Citrus Sinensis ID: 009640

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530
Protein Sequence
MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVVRSPENWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGRKGV
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcccccEEEEEEEEcccccccccHHHHHHHHHHHcccccccccccEEEEccccccccEEEEEccccEEEEEEccEEEEEEEEEcccccccccEEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHccEEEEEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHHccHHHHHHHcccccccEEEEccccccHHHHHHHHHHHHcccEEEEcccccccHHHHHHHHHcccccEEEEEEcccccccccHHHccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccccccccccEEEEcccccHHHHHHHHHHHcccccccccHHHHHHHHHccccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHcccccccccccccccccccccccccccccccccccEEEEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccEEEEEEEcccccccccHHHHHHHHHHHHHHccccccHccEEEEccccccccEEEEEccccEEEEEEccEEEEEEEEEEcccccccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEcccccccccccccccccccccHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccEEEEccccccHHHHHHHHHHHccccEEEEEccEccccHHHHHHHHcccccEEEEEEEcccEEEccccccccccccccccccccccccccccccccccccccccccccccccEEEEHHHHHHHccHHccccccEEEEEEcccHHcccHHHcccccccEEEEEccccHHHHHHHHHHHccccccccHHHHHHHHHHHcccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEcccccccccccccccccccccccccEEEEEEEEEcccccccccccc
Coil and Loop (DISEMBL)
MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLqdlfspysyfeipefngycgvdvndlYRHVNLYLnsvnpagsstcrrltlsrsrssnrisftvapnhtvhdsfsghslswtHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRlftnnghgsydsgwvsvpfrhpstfetlalepQLKKQITEDLTAFANGKEFYHRVGRAWKRgyllygppgsgksSLIAAMANYLCYdvydleltkvtdnSELRALLLQTTNRSIIviedidcsvdltadrmlkssntsttaktkRSSSIKEMGSriasstcgnnnnnngeesGRVTLSGLLNFtdglwsccseeKIIVFTtnhrdsvdpalircgrmdvhvslgtcgpHAFKVLAKNYLGIESHHALFDVVESCIraggaltpaqIGEVLLRNRGNVDLAMKEVVSAMQAKIlsgrevmecdelvitrspesvvvvrspenwdsspggkygnrskkrkegtkaNFLVRLRSltksdsgrkgv
Flexible Loop (DISEMBL)
MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLnsvnpagsstcRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSftlklpkrhrQTLLSAYLDHVTSRAEEFERVSRErrlftnnghgsydsgwVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLlqttnrsiivieDIDCSVDLTAdrmlkssntsttaktkrsssikemgsriasstcgnnnnnngEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAkilsgrevmECDELvitrspesvvvvrspenwdsspggkygnrskkrkegtkanflvrlrsltksdsgrkgv
Low Complexity Region (SEG)
MEILSQMWSllglltvlqnvlPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGsstcrrltlsrsrssnrisFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLkssntsttaktkrsssikEMGSRIASSTCGnnnnnnGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITrspesvvvvrspeNWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGRKGV
Disordered region (IsUnstruct)
***LSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPA********************FTVAPNHTVHDSFSGHSLSWTHHVDTV**********TLKL***HRQTLLSAYLDHVTS***********RRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTA**********************************************VTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVV**********************************************
Disordered Region (DISOPRED)
*EILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGSSTCR****************VAPNHTVHDSFSGHSLSWTH**************FTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDL*******************************************************NFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS***********************************************************L****************
Disordered Region (DISEMBL)
MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLK*************************STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVVRS********************EGTKANFLVRLRSLT*********
Disordered Region (DISPRO)
*EILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLT********************************************SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREV*****************************************GTKANFLVRLRSL**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVVRSPENWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGRKGV
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	530	2.2.26 [Sep-21-2011]
Q9P6Q3	449	Probable mitochondrial ch	yes	no	0.367	0.434	0.340	2e-26
Q54DY9	458	Probable mitochondrial ch	yes	no	0.437	0.506	0.314	4e-26
Q9Y276	419	Mitochondrial chaperone B	yes	no	0.405	0.513	0.288	4e-22
Q7ZTL7	419	Mitochondrial chaperone B	N/A	no	0.313	0.396	0.328	7e-22
Q5E9H5	419	Mitochondrial chaperone B	yes	no	0.4	0.505	0.277	1e-21
P32839	456	Mitochondrial chaperone B	yes	no	0.416	0.484	0.319	2e-21
Q7ZV60	420	Mitochondrial chaperone B	yes	no	0.390	0.492	0.294	3e-21
Q9CZP5	418	Mitochondrial chaperone B	yes	no	0.401	0.509	0.282	1e-20
Q54HY8	421	Probable mitochondrial ch	no	no	0.449	0.565	0.281	5e-19
Q5UR45	196	Putative AAA family ATPas	N/A	no	0.364	0.984	0.280	4e-14

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

 Score =  120 bits (302), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/241 (34%), Positives = 119/241 (49%), Gaps = 46/241 (19%)

Query: 186 PFRHPST---FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKS 242
           PF HP +     ++ LE  +KK IT+D+  F    ++Y   G  ++RGYLLYGPPGSGK+
Sbjct: 197 PFGHPRSKRMLSSVVLESNVKKMITDDVHDFLRNSQWYDTRGIPYRRGYLLYGPPGSGKT 256

Query: 243 SLIAAMANYLCYDVYDLELTK--VTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRML 300
           S + A+A  L YD+  L L +  +TD+  L  LL     ++++++ED+D +         
Sbjct: 257 SFLYALAGELDYDICVLNLAEKGLTDD-RLNHLLSNVPPKAVVLLEDVDSAFQ------- 308

Query: 301 KSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCS 360
                                 R  S   G + N        VT SGLLN  DG+ S  S
Sbjct: 309 ---------------------GRERSGEVGFHAN--------VTFSGLLNALDGVTS--S 337

Query: 361 EEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHA--LFDV 418
           +E+II  TTNH + +DPAL+R GR+DV   LG   P   + +   + G     A  L D+
Sbjct: 338 DERIIFMTTNHPEKLDPALVRPGRVDVKAYLGNATPEQVREMFTRFYGHSPEMADDLSDI 397

Query: 419 V 419
           V
Sbjct: 398 V 398

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

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

 Score =  120 bits (300), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 80/254 (31%), Positives = 130/254 (51%), Gaps = 22/254 (8%)

Query: 187 FRHPS---TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSS 243
           F HP       ++ L+    + I +D+  F N  ++Y+  G  ++RGYLLYGPPG+GKSS
Sbjct: 197 FGHPRRKRPISSVILDKGKSELIIQDVKKFLNNSDWYNDRGIPYRRGYLLYGPPGTGKSS 256

Query: 244 LIAAMANYLCYDVYDLELT-KVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKS 302
            I A+A  L   +  L L  K   ++ L  LL     RSII++EDID ++  T +  L +
Sbjct: 257 FITALAGELQLSICILNLAGKSVSDTSLNQLLATAPQRSIILLEDIDSAIQ-TGNHDLSA 315

Query: 303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEE 362
            + S  A +  S  ++  G        GN + ++G  +  +T SGLLN  DG+    SE 
Sbjct: 316 KSNSANAPSISSGGLQYQG------YYGNPSVSSGGSA--LTFSGLLNALDGV--AASEG 365

Query: 363 KIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESC 422
           +I+  TTNH + +D  LIR GR+D+ + +G C  +  + +   +   +     FD+ +  
Sbjct: 366 RILFMTTNHLEKLDKVLIRPGRVDLQIEIGLCSSYQMEQMFLKFYPTD-----FDLAKQF 420

Query: 423 IRA--GGALTPAQI 434
           +        +PAQ+
Sbjct: 421 VEKLENYKFSPAQL 434

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 =  106 bits (265), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 119/253 (47%), Gaps = 38/253 (15%)

Query: 186 PFRHPS---TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKS 242
           PF +P       ++ L+  L  +I  D+  F +  ++Y   G  ++RGYLLYGPPG GKS
Sbjct: 178 PFGYPRRRRPLNSVVLQQGLADRIVRDVQEFIDNPKWYTDRGIPYRRGYLLYGPPGCGKS 237

Query: 243 SLIAAMANYLCYDV-YDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLK 301
           S I A+A  L + +           +  L  LL     +S++++ED+D +  L+ D  ++
Sbjct: 238 SFITALAGELEHSICLLSLTDSSLSDDRLNHLLSVAPQQSLVLLEDVDAAF-LSRDLAVE 296

Query: 302 SSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSE 361
           +              +K  G                   GR+T SGLLN  DG+    +E
Sbjct: 297 NP-------------VKYQGL------------------GRLTFSGLLNALDGV--ASTE 323

Query: 362 EKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVES 421
            +I+  TTNH D +DPALIR GR+D+   +G C       + + +   ++     +  E 
Sbjct: 324 ARIVFMTTNHVDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQRFYPGQAPSLAENFAEH 383

Query: 422 CIRAGGALTPAQI 434
            +RA   ++PAQ+
Sbjct: 384 VLRATNQISPAQV 396

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

 Score =  105 bits (263), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 66/201 (32%), Positives = 94/201 (46%), Gaps = 35/201 (17%)

Query: 195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY 254
           ++ LE  + ++I +D+  F    ++Y   G  ++RGYLLYGPPG GKSS I A+A  L Y
Sbjct: 190 SVVLEQGISEKIVQDVKGFIENPKWYSDRGIPYRRGYLLYGPPGCGKSSFITALAGELEY 249

Query: 255 DV-YDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKR 313
            +           +  L  LL     +SII++ED+D +                      
Sbjct: 250 SICLMSLSDSSLSDDRLNHLLSVAPQQSIILLEDVDAA---------------------- 287

Query: 314 SSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD 373
                       S      N    +  GR+T SGLLN  DG+    +E +I+  TTNH D
Sbjct: 288 ----------FVSRDLNKQNPTAYQGMGRLTFSGLLNALDGV--ASTEARIVFMTTNHID 335

Query: 374 SVDPALIRCGRMDVHVSLGTC 394
            +DPALIR GR+DV   +G C
Sbjct: 336 RLDPALIRPGRVDVKQYVGHC 356

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

Xenopus laevis (taxid: 8355)

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

 Score =  105 bits (261), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 71/256 (27%), Positives = 117/256 (45%), Gaps = 44/256 (17%)

Query: 186 PFRHPS---TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKS 242
           PF +P       ++ LE  + ++I  D+  F +  ++Y   G  ++RGYLLYGPPG GKS
Sbjct: 178 PFGYPRRRRPLNSVVLEQGVTERIVRDIREFIDNPKWYIDRGIPYRRGYLLYGPPGCGKS 237

Query: 243 SLIAAMANYLCYDV-YDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSV---DLTADR 298
           S I A+A  L + +           +  L  LL     +S++++ED+D +    DL A+ 
Sbjct: 238 SFITALAGELQHSICLLSLTDSSLSDDRLNHLLSVAPQQSLVLLEDVDAAFLSRDLAAEN 297

Query: 299 MLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSC 358
            +K                                       GR+T SGLLN  DG+   
Sbjct: 298 PIKYQGL-----------------------------------GRLTFSGLLNALDGV--A 320

Query: 359 CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV 418
            +E +I+  TTNH D +DPALIR GR+D+   +G C       + + +   ++     + 
Sbjct: 321 STEARIVFMTTNHIDRLDPALIRPGRVDMKEYVGHCSRWQLTQMFQRFYPGQATSLAENF 380

Query: 419 VESCIRAGGALTPAQI 434
            +  ++A   ++PAQ+
Sbjct: 381 ADRVLQATTQISPAQV 396

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

 Score =  104 bits (259), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 129/269 (47%), Gaps = 48/269 (17%)

Query: 195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY 254
           ++ L+  +K+ I +D+  F    ++Y   G  ++RGYLLYGPPGSGK+S I A+A  L Y
Sbjct: 227 SVILDSGIKEGILDDVYDFMKNGKWYSDRGIPYRRGYLLYGPPGSGKTSFIQALAGELDY 286

Query: 255 DVYDLELTK--VTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTK 312
           ++  L L++  +TD+  L  L+     RSI+++EDID + +                  K
Sbjct: 287 NICILNLSENNLTDD-RLNHLMNNMPERSILLLEDIDAAFN------------------K 327

Query: 313 RSSSIKEMGSRIASSTCGNNNNNNGEES--GRVTLSGLLNFTDGLWSCCSEEKIIVFTTN 370
           RS +                    GE+     VT SGLLN  DG+ S  SEE I   TTN
Sbjct: 328 RSQT--------------------GEQGFHSSVTFSGLLNALDGVTS--SEETITFMTTN 365

Query: 371 HRDSVDPALIRCGRMDVHVSLGTCGPHAF-KVLAKNYLGIESHHALFDVVESCIRAGGAL 429
           H + +D A++R GR+D  V +G   P+   K+  K Y G       F  V S       +
Sbjct: 366 HPEKLDAAIMRPGRIDYKVFVGNATPYQVEKMFMKFYPGETDICKKF--VNSVKELDITV 423

Query: 430 TPAQIGEVLLRNRGNVDLAMKEVVSAMQA 458
           + AQ+  + + N+     A+K V S   A
Sbjct: 424 STAQLQGLFVMNKDAPHDALKMVSSLRNA 452

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

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

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

 Score =  103 bits (257), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 113/241 (46%), Gaps = 34/241 (14%)

Query: 195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY 254
           ++ LE  + ++I +D+  F    ++Y   G  ++RGYLLYGPPG GKSS I A+A  L Y
Sbjct: 190 SVVLESGVAERIVDDVKEFIGNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELGY 249

Query: 255 DVYDLELT-KVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKR 313
            +  + L+ +   +  L  LL     +SII++ED+D +    +  +L + N         
Sbjct: 250 SICLMSLSDRSLSDDRLNHLLSVAPQQSIILLEDVDAA--FVSRELLPTENPLAY----- 302

Query: 314 SSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD 373
                                   +  GR+T SGLLN  DG+    SE +I+  TTN  +
Sbjct: 303 ------------------------QGMGRLTFSGLLNALDGV--ASSEARIVFMTTNFIE 336

Query: 374 SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQ 433
            +DPAL+R GR+D+   +G C       + + +   ES        E  + A   L+ AQ
Sbjct: 337 RLDPALVRPGRVDLKQYVGHCSHWQLTQMFRRFYPQESAAEADHFSEQALAAHTDLSAAQ 396

Query: 434 I 434
           +
Sbjct: 397 V 397

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

Danio rerio (taxid: 7955)

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

 Score =  101 bits (252), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 118/248 (47%), Gaps = 35/248 (14%)

Query: 188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAA 247
           R     +++ L+  L  +I +D+  F +  ++Y   G  ++RGYLLYGPPG GKSS I A
Sbjct: 183 RRRRPLDSVVLQQGLADRIVKDIREFIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITA 242

Query: 248 MANYLCYDV-YDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTS 306
           +A  L + +           +  L  LL     +S++++ED+D +  L+ D  +++    
Sbjct: 243 LAGELEHSICLLSLTDSSLSDDRLNHLLSVAPQQSLVLLEDVDAAF-LSRDLAVENP--- 298

Query: 307 TTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIV 366
                     IK  G                   GR+T SGLLN  DG+    +E +I+ 
Sbjct: 299 ----------IKYQGL------------------GRLTFSGLLNALDGV--ASTEARIVF 328

Query: 367 FTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAG 426
            TTN+ D +DPALIR GR+D+   +G C       + + +   ++     +  E  ++A 
Sbjct: 329 MTTNYIDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQRFYPGQAPSLAENFAEHVLKAT 388

Query: 427 GALTPAQI 434
             ++PAQ+
Sbjct: 389 SEISPAQV 396

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

 Score = 96.3 bits (238), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 84/298 (28%), Positives = 137/298 (45%), Gaps = 60/298 (20%)

Query: 169 LFTNNGHGSYDSGWVSVPFRHPSTFETLA---LEPQLKKQITEDLTAFANGKEFYHRVGR 225
           ++ N G+G+++       F +P +  +L+   L   LK ++ ED+ +F   + +Y   G 
Sbjct: 165 IYINGGNGNWER------FGNPRSIRSLSSVILADDLKSKLIEDIKSFITNESWYRNRGI 218

Query: 226 AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL-TKVTDNSELRALLLQTTNRSIIV 284
            ++RGYLLYG PG+GKSSLI A+A  L  D+  + L +K  D+ ++  LL     +SI++
Sbjct: 219 PYRRGYLLYGEPGNGKSSLINAIAGELNLDICIVSLSSKDIDDKQINHLLNNAPPKSILL 278

Query: 285 IEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVT 344
           IEDID +     D +  ++N S    +                               +T
Sbjct: 279 IEDIDAAFKSHRDNVDSNNNNSNNNNS-------------------------------LT 307

Query: 345 LSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP-------- 396
            SGLLN  DG+     E +I+  TTN  + +D ALIR GR+D+ + +             
Sbjct: 308 YSGLLNALDGV--ASQEGRILFMTTNKIELLDSALIREGRIDLKIKVSNATKSQAAQLFT 365

Query: 397 HAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS 454
           H + +   N L I     L D           L+ +QI   LL+   + + A++EV S
Sbjct: 366 HFYNLPTDNQLAIRFSENLHD---------HQLSMSQIQGFLLKYINSPEKAIEEVQS 414

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

Dictyostelium discoideum (taxid: 44689)

>sp|Q5UR45|YL572_MIMIV Putative AAA family ATPase L572 OS=Acanthamoeba polyphaga mimivirus GN=MIMI_L572 PE=3 SV=1

 Score = 80.1 bits (196), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 108/210 (51%), Gaps = 17/210 (8%)

Query: 244 LIAAMANYLCYDVYDLELTKVTDNSELRALLLQTT-NRSIIVIEDIDCSVDLTADRMLKS 302
           +I A++ +    ++ L L  + D++EL  LL       +I+V+EDIDC+ +    R  K 
Sbjct: 1   MIKAISTHTKRHIHYLILNNIQDDNELINLLNAVNCKETILVLEDIDCASEAVKSRA-KE 59

Query: 303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEE 362
             T     T   S+++   ++I +           E+  ++TLSG+LN  DG+++  SE 
Sbjct: 60  EETVVEKVTDDKSTLE---NKILADQLKK-----VEKVSKLTLSGILNSLDGIFN--SEG 109

Query: 363 KIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESC 422
           +I++ TTNH + +DPALIR GR+D+ +    C  +    + +N+ G  +   +   + S 
Sbjct: 110 RIVIMTTNHSEVLDPALIRRGRIDMQIEFSNCDRYQIAKMYENFYGKNADSDILSKIPSD 169

Query: 423 IRAGGALTPAQIGEVLLRNRGNVDLAMKEV 452
           I      +PA +  +LL  R N + ++ E+
Sbjct: 170 I-----YSPAHVSGLLLSYRNNPENSLIEL 194

Acanthamoeba polyphaga (taxid: 5757)

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	530
225450283	516	PREDICTED: ATPase family gene 2 protein-	0.945	0.970	0.767	0.0
255542265	517	ATP binding protein, putative [Ricinus c	0.956	0.980	0.783	0.0
449468065	503	PREDICTED: probable mitochondrial chaper	0.933	0.984	0.713	0.0
356557096	521	PREDICTED: uncharacterized protein LOC10	0.971	0.988	0.726	0.0
356525695	516	PREDICTED: uncharacterized protein LOC10	0.958	0.984	0.715	0.0
224104521	432	predicted protein [Populus trichocarpa]	0.811	0.995	0.813	0.0
224121086	362	predicted protein [Populus trichocarpa]	0.681	0.997	0.816	1e-174
326513926	514	predicted protein [Hordeum vulgare subsp	0.952	0.982	0.545	1e-151
242044842	522	hypothetical protein SORBIDRAFT_02g02609	0.960	0.975	0.526	1e-149
226495729	519	uncharacterized protein LOC100278733 pre	0.956	0.976	0.531	1e-148

>gi|225450283|ref|XP_002267624.1| PREDICTED: ATPase family gene 2 protein-like [Vitis vinifera]

 Score =  837 bits (2161), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/543 (76%), Positives = 466/543 (85%), Gaps = 42/543 (7%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           MEILSQMWS LGLLTVLQNVLPSQ+LSLLHSFYESLQD FSP++YFEIPEFN YCGVDVN
Sbjct: 1   MEILSQMWSFLGLLTVLQNVLPSQILSLLHSFYESLQDFFSPFAYFEIPEFNDYCGVDVN 60

Query: 61  DLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHV 120
           DLYRHVNLYLNSVNPA  +TCRR TLSRS+SSNRISFTVAPNHTVHDSF+GH+LSWTHHV
Sbjct: 61  DLYRHVNLYLNSVNPA--TTCRRFTLSRSKSSNRISFTVAPNHTVHDSFNGHTLSWTHHV 118

Query: 121 DTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDS 180
           +TVQDS++E+RSF+LKLPKRHRQ LLS YL+ VTSRAEEFERVSRERRLFTNNGHGSY+S
Sbjct: 119 ETVQDSLDERRSFSLKLPKRHRQALLSPYLELVTSRAEEFERVSRERRLFTNNGHGSYES 178

Query: 181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSG 240
           GWVSVPFRHPSTFETLALEPQL++QIT+DLTAFANGKEFYHRVGRAWKRGYLLYGPPGSG
Sbjct: 179 GWVSVPFRHPSTFETLALEPQLRQQITDDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSG 238

Query: 241 KSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRML 300
           KSSLIAAMANYLCYDVYDLELTKV+DNSELRALL+QTTNRSIIVIEDIDCSVDLTADR+ 
Sbjct: 239 KSSLIAAMANYLCYDVYDLELTKVSDNSELRALLIQTTNRSIIVIEDIDCSVDLTADRL- 297

Query: 301 KSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCS 360
                   +KTKR++  K             ++ + GEE+GRVTLSGLLNFTDGLWSCC 
Sbjct: 298 --------SKTKRTTPAK------------GSSRDEGEENGRVTLSGLLNFTDGLWSCCG 337

Query: 361 EEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE 420
           EE+IIVFTTNHRD+VDPAL+RCGRMDVHVSLGTCG HAFK LA NYLG+ES H LFDVVE
Sbjct: 338 EERIIVFTTNHRDNVDPALVRCGRMDVHVSLGTCGIHAFKALAANYLGLES-HPLFDVVE 396

Query: 421 SCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSG-REVMECDELVITRSPE 479
           SCIR+GG LTPAQ+GE+LLRNR + ++A+K V+SAMQA+IL   RE +E +E+   +SPE
Sbjct: 397 SCIRSGGTLTPAQVGEILLRNRRDAEVAIKAVISAMQARILGAEREPIEYEEMA--KSPE 454

Query: 480 SVV--VVRSPENWDSSPGGKYGNRSKKRKEGT-----------KANFLVRLRSLTKSDSG 526
           SV   ++ SPENW++S  GKY    KKRKEG            K  FLVRLRSLTKSDSG
Sbjct: 455 SVERGLMESPENWETSSPGKYVR--KKRKEGGSVTGSGSSWEKKVKFLVRLRSLTKSDSG 512

Query: 527 RKG 529
           R+G
Sbjct: 513 RRG 515

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542265|ref|XP_002512196.1| ATP binding protein, putative [Ricinus communis] gi|223548740|gb|EEF50230.1| ATP binding protein, putative [Ricinus communis]

 Score =  830 bits (2143), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 423/540 (78%), Positives = 462/540 (85%), Gaps = 33/540 (6%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           MEILSQMWS+LGLLTVLQN+LP+QLLSLLHS YES QDL SPYSYF+IPEFNGYCGVD+N
Sbjct: 1   MEILSQMWSVLGLLTVLQNILPTQLLSLLHSIYESFQDLISPYSYFDIPEFNGYCGVDIN 60

Query: 61  DLYRHVNLYLNSVNPAGSST-CRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHH 119
           DLYRHVNLYLNSV+ + S+  CRRLTLSRS+SSN ISFTVAPN TVHD+FSGHSL WTHH
Sbjct: 61  DLYRHVNLYLNSVSSSTSAAACRRLTLSRSKSSNCISFTVAPNQTVHDTFSGHSLYWTHH 120

Query: 120 VDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYD 179
           V+TVQDS+EEKRSFTLKLPKRHR  LL  YL HVTSRAEEFERVSRERRLFTNNG+ S++
Sbjct: 121 VETVQDSLEEKRSFTLKLPKRHRCNLLGPYLQHVTSRAEEFERVSRERRLFTNNGNASHE 180

Query: 180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGS 239
           SGWVSVPFRHPSTFETLALEPQLKKQI  DL AF+NGK FYHRVGRAWKRGYLL+GPPGS
Sbjct: 181 SGWVSVPFRHPSTFETLALEPQLKKQIMGDLKAFSNGKAFYHRVGRAWKRGYLLHGPPGS 240

Query: 240 GKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRM 299
           GKSSLIAAMANYLCYDVYDLELTKVTDNSELRALL+QTTNRSIIVIEDIDCSVDLT DRM
Sbjct: 241 GKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLIQTTNRSIIVIEDIDCSVDLTTDRM 300

Query: 300 LKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCC 359
           +K+S        KRS+           S+C +++N   EESGRVTLSGLLNFTDGLWSCC
Sbjct: 301 VKTSR-------KRSN----------LSSCKDSSNE--EESGRVTLSGLLNFTDGLWSCC 341

Query: 360 SEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV 419
            EEKIIVFTTNHRD+VDPAL+RCGRMDVHVSLGTCG HAFK LA NYLGI+S H+LFDV 
Sbjct: 342 GEEKIIVFTTNHRDNVDPALVRCGRMDVHVSLGTCGMHAFKALAMNYLGIDS-HSLFDVA 400

Query: 420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSG----REVMECDELVIT 475
           ESCIR+GGALTPAQIGE+LLRNRGN D+A+KEVVSAMQA+ILS     +E +   E   T
Sbjct: 401 ESCIRSGGALTPAQIGEILLRNRGNTDVALKEVVSAMQARILSSSGTHKEHLTDYEDTAT 460

Query: 476 RSPESVVVVRSPENWDSSPGGKYGNRSKKRKEG-----TKANFLVRLRSLTKSDSGRKGV 530
           RSP+SV+ V SPENWDSSPG   G   KKRKEG      KA FLVRLRSLTKSDSGR+GV
Sbjct: 461 RSPQSVLTVGSPENWDSSPGRIGG---KKRKEGGNNCDKKAKFLVRLRSLTKSDSGRRGV 517

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468065|ref|XP_004151742.1| PREDICTED: probable mitochondrial chaperone BCS1-A-like [Cucumis sativus] gi|449531295|ref|XP_004172622.1| PREDICTED: probable mitochondrial chaperone BCS1-A-like [Cucumis sativus]

 Score =  754 bits (1947), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/538 (71%), Positives = 442/538 (82%), Gaps = 43/538 (7%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           MEILSQ+WS LGLLTVLQN+LPSQ LSLLHS YESLQD F+P+SYF+IPEFNGYC VD+N
Sbjct: 1   MEILSQLWSFLGLLTVLQNILPSQFLSLLHSLYESLQDFFTPFSYFDIPEFNGYCSVDLN 60

Query: 61  DLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHV 120
           +LYRHV LYLNS++   S+ CRRL+LSRS+SSNRISFTVAPN +VH +F+G  +SWTH V
Sbjct: 61  ELYRHVTLYLNSLH--NSAACRRLSLSRSKSSNRISFTVAPNQSVHVTFNGQRISWTHQV 118

Query: 121 DTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGS-YD 179
           +TVQDS++EKRSF+LK+PKRHRQ LL  YLDH+T+ A EFER SRERRLFTNNG+ S YD
Sbjct: 119 ETVQDSLDEKRSFSLKIPKRHRQALLPLYLDHITATAAEFERTSRERRLFTNNGNASSYD 178

Query: 180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGS 239
           SGWVSVPFRHPSTFETLALE +LKKQI  DL AFA G+EFY RVGRAWKRGYLLYGPPGS
Sbjct: 179 SGWVSVPFRHPSTFETLALETELKKQIMNDLMAFAAGREFYSRVGRAWKRGYLLYGPPGS 238

Query: 240 GKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRM 299
           GKSSLIAAMAN+LCYDVYDLELTKV+DNSELR+LL+QTTNRS+IVIEDIDCSVDLTADR+
Sbjct: 239 GKSSLIAAMANFLCYDVYDLELTKVSDNSELRSLLIQTTNRSVIVIEDIDCSVDLTADRV 298

Query: 300 LKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCC 359
            K +                               ++ EE GRVTLSGLLNFTDGLWSCC
Sbjct: 299 TKVA----------------------------AREDHEEEMGRVTLSGLLNFTDGLWSCC 330

Query: 360 SEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV 419
            EE+I+VFTTN+R+ +DPAL+RCGRMDVHVSLGTCGP AF+ L KNYL IES HALFDVV
Sbjct: 331 GEERIVVFTTNYREKIDPALVRCGRMDVHVSLGTCGPAAFRTLVKNYLEIES-HALFDVV 389

Query: 420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKIL---SGREVMECDELVITR 476
           +SCIR+GG LTPAQIGE+LLRNR + D+AM+EVV+A+QA++L    GR   E +E+V+ R
Sbjct: 390 DSCIRSGGGLTPAQIGEILLRNRRDADVAMREVVAALQARVLGSGGGRGAAEYEEIVM-R 448

Query: 477 SPESVVVVRSPENWDSSPGGKYGNRSKKRKEG----TKANFLVRLRSLTKSDSGRKGV 530
           SPESV+VV SPENWDSSPG   G   K+RKEG     K NFLVRLRSLTKSDSGR+GV
Sbjct: 449 SPESVLVVGSPENWDSSPGKYVG---KRRKEGPASEKKVNFLVRLRSLTKSDSGRRGV 503

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557096|ref|XP_003546854.1| PREDICTED: uncharacterized protein LOC100820437 [Glycine max]

 Score =  750 bits (1936), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/533 (72%), Positives = 438/533 (82%), Gaps = 18/533 (3%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           MEILSQMWSLLGLLTVLQNVLPSQLLSLLHS YESLQDL SPYSYFEIPEFNGYCGVD+N
Sbjct: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSLYESLQDLLSPYSYFEIPEFNGYCGVDLN 60

Query: 61  DLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHV 120
           DLYRH +LYLN+ N A ++ CRRLTLSRS SSNRISF VAPNHTVHD+F GH ++WTHHV
Sbjct: 61  DLYRHAHLYLNASNHAPATACRRLTLSRSPSSNRISFAVAPNHTVHDAFRGHRVAWTHHV 120

Query: 121 DTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNN--GHGSY 178
           +T QDS+EE+RSFTL+LPKRHR  LLS YL HVTSRAEEFERVSRERRLFTNN    GS+
Sbjct: 121 ETAQDSLEERRSFTLRLPKRHRHALLSPYLAHVTSRAEEFERVSRERRLFTNNTTSSGSF 180

Query: 179 DSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPG 238
           +SGWVSVPFRHPSTFETLA+EP+LKK I  DLTAFA GKEFY RVGRAWKRGYLL+GPPG
Sbjct: 181 ESGWVSVPFRHPSTFETLAMEPELKKNIKNDLTAFAEGKEFYKRVGRAWKRGYLLHGPPG 240

Query: 239 SGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADR 298
           SGKSSLIAAMAN+LCYDVYDLELTKV+DNSELR+LL+QTTNRSIIVIEDIDCSVDLTADR
Sbjct: 241 SGKSSLIAAMANFLCYDVYDLELTKVSDNSELRSLLIQTTNRSIIVIEDIDCSVDLTADR 300

Query: 299 MLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSC 358
            +K +      K    SS K+  +  + + C        EESGRVTLSGLLNFTDGLWSC
Sbjct: 301 TVKKTQ---AGKLSLRSSNKKTTTTSSFTRC--------EESGRVTLSGLLNFTDGLWSC 349

Query: 359 CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV 418
           C EE+I+VFTTNHRDSVDPAL+RCGRMDVHVSL TCG HAF+ LA+NYLG+ES H LF  
Sbjct: 350 CGEERIVVFTTNHRDSVDPALVRCGRMDVHVSLATCGAHAFRELARNYLGLES-HVLFQA 408

Query: 419 VESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKIL----SGREVMECDELVI 474
           VE CIR GGALTPAQ+GE+LLRNRG+ D+AM+EV++AMQ ++L    +  +  E +E V 
Sbjct: 409 VEGCIRGGGALTPAQVGEILLRNRGDADVAMREVLAAMQGRMLAVAAAANDQAENEEAVG 468

Query: 475 TRSPESVVVVRSPENWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGR 527
            RSPESV+++ SPENWD+  G K   +        K  F VRLRSLT+SD GR
Sbjct: 469 VRSPESVLLMGSPENWDAFSGKKRKEQHGCNNLDKKVKFFVRLRSLTRSDPGR 521

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525695|ref|XP_003531459.1| PREDICTED: uncharacterized protein LOC100783574 [Glycine max]

 Score =  736 bits (1901), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/535 (71%), Positives = 438/535 (81%), Gaps = 27/535 (5%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           MEILSQMWSLLGLLTVLQNVLPSQLLSLLHS YESLQDL SPYSYFEIPEFNGYCGV++N
Sbjct: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSLYESLQDLLSPYSYFEIPEFNGYCGVELN 60

Query: 61  DLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHV 120
           DLYRHV+LYLN+ N A ++ CRRLTLS S SSNRISF VAPNHTVHD+F GH + WTHHV
Sbjct: 61  DLYRHVHLYLNAANHAPAAACRRLTLSCSPSSNRISFAVAPNHTVHDAFRGHRVGWTHHV 120

Query: 121 DTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNN--GHGSY 178
           +T QDS+EE+RSFTL+LPKRHR  LLS YL HVTSRAEEFERVSRERRLFTNN    GS+
Sbjct: 121 ETAQDSLEERRSFTLRLPKRHRHALLSPYLAHVTSRAEEFERVSRERRLFTNNTTASGSF 180

Query: 179 DSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPG 238
           +SGWVSVPFRHPSTFETLALEP+LKKQI  DLTAFA+GKEFY RVGRAWKRGYLL+GPPG
Sbjct: 181 ESGWVSVPFRHPSTFETLALEPELKKQIKNDLTAFADGKEFYKRVGRAWKRGYLLHGPPG 240

Query: 239 SGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADR 298
           SGKSSLIAAMAN+LCYDVYDLELTKV+DNSELR+LL+QTTNRSIIVIEDIDCSVD+TADR
Sbjct: 241 SGKSSLIAAMANFLCYDVYDLELTKVSDNSELRSLLIQTTNRSIIVIEDIDCSVDITADR 300

Query: 299 MLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSC 358
                    T K K+S      G++++  +         EESGRVTLSGLLNFTDGLWSC
Sbjct: 301 ---------TVKVKKS-----QGAKLSLRSSNKKGQTGCEESGRVTLSGLLNFTDGLWSC 346

Query: 359 CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV 418
           C EE+I+VFTTNHRDSVDPAL+RCGRMDVHVSLGTCG HAF+ LA+NYLG++S H LF+ 
Sbjct: 347 CGEERIVVFTTNHRDSVDPALLRCGRMDVHVSLGTCGTHAFRELARNYLGVDS-HVLFEA 405

Query: 419 VESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGR------EVMECDEL 472
           VE CIR+GG+LTPA +GE+LLRNRG+VD+AM+EV++AMQ ++L         E  E    
Sbjct: 406 VEGCIRSGGSLTPAHVGEILLRNRGDVDVAMREVLAAMQGRMLVATAAADQPENEEASTA 465

Query: 473 VITRSPESVVVVRSPENWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGR 527
              RSPESV+++ SPENWD     ++G  +  +    K  F VRLRSLT+SD GR
Sbjct: 466 AGVRSPESVLMMGSPENWDVKRKEQHGCNNLDK----KVKFFVRLRSLTRSDPGR 516

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224104521|ref|XP_002313465.1| predicted protein [Populus trichocarpa] gi|222849873|gb|EEE87420.1| predicted protein [Populus trichocarpa]

 Score =  710 bits (1832), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/440 (81%), Positives = 389/440 (88%), Gaps = 10/440 (2%)

Query: 23  SQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNP-AGSSTC 81
           +QLLSLLHS  ESLQDL S YSYF+IPEFNGYCGVD+NDLYRHVNLYLNSVN  A +STC
Sbjct: 1   AQLLSLLHSLIESLQDLISQYSYFDIPEFNGYCGVDINDLYRHVNLYLNSVNSSATASTC 60

Query: 82  RRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRH 141
           RR +LSRSRSSN ISFT+APNHT+HDSF+GHSL WTH VDTVQDS+EEKRSFTLKLPKRH
Sbjct: 61  RRFSLSRSRSSNCISFTIAPNHTIHDSFNGHSLCWTHQVDTVQDSLEEKRSFTLKLPKRH 120

Query: 142 RQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQ 201
           R  LLS YL HVTSRAEEFERVSRERRLFTNNG+ SY+SGWVSVPFRHPSTFETLALEPQ
Sbjct: 121 RHMLLSPYLQHVTSRAEEFERVSRERRLFTNNGNASYESGWVSVPFRHPSTFETLALEPQ 180

Query: 202 LKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL 261
           LK+QI EDL AFA+G+E+YHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL
Sbjct: 181 LKRQIMEDLKAFASGREYYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL 240

Query: 262 TKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMG 321
           TKVTDNS+LRALL+QT+NRSIIVIEDIDCS+DLTADRMLK++ T+T  + KRSSS     
Sbjct: 241 TKVTDNSDLRALLIQTSNRSIIVIEDIDCSLDLTADRMLKAT-TATATRRKRSSSSG--- 296

Query: 322 SRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIR 381
               +   G+ N    EESGRVTLSGLLNFTDGLWSCC EE+IIVFTTNHRD VDPAL+R
Sbjct: 297 ---YNKDPGSGNYQLLEESGRVTLSGLLNFTDGLWSCCGEERIIVFTTNHRDKVDPALVR 353

Query: 382 CGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRN 441
           CGRMDVHVSLG CG HAFK LA NYLGIE  H+LFDVVESCIR+GGALTPAQIGE+LLRN
Sbjct: 354 CGRMDVHVSLGPCGMHAFKALAMNYLGIE-EHSLFDVVESCIRSGGALTPAQIGEILLRN 412

Query: 442 RG-NVDLAMKEVVSAMQAKI 460
           RG N DLAM EVVSAMQ +I
Sbjct: 413 RGSNADLAMTEVVSAMQTRI 432

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224121086|ref|XP_002330900.1| predicted protein [Populus trichocarpa] gi|222872722|gb|EEF09853.1| predicted protein [Populus trichocarpa]

 Score =  617 bits (1591), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 302/370 (81%), Positives = 331/370 (89%), Gaps = 9/370 (2%)

Query: 89  SRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSA 148
           S+SSN ISFT+APNHT+HDSF+GHSLSWTHHVDTVQDS+EEKRSFTLKLPKR R  LLS 
Sbjct: 1   SKSSNCISFTIAPNHTIHDSFNGHSLSWTHHVDTVQDSLEEKRSFTLKLPKRLRHLLLSP 60

Query: 149 YLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITE 208
           Y+ HVTSRAEEFERVSRERRLFTNNG+ SY+SGWVSVPFRHPSTFETLALEP LKKQ+ E
Sbjct: 61  YIQHVTSRAEEFERVSRERRLFTNNGNASYESGWVSVPFRHPSTFETLALEPHLKKQMME 120

Query: 209 DLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS 268
           DL AFA+G+EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS
Sbjct: 121 DLKAFASGREFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS 180

Query: 269 ELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST 328
           ELRALL+QT+NRSIIVIEDIDCS+DLTADRM+K++ T+T  + KRSSS         +  
Sbjct: 181 ELRALLIQTSNRSIIVIEDIDCSLDLTADRMMKAT-TATATRRKRSSSSG------YNKD 233

Query: 329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVH 388
            G  N+   EESGRVTLSGLLNFTDGLWSCC EE+IIVFTTNHR++VDPAL+RCGRMDVH
Sbjct: 234 LGTGNDQLLEESGRVTLSGLLNFTDGLWSCCGEERIIVFTTNHRENVDPALVRCGRMDVH 293

Query: 389 VSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRG-NVDL 447
           VSLGTCG HAFK LA NYLGIE H + FDVVESCIR+GGALTPAQIGE+LLRNRG NVDL
Sbjct: 294 VSLGTCGMHAFKALAMNYLGIEWHSS-FDVVESCIRSGGALTPAQIGEILLRNRGNNVDL 352

Query: 448 AMKEVVSAMQ 457
           A+KEVVSAMQ
Sbjct: 353 AIKEVVSAMQ 362

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326513926|dbj|BAJ92113.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  540 bits (1391), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 294/539 (54%), Positives = 368/539 (68%), Gaps = 34/539 (6%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           ME LSQMWSLLGLLT+LQNVLP+QLLSLLHS ++SLQD  +PYSYF++PEF G   V+ N
Sbjct: 1   MEFLSQMWSLLGLLTILQNVLPTQLLSLLHSLWQSLQDSLTPYSYFDVPEFLGSAAVEPN 60

Query: 61  DLYRHVNLYLNSVNPAGSSTCRRLTLSRSRS--------SNRISFTVAPNHTVHDSFSGH 112
            LYRHV LYL+      S +  RLTLS  RS        +   S +++PNH+V D+F+GH
Sbjct: 61  ALYRHVQLYLHRSLLLSSPSPPRLTLSLPRSVAGNAGAAAPPPSVSLSPNHSVPDAFNGH 120

Query: 113 SLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTN 172
              WTHH DT+QDS+EE+RSF+L+LPKRH   +L AYL H+ + A+  ER SR RRL TN
Sbjct: 121 RAVWTHHADTLQDSLEERRSFSLRLPKRHAAAVLPAYLAHLAAAADSLERSSRARRLHTN 180

Query: 173 NGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYL 232
                  + W SVPF HPSTFETLAL+P+LK ++  DLTAFA+G+EFY R GR WKRGYL
Sbjct: 181 AASPRGSASWSSVPFCHPSTFETLALDPELKARLLADLTAFADGREFYRRTGRPWKRGYL 240

Query: 233 LYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSV 292
           L+GPPGSGKSSLIAAMAN+L YDV+DLELT+VT N++LRALL+QTTNRS+IVIEDIDCS+
Sbjct: 241 LHGPPGSGKSSLIAAMANHLRYDVFDLELTRVTTNADLRALLIQTTNRSLIVIEDIDCSL 300

Query: 293 DLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFT 352
            LT DR L S         +R ++  +  S       G +N+      G+VTLSGLLNFT
Sbjct: 301 HLTGDRGLASMRR----HKRRRTAASDDSSDSDDDVMGADNHR-----GKVTLSGLLNFT 351

Query: 353 DGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIE-S 411
           DGLWSCC EE+IIVFTTNH D +DPAL+R GRMDVHV LG CG HA + L + Y+G+   
Sbjct: 352 DGLWSCCGEERIIVFTTNHVDGIDPALLRPGRMDVHVRLGPCGVHAMRELVERYVGVSVG 411

Query: 412 HHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDE 471
              + D  E CIR G  +TPA++GEVLLRNR   + A+ E+ + ++A++ +  ++   D 
Sbjct: 412 DQDMLDAAEGCIRDGAEMTPAEVGEVLLRNRDEPETAVTELAAELKARVNAADDLQWEDS 471

Query: 472 LVITRSPESVVVVRSPENWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGRKGV 530
                         + E  D SP  K G +     EG K   L RLRSLTKSDSGR+GV
Sbjct: 472 --------------AAELSDESP-TKKGRKGFGGWEG-KVRILGRLRSLTKSDSGRRGV 514

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242044842|ref|XP_002460292.1| hypothetical protein SORBIDRAFT_02g026090 [Sorghum bicolor] gi|241923669|gb|EER96813.1| hypothetical protein SORBIDRAFT_02g026090 [Sorghum bicolor]

 Score =  536 bits (1381), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 285/541 (52%), Positives = 360/541 (66%), Gaps = 32/541 (5%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           ME LSQMWSLLGLLT+LQNVLP+QLLSLLHS ++SLQD  +PYSYF++PEF G   V+ N
Sbjct: 1   MEFLSQMWSLLGLLTILQNVLPTQLLSLLHSLWQSLQDSLTPYSYFDVPEFLGSAAVEPN 60

Query: 61  DLYRHVNLYLNSVNPAGSSTCRRL-TLSRSRSS------------NRISFTVAPNHTVHD 107
            LYRHV LYL+      SS      TLS  RSS            +  S +++PNH+V D
Sbjct: 61  ALYRHVQLYLHRSLLLSSSPPPPRLTLSLPRSSAVSGGQAHGAAPSPPSVSLSPNHSVAD 120

Query: 108 SFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRER 167
           +F+GH   WTHH DT+QDS+EE+RSF+L+LPKRH   +L AYL H+   A+  ER SR R
Sbjct: 121 TFNGHRAVWTHHADTLQDSLEERRSFSLRLPKRHAAAVLPAYLAHLADAADHLERSSRAR 180

Query: 168 RLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAW 227
           RL TN       + W SVPF HP+TF+TLAL+P LK ++  DLTAF+ G+EFY R GR W
Sbjct: 181 RLHTNAASPRGAAAWASVPFCHPATFDTLALDPGLKARLLADLTAFSEGREFYRRTGRPW 240

Query: 228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIED 287
           KRGYLL+GPPGSGKSSLIAAMAN+L YDV+DLELT+V  N++LRALL+QTTNRS+IVIED
Sbjct: 241 KRGYLLHGPPGSGKSSLIAAMANHLRYDVFDLELTRVATNADLRALLIQTTNRSLIVIED 300

Query: 288 IDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSG 347
           IDCS+ LT DR L S       K   +S   +       +  G N ++N    G+VTLSG
Sbjct: 301 IDCSLHLTGDRGLASERMHKRRKLHATSYNDDSSDSDDDAEAGANGDDN--HRGKVTLSG 358

Query: 348 LLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL 407
           +LNFTDGLWSCC EE+IIVFTTNH D +DPAL+R GRMDVHV L  CG HA + L + Y+
Sbjct: 359 ILNFTDGLWSCCGEERIIVFTTNHVDGIDPALLRPGRMDVHVRLDACGTHAMRELVQRYV 418

Query: 408 GIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVM 467
           G+  H  + D  E  IR G  +TPA++GEVLLRNR   + A+ E+ + ++A+  +  ++ 
Sbjct: 419 GVGDHE-MLDAAEDSIRRGAEMTPAEVGEVLLRNRDEPEAAVTELAAELKARRSAADDLH 477

Query: 468 ECDELVITRSPESVVVVRSPENWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGR 527
           + ++              + E  D SP  K   R     EG K   L RLRSLTKS+SGR
Sbjct: 478 QWED-------------SAAELSDGSPTKK--GRKGLGWEG-KVRILGRLRSLTKSESGR 521

Query: 528 K 528
           +
Sbjct: 522 R 522

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226495729|ref|NP_001145385.1| uncharacterized protein LOC100278733 precursor [Zea mays] gi|194699030|gb|ACF83599.1| unknown [Zea mays] gi|195655401|gb|ACG47168.1| hypothetical protein [Zea mays] gi|414885676|tpg|DAA61690.1| TPA: hypothetical protein ZEAMMB73_545222 [Zea mays]

 Score =  532 bits (1371), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 287/540 (53%), Positives = 357/540 (66%), Gaps = 33/540 (6%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVN 60
           ME LSQMWSLLGLLT+LQNVLP+QLLSLLHS ++SLQD  +PYSYF++PEF G   V+ N
Sbjct: 1   MEFLSQMWSLLGLLTILQNVLPTQLLSLLHSLWQSLQDSLTPYSYFDVPEFLGSAAVEPN 60

Query: 61  DLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSS------------NRISFTVAPNHTVHDS 108
            LYRH+ LYL+      S    RLTLS  RSS            +  S +++PNH+V D+
Sbjct: 61  ALYRHIQLYLHRSLLLSSPPPPRLTLSLPRSSAGSGGHAHGAAPSPPSVSLSPNHSVADT 120

Query: 109 FSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERR 168
           F+GH   WTHH DT+QDS+EE+RSF+L+LPKRH   +L AYL H+   A+  ER SR RR
Sbjct: 121 FNGHRAVWTHHADTLQDSLEERRSFSLRLPKRHAAAVLPAYLAHLADAADHLERSSRARR 180

Query: 169 LFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWK 228
           L TN       + W SVPF HP+TF+TLAL+P LK ++  DLTAF+ G+EFY R GR WK
Sbjct: 181 LHTNAASPRGAAAWASVPFCHPATFDTLALDPGLKARLLADLTAFSQGREFYRRTGRPWK 240

Query: 229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDI 288
           RGYLL+GPPGSGKSSLIAAMAN+L YDV+DLELT+V  N++LRALL+QTTNRS+IVIEDI
Sbjct: 241 RGYLLHGPPGSGKSSLIAAMANHLRYDVFDLELTRVATNADLRALLIQTTNRSLIVIEDI 300

Query: 289 DCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGL 348
           DCS+ LT DR L S       K   +S         + S      N +    G+VTLSGL
Sbjct: 301 DCSLHLTGDRGLASERLHKRRKLHAAS----YNDDSSDSDDDAGANGDDNHRGKVTLSGL 356

Query: 349 LNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG 408
           LNFTDGLWSCC EE+IIVFTTNH D +DPAL+R GRMDVHV L  CG HA + L + Y+G
Sbjct: 357 LNFTDGLWSCCGEERIIVFTTNHVDGIDPALLRPGRMDVHVRLDACGTHAMRELVQRYVG 416

Query: 409 IESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVME 468
           +  H  + D  E  IR G  +TPA++GEVLLRNR   + A+ E+ + ++A+  +   + E
Sbjct: 417 VGDHE-MVDAAEDSIRGGAEMTPAEVGEVLLRNRDEPEAAVTELAAELKARRSAADNIHE 475

Query: 469 CDELVITRSPESVVVVRSPENWDSSPGGKYGNRSKKRKEGTKANFLVRLRSLTKSDSGRK 528
            D+              + E  D SP  K   R     EG K   L RLRSLTKS+SGR+
Sbjct: 476 WDD-------------SAAELSDGSPTKK--GRKGLGWEG-KIRILGRLRSLTKSESGRR 519

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	530
TAIR|locus:2174502	520	AT5G57480 [Arabidopsis thalian	0.794	0.809	0.438	2.4e-92
TAIR|locus:2128916	519	AT4G30250 [Arabidopsis thalian	0.790	0.807	0.449	2.1e-91
TAIR|locus:505006520	506	AT4G25835 [Arabidopsis thalian	0.781	0.818	0.431	2e-88
TAIR|locus:2098658	530	AT3G28510 [Arabidopsis thalian	0.811	0.811	0.397	9.7e-80
TAIR|locus:2039981	491	AT2G46620 [Arabidopsis thalian	0.483	0.521	0.389	1.2e-77
TAIR|locus:2095532	477	AT3G28600 [Arabidopsis thalian	0.494	0.549	0.392	1.5e-77
TAIR|locus:2098648	510	AT3G28540 [Arabidopsis thalian	0.818	0.850	0.389	3.4e-77
TAIR|locus:2178067	514	AATP1 "AAA-ATPase 1" [Arabidop	0.501	0.517	0.403	5.2e-77
TAIR|locus:2095537	474	AT3G28610 [Arabidopsis thalian	0.490	0.548	0.404	5.2e-77
TAIR|locus:2078007	451	AT3G50940 [Arabidopsis thalian	0.496	0.583	0.392	1.4e-76

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

 Score = 920 (328.9 bits), Expect = 2.4e-92, P = 2.4e-92
 Identities = 199/454 (43%), Positives = 280/454 (61%)

Query:    22 PSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNS-VNPAGXXX 80
             P +L      F+  +  +FS Y YF+I E +G   V+ N+LY  V LYL+S V+ AG   
Sbjct:    27 PPELRFAFLKFFNRIFHVFSSYCYFDITEIDG---VNTNELYNAVQLYLSSSVSIAGNRL 83

Query:    81 XXXXXXXXXXXXXXXXFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSV-------EEKRSF 133
                             F ++ N ++ D+F+G ++ W H V   Q          EEKR F
Sbjct:    84 SLTRAVNSSSIT----FGLSNNDSIVDTFNGVTVLWEHVVTQRQTQTFAWRPLPEEKRGF 139

Query:   134 TLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDS-G--WVSVPFRHP 190
             TL++ K+ +  +L++YLD++  RA E  R +++R L+TN+  GS DS G  W SVPF+HP
Sbjct:   140 TLRIKKKDKTLILNSYLDYIMERANEIRRKNQDRLLYTNSRGGSLDSRGHPWESVPFKHP 199

Query:   191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN 250
             STFETLA++P+ K+QI +DL  FA G+ FY + GRAWKRGYLLYGPPG+GKSS+IAAMAN
Sbjct:   200 STFETLAMDPRKKQQIMDDLKDFAEGQVFYQKTGRAWKRGYLLYGPPGTGKSSMIAAMAN 259

Query:   251 YLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLXXXXXXXXXX 310
             YL YD+YDLELT+V  NSELR LL++T+++SIIVIEDIDCS++LT  +            
Sbjct:   260 YLGYDIYDLELTEVHSNSELRKLLMKTSSKSIIVIEDIDCSINLTNRKK-------NSSN 312

Query:   311 XXXXXXXXEMGSRIASSTCGXXXXXXGEESGR---VTLSGLLNFTDGLWSCCSEEKIIVF 367
                     +  +R  S   G      GEE G    +TLSGLLNFTDGLWSCC  E+I VF
Sbjct:   313 VSSQRSYYDAETRNGS---GSGSGGSGEEGGNGNTITLSGLLNFTDGLWSCCGSERIFVF 369

Query:   368 TTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESC--IRA 425
             TTNH + +DPAL+R GRMD+H+ +  C   + K+L KNYLG        DV++    +  
Sbjct:   370 TTNHIEKLDPALLRSGRMDMHIYMSFCNFPSLKILLKNYLGYGVEDINGDVLKEMEMVVE 429

Query:   426 GGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAK 459
                +TPA + E L++NR + + A++E++  ++++
Sbjct:   430 KAEMTPADVSEALIKNRRDKEKAIRELLEDLKSR 463

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:2128916 AT4G30250 [Arabidopsis thaliana (taxid:3702)]

 Score = 911 (325.7 bits), Expect = 2.1e-91, P = 2.1e-91
 Identities = 209/465 (44%), Positives = 281/465 (60%)

Query:    22 PSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNS---VNPAGX 78
             P   L+ LH F   ++ +FS + YF+I E +G   V+ N+LY  V LYL+S   VN A  
Sbjct:    28 PELRLAFLH-FLTRIRHVFSSHIYFDITEIDG---VNTNELYNAVQLYLSSSVTVNDAVS 83

Query:    79 XXXXXXXXXXXXX--XXXXXFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSV--------- 127
                                 F ++ N  + D F+G ++ W H V  VQ  V         
Sbjct:    84 SSNNNTRLSLTRVPNSSSVTFGLSNNDRITDVFNGVTILWEHVV--VQRQVQSFSWRPMP 141

Query:   128 EEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSG---WVS 184
             EEKR FTL++ KR +  +L +YLD++  ++EE  R + ER L+TN+   S D+    W S
Sbjct:   142 EEKRGFTLQINKRDKALVLDSYLDYIVGKSEEIRRRNEERLLYTNSRGVSLDARSHPWDS 201

Query:   185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSL 244
             V F+HPSTF+TLA++P+ KK+I EDL  FANG+ FY + GRAWKRGYLLYGPPG+GKSSL
Sbjct:   202 VRFKHPSTFDTLAMDPEKKKRIMEDLREFANGQGFYQKTGRAWKRGYLLYGPPGTGKSSL 261

Query:   245 IAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLXXXX 304
             IAAMANYL YD+YDLELT+V +NSELR LL++T+++SIIVIEDIDCS+ LT         
Sbjct:   262 IAAMANYLGYDIYDLELTEVQNNSELRKLLMKTSSKSIIVIEDIDCSISLTK-------- 313

Query:   305 XXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGR-VTLSGLLNFTDGLWSCCSEEK 363
                           + GS       G       EE G  VTLSGLLNFTDGLWSCC  EK
Sbjct:   314 --------RGKNKKKNGSYEYDP--GLTNGSGLEEPGSSVTLSGLLNFTDGLWSCCGSEK 363

Query:   364 IIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHH---ALFDVVE 420
             I VFTTNH + +D AL+R GRMD+HV +G C   A K+L KNYL +E       +   +E
Sbjct:   364 IFVFTTNHIEKLDSALMRSGRMDMHVHMGFCKFPALKILLKNYLRLEEEDMDSVVLKEME 423

Query:   421 SCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGRE 465
              C+     +TPA + EVL+RNR + + A++E+VS ++ +++  R+
Sbjct:   424 ECVEEA-EITPADVSEVLIRNRSDAEKAVREIVSVLKERVVKRRK 467

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:505006520 AT4G25835 [Arabidopsis thaliana (taxid:3702)]

 Score = 883 (315.9 bits), Expect = 2.0e-88, P = 2.0e-88
 Identities = 196/454 (43%), Positives = 277/454 (61%)

Query:    22 PSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNS-VNPAGXXX 80
             P +L   +   +     LFS + YF+I E +G   V+ N+LY  V LYL+S V+ AG   
Sbjct:    27 PPELRFAISKLFNKFFKLFSTFCYFDITEIDG---VNTNELYNAVQLYLSSSVSIAGNRL 83

Query:    81 XXXXXXXXXXXXXXXXFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSV-------EEKRSF 133
                             F ++ N ++ D+F+  ++ W H V   Q          EEKR F
Sbjct:    84 SLTRAVNSSSVT----FGLSNNDSIVDTFNSVTVVWEHIVTQRQTQTFAWRPMPEEKRGF 139

Query:   134 TLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDS-G--WVSVPFRHP 190
             TL++ K+ +  +L +YLD++  +A E  R++++R L+TN+  GS DS G  W SVPF+HP
Sbjct:   140 TLRIKKKDKNLILDSYLDYIMEKANEIRRLNQDRLLYTNSRGGSLDSRGLPWESVPFKHP 199

Query:   191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN 250
             STF+TLA++P  K+QI EDL  FA  + FY R GRAWKRGYLLYGPPG+GKSS+IAAMAN
Sbjct:   200 STFDTLAMDPVKKQQIMEDLKDFAECQSFYERTGRAWKRGYLLYGPPGTGKSSMIAAMAN 259

Query:   251 YLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLXXXXXXXXXX 310
             YL YD+YDLELT+V  NSELR LL++T+++SIIVIEDIDCS++LT +R            
Sbjct:   260 YLRYDIYDLELTEVKSNSELRKLLMKTSSKSIIVIEDIDCSINLT-NR--------NKKQ 310

Query:   311 XXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTN 370
                     EM   +  S  G        +   +TLSGLLNFTDGLWSCC  E+I VFTTN
Sbjct:   311 STGSYNEPEM---LTGSGLGDDLG----DGNTITLSGLLNFTDGLWSCCGSERIFVFTTN 363

Query:   371 HRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHH----ALFDVVESCIRAG 426
             H + +DPAL+R GRMD+H+ +  C   + K+L +NYLG E        L ++ E   RA 
Sbjct:   364 HIEKLDPALLRSGRMDMHIHMSYCTFSSVKILLRNYLGFEEGDLNDVVLKELAEVVDRA- 422

Query:   427 GALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKI 460
               +TPA + E L++NR + + A++E++  +++++
Sbjct:   423 -EITPADVSEALIKNRRDKERAVRELLVDLRSRV 455

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:2098658 AT3G28510 [Arabidopsis thaliana (taxid:3702)]

 Score = 801 (287.0 bits), Expect = 9.7e-80, P = 9.7e-80
 Identities = 184/463 (39%), Positives = 260/463 (56%)

Query:    22 PSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGXXXX 81
             P+   + +  ++  +    S Y   +  E+    G+  +  Y  +  YL S + A     
Sbjct:    30 PAHFRAYVERYFHKMIGWISYYVDIKFTEYTDE-GLKRSQAYDSIRNYLASKSTA---LA 85

Query:    82 XXXXXXXXXXXXXXXFTVAPNHTVHDSFSGHSLSWTHHVDTVQD-------SVEEKRSFT 134
                            F++  +  + D F G  + W  +V  +Q        S EE+R FT
Sbjct:    86 KRLKANETKNSKSLVFSMDDHEEIEDEFEGVKVKWYSNVKVIQPQSNYGQRSSEERRHFT 145

Query:   135 LKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSY---DSG-WVSVPFRHP 190
             L   +RHR  ++  YLDHV    +    ++RER+L+TNN    +    SG W +VPF HP
Sbjct:   146 LSFHRRHRGMIIETYLDHVLREGKAIGLMNRERKLYTNNSSQEWYPWRSGKWSNVPFHHP 205

Query:   191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN 250
             +TFETLA++P+ K+ I +DL  F+ GK++Y +VG+ WKRGYLL+GPPG+GKS++IAA+AN
Sbjct:   206 ATFETLAMDPEKKEGIKKDLIKFSKGKDYYKKVGKPWKRGYLLFGPPGTGKSTMIAAIAN 265

Query:   251 YLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLXXXXXXXXXX 310
             +L YDVYDLELT V DNSEL+ LLL TT++SIIVIEDIDCS+DLT  R            
Sbjct:   266 FLDYDVYDLELTTVKDNSELKKLLLDTTSKSIIVIEDIDCSLDLTGQRK----------- 314

Query:   311 XXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTN 370
                     E G        G       ++  +VTLSGLLN  DGLWS CS EKIIVFTTN
Sbjct:   315 KKKEEDEEEDGEEKKE---GEKKPKVDDKQSKVTLSGLLNSIDGLWSACSGEKIIVFTTN 371

Query:   371 HRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALT 430
               D +DPALIR GRMD H+ +  C   AFKVLAKNYL IE+H  L+  +E  +     ++
Sbjct:   372 FVDKLDPALIRRGRMDNHIEMSYCKFEAFKVLAKNYLEIETHD-LYGEIERKLEETD-MS 429

Query:   431 PAQIGEVLL--RNRGNVDLAMKEVVSAMQAKILSGREVMECDE 471
             PA + E L+   +  + D+ +K +V  ++ +    R++ E +E
Sbjct:   430 PADVAETLMPKSDEEDADICIKRLVKTLEEEKEKARKLAEEEE 472

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:2039981 AT2G46620 [Arabidopsis thaliana (taxid:3702)]

 Score = 503 (182.1 bits), Expect = 1.2e-77, Sum P(2) = 1.2e-77
 Identities = 106/272 (38%), Positives = 161/272 (59%)

Query:    25 LLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGXXXXXXX 84
             L+ ++  +   + D F  Y ++++PEFN    V  N LY+ V +YLNS++          
Sbjct:    30 LIYMVKLWRRKIIDWFHVYQFYKVPEFND--NVQENHLYQKVYMYLNSLS--SIENSDFT 85

Query:    85 XXXXXXXXXXXXFTVAPNHTVHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHRQT 144
                           +  N  V D F G  + W +  D  +D     R+F LK+ K  ++ 
Sbjct:    86 NLFTGKKSNEIILRLDRNQVVGDEFLGARVCWINGED--EDGA---RNFVLKIRKADKRR 140

Query:   145 LLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSY------DSG-WVSVPFRHPSTFETLA 197
             +L +YL H+ + ++E E+ + E +LF N G   +       +G W S+PF HP TF+ +A
Sbjct:   141 ILGSYLQHIHTVSDELEQRNTELKLFINVGIDDHLNKKKKKNGRWRSIPFDHPCTFDNIA 200

Query:   198 LEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVY 257
             +E  LK ++  DL +F  GK++Y+R+GR WKR YLLYGP G+GKSS +AAMAN+L YDVY
Sbjct:   201 METDLKNKVKSDLESFLKGKQYYNRLGRVWKRSYLLYGPSGTGKSSFVAAMANFLDYDVY 260

Query:   258 DLELTKVTDNSELRALLLQTTNRSIIVIEDID 289
             D++L+KV D+S+L+ LLLQT  +S+IVIED+D
Sbjct:   261 DIDLSKVVDDSDLKMLLLQTRGKSVIVIEDLD 292

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:2095532 AT3G28600 [Arabidopsis thaliana (taxid:3702)]

 Score = 488 (176.8 bits), Expect = 1.5e-77, Sum P(2) = 1.5e-77
 Identities = 110/280 (39%), Positives = 159/280 (56%)

Query:    24 QLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGXXXXXX 83
             Q LS +  F +   + FSPY   EI  F+ Y     N  +  +  YL +           
Sbjct:    42 QQLSFVQRFSDRFINFFSPY--VEI-SFSQYEDYQFNHAFAAIETYLGA-----KATDKA 93

Query:    84 XXXXXXXXXXXXXFTVAPNHT-VHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLPKRHR 142
                            +  + T V D + G ++ W    D+        R+F L   +R R
Sbjct:    94 KHLRASQVKESKGLVLKRDETKVRDEYEGGTVWWEMETDSTG-----YRTFKLTFHRRSR 148

Query:   143 QTLLSAYLDHVTSRAEEFERVSRERRLFTNN--GH-G-SYDSGWVSVPFRHPSTFETLAL 198
               +  +Y+ +V    +  +  S++ +LFTNN   H G S  S W  + F HP++F TLA+
Sbjct:   149 DIVTDSYIKYVFEEGKSIQAKSKQMKLFTNNPSSHWGTSKKSFWRYIDFEHPASFHTLAM 208

Query:   199 EPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD 258
             + + K++I  DL AF+NGKE+Y ++G+AWKRGYLL+GPPG+GKS++IAAMAN+L Y +YD
Sbjct:   209 DTKKKEEILNDLAAFSNGKEYYKKIGKAWKRGYLLHGPPGTGKSTMIAAMANHLNYSIYD 268

Query:   259 LELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADR 298
             LELT + +NSELR LL  T+++SIIVIEDIDCS+DLT  R
Sbjct:   269 LELTAIRNNSELRKLLTATSSKSIIVIEDIDCSLDLTGKR 308

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:2098648 AT3G28540 [Arabidopsis thaliana (taxid:3702)]

 Score = 777 (278.6 bits), Expect = 3.4e-77, P = 3.4e-77
 Identities = 179/460 (38%), Positives = 254/460 (55%)

Query:    22 PSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGXXXX 81
             P Q+   L   +  +  L S   + +  E+    G+  +  Y  +  YL+S + A     
Sbjct:    30 PYQIRDYLEKCFYKMFGLVSNSVHIKFTEYTEDKGLKKSQAYDLIRNYLSSKSTARAQRL 89

Query:    82 XXXXXXXXXXXXXXXFTVAPNH-TVHDSFSGHSLSWTHHVDTVQDSVE--EKRSFTLKLP 138
                                 NH  V D F G  + W+  V    D  +  EKR  TL   
Sbjct:    90 KANESKNSKSLVLSL----DNHEAVEDVFQGVKVVWSLSVWKSNDQADSSEKRYLTLSFH 145

Query:   139 KRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDS---G-WVSVPFRHPSTFE 194
              R+R+ + + YLDHV    +E    +RER+L+TNN    Y +   G W +VPF HP+TFE
Sbjct:   146 NRYREMITTTYLDHVLREGKEIGLKNRERKLYTNNSSQDYSAWREGRWSNVPFDHPATFE 205

Query:   195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY 254
             TLA++ + K+ + +DL  F  GK++Y +VG+ WKRGYLL+GPPG+GKS++I+AMAN+L Y
Sbjct:   206 TLAMDLEKKEGMKKDLIKFTKGKDYYRKVGKPWKRGYLLFGPPGTGKSTMISAMANFLEY 265

Query:   255 DVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXX 314
             DVYDLELT V DNSEL+ L+L T  +SI+VIEDIDCS+DLT  R                
Sbjct:   266 DVYDLELTTVKDNSELKKLMLDTKGKSIVVIEDIDCSLDLTGQRKKKKEEDEDEEEEEKK 325

Query:   315 XXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS 374
                 ++  R             GE   +VTLSGLLN  DGLWS CS EKIIVFTTN+ D 
Sbjct:   326 KEAEKLLKR-----------ERGERESKVTLSGLLNAIDGLWSACSGEKIIVFTTNYLDK 374

Query:   375 VDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQI 434
             +DPALIR GRMD H+ +  C   AFKVLAKNYL IESH  LF  ++  +     ++PA +
Sbjct:   375 LDPALIRRGRMDNHIEMSYCRFEAFKVLAKNYLEIESHD-LFGEIKRLVEETD-MSPADV 432

Query:   435 GEVLL--RNRGNVDLAMKEVVSAMQAKILSGREVMECDEL 472
              E L+   +  + D+ +  +V +++ +    +++ E +++
Sbjct:   433 AENLMPKSDEDDADICLTRLVKSLEEEKEKAKKLAEEEKM 472

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 = 504 (182.5 bits), Expect = 5.2e-77, Sum P(2) = 5.2e-77
 Identities = 115/285 (40%), Positives = 165/285 (57%)

Query:    29 LHSFYESL-QDLFS-PYSYFEIPEFNGYCGVDV--NDLYRHVNLYLNSVNPAGXXXXXXX 84
             L   +E L Q L    Y Y +I  F+ Y G     +D+Y  +  YL+  + +        
Sbjct:    33 LREHFEPLAQSLIGFIYPYIQIT-FHEYSGERFKRSDVYDAIQSYLSKDSSS---RAKKL 88

Query:    85 XXXXXXXXXXXXFTVAPNHTVHDSFSGHSLSWT---HHVDTVQDS----VEEKRSFTLKL 137
                          ++  +  + D F G  + W    H  ++   S     +E R + LK 
Sbjct:    89 TANTIKGNKSIILSMDDHEEITDEFQGVKVWWQSKKHQSESRAISFYPKADESRFYMLKF 148

Query:   138 PKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGH----GSYDSGWVSVPFRHPSTF 193
              +R R+ +   YL+HV S  +  E  +RER+L++NN      G   + W  V F HP+TF
Sbjct:   149 HRRDREVITKKYLNHVISEGKTIEVKNRERKLYSNNPSQNWSGYKQTKWSHVTFEHPATF 208

Query:   194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC 253
             +TLA+E + K++I  DL  F+N K++Y ++G+AWKRGYLL+GPPG+GKS++IAAMAN L 
Sbjct:   209 DTLAMEYKKKEEIKNDLIKFSNSKDYYKKIGKAWKRGYLLFGPPGTGKSTMIAAMANLLE 268

Query:   254 YDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADR 298
             YDVYDLELT V DN+ELR LL++T+ +SIIVIEDIDCS+DLT  R
Sbjct:   269 YDVYDLELTTVKDNTELRRLLIETSGKSIIVIEDIDCSLDLTGQR 313

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:2095537 AT3G28610 [Arabidopsis thaliana (taxid:3702)]

 Score = 500 (181.1 bits), Expect = 5.2e-77, Sum P(2) = 5.2e-77
 Identities = 114/282 (40%), Positives = 160/282 (56%)

Query:    24 QLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGXXXXXX 83
             Q +S    F +   + FSPY      E+  Y    VN  +  +  YL +           
Sbjct:    41 QQISFAKRFSDKFINFFSPYVQINFSEYEDY---RVNHAFDPIETYLGA-----KATDKA 92

Query:    84 XXXXXXXXXXXXXFTVAPNHT-VHDSFSGHSLSWTHHVDTVQDSVEEKRSFTLKLP--KR 140
                            +  + T V D + G  + W   ++T  DS   K   TLKL   +R
Sbjct:    93 KHLRASQVRESKGLVLKRDETKVRDEYEGIRVWW--EMET--DSAGYK---TLKLTFHRR 145

Query:   141 HRQTLLSAYLDHVTSRAEEFERVSRERRLFTNN--GH--GSYDSGWVSVPFRHPSTFETL 196
              R  + ++Y+ +V    +  +  +++ +LFTNN   H   S  S W  + F HP+TFETL
Sbjct:   146 SRDIVTNSYIKYVVEEGKSIDAKNKKMKLFTNNPSSHWGSSKTSFWRYIDFEHPATFETL 205

Query:   197 ALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDV 256
             A++P+ K+QI  DL AF NGK++Y ++G+AWKRGYLLYGPPG+GKS++IAAMAN L Y +
Sbjct:   206 AMDPKKKEQILNDLAAFNNGKDYYKKIGKAWKRGYLLYGPPGTGKSTMIAAMANLLNYSI 265

Query:   257 YDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADR 298
             YDLELT + +NSELR +L  T+N+SIIVIEDIDCS+DLT  R
Sbjct:   266 YDLELTAIQNNSELRKILTATSNKSIIVIEDIDCSLDLTGKR 307

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:0042991 "transcription factor import into nucleus" evidence=RCA

TAIR|locus:2078007 AT3G50940 [Arabidopsis thaliana (taxid:3702)]

 Score = 479 (173.7 bits), Expect = 1.4e-76, Sum P(2) = 1.4e-76
 Identities = 111/283 (39%), Positives = 157/283 (55%)

Query:    29 LHSFYE-SLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGXXXXXXXXXX 87
             +H +     +  FS +SY        + G + N ++     YL++               
Sbjct:    41 VHEYISHGFRRFFSYFSYQMTAVIEEFGGFEHNQVFEAAEAYLSTKI---SNSTRRIKVN 97

Query:    88 XXXXXXXXXFTVAPNHTVHDSFSGHSLSWT---HHVDT--------VQDSVE-EKRSFTL 135
                       TV  +  V D F G  LSW     HVD         +  +++ E RS+ L
Sbjct:    98 KLEKQSNYSVTVERDEEVVDIFDGVKLSWILVCRHVDKKDFRNPRDLNSTLKSEVRSYEL 157

Query:   136 KLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFET 195
                K+ +  +L +YL  V  +A   ++  +  ++FT +   SY   W SV   HPSTF T
Sbjct:   158 SFRKKFKNMVLESYLPFVVEQAASIKQKFKTLKIFTVD---SYSVEWTSVTLDHPSTFRT 214

Query:   196 LALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD 255
             LAL+P++KK + EDL  F   K FY RVG+AWKRGYLLYGPPG+GKSSLIAA+AN+L +D
Sbjct:   215 LALDPEVKKNLVEDLDRFVQRKGFYGRVGKAWKRGYLLYGPPGTGKSSLIAAIANHLNFD 274

Query:   256 VYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADR 298
             +YDL+LT + +N+ELR LL+ T NRSI+V+EDIDCS++L  DR
Sbjct:   275 IYDLDLTSLNNNAELRRLLMSTANRSILVVEDIDCSIELK-DR 316

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.4	LOW CONFIDENCE prediction!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00003720001 SubName- Full=Chromosome chr13 scaffold_149, whole genome shotgun sequence; (477 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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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	530
pfam14363	100	pfam14363, AAA_assoc, Domain associated at C-termi	4e-19
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	3e-15
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	5e-09
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	2e-08
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	3e-07
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	7e-07
CHL00206	2281	CHL00206, ycf2, Ycf2; Provisional	6e-06
PRK08116	268	PRK08116, PRK08116, hypothetical protein; Validate	1e-05
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	2e-05
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	6e-05
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	6e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-05
COG1484	254	COG1484, DnaC, DNA replication protein [DNA replic	2e-04
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	3e-04
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	4e-04
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	5e-04
smart00382	148	smart00382, AAA, ATPases associated with a variety	6e-04
TIGR00678	188	TIGR00678, holB, DNA polymerase III, delta' subuni	0.001
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	0.002
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	0.002
pfam13207	114	pfam13207, AAA_17, AAA domain	0.002
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	0.002
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	0.002
PRK06851	367	PRK06851, PRK06851, hypothetical protein; Provisio	0.004

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

 Score = 82.2 bits (204), Expect = 4e-19
 Identities = 30/106 (28%), Positives = 45/106 (42%), Gaps = 9/106 (8%)

Query: 20  VLPSQLLSLLHS-FYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGS 78
           +LP +L   L S         FSPY    I E++G+     N LY     YL++     S
Sbjct: 1   LLPHELREYLSSLLRRLFGSRFSPYLTIVIDEYDGF---SRNQLYDAAEAYLST---KIS 54

Query: 79  STCRRLTLSRSRSSN--RISFTVAPNHTVHDSFSGHSLSWTHHVDT 122
            + RRL  S+++ S    +  ++     V D F G  + WT  V  
Sbjct: 55  PSARRLKASKAKKSKNSSLVLSLDDGEEVTDVFEGVKVWWTSVVTE 100

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

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

 Score = 72.2 bits (178), Expect = 3e-15
 Identities = 44/168 (26%), Positives = 66/168 (39%), Gaps = 50/168 (29%)

Query: 231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN------SELRALL--LQTTNRSI 282
            LLYGPPG+GK++L  A+A  L     ++  +++           LR L    +     +
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60

Query: 283 IVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGR 342
           I I++ID                                  +A S       + G+   R
Sbjct: 61  IFIDEID---------------------------------ALAGS-----RGSGGDSESR 82

Query: 343 VTLSGLLNFTDGLWSCCSEEKIIVF-TTNHRDSVDPALIRCGRMDVHV 389
             ++ LL   DG  S  S  K+IV   TN  D +DPAL+R GR D  +
Sbjct: 83  RVVNQLLTELDGFTS--SLSKVIVIAATNRPDKLDPALLR-GRFDRII 127

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

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

 Score = 58.8 bits (142), Expect = 5e-09
 Identities = 55/218 (25%), Positives = 78/218 (35%), Gaps = 75/218 (34%)

Query: 183 VSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKS 242
           V +P +HP  FE L +EP                            +G LLYGPPG+GK+
Sbjct: 194 VELPMKHPELFEHLGIEP---------------------------PKGVLLYGPPGTGKT 226

Query: 243 SLIAAMANYLCYDVYDLE----LTKVTDNSE--LRALLLQTTNR--SIIVIEDIDCSVDL 294
            L  A+AN        +     ++K    SE  LR +  +      SII I++ID     
Sbjct: 227 LLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEID----- 281

Query: 295 TADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG 354
                            KR     E+  R+ +                     LL   DG
Sbjct: 282 -------------AIAPKREEVTGEVEKRVVAQ--------------------LLTLMDG 308

Query: 355 LWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
           L        I++  TN  D++DPAL R GR D  + + 
Sbjct: 309 LKG--RGRVIVIGATNRPDALDPALRRPGRFDREIVIR 344

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

 Score = 56.3 bits (136), Expect = 2e-08
 Identities = 53/177 (29%), Positives = 77/177 (43%), Gaps = 45/177 (25%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---YDVYDLELTK--VTDNSELRA 272
           E Y  +G    +G +LYGPPG+GK+ L  A+AN        V   EL +  + D  +L  
Sbjct: 207 ELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVR 266

Query: 273 LLLQTTNR---SIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTC 329
            L +       SI+ I++ID                     TKR  +             
Sbjct: 267 ELFRVAEENAPSIVFIDEID------------------AIGTKRYDA------------- 295

Query: 330 GNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMD 386
                + GE+  + T+  LLN  DG  S   + K+I+  TN  +S+DPALIR GR+D
Sbjct: 296 ----TSGGEKEIQRTMLELLNQLDGFDSR-GDVKVIM-ATNRIESLDPALIRPGRID 346

Length = 438

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

 Score = 52.5 bits (126), Expect = 3e-07
 Identities = 48/198 (24%), Positives = 72/198 (36%), Gaps = 56/198 (28%)

Query: 201 QLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-------- 252
           + K+++ E +       E + ++G    +G LLYGPPG+GK+ L  A+A           
Sbjct: 249 EAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVK 308

Query: 253 ---CYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTA 309
                  +  E  K       +A  L     SII I++ID                  + 
Sbjct: 309 GSELLSKWVGESEKNIRELFEKARKLA---PSIIFIDEID------------------SL 347

Query: 310 KTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVF-T 368
            + R  S    G R+                       LL   DG+      E ++V   
Sbjct: 348 ASGRGPSEDGSGRRVVGQ--------------------LLTELDGI---EKAEGVLVIAA 384

Query: 369 TNHRDSVDPALIRCGRMD 386
           TN  D +DPAL+R GR D
Sbjct: 385 TNRPDDLDPALLRPGRFD 402

Length = 494

>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 = 48.7 bits (116), Expect = 7e-07
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 14/76 (18%)

Query: 228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL------ELTKVTDNSEL--------RAL 273
            +  LLYGPPG+GK++L  A+AN L             +L +    +EL           
Sbjct: 19  PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFE 78

Query: 274 LLQTTNRSIIVIEDID 289
           L +     ++ I++ID
Sbjct: 79  LAEKAKPGVLFIDEID 94

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|214396 CHL00206, ycf2, Ycf2; Provisional

 Score = 49.1 bits (117), Expect = 6e-06
 Identities = 79/335 (23%), Positives = 125/335 (37%), Gaps = 25/335 (7%)

Query: 74   NPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSL-SWTHHVDTVQDSVEEKRS 132
            NP    T  R T   S +S  I   +     V+  +    + SW  + D++ D   E+R 
Sbjct: 1465 NPINRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDDKIESWVANSDSIDD---EERE 1521

Query: 133  F-----TLKLPKRHRQTLLSAYL-DHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVP 186
            F     TL   KR  Q LLS    DH++     ++ + +   ++       +    ++  
Sbjct: 1522 FLVQFSTLTTEKRIDQILLSLTHSDHLSKNDSGYQMIEQPGSIYLRYLVDIHKKYLMNYE 1581

Query: 187  FRHPSTFET---LALEPQ-LKKQITEDLTAF---ANGKEFYHRVGRAWKRGYLLYGPPGS 239
            F      E    LA        Q +    +F   ++GK F  R+  +  RG L+ G  G+
Sbjct: 1582 FNTSCLAERRIFLAHYQTITYSQTSCGANSFHFPSHGKPFSLRLALSPSRGILVIGSIGT 1641

Query: 240  GKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRM 299
            G+S L+  +A         + L K  DN     L+          I+D D         +
Sbjct: 1642 GRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTEL 1701

Query: 300  LKSSNTST---TAKTKRSSSIKEMGSRIASSTC----GNNNNNNGEESGRVTLSGLLNFT 352
            L   N  T     K  R     +     A S C     N ++ N  ES  ++L  L+N  
Sbjct: 1702 LTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVNESNYLSLGLLVNSL 1761

Query: 353  DGLWSCCSEEKIIVFTTNHRDS-VDPALIRCGRMD 386
                  CS   I+V  + H    VDPALI   +++
Sbjct: 1762 SRDCERCSTRNILVIASTHIPQKVDPALIAPNKLN 1796

Length = 2281

>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated

 Score = 46.9 bits (112), Expect = 1e-05
 Identities = 29/100 (29%), Positives = 41/100 (41%), Gaps = 20/100 (20%)

Query: 156 RAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFAN 215
             E  E+  R  RL +N+             FR+ STFE    +   +K       A   
Sbjct: 56  EEENREKQRRIERLKSNSLLDEK--------FRN-STFENFLFDKGSEKAY---KIARKY 103

Query: 216 GKEFYHRVGRAWKR---GYLLYGPPGSGKSSLIAAMANYL 252
            K+F        K+   G LL+G  G+GK+ L A +AN L
Sbjct: 104 VKKF-----EEMKKENVGLLLWGSVGTGKTYLAACIANEL 138

Length = 268

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

 Score = 46.5 bits (111), Expect = 2e-05
 Identities = 54/187 (28%), Positives = 70/187 (37%), Gaps = 65/187 (34%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT----DNSEL--- 270
           E +  +G    +G LLYGPPG+GK+ L  A+AN           T  T      SEL   
Sbjct: 175 ELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQ----------TDATFIRVVGSELVQK 224

Query: 271 ---------RAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKE 319
                    R L  L +    SII I++ID                          +I  
Sbjct: 225 YIGEGARLVRELFELAREKAPSIIFIDEID--------------------------AIG- 257

Query: 320 MGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPAL 379
              R  S T G+       E  R T+  LLN  DG          ++  TN  D +DPAL
Sbjct: 258 -AKRFDSGTSGDR------EVQR-TMLELLNQLDGFDP--RGNVKVIMATNRPDILDPAL 307

Query: 380 IRCGRMD 386
           +R GR D
Sbjct: 308 LRPGRFD 314

Length = 406

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

 Score = 45.2 bits (107), Expect = 6e-05
 Identities = 59/212 (27%), Positives = 81/212 (38%), Gaps = 72/212 (33%)

Query: 183 VSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKS 242
           V +P +HP  FE + +EP                            +G LLYGPPG+GK+
Sbjct: 138 VELPLKHPELFEEVGIEP---------------------------PKGVLLYGPPGTGKT 170

Query: 243 SLIAAMA---NYLCYDVYDLELTK--VTDNSELRALLLQTTNR---SIIVIEDIDCSVDL 294
            L  A+A   N     V   EL +  + + + L   + +       SII I++ID     
Sbjct: 171 LLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEID----- 225

Query: 295 TADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG 354
                      +  AK            R  S T G+       E  R TL  LL   DG
Sbjct: 226 -----------AIAAK------------RTDSGTSGD------REVQR-TLMQLLAELDG 255

Query: 355 LWSCCSEEKIIVFTTNHRDSVDPALIRCGRMD 386
            +      K+I   TN  D +DPAL+R GR D
Sbjct: 256 -FDPRGNVKVIA-ATNRPDILDPALLRPGRFD 285

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

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

 Score = 45.4 bits (108), Expect = 6e-05
 Identities = 50/211 (23%), Positives = 87/211 (41%), Gaps = 50/211 (23%)

Query: 192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
           TF  +A   + K++  E++ +F    E +  VG    +G LL GPPG+GK+ L  A+A  
Sbjct: 181 TFRDIAGIEEAKEEF-EEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE 239

Query: 252 LCYDVYDLELTKVTD------NSELRALLLQTTNRS--IIVIEDIDCSVDLTADRMLKSS 303
                + +  ++  +       + +R L  +    S  I+ I++ID              
Sbjct: 240 AEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEID-------------- 285

Query: 304 NTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEK 363
                      +  ++ G+ I         N+  E+    TL+ LL   DG        K
Sbjct: 286 -----------AVGRQRGAGI------GGGNDEREQ----TLNQLLTEMDGF----KGNK 320

Query: 364 --IIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
             I++  TN  D +D AL+R GR D  +++ 
Sbjct: 321 GVIVIAATNRVDILDAALLRPGRFDRQITVS 351

Length = 638

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

 Score = 44.9 bits (107), Expect = 8e-05
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 9/70 (12%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA 249
           P T   +    + K+Q+ E + ++  GK          K+  LLYGPPG GK+SL  A+A
Sbjct: 10  PKTLSDVVGNEKAKEQLREWIESWLKGKP---------KKALLLYGPPGVGKTSLAHALA 60

Query: 250 NYLCYDVYDL 259
           N   ++V +L
Sbjct: 61  NDYGWEVIEL 70

Length = 482

>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]

 Score = 42.8 bits (101), Expect = 2e-04
 Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 10/69 (14%)

Query: 187 FRHPSTFET--LALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSL 244
           F    TFE      +P + K+  EDL +     EF+ R         +L GPPG GK+ L
Sbjct: 70  FPAKKTFEEFDFEFQPGIDKKALEDLASLV---EFFER-----GENLVLLGPPGVGKTHL 121

Query: 245 IAAMANYLC 253
             A+ N L 
Sbjct: 122 AIAIGNELL 130

Length = 254

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

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 50/210 (23%), Positives = 85/210 (40%), Gaps = 46/210 (21%)

Query: 191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN 250
           +TF  +A   + K+++ E L  +      + ++G    +G L+ GPPG+GK+ L  A+A 
Sbjct: 149 TTFADVAGCDEAKEEVAE-LVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG 207

Query: 251 YLCYDVYDL------ELTKVTDNSELRALLLQTTNRS--IIVIEDIDCSVDLTADRMLKS 302
                 + +      E+      S +R +  Q    +  II I++ID             
Sbjct: 208 EAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDA------------ 255

Query: 303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEE 362
                            +G +  +   G      G +    TL+ +L   DG     +E 
Sbjct: 256 -----------------VGRQRGAGLGG------GHDEREQTLNQMLVEMDGFEG--NEG 290

Query: 363 KIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
            I++  TN  D +DPAL+R GR D  V +G
Sbjct: 291 IIVIAATNRPDVLDPALLRPGRFDRQVVVG 320

Length = 644

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

 Score = 42.4 bits (100), Expect = 4e-04
 Identities = 17/34 (50%), Positives = 24/34 (70%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
           E Y ++G    RG LLYGPPG+GK+ L  A+A++
Sbjct: 169 ELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH 202

Length = 398

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

 Score = 42.4 bits (100), Expect = 5e-04
 Identities = 20/38 (52%), Positives = 23/38 (60%), Gaps = 2/38 (5%)

Query: 217 KEFYHRVGRAWKRGYLLYGPPGSGKSSLIA-AMANYLC 253
            E Y   G    +G LLYGPPG GK +LIA A+AN L 
Sbjct: 205 PELYREYGLKPPKGVLLYGPPGCGK-TLIAKAVANSLA 241

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 512

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

 Score = 40.0 bits (93), Expect = 6e-04
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 228 KRGYLLYGPPGSGKSSLIAAMANYL 252
               L+ GPPGSGK++L  A+A  L
Sbjct: 2   GEVILIVGPPGSGKTTLARALAREL 26

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|233087 TIGR00678, holB, DNA polymerase III, delta' subunit

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 32/116 (27%), Positives = 44/116 (37%), Gaps = 44/116 (37%)

Query: 220 YHRVGRAWKRG-----YLLYGPPGSGKSSLIAAMANYL----------------CY---- 254
           Y ++ RA ++G     YL  GP G GK  L  A+A  L                C     
Sbjct: 1   YQQLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEA 60

Query: 255 ----DVYDLELT----KVTDNSELRALLLQTT---NRSIIVIEDIDCSVDLTADRM 299
               D++ LE      KV    EL   L +T     R +++IED        A+RM
Sbjct: 61  GNHPDLHRLEPEGQSIKVDQVRELVEFLSRTPQESGRRVVIIED--------AERM 108

This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 188

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

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 42/178 (23%), Positives = 69/178 (38%), Gaps = 47/178 (26%)

Query: 217 KEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE----LTKVTDNSELRA 272
            E + ++G    +G LL+GPPG+GK+ L  A+A     +   +     L+K    SE   
Sbjct: 476 PEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESEKAI 535

Query: 273 LLLQTTNR----SIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST 328
             +    R    +II  ++ID      A       +TS T +      + ++ +      
Sbjct: 536 REIFRKARQAAPAIIFFDEIDA----IAPARGARFDTSVTDRI-----VNQLLT------ 580

Query: 329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMD 386
                    E  G   LS +               +++  TN  D +DPAL+R GR D
Sbjct: 581 ---------EMDGIQELSNV---------------VVIAATNRPDILDPALLRPGRFD 614

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

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 50/182 (27%), Positives = 66/182 (36%), Gaps = 53/182 (29%)

Query: 220 YHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT---------KVTDNSEL 270
           Y  +G    +G LL GPPG+GK+ L  A+A      V    ++          V   S +
Sbjct: 175 YQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA--GVPFFSISGSDFVEMFVGV-GASRV 231

Query: 271 RALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST 328
           R L  Q       II I++ID                       R         R A   
Sbjct: 232 RDLFEQAKKNAPCIIFIDEID--------------------AVGR--------QRGAGLG 263

Query: 329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFT-TNHRDSVDPALIRCGRMDV 387
            GN+           TL+ LL   DG       E +IV   TN  D +DPAL+R GR D 
Sbjct: 264 GGNDER-------EQTLNQLLVEMDGFG---GNEGVIVIAATNRPDVLDPALLRPGRFDR 313

Query: 388 HV 389
            +
Sbjct: 314 QI 315

Length = 596

>gnl|CDD|221983 pfam13207, AAA_17, AAA domain

 Score = 38.0 bits (88), Expect = 0.002
 Identities = 14/30 (46%), Positives = 18/30 (60%)

Query: 231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE 260
            L+ GPPGSGKS+L   +A  L   V  L+
Sbjct: 2   ILITGPPGSGKSTLAKKLAEKLGIPVISLD 31

Length = 114

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

 Score = 40.5 bits (96), Expect = 0.002
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 8/55 (14%)

Query: 232 LLYGPPGSGKSSLIAAMANYLCYDVYDL--------ELTKVTDNSELRALLLQTT 278
           +L+GPPG+GK++L   +A         L        +L +V + +  R    + T
Sbjct: 40  ILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGVKDLREVIEEARQRRSAGRRT 94

Length = 413

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

 Score = 40.3 bits (95), Expect = 0.002
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 9/63 (14%)

Query: 233 LYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN-SELRALL------LQTTNRSIIVI 285
           L+GPPG+GK++L   +A           L+ VT    +LR ++           R+I+ +
Sbjct: 53  LWGPPGTGKTTLARLIAGTTNAAFE--ALSAVTSGVKDLREIIEEARKNRLLGRRTILFL 110

Query: 286 EDI 288
           ++I
Sbjct: 111 DEI 113

Length = 436

>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional

 Score = 39.6 bits (93), Expect = 0.004
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 219 FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-DNSELRALLLQT 277
            Y  +     R ++L G PG+GKS+L+  +        YD+E    + DN  L  +++  
Sbjct: 21  LYDSIIDGANRIFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFLHCSSDNDSLDGVIIPE 80

Query: 278 TNRSII 283
              +I+
Sbjct: 81  LKIAIL 86

Length = 367

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	530
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	100.0
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0730	693	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
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	100.0
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	100.0
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	100.0
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	100.0
PRK03992	389	proteasome-activating nucleotidase; Provisional	100.0
CHL00195	489	ycf46 Ycf46; Provisional	100.0
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	100.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	100.0
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	100.0
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.98
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.98
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.98
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.97
CHL00176	638	ftsH cell division protein; Validated	99.97
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.97
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.96
CHL00206	2281	ycf2 Ycf2; Provisional	99.96
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.96
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.96
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.96
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.96
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.96
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.95
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.95
PF14363	98	AAA_assoc: Domain associated at C-terminal with AA	99.87
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.85
PF00004	132	AAA: ATPase family associated with various cellula	99.83
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.83
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.78
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.77
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.76
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.75
PRK04195	482	replication factor C large subunit; Provisional	99.74
CHL00181	287	cbbX CbbX; Provisional	99.73
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.72
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.72
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.7
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.7
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.69
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.69
PHA02544	316	44 clamp loader, small subunit; Provisional	99.68
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.68
PLN03025	319	replication factor C subunit; Provisional	99.68
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.68
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.68
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.68
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.66
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.65
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.65
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.65
PRK13342	413	recombination factor protein RarA; Reviewed	99.64
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.63
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.62
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.62
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.62
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.61
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.61
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.61
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.61
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.6
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.6
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.59
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.59
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.59
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.58
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK06893	229	DNA replication initiation factor; Validated	99.57
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.57
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.57
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.57
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.57
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.56
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.56
PRK12402	337	replication factor C small subunit 2; Reviewed	99.55
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.55
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.54
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.53
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.53
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.52
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.52
PRK13341	725	recombination factor protein RarA/unknown domain f	99.52
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.52
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.51
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.5
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.5
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.5
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.49
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.48
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.48
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.48
PRK08727	233	hypothetical protein; Validated	99.48
PRK10865	857	protein disaggregation chaperone; Provisional	99.47
PRK08084	235	DNA replication initiation factor; Provisional	99.47
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.47
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.46
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.45
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.45
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.44
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.44
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.44
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.43
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.43
KOG2028	554	consensus ATPase related to the helicase subunit o	99.42
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.42
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.4
CHL00095	821	clpC Clp protease ATP binding subunit	99.39
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.38
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.38
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.38
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.37
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.36
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.35
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.35
PRK05642	234	DNA replication initiation factor; Validated	99.35
PRK12422	445	chromosomal replication initiation protein; Provis	99.35
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.34
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.33
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.32
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.32
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.32
PRK06620	214	hypothetical protein; Validated	99.31
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.31
PHA02244	383	ATPase-like protein	99.3
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.3
PRK08181	269	transposase; Validated	99.28
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.28
PRK06526	254	transposase; Provisional	99.28
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.27
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.27
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.27
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.26
PRK07952	244	DNA replication protein DnaC; Validated	99.26
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.25
COG0714	329	MoxR-like ATPases [General function prediction onl	99.25
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.23
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.22
PRK10865	857	protein disaggregation chaperone; Provisional	99.2
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.19
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.19
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.18
PRK09087	226	hypothetical protein; Validated	99.18
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.17
CHL00095	821	clpC Clp protease ATP binding subunit	99.15
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.14
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.13
PRK08116	268	hypothetical protein; Validated	99.12
PRK12377	248	putative replication protein; Provisional	99.08
PRK09183	259	transposase/IS protein; Provisional	99.08
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.07
smart00382	148	AAA ATPases associated with a variety of cellular	99.06
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.05
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.05
PRK04132	846	replication factor C small subunit; Provisional	99.04
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.04
PRK08939	306	primosomal protein DnaI; Reviewed	99.04
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.03
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.02
PF07726	131	AAA_3: ATPase family associated with various cellu	99.02
PRK13531	498	regulatory ATPase RavA; Provisional	99.02
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.0
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.0
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.98
PRK06964	342	DNA polymerase III subunit delta'; Validated	98.95
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.93
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.92
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	98.91
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.91
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.88
smart00350	509	MCM minichromosome maintenance proteins.	98.87
PRK07993	334	DNA polymerase III subunit delta'; Validated	98.86
PRK08769	319	DNA polymerase III subunit delta'; Validated	98.84
PRK06835	329	DNA replication protein DnaC; Validated	98.82
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.81
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	98.76
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.76
PRK06871	325	DNA polymerase III subunit delta'; Validated	98.76
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.75
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	98.74
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.73
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.72
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.72
PRK06090	319	DNA polymerase III subunit delta'; Validated	98.71
PRK11608	326	pspF phage shock protein operon transcriptional ac	98.7
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	98.69
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.68
PRK06921	266	hypothetical protein; Provisional	98.68
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.62
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.62
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	98.57
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.57
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	98.56
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.54
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.54
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	98.51
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.5
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	98.47
PRK09862	506	putative ATP-dependent protease; Provisional	98.47
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.46
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.46
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	98.45
PHA02624	647	large T antigen; Provisional	98.44
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.43
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.42
PF13173	128	AAA_14: AAA domain	98.41
KOG1514	767	consensus Origin recognition complex, subunit 1, a	98.39
PHA00729	226	NTP-binding motif containing protein	98.36
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.34
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.34
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.33
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.32
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.32
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.32
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.27
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.26
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	98.24
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.24
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.24
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.21
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.21
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.2
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.2
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.2
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.2
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.19
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.17
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.17
PF05729	166	NACHT: NACHT domain	98.16
PHA02774	613	E1; Provisional	98.16
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.15
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.14
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.08
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.06
PRK15115	444	response regulator GlrR; Provisional	97.99
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	97.97
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	97.96
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	97.95
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	97.85
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.83
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.82
PRK10365	441	transcriptional regulatory protein ZraR; Provision	97.8
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.8
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	97.8
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	97.74
PRK15455	644	PrkA family serine protein kinase; Provisional	97.73
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	97.72
COG2204	464	AtoC Response regulator containing CheY-like recei	97.71
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.7
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.7
PRK00131	175	aroK shikimate kinase; Reviewed	97.68
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.68
) 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	97.67
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.63
PF08740	187	BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA A	97.62
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.6
PRK07261	171	topology modulation protein; Provisional	97.6
PRK08118	167	topology modulation protein; Reviewed	97.57
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.5
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.49
COG1241	682	MCM2 Predicted ATPase involved in replication cont	97.44
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.43
PRK06067	234	flagellar accessory protein FlaH; Validated	97.42
PRK06581	263	DNA polymerase III subunit delta'; Validated	97.42
PRK13947	171	shikimate kinase; Provisional	97.41
PRK03839	180	putative kinase; Provisional	97.4
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.4
PF14516	331	AAA_35: AAA-like domain	97.4
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.4
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.37
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.36
PRK00625	173	shikimate kinase; Provisional	97.34
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.33
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.33
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.32
PRK13949	169	shikimate kinase; Provisional	97.31
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.31
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	97.3
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.3
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.29
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	97.28
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.28
PRK13765	637	ATP-dependent protease Lon; Provisional	97.27
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.27
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	97.26
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.25
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.25
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.23
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.23
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.22
PRK04296	190	thymidine kinase; Provisional	97.22
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.21
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.18
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.18
PRK14532	188	adenylate kinase; Provisional	97.17
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.17
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.17
PRK14531	183	adenylate kinase; Provisional	97.16
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.16
COG1485	367	Predicted ATPase [General function prediction only	97.16
PRK13948	182	shikimate kinase; Provisional	97.16
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.15
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.15
PRK06217	183	hypothetical protein; Validated	97.13
PRK04841	903	transcriptional regulator MalT; Provisional	97.12
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.11
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.09
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.08
PRK12608	380	transcription termination factor Rho; Provisional	97.08
PRK13946	184	shikimate kinase; Provisional	97.07
TIGR00767	415	rho transcription termination factor Rho. Members	97.07
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.07
PRK11823	446	DNA repair protein RadA; Provisional	97.07
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.06
PRK05057	172	aroK shikimate kinase I; Reviewed	97.06
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.03
PRK09376	416	rho transcription termination factor Rho; Provisio	97.03
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	97.03
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.01
PF13245	76	AAA_19: Part of AAA domain	97.0
PRK03731	171	aroL shikimate kinase II; Reviewed	96.98
PRK08233	182	hypothetical protein; Provisional	96.97
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.96
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.96
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.94
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.94
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.94
PRK13764	602	ATPase; Provisional	96.93
PRK14530	215	adenylate kinase; Provisional	96.92
PRK05973	237	replicative DNA helicase; Provisional	96.92
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	96.92
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	96.9
PRK13695	174	putative NTPase; Provisional	96.89
PRK02496	184	adk adenylate kinase; Provisional	96.89
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.88
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	96.88
PRK06547	172	hypothetical protein; Provisional	96.88
COG1855	604	ATPase (PilT family) [General function prediction	96.87
PRK06762	166	hypothetical protein; Provisional	96.87
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.87
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.87
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.87
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.86
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.86
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	96.85
PRK14528	186	adenylate kinase; Provisional	96.85
PTZ00088	229	adenylate kinase 1; Provisional	96.84
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.82
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.81
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.81
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.79
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	96.79
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.78
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	96.77
PRK00279	215	adk adenylate kinase; Reviewed	96.76
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.76
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	96.74
PLN02200	234	adenylate kinase family protein	96.74
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	96.73
PRK04182	180	cytidylate kinase; Provisional	96.73
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.72
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.72
COG4619	223	ABC-type uncharacterized transport system, ATPase	96.71
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.71
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	96.68
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.67
PRK14527	191	adenylate kinase; Provisional	96.67
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	96.66
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.65
PRK09354	349	recA recombinase A; Provisional	96.64
cd03246	173	ABCC_Protease_Secretion This family represents the	96.63
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.61
smart00487	201	DEXDc DEAD-like helicases superfamily.	96.6
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.6
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	96.6
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.59
PRK04040	188	adenylate kinase; Provisional	96.58
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.57
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.57
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	96.57
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.56
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.56
PRK01184	184	hypothetical protein; Provisional	96.55
PF13479	213	AAA_24: AAA domain	96.53
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	96.53
PRK10436	462	hypothetical protein; Provisional	96.52
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	96.52
PRK14526	211	adenylate kinase; Provisional	96.51
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.51
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.5
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.5
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	96.49
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	96.48
PRK10646	153	ADP-binding protein; Provisional	96.48
PLN02199	303	shikimate kinase	96.47
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.46
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.45
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.45
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.44
PHA02530	300	pseT polynucleotide kinase; Provisional	96.43
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.42
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.41
PRK06696	223	uridine kinase; Validated	96.37
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	96.37
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.36
PRK09302	509	circadian clock protein KaiC; Reviewed	96.34
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.31
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.31
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	96.3
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.29
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	96.29
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.29
PHA00350	399	putative assembly protein	96.28
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	96.28
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.28
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.28
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.27
PRK00409	782	recombination and DNA strand exchange inhibitor pr	96.27
COG4133	209	CcmA ABC-type transport system involved in cytochr	96.26
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.25
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.24
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.19
cd03239	178	ABC_SMC_head The structural maintenance of chromos	96.18
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.18
PRK14529	223	adenylate kinase; Provisional	96.17
KOG2383	467	consensus Predicted ATPase [General function predi	96.17
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	96.15
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.15
PLN02674	244	adenylate kinase	96.15
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.14
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.12
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.09
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.08
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.07
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	96.04
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.04
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.04
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	96.02
PLN02459	261	probable adenylate kinase	96.0
cd01128	249	rho_factor Transcription termination factor rho is	95.99
PRK12338	319	hypothetical protein; Provisional	95.99
PRK14021	542	bifunctional shikimate kinase/3-dehydroquinate syn	95.99
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.99
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.98
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	95.97
PF13555	62	AAA_29: P-loop containing region of AAA domain	95.96
PRK09825	176	idnK D-gluconate kinase; Provisional	95.93
TIGR02236	310	recomb_radA DNA repair and recombination protein R	95.93
PRK05541	176	adenylylsulfate kinase; Provisional	95.91
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	95.91
PRK13889	988	conjugal transfer relaxase TraA; Provisional	95.9
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.88
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.87
PRK13808	333	adenylate kinase; Provisional	95.85
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	95.84
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	95.84
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.84
PRK11545	163	gntK gluconate kinase 1; Provisional	95.82
PRK04328	249	hypothetical protein; Provisional	95.8
PRK06761	282	hypothetical protein; Provisional	95.8
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.8
PRK09519	790	recA DNA recombination protein RecA; Reviewed	95.78
PRK00889	175	adenylylsulfate kinase; Provisional	95.77
COG3378	517	Phage associated DNA primase [General function pre	95.76
PRK13851	344	type IV secretion system protein VirB11; Provision	95.75
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.74
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	95.71
COG4650	531	RtcR Sigma54-dependent transcription regulator con	95.71
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	95.7
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.7
PRK00300	205	gmk guanylate kinase; Provisional	95.69
PLN02165	334	adenylate isopentenyltransferase	95.69
PRK06851	367	hypothetical protein; Provisional	95.69
PRK10416	318	signal recognition particle-docking protein FtsY;	95.68
PRK04301	317	radA DNA repair and recombination protein RadA; Va	95.66
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.66
PRK05480	209	uridine/cytidine kinase; Provisional	95.65
PRK14730	195	coaE dephospho-CoA kinase; Provisional	95.64
PTZ00202	550	tuzin; Provisional	95.64
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	95.63
PRK13975	196	thymidylate kinase; Provisional	95.61
KOG0481	729	consensus DNA replication licensing factor, MCM5 c	95.61
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.6
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.57
PRK14737	186	gmk guanylate kinase; Provisional	95.55

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

Probab=100.00  E-value=5.8e-94  Score=736.48  Aligned_cols=426  Identities=48%  Similarity=0.803  Sum_probs=390.6

Q ss_pred             ChhhHHHHHHHHHH----HHHHhhChHHHHHHHHHHHHHhhhhcCCceEEEEecccCCCCCCcChHHHHHHHHhhccCCC
Q 009640            1 MEILSQMWSLLGLL----TVLQNVLPSQLLSLLHSFYESLQDLFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPA   76 (530)
Q Consensus         1 ~~~~s~~~s~~~~~----~~~~~~~p~~l~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~n~~~~a~~~yl~~~~~~   76 (530)
                      +.+|+.++|++|++    +|+++++|..++.|+.++.++|+.++++|.++.+.|+.|   +.+|++|.|+|.||++++..
T Consensus         1 ~~~~~~~~s~~~~~~~~~~~~~~~~p~~~~~y~~~~~~~l~g~~s~~~~~~~~e~~g---~~~n~~~~aie~yl~~k~~~   77 (457)
T KOG0743|consen    1 SSVFTAYASLLGSLMFIKSMLQDIIPPSINPYFISALRGLFGVFSSYALIRIGEQDG---VFRNQLYVAIEVYLSSKSSA   77 (457)
T ss_pred             CCccchhHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHhhccCcccEEEEeehhcc---chHHHHHHHHHHhhhccchh
Confidence            45777777777744    999999999999999999999999999999999999987   49999999999999999777


Q ss_pred             CCccccceeecccCCCCceEEEeCCCCeEeecccCeEEEEEEEeeccccc-----ccccceEEEecccchhhhhHHHHHH
Q 009640           77 GSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLSWTHHVDTVQDS-----VEEKRSFTLKLPKRHRQTLLSAYLD  151 (530)
Q Consensus        77 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~d~f~g~~~~w~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~vl~~yl~  151 (530)
                      .+   +|++.+...+++++++.+++|++|.|.|+|++++|.+.+......     ..++|+|+|+|++++++.|+.+||+
T Consensus        78 ~~---~rl~~~~~~~s~~~~l~~~~~~~i~d~f~gv~~~w~~~~~~~~~~~~~~~~~~~r~~~L~f~k~~~e~V~~syl~  154 (457)
T KOG0743|consen   78 IA---KRLTQNLSKNSKSLVLGLDDNEEISDEFEGVPVKWRHFVDYNEKWIFVEREREKRYFELTFHKKPRELVTLSYLP  154 (457)
T ss_pred             hh---hhhhhhhccccccceEEecCCcEEEEEEeceEEEEEEEEEecCcccccccCCcceEEEEEecCccHHHhHHhHHH
Confidence            65   799999999999999999999999999999999999987654432     5678999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhccccCCCCC----CCCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCC
Q 009640          152 HVTSRAEEFERVSRERRLFTNNGHGS----YDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAW  227 (530)
Q Consensus       152 ~v~~~~~~~~~~~~~~~l~~~~~~~~----~~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~  227 (530)
                      ++...+++|.++++++++|++.+...    ....|.++++.||++|++|+|++++|+.|++|+..|+++++||+++|+||
T Consensus       155 ~v~~~~k~I~~~~r~~kl~t~~~~~~~~~~~~~~W~~v~f~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkaw  234 (457)
T KOG0743|consen  155 YVVSKAKEILEENRELKLYTNSGKTVIYTAKGGEWRSVGFPHPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAW  234 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCcccccccCCcceecCCCCCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcch
Confidence            99999999999999999999976433    35679999999999999999999999999999999999999999999999


Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCcc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTST  307 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~  307 (530)
                      +||||||||||||||||++||||+|++++|+++++++.++++|++||..++++||||||||||.++++.++..+.+.   
T Consensus       235 KRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n~dLr~LL~~t~~kSIivIEDIDcs~~l~~~~~~~~~~---  311 (457)
T KOG0743|consen  235 KRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLDSDLRHLLLATPNKSILLIEDIDCSFDLRERRKKKKEN---  311 (457)
T ss_pred             hccceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCcHHHHHHHHhCCCCcEEEEeeccccccccccccccccc---
Confidence            99999999999999999999999999999999999999999999999999999999999999999888876553210   


Q ss_pred             ccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeE
Q 009640          308 TAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDV  387 (530)
Q Consensus       308 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~  387 (530)
                                                  .....+++|+|||||++||+||+|+++|||||||||+++|||||+||||||+
T Consensus       312 ----------------------------~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDm  363 (457)
T KOG0743|consen  312 ----------------------------FEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDM  363 (457)
T ss_pred             ----------------------------ccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCccee
Confidence                                        0113478999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHhhCCcC-ccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhhhcccc
Q 009640          388 HVSLGTCGPHAFKVLAKNYLGIES-HHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGRE  465 (530)
Q Consensus       388 ~I~~~~p~~~~r~~i~~~~l~~~~-~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~~~~~~  465 (530)
                      ||+|++|++++++.|+++||+... |. ++++++++.. +..+|||||++.+|+++.|++.|++++++.++.++.....
T Consensus       364 hI~mgyCtf~~fK~La~nYL~~~~~h~-L~~eie~l~~-~~~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~~~~~~~~~  440 (457)
T KOG0743|consen  364 HIYMGYCTFEAFKTLASNYLGIEEDHR-LFDEIERLIE-ETEVTPAQVAEELMKNKNDADVALKGLVEALESKKEKRNK  440 (457)
T ss_pred             EEEcCCCCHHHHHHHHHHhcCCCCCcc-hhHHHHHHhh-cCccCHHHHHHHHhhccccHHHHHHHHHHHHHhhhhhhcc
Confidence            999999999999999999999975 77 9999999776 6999999999999999989999999999999988764433

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

Probab=100.00  E-value=1.1e-44  Score=361.68  Aligned_cols=220  Identities=25%  Similarity=0.287  Sum_probs=191.0

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++|+|.++++++|++.++.++.+|+.|.++|+.+|+|+|||||||||||.||+|+|++.+..|+.+..+++
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            55678889999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      +..-++.+|.-+  .+||||||||||++.                  .+|.++                 +.+
T Consensus       222 VqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg------------------~kR~d~-----------------~t~  266 (406)
T COG1222         222 VQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIG------------------AKRFDS-----------------GTS  266 (406)
T ss_pred             HHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhh------------------cccccC-----------------CCC
Confidence            2      334467787755  799999999999983                  233221                 113


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      ++..-++|+-+|||+|||+.+  .+++=|||+||+++.|||||+||||||++|+||+||.++|..||+.+......... 
T Consensus       267 gDrEVQRTmleLL~qlDGFD~--~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~d-  343 (406)
T COG1222         267 GDREVQRTMLELLNQLDGFDP--RGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADD-  343 (406)
T ss_pred             chHHHHHHHHHHHHhccCCCC--CCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccC-
Confidence            456678899999999999987  58899999999999999999999999999999999999999999999886554422 


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      -.++.++..+.++|+|||+.+|..+.
T Consensus       344 vd~e~la~~~~g~sGAdlkaictEAG  369 (406)
T COG1222         344 VDLELLARLTEGFSGADLKAICTEAG  369 (406)
T ss_pred             cCHHHHHHhcCCCchHHHHHHHHHHh
Confidence            23788888899999999999997654

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

Probab=100.00  E-value=5.5e-41  Score=356.61  Aligned_cols=244  Identities=22%  Similarity=0.268  Sum_probs=205.4

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc-
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV-  264 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~-  264 (530)
                      ...++.+|++|+|.+++|+++.+.+..++++++.|.++|+.+++|+|||||||||||++|+|+|++.+.+|+.+...++ 
T Consensus       426 ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~  505 (693)
T KOG0730|consen  426 VEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELF  505 (693)
T ss_pred             ccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHH
Confidence            3457889999999999999999999999999999999999999999999999999999999999999999999976655 


Q ss_pred             -----CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          265 -----TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       265 -----~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                           .++..++++|.++  .+||||||||||++..   +               |..                    +.
T Consensus       506 sk~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~---~---------------R~g--------------------~~  547 (693)
T KOG0730|consen  506 SKYVGESERAIREVFRKARQVAPCIIFFDEIDALAG---S---------------RGG--------------------SS  547 (693)
T ss_pred             HHhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhh---c---------------cCC--------------------Cc
Confidence                 3567799999987  6899999999999842   1               110                    12


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD  417 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~  417 (530)
                      .....+++++||++|||+..  ..+++||++||+|+.||+||+||||||+.|++++||.++|.+|++.++........ .
T Consensus       548 ~~v~~RVlsqLLtEmDG~e~--~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~-v  624 (693)
T KOG0730|consen  548 SGVTDRVLSQLLTEMDGLEA--LKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSED-V  624 (693)
T ss_pred             cchHHHHHHHHHHHcccccc--cCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCcc-c
Confidence            35678899999999999986  46899999999999999999999999999999999999999999999987665523 4


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhhhccccccccccccccC
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITR  476 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~~~~~~~~~~~~~~~~~  476 (530)
                      .+++++..|.+||+|||.++|..+.      +-.+.+.++...+...++.++...++++
T Consensus       625 dl~~La~~T~g~SGAel~~lCq~A~------~~a~~e~i~a~~i~~~hf~~al~~~r~s  677 (693)
T KOG0730|consen  625 DLEELAQATEGYSGAEIVAVCQEAA------LLALRESIEATEITWQHFEEALKAVRPS  677 (693)
T ss_pred             cHHHHHHHhccCChHHHHHHHHHHH------HHHHHHhcccccccHHHHHHHHHhhccc
Confidence            5889999999999999999997543      3333444444555566666666555443

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

Probab=100.00  E-value=8.4e-40  Score=338.19  Aligned_cols=211  Identities=25%  Similarity=0.340  Sum_probs=185.5

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc----
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV----  264 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~----  264 (530)
                      ...+|+++-|.++.|+++.+ +..|+++|..|.++|-..|+|+||.||||||||+||+|+|.+.+.+||..+.+++    
T Consensus       299 ~nv~F~dVkG~DEAK~ELeE-iVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdEm~  377 (752)
T KOG0734|consen  299 KNVTFEDVKGVDEAKQELEE-IVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMF  377 (752)
T ss_pred             cccccccccChHHHHHHHHH-HHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhhhh
Confidence            35689999999999999988 7899999999999999999999999999999999999999999999999988876    


Q ss_pred             --CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          265 --TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       265 --~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                        .+...+|.||..+  .+||||||||||++-                  .+|..                    .+...
T Consensus       378 VGvGArRVRdLF~aAk~~APcIIFIDEiDavG------------------~kR~~--------------------~~~~y  419 (752)
T KOG0734|consen  378 VGVGARRVRDLFAAAKARAPCIIFIDEIDAVG------------------GKRNP--------------------SDQHY  419 (752)
T ss_pred             hcccHHHHHHHHHHHHhcCCeEEEEechhhhc------------------ccCCc--------------------cHHHH
Confidence              3677899999977  789999999999983                  12221                    11226


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE  420 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~  420 (530)
                      .+.|+++||..|||+..  ++++|||++||.|+.||+||+||||||+||.+|.||...|.+|++.|+....+.... +..
T Consensus       420 ~kqTlNQLLvEmDGF~q--NeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~V-D~~  496 (752)
T KOG0734|consen  420 AKQTLNQLLVEMDGFKQ--NEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDV-DPK  496 (752)
T ss_pred             HHHHHHHHHHHhcCcCc--CCceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCC-CHh
Confidence            78899999999999987  589999999999999999999999999999999999999999999999876655222 366


Q ss_pred             HHHHhCCCCCHHHHHHHHHHh
Q 009640          421 SCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~  441 (530)
                      -+++.|.||++||+++++..+
T Consensus       497 iiARGT~GFsGAdLaNlVNqA  517 (752)
T KOG0734|consen  497 IIARGTPGFSGADLANLVNQA  517 (752)
T ss_pred             HhccCCCCCchHHHHHHHHHH
Confidence            778889999999999998643

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

Probab=100.00  E-value=4.1e-39  Score=337.75  Aligned_cols=222  Identities=24%  Similarity=0.313  Sum_probs=189.3

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc-----
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV-----  264 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~-----  264 (530)
                      ...|++|+|.+....++.+.+.. +.+|+.|..+|..++||+|||||||||||+||+|+|++++.+|+.++.+++     
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            45899999999999999886665 999999999999999999999999999999999999999999999998876     


Q ss_pred             -CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          265 -TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       265 -~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                       .++..++.+|.++  .+||||||||||++-                  ++|....                    .+..
T Consensus       265 GESEkkiRelF~~A~~~aPcivFiDeIDAI~------------------pkRe~aq--------------------reME  306 (802)
T KOG0733|consen  265 GESEKKIRELFDQAKSNAPCIVFIDEIDAIT------------------PKREEAQ--------------------REME  306 (802)
T ss_pred             cccHHHHHHHHHHHhccCCeEEEeecccccc------------------cchhhHH--------------------HHHH
Confidence             3577899999998  689999999999983                  3444332                    3345


Q ss_pred             hhhHHHHhhhccCCccCC--CCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          342 RVTLSGLLNFTDGLWSCC--SEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       342 ~~~ls~LLn~lDgl~s~~--~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ++++++||+.||++....  +..++||+|||+|+.|||||+|+||||+.|.+..|+..+|..|++.++....+...+ ..
T Consensus       307 rRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~-d~  385 (802)
T KOG0733|consen  307 RRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDF-DF  385 (802)
T ss_pred             HHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCc-CH
Confidence            778999999999997542  577999999999999999999999999999999999999999999998765555233 36


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHH
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS  454 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~  454 (530)
                      .++|..|.||.+||+..+|..+.   ..|++++.+
T Consensus       386 ~qlA~lTPGfVGADL~AL~~~Aa---~vAikR~ld  417 (802)
T KOG0733|consen  386 KQLAKLTPGFVGADLMALCREAA---FVAIKRILD  417 (802)
T ss_pred             HHHHhcCCCccchhHHHHHHHHH---HHHHHHHhh
Confidence            77888899999999999987654   455555443

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

Probab=100.00  E-value=2.7e-38  Score=331.53  Aligned_cols=224  Identities=21%  Similarity=0.301  Sum_probs=187.8

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc---
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV---  264 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~---  264 (530)
                      .+..+|++|++.++++.++...+..++++|+.|+.+|+..+.|+|||||||||||.||+|+||+.+.+|+.+...++   
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            46789999999999999999999999999999999999999999999999999999999999999999999986554   


Q ss_pred             ---CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          265 ---TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       265 ---~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                         .++..+|.+|.++  ++||||||||||++.+.                  |++                    ....
T Consensus       585 YVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~------------------R~~--------------------~~s~  626 (802)
T KOG0733|consen  585 YVGESERAVRQVFQRARASAPCVIFFDEIDALVPR------------------RSD--------------------EGSS  626 (802)
T ss_pred             HhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcc------------------cCC--------------------CCch
Confidence               2455689999987  78999999999998532                  211                    2345


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccc-hHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHA-LFDV  418 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~-~~~~  418 (530)
                      .+.+++++||..|||+..  ..++.||++||+|+.+|||++||||||+.+++++|+.++|..|++........+. ..-.
T Consensus       627 ~s~RvvNqLLtElDGl~~--R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVd  704 (802)
T KOG0733|consen  627 VSSRVVNQLLTELDGLEE--RRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVD  704 (802)
T ss_pred             hHHHHHHHHHHHhccccc--ccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccC
Confidence            577899999999999976  4789999999999999999999999999999999999999999999987422110 1123


Q ss_pred             HHHHHHhC--CCCCHHHHHHHHHHhccCHHHHHHHHHH
Q 009640          419 VESCIRAG--GALTPAQIGEVLLRNRGNVDLAMKEVVS  454 (530)
Q Consensus       419 i~~l~~~~--~~~spadi~~~l~~~~~d~~~al~~l~~  454 (530)
                      +++++..+  .+||+|||+.++..+.   ..||+.-+.
T Consensus       705 l~eia~~~~c~gftGADLaaLvreAs---i~AL~~~~~  739 (802)
T KOG0733|consen  705 LDEIARNTKCEGFTGADLAALVREAS---ILALRESLF  739 (802)
T ss_pred             HHHHhhcccccCCchhhHHHHHHHHH---HHHHHHHHh
Confidence            55666644  4999999999997655   455554333

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

Probab=100.00  E-value=4.5e-38  Score=315.85  Aligned_cols=261  Identities=23%  Similarity=0.296  Sum_probs=202.1

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC---
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT---  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~---  265 (530)
                      +...|++|+|..+.|+-|.+.+..++.-|++|+.+-.|| +|+|++||||||||+||+|+|.+++..|+.|+.+.+.   
T Consensus       207 p~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPW-kgvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstltSKw  285 (491)
T KOG0738|consen  207 PNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPW-KGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKW  285 (491)
T ss_pred             CCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhccccc-ceeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhhhhh
Confidence            445679999999999999999999999999999999999 7999999999999999999999999999999988773   


Q ss_pred             --ChHHHHHHHHhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          266 --DNSELRALLLQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       266 --~~~~L~~l~~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                        ....|.++|..+   .+||+|||||||+++.                                     .+++..+++.
T Consensus       286 RGeSEKlvRlLFemARfyAPStIFiDEIDslcs-------------------------------------~RG~s~EHEa  328 (491)
T KOG0738|consen  286 RGESEKLVRLLFEMARFYAPSTIFIDEIDSLCS-------------------------------------QRGGSSEHEA  328 (491)
T ss_pred             ccchHHHHHHHHHHHHHhCCceeehhhHHHHHh-------------------------------------cCCCccchhH
Confidence              234466665543   7999999999999852                                     2222356788


Q ss_pred             hhhhHHHHhhhccCCccCCCCC---eEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEE---KIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD  417 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~---~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~  417 (530)
                      +++..++||.+|||+.... ++   ++|+++||.||+||+||+|  ||.+.|++|+|+.++|..|++..|+..... ..-
T Consensus       329 SRRvKsELLvQmDG~~~t~-e~~k~VmVLAATN~PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~-~~~  404 (491)
T KOG0738|consen  329 SRRVKSELLVQMDGVQGTL-ENSKVVMVLAATNFPWDIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELD-DPV  404 (491)
T ss_pred             HHHHHHHHHHHhhcccccc-ccceeEEEEeccCCCcchHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCC-CCc
Confidence            9999999999999998653 34   6778899999999999999  999999999999999999999999854433 222


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHh------------hhccccccccccccccCCCCcccccC
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAK------------ILSGREVMECDELVITRSPESVVVVR  485 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~  485 (530)
                      .++.+++.+.|||++||.++|..+.   +-++++.+..+...            .....++..+...+.|+.  +-..+.
T Consensus       405 ~~~~lae~~eGySGaDI~nvCreAs---m~~mRR~i~g~~~~ei~~lakE~~~~pv~~~Dfe~Al~~v~pSv--s~~d~~  479 (491)
T KOG0738|consen  405 NLEDLAERSEGYSGADITNVCREAS---MMAMRRKIAGLTPREIRQLAKEEPKMPVTNEDFEEALRKVRPSV--SAADLE  479 (491)
T ss_pred             cHHHHHHHhcCCChHHHHHHHHHHH---HHHHHHHHhcCCcHHhhhhhhhccccccchhhHHHHHHHcCcCC--CHHHHH
Confidence            3677888889999999999997654   44444333222111            122233333433333322  224566


Q ss_pred             CCCcccCCCCC
Q 009640          486 SPENWDSSPGG  496 (530)
Q Consensus       486 ~~~~w~~~~g~  496 (530)
                      .+++|.+..|+
T Consensus       480 k~ekW~~efGS  490 (491)
T KOG0738|consen  480 KYEKWMDEFGS  490 (491)
T ss_pred             HHHHHHHHhcC
Confidence            67788877765

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

Probab=100.00  E-value=2.9e-36  Score=329.44  Aligned_cols=216  Identities=24%  Similarity=0.320  Sum_probs=185.9

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc---
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV---  264 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~---  264 (530)
                      ..+.+|.|++|.+++|++|++ +..|+++|+.|.++|...|+|+||+||||||||.||+|+|.+.+.+|+.++.+++   
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            445799999999999999999 7799999999999999999999999999999999999999999999999998886   


Q ss_pred             ---CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          265 ---TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       265 ---~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                         ...+.++.+|..+  .+||||||||||++...++   .                               ......+.
T Consensus       384 ~~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~---G-------------------------------~~~~~~~~  429 (774)
T KOG0731|consen  384 FVGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRG---G-------------------------------KGTGGGQD  429 (774)
T ss_pred             hcccchHHHHHHHHHhhccCCeEEEeccccccccccc---c-------------------------------cccCCCCh
Confidence               3578899999877  6899999999999831110   0                               00112345


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ....++++||..|||..+  ..++||+++||+++.||+||+||||||++|+++.||...|..|++.|+...........+
T Consensus       430 e~e~tlnQll~emDgf~~--~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl  507 (774)
T KOG0731|consen  430 EREQTLNQLLVEMDGFET--SKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDL  507 (774)
T ss_pred             HHHHHHHHHHHHhcCCcC--CCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhH
Confidence            567899999999999987  478999999999999999999999999999999999999999999999865443223335


Q ss_pred             HHHHHhCCCCCHHHHHHHHHH
Q 009640          420 ESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~  440 (530)
                      ..++..|.+|++|||+++|..
T Consensus       508 ~~~a~~t~gf~gadl~n~~ne  528 (774)
T KOG0731|consen  508 SKLASLTPGFSGADLANLCNE  528 (774)
T ss_pred             HHHHhcCCCCcHHHHHhhhhH
Confidence            558888999999999999864

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

Probab=100.00  E-value=2.2e-36  Score=288.65  Aligned_cols=218  Identities=23%  Similarity=0.310  Sum_probs=186.0

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-  265 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-  265 (530)
                      ..+..++.+++|.+-+|++|++.++.++.+.++|+++|+.+|||+|||||||||||+|++|+|++....|+.+..+++. 
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            4567799999999999999999999999999999999999999999999999999999999999999999999887762 


Q ss_pred             -----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          266 -----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       266 -----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                           +..-++.+|.-+  ++|+||||||||++.                  ++|.+.          +       .+.+
T Consensus       228 kylgegprmvrdvfrlakenapsiifideidaia------------------tkrfda----------q-------tgad  272 (408)
T KOG0727|consen  228 KYLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIA------------------TKRFDA----------Q-------TGAD  272 (408)
T ss_pred             HHhccCcHHHHHHHHHHhccCCcEEEeehhhhHh------------------hhhccc----------c-------cccc
Confidence                 445577887654  799999999999983                  333322          1       1234


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV  418 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~  418 (530)
                      ..-++.+-.|||+|||+..  ..++-|||+||+.+.|||||+||||+|++|+||+||..+++-+|.......... ....
T Consensus       273 revqril~ellnqmdgfdq--~~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls-~~vd  349 (408)
T KOG0727|consen  273 REVQRILIELLNQMDGFDQ--TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLS-DEVD  349 (408)
T ss_pred             HHHHHHHHHHHHhccCcCc--ccceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCC-cccC
Confidence            5567889999999999987  477999999999999999999999999999999999999999998877665444 2234


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          419 VESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       419 i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ++.++...+.+|+|||..+|..+.
T Consensus       350 le~~v~rpdkis~adi~aicqeag  373 (408)
T KOG0727|consen  350 LEDLVARPDKISGADINAICQEAG  373 (408)
T ss_pred             HHHHhcCccccchhhHHHHHHHHh
Confidence            777877789999999999997544

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

Probab=100.00  E-value=2.6e-36  Score=323.62  Aligned_cols=236  Identities=20%  Similarity=0.290  Sum_probs=188.6

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      .|..+..+|+||+|.+++|.+|.+.|..++++|++|.. |...+.|+|||||||||||.||+|+|.++..+|..+...++
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            45678889999999999999999999999999999865 56667899999999999999999999999999999976655


Q ss_pred             ------CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 ------TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ------~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                            +++.++|++|.++  .+|||||+||+|++.+.+|.                  +             +     .
T Consensus       742 LNMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~------------------s-------------G-----D  785 (953)
T KOG0736|consen  742 LNMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGR------------------S-------------G-----D  785 (953)
T ss_pred             HHHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCC------------------C-------------C-----C
Confidence                  5788999999988  68999999999998532221                  1             0     1


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC-HHHHHHHHHHhhCCcCccch
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG-PHAFKVLAKNYLGIESHHAL  415 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~-~~~r~~i~~~~l~~~~~~~~  415 (530)
                      ......+++|+||.+|||+.......++||++||+||-|||||+||||||+-++++.|+ .+.+..+++.....-..+..
T Consensus       786 SGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLded  865 (953)
T KOG0736|consen  786 SGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDED  865 (953)
T ss_pred             ccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCC
Confidence            24567789999999999999655788999999999999999999999999999999884 45566677665543222211


Q ss_pred             HHHHHHHHH-hCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhhh
Q 009640          416 FDVVESCIR-AGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKIL  461 (530)
Q Consensus       416 ~~~i~~l~~-~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~~  461 (530)
                      .+ +.++|+ -...||+||+-.+|..+.   ..|+++.+..++....
T Consensus       866 Vd-L~eiAk~cp~~~TGADlYsLCSdA~---l~AikR~i~~ie~g~~  908 (953)
T KOG0736|consen  866 VD-LVEIAKKCPPNMTGADLYSLCSDAM---LAAIKRTIHDIESGTI  908 (953)
T ss_pred             cC-HHHHHhhCCcCCchhHHHHHHHHHH---HHHHHHHHHHhhhccc
Confidence            11 222332 257999999999997554   6677777776665543

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

Probab=100.00  E-value=3.9e-37  Score=298.84  Aligned_cols=221  Identities=26%  Similarity=0.305  Sum_probs=186.1

Q ss_pred             ccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          184 SVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       184 ~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      .+...+..+|.+++|.+.+.++|.+.++.++.+|++|...|+.+|+|++|||+||||||.||+|+||.....|..+-.++
T Consensus       175 K~eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvGse  254 (440)
T KOG0726|consen  175 KVEKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSE  254 (440)
T ss_pred             ecccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhhhHH
Confidence            35567888999999999999999999999999999999999999999999999999999999999999999998887666


Q ss_pred             cC------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          264 VT------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       264 ~~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                      +.      +..-++++|.-+  .+|||+||||||++-                  +||-++                 ++
T Consensus       255 LiQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiG------------------tKRyds-----------------~S  299 (440)
T KOG0726|consen  255 LIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIG------------------TKRYDS-----------------NS  299 (440)
T ss_pred             HHHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhc------------------cccccC-----------------CC
Confidence            52      334467777655  799999999999982                  333322                 11


Q ss_pred             CCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccch
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHAL  415 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~  415 (530)
                      ++...-++++-.|||++||+.+  .+.+-|||+||+.+.|||||+||||+|++|+|+.||...++.||..+....... .
T Consensus       300 ggerEiQrtmLELLNQldGFds--rgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~-~  376 (440)
T KOG0726|consen  300 GGEREIQRTMLELLNQLDGFDS--RGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLA-E  376 (440)
T ss_pred             ccHHHHHHHHHHHHHhccCccc--cCCeEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchh-c
Confidence            3445567788899999999998  578999999999999999999999999999999999999999998776654333 2


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          416 FDVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       416 ~~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ...++.++...+.+|+|||+.+|..+.
T Consensus       377 dVnle~li~~kddlSGAdIkAictEaG  403 (440)
T KOG0726|consen  377 DVNLEELIMTKDDLSGADIKAICTEAG  403 (440)
T ss_pred             cccHHHHhhcccccccccHHHHHHHHh
Confidence            223777777779999999999997654

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

Probab=100.00  E-value=2.6e-36  Score=287.81  Aligned_cols=220  Identities=24%  Similarity=0.277  Sum_probs=184.3

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+++.++|.+.+.++|.+.++.+.++|++|..+|++.|+|+|||||||||||.||+|+|++.++.|+.++.+++
T Consensus       138 VeKvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht~c~firvsgsel  217 (404)
T KOG0728|consen  138 VEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSEL  217 (404)
T ss_pred             hhhCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhcceEEEEechHHH
Confidence            44557788999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      +..-++.+|.-+  ++|||||+||||++-..+.                                   .++.+
T Consensus       218 vqk~igegsrmvrelfvmarehapsiifmdeidsigs~r~-----------------------------------e~~~g  262 (404)
T KOG0728|consen  218 VQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRV-----------------------------------ESGSG  262 (404)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhcCCceEeeecccccccccc-----------------------------------cCCCC
Confidence            2      334467777655  8999999999999831111                                   11113


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      +++.-+++.-.|||++||+..  ..++-||++||+.+.|||||+||||+|++|+||+|+.++|.+|++.+......- .-
T Consensus       263 gdsevqrtmlellnqldgfea--tknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~-rg  339 (404)
T KOG0728|consen  263 GDSEVQRTMLELLNQLDGFEA--TKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLT-RG  339 (404)
T ss_pred             ccHHHHHHHHHHHHhcccccc--ccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchh-cc
Confidence            456678899999999999987  477889999999999999999999999999999999999999999876543321 11


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      -.+..+++...|.|+|+++.+|..+.
T Consensus       340 i~l~kiaekm~gasgaevk~vcteag  365 (404)
T KOG0728|consen  340 INLRKIAEKMPGASGAEVKGVCTEAG  365 (404)
T ss_pred             cCHHHHHHhCCCCccchhhhhhhhhh
Confidence            12566777779999999999997654

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

Probab=100.00  E-value=4e-35  Score=281.09  Aligned_cols=220  Identities=24%  Similarity=0.288  Sum_probs=183.8

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..++++++|.+.+.+++.+.+..++.+++.|.++|+.+|+|+|+|||||||||.||+|.|...+..|..+-...+
T Consensus       162 vDekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQL  241 (424)
T KOG0652|consen  162 VDEKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQL  241 (424)
T ss_pred             eccCCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcchHH
Confidence            44567778999999999999999999999999999999999999999999999999999999999999988877754443


Q ss_pred             -----CChH-HHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 -----TDNS-ELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 -----~~~~-~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                           .+.. -++..|.-+  .+|+||||||+|++-                  +||.++                 ...
T Consensus       242 VQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIG------------------tKRfDS-----------------ek~  286 (424)
T KOG0652|consen  242 VQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIG------------------TKRFDS-----------------EKA  286 (424)
T ss_pred             HhhhhcchHHHHHHHHHHhhccCCeEEEEechhhhc------------------cccccc-----------------ccc
Confidence                 2333 356666544  789999999999982                  344333                 113


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      ++...++++-.|||++||+.+  .+.+-||++||+.+.|||||+|.||+|++|+||.|+.++|..|++.+....... ..
T Consensus       287 GDREVQRTMLELLNQLDGFss--~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~-~D  363 (424)
T KOG0652|consen  287 GDREVQRTMLELLNQLDGFSS--DDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVS-DD  363 (424)
T ss_pred             ccHHHHHHHHHHHHhhcCCCC--ccceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCC-CC
Confidence            455677889999999999998  578889999999999999999999999999999999999999999887754433 22


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ...++|+..+++|.+|+.+.+|..+.
T Consensus       364 vNfeELaRsTddFNGAQcKAVcVEAG  389 (424)
T KOG0652|consen  364 VNFEELARSTDDFNGAQCKAVCVEAG  389 (424)
T ss_pred             CCHHHHhhcccccCchhheeeehhhh
Confidence            23678888899999999999887554

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

Probab=100.00  E-value=3.6e-34  Score=301.43  Aligned_cols=219  Identities=21%  Similarity=0.295  Sum_probs=181.8

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT  265 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~  265 (530)
                      ...+..+|++|+|.+.+|++|.+.+..++.+++.|.++|+++++|+|||||||||||++++++|++++.+++.+..+.+.
T Consensus       137 ~~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l~  216 (398)
T PTZ00454        137 SEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFV  216 (398)
T ss_pred             cCCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHH
Confidence            34577899999999999999999999999999999999999999999999999999999999999999999998765541


Q ss_pred             ------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          266 ------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       266 ------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                            +...++.+|..+  .+||||||||||+++..+                  .+.                 ..+.
T Consensus       217 ~k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r------------------~~~-----------------~~~~  261 (398)
T PTZ00454        217 QKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKR------------------FDA-----------------QTGA  261 (398)
T ss_pred             HHhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhcccc------------------ccc-----------------cCCc
Confidence                  234577777654  789999999999985211                  000                 0011


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD  417 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~  417 (530)
                      +.....++..||+.+||+..  ..+++||+|||+++.||||++||||||.+|+|++|+.++|..|++.++...... ...
T Consensus       262 d~~~~r~l~~LL~~ld~~~~--~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~-~dv  338 (398)
T PTZ00454        262 DREVQRILLELLNQMDGFDQ--TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLS-EEV  338 (398)
T ss_pred             cHHHHHHHHHHHHHhhccCC--CCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCC-ccc
Confidence            23345688999999999876  367899999999999999999999999999999999999999999998754433 222


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      .+..++..+.+||||||..+|..+.
T Consensus       339 d~~~la~~t~g~sgaDI~~l~~eA~  363 (398)
T PTZ00454        339 DLEDFVSRPEKISAADIAAICQEAG  363 (398)
T ss_pred             CHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            3677888899999999999997654

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

Probab=100.00  E-value=6e-35  Score=284.44  Aligned_cols=262  Identities=23%  Similarity=0.293  Sum_probs=204.7

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-  265 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-  265 (530)
                      ..+...|++|+|.+..|+.+.+.+..+++-|.+|..-..|| +|+|||||||||||.||+|+|.+.+..|+.++.+++. 
T Consensus       126 EKPNVkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~Pw-rgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLvS  204 (439)
T KOG0739|consen  126 EKPNVKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPW-RGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS  204 (439)
T ss_pred             cCCCCchhhhccchhHHHHHHhheeecccchhhhcCCCCcc-eeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHHHH
Confidence            35667889999999999999999999999999999888888 8999999999999999999999999999999988763 


Q ss_pred             -----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          266 -----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       266 -----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                           ++.-++.||.-+  +.||||||||||++.+.   |                                   +.+++
T Consensus       205 KWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~---r-----------------------------------~enEs  246 (439)
T KOG0739|consen  205 KWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGS---R-----------------------------------SENES  246 (439)
T ss_pred             HHhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccC---C-----------------------------------CCCch
Confidence                 233456676644  79999999999987421   1                                   11345


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV  418 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~  418 (530)
                      +.++++...||.+|.|+-.. .++++|+++||-|+.||.|++|  ||++.|++|+|+..+|..+|+.++|...|......
T Consensus       247 easRRIKTEfLVQMqGVG~d-~~gvLVLgATNiPw~LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d  323 (439)
T KOG0739|consen  247 EASRRIKTEFLVQMQGVGND-NDGVLVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQD  323 (439)
T ss_pred             HHHHHHHHHHHHhhhccccC-CCceEEEecCCCchhHHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhh
Confidence            66788899999999999764 6889999999999999999999  99999999999999999999999999999866778


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhhhccc-cccccccccccCCCCcccccCCCCcccCCCC
Q 009640          419 VESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGR-EVMECDELVITRSPESVVVVRSPENWDSSPG  495 (530)
Q Consensus       419 i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~g  495 (530)
                      +..|+..|+|||++||.-++..+-   +..++.+..+..-++.... +......+.+|-+|.+...++.  .|.+..+
T Consensus       324 ~~eL~~kTeGySGsDisivVrDal---mePvRkvqsAthFk~v~~~s~~~~~~~lltpcspgd~ga~em--~w~dv~~  396 (439)
T KOG0739|consen  324 FKELARKTEGYSGSDISIVVRDAL---MEPVRKVQSATHFKKVSGPSNPSEVDDLLTPCSPGDPGAIEM--SWMDVPA  396 (439)
T ss_pred             HHHHHhhcCCCCcCceEEEehhhh---hhhHHHhhhhhhhhccCCCCChhhhccccCCCCCCCcchhhh--hhccCCH
Confidence            999999999999999976654322   3344555555544443321 1111234444444444333332  3555544

>TIGR03689 pup_AAA proteasome ATPase

Probab=100.00  E-value=4.8e-34  Score=306.30  Aligned_cols=268  Identities=20%  Similarity=0.292  Sum_probs=191.4

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc----------E
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD----------V  256 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~----------i  256 (530)
                      ..++.+|++|+|.+..+++|.+.+..++.+++.|...|+++++|+|||||||||||++++|+|++++.+          +
T Consensus       175 ~~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~f  254 (512)
T TIGR03689       175 EVPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYF  254 (512)
T ss_pred             cCCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeE
Confidence            346789999999999999999999999999999999999999999999999999999999999999765          2


Q ss_pred             EEEecCcc------CChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccc
Q 009640          257 YDLELTKV------TDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRI  324 (530)
Q Consensus       257 ~~l~l~~~------~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~  324 (530)
                      +.+....+      .+...++.+|..+      ..||||||||||+++..++.                           
T Consensus       255 l~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~---------------------------  307 (512)
T TIGR03689       255 LNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGS---------------------------  307 (512)
T ss_pred             EeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCC---------------------------
Confidence            33332222      1234567777654      36999999999998631110                           


Q ss_pred             ccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          325 ASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       325 ~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                                ...+...+.++++||+.|||+.+  .++++||+|||+++.|||||+||||||++|+|++|+.++|++|++
T Consensus       308 ----------~~s~d~e~~il~~LL~~LDgl~~--~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~  375 (512)
T TIGR03689       308 ----------GVSSDVETTVVPQLLSELDGVES--LDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFS  375 (512)
T ss_pred             ----------CccchHHHHHHHHHHHHhccccc--CCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHH
Confidence                      01122345678999999999986  367999999999999999999999999999999999999999999


Q ss_pred             HhhCCcCcc-------------chHHHHHHHHH-------------------------hCCCCCHHHHHHHHHHhccCHH
Q 009640          405 NYLGIESHH-------------ALFDVVESCIR-------------------------AGGALTPAQIGEVLLRNRGNVD  446 (530)
Q Consensus       405 ~~l~~~~~~-------------~~~~~i~~l~~-------------------------~~~~~spadi~~~l~~~~~d~~  446 (530)
                      .|+......             .....+.+.+.                         .++.+|+|+|++++.++.   .
T Consensus       376 ~~l~~~l~l~~~l~~~~g~~~a~~~al~~~av~~~~a~~~~~~~l~~~~~~g~~~~l~~~d~~sGa~i~~iv~~a~---~  452 (512)
T TIGR03689       376 KYLTDSLPLDADLAEFDGDREATAAALIQRAVDHLYATSEENRYVEVTYANGSTEVLYFKDFVSGAMIANIVDRAK---K  452 (512)
T ss_pred             HHhhccCCchHHHHHhcCCCHHHHHHHHHHHHHHHhhhhcccceeEEEecCCceeeEeecccccHHHHHHHHHHHH---H
Confidence            998642110             00011111100                         135688888888887766   5


Q ss_pred             HHHHHHHHHHHHhhhccccccccccccccCCCCcccccCCCCcccCCCCCCC
Q 009640          447 LAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVVRSPENWDSSPGGKY  498 (530)
Q Consensus       447 ~al~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~g~~~  498 (530)
                      .|+++.+... ...++..+...+..-. ....++.--...|++|..+-|..|
T Consensus       453 ~ai~~~~~~~-~~~~~~~~l~~a~~~e-~~~~~~~~~~~~~~~w~~~~~~~~  502 (512)
T TIGR03689       453 RAIKDHITGG-QVGLRIEHLLAAVLDE-FRESEDLPNTTNPDDWARISGKKG  502 (512)
T ss_pred             HHHHHHHhcC-CcCcCHHHHHHHHHHh-hcccccCCCCCCHHHHhhhhCCCC
Confidence            5555544221 1233333333332211 122334455677889999866653

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.

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

Probab=100.00  E-value=1.4e-33  Score=303.79  Aligned_cols=233  Identities=24%  Similarity=0.334  Sum_probs=194.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc---
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV---  264 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~---  264 (530)
                      ....+|.+++|.++.|+++.+ +..|+++|..|..+|...|+|+||+||||||||+||+|+|.+.+.+++.++.+++   
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            456799999999999999999 7789999999999999999999999999999999999999999999999998886   


Q ss_pred             ---CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          265 ---TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       265 ---~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                         .+.+.+|.+|.++  ++||||||||||++-..++   .                                +-..++.
T Consensus       223 fVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg---~--------------------------------g~Gggnd  267 (596)
T COG0465         223 FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRG---A--------------------------------GLGGGND  267 (596)
T ss_pred             hcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccC---C--------------------------------CCCCCch
Confidence               3678999999998  5799999999999731110   0                                0013455


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ....|+++||.+|||...  ++++|||++||+|+-|||||+||||||++|.++.||...|.+|++.+....... ....+
T Consensus       268 erEQTLNQlLvEmDGF~~--~~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~-~~Vdl  344 (596)
T COG0465         268 EREQTLNQLLVEMDGFGG--NEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLA-EDVDL  344 (596)
T ss_pred             HHHHHHHHHHhhhccCCC--CCceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCC-CcCCH
Confidence            667899999999999985  588999999999999999999999999999999999999999999888765544 22224


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhc-------------cCHHHHHHHHHHHHHHh
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNR-------------GNVDLAMKEVVSAMQAK  459 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~-------------~d~~~al~~l~~~l~~~  459 (530)
                      ..++..+.||++||+.+++..+.             .+.+.|.+.++...+.+
T Consensus       345 ~~iAr~tpGfsGAdL~nl~NEAal~aar~n~~~i~~~~i~ea~drv~~G~erk  397 (596)
T COG0465         345 KKIARGTPGFSGADLANLLNEAALLAARRNKKEITMRDIEEAIDRVIAGPERK  397 (596)
T ss_pred             HHHhhhCCCcccchHhhhHHHHHHHHHHhcCeeEeccchHHHHHHHhcCcCcC
Confidence            55888899999999999984311             25666666666554433

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

Probab=100.00  E-value=4.8e-33  Score=296.02  Aligned_cols=211  Identities=20%  Similarity=0.247  Sum_probs=185.1

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc------
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV------  264 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~------  264 (530)
                      ..|++++|..++|+.+.+.+..+.+.|..|.+.+...+.|+|||||||||||.||.|+|..+++.|+.+...++      
T Consensus       664 i~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fisvKGPElL~KyIG  743 (952)
T KOG0735|consen  664 IRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFISVKGPELLSKYIG  743 (952)
T ss_pred             CCceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEEecCHHHHHHHhc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999986655      


Q ss_pred             CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchh
Q 009640          265 TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGR  342 (530)
Q Consensus       265 ~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (530)
                      .++..+|.+|.++  .+|||+|+||+|++.+                  +|..                    ...+...
T Consensus       744 aSEq~vR~lF~rA~~a~PCiLFFDEfdSiAP------------------kRGh--------------------DsTGVTD  785 (952)
T KOG0735|consen  744 ASEQNVRDLFERAQSAKPCILFFDEFDSIAP------------------KRGH--------------------DSTGVTD  785 (952)
T ss_pred             ccHHHHHHHHHHhhccCCeEEEeccccccCc------------------ccCC--------------------CCCCchH
Confidence            3678899999987  6899999999999842                  2221                    1234567


Q ss_pred             hhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHH
Q 009640          343 VTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESC  422 (530)
Q Consensus       343 ~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l  422 (530)
                      +++++||.+|||...  -.++.|+++|.+|+.|||||+||||+|++++.+.|+..+|.+|++..-.....+ ...+++-+
T Consensus       786 RVVNQlLTelDG~Eg--l~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~-~~vdl~~~  862 (952)
T KOG0735|consen  786 RVVNQLLTELDGAEG--LDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKD-TDVDLECL  862 (952)
T ss_pred             HHHHHHHHhhccccc--cceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCc-cccchHHH
Confidence            789999999999987  478999999999999999999999999999999999999999999876644443 33457788


Q ss_pred             HHhCCCCCHHHHHHHHHHhc
Q 009640          423 IRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       423 ~~~~~~~spadi~~~l~~~~  442 (530)
                      +..|+|||+||++.+|..+.
T Consensus       863 a~~T~g~tgADlq~ll~~A~  882 (952)
T KOG0735|consen  863 AQKTDGFTGADLQSLLYNAQ  882 (952)
T ss_pred             hhhcCCCchhhHHHHHHHHH
Confidence            88899999999999997554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=100.00  E-value=1.1e-32  Score=290.95  Aligned_cols=220  Identities=23%  Similarity=0.245  Sum_probs=181.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++|+|.++++++|.+.+..++.+++.|..+|+.+++|+|||||||||||++|+|+|++++.+++.+..+.+
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            44456778999999999999999999999999999999999999999999999999999999999999999999987765


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      +...++.+|..+  .+||||||||||.++..+.+                                   ....
T Consensus       202 ~~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~-----------------------------------~~~~  246 (389)
T PRK03992        202 VQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTD-----------------------------------SGTS  246 (389)
T ss_pred             hHhhccchHHHHHHHHHHHHhcCCeEEEEechhhhhccccc-----------------------------------CCCC
Confidence            2      234567777765  57999999999998521100                                   0001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .+.....++..||+.+||+..  ..+++||+|||+++.||+||+||||||..|+|++|+.++|..|++.++...... ..
T Consensus       247 ~~~~~~~~l~~lL~~ld~~~~--~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~-~~  323 (389)
T PRK03992        247 GDREVQRTLMQLLAEMDGFDP--RGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLA-DD  323 (389)
T ss_pred             ccHHHHHHHHHHHHhccccCC--CCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCC-Cc
Confidence            122345678899999999875  467899999999999999999999999999999999999999999998754433 11


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ..+..++..+.+|+++||..+|..+.
T Consensus       324 ~~~~~la~~t~g~sgadl~~l~~eA~  349 (389)
T PRK03992        324 VDLEELAELTEGASGADLKAICTEAG  349 (389)
T ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            23677888899999999999997554

>CHL00195 ycf46 Ycf46; Provisional

Probab=100.00  E-value=6.2e-33  Score=298.01  Aligned_cols=252  Identities=18%  Similarity=0.211  Sum_probs=197.0

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC---
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT---  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~---  265 (530)
                      +..+|++|+|.+.+|+.+.+....|..   .+.+.|.+.++|+|||||||||||++|+|+|++++.+++.++.+.+.   
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            456899999999999988876655532   34567999999999999999999999999999999999999876542   


Q ss_pred             ---ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          266 ---DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       266 ---~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                         ++..++++|..+  .+||||||||||.++.-..                                     ..++...
T Consensus       300 vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~-------------------------------------~~~d~~~  342 (489)
T CHL00195        300 VGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSE-------------------------------------SKGDSGT  342 (489)
T ss_pred             cChHHHHHHHHHHHHHhcCCcEEEehhhhhhhcccc-------------------------------------CCCCchH
Confidence               456788888754  7899999999999852000                                     0012334


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccc-hHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHA-LFDVV  419 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~-~~~~i  419 (530)
                      ....++.||+.|+..    ...++||+|||+++.|||||+||||||..|+++.|+.++|..||+.|+....... ....+
T Consensus       343 ~~rvl~~lL~~l~~~----~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl  418 (489)
T CHL00195        343 TNRVLATFITWLSEK----KSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDI  418 (489)
T ss_pred             HHHHHHHHHHHHhcC----CCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCH
Confidence            567888999988853    4578999999999999999999999999999999999999999999997643221 12347


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhhhccccccccccccccCCCCcccccCCCCcccCC
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVVRSPENWDSS  493 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~  493 (530)
                      +.++..+.|||+|||.+++..+.   ..|      ..+.+.++..++..+...+.|.+....+.+....+|...
T Consensus       419 ~~La~~T~GfSGAdI~~lv~eA~---~~A------~~~~~~lt~~dl~~a~~~~~Pls~~~~e~i~~~~~Wa~~  483 (489)
T CHL00195        419 KKLSKLSNKFSGAEIEQSIIEAM---YIA------FYEKREFTTDDILLALKQFIPLAQTEKEQIEALQNWASS  483 (489)
T ss_pred             HHHHhhcCCCCHHHHHHHHHHHH---HHH------HHcCCCcCHHHHHHHHHhcCCCcccCHHHHHHHHHHHHc
Confidence            88888899999999999986543   111      123456777777888777777665555667777788765

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

Probab=100.00  E-value=9.4e-33  Score=265.52  Aligned_cols=219  Identities=23%  Similarity=0.265  Sum_probs=181.0

Q ss_pred             ccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          184 SVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       184 ~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      .+...+..|+.+++|..++.+.|++.++.++.+|+.|.++|+.+++|+|||||||||||.+|+|+||..+.-|+.+-.++
T Consensus       167 ~veekpdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdacfirvigse  246 (435)
T KOG0729|consen  167 QVEEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSE  246 (435)
T ss_pred             EeecCCCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCceEEeehhHH
Confidence            45667888999999999999999999999999999999999999999999999999999999999999999999987776


Q ss_pred             cC------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          264 VT------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       264 ~~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                      +.      +..-++.+|.-+  .+-||||+||||++-+.+=+                                   ...
T Consensus       247 lvqkyvgegarmvrelf~martkkaciiffdeidaiggarfd-----------------------------------dg~  291 (435)
T KOG0729|consen  247 LVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFD-----------------------------------DGA  291 (435)
T ss_pred             HHHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCcccc-----------------------------------CCC
Confidence            52      234467777655  56799999999998321110                                   011


Q ss_pred             CCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCcc--
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHH--  413 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~--  413 (530)
                      +++...++++-.|+|++||+..  .+++-|+|+||+|+.|||||+||||+|++++|.+||.+.|..|++.+......+  
T Consensus       292 ggdnevqrtmleli~qldgfdp--rgnikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverd  369 (435)
T KOG0729|consen  292 GGDNEVQRTMLELINQLDGFDP--RGNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERD  369 (435)
T ss_pred             CCcHHHHHHHHHHHHhccCCCC--CCCeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccc
Confidence            3445567889999999999987  578889999999999999999999999999999999999999998776543322  


Q ss_pred             chHHHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          414 ALFDVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       414 ~~~~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      -.++.+..   ....-|+|+|..+|..+.
T Consensus       370 ir~ellar---lcpnstgaeirsvcteag  395 (435)
T KOG0729|consen  370 IRFELLAR---LCPNSTGAEIRSVCTEAG  395 (435)
T ss_pred             hhHHHHHh---hCCCCcchHHHHHHHHhh
Confidence            13444444   467899999999997543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=100.00  E-value=2.4e-32  Score=310.08  Aligned_cols=215  Identities=20%  Similarity=0.249  Sum_probs=183.3

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc---
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV---  264 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~---  264 (530)
                      .+..+|++++|.+.+|+.|.+.+..++.+++.|.++|..+++|+|||||||||||++|+|+|++++.+++.++.+++   
T Consensus       447 ~~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~~  526 (733)
T TIGR01243       447 VPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSK  526 (733)
T ss_pred             ccccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhhc
Confidence            34668999999999999999999999999999999999999999999999999999999999999999999987654   


Q ss_pred             ---CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          265 ---TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       265 ---~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                         .++..++.+|..+  ..||||||||||.+++.++.                                     .....
T Consensus       527 ~vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~-------------------------------------~~~~~  569 (733)
T TIGR01243       527 WVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGA-------------------------------------RFDTS  569 (733)
T ss_pred             ccCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCC-------------------------------------CCCcc
Confidence               2456789999876  68999999999998631110                                     01123


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      .....+++||+.|||+..  ..+++||+|||+|+.||||++||||||++|++++|+.++|.+||+.++...... ....+
T Consensus       570 ~~~~~~~~lL~~ldg~~~--~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~-~~~~l  646 (733)
T TIGR01243       570 VTDRIVNQLLTEMDGIQE--LSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLA-EDVDL  646 (733)
T ss_pred             HHHHHHHHHHHHhhcccC--CCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCC-ccCCH
Confidence            356788999999999976  467999999999999999999999999999999999999999999988755443 22237


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhc
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      +.++..+.|||+|||..+|..+.
T Consensus       647 ~~la~~t~g~sgadi~~~~~~A~  669 (733)
T TIGR01243       647 EELAEMTEGYTGADIEAVCREAA  669 (733)
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHH
Confidence            78888899999999999986544

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.

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

Probab=100.00  E-value=2.3e-32  Score=289.65  Aligned_cols=220  Identities=25%  Similarity=0.299  Sum_probs=180.9

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...++.+|++|+|.++++++|.+.+..++.++++|..+|+.+++|+|||||||||||++|+|||++++.+++.+..+.+
T Consensus       174 ~~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~seL  253 (438)
T PTZ00361        174 VDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSEL  253 (438)
T ss_pred             cccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEecchh
Confidence            44567789999999999999999999999999999999999999999999999999999999999999999999887665


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      +...++.+|..+  ..||||||||||+++..+.+                  .                 ..+
T Consensus       254 ~~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~------------------~-----------------~sg  298 (438)
T PTZ00361        254 IQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYD------------------A-----------------TSG  298 (438)
T ss_pred             hhhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCC------------------C-----------------CCc
Confidence            2      233467777654  68999999999998521100                  0                 001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .......++..||+.+||+..  ..++.||+|||+++.|||||+||||||.+|+|++|+.++|..|++.++...... ..
T Consensus       299 g~~e~qr~ll~LL~~Ldg~~~--~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~-~d  375 (438)
T PTZ00361        299 GEKEIQRTMLELLNQLDGFDS--RGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLA-ED  375 (438)
T ss_pred             ccHHHHHHHHHHHHHHhhhcc--cCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCC-cC
Confidence            222345677899999999875  467899999999999999999999999999999999999999999998754433 11


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ..++.++..+.+||+|||..+|..+.
T Consensus       376 vdl~~la~~t~g~sgAdI~~i~~eA~  401 (438)
T PTZ00361        376 VDLEEFIMAKDELSGADIKAICTEAG  401 (438)
T ss_pred             cCHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            23677777889999999999987543

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.98  E-value=6.5e-32  Score=293.90  Aligned_cols=216  Identities=24%  Similarity=0.320  Sum_probs=180.1

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-  265 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-  265 (530)
                      ..+..+|++++|.+++|+++.+ +..++.+++.|.+.|...++|+|||||||||||++++++|++++.+++.++.+.+. 
T Consensus        48 ~~~~~~~~di~g~~~~k~~l~~-~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~  126 (495)
T TIGR01241        48 EKPKVTFKDVAGIDEAKEELME-IVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVE  126 (495)
T ss_pred             CCCCCCHHHhCCHHHHHHHHHH-HHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHHH
Confidence            3567899999999999999997 45578999999999999999999999999999999999999999999999876542 


Q ss_pred             -----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          266 -----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       266 -----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                           +...++.+|..+  .+||||||||||++...++..                                   ....+
T Consensus       127 ~~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~-----------------------------------~~~~~  171 (495)
T TIGR01241       127 MFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAG-----------------------------------LGGGN  171 (495)
T ss_pred             HHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccC-----------------------------------cCCcc
Confidence                 456788898876  689999999999985211100                                   00112


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV  418 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~  418 (530)
                      .....+++.||+.|||+.+  .++++||+|||+++.|||||+||||||++|+++.|+.++|.+|++.++...... ....
T Consensus       172 ~~~~~~~~~lL~~~d~~~~--~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~-~~~~  248 (495)
T TIGR01241       172 DEREQTLNQLLVEMDGFGT--NTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLA-PDVD  248 (495)
T ss_pred             HHHHHHHHHHHhhhccccC--CCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCC-cchh
Confidence            3345788999999999976  467999999999999999999999999999999999999999999999765443 2234


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHh
Q 009640          419 VESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       419 i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      +..++..+.+||++||..++..+
T Consensus       249 l~~la~~t~G~sgadl~~l~~eA  271 (495)
T TIGR01241       249 LKAVARRTPGFSGADLANLLNEA  271 (495)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHH
Confidence            67888889999999999998643

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.

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

Probab=99.98  E-value=9.3e-32  Score=258.05  Aligned_cols=207  Identities=17%  Similarity=0.237  Sum_probs=173.6

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC--
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD--  266 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~--  266 (530)
                      +..+|++++|+++.|+.- ..|..|+.+|+.|..+   .|+.+|||||||||||+||+|+||+++.+++.+..+++.+  
T Consensus       116 ~~it~ddViGqEeAK~kc-rli~~yLenPe~Fg~W---APknVLFyGppGTGKTm~Akalane~kvp~l~vkat~liGeh  191 (368)
T COG1223         116 SDITLDDVIGQEEAKRKC-RLIMEYLENPERFGDW---APKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEH  191 (368)
T ss_pred             ccccHhhhhchHHHHHHH-HHHHHHhhChHHhccc---CcceeEEECCCCccHHHHHHHHhcccCCceEEechHHHHHHH
Confidence            456899999999998865 4577899999988765   3789999999999999999999999999999999887732  


Q ss_pred             ----hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          267 ----NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       267 ----~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                          ...+++++..+  .+|||+||||+|++.  -.+|..                                   .-.+.
T Consensus       192 VGdgar~Ihely~rA~~~aPcivFiDE~DAia--LdRryQ-----------------------------------elRGD  234 (368)
T COG1223         192 VGDGARRIHELYERARKAAPCIVFIDELDAIA--LDRRYQ-----------------------------------ELRGD  234 (368)
T ss_pred             hhhHHHHHHHHHHHHHhcCCeEEEehhhhhhh--hhhhHH-----------------------------------Hhccc
Confidence                34688888877  689999999999982  111111                                   11233


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE  420 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~  420 (530)
                      -..+++.||..|||+..  +++++.|++||+|+.||||+++  ||...|+|.+|+.++|..|++.|......+ ....++
T Consensus       235 VsEiVNALLTelDgi~e--neGVvtIaaTN~p~~LD~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plp-v~~~~~  309 (368)
T COG1223         235 VSEIVNALLTELDGIKE--NEGVVTIAATNRPELLDPAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLP-VDADLR  309 (368)
T ss_pred             HHHHHHHHHHhccCccc--CCceEEEeecCChhhcCHHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCc-cccCHH
Confidence            45688999999999997  6899999999999999999999  999999999999999999999999877666 333477


Q ss_pred             HHHHhCCCCCHHHHHHHHHHh
Q 009640          421 SCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~  441 (530)
                      .++..+.|||+.||.+-+++.
T Consensus       310 ~~~~~t~g~SgRdikekvlK~  330 (368)
T COG1223         310 YLAAKTKGMSGRDIKEKVLKT  330 (368)
T ss_pred             HHHHHhCCCCchhHHHHHHHH
Confidence            888889999999999887753

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

Probab=99.98  E-value=1.9e-31  Score=290.60  Aligned_cols=216  Identities=24%  Similarity=0.295  Sum_probs=185.6

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-  265 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-  265 (530)
                      ..+..+|++++|.+.+|+.+.+.+..++..++.|.+.|...++|+|||||||||||+||+|+|++++.+|+.+..+++. 
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            4566789999999999999999999999999999999999999999999999999999999999999999999877653 


Q ss_pred             -----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          266 -----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       266 -----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                           ++..++++|..+  .+||||||||||+++..++.                                      ..+
T Consensus       315 k~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~--------------------------------------~~~  356 (494)
T COG0464         315 KWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGP--------------------------------------SED  356 (494)
T ss_pred             cccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCC--------------------------------------CCc
Confidence                 467799999887  68999999999998531110                                      112


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCcc-chHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHH-ALFD  417 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~-~~~~  417 (530)
                      ......+++||.+|||+..  ..+++||+|||+|+.||||++||||||..|+++.||.++|..|++.++...... ....
T Consensus       357 ~~~~r~~~~lL~~~d~~e~--~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~  434 (494)
T COG0464         357 GSGRRVVGQLLTELDGIEK--AEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDV  434 (494)
T ss_pred             hHHHHHHHHHHHHhcCCCc--cCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhh
Confidence            2236789999999999987  577999999999999999999999999999999999999999999999855443 1223


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      .++.++..+.+||++||..+|..+.
T Consensus       435 ~~~~l~~~t~~~sgadi~~i~~ea~  459 (494)
T COG0464         435 DLEELAEITEGYSGADIAALVREAA  459 (494)
T ss_pred             hHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            4667777789999999999997554

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

Probab=99.97  E-value=3.1e-32  Score=273.91  Aligned_cols=213  Identities=21%  Similarity=0.279  Sum_probs=181.5

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhc-CCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC-
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVG-RAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD-  266 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g-~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~-  266 (530)
                      -..+|++|+|.+++++++.+.+..++.+|++|..-+ ..+++|+|||||||||||++|+|+|++.+.+++.+..+.+.+ 
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            456899999999999999999999999999997433 235789999999999999999999999999999999998753 


Q ss_pred             -----hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          267 -----NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       267 -----~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                           +.-++.+|.-+  -+||||||||||.++..++                                      ..+++
T Consensus       167 WfgE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R~--------------------------------------s~dHE  208 (386)
T KOG0737|consen  167 WFGEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRR--------------------------------------STDHE  208 (386)
T ss_pred             hHHHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhcc--------------------------------------cchHH
Confidence                 23355556555  4799999999999863221                                      13566


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      .....-++|...+||+.+..+..++|+++||+|.+||.|++|  ||...++++.|+..+|..|++.+|..+..+..++ +
T Consensus       209 a~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD-~  285 (386)
T KOG0737|consen  209 ATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVD-L  285 (386)
T ss_pred             HHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccC-H
Confidence            677888999999999999766678888999999999999999  9999999999999999999999999876653444 7


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhc
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      .+++..+.|||+.||.++|..+.
T Consensus       286 ~~iA~~t~GySGSDLkelC~~Aa  308 (386)
T KOG0737|consen  286 DEIAQMTEGYSGSDLKELCRLAA  308 (386)
T ss_pred             HHHHHhcCCCcHHHHHHHHHHHh
Confidence            77888899999999999998655

>CHL00176 ftsH cell division protein; Validated

Probab=99.97  E-value=1.5e-30  Score=287.77  Aligned_cols=215  Identities=23%  Similarity=0.309  Sum_probs=179.6

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-  265 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-  265 (530)
                      .....+|++++|.+++++++.+ +..+++.++.|..+|...++|+|||||||||||++|+|+|++++.+++.++.+.+. 
T Consensus       176 ~~~~~~f~dv~G~~~~k~~l~e-iv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~~  254 (638)
T CHL00176        176 ADTGITFRDIAGIEEAKEEFEE-VVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVE  254 (638)
T ss_pred             cCCCCCHHhccChHHHHHHHHH-HHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHHH
Confidence            3456799999999999998876 56778999999999999999999999999999999999999999999999877652 


Q ss_pred             -----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          266 -----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       266 -----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                           ....++.+|..+  ..||||||||||++...++..                                   ....+
T Consensus       255 ~~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~-----------------------------------~~~~~  299 (638)
T CHL00176        255 MFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAG-----------------------------------IGGGN  299 (638)
T ss_pred             HhhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCC-----------------------------------CCCCc
Confidence                 345678888876  589999999999984211100                                   00123


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV  418 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~  418 (530)
                      .....+++.||+.+||+..  ..+++||+|||+++.|||||+||||||.+|+++.|+.++|..|++.++...... ....
T Consensus       300 ~e~~~~L~~LL~~~dg~~~--~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~-~d~~  376 (638)
T CHL00176        300 DEREQTLNQLLTEMDGFKG--NKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLS-PDVS  376 (638)
T ss_pred             HHHHHHHHHHHhhhccccC--CCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccc-hhHH
Confidence            3456789999999999876  467999999999999999999999999999999999999999999999764433 3345


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHH
Q 009640          419 VESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       419 i~~l~~~~~~~spadi~~~l~~  440 (530)
                      +..++..+.||+++||.+++..
T Consensus       377 l~~lA~~t~G~sgaDL~~lvne  398 (638)
T CHL00176        377 LELIARRTPGFSGADLANLLNE  398 (638)
T ss_pred             HHHHHhcCCCCCHHHHHHHHHH
Confidence            7788888999999999998864

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

Probab=99.97  E-value=4.8e-30  Score=273.38  Aligned_cols=252  Identities=23%  Similarity=0.274  Sum_probs=213.4

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc----
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV----  264 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~----  264 (530)
                      ++.+ ++++|.......+.+.+..++..+..|...|.++++|+|+|||||||||.+++|+|++.+..++.++..++    
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            5666 78899999999999999999999999999999999999999999999999999999999999999987765    


Q ss_pred             --CChHHHHHHHHhc--CC-CeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          265 --TDNSELRALLLQT--TN-RSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       265 --~~~~~L~~l~~~~--~~-~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                        .+++.|++.|.++  .+ |+||||||||.+.+                  +|..                     .+.
T Consensus       259 ~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p------------------~r~~---------------------~~~  299 (693)
T KOG0730|consen  259 PGETESNLRKAFAEALKFQVPSIIFIDELDALCP------------------KREG---------------------ADD  299 (693)
T ss_pred             ccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCC------------------cccc---------------------cch
Confidence              4678899999987  45 99999999999852                  1111                     112


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ...++.++|+..+||+.+  ...+|||+|||+|+.|||++.| ||||..+++..|+..+|.+|++.+.....+. ....+
T Consensus       300 ~e~Rv~sqlltL~dg~~~--~~~vivl~atnrp~sld~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~-~~~~l  375 (693)
T KOG0730|consen  300 VESRVVSQLLTLLDGLKP--DAKVIVLAATNRPDSLDPALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLL-SDVDL  375 (693)
T ss_pred             HHHHHHHHHHHHHhhCcC--cCcEEEEEecCCccccChhhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCc-chhhH
Confidence            467789999999999985  5789999999999999999999 9999999999999999999999999877666 45568


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhhhccccccccccccccCCCCcccccCCCCcccCCCCCC
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVVRSPENWDSSPGGK  497 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~g~~  497 (530)
                      +.++..++||++||+..+|..+.   ..++++          +...+..+.....|++.+......+.+.|+++||..
T Consensus       376 ~~iA~~thGyvGaDL~~l~~ea~---~~~~r~----------~~~~~~~A~~~i~psa~Re~~ve~p~v~W~dIGGlE  440 (693)
T KOG0730|consen  376 EDIAVSTHGYVGADLAALCREAS---LQATRR----------TLEIFQEALMGIRPSALREILVEMPNVSWDDIGGLE  440 (693)
T ss_pred             HHHHHHccchhHHHHHHHHHHHH---HHHhhh----------hHHHHHHHHhcCCchhhhheeccCCCCChhhccCHH
Confidence            88888899999999999997554   233332          333444555566677888888888999999999875

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.96  E-value=2.4e-29  Score=263.75  Aligned_cols=220  Identities=22%  Similarity=0.249  Sum_probs=177.2

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++++|.++++++|.+.+..++.+++.|..+|+.+++|+|||||||||||++++++|++++.+++.+....+
T Consensus       113 ~~~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~~~~l  192 (364)
T TIGR01242       113 VEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSEL  192 (364)
T ss_pred             eccCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEecchHHH
Confidence            34456778999999999999999999999999999999999999999999999999999999999999999988875543


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      ....++.+|..+  ..|+||||||||.+...+.   .                                ...+
T Consensus       193 ~~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~---~--------------------------------~~~~  237 (364)
T TIGR01242       193 VRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRT---D--------------------------------SGTS  237 (364)
T ss_pred             HHHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccc---c--------------------------------CCCC
Confidence            2      123356666544  5799999999999842100   0                                0001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .+.....++..+++.+|++..  .++++||+|||+++.+|++++||||||..|+|+.|+.++|..|++.++........ 
T Consensus       238 ~~~~~~~~l~~ll~~ld~~~~--~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~-  314 (364)
T TIGR01242       238 GDREVQRTLMQLLAELDGFDP--RGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAED-  314 (364)
T ss_pred             ccHHHHHHHHHHHHHhhCCCC--CCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCcc-
Confidence            223345678899999998865  36789999999999999999999999999999999999999999998865433211 


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ..+..++..+.+|+++||..+|..+.
T Consensus       315 ~~~~~la~~t~g~sg~dl~~l~~~A~  340 (364)
T TIGR01242       315 VDLEAIAKMTEGASGADLKAICTEAG  340 (364)
T ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            13677777789999999999987544

Many proteins may score above the trusted cutoff because an internal

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.96  E-value=1.6e-29  Score=293.16  Aligned_cols=200  Identities=17%  Similarity=0.124  Sum_probs=153.6

Q ss_pred             cChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC----------------------------
Q 009640          215 NGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD----------------------------  266 (530)
Q Consensus       215 ~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~----------------------------  266 (530)
                      .++..+.++|..+++|+||+||||||||+||+|+|++++++++.++++++..                            
T Consensus      1617 ~~kP~slrLGl~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~ 1696 (2281)
T CHL00206       1617 HGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRD 1696 (2281)
T ss_pred             cCcCHHHHcCCCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhcccccccccccccccccccccccccccc
Confidence            3456778899999999999999999999999999999999999998766531                            


Q ss_pred             ---------------------hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccc
Q 009640          267 ---------------------NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSR  323 (530)
Q Consensus       267 ---------------------~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~  323 (530)
                                           ...++.+|..|  .+||||+|||||++..                              
T Consensus      1697 ~~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~------------------------------ 1746 (2281)
T CHL00206       1697 LDTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNV------------------------------ 1746 (2281)
T ss_pred             cchhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCC------------------------------
Confidence                                 01256677665  7899999999999831                              


Q ss_pred             cccccCCCCCCCCCCcchhhhHHHHhhhccCCccC-CCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHH
Q 009640          324 IASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSC-CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVL  402 (530)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~-~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i  402 (530)
                                    .+....+++.||+.|||.... ...++|||+|||+|+.|||||+||||||++|+++.|+..+|+++
T Consensus      1747 --------------~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~ki 1812 (2281)
T CHL00206       1747 --------------NESNYLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKH 1812 (2281)
T ss_pred             --------------CccceehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHH
Confidence                          112335689999999987532 24679999999999999999999999999999999999999998


Q ss_pred             HHHhhCCc--CccchHHHHHHHHHhCCCCCHHHHHHHHHHhc-------------cCHHHHHHHHHHHHHH
Q 009640          403 AKNYLGIE--SHHALFDVVESCIRAGGALTPAQIGEVLLRNR-------------GNVDLAMKEVVSAMQA  458 (530)
Q Consensus       403 ~~~~l~~~--~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~-------------~d~~~al~~l~~~l~~  458 (530)
                      +...+...  ........+..+|..|.|||+|||+++|..+.             .+.+.|+.+.+-.++.
T Consensus      1813 L~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanLvNEAaliAirq~ks~Id~~~I~~Al~Rq~~g~~~ 1883 (2281)
T CHL00206       1813 FFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALTNEALSISITQKKSIIDTNTIRSALHRQTWDLRS 1883 (2281)
T ss_pred             HHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHHhhhhh
Confidence            87654221  11101123678888899999999999986422             2455666665544443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.96  E-value=4.8e-29  Score=283.14  Aligned_cols=265  Identities=22%  Similarity=0.286  Sum_probs=205.4

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC---
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT---  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~---  265 (530)
                      +..+|++|+|.+++++.|.+.+..++.+++.|..+|+.+++|+|||||||||||+|+++||++++.+++.++...+.   
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            56789999999999999999999999999999999999999999999999999999999999999999999866542   


Q ss_pred             ---ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          266 ---DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       266 ---~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                         ....++.+|..+  ..|+||||||||++...++                  .                    .....
T Consensus       253 ~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~------------------~--------------------~~~~~  294 (733)
T TIGR01243       253 YGESEERLREIFKEAEENAPSIIFIDEIDAIAPKRE------------------E--------------------VTGEV  294 (733)
T ss_pred             ccHHHHHHHHHHHHHHhcCCcEEEeehhhhhccccc------------------C--------------------CcchH
Confidence               245688888765  6789999999999852110                  0                    11223


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE  420 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~  420 (530)
                      ...+++.|++.||++..  ...++||+|||+++.|||+++|+||||.+|+++.|+.++|..|++.++...... ....+.
T Consensus       295 ~~~~~~~Ll~~ld~l~~--~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~-~d~~l~  371 (733)
T TIGR01243       295 EKRVVAQLLTLMDGLKG--RGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLA-EDVDLD  371 (733)
T ss_pred             HHHHHHHHHHHhhcccc--CCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCc-cccCHH
Confidence            35678899999999976  467889999999999999999999999999999999999999999887654332 122366


Q ss_pred             HHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHH--------------HHHhhhccccccccccccccCCCCcccccCC
Q 009640          421 SCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSA--------------MQAKILSGREVMECDELVITRSPESVVVVRS  486 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~--------------l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  486 (530)
                      .++..+.+|+++|+..++..+.   ..+++.+...              ++....+..++..+...+.|+.........+
T Consensus       372 ~la~~t~G~~gadl~~l~~~a~---~~al~r~~~~~~~~~~~~~i~~~~~~~~~v~~~df~~Al~~v~ps~~~~~~~~~~  448 (733)
T TIGR01243       372 KLAEVTHGFVGADLAALAKEAA---MAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPSAIREVLVEVP  448 (733)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHH---HHHHHHHhhccccccccccccchhcccccccHHHHHHHHhhccccccchhhcccc
Confidence            7777899999999999886543   4444443321              1112233444555555555655555555567


Q ss_pred             CCcccCCCCCC
Q 009640          487 PENWDSSPGGK  497 (530)
Q Consensus       487 ~~~w~~~~g~~  497 (530)
                      ...|++++|..
T Consensus       449 ~~~~~di~g~~  459 (733)
T TIGR01243       449 NVRWSDIGGLE  459 (733)
T ss_pred             ccchhhcccHH
Confidence            88999998754

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.

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

Probab=99.96  E-value=4.9e-30  Score=251.80  Aligned_cols=213  Identities=24%  Similarity=0.322  Sum_probs=173.9

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC--
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD--  266 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~--  266 (530)
                      ...+|+.+.|.-++..++++-++.++.+++.|.++|+.+|.|+|||||||||||.+++++|..++.+++.+..+.+.+  
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            345899999999999999999999999999999999999999999999999999999999999999999999887743  


Q ss_pred             ----hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          267 ----NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       267 ----~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                          ..-+++.|..+  ..|||||+||||++.+   ++..                                .....+..
T Consensus       207 iGEsaRlIRemf~yA~~~~pciifmdeiDAigG---Rr~s--------------------------------e~Ts~dre  251 (388)
T KOG0651|consen  207 IGESARLIRDMFRYAREVIPCIIFMDEIDAIGG---RRFS--------------------------------EGTSSDRE  251 (388)
T ss_pred             cccHHHHHHHHHHHHhhhCceEEeehhhhhhcc---EEec--------------------------------cccchhHH
Confidence                23367777766  5799999999999842   1100                                00022345


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC-cCccchHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI-ESHHALFDVV  419 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~-~~~~~~~~~i  419 (530)
                      -+.||-.|||+|||...  -+.+-+|+|||+|+.|||||+||||+|+.|+.|.|+...|..|++.+-.. ..|.++.  .
T Consensus       252 iqrTLMeLlnqmdgfd~--l~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid--~  327 (388)
T KOG0651|consen  252 IQRTLMELLNQMDGFDT--LHRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEID--D  327 (388)
T ss_pred             HHHHHHHHHHhhccchh--cccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEeecccccccccccc--H
Confidence            67899999999999987  46788999999999999999999999999999999999999988766543 2233121  3


Q ss_pred             HHHHHhCCCCCHHHHHHHHHH
Q 009640          420 ESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~  440 (530)
                      +++.+-.+++.++|+.+.|..
T Consensus       328 eaivK~~d~f~gad~rn~~tE  348 (388)
T KOG0651|consen  328 EAILKLVDGFNGADLRNVCTE  348 (388)
T ss_pred             HHHHHHHhccChHHHhhhccc
Confidence            444444689999998888764

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

Probab=99.96  E-value=1.5e-29  Score=262.78  Aligned_cols=266  Identities=19%  Similarity=0.198  Sum_probs=213.0

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC---
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT---  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~---  265 (530)
                      ++..|++++|...+|+.+.+.+..++.+++.|..+. ++.+|+||+||||||||+|++|||.+++..+++++.+++.   
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 RNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLR-EPVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSLTSKY  226 (428)
T ss_pred             CcccccCCcchhhHHHHhhhhhhhcccchHhhhccc-cccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHhhhhc
Confidence            446779999999999999999999999999998874 4458999999999999999999999999999999988773   


Q ss_pred             ---ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          266 ---DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       266 ---~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                         ++.-++.+|.-+  .+|+||||||||.++..+                  .                    .+.++.
T Consensus       227 ~Ge~eK~vralf~vAr~~qPsvifidEidslls~R------------------s--------------------~~e~e~  268 (428)
T KOG0740|consen  227 VGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKR------------------S--------------------DNEHES  268 (428)
T ss_pred             cChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhc------------------C--------------------Cccccc
Confidence               234466676544  789999999999997311                  0                    034566


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE  420 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~  420 (530)
                      ++....++|..++|..+...+.++||+|||.|+.+|.|++|  ||-+.+++|.|+.++|..+|++++....+......++
T Consensus       269 srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~  346 (428)
T KOG0740|consen  269 SRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDIS  346 (428)
T ss_pred             chhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHH
Confidence            77888999999999999877889999999999999999999  9999999999999999999999999886664557899


Q ss_pred             HHHHhCCCCCHHHHHHHHHHhccCHHHHHHHH--H---HHHHHhhhccccccccccccccCCCCcccccCCCCcccCCCC
Q 009640          421 SCIRAGGALTPAQIGEVLLRNRGNVDLAMKEV--V---SAMQAKILSGREVMECDELVITRSPESVVVVRSPENWDSSPG  495 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~~~d~~~al~~l--~---~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~g  495 (530)
                      .++..+.||++.||.++|..+..++...+..-  +   .+...+.....++..+...+.+..  +......+.+|+...|
T Consensus       347 ~l~~~Tegysgsdi~~l~kea~~~p~r~~~~~~~~~~~~~~~~r~i~~~df~~a~~~i~~~~--s~~~l~~~~~~~~~fg  424 (428)
T KOG0740|consen  347 LLAKVTEGYSGSDITALCKEAAMGPLRELGGTTDLEFIDADKIRPITYPDFKNAFKNIKPSV--SLEGLEKYEKWDKEFG  424 (428)
T ss_pred             HHHHHhcCcccccHHHHHHHhhcCchhhcccchhhhhcchhccCCCCcchHHHHHHhhcccc--CccccchhHHHhhhhc
Confidence            99999999999999999988776666655542  2   222234444555555555554433  3355666777777666


Q ss_pred             CC
Q 009640          496 GK  497 (530)
Q Consensus       496 ~~  497 (530)
                      ..
T Consensus       425 ~~  426 (428)
T KOG0740|consen  425 SS  426 (428)
T ss_pred             cc
Confidence            53

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.96  E-value=1.7e-28  Score=273.84  Aligned_cols=216  Identities=23%  Similarity=0.314  Sum_probs=176.5

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC--
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT--  265 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~--  265 (530)
                      ....+|+++.+.+..++.+.+. ..++..+..|..+|...++|+||+||||||||++++++|++++.+++.++.+.+.  
T Consensus       146 ~~~~~~~di~g~~~~~~~l~~i-~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~~  224 (644)
T PRK10733        146 QIKTTFADVAGCDEAKEEVAEL-VEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM  224 (644)
T ss_pred             hhhCcHHHHcCHHHHHHHHHHH-HHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHHh
Confidence            4456899999999999988774 4567778888889999999999999999999999999999999999999876542  


Q ss_pred             ----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          266 ----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       266 ----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                          +...++.+|..+  .+||||||||||++...++   .                                +..+.+.
T Consensus       225 ~~g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~---~--------------------------------~~~g~~~  269 (644)
T PRK10733        225 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG---A--------------------------------GLGGGHD  269 (644)
T ss_pred             hhcccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccC---C--------------------------------CCCCCch
Confidence                345678888776  5899999999999842110   0                                0001233


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ....+++.||..|||+.+  ..+++||+|||+|+.|||||+||||||++|++++|+.++|.+|++.|+........ ..+
T Consensus       270 ~~~~~ln~lL~~mdg~~~--~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~-~d~  346 (644)
T PRK10733        270 EREQTLNQMLVEMDGFEG--NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPD-IDA  346 (644)
T ss_pred             HHHHHHHHHHHhhhcccC--CCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCc-CCH
Confidence            456789999999999976  46799999999999999999999999999999999999999999999976543312 235


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhc
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ..++..+.|||+|||.++|..+.
T Consensus       347 ~~la~~t~G~sgadl~~l~~eAa  369 (644)
T PRK10733        347 AIIARGTPGFSGADLANLVNEAA  369 (644)
T ss_pred             HHHHhhCCCCCHHHHHHHHHHHH
Confidence            66788899999999999997543

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

Probab=99.96  E-value=9.2e-28  Score=244.11  Aligned_cols=166  Identities=15%  Similarity=0.121  Sum_probs=131.3

Q ss_pred             hHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC------ChHHHHHHHHhc-------CCCeEEEE
Q 009640          219 FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT------DNSELRALLLQT-------TNRSIIVI  285 (530)
Q Consensus       219 ~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~------~~~~L~~l~~~~-------~~~sII~I  285 (530)
                      +....|+.+|+|+|||||||||||++++|+|++++.+++.++..++.      ++..++++|..+       .+||||||
T Consensus       139 ~l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFI  218 (413)
T PLN00020        139 FLALPNIKVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFI  218 (413)
T ss_pred             hhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEE
Confidence            33447889999999999999999999999999999999999987763      457799999866       26999999


Q ss_pred             cCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCC--------c-
Q 009640          286 EDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGL--------W-  356 (530)
Q Consensus       286 DeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl--------~-  356 (530)
                      ||||++++-++                                     ........+.+...|||.+|++        | 
T Consensus       219 DEIDA~~g~r~-------------------------------------~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~  261 (413)
T PLN00020        219 NDLDAGAGRFG-------------------------------------TTQYTVNNQMVNGTLMNIADNPTNVSLGGDWR  261 (413)
T ss_pred             ehhhhcCCCCC-------------------------------------CCCcchHHHHHHHHHHHHhcCCcccccccccc
Confidence            99999853110                                     0011222455568999998864        4 


Q ss_pred             -cCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHh
Q 009640          357 -SCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRA  425 (530)
Q Consensus       357 -s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~  425 (530)
                       .....+++||+|||+|+.|||||+||||||+.|  ..|+.++|..|++.++......  ...+..++..
T Consensus       262 ~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~--~~dv~~Lv~~  327 (413)
T PLN00020        262 EKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVS--REDVVKLVDT  327 (413)
T ss_pred             ccccCCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCC--HHHHHHHHHc
Confidence             112466899999999999999999999999975  5899999999999999876544  3567777764

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

Probab=99.95  E-value=1.8e-27  Score=266.73  Aligned_cols=214  Identities=23%  Similarity=0.241  Sum_probs=180.2

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----CcEEEEec
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----YDVYDLEL  261 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----~~i~~l~l  261 (530)
                      ......|++|+|.+.++.++.+-+..++..|++|.++++.++||+|||||||||||++++|+|..+.     ..+|.-..
T Consensus       258 ~~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkg  337 (1080)
T KOG0732|consen  258 VDSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKG  337 (1080)
T ss_pred             hhcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcC
Confidence            3456689999999999999999999999999999999999999999999999999999999999882     23332222


Q ss_pred             ----Ccc--CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCC
Q 009640          262 ----TKV--TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNN  333 (530)
Q Consensus       262 ----~~~--~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~  333 (530)
                          +..  ..+.+|+-+|.++  ..|||||+||||-+.+                  .|++.                 
T Consensus       338 aD~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlap------------------vrSsk-----------------  382 (1080)
T KOG0732|consen  338 ADCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAP------------------VRSSK-----------------  382 (1080)
T ss_pred             chhhccccCcHHHHHHHHHHHHhccCceEEeccccccccc------------------cccch-----------------
Confidence                222  2356788899887  6899999999998742                  22211                 


Q ss_pred             CCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCcc
Q 009640          334 NNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHH  413 (530)
Q Consensus       334 ~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~  413 (530)
                         .......+++.||..|||+.+  .+.++||++||+|+.+||||+||||||+.++|++|+.++|..|+..+-..-.+.
T Consensus       383 ---qEqih~SIvSTLLaLmdGlds--RgqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~  457 (1080)
T KOG0732|consen  383 ---QEQIHASIVSTLLALMDGLDS--RGQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPP  457 (1080)
T ss_pred             ---HHHhhhhHHHHHHHhccCCCC--CCceEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCC
Confidence               123345678999999999998  588999999999999999999999999999999999999999999888776666


Q ss_pred             chHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009640          414 ALFDVVESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       414 ~~~~~i~~l~~~~~~~spadi~~~l~~  440 (530)
                      .....+..++..+.||-+|||+.+|..
T Consensus       458 i~~~l~~~la~~t~gy~gaDlkaLCTe  484 (1080)
T KOG0732|consen  458 ISRELLLWLAEETSGYGGADLKALCTE  484 (1080)
T ss_pred             CCHHHHHHHHHhccccchHHHHHHHHH
Confidence            566778889999999999999999974

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

Probab=99.95  E-value=6e-28  Score=250.33  Aligned_cols=248  Identities=17%  Similarity=0.251  Sum_probs=181.4

Q ss_pred             CCCCCCcccc--cC-ChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcE-EEEecC
Q 009640          187 FRHPSTFETL--AL-EPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDV-YDLELT  262 (530)
Q Consensus       187 ~~~~~~f~~l--~~-~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i-~~l~l~  262 (530)
                      ..+...|+++  +| +.+.-...+..+..-+..|+.-.++|+++-+|+|||||||||||.+|+.|..-|+..- -.++..
T Consensus       212 i~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGP  291 (744)
T KOG0741|consen  212 INPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGP  291 (744)
T ss_pred             cCCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcH
Confidence            3455578887  23 3344444455555555689999999999999999999999999999999999997543 233333


Q ss_pred             cc------CChHHHHHHHHhc----------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          263 KV------TDNSELRALLLQT----------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       263 ~~------~~~~~L~~l~~~~----------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      ++      .++.++|+||..+          +.-.||++||||+++..++..                            
T Consensus       292 eIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~----------------------------  343 (744)
T KOG0741|consen  292 EILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSM----------------------------  343 (744)
T ss_pred             HHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCC----------------------------
Confidence            22      4678899999876          234699999999997322211                            


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                              .++......++++||.-|||+.+  -.+++||+-||+++.+|+||+||||+..++++++||++.|.+|++.+
T Consensus       344 --------~g~TGVhD~VVNQLLsKmDGVeq--LNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IH  413 (744)
T KOG0741|consen  344 --------AGSTGVHDTVVNQLLSKMDGVEQ--LNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIH  413 (744)
T ss_pred             --------CCCCCccHHHHHHHHHhcccHHh--hhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhh
Confidence                    02345567789999999999987  47899999999999999999999999999999999999999999877


Q ss_pred             hCCcC-ccc--hHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHH----------HHHHhhhcccccccccccc
Q 009640          407 LGIES-HHA--LFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS----------AMQAKILSGREVMECDELV  473 (530)
Q Consensus       407 l~~~~-~~~--~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~----------~l~~~~~~~~~~~~~~~~~  473 (530)
                      ..... +..  ....+++++..|..||+|+|..++..+.   ..|+.+.+.          .++.-+.+..++..+.+-+
T Consensus       414 T~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVksA~---S~A~nR~vk~~~~~~~~~~~~e~lkV~r~DFl~aL~dV  490 (744)
T KOG0741|consen  414 TKRMRENNKLSADVDLKELAALTKNFSGAELEGLVKSAQ---SFAMNRHVKAGGKVEVDPVAIENLKVTRGDFLNALEDV  490 (744)
T ss_pred             hhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHHHHH---HHHHHhhhccCcceecCchhhhheeecHHHHHHHHHhc
Confidence            65321 110  1224778888899999999999997655   445544432          2233344555555555554


Q ss_pred             cc
Q 009640          474 IT  475 (530)
Q Consensus       474 ~~  475 (530)
                      .|
T Consensus       491 kP  492 (744)
T KOG0741|consen  491 KP  492 (744)
T ss_pred             Cc
Confidence            44

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

Probab=99.87  E-value=6.2e-22  Score=168.61  Aligned_cols=96  Identities=34%  Similarity=0.585  Sum_probs=89.6

Q ss_pred             hChHHHHHHHHHHHHHhhh-hcCCceEEEEecccCCCCCCcChHHHHHHHHhhccCCCCCccccceeecccCCCCceEEE
Q 009640           20 VLPSQLLSLLHSFYESLQD-LFSPYSYFEIPEFNGYCGVDVNDLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFT   98 (530)
Q Consensus        20 ~~p~~l~~~~~~~~~~~~~-~~~~~~~~~i~e~~~~~~~~~n~~~~a~~~yl~~~~~~~~~~~~~l~~~~~~~~~~~~~~   98 (530)
                      |+|++|++++.+++++++. +++||+||+|+|++|.   ++|++|+|+++||+++++..+   +||++++++++++++++
T Consensus         1 ~~P~~lr~~~~~~~~~~~~~~~s~~~ti~I~E~~g~---~~N~ly~a~~~YL~s~~s~~a---~rL~~~~~~~~~~~~l~   74 (98)
T PF14363_consen    1 LLPHELRSYLRSLLRRLFSSRFSPYLTIVIPEFDGL---SRNELYDAAQAYLSSKISPSA---RRLKASKSKNSKNLVLS   74 (98)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCCcEEEEEEeCCCc---cccHHHHHHHHHHhhccCccc---ceeeecccCCCCceEEe
Confidence            6899999999999987665 9999999999999974   899999999999999987776   89999999999999999


Q ss_pred             eCCCCeEeecccCeEEEEEEEee
Q 009640           99 VAPNHTVHDSFSGHSLSWTHHVD  121 (530)
Q Consensus        99 ~~~~~~~~d~f~g~~~~w~~~~~  121 (530)
                      |++||+|+|+|+|+++||+++++
T Consensus        75 l~~~e~V~D~F~Gv~v~W~~~~~   97 (98)
T PF14363_consen   75 LDDGEEVVDVFEGVKVWWSSVCT   97 (98)
T ss_pred             cCCCCEEEEEECCEEEEEEEEcc
Confidence            99999999999999999998764

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

Probab=99.85  E-value=7.8e-21  Score=192.58  Aligned_cols=248  Identities=23%  Similarity=0.264  Sum_probs=173.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHhhhhccccC----CCCCCCCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChh
Q 009640          143 QTLLSAYLDHVTSRAEEFERVSRERRLFTNN----GHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKE  218 (530)
Q Consensus       143 ~~vl~~yl~~v~~~~~~~~~~~~~~~l~~~~----~~~~~~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~  218 (530)
                      ..|...|+..++-.-.-+++..+-+.-+...    .++-.  .-..........|++|+..+.+++.|.+.-..-.+.+.
T Consensus       302 ~~V~w~yi~r~LGqPSLiREsSrg~~pw~gsls~~k~~i~--~~~~~s~~gk~pl~~ViL~psLe~Rie~lA~aTaNTK~  379 (630)
T KOG0742|consen  302 TLVTWRYIERRLGQPSLIRESSRGRFPWIGSLSALKHPIQ--GSRSASSRGKDPLEGVILHPSLEKRIEDLAIATANTKK  379 (630)
T ss_pred             chhHHHHHHHHcCCchhhhhhccccCCCcccHHHHhchhh--hhHhhhhcCCCCcCCeecCHHHHHHHHHHHHHhccccc
Confidence            3677778777776655555444322111000    00000  00112234455699999999999998886665555443


Q ss_pred             hHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-----ChHHHHHHHHhc---CCCeEEEEcCccc
Q 009640          219 FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-----DNSELRALLLQT---TNRSIIVIEDIDC  290 (530)
Q Consensus       219 ~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-----~~~~L~~l~~~~---~~~sII~IDeID~  290 (530)
                      .     ..+-|++|||||||||||++++-||.+.|+++-.+...++.     .-+.+.++|..+   ...-+|||||.|+
T Consensus       380 h-----~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS~rGLllFIDEADA  454 (630)
T KOG0742|consen  380 H-----QAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRGLLLFIDEADA  454 (630)
T ss_pred             c-----cchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCccccchHHHHHHHHHHHHHhhcccceEEEehhhHH
Confidence            1     22348899999999999999999999999999888777663     346688888866   3456899999999


Q ss_pred             hhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeC
Q 009640          291 SVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTN  370 (530)
Q Consensus       291 ~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN  370 (530)
                      ++-                  +|.+.                   ..++..+..|+.||--. |-.   +..++++.+||
T Consensus       455 FLc------------------eRnkt-------------------ymSEaqRsaLNAlLfRT-Gdq---SrdivLvlAtN  493 (630)
T KOG0742|consen  455 FLC------------------ERNKT-------------------YMSEAQRSALNALLFRT-GDQ---SRDIVLVLATN  493 (630)
T ss_pred             HHH------------------Hhchh-------------------hhcHHHHHHHHHHHHHh-ccc---ccceEEEeccC
Confidence            862                  22211                   22344567788887544 333   35688899999


Q ss_pred             CCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCc-------Cc-------------------cchHHHHHHHHH
Q 009640          371 HRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIE-------SH-------------------HALFDVVESCIR  424 (530)
Q Consensus       371 ~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~-------~~-------------------~~~~~~i~~l~~  424 (530)
                      +|.+||.|+-.  |||..|+||+|..++|..|+..||...       ..                   .+....+.+.+.
T Consensus       494 rpgdlDsAV~D--Ride~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAk  571 (630)
T KOG0742|consen  494 RPGDLDSAVND--RIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAK  571 (630)
T ss_pred             CccchhHHHHh--hhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHH
Confidence            99999999999  999999999999999999999988521       10                   012345677888


Q ss_pred             hCCCCCHHHHHHHHHH
Q 009640          425 AGGALTPAQIGEVLLR  440 (530)
Q Consensus       425 ~~~~~spadi~~~l~~  440 (530)
                      .|.|||+.+|+.++..
T Consensus       572 kTeGfSGREiakLva~  587 (630)
T KOG0742|consen  572 KTEGFSGREIAKLVAS  587 (630)
T ss_pred             hccCCcHHHHHHHHHH
Confidence            8999999999998763

>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=99.83  E-value=1.7e-20  Score=166.85  Aligned_cols=123  Identities=28%  Similarity=0.496  Sum_probs=100.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC------ChHHHHHHHHhc--CC-CeEEEEcCccchhhhhhhhhhc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT------DNSELRALLLQT--TN-RSIIVIEDIDCSVDLTADRMLK  301 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~------~~~~L~~l~~~~--~~-~sII~IDeID~~~~~~~~r~~~  301 (530)
                      +|||||||||||++++++|++++.+++.++...+.      ....+..+|.++  .. |+||+|||+|.+++..      
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~------   74 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKS------   74 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHC------
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccc------
Confidence            68999999999999999999999999999987764      345677778775  44 8999999999985311      


Q ss_pred             ccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhc
Q 009640          302 SSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIR  381 (530)
Q Consensus       302 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlR  381 (530)
                                                      ...........+..|++.++..... ..+++||+|||.++.+||+|+|
T Consensus        75 --------------------------------~~~~~~~~~~~~~~L~~~l~~~~~~-~~~~~vI~ttn~~~~i~~~l~~  121 (132)
T PF00004_consen   75 --------------------------------QPSSSSFEQRLLNQLLSLLDNPSSK-NSRVIVIATTNSPDKIDPALLR  121 (132)
T ss_dssp             --------------------------------STSSSHHHHHHHHHHHHHHHTTTTT-SSSEEEEEEESSGGGSCHHHHS
T ss_pred             --------------------------------ccccccccccccceeeecccccccc-cccceeEEeeCChhhCCHhHHh
Confidence                                            0022344667889999999988763 4569999999999999999999


Q ss_pred             CCceeEEEEeCC
Q 009640          382 CGRMDVHVSLGT  393 (530)
Q Consensus       382 pGR~d~~I~~~~  393 (530)
                       +||+..|+++.
T Consensus       122 -~rf~~~i~~~~  132 (132)
T PF00004_consen  122 -SRFDRRIEFPL  132 (132)
T ss_dssp             -TTSEEEEEE-S
T ss_pred             -CCCcEEEEcCC
Confidence             99999999974

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 ....

>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=3.6e-19  Score=170.97  Aligned_cols=167  Identities=19%  Similarity=0.195  Sum_probs=113.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN  267 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~  267 (530)
                      .+|.+|++++|+++++..+.-.+.....+.+.        -..+||||||||||||||..||++++.++..++...+...
T Consensus        18 lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~~~--------l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i~k~   89 (233)
T PF05496_consen   18 LRPKSLDEFIGQEHLKGNLKILIRAAKKRGEA--------LDHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAIEKA   89 (233)
T ss_dssp             TS-SSCCCS-S-HHHHHHHHHHHHHHHCTTS-----------EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC--SC
T ss_pred             cCCCCHHHccCcHHHHhhhHHHHHHHHhcCCC--------cceEEEECCCccchhHHHHHHHhccCCCeEeccchhhhhH
Confidence            47889999999999998877666655443321        2479999999999999999999999999999988777778


Q ss_pred             HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHH
Q 009640          268 SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSG  347 (530)
Q Consensus       268 ~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~  347 (530)
                      .++..++.....+.|||||||+.+-..                                                 ....
T Consensus        90 ~dl~~il~~l~~~~ILFIDEIHRlnk~-------------------------------------------------~qe~  120 (233)
T PF05496_consen   90 GDLAAILTNLKEGDILFIDEIHRLNKA-------------------------------------------------QQEI  120 (233)
T ss_dssp             HHHHHHHHT--TT-EEEECTCCC--HH-------------------------------------------------HHHH
T ss_pred             HHHHHHHHhcCCCcEEEEechhhccHH-------------------------------------------------HHHH
Confidence            899999999989999999999998211                                                 1112


Q ss_pred             HhhhccCCc-----cCC---------CCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCcc
Q 009640          348 LLNFTDGLW-----SCC---------SEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHH  413 (530)
Q Consensus       348 LLn~lDgl~-----s~~---------~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~  413 (530)
                      |+..|+...     ..+         -...-+|++|++...|.++|+.  ||.....+.+.+.++...|+++........
T Consensus       121 LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~  198 (233)
T PF05496_consen  121 LLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRD--RFGIVLRLEFYSEEELAKIVKRSARILNIE  198 (233)
T ss_dssp             HHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCT--TSSEEEE----THHHHHHHHHHCCHCTT-E
T ss_pred             HHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhHHh--hcceecchhcCCHHHHHHHHHHHHHHhCCC
Confidence            233222111     000         1234689999999999999999  999999999999999999998766554444

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.

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

Probab=99.78  E-value=1.8e-18  Score=185.42  Aligned_cols=253  Identities=17%  Similarity=0.203  Sum_probs=175.9

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC----CcEEEEecCccCC--h
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC----YDVYDLELTKVTD--N  267 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~----~~i~~l~l~~~~~--~  267 (530)
                      .+++..+..|++..++...+           +.....+||+||+|||||.|++++++++.    +++..++++.+..  -
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            44555555555554433222           33346899999999999999999999984    3344556665532  2


Q ss_pred             HH----HHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          268 SE----LRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       268 ~~----L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                      ..    |+.+|..+  .+||||++||+||++..                                    ...+++.....
T Consensus       477 e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~------------------------------------s~~e~~q~~~~  520 (952)
T KOG0735|consen  477 EKIQKFLNNVFSEALWYAPSIIVLDDLDCLASA------------------------------------SSNENGQDGVV  520 (952)
T ss_pred             HHHHHHHHHHHHHHHhhCCcEEEEcchhhhhcc------------------------------------CcccCCcchHH
Confidence            23    44555555  79999999999999630                                    00111223333


Q ss_pred             hhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHH
Q 009640          342 RVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVES  421 (530)
Q Consensus       342 ~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~  421 (530)
                      ...+..+||.+--.....+..+.+|+|.+....|+|-|..|++|+.++.++.|+..+|.+|+++.+........++.++-
T Consensus       521 ~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~  600 (952)
T KOG0735|consen  521 SERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDF  600 (952)
T ss_pred             HHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHH
Confidence            44556666554333322344568899999999999999999999999999999999999999999876543335566666


Q ss_pred             HHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhhhccccccccccccccCCCCcccccCCC-CcccCCCCCC
Q 009640          422 CIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSGREVMECDELVITRSPESVVVVRSP-ENWDSSPGGK  497 (530)
Q Consensus       422 l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~w~~~~g~~  497 (530)
                      ++..|.||.+-|+.-++.++-.   .|+...+...+ +-++...+..+.+-+.|...+++....+. -.|.++||..
T Consensus       601 ls~~TEGy~~~DL~ifVeRai~---~a~leris~~~-klltke~f~ksL~~F~P~aLR~ik~~k~tgi~w~digg~~  673 (952)
T KOG0735|consen  601 LSVKTEGYLATDLVIFVERAIH---EAFLERISNGP-KLLTKELFEKSLKDFVPLALRGIKLVKSTGIRWEDIGGLF  673 (952)
T ss_pred             HHHhcCCccchhHHHHHHHHHH---HHHHHHhccCc-ccchHHHHHHHHHhcChHHhhhccccccCCCCceecccHH
Confidence            8888999999999999865442   22211111111 25677778888888889999999877766 8999998864

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.77  E-value=1.2e-17  Score=173.07  Aligned_cols=192  Identities=16%  Similarity=0.166  Sum_probs=136.1

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD  266 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~  266 (530)
                      ...|.+|++++|.++.++.+...+.......        ...+++|||||||||||++|+++|++++.++..++...+..
T Consensus        18 ~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~~--------~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~~~   89 (328)
T PRK00080         18 SLRPKSLDEFIGQEKVKENLKIFIEAAKKRG--------EALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEK   89 (328)
T ss_pred             hcCcCCHHHhcCcHHHHHHHHHHHHHHHhcC--------CCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccccC
Confidence            3467899999999999998887776544322        22468999999999999999999999999988877766666


Q ss_pred             hHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHH
Q 009640          267 NSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLS  346 (530)
Q Consensus       267 ~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls  346 (530)
                      ..++..++.....++||||||||.+.....+                                                 
T Consensus        90 ~~~l~~~l~~l~~~~vl~IDEi~~l~~~~~e-------------------------------------------------  120 (328)
T PRK00080         90 PGDLAAILTNLEEGDVLFIDEIHRLSPVVEE-------------------------------------------------  120 (328)
T ss_pred             hHHHHHHHHhcccCCEEEEecHhhcchHHHH-------------------------------------------------
Confidence            7788888888888999999999987311100                                                 


Q ss_pred             HHhhhccCC---------ccC-----CCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCc
Q 009640          347 GLLNFTDGL---------WSC-----CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESH  412 (530)
Q Consensus       347 ~LLn~lDgl---------~s~-----~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~  412 (530)
                      .|.+.|+..         .+.     .-....+|++||++..++++|.+  ||+..+.|++++.+++..|++...+....
T Consensus       121 ~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~  198 (328)
T PRK00080        121 ILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGV  198 (328)
T ss_pred             HHHHHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCC
Confidence            011111110         000     01235789999999999999998  99999999999999999999987765443


Q ss_pred             cchHHHHHHHHHhCCCCCHHHHHHHH
Q 009640          413 HALFDVVESCIRAGGALTPAQIGEVL  438 (530)
Q Consensus       413 ~~~~~~i~~l~~~~~~~spadi~~~l  438 (530)
                      ....+.+..++.. .+-+|..+..++
T Consensus       199 ~~~~~~~~~ia~~-~~G~pR~a~~~l  223 (328)
T PRK00080        199 EIDEEGALEIARR-SRGTPRIANRLL  223 (328)
T ss_pred             CcCHHHHHHHHHH-cCCCchHHHHHH
Confidence            3222334444443 223444444444

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.76  E-value=2.1e-17  Score=169.19  Aligned_cols=159  Identities=18%  Similarity=0.194  Sum_probs=120.0

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHH
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELR  271 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~  271 (530)
                      +|++++|++++++.|...+......+.        ...+++||||||||||+|++++|++++.++..+..+.......+.
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~~~--------~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~~~~l~   73 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMRQE--------ALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLA   73 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhcCC--------CCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcCchhHH
Confidence            689999999999998887765544332        235799999999999999999999999998777666555566777


Q ss_pred             HHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhh
Q 009640          272 ALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF  351 (530)
Q Consensus       272 ~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~  351 (530)
                      ..+.....+.||||||||.+.+..                                                 ...|++.
T Consensus        74 ~~l~~~~~~~vl~iDEi~~l~~~~-------------------------------------------------~e~l~~~  104 (305)
T TIGR00635        74 AILTNLEEGDVLFIDEIHRLSPAV-------------------------------------------------EELLYPA  104 (305)
T ss_pred             HHHHhcccCCEEEEehHhhhCHHH-------------------------------------------------HHHhhHH
Confidence            777777888999999999873100                                                 0111111


Q ss_pred             ccCCc--------------cCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          352 TDGLW--------------SCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       352 lDgl~--------------s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      ++...              .......++|++||++..++++|++  ||...+.+++++.++...+++...+.
T Consensus       105 ~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~  174 (305)
T TIGR00635       105 MEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGL  174 (305)
T ss_pred             HhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHH
Confidence            11100              0001336789999999999999999  99999999999999999999877653

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.

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

Probab=99.75  E-value=3.8e-18  Score=169.08  Aligned_cols=178  Identities=23%  Similarity=0.321  Sum_probs=129.8

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhh-hcCCCCceEEEECCCCCChhHHHHHHHHHcCC---------cEEEEec
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHR-VGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY---------DVYDLEL  261 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~-~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~---------~i~~l~l  261 (530)
                      -|+.++.+..+|+.+..+...-+.-.+.-.. --+.|.|-+|||||||||||+|++|+|..|..         .++.++.
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            4688899999999999887765542221111 22688999999999999999999999999832         3344554


Q ss_pred             Ccc------CChHHHHHHHHhc-------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccccc
Q 009640          262 TKV------TDNSELRALLLQT-------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST  328 (530)
Q Consensus       262 ~~~------~~~~~L~~l~~~~-------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~  328 (530)
                      .++      .+...+.++|.+.       ..--.++|||++++.-   .|....                          
T Consensus       220 hsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~---aR~s~~--------------------------  270 (423)
T KOG0744|consen  220 HSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAA---ARTSAS--------------------------  270 (423)
T ss_pred             hHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHH---HHHhhh--------------------------
Confidence            333      1223355555543       1224577999999732   121100                          


Q ss_pred             CCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       329 ~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                           +.++....-++++.||.+||.+..  ..++++++|+|-.+.||-|+..  |-|...++++|+.+++..|++..+
T Consensus       271 -----S~~EpsDaIRvVNalLTQlDrlK~--~~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~Ilksci  340 (423)
T KOG0744|consen  271 -----SRNEPSDAIRVVNALLTQLDRLKR--YPNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCI  340 (423)
T ss_pred             -----cCCCCchHHHHHHHHHHHHHHhcc--CCCEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHH
Confidence                 002233455788999999999987  4789999999999999999999  999999999999999999998776

>PRK04195 replication factor C large subunit; Provisional

Probab=99.74  E-value=5.6e-17  Score=176.32  Aligned_cols=165  Identities=22%  Similarity=0.365  Sum_probs=127.1

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .|  +..+.|.+|++++|++++++.+...+..+.++.        + ++++|||||||||||++|+++|++++++++.++
T Consensus         3 ~W--~eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~g~--------~-~~~lLL~GppG~GKTtla~ala~el~~~~ieln   71 (482)
T PRK04195          3 PW--VEKYRPKTLSDVVGNEKAKEQLREWIESWLKGK--------P-KKALLLYGPPGVGKTSLAHALANDYGWEVIELN   71 (482)
T ss_pred             Cc--hhhcCCCCHHHhcCCHHHHHHHHHHHHHHhcCC--------C-CCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEc
Confidence            57  778999999999999999999999888776422        2 579999999999999999999999999999999


Q ss_pred             cCccCChHHHHHHHHhc--------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          261 LTKVTDNSELRALLLQT--------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       261 l~~~~~~~~L~~l~~~~--------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      .+...+...+..++...        ..+.||||||+|.+..                                       
T Consensus        72 asd~r~~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~---------------------------------------  112 (482)
T PRK04195         72 ASDQRTADVIERVAGEAATSGSLFGARRKLILLDEVDGIHG---------------------------------------  112 (482)
T ss_pred             ccccccHHHHHHHHHHhhccCcccCCCCeEEEEecCccccc---------------------------------------
Confidence            98877666666655432        2578999999998731                                       


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                            ......+..|++.++.      ....||++||.+..+++.-+|  +....|.|+.|+..+...+++..+..
T Consensus       113 ------~~d~~~~~aL~~~l~~------~~~~iIli~n~~~~~~~k~Lr--sr~~~I~f~~~~~~~i~~~L~~i~~~  175 (482)
T PRK04195        113 ------NEDRGGARAILELIKK------AKQPIILTANDPYDPSLRELR--NACLMIEFKRLSTRSIVPVLKRICRK  175 (482)
T ss_pred             ------ccchhHHHHHHHHHHc------CCCCEEEeccCccccchhhHh--ccceEEEecCCCHHHHHHHHHHHHHH
Confidence                  0011234567777662      223477789999988873344  34467999999999999988877643

>CHL00181 cbbX CbbX; Provisional

Probab=99.73  E-value=6.7e-17  Score=164.01  Aligned_cols=169  Identities=19%  Similarity=0.291  Sum_probs=122.9

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCC-ce--EEEECCCCCChhHHHHHHHHHcC-------CcEEEEecCc
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWK-RG--YLLYGPPGSGKSSLIAAMANYLC-------YDVYDLELTK  263 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~-rG--~LL~GPPGTGKTsLa~AiA~~l~-------~~i~~l~l~~  263 (530)
                      ++++|.+++|++|.+.+ .++..+..+.+.|...+ .|  +||+||||||||++|+++|..+.       .+++.++.+.
T Consensus        23 ~~l~Gl~~vK~~i~e~~-~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~  101 (287)
T CHL00181         23 EELVGLAPVKTRIREIA-ALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDD  101 (287)
T ss_pred             HhcCCcHHHHHHHHHHH-HHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHH
Confidence            47999999999999865 44555677777887654 24  89999999999999999999862       2467766544


Q ss_pred             cC------ChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          264 VT------DNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       264 ~~------~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                      +.      +......+|.++ .++||||||+|.+....                                        ..
T Consensus       102 l~~~~~g~~~~~~~~~l~~a-~ggVLfIDE~~~l~~~~----------------------------------------~~  140 (287)
T CHL00181        102 LVGQYIGHTAPKTKEVLKKA-MGGVLFIDEAYYLYKPD----------------------------------------NE  140 (287)
T ss_pred             HHHHHhccchHHHHHHHHHc-cCCEEEEEccchhccCC----------------------------------------Cc
Confidence            31      223445566665 45899999999873100                                        11


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCc
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIE  410 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~  410 (530)
                      ..........|+..|+..    ...++||++++...     .++|+|.+  ||+.+|+|+.++.+++..|+..++...
T Consensus       141 ~~~~~e~~~~L~~~me~~----~~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~  212 (287)
T CHL00181        141 RDYGSEAIEILLQVMENQ----RDDLVVIFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQ  212 (287)
T ss_pred             cchHHHHHHHHHHHHhcC----CCCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHh
Confidence            122355677888888743    24577777775422     34799999  999999999999999999999998643

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.72  E-value=2e-16  Score=158.60  Aligned_cols=169  Identities=12%  Similarity=0.215  Sum_probs=118.9

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCC---CceEEEECCCCCChhHHHHHHHHHcC-------CcEEEEecC
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAW---KRGYLLYGPPGSGKSSLIAAMANYLC-------YDVYDLELT  262 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~---~rG~LL~GPPGTGKTsLa~AiA~~l~-------~~i~~l~l~  262 (530)
                      +++++|.+++|++|.+.+...... ....+.|...   ..++|||||||||||++|+++|+.+.       .+++.++.+
T Consensus         5 l~~~~Gl~~vk~~i~~~~~~~~~~-~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~   83 (261)
T TIGR02881         5 LSRMVGLDEVKALIKEIYAWIQIN-EKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA   83 (261)
T ss_pred             HHHhcChHHHHHHHHHHHHHHHHH-HHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH
Confidence            578999999999999866554333 3344455542   34689999999999999999998762       245555544


Q ss_pred             ccC------ChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          263 KVT------DNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       263 ~~~------~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .+.      ....++.+|..+. ++||||||+|.+..  +                                       .
T Consensus        84 ~l~~~~~g~~~~~~~~~~~~a~-~~VL~IDE~~~L~~--~---------------------------------------~  121 (261)
T TIGR02881        84 DLVGEYIGHTAQKTREVIKKAL-GGVLFIDEAYSLAR--G---------------------------------------G  121 (261)
T ss_pred             HhhhhhccchHHHHHHHHHhcc-CCEEEEechhhhcc--C---------------------------------------C
Confidence            432      2345667776654 58999999999731  0                                       0


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCc
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIE  410 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~  410 (530)
                      ........+..|++.|+...    ...++|++++..+     .++|+|.+  ||+.+|+|+.++.+++..|++.++...
T Consensus       122 ~~~~~~~~i~~Ll~~~e~~~----~~~~vila~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~  194 (261)
T TIGR02881       122 EKDFGKEAIDTLVKGMEDNR----NEFVLILAGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKER  194 (261)
T ss_pred             ccchHHHHHHHHHHHHhccC----CCEEEEecCCcchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHc
Confidence            11112345677888887542    3456666654332     47899999  999999999999999999999998644

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.72  E-value=1.6e-16  Score=161.19  Aligned_cols=169  Identities=17%  Similarity=0.249  Sum_probs=124.5

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCC---CceEEEECCCCCChhHHHHHHHHHcCC-------cEEEEecCcc
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAW---KRGYLLYGPPGSGKSSLIAAMANYLCY-------DVYDLELTKV  264 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~---~rG~LL~GPPGTGKTsLa~AiA~~l~~-------~i~~l~l~~~  264 (530)
                      .++|.+++|++|.+.+.. +..++.+.+.|.+.   ..++||+||||||||++|+++|..+..       +++.++...+
T Consensus        23 ~l~Gl~~vk~~i~e~~~~-~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l  101 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAAL-LLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDL  101 (284)
T ss_pred             hccCHHHHHHHHHHHHHH-HHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHH
Confidence            689999999999885554 66777788888764   348999999999999999999988732       5666665433


Q ss_pred             C------ChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          265 T------DNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       265 ~------~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                      .      +...++.+|.++ .++||||||||.+....                                        ...
T Consensus       102 ~~~~~g~~~~~~~~~~~~a-~~gvL~iDEi~~L~~~~----------------------------------------~~~  140 (284)
T TIGR02880       102 VGQYIGHTAPKTKEILKRA-MGGVLFIDEAYYLYRPD----------------------------------------NER  140 (284)
T ss_pred             hHhhcccchHHHHHHHHHc-cCcEEEEechhhhccCC----------------------------------------Ccc
Confidence            1      234456667665 45899999999873100                                        011


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC--C---CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR--D---SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~--~---~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                      .........|++.|+.-    ..+++||++++..  +   .++|+|.+  ||+.+|+|+.++.+++..|+++++....
T Consensus       141 ~~~~~~~~~Ll~~le~~----~~~~~vI~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~  212 (284)
T TIGR02880       141 DYGQEAIEILLQVMENQ----RDDLVVILAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQ  212 (284)
T ss_pred             chHHHHHHHHHHHHhcC----CCCEEEEEeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhc
Confidence            22345667888888743    3567777776543  3   35899999  9999999999999999999999987543

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.

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

Probab=99.70  E-value=5e-16  Score=152.20  Aligned_cols=179  Identities=18%  Similarity=0.199  Sum_probs=132.0

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN  267 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~  267 (530)
                      .+|.+|++.+|++++|+++.-.+..-..+.+.        --.+|||||||.||||||.-||+++|.++-..+...+...
T Consensus        20 lRP~~l~efiGQ~~vk~~L~ifI~AAk~r~e~--------lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK~   91 (332)
T COG2255          20 LRPKTLDEFIGQEKVKEQLQIFIKAAKKRGEA--------LDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKP   91 (332)
T ss_pred             cCcccHHHhcChHHHHHHHHHHHHHHHhcCCC--------cCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccccCh
Confidence            47889999999999999888777766555442        2579999999999999999999999999999988888889


Q ss_pred             HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHH
Q 009640          268 SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSG  347 (530)
Q Consensus       268 ~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~  347 (530)
                      .+|..+|.......|+|||||+.+.....+-                 .+..|++-...-..+.      +...+.+   
T Consensus        92 gDlaaiLt~Le~~DVLFIDEIHrl~~~vEE~-----------------LYpaMEDf~lDI~IG~------gp~Arsv---  145 (332)
T COG2255          92 GDLAAILTNLEEGDVLFIDEIHRLSPAVEEV-----------------LYPAMEDFRLDIIIGK------GPAARSI---  145 (332)
T ss_pred             hhHHHHHhcCCcCCeEEEehhhhcChhHHHH-----------------hhhhhhheeEEEEEcc------CCccceE---
Confidence            9999999999999999999999984211110                 0111111000000000      0000100   


Q ss_pred             HhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          348 LLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       348 LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                         .||      -...-+|++|.+...|...|..  ||....++.+.+.++...|+++.-....
T Consensus       146 ---~ld------LppFTLIGATTr~G~lt~PLrd--RFGi~~rlefY~~~eL~~Iv~r~a~~l~  198 (332)
T COG2255         146 ---RLD------LPPFTLIGATTRAGMLTNPLRD--RFGIIQRLEFYTVEELEEIVKRSAKILG  198 (332)
T ss_pred             ---ecc------CCCeeEeeeccccccccchhHH--hcCCeeeeecCCHHHHHHHHHHHHHHhC
Confidence               011      1335689999999999999999  9999999999999999999987755433

>TIGR00763 lon ATP-dependent protease La

Probab=99.70  E-value=4.2e-16  Score=178.17  Aligned_cols=158  Identities=25%  Similarity=0.242  Sum_probs=115.5

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh-------
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN-------  267 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~-------  267 (530)
                      ++.|++++|+.|.+.+.......       ......+||+||||||||++|++||+.++.+++.++++.+.+.       
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~-------~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~  393 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRG-------KMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHR  393 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhc-------CCCCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCC
Confidence            47888999999888776543222       1223479999999999999999999999999999987655332       


Q ss_pred             --------HHHHHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          268 --------SELRALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       268 --------~~L~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                              ..+.+.|..+ ..+.||||||||.+..                                          .  
T Consensus       394 ~~~~g~~~g~i~~~l~~~~~~~~villDEidk~~~------------------------------------------~--  429 (775)
T TIGR00763       394 RTYVGAMPGRIIQGLKKAKTKNPLFLLDEIDKIGS------------------------------------------S--  429 (775)
T ss_pred             CceeCCCCchHHHHHHHhCcCCCEEEEechhhcCC------------------------------------------c--
Confidence                    2344555554 3445999999999831                                          0  


Q ss_pred             cchhhhHHHHhhhccCCc----cC-------CCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          339 ESGRVTLSGLLNFTDGLW----SC-------CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~----s~-------~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                       ......+.||..||...    ..       .-.++++|+|||.++.|||+|++  ||+ .|+|+.|+.+++..|+++|+
T Consensus       430 -~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       430 -FRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             -cCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCchhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHH
Confidence             00112356666666310    00       01468899999999999999999  996 68999999999999999987

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.69  E-value=6.8e-16  Score=166.29  Aligned_cols=154  Identities=19%  Similarity=0.324  Sum_probs=115.7

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ...+|.+|++++|++++++.+...+    ....        .+.+|||||||||||||+|+++|+.++.           
T Consensus         6 ~kyRP~~~~divGq~~i~~~L~~~i----~~~~--------l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~   73 (472)
T PRK14962          6 RKYRPKTFSEVVGQDHVKKLIINAL----KKNS--------ISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNE   73 (472)
T ss_pred             HHHCCCCHHHccCcHHHHHHHHHHH----HcCC--------CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcc
Confidence            3568999999999998866655533    3222        2457999999999999999999999865           


Q ss_pred             -------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          255 -------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       255 -------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                                   +++.++.+.-.+-..++++...+      ....||||||+|.+-                       
T Consensus        74 c~~c~~i~~g~~~dv~el~aa~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt-----------------------  130 (472)
T PRK14962         74 CRACRSIDEGTFMDVIELDAASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLT-----------------------  130 (472)
T ss_pred             cHHHHHHhcCCCCccEEEeCcccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhH-----------------------
Confidence                         57777765444556677665443      245799999999872                       


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                                ...+..||..++..    ++.+++|++||.+..++++|++  |+. .+.|..++
T Consensus       131 --------------------------~~a~~~LLk~LE~p----~~~vv~Ilattn~~kl~~~L~S--R~~-vv~f~~l~  177 (472)
T PRK14962        131 --------------------------KEAFNALLKTLEEP----PSHVVFVLATTNLEKVPPTIIS--RCQ-VIEFRNIS  177 (472)
T ss_pred             --------------------------HHHHHHHHHHHHhC----CCcEEEEEEeCChHhhhHHHhc--CcE-EEEECCcc
Confidence                                      12356788888743    3567788888888999999998  764 69999999


Q ss_pred             HHHHHHHHHHhh
Q 009640          396 PHAFKVLAKNYL  407 (530)
Q Consensus       396 ~~~r~~i~~~~l  407 (530)
                      .++...+++..+
T Consensus       178 ~~el~~~L~~i~  189 (472)
T PRK14962        178 DELIIKRLQEVA  189 (472)
T ss_pred             HHHHHHHHHHHH
Confidence            999888877665

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.69  E-value=8.4e-16  Score=169.42  Aligned_cols=157  Identities=18%  Similarity=0.296  Sum_probs=120.5

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      .+++|.+|++|+|++++++.|...+.    ...        ....||||||||||||++++++|+.+++           
T Consensus         8 rKYRPqtFdEVIGQe~Vv~~L~~aL~----~gR--------L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~   75 (830)
T PRK07003          8 RKWRPKDFASLVGQEHVVRALTHALD----GGR--------LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGV   75 (830)
T ss_pred             HHhCCCcHHHHcCcHHHHHHHHHHHh----cCC--------CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcc
Confidence            34689999999999998887766542    211        2457999999999999999999998854           


Q ss_pred             -------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          255 -------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       255 -------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                                   +++.++..+-.+-.+++.++...      ....||||||+|.+-                       
T Consensus        76 C~sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT-----------------------  132 (830)
T PRK07003         76 CRACREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLT-----------------------  132 (830)
T ss_pred             cHHHHHHhcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCC-----------------------
Confidence                         45666555434456677777653      245799999999872                       


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                                ....+.||..|+..    ...++||++||.+++|.+.+++  |+ .++.|..++
T Consensus       133 --------------------------~~A~NALLKtLEEP----P~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls  179 (830)
T PRK07003        133 --------------------------NHAFNAMLKTLEEP----PPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMP  179 (830)
T ss_pred             --------------------------HHHHHHHHHHHHhc----CCCeEEEEEECChhhccchhhh--he-EEEecCCcC
Confidence                                      22467788888753    3568899999999999999998  77 679999999


Q ss_pred             HHHHHHHHHHhhCCc
Q 009640          396 PHAFKVLAKNYLGIE  410 (530)
Q Consensus       396 ~~~r~~i~~~~l~~~  410 (530)
                      .++....++..++.+
T Consensus       180 ~eeIv~~L~~Il~~E  194 (830)
T PRK07003        180 AGHIVSHLERILGEE  194 (830)
T ss_pred             HHHHHHHHHHHHHHc
Confidence            999988888877543

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.68  E-value=2e-15  Score=155.26  Aligned_cols=196  Identities=15%  Similarity=0.174  Sum_probs=135.6

Q ss_pred             CCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          179 DSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       179 ~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      +..|  +..++|.+|+++++++++++.+...+.    ..        ..+..+|||||||||||++++++|++++.+++.
T Consensus         8 ~~~w--~~kyrP~~~~~~~~~~~~~~~l~~~~~----~~--------~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~   73 (316)
T PHA02544          8 EFMW--EQKYRPSTIDECILPAADKETFKSIVK----KG--------RIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLF   73 (316)
T ss_pred             CCcc--eeccCCCcHHHhcCcHHHHHHHHHHHh----cC--------CCCeEEEeeCcCCCCHHHHHHHHHHHhCccceE
Confidence            3468  778899999999999998887776553    11        124567779999999999999999999999999


Q ss_pred             EecCccCChHHHHHHH----Hhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          259 LELTKVTDNSELRALL----LQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       259 l~l~~~~~~~~L~~l~----~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      ++.+. .....++..+    ...   ..+.||||||+|.+..                                      
T Consensus        74 i~~~~-~~~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~--------------------------------------  114 (316)
T PHA02544         74 VNGSD-CRIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGL--------------------------------------  114 (316)
T ss_pred             eccCc-ccHHHHHHHHHHHHHhhcccCCCeEEEEECcccccC--------------------------------------
Confidence            98877 3233333322    111   3678999999997610                                      


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                            .    .....|.+.++...    ....+|+|||.+..++|++.+  |+. .+.++.|+.+++..+++.++..  
T Consensus       115 ------~----~~~~~L~~~le~~~----~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~~~~il~~~~~~--  175 (316)
T PHA02544        115 ------A----DAQRHLRSFMEAYS----KNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEEQIEMMKQMIVR--  175 (316)
T ss_pred             ------H----HHHHHHHHHHHhcC----CCceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHHHHHHHHHHHHH--
Confidence                  0    01223444455432    456788999999999999999  885 6899999999999887764321  


Q ss_pred             ccchHHHHHHHH-HhCCCCCHHHHHHHHHHhccCHHHHHHHHH
Q 009640          412 HHALFDVVESCI-RAGGALTPAQIGEVLLRNRGNVDLAMKEVV  453 (530)
Q Consensus       412 ~~~~~~~i~~l~-~~~~~~spadi~~~l~~~~~d~~~al~~l~  453 (530)
                             +...+ .....++++.+..++....++...++..+.
T Consensus       176 -------~~~~~~~~~~~i~~~al~~l~~~~~~d~r~~l~~l~  211 (316)
T PHA02544        176 -------CKGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQ  211 (316)
T ss_pred             -------HHHHHHhcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Confidence                   11111 224566666666666666666665555444

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.68  E-value=7e-16  Score=164.29  Aligned_cols=156  Identities=13%  Similarity=0.254  Sum_probs=115.8

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------  254 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------  254 (530)
                      ...++|.+|++++|++.+.+.|...+.    ...        .+..||||||||||||++|+++|+.++.          
T Consensus         9 ~~KyRP~~f~dvVGQe~iv~~L~~~i~----~~r--------i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg   76 (484)
T PRK14956          9 SRKYRPQFFRDVIHQDLAIGALQNALK----SGK--------IGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCN   76 (484)
T ss_pred             HHHhCCCCHHHHhChHHHHHHHHHHHH----cCC--------CCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccC
Confidence            446789999999999998877666543    211        1346999999999999999999999865          


Q ss_pred             --------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          255 --------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       255 --------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                    +++.++...-.+-.+++.+....      ....|+||||+|.+-                      
T Consensus        77 ~C~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls----------------------  134 (484)
T PRK14956         77 ECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLT----------------------  134 (484)
T ss_pred             CCcHHHHHHccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcC----------------------
Confidence                          35555543333445566665433      245699999999871                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.||..|+.-    ...+++|++||.++.|.+++++  |+ .++.|..+
T Consensus       135 ---------------------------~~A~NALLKtLEEP----p~~viFILaTte~~kI~~TI~S--RC-q~~~f~~l  180 (484)
T PRK14956        135 ---------------------------DQSFNALLKTLEEP----PAHIVFILATTEFHKIPETILS--RC-QDFIFKKV  180 (484)
T ss_pred             ---------------------------HHHHHHHHHHhhcC----CCceEEEeecCChhhccHHHHh--hh-heeeecCC
Confidence                                       23567888888742    3678899999999999999998  87 45888888


Q ss_pred             CHHHHHHHHHHhhC
Q 009640          395 GPHAFKVLAKNYLG  408 (530)
Q Consensus       395 ~~~~r~~i~~~~l~  408 (530)
                      +.++....++..+.
T Consensus       181 s~~~i~~~L~~i~~  194 (484)
T PRK14956        181 PLSVLQDYSEKLCK  194 (484)
T ss_pred             CHHHHHHHHHHHHH
Confidence            88877777766554

>PLN03025 replication factor C subunit; Provisional

Probab=99.68  E-value=5.8e-16  Score=159.78  Aligned_cols=188  Identities=15%  Similarity=0.233  Sum_probs=132.7

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----Cc
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----YD  255 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----~~  255 (530)
                      +|  +..++|.+|++++|++++.+.|...    +....         ...+|||||||||||++|.++|+++.     ..
T Consensus         2 ~w--~~kyrP~~l~~~~g~~~~~~~L~~~----~~~~~---------~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~   66 (319)
T PLN03025          2 PW--VEKYRPTKLDDIVGNEDAVSRLQVI----ARDGN---------MPNLILSGPPGTGKTTSILALAHELLGPNYKEA   66 (319)
T ss_pred             Ch--hhhcCCCCHHHhcCcHHHHHHHHHH----HhcCC---------CceEEEECCCCCCHHHHHHHHHHHHhcccCccc
Confidence            47  6788999999999999877766543    22221         13699999999999999999999972     23


Q ss_pred             EEEEecCccCChHHHHHHHH---hc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          256 VYDLELTKVTDNSELRALLL---QT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       256 i~~l~l~~~~~~~~L~~l~~---~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      +..++.++..+-..++..+.   +.      ..+.||+|||+|.+..                                 
T Consensus        67 ~~eln~sd~~~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~---------------------------------  113 (319)
T PLN03025         67 VLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTS---------------------------------  113 (319)
T ss_pred             eeeecccccccHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCH---------------------------------
Confidence            55666665544444554432   21      2467999999998721                                 


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                                      ...+.|+..|+-..    ....+|++||.+..+.++|.+  |+ ..+.|+.|+.++....++..
T Consensus       114 ----------------~aq~aL~~~lE~~~----~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~~~~l~~~L~~i  170 (319)
T PLN03025        114 ----------------GAQQALRRTMEIYS----NTTRFALACNTSSKIIEPIQS--RC-AIVRFSRLSDQEILGRLMKV  170 (319)
T ss_pred             ----------------HHHHHHHHHHhccc----CCceEEEEeCCccccchhHHH--hh-hcccCCCCCHHHHHHHHHHH
Confidence                            12345666665432    334578899999999999998  65 46899999998887776654


Q ss_pred             hCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHH
Q 009640          407 LGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS  454 (530)
Q Consensus       407 l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~  454 (530)
                      +..               ++..++++.+..++..+.+|...++..+..
T Consensus       171 ~~~---------------egi~i~~~~l~~i~~~~~gDlR~aln~Lq~  203 (319)
T PLN03025        171 VEA---------------EKVPYVPEGLEAIIFTADGDMRQALNNLQA  203 (319)
T ss_pred             HHH---------------cCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            422               234577777777777777888888877763

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.68  E-value=5.2e-16  Score=169.13  Aligned_cols=157  Identities=18%  Similarity=0.302  Sum_probs=122.2

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++|+|++++++.|...+..    .+        ....|||+||+|||||++++++|+.++.           
T Consensus         8 rKYRPqtFddVIGQe~vv~~L~~al~~----gR--------LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~   75 (700)
T PRK12323          8 RKWRPRDFTTLVGQEHVVRALTHALEQ----QR--------LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITA   75 (700)
T ss_pred             HHhCCCcHHHHcCcHHHHHHHHHHHHh----CC--------CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCC
Confidence            356899999999999988877765532    11        2357999999999999999999999865           


Q ss_pred             ------------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccc
Q 009640          255 ------------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAK  310 (530)
Q Consensus       255 ------------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~  310 (530)
                                        +++.++..+-.+-.++++++...      ....|+||||+|.+-                  
T Consensus        76 ~PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls------------------  137 (700)
T PRK12323         76 QPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLT------------------  137 (700)
T ss_pred             CCCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcC------------------
Confidence                              55666655444556777776653      245799999999871                  


Q ss_pred             cccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEE
Q 009640          311 TKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVS  390 (530)
Q Consensus       311 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~  390 (530)
                                                     ....+.||+.|+.-    ...++||++||.+++|.+.+++  |+ .++.
T Consensus       138 -------------------------------~~AaNALLKTLEEP----P~~v~FILaTtep~kLlpTIrS--RC-q~f~  179 (700)
T PRK12323        138 -------------------------------NHAFNAMLKTLEEP----PEHVKFILATTDPQKIPVTVLS--RC-LQFN  179 (700)
T ss_pred             -------------------------------HHHHHHHHHhhccC----CCCceEEEEeCChHhhhhHHHH--HH-Hhcc
Confidence                                           23467899988853    3568899999999999999998  76 6789


Q ss_pred             eCCCCHHHHHHHHHHhhCCc
Q 009640          391 LGTCGPHAFKVLAKNYLGIE  410 (530)
Q Consensus       391 ~~~p~~~~r~~i~~~~l~~~  410 (530)
                      |..++.++....++..+..+
T Consensus       180 f~~ls~eei~~~L~~Il~~E  199 (700)
T PRK12323        180 LKQMPPGHIVSHLDAILGEE  199 (700)
T ss_pred             cCCCChHHHHHHHHHHHHHc
Confidence            99999999888888776543

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

Probab=99.68  E-value=6.4e-16  Score=167.50  Aligned_cols=190  Identities=14%  Similarity=0.201  Sum_probs=140.2

Q ss_pred             HHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC------ChHHHHHHHHhc--CCC
Q 009640          209 DLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT------DNSELRALLLQT--TNR  280 (530)
Q Consensus       209 ~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~------~~~~L~~l~~~~--~~~  280 (530)
                      .+..++..+.--...++.....+||||+||||||++++++|.++|.+++.+++.++.      ++..+...|.++  .+|
T Consensus       412 ~l~~vl~p~~~~s~~~~~~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~p  491 (953)
T KOG0736|consen  412 ELVAVLSPQKQPSGALLTLNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSP  491 (953)
T ss_pred             HHHHHhCcccCcchhccccceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCc
Confidence            344444443333333444556799999999999999999999999999999987763      456788888877  689


Q ss_pred             eEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCC
Q 009640          281 SIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCS  360 (530)
Q Consensus       281 sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~  360 (530)
                      +||||-++|.+.-   ++                                 ++  +.+-.-...+..++. +|-.... .
T Consensus       492 avifl~~~dvl~i---d~---------------------------------dg--ged~rl~~~i~~~ls-~e~~~~~-~  531 (953)
T KOG0736|consen  492 AVLFLRNLDVLGI---DQ---------------------------------DG--GEDARLLKVIRHLLS-NEDFKFS-C  531 (953)
T ss_pred             eEEEEeccceeee---cC---------------------------------CC--chhHHHHHHHHHHHh-cccccCC-C
Confidence            9999999998730   00                                 00  111111223333443 3333322 4


Q ss_pred             CCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009640          361 EEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       361 ~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~  440 (530)
                      ...|||+||+..+.|++.+.+  -|-..|.++.|+.++|.+|++.|+...... .......++..+.+|+.+|+..++..
T Consensus       532 ~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y~~~~~~n-~~v~~k~~a~~t~gfs~~~L~~l~~~  608 (953)
T KOG0736|consen  532 PPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWYLNHLPLN-QDVNLKQLARKTSGFSFGDLEALVAH  608 (953)
T ss_pred             CceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHhccccc-hHHHHHHHHHhcCCCCHHHHHHHhcC
Confidence            679999999999999999999  888899999999999999999999866544 34456788888999999999998854


Q ss_pred             h
Q 009640          441 N  441 (530)
Q Consensus       441 ~  441 (530)
                      .
T Consensus       609 ~  609 (953)
T KOG0736|consen  609 S  609 (953)
T ss_pred             c
Confidence            4

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

Probab=99.68  E-value=6.3e-16  Score=167.37  Aligned_cols=159  Identities=24%  Similarity=0.248  Sum_probs=119.9

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHH---
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELR---  271 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~---  271 (530)
                      +-.|.+++|+.|++++.--...+..       ...-++|.||||+|||||+++||..++..|+.+++..+.+++++|   
T Consensus       324 dHYGLekVKeRIlEyLAV~~l~~~~-------kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHR  396 (782)
T COG0466         324 DHYGLEKVKERILEYLAVQKLTKKL-------KGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGHR  396 (782)
T ss_pred             cccCchhHHHHHHHHHHHHHHhccC-------CCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhcccc
Confidence            4468899999999988654433321       113478999999999999999999999999999999999888765   


Q ss_pred             ------------HHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          272 ------------ALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       272 ------------~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                                  +-+.++ ...-+++|||||.+..                                             
T Consensus       397 RTYIGamPGrIiQ~mkka~~~NPv~LLDEIDKm~s---------------------------------------------  431 (782)
T COG0466         397 RTYIGAMPGKIIQGMKKAGVKNPVFLLDEIDKMGS---------------------------------------------  431 (782)
T ss_pred             ccccccCChHHHHHHHHhCCcCCeEEeechhhccC---------------------------------------------
Confidence                        223333 4566889999999721                                             


Q ss_pred             cchhhhHHHHhhhccCCccC-----------CCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          339 ESGRVTLSGLLNFTDGLWSC-----------CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~-----------~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                      +....--|.||..+|-=.+.           .-..+++|+|+|..+.++.+|+.  ||.. |+++-.+.++...|+++||
T Consensus       432 s~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlD--RMEi-I~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         432 SFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLD--RMEV-IRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             CCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhc--ceee-eeecCCChHHHHHHHHHhc
Confidence            00111235667666622111           12458999999999999999999  9965 9999999999999999998


Q ss_pred             C
Q 009640          408 G  408 (530)
Q Consensus       408 ~  408 (530)
                      =
T Consensus       509 i  509 (782)
T COG0466         509 I  509 (782)
T ss_pred             c
Confidence            4

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

Probab=99.66  E-value=1.5e-15  Score=155.23  Aligned_cols=195  Identities=19%  Similarity=0.252  Sum_probs=129.6

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN  267 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~  267 (530)
                      -+|.++++++|++++.-. -.-+...+....         -..++|||||||||||||+.||+.++.+|+.++... .+-
T Consensus        18 mRP~~lde~vGQ~HLlg~-~~~lrr~v~~~~---------l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~-~gv   86 (436)
T COG2256          18 LRPKSLDEVVGQEHLLGE-GKPLRRAVEAGH---------LHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVT-SGV   86 (436)
T ss_pred             hCCCCHHHhcChHhhhCC-CchHHHHHhcCC---------CceeEEECCCCCCHHHHHHHHHHhhCCceEEecccc-ccH
Confidence            478999999999886422 111222232222         357999999999999999999999999999998765 356


Q ss_pred             HHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          268 SELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       268 ~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                      .+++.++.++      ..+.|||||||+.+-                                                 
T Consensus        87 kdlr~i~e~a~~~~~~gr~tiLflDEIHRfn-------------------------------------------------  117 (436)
T COG2256          87 KDLREIIEEARKNRLLGRRTILFLDEIHRFN-------------------------------------------------  117 (436)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEehhhhcC-------------------------------------------------
Confidence            7889888876      357999999999972                                                 


Q ss_pred             hhhHHHHhhhccCCccCCCCCeEEEEE-e-CCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          342 RVTLSGLLNFTDGLWSCCSEEKIIVFT-T-NHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       342 ~~~ls~LLn~lDgl~s~~~~~~ivI~T-T-N~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      +.....||-.++      .+.+++|++ | |..-.|.+||++  |. +..++...+.+..+.++++-+..+... +.   
T Consensus       118 K~QQD~lLp~vE------~G~iilIGATTENPsF~ln~ALlS--R~-~vf~lk~L~~~di~~~l~ra~~~~~rg-l~---  184 (436)
T COG2256         118 KAQQDALLPHVE------NGTIILIGATTENPSFELNPALLS--RA-RVFELKPLSSEDIKKLLKRALLDEERG-LG---  184 (436)
T ss_pred             hhhhhhhhhhhc------CCeEEEEeccCCCCCeeecHHHhh--hh-heeeeecCCHHHHHHHHHHHHhhhhcC-CC---
Confidence            111234666665      355777774 4 455689999998  54 347888999999999888744322211 00   


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHh
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAK  459 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~  459 (530)
                          .....+++.-+..++..+.+|.+.+|..+.......
T Consensus       185 ----~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~  220 (436)
T COG2256         185 ----GQIIVLDEEALDYLVRLSNGDARRALNLLELAALSA  220 (436)
T ss_pred             ----cccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhc
Confidence                001123444444444455567777776665554433

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

Probab=99.65  E-value=1e-14  Score=142.15  Aligned_cols=199  Identities=19%  Similarity=0.262  Sum_probs=153.1

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEE
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVY  257 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~  257 (530)
                      ....+....+..+++|.|.+.+|+.|.+....|+....         ...+||||++||||||+++|+.+++   |+.++
T Consensus        14 ~l~~i~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~p---------annvLL~G~rGtGKSSlVkall~~y~~~GLRlI   84 (249)
T PF05673_consen   14 YLEPIKHPDPIRLDDLIGIERQKEALIENTEQFLQGLP---------ANNVLLWGARGTGKSSLVKALLNEYADQGLRLI   84 (249)
T ss_pred             cEEecCCCCCCCHHHhcCHHHHHHHHHHHHHHHHcCCC---------CcceEEecCCCCCHHHHHHHHHHHHhhcCceEE
Confidence            46678888999999999999999999999999998643         4789999999999999999999987   77788


Q ss_pred             EEecCccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          258 DLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       258 ~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                      .+.-..+.+-..|...+...+.+-|||+||+.  |+                                           .
T Consensus        85 ev~k~~L~~l~~l~~~l~~~~~kFIlf~DDLs--Fe-------------------------------------------~  119 (249)
T PF05673_consen   85 EVSKEDLGDLPELLDLLRDRPYKFILFCDDLS--FE-------------------------------------------E  119 (249)
T ss_pred             EECHHHhccHHHHHHHHhcCCCCEEEEecCCC--CC-------------------------------------------C
Confidence            88877777888888888888899999999865  31                                           0


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCCh-----------------------hhhcCCceeEEEEeCCC
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDP-----------------------ALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDp-----------------------ALlRpGR~d~~I~~~~p  394 (530)
                         .......|-..|||--...+++++|.+|+|+-.-+++                       +|-.  ||...|.|..|
T Consensus       120 ---~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsD--RFGL~l~F~~~  194 (249)
T PF05673_consen  120 ---GDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSD--RFGLWLSFYPP  194 (249)
T ss_pred             ---CcHHHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHH--hCCcEEEecCC
Confidence               1123467778888876666889999999998654433                       3334  99999999999


Q ss_pred             CHHHHHHHHHHhhCCcCcc----chHHHHHHHHHhCCCCCHHHHHHHH
Q 009640          395 GPHAFKVLAKNYLGIESHH----ALFDVVESCIRAGGALTPAQIGEVL  438 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~~~~~----~~~~~i~~l~~~~~~~spadi~~~l  438 (530)
                      +.++..+|+++|+......    .+.......+..-.+.||.--.+++
T Consensus       195 ~q~~YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~rg~RSGRtA~QF~  242 (249)
T PF05673_consen  195 DQEEYLAIVRHYAERYGLELDEEELRQEALQWALRRGGRSGRTARQFI  242 (249)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            9999999999999543332    1223334444444566665444443

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=3.1e-15  Score=163.43  Aligned_cols=156  Identities=17%  Similarity=0.280  Sum_probs=119.5

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++|+|++.+++.|...+.    ..        ..+..|||+||||||||++|+++|+.++.           
T Consensus         7 rKyRPktFddVIGQe~vv~~L~~aI~----~g--------rl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~   74 (702)
T PRK14960          7 RKYRPRNFNELVGQNHVSRALSSALE----RG--------RLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEV   74 (702)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHH----cC--------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCcc
Confidence            34689999999999998887776553    11        11368999999999999999999999865           


Q ss_pred             -------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          255 -------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       255 -------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                                   +++.++.++-.+-.+++.++...      .+..|+||||+|.+-                       
T Consensus        75 C~sC~~I~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS-----------------------  131 (702)
T PRK14960         75 CATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLS-----------------------  131 (702)
T ss_pred             CHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcC-----------------------
Confidence                         56666665444556778777654      245799999999871                       


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                                ....+.||..|+..    .+.+.+|++|+.+.++.+.+++  |+ .++.|..++
T Consensus       132 --------------------------~~A~NALLKtLEEP----P~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs  178 (702)
T PRK14960        132 --------------------------THSFNALLKTLEEP----PEHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLA  178 (702)
T ss_pred             --------------------------HHHHHHHHHHHhcC----CCCcEEEEEECChHhhhHHHHH--hh-heeeccCCC
Confidence                                      22456788888753    3557888889999999999887  76 568999999


Q ss_pred             HHHHHHHHHHhhCC
Q 009640          396 PHAFKVLAKNYLGI  409 (530)
Q Consensus       396 ~~~r~~i~~~~l~~  409 (530)
                      .++....++..+..
T Consensus       179 ~eEI~k~L~~Il~k  192 (702)
T PRK14960        179 VDEITKHLGAILEK  192 (702)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99988888777654

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=6.5e-15  Score=154.58  Aligned_cols=155  Identities=17%  Similarity=0.274  Sum_probs=113.7

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      .++|.+|++++|++++++.+...+.    ..        ..+..|||+||||||||++|+++|+.+..            
T Consensus         9 kyrP~~~~~iiGq~~~~~~l~~~~~----~~--------~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c   76 (363)
T PRK14961          9 KWRPQYFRDIIGQKHIVTAISNGLS----LG--------RIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKC   76 (363)
T ss_pred             HhCCCchhhccChHHHHHHHHHHHH----cC--------CCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCC
Confidence            4588999999999998887665442    11        12457999999999999999999998852            


Q ss_pred             ------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          255 ------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       255 ------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                  +++.++..+-..-..++.++...      ....|+||||+|.+-                        
T Consensus        77 ~~c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~------------------------  132 (363)
T PRK14961         77 IICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLS------------------------  132 (363)
T ss_pred             HHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcC------------------------
Confidence                        44555443323345566666543      235699999999871                        


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                               ....+.||..++..    .....+|++|+.++.+.+++.+  |+ ..++|+.++.
T Consensus       133 -------------------------~~a~naLLk~lEe~----~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~  180 (363)
T PRK14961        133 -------------------------RHSFNALLKTLEEP----PQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISE  180 (363)
T ss_pred             -------------------------HHHHHHHHHHHhcC----CCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCH
Confidence                                     12345688887743    3456788888889999999987  66 5689999999


Q ss_pred             HHHHHHHHHhhCC
Q 009640          397 HAFKVLAKNYLGI  409 (530)
Q Consensus       397 ~~r~~i~~~~l~~  409 (530)
                      ++...++...+..
T Consensus       181 ~el~~~L~~~~~~  193 (363)
T PRK14961        181 EKIFNFLKYILIK  193 (363)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999888776544

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.64  E-value=4.4e-15  Score=158.49  Aligned_cols=152  Identities=21%  Similarity=0.303  Sum_probs=112.3

Q ss_pred             cCCCCCCCcccccCChhhhHH---HHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          185 VPFRHPSTFETLALEPQLKKQ---ITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~---i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      ....+|.+|++++|++++...   +...+    ....         ..++|||||||||||++|+++|+.++.+++.++.
T Consensus         3 a~~~RP~~l~d~vGq~~~v~~~~~L~~~i----~~~~---------~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a   69 (413)
T PRK13342          3 AERMRPKTLDEVVGQEHLLGPGKPLRRMI----EAGR---------LSSMILWGPPGTGKTTLARIIAGATDAPFEALSA   69 (413)
T ss_pred             hhhhCCCCHHHhcCcHHHhCcchHHHHHH----HcCC---------CceEEEECCCCCCHHHHHHHHHHHhCCCEEEEec
Confidence            345688999999999887544   44433    2221         3489999999999999999999999999999987


Q ss_pred             CccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          262 TKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       262 ~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                      ... +...++.++..+      ..+.||||||||.+.                                           
T Consensus        70 ~~~-~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~-------------------------------------------  105 (413)
T PRK13342         70 VTS-GVKDLREVIEEARQRRSAGRRTILFIDEIHRFN-------------------------------------------  105 (413)
T ss_pred             ccc-cHHHHHHHHHHHHHhhhcCCceEEEEechhhhC-------------------------------------------
Confidence            643 345566666554      267899999999872                                           


Q ss_pred             CCCcchhhhHHHHhhhccCCccCCCCCeEEEEEe--CCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTT--NHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TT--N~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                            ......|+..++.      ..+++|++|  |....++++|++  |+ ..+.|+.++.++...+++..+.
T Consensus       106 ------~~~q~~LL~~le~------~~iilI~att~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~lL~~~l~  165 (413)
T PRK13342        106 ------KAQQDALLPHVED------GTITLIGATTENPSFEVNPALLS--RA-QVFELKPLSEEDIEQLLKRALE  165 (413)
T ss_pred             ------HHHHHHHHHHhhc------CcEEEEEeCCCChhhhccHHHhc--cc-eeeEeCCCCHHHHHHHHHHHHH
Confidence                  1123456666652      345666654  345689999999  87 6789999999999999988764

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.63  E-value=1.1e-14  Score=157.81  Aligned_cols=157  Identities=19%  Similarity=0.285  Sum_probs=118.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------  254 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------  254 (530)
                      ...++|.+|++++|++.+.+.+...+.   .+         ..+.+|||+||||||||++|+++|+.++.          
T Consensus        12 a~kyRP~~f~dliGq~~vv~~L~~ai~---~~---------ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~   79 (507)
T PRK06645         12 ARKYRPSNFAELQGQEVLVKVLSYTIL---ND---------RLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTI   79 (507)
T ss_pred             hhhhCCCCHHHhcCcHHHHHHHHHHHH---cC---------CCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCc
Confidence            456799999999999998776655332   11         11458999999999999999999999854          


Q ss_pred             ------------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccc
Q 009640          255 ------------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAK  310 (530)
Q Consensus       255 ------------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~  310 (530)
                                        +++.++..+-.+-.+++.++..+      ....|+||||+|.+-                  
T Consensus        80 ~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls------------------  141 (507)
T PRK06645         80 KTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLS------------------  141 (507)
T ss_pred             CCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcC------------------
Confidence                              44445544434556788877655      245799999999871                  


Q ss_pred             cccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEE
Q 009640          311 TKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVS  390 (530)
Q Consensus       311 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~  390 (530)
                                                     ....+.||..|+..    ....++|++|+.++++++++++  |+ ..++
T Consensus       142 -------------------------------~~a~naLLk~LEep----p~~~vfI~aTte~~kI~~tI~S--Rc-~~~e  183 (507)
T PRK06645        142 -------------------------------KGAFNALLKTLEEP----PPHIIFIFATTEVQKIPATIIS--RC-QRYD  183 (507)
T ss_pred             -------------------------------HHHHHHHHHHHhhc----CCCEEEEEEeCChHHhhHHHHh--cc-eEEE
Confidence                                           22456788888742    4567888889999999999998  66 5688


Q ss_pred             eCCCCHHHHHHHHHHhhCC
Q 009640          391 LGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       391 ~~~p~~~~r~~i~~~~l~~  409 (530)
                      |..++.++...+++..+..
T Consensus       184 f~~ls~~el~~~L~~i~~~  202 (507)
T PRK06645        184 LRRLSFEEIFKLLEYITKQ  202 (507)
T ss_pred             ccCCCHHHHHHHHHHHHHH
Confidence            9999999999888877754

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.62  E-value=1.1e-14  Score=156.64  Aligned_cols=156  Identities=16%  Similarity=0.239  Sum_probs=120.5

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc--------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL--------------  252 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l--------------  252 (530)
                      .++|.+|++++|++.+.+.+...+.    ..        ..+.+|||+|||||||||+|+++|+.+              
T Consensus         6 KyRP~~f~dliGQe~vv~~L~~a~~----~~--------ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C   73 (491)
T PRK14964          6 KYRPSSFKDLVGQDVLVRILRNAFT----LN--------KIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTC   73 (491)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHH----cC--------CCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCcccc
Confidence            4689999999999998776654332    11        124689999999999999999999865              


Q ss_pred             ----------CCcEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          253 ----------CYDVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       253 ----------~~~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                ..+++.++.++-.+-.+++.++...      ...-|+||||+|.+-                        
T Consensus        74 ~~C~~i~~~~~~Dv~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls------------------------  129 (491)
T PRK14964         74 HNCISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLS------------------------  129 (491)
T ss_pred             HHHHHHhccCCCCEEEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCC------------------------
Confidence                      2467778777666667788887654      245699999999871                        


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                               ....+.||..|+..    .+..++|++|+.+++|.+.+++  |+ ..++|..++.
T Consensus       130 -------------------------~~A~NaLLK~LEeP----p~~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~  177 (491)
T PRK14964        130 -------------------------NSAFNALLKTLEEP----APHVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPT  177 (491)
T ss_pred             -------------------------HHHHHHHHHHHhCC----CCCeEEEEEeCChHHHHHHHHH--hh-eeeecccccH
Confidence                                     22467899998854    3568889999999999999998  66 5589999999


Q ss_pred             HHHHHHHHHhhCCc
Q 009640          397 HAFKVLAKNYLGIE  410 (530)
Q Consensus       397 ~~r~~i~~~~l~~~  410 (530)
                      ++....+...+..+
T Consensus       178 ~el~~~L~~ia~~E  191 (491)
T PRK14964        178 DKLVEHLVDIAKKE  191 (491)
T ss_pred             HHHHHHHHHHHHHc
Confidence            99888888776543

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.62  E-value=1.3e-14  Score=160.31  Aligned_cols=154  Identities=17%  Similarity=0.287  Sum_probs=117.7

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      ..+|.+|++|+|++.+++.|...+..    ..        .+..|||+||||||||++|+++|+.++.            
T Consensus         9 KyRP~~f~divGQe~vv~~L~~~l~~----~r--------l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C   76 (647)
T PRK07994          9 KWRPQTFAEVVGQEHVLTALANALDL----GR--------LHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGEC   76 (647)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHc----CC--------CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCC
Confidence            35889999999999988876654432    11        2457999999999999999999999865            


Q ss_pred             ------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          255 ------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       255 ------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                  +++.++..+-.+-.+++.++...      ...-|+||||+|.+                         
T Consensus        77 ~~C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~L-------------------------  131 (647)
T PRK07994         77 DNCREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHML-------------------------  131 (647)
T ss_pred             HHHHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhC-------------------------
Confidence                        44555554323445677776553      24569999999987                         


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                              +....+.||..|+.-    .+.+++|++|+.+.+|.+.+++  |+ .+++|..++.
T Consensus       132 ------------------------s~~a~NALLKtLEEP----p~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~  180 (647)
T PRK07994        132 ------------------------SRHSFNALLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDV  180 (647)
T ss_pred             ------------------------CHHHHHHHHHHHHcC----CCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCH
Confidence                                    223577899999853    3567888889999999999998  75 8899999999


Q ss_pred             HHHHHHHHHhhC
Q 009640          397 HAFKVLAKNYLG  408 (530)
Q Consensus       397 ~~r~~i~~~~l~  408 (530)
                      ++....+...+.
T Consensus       181 ~ei~~~L~~il~  192 (647)
T PRK07994        181 EQIRQQLEHILQ  192 (647)
T ss_pred             HHHHHHHHHHHH
Confidence            998888887764

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.62  E-value=9.1e-15  Score=159.13  Aligned_cols=156  Identities=15%  Similarity=0.295  Sum_probs=117.1

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------  254 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------  254 (530)
                      ...++|.+|++|+|++.+++.+...+..    ..        .+..||||||||||||++|+++|+.++.          
T Consensus         7 ~~kyRP~~f~divGq~~v~~~L~~~~~~----~~--------l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg   74 (509)
T PRK14958          7 ARKWRPRCFQEVIGQAPVVRALSNALDQ----QY--------LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCN   74 (509)
T ss_pred             HHHHCCCCHHHhcCCHHHHHHHHHHHHh----CC--------CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCC
Confidence            3456899999999999988877765532    11        1357999999999999999999999854          


Q ss_pred             --------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          255 --------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       255 --------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                    +++.++..+-.+-.+++.++...      ....|++|||+|.+-                      
T Consensus        75 ~C~~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls----------------------  132 (509)
T PRK14958         75 DCENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLS----------------------  132 (509)
T ss_pred             CCHHHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcC----------------------
Confidence                          36667665545566778777653      234699999999872                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.||..|+..    .+.+++|++|+.+.++.+.+++  |+ ..++|..+
T Consensus       133 ---------------------------~~a~naLLk~LEep----p~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l  178 (509)
T PRK14958        133 ---------------------------GHSFNALLKTLEEP----PSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQL  178 (509)
T ss_pred             ---------------------------HHHHHHHHHHHhcc----CCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCC
Confidence                                       22457888888854    3567888888999999999887  66 55788888


Q ss_pred             CHHHHHHHHHHhhC
Q 009640          395 GPHAFKVLAKNYLG  408 (530)
Q Consensus       395 ~~~~r~~i~~~~l~  408 (530)
                      +.++....++..+.
T Consensus       179 ~~~~i~~~l~~il~  192 (509)
T PRK14958        179 PPLQIAAHCQHLLK  192 (509)
T ss_pred             CHHHHHHHHHHHHH
Confidence            88877776666554

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.61  E-value=2.4e-14  Score=155.54  Aligned_cols=155  Identities=17%  Similarity=0.326  Sum_probs=115.2

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      .++|.+|++|+|++++++.|...+..    .        ..+..||||||||||||++|+++|+.+..            
T Consensus         7 KyRP~~~~dvvGq~~v~~~L~~~i~~----~--------~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~   74 (504)
T PRK14963          7 RARPITFDEVVGQEHVKEVLLAALRQ----G--------RLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECE   74 (504)
T ss_pred             hhCCCCHHHhcChHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcCh
Confidence            45899999999999988777665543    1        12346899999999999999999998843            


Q ss_pred             -----------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhh
Q 009640          255 -----------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSI  317 (530)
Q Consensus       255 -----------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~  317 (530)
                                 +++.++.....+-..++.+...+      ..+.||||||+|.+                          
T Consensus        75 sc~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~l--------------------------  128 (504)
T PRK14963         75 SCLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMM--------------------------  128 (504)
T ss_pred             hhHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECcccc--------------------------
Confidence                       35556554333445566653322      35679999999976                          


Q ss_pred             hhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHH
Q 009640          318 KEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPH  397 (530)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~  397 (530)
                                             +...++.||..|+..    ....++|++||.+..+.+++.+  |+. +++|..++.+
T Consensus       129 -----------------------s~~a~naLLk~LEep----~~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls~~  178 (504)
T PRK14963        129 -----------------------SKSAFNALLKTLEEP----PEHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLTEE  178 (504)
T ss_pred             -----------------------CHHHHHHHHHHHHhC----CCCEEEEEEcCChhhCChHHhc--ceE-EEEecCCCHH
Confidence                                   123467788888743    3567888899999999999998  664 6999999999


Q ss_pred             HHHHHHHHhhCC
Q 009640          398 AFKVLAKNYLGI  409 (530)
Q Consensus       398 ~r~~i~~~~l~~  409 (530)
                      +....++..+..
T Consensus       179 el~~~L~~i~~~  190 (504)
T PRK14963        179 EIAGKLRRLLEA  190 (504)
T ss_pred             HHHHHHHHHHHH
Confidence            998888876643

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

Probab=99.61  E-value=6.7e-15  Score=167.47  Aligned_cols=158  Identities=19%  Similarity=0.229  Sum_probs=114.0

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEE
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYD  258 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~  258 (530)
                      .+..++.++|.++..+.+.+.+    .++         .+.++||+||||||||++++++|..+          +..++.
T Consensus       177 r~~~l~~~igr~~ei~~~~~~L----~~~---------~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~  243 (731)
T TIGR02639       177 KNGKIDPLIGREDELERTIQVL----CRR---------KKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS  243 (731)
T ss_pred             hcCCCCcccCcHHHHHHHHHHH----hcC---------CCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE
Confidence            5667888999887666555433    222         25689999999999999999999987          788999


Q ss_pred             EecCccCC--------hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccccc
Q 009640          259 LELTKVTD--------NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST  328 (530)
Q Consensus       259 l~l~~~~~--------~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~  328 (530)
                      ++++.+..        +..++++|..+  ..++||||||||.+++...                                
T Consensus       244 ~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~--------------------------------  291 (731)
T TIGR02639       244 LDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGA--------------------------------  291 (731)
T ss_pred             ecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCC--------------------------------
Confidence            88766532        35788888875  4589999999999853110                                


Q ss_pred             CCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHH
Q 009640          329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLA  403 (530)
Q Consensus       329 ~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~  403 (530)
                              ....+....+-|+..+.      .+.+.+|++||..+     .+|+||.|  ||. .|+++.|+.+++..|+
T Consensus       292 --------~~~~~~~~~~~L~~~l~------~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il  354 (731)
T TIGR02639       292 --------TSGGSMDASNLLKPALS------SGKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKIL  354 (731)
T ss_pred             --------CCCccHHHHHHHHHHHh------CCCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHH
Confidence                    00001111122333332      36788999888743     57999999  997 6999999999999999


Q ss_pred             HHhhC
Q 009640          404 KNYLG  408 (530)
Q Consensus       404 ~~~l~  408 (530)
                      +....
T Consensus       355 ~~~~~  359 (731)
T TIGR02639       355 KGLKE  359 (731)
T ss_pred             HHHHH
Confidence            97654

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.61  E-value=2.2e-14  Score=160.98  Aligned_cols=155  Identities=19%  Similarity=0.307  Sum_probs=114.6

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc-----------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD-----------  255 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~-----------  255 (530)
                      .++|.+|++|+|++.+++.|...+.    ...        .+..||||||||||||++|+++|+.++..           
T Consensus         9 KyRP~tFddIIGQe~Iv~~LknaI~----~~r--------l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C   76 (944)
T PRK14949          9 KWRPATFEQMVGQSHVLHALTNALT----QQR--------LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVC   76 (944)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHH----hCC--------CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCc
Confidence            4588999999999998877655442    221        24578999999999999999999998653           


Q ss_pred             -------------EEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          256 -------------VYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       256 -------------i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                   ++.++..+...-..++.+....      ...-|+||||+|.+                         
T Consensus        77 ~sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~L-------------------------  131 (944)
T PRK14949         77 SSCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHML-------------------------  131 (944)
T ss_pred             hHHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhc-------------------------
Confidence                         2333333222334566665443      23569999999987                         


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                              +....+.||..|+..    .+.+++|++|+.+.+|.+.+++  |+ .++.|..++.
T Consensus       132 ------------------------T~eAqNALLKtLEEP----P~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~  180 (944)
T PRK14949        132 ------------------------SRSSFNALLKTLEEP----PEHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQ  180 (944)
T ss_pred             ------------------------CHHHHHHHHHHHhcc----CCCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCH
Confidence                                    233578899999853    3567788888889999999997  76 6789999999


Q ss_pred             HHHHHHHHHhhCC
Q 009640          397 HAFKVLAKNYLGI  409 (530)
Q Consensus       397 ~~r~~i~~~~l~~  409 (530)
                      ++....++..+..
T Consensus       181 eEI~~~L~~il~~  193 (944)
T PRK14949        181 DEIGTQLNHILTQ  193 (944)
T ss_pred             HHHHHHHHHHHHH
Confidence            9988888776654

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.61  E-value=7e-15  Score=145.59  Aligned_cols=151  Identities=20%  Similarity=0.271  Sum_probs=103.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-cE-----EE
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-DV-----YD  258 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-~i-----~~  258 (530)
                      ...+.|.+|+++++++.+.+.+...+.. ...            ..|||||||||||||.|.|+|.++.. +.     .+
T Consensus        27 teKYrPkt~de~~gQe~vV~~L~~a~~~-~~l------------p~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~   93 (346)
T KOG0989|consen   27 TEKYRPKTFDELAGQEHVVQVLKNALLR-RIL------------PHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLE   93 (346)
T ss_pred             HHHhCCCcHHhhcchHHHHHHHHHHHhh-cCC------------ceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhh
Confidence            6788999999999999999988887755 222            37999999999999999999999855 22     22


Q ss_pred             EecCccCC----------hHHHHHHHHhc-----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccc
Q 009640          259 LELTKVTD----------NSELRALLLQT-----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSR  323 (530)
Q Consensus       259 l~l~~~~~----------~~~L~~l~~~~-----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~  323 (530)
                      ++.+.-.+          -+.+.......     +..-||+|||.|.+                                
T Consensus        94 lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsm--------------------------------  141 (346)
T KOG0989|consen   94 LNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSM--------------------------------  141 (346)
T ss_pred             hcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhh--------------------------------
Confidence            23332211          12222222111     12259999999987                                


Q ss_pred             cccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHH
Q 009640          324 IASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLA  403 (530)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~  403 (530)
                                       .....+.|.+.||...    ....+|+.||+++.|.+.+.+  |..+ +.|+..+.+.....+
T Consensus       142 -----------------tsdaq~aLrr~mE~~s----~~trFiLIcnylsrii~pi~S--RC~K-frFk~L~d~~iv~rL  197 (346)
T KOG0989|consen  142 -----------------TSDAQAALRRTMEDFS----RTTRFILICNYLSRIIRPLVS--RCQK-FRFKKLKDEDIVDRL  197 (346)
T ss_pred             -----------------hHHHHHHHHHHHhccc----cceEEEEEcCChhhCChHHHh--hHHH-hcCCCcchHHHHHHH
Confidence                             2335678999998643    457899999999999999998  7654 445444443333333


Q ss_pred             H
Q 009640          404 K  404 (530)
Q Consensus       404 ~  404 (530)
                      +
T Consensus       198 ~  198 (346)
T KOG0989|consen  198 E  198 (346)
T ss_pred             H
Confidence            3

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.60  E-value=1.6e-14  Score=159.18  Aligned_cols=157  Identities=18%  Similarity=0.297  Sum_probs=118.0

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++|+|++.+++.|...+..    .        ..+.+|||+||||||||++|+++|+.++.           
T Consensus         8 rKYRP~tFddIIGQe~vv~~L~~ai~~----~--------rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~   75 (709)
T PRK08691          8 RKWRPKTFADLVGQEHVVKALQNALDE----G--------RLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGV   75 (709)
T ss_pred             HHhCCCCHHHHcCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcc
Confidence            356899999999999988877776542    1        12468999999999999999999998743           


Q ss_pred             -------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          255 -------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       255 -------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                                   +++.++..+-.+...++.++..+      ....||||||+|.+-                       
T Consensus        76 C~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls-----------------------  132 (709)
T PRK08691         76 CQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLS-----------------------  132 (709)
T ss_pred             cHHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccC-----------------------
Confidence                         34455544434556777777643      345799999999761                       


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                                ....+.||..|+..    .+.+++|++||.+.++.+.+++  |+ ..+.|..++
T Consensus       133 --------------------------~~A~NALLKtLEEP----p~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls  179 (709)
T PRK08691        133 --------------------------KSAFNAMLKTLEEP----PEHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMT  179 (709)
T ss_pred             --------------------------HHHHHHHHHHHHhC----CCCcEEEEEeCCccccchHHHH--HH-hhhhcCCCC
Confidence                                      22456788888753    3557888999999999999886  77 667888999


Q ss_pred             HHHHHHHHHHhhCCc
Q 009640          396 PHAFKVLAKNYLGIE  410 (530)
Q Consensus       396 ~~~r~~i~~~~l~~~  410 (530)
                      .++....++..+..+
T Consensus       180 ~eeI~~~L~~Il~kE  194 (709)
T PRK08691        180 AQQVADHLAHVLDSE  194 (709)
T ss_pred             HHHHHHHHHHHHHHc
Confidence            998888887776543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.60  E-value=3.2e-14  Score=148.57  Aligned_cols=158  Identities=17%  Similarity=0.313  Sum_probs=116.8

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----------  253 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----------  253 (530)
                      ....+|.+|++++|++++++.+...+..    .        ..+..||||||||+|||++++++|..+.           
T Consensus         5 ~~~~rp~~~~~iig~~~~~~~l~~~~~~----~--------~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~   72 (355)
T TIGR02397         5 ARKYRPQTFEDVIGQEHIVQTLKNAIKN----G--------RIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCN   72 (355)
T ss_pred             HHHhCCCcHhhccCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCC
Confidence            4556889999999999988877775532    1        1245799999999999999999999873           


Q ss_pred             -------------CcEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          254 -------------YDVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       254 -------------~~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                   .+++.++.....+...++.++..+      ..+.||+|||+|.+-                      
T Consensus        73 ~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~----------------------  130 (355)
T TIGR02397        73 ECESCKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLS----------------------  130 (355)
T ss_pred             CCHHHHHHhcCCCCCEEEeeccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcC----------------------
Confidence                         234445444333444566676654      244699999999761                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.||..++..    ....++|++||.++.|.+++.+  |+ ..++|+.|
T Consensus       131 ---------------------------~~~~~~Ll~~le~~----~~~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~  176 (355)
T TIGR02397       131 ---------------------------KSAFNALLKTLEEP----PEHVVFILATTEPHKIPATILS--RC-QRFDFKRI  176 (355)
T ss_pred             ---------------------------HHHHHHHHHHHhCC----ccceeEEEEeCCHHHHHHHHHh--he-eEEEcCCC
Confidence                                       12356788888753    3567888899999999999998  76 46899999


Q ss_pred             CHHHHHHHHHHhhCCc
Q 009640          395 GPHAFKVLAKNYLGIE  410 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~~  410 (530)
                      +.++...++..++...
T Consensus       177 ~~~~l~~~l~~~~~~~  192 (355)
T TIGR02397       177 PLEDIVERLKKILDKE  192 (355)
T ss_pred             CHHHHHHHHHHHHHHc
Confidence            9999999988876543

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.59  E-value=5e-14  Score=155.20  Aligned_cols=156  Identities=17%  Similarity=0.299  Sum_probs=118.7

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-------------  253 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-------------  253 (530)
                      ..+|.+|++++|++++.+.+...+..    .        ..+..||||||||||||++|+.+|+.++             
T Consensus         9 k~rP~~f~~viGq~~v~~~L~~~i~~----~--------~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C   76 (559)
T PRK05563          9 KWRPQTFEDVVGQEHITKTLKNAIKQ----G--------KISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNEC   76 (559)
T ss_pred             HhCCCcHHhccCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            35899999999999988877765543    1        1246799999999999999999999874             


Q ss_pred             -----------CcEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          254 -----------YDVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       254 -----------~~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                 .+++.++..+..+-..++.+...+      ...-|++|||+|.+-                        
T Consensus        77 ~~C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt------------------------  132 (559)
T PRK05563         77 EICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLS------------------------  132 (559)
T ss_pred             HHHHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC------------------------
Confidence                       456666665544556677776654      235699999999872                        


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                               ....+.||..++..    ...+++|++|+.+++|++.+++  |+. .+.|..|+.
T Consensus       133 -------------------------~~a~naLLKtLEep----p~~~ifIlatt~~~ki~~tI~S--Rc~-~~~f~~~~~  180 (559)
T PRK05563        133 -------------------------TGAFNALLKTLEEP----PAHVIFILATTEPHKIPATILS--RCQ-RFDFKRISV  180 (559)
T ss_pred             -------------------------HHHHHHHHHHhcCC----CCCeEEEEEeCChhhCcHHHHh--Hhe-EEecCCCCH
Confidence                                     12466888888754    3567888888899999999997  664 578999999


Q ss_pred             HHHHHHHHHhhCCc
Q 009640          397 HAFKVLAKNYLGIE  410 (530)
Q Consensus       397 ~~r~~i~~~~l~~~  410 (530)
                      ++....++..+...
T Consensus       181 ~ei~~~L~~i~~~e  194 (559)
T PRK05563        181 EDIVERLKYILDKE  194 (559)
T ss_pred             HHHHHHHHHHHHHc
Confidence            99888887766533

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=2.7e-14  Score=157.53  Aligned_cols=156  Identities=19%  Similarity=0.297  Sum_probs=116.4

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++++|++.+.+.|...+.    ...        .+..||||||+|||||++++++|+.+++           
T Consensus         8 ~KyRP~~f~dviGQe~vv~~L~~~l~----~~r--------l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~   75 (618)
T PRK14951          8 RKYRPRSFSEMVGQEHVVQALTNALT----QQR--------LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITA   75 (618)
T ss_pred             HHHCCCCHHHhcCcHHHHHHHHHHHH----cCC--------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCC
Confidence            45689999999999988776666443    221        1357999999999999999999999864           


Q ss_pred             ------------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccc
Q 009640          255 ------------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAK  310 (530)
Q Consensus       255 ------------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~  310 (530)
                                        +++.++..+-.+-.+++.++...      ...-|++|||+|.+.                  
T Consensus        76 ~pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls------------------  137 (618)
T PRK14951         76 TPCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLT------------------  137 (618)
T ss_pred             CCCCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCC------------------
Confidence                              34555544334455777777654      124599999999872                  


Q ss_pred             cccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEE
Q 009640          311 TKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVS  390 (530)
Q Consensus       311 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~  390 (530)
                                                     ....+.||..|+..    .+..++|++|+.+.++.+.+++  |+ ..++
T Consensus       138 -------------------------------~~a~NaLLKtLEEP----P~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~  179 (618)
T PRK14951        138 -------------------------------NTAFNAMLKTLEEP----PEYLKFVLATTDPQKVPVTVLS--RC-LQFN  179 (618)
T ss_pred             -------------------------------HHHHHHHHHhcccC----CCCeEEEEEECCchhhhHHHHH--hc-eeee
Confidence                                           22467788888753    3567888888899999999888  65 6789


Q ss_pred             eCCCCHHHHHHHHHHhhCC
Q 009640          391 LGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       391 ~~~p~~~~r~~i~~~~l~~  409 (530)
                      |..++.++....++..+..
T Consensus       180 f~~Ls~eei~~~L~~i~~~  198 (618)
T PRK14951        180 LRPMAPETVLEHLTQVLAA  198 (618)
T ss_pred             cCCCCHHHHHHHHHHHHHH
Confidence            9999999888888776643

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.59  E-value=4e-14  Score=149.39  Aligned_cols=156  Identities=22%  Similarity=0.255  Sum_probs=114.5

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc----------------
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD----------------  255 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~----------------  255 (530)
                      .|++|+|++.+++.+...+.....   .+...+...+.+||||||||+|||++|.++|+.+..+                
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            579999999999998887765443   2334455567899999999999999999999977442                


Q ss_pred             -------EEEEecCc-cCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhc
Q 009640          256 -------VYDLELTK-VTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMG  321 (530)
Q Consensus       256 -------i~~l~l~~-~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~  321 (530)
                             ++.+.... ...-.+++.++..+      ....|+||||+|.+-                             
T Consensus        80 ~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~-----------------------------  130 (394)
T PRK07940         80 LAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLT-----------------------------  130 (394)
T ss_pred             hcCCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcC-----------------------------
Confidence                   33333221 12345677777654      234699999999872                             


Q ss_pred             cccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHH
Q 009640          322 SRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKV  401 (530)
Q Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~  401 (530)
                                          ....+.||..|+.-    ..+.++|++|+.++.|.|++++  |+ ..|.|+.|+.++...
T Consensus       131 --------------------~~aanaLLk~LEep----~~~~~fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~~~i~~  183 (394)
T PRK07940        131 --------------------ERAANALLKAVEEP----PPRTVWLLCAPSPEDVLPTIRS--RC-RHVALRTPSVEAVAE  183 (394)
T ss_pred             --------------------HHHHHHHHHHhhcC----CCCCeEEEEECChHHChHHHHh--hC-eEEECCCCCHHHHHH
Confidence                                11346788888753    3456777777779999999998  76 689999999999887


Q ss_pred             HHHHh
Q 009640          402 LAKNY  406 (530)
Q Consensus       402 i~~~~  406 (530)
                      ++...
T Consensus       184 ~L~~~  188 (394)
T PRK07940        184 VLVRR  188 (394)
T ss_pred             HHHHh
Confidence            77643

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

Probab=99.59  E-value=1.6e-14  Score=155.75  Aligned_cols=161  Identities=24%  Similarity=0.306  Sum_probs=116.7

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHH--
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELR--  271 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~--  271 (530)
                      ++-.|.+++|+.|++.|.--.-+       |-....-++|+||||.||||++++||..||..|+.+++..+.+.++++  
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLr-------gs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGH  483 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLR-------GSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGH  483 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhc-------ccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhccc
Confidence            45577889999999877532211       111223478999999999999999999999999999998887665543  


Q ss_pred             -------------HHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          272 -------------ALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       272 -------------~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                                   +-|... ...-+++|||||.+-.  +                                         
T Consensus       484 RRTYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~--g-----------------------------------------  520 (906)
T KOG2004|consen  484 RRTYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGS--G-----------------------------------------  520 (906)
T ss_pred             ceeeeccCChHHHHHHHhhCCCCceEEeehhhhhCC--C-----------------------------------------
Confidence                         334443 4566889999999820  0                                         


Q ss_pred             CcchhhhHHHHhhhccCCccC-----------CCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          338 EESGRVTLSGLLNFTDGLWSC-----------CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~-----------~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                        ....--+.||..||--.++           .-..+++|+|.|..+.|+|+|+.  ||.+ |+++-...++...|+++|
T Consensus       521 --~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~idtIP~pLlD--RMEv-IelsGYv~eEKv~IA~~y  595 (906)
T KOG2004|consen  521 --HQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVIDTIPPPLLD--RMEV-IELSGYVAEEKVKIAERY  595 (906)
T ss_pred             --CCCChHHHHHHhcChhhccchhhhccccccchhheEEEEeccccccCChhhhh--hhhe-eeccCccHHHHHHHHHHh
Confidence              0011124455554421111           12568999999999999999999  9976 999999999999999999


Q ss_pred             hCC
Q 009640          407 LGI  409 (530)
Q Consensus       407 l~~  409 (530)
                      |-.
T Consensus       596 Lip  598 (906)
T KOG2004|consen  596 LIP  598 (906)
T ss_pred             hhh
Confidence            853

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

Probab=99.58  E-value=1.5e-14  Score=157.93  Aligned_cols=236  Identities=21%  Similarity=0.245  Sum_probs=168.1

Q ss_pred             HcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc------CChHHHHHHHHhc--CCCeEEEE
Q 009640          214 ANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV------TDNSELRALLLQT--TNRSIIVI  285 (530)
Q Consensus       214 l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~------~~~~~L~~l~~~~--~~~sII~I  285 (530)
                      +..++.+...+...++|+++|||||||||++++++|++ +.....++...+      .+...++.+|..+  ..|+|+++
T Consensus         4 ~~~~~~~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~   82 (494)
T COG0464           4 LKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFI   82 (494)
T ss_pred             ccCHHHHHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEee
Confidence            34667788899999999999999999999999999999 444433333322      1345567777665  67899999


Q ss_pred             cCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEE
Q 009640          286 EDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKII  365 (530)
Q Consensus       286 DeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~iv  365 (530)
                      ||+|.+.+.+..                                      ..........+.|+..+|++.  .+. +++
T Consensus        83 d~~~~~~~~~~~--------------------------------------~~~~~~~~v~~~l~~~~d~~~--~~~-v~~  121 (494)
T COG0464          83 DEIDALAPKRSS--------------------------------------DQGEVERRVVAQLLALMDGLK--RGQ-VIV  121 (494)
T ss_pred             chhhhcccCccc--------------------------------------cccchhhHHHHHHHHhccccc--CCc-eEE
Confidence            999998532111                                      122345667899999999998  356 888


Q ss_pred             EEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCH
Q 009640          366 VFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNV  445 (530)
Q Consensus       366 I~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~  445 (530)
                      ++.||.+..+|+++++|||++..+.+..|+...+..++.......... .......++..+.+++.+++..++....   
T Consensus       122 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~~~l~~~~~---  197 (494)
T COG0464         122 IGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLG-PPGTGKTLAARTVGKSGADLGALAKEAA---  197 (494)
T ss_pred             EeecCCccccChhHhCccccceeeecCCCCHHHHHHHHHHHHhcCCCc-ccccHHHHHHhcCCccHHHHHHHHHHHH---
Confidence            889999999999999999999999999999999988887766543322 1223667777789999999999986433   


Q ss_pred             HHHHHHHH-HHHHHhhhccccccccccccccCCCCcccccCCCCcccCCCCCC
Q 009640          446 DLAMKEVV-SAMQAKILSGREVMECDELVITRSPESVVVVRSPENWDSSPGGK  497 (530)
Q Consensus       446 ~~al~~l~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~g~~  497 (530)
                      ..++.... ........+..++..+...+.+.  ..+....+.+.|.+++|..
T Consensus       198 ~~~~~r~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~v~~~diggl~  248 (494)
T COG0464         198 LRELRRAIDLVGEYIGVTEDDFEEALKKVLPS--RGVLFEDEDVTLDDIGGLE  248 (494)
T ss_pred             HHHHHhhhccCcccccccHHHHHHHHHhcCcc--cccccCCCCcceehhhcHH
Confidence            22222221 11222233334444444444333  4667788889999998854

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=2.7e-14  Score=156.31  Aligned_cols=154  Identities=18%  Similarity=0.322  Sum_probs=115.9

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      ..+|.+|++|+|++.+++.+...+..    ..        .+..||||||||||||++|+++|+.++.            
T Consensus         9 k~rP~~f~divGq~~v~~~L~~~i~~----~~--------~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C   76 (527)
T PRK14969          9 KWRPKSFSELVGQEHVVRALTNALEQ----QR--------LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVC   76 (527)
T ss_pred             HhCCCcHHHhcCcHHHHHHHHHHHHc----CC--------CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCC
Confidence            34789999999999988877665532    11        1357999999999999999999999854            


Q ss_pred             ------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          255 ------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       255 ------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                  +++.++...-..-.+++.++..+      ....|+||||+|.+-                        
T Consensus        77 ~~C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls------------------------  132 (527)
T PRK14969         77 SACLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLS------------------------  132 (527)
T ss_pred             HHHHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCC------------------------
Confidence                        45555544334456677776654      235699999999871                        


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                               ....+.||..|+..    .+..++|++|+.++++.+.+++  |+ ..++|..++.
T Consensus       133 -------------------------~~a~naLLK~LEep----p~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~  180 (527)
T PRK14969        133 -------------------------KSAFNAMLKTLEEP----PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPP  180 (527)
T ss_pred             -------------------------HHHHHHHHHHHhCC----CCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCH
Confidence                                     22456899988863    3567888888889999988887  65 6689999999


Q ss_pred             HHHHHHHHHhhC
Q 009640          397 HAFKVLAKNYLG  408 (530)
Q Consensus       397 ~~r~~i~~~~l~  408 (530)
                      ++....+...+.
T Consensus       181 ~~i~~~L~~il~  192 (527)
T PRK14969        181 PLIVSHLQHILE  192 (527)
T ss_pred             HHHHHHHHHHHH
Confidence            988887777664

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=5.2e-14  Score=153.41  Aligned_cols=155  Identities=17%  Similarity=0.275  Sum_probs=114.0

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ...+|.+|++++|++.+++.+...+.    ...        .+..||||||||||||++|+++|+.+..           
T Consensus         8 ~KyRP~~f~diiGq~~~v~~L~~~i~----~~r--------l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~   75 (546)
T PRK14957          8 RKYRPQSFAEVAGQQHALNSLVHALE----TQK--------VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNK   75 (546)
T ss_pred             HHHCcCcHHHhcCcHHHHHHHHHHHH----cCC--------CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcc
Confidence            34588999999999998887665443    111        1357999999999999999999998853           


Q ss_pred             -------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          255 -------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       255 -------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                                   +++.++...-.+-.+++.++...      ...-|+||||+|.+-                       
T Consensus        76 C~sC~~i~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls-----------------------  132 (546)
T PRK14957         76 CENCVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLS-----------------------  132 (546)
T ss_pred             cHHHHHHhcCCCCceEEeecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhcc-----------------------
Confidence                         55556553333445566665443      346799999999871                       


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                                ....+.||..|+..    .+.+++|++|+.+..+.+++++  |+ ..++|..++
T Consensus       133 --------------------------~~a~naLLK~LEep----p~~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls  179 (546)
T PRK14957        133 --------------------------KQSFNALLKTLEEP----PEYVKFILATTDYHKIPVTILS--RC-IQLHLKHIS  179 (546)
T ss_pred             --------------------------HHHHHHHHHHHhcC----CCCceEEEEECChhhhhhhHHH--he-eeEEeCCCC
Confidence                                      22456889888853    3567788888889999989887  66 679999999


Q ss_pred             HHHHHHHHHHhhC
Q 009640          396 PHAFKVLAKNYLG  408 (530)
Q Consensus       396 ~~~r~~i~~~~l~  408 (530)
                      .++....++..+.
T Consensus       180 ~~eI~~~L~~il~  192 (546)
T PRK14957        180 QADIKDQLKIILA  192 (546)
T ss_pred             HHHHHHHHHHHHH
Confidence            9988877776554

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=5.1e-14  Score=154.78  Aligned_cols=157  Identities=21%  Similarity=0.347  Sum_probs=116.6

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++|+|++.+++.|...+.    ...        .+..|||||||||||||+|+++|+.++.           
T Consensus         5 ~kyRP~~f~eivGq~~i~~~L~~~i~----~~r--------~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~   72 (584)
T PRK14952          5 RKYRPATFAEVVGQEHVTEPLSSALD----AGR--------INHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGV   72 (584)
T ss_pred             HHhCCCcHHHhcCcHHHHHHHHHHHH----cCC--------CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccc
Confidence            34689999999999998877666543    211        2346999999999999999999998752           


Q ss_pred             ---------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCcccccccc
Q 009640          255 ---------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKR  313 (530)
Q Consensus       255 ---------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r  313 (530)
                                     +++.++..+..+-.+++.+....      ...-|+||||+|.+-                     
T Consensus        73 C~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt---------------------  131 (584)
T PRK14952         73 CESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVT---------------------  131 (584)
T ss_pred             cHHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCC---------------------
Confidence                           34555544433455666654432      345699999999871                     


Q ss_pred             chhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCC
Q 009640          314 SSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGT  393 (530)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~  393 (530)
                                                  ....+.||..|+..    .+.+++|++|+.+++|.+++++  |. .+++|..
T Consensus       132 ----------------------------~~A~NALLK~LEEp----p~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~  176 (584)
T PRK14952        132 ----------------------------TAGFNALLKIVEEP----PEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRL  176 (584)
T ss_pred             ----------------------------HHHHHHHHHHHhcC----CCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeC
Confidence                                        12467889988853    4578899999999999999998  64 6799999


Q ss_pred             CCHHHHHHHHHHhhCCc
Q 009640          394 CGPHAFKVLAKNYLGIE  410 (530)
Q Consensus       394 p~~~~r~~i~~~~l~~~  410 (530)
                      ++.++....+..++...
T Consensus       177 l~~~~i~~~L~~i~~~e  193 (584)
T PRK14952        177 LPPRTMRALIARICEQE  193 (584)
T ss_pred             CCHHHHHHHHHHHHHHc
Confidence            99998888887766543

>PRK06893 DNA replication initiation factor; Validated

Probab=99.57  E-value=5.6e-14  Score=138.29  Aligned_cols=162  Identities=14%  Similarity=0.185  Sum_probs=102.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      +...++.+|+++++.+...  ....+..-      +.   ....+.++||||||||||+|+.|+|+++   +..+..+++
T Consensus         7 ~~~~~~~~fd~f~~~~~~~--~~~~~~~~------~~---~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~   75 (229)
T PRK06893          7 IHQIDDETLDNFYADNNLL--LLDSLRKN------FI---DLQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPL   75 (229)
T ss_pred             CCCCCcccccccccCChHH--HHHHHHHH------hh---ccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeH
Confidence            4556788999998766431  22222111      11   1112457999999999999999999987   345555555


Q ss_pred             CccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          262 TKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       262 ~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                      ....  ....+++....+..+|+|||||.+.+                                            ....
T Consensus        76 ~~~~--~~~~~~~~~~~~~dlLilDDi~~~~~--------------------------------------------~~~~  109 (229)
T PRK06893         76 SKSQ--YFSPAVLENLEQQDLVCLDDLQAVIG--------------------------------------------NEEW  109 (229)
T ss_pred             HHhh--hhhHHHHhhcccCCEEEEeChhhhcC--------------------------------------------ChHH
Confidence            4221  11234555566778999999998621                                            1112


Q ss_pred             hhhHHHHhhhccCCccCCCCCeEEEEEeC-CCCCCC---hhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          342 RVTLSGLLNFTDGLWSCCSEEKIIVFTTN-HRDSVD---PALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       342 ~~~ls~LLn~lDgl~s~~~~~~ivI~TTN-~~~~LD---pALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      ...+-.++|.+   ..  .+..++|+|+| .|..++   |.|.++.+.+..+.++.|+.+.+..|++....
T Consensus       110 ~~~l~~l~n~~---~~--~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~  175 (229)
T PRK06893        110 ELAIFDLFNRI---KE--QGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAY  175 (229)
T ss_pred             HHHHHHHHHHH---HH--cCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHH
Confidence            22344444433   22  23445555555 566654   89998556678899999999999999987653

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.57  E-value=5.8e-14  Score=159.75  Aligned_cols=201  Identities=18%  Similarity=0.267  Sum_probs=138.2

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++|+|++.+++.|...+..    ..        ....||||||+|||||++++++|+.|++           
T Consensus         7 ~KyRP~~f~eiiGqe~v~~~L~~~i~~----~r--------i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~   74 (824)
T PRK07764          7 RRYRPATFAEVIGQEHVTEPLSTALDS----GR--------INHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGE   74 (824)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHh----CC--------CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcc
Confidence            457899999999999988876665532    11        1357999999999999999999999853           


Q ss_pred             ---------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCcccccccc
Q 009640          255 ---------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKR  313 (530)
Q Consensus       255 ---------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r  313 (530)
                                     +++.++..+..+-.+++.+....      ...-|+||||+|.+-                     
T Consensus        75 C~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt---------------------  133 (824)
T PRK07764         75 CDSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVT---------------------  133 (824)
T ss_pred             cHHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcC---------------------
Confidence                           34555443333445666654332      356799999999871                     


Q ss_pred             chhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCC
Q 009640          314 SSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGT  393 (530)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~  393 (530)
                                                  ....+.||+.|+..    ....+|||+|+.+++|-+.|++  |+ .+|.|..
T Consensus       134 ----------------------------~~a~NaLLK~LEEp----P~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~  178 (824)
T PRK07764        134 ----------------------------PQGFNALLKIVEEP----PEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRL  178 (824)
T ss_pred             ----------------------------HHHHHHHHHHHhCC----CCCeEEEEEeCChhhhhHHHHh--he-eEEEeeC
Confidence                                        22456899999864    3568899999999999999988  65 6789999


Q ss_pred             CCHHHHHHHHHHhhCCcCcc------------------chHHHHHHHHHh--CCCCCHHHHHHHHHHhccCHHHHHHHHH
Q 009640          394 CGPHAFKVLAKNYLGIESHH------------------ALFDVVESCIRA--GGALTPAQIGEVLLRNRGNVDLAMKEVV  453 (530)
Q Consensus       394 p~~~~r~~i~~~~l~~~~~~------------------~~~~~i~~l~~~--~~~~spadi~~~l~~~~~d~~~al~~l~  453 (530)
                      ++.+....++...+..+...                  .....+++|+..  ...+|..++..++-...   ...+..++
T Consensus       179 l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~allg~~~---~~~I~~li  255 (824)
T PRK07764        179 VPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAVALLGVTD---SALIDEAV  255 (824)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHhcCCC---HHHHHHHH
Confidence            99999888888776432211                  112233444321  24566777777664332   45566666


Q ss_pred             HHHH
Q 009640          454 SAMQ  457 (530)
Q Consensus       454 ~~l~  457 (530)
                      +++.
T Consensus       256 dAL~  259 (824)
T PRK07764        256 DALA  259 (824)
T ss_pred             HHHH
Confidence            6665

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

Probab=99.57  E-value=3.4e-14  Score=161.54  Aligned_cols=158  Identities=22%  Similarity=0.221  Sum_probs=115.9

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHH----
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSEL----  270 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L----  270 (530)
                      +..|.+++|+.|.+.+........       .....++|+||||||||++++++|+.++.+++.++++.+.+..++    
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~~~~-------~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~  395 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSRVNK-------IKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHR  395 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHhccc-------CCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccch
Confidence            378899999999987775443211       123468999999999999999999999999999998877554443    


Q ss_pred             -----------HHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          271 -----------RALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       271 -----------~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                                 .+.+..+ ....||+|||||.+..                                             
T Consensus       396 ~~~~g~~~G~~~~~l~~~~~~~~villDEidk~~~---------------------------------------------  430 (784)
T PRK10787        396 RTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSS---------------------------------------------  430 (784)
T ss_pred             hccCCCCCcHHHHHHHhcCCCCCEEEEEChhhccc---------------------------------------------
Confidence                       2233333 2445899999998721                                             


Q ss_pred             cchhhhHHHHhhhccCCc----c-------CCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          339 ESGRVTLSGLLNFTDGLW----S-------CCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~----s-------~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                      .......+.||..+|--.    .       ..-+++++|+|||.. .|+|||+.  ||+ .|.++.++.++...|+++||
T Consensus       431 ~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~--R~~-ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        431 DMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLD--RME-VIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             ccCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhc--cee-eeecCCCCHHHHHHHHHHhh
Confidence            001123567777776310    0       012568999999987 59999999  996 58999999999999999998


Q ss_pred             C
Q 009640          408 G  408 (530)
Q Consensus       408 ~  408 (530)
                      .
T Consensus       507 ~  507 (784)
T PRK10787        507 L  507 (784)
T ss_pred             h
Confidence            4

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=1.3e-13  Score=144.90  Aligned_cols=156  Identities=14%  Similarity=0.288  Sum_probs=113.2

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------  254 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------  254 (530)
                      ...++|.+|++++|++.+.+.+...+..    .        ..+.+||||||||+|||++++++|+.+..          
T Consensus         8 ~~k~rP~~~~~iig~~~~~~~l~~~i~~----~--------~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~   75 (367)
T PRK14970          8 ARKYRPQTFDDVVGQSHITNTLLNAIEN----N--------HLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDF   75 (367)
T ss_pred             HHHHCCCcHHhcCCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCC
Confidence            4456899999999999987766665532    1        12468999999999999999999998743          


Q ss_pred             --cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          255 --DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       255 --~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                        ++++++.....+...++.++..+      ..+.||+|||+|.+.                                  
T Consensus        76 ~~~~~~l~~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~----------------------------------  121 (367)
T PRK14970         76 SFNIFELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLS----------------------------------  121 (367)
T ss_pred             CcceEEeccccCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcC----------------------------------
Confidence              33444333333346777777643      245799999999762                                  


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                                     ...++.|++.++..    ....++|++||.+..+.+++.+  |+ ..++++.|+.++...++...
T Consensus       122 ---------------~~~~~~ll~~le~~----~~~~~~Il~~~~~~kl~~~l~s--r~-~~v~~~~~~~~~l~~~l~~~  179 (367)
T PRK14970        122 ---------------SAAFNAFLKTLEEP----PAHAIFILATTEKHKIIPTILS--RC-QIFDFKRITIKDIKEHLAGI  179 (367)
T ss_pred             ---------------HHHHHHHHHHHhCC----CCceEEEEEeCCcccCCHHHHh--cc-eeEecCCccHHHHHHHHHHH
Confidence                           11356788877753    3456788888889999999998  54 35899999999888777765


Q ss_pred             hC
Q 009640          407 LG  408 (530)
Q Consensus       407 l~  408 (530)
                      +.
T Consensus       180 ~~  181 (367)
T PRK14970        180 AV  181 (367)
T ss_pred             HH
Confidence            53

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.57  E-value=4.4e-14  Score=154.28  Aligned_cols=156  Identities=16%  Similarity=0.290  Sum_probs=115.9

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----------  253 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----------  253 (530)
                      ...++|.+|++++|++.+++.+...+..   +         ..+.+|||+||||||||++|+++|+.+.           
T Consensus         7 ~~KyRP~~F~dIIGQe~iv~~L~~aI~~---~---------rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg   74 (605)
T PRK05896          7 YRKYRPHNFKQIIGQELIKKILVNAILN---N---------KLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCN   74 (605)
T ss_pred             HHHhCCCCHHHhcCcHHHHHHHHHHHHc---C---------CCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCc
Confidence            4557899999999999988777664421   1         1136899999999999999999999874           


Q ss_pred             -------------CcEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          254 -------------YDVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       254 -------------~~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                   .+++.++..+..+-.+++.+....      ....|++|||+|.+-                      
T Consensus        75 ~C~sCr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt----------------------  132 (605)
T PRK05896         75 SCSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLS----------------------  132 (605)
T ss_pred             ccHHHHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCC----------------------
Confidence                         255556554434455677766543      245699999999861                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.||..|+..    .+..++|++|+.+..|.+++++  |+. .++|..+
T Consensus       133 ---------------------------~~A~NaLLKtLEEP----p~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~L  178 (605)
T PRK05896        133 ---------------------------TSAWNALLKTLEEP----PKHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKL  178 (605)
T ss_pred             ---------------------------HHHHHHHHHHHHhC----CCcEEEEEECCChHhhhHHHHh--hhh-hcccCCC
Confidence                                       11346788888753    3567888899999999999998  764 6899999


Q ss_pred             CHHHHHHHHHHhhC
Q 009640          395 GPHAFKVLAKNYLG  408 (530)
Q Consensus       395 ~~~~r~~i~~~~l~  408 (530)
                      +.++....+...+.
T Consensus       179 s~~eL~~~L~~il~  192 (605)
T PRK05896        179 NNSELQELLKSIAK  192 (605)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99998888777654

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.56  E-value=1e-13  Score=154.15  Aligned_cols=156  Identities=17%  Similarity=0.320  Sum_probs=116.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------  254 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------  254 (530)
                      ...++|.+|++|+|++.+++.+...+..    .        ..+..||||||||||||++|+++|+.+..          
T Consensus         9 ~~KyRP~~f~dIiGQe~~v~~L~~aI~~----~--------rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC   76 (725)
T PRK07133          9 YRKYRPKTFDDIVGQDHIVQTLKNIIKS----N--------KISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPC   76 (725)
T ss_pred             HHHhCCCCHHHhcCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCch
Confidence            4567899999999999988877776642    1        12468999999999999999999998743          


Q ss_pred             -----------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhh
Q 009640          255 -----------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSI  317 (530)
Q Consensus       255 -----------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~  317 (530)
                                 +++.++...-.+-.+++.+...+      ....|++|||+|.+-                         
T Consensus        77 ~~C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT-------------------------  131 (725)
T PRK07133         77 QECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLS-------------------------  131 (725)
T ss_pred             hHHHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCC-------------------------
Confidence                       23334332222345577766544      345799999999871                         


Q ss_pred             hhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHH
Q 009640          318 KEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPH  397 (530)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~  397 (530)
                                              ....+.||..|+..    .+.+++|++|+.+++|.+++++  |+ .++.|..++.+
T Consensus       132 ------------------------~~A~NALLKtLEEP----P~~tifILaTte~~KLl~TI~S--Rc-q~ieF~~L~~e  180 (725)
T PRK07133        132 ------------------------KSAFNALLKTLEEP----PKHVIFILATTEVHKIPLTILS--RV-QRFNFRRISED  180 (725)
T ss_pred             ------------------------HHHHHHHHHHhhcC----CCceEEEEEcCChhhhhHHHHh--hc-eeEEccCCCHH
Confidence                                    12467889988854    3567888899999999999998  77 47999999999


Q ss_pred             HHHHHHHHhhC
Q 009640          398 AFKVLAKNYLG  408 (530)
Q Consensus       398 ~r~~i~~~~l~  408 (530)
                      +....+...+.
T Consensus       181 eI~~~L~~il~  191 (725)
T PRK07133        181 EIVSRLEFILE  191 (725)
T ss_pred             HHHHHHHHHHH
Confidence            98888876654

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=6.7e-14  Score=153.60  Aligned_cols=156  Identities=16%  Similarity=0.256  Sum_probs=113.9

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc---------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD---------  255 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~---------  255 (530)
                      ...++|.+|++|+|++.+++.|...+.    ...        ....||||||||||||++|+++|+.+...         
T Consensus         7 a~KyRP~sf~dIiGQe~v~~~L~~ai~----~~r--------i~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg   74 (624)
T PRK14959          7 TARYRPQTFAEVAGQETVKAILSRAAQ----ENR--------VAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCN   74 (624)
T ss_pred             HHHhCCCCHHHhcCCHHHHHHHHHHHH----cCC--------CCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCc
Confidence            455789999999999998777666543    211        13589999999999999999999998642         


Q ss_pred             ---------------EEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          256 ---------------VYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       256 ---------------i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                     ++.++...-..-..++.+....      ....||||||+|.+-                      
T Consensus        75 ~C~sC~~i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt----------------------  132 (624)
T PRK14959         75 TCEQCRKVTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLT----------------------  132 (624)
T ss_pred             ccHHHHHHhcCCCCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCC----------------------
Confidence                           5555443222334455543222      356799999999871                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.||..|+..    ....++|++||.+..+.+.|++  |+ .+|+|..+
T Consensus       133 ---------------------------~~a~naLLk~LEEP----~~~~ifILaTt~~~kll~TI~S--Rc-q~i~F~pL  178 (624)
T PRK14959        133 ---------------------------REAFNALLKTLEEP----PARVTFVLATTEPHKFPVTIVS--RC-QHFTFTRL  178 (624)
T ss_pred             ---------------------------HHHHHHHHHHhhcc----CCCEEEEEecCChhhhhHHHHh--hh-hccccCCC
Confidence                                       22357788888753    3568899999999999999887  76 46899999


Q ss_pred             CHHHHHHHHHHhhC
Q 009640          395 GPHAFKVLAKNYLG  408 (530)
Q Consensus       395 ~~~~r~~i~~~~l~  408 (530)
                      +.++...++...+.
T Consensus       179 s~~eL~~~L~~il~  192 (624)
T PRK14959        179 SEAGLEAHLTKVLG  192 (624)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99998888776554

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.55  E-value=1.3e-13  Score=142.75  Aligned_cols=158  Identities=13%  Similarity=0.242  Sum_probs=105.9

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----c
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----D  255 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----~  255 (530)
                      .|  +..+.|.+|++++|++++++.+...+.    .+.         ..++|||||||||||++|+++|+++..     +
T Consensus         4 ~w--~~ky~P~~~~~~~g~~~~~~~L~~~~~----~~~---------~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~   68 (337)
T PRK12402          4 LW--TEKYRPALLEDILGQDEVVERLSRAVD----SPN---------LPHLLVQGPPGSGKTAAVRALARELYGDPWENN   68 (337)
T ss_pred             ch--HHhhCCCcHHHhcCCHHHHHHHHHHHh----CCC---------CceEEEECCCCCCHHHHHHHHHHHhcCcccccc
Confidence            57  677899999999999987777666442    221         237999999999999999999999842     3


Q ss_pred             EEEEecCccCC--------------------------hHHHHHHHHhc-------CCCeEEEEcCccchhhhhhhhhhcc
Q 009640          256 VYDLELTKVTD--------------------------NSELRALLLQT-------TNRSIIVIEDIDCSVDLTADRMLKS  302 (530)
Q Consensus       256 i~~l~l~~~~~--------------------------~~~L~~l~~~~-------~~~sII~IDeID~~~~~~~~r~~~~  302 (530)
                      +..+++..+..                          ...++.++...       ..+.+|+|||+|.+-+         
T Consensus        69 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~---------  139 (337)
T PRK12402         69 FTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALRE---------  139 (337)
T ss_pred             eEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCH---------
Confidence            45555543210                          11222222211       3456999999997610         


Q ss_pred             cCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcC
Q 009640          303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRC  382 (530)
Q Consensus       303 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRp  382 (530)
                                                              .....|+..++...    ....+|+||+.+..+.++|.+ 
T Consensus       140 ----------------------------------------~~~~~L~~~le~~~----~~~~~Il~~~~~~~~~~~L~s-  174 (337)
T PRK12402        140 ----------------------------------------DAQQALRRIMEQYS----RTCRFIIATRQPSKLIPPIRS-  174 (337)
T ss_pred             ----------------------------------------HHHHHHHHHHHhcc----CCCeEEEEeCChhhCchhhcC-
Confidence                                                    01234555555332    234466777778888888887 


Q ss_pred             CceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          383 GRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       383 GR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                       |+ ..+.|.+|+.++...+++..+..
T Consensus       175 -r~-~~v~~~~~~~~~~~~~l~~~~~~  199 (337)
T PRK12402        175 -RC-LPLFFRAPTDDELVDVLESIAEA  199 (337)
T ss_pred             -Cc-eEEEecCCCHHHHHHHHHHHHHH
Confidence             65 56899999999998888876543

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.55  E-value=1.1e-13  Score=153.18  Aligned_cols=154  Identities=16%  Similarity=0.260  Sum_probs=114.9

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      .++|.+|++|+|++++++.+...+..    .        ..+..||||||||||||++++++|+.++.            
T Consensus         9 k~RP~~f~~iiGq~~v~~~L~~~i~~----~--------~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c   76 (576)
T PRK14965          9 KYRPQTFSDLTGQEHVSRTLQNAIDT----G--------RVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVC   76 (576)
T ss_pred             HhCCCCHHHccCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCcc
Confidence            45889999999999988877765532    1        12468999999999999999999999853            


Q ss_pred             ------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          255 ------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       255 ------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                  +++.++..+...-.+++.+....      ...-|+||||+|.+-                        
T Consensus        77 ~~c~~i~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt------------------------  132 (576)
T PRK14965         77 PPCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLS------------------------  132 (576)
T ss_pred             HHHHHHhcCCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCC------------------------
Confidence                        24455444333445677766543      234699999999871                        


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                               ....+.||..|+..    .+.+++|++||.+++|.+.+++  |+ ..+.|..++.
T Consensus       133 -------------------------~~a~naLLk~LEep----p~~~~fIl~t~~~~kl~~tI~S--Rc-~~~~f~~l~~  180 (576)
T PRK14965        133 -------------------------TNAFNALLKTLEEP----PPHVKFIFATTEPHKVPITILS--RC-QRFDFRRIPL  180 (576)
T ss_pred             -------------------------HHHHHHHHHHHHcC----CCCeEEEEEeCChhhhhHHHHH--hh-hhhhcCCCCH
Confidence                                     22457899988853    3568899999999999999997  65 4688999998


Q ss_pred             HHHHHHHHHhhC
Q 009640          397 HAFKVLAKNYLG  408 (530)
Q Consensus       397 ~~r~~i~~~~l~  408 (530)
                      ++....+...+.
T Consensus       181 ~~i~~~L~~i~~  192 (576)
T PRK14965        181 QKIVDRLRYIAD  192 (576)
T ss_pred             HHHHHHHHHHHH
Confidence            888777776654

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=2.5e-13  Score=147.50  Aligned_cols=157  Identities=18%  Similarity=0.277  Sum_probs=116.8

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----------  253 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----------  253 (530)
                      ...++|.+|++++|++.+++.+...+.    ..        ..+..||||||||||||++|+++|+.+.           
T Consensus         5 ~~KyRP~~fdeiiGqe~v~~~L~~~I~----~g--------rl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~   72 (535)
T PRK08451          5 ALKYRPKHFDELIGQESVSKTLSLALD----NN--------RLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCD   72 (535)
T ss_pred             HHHHCCCCHHHccCcHHHHHHHHHHHH----cC--------CCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCc
Confidence            345689999999999998877766553    21        1246799999999999999999999873           


Q ss_pred             -------------CcEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          254 -------------YDVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       254 -------------~~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                   .+++.++..+-.+-..++.+....      ...-|++|||+|.+-                      
T Consensus        73 ~C~~C~~~~~~~h~dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt----------------------  130 (535)
T PRK08451         73 TCIQCQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLT----------------------  130 (535)
T ss_pred             ccHHHHHHhhcCCCeEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC----------------------
Confidence                         245555544333456777777553      234699999999871                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.||..|+..    .....+|++|+.+.+|.+++++  |. .+++|..+
T Consensus       131 ---------------------------~~A~NALLK~LEEp----p~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~L  176 (535)
T PRK08451        131 ---------------------------KEAFNALLKTLEEP----PSYVKFILATTDPLKLPATILS--RT-QHFRFKQI  176 (535)
T ss_pred             ---------------------------HHHHHHHHHHHhhc----CCceEEEEEECChhhCchHHHh--hc-eeEEcCCC
Confidence                                       23467888888854    3456788888889999999998  74 57999999


Q ss_pred             CHHHHHHHHHHhhCC
Q 009640          395 GPHAFKVLAKNYLGI  409 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~  409 (530)
                      +.++....+...+..
T Consensus       177 s~~ei~~~L~~Il~~  191 (535)
T PRK08451        177 PQNSIISHLKTILEK  191 (535)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            998888877766543

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.53  E-value=2.5e-13  Score=147.12  Aligned_cols=157  Identities=15%  Similarity=0.284  Sum_probs=114.3

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------  254 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------  254 (530)
                      ...++|.+|++++|++.+.+.+...+..    .        ..+..||||||||||||++|+++|..++.          
T Consensus         7 ~~kyRP~~f~diiGq~~i~~~L~~~i~~----~--------~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~   74 (486)
T PRK14953          7 ARKYRPKFFKEVIGQEIVVRILKNAVKL----Q--------RVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCG   74 (486)
T ss_pred             HHhhCCCcHHHccChHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCC
Confidence            4456899999999999988777665532    1        12457999999999999999999998752          


Q ss_pred             --------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          255 --------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       255 --------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                    +++.++.+...+-..++.+...+      ..+-|++|||+|.+-                      
T Consensus        75 ~c~nc~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt----------------------  132 (486)
T PRK14953         75 KCENCVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLT----------------------  132 (486)
T ss_pred             ccHHHHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcC----------------------
Confidence                          34555543333444555554432      346799999999761                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.||..++..    ....++|++|+.++.+.+++.+  |+. .+.|..+
T Consensus       133 ---------------------------~~a~naLLk~LEep----p~~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~l  178 (486)
T PRK14953        133 ---------------------------KEAFNALLKTLEEP----PPRTIFILCTTEYDKIPPTILS--RCQ-RFIFSKP  178 (486)
T ss_pred             ---------------------------HHHHHHHHHHHhcC----CCCeEEEEEECCHHHHHHHHHH--hce-EEEcCCC
Confidence                                       11346788887753    3457788888888999999988  654 6999999


Q ss_pred             CHHHHHHHHHHhhCC
Q 009640          395 GPHAFKVLAKNYLGI  409 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~  409 (530)
                      +.++....+...+..
T Consensus       179 s~~el~~~L~~i~k~  193 (486)
T PRK14953        179 TKEQIKEYLKRICNE  193 (486)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999999888876653

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.53  E-value=4e-13  Score=137.94  Aligned_cols=188  Identities=15%  Similarity=0.217  Sum_probs=122.5

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----C
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----Y  254 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----~  254 (530)
                      ..|  +..+.|.+|+++++.+++++.+...+.    ...         ..++|||||||||||++++++++++.     .
T Consensus         5 ~~w--~~kyrP~~~~~~~g~~~~~~~l~~~i~----~~~---------~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~   69 (319)
T PRK00440          5 EIW--VEKYRPRTLDEIVGQEEIVERLKSYVK----EKN---------MPHLLFAGPPGTGKTTAALALARELYGEDWRE   69 (319)
T ss_pred             Ccc--chhhCCCcHHHhcCcHHHHHHHHHHHh----CCC---------CCeEEEECCCCCCHHHHHHHHHHHHcCCcccc
Confidence            368  788899999999999988777666542    211         13589999999999999999999973     2


Q ss_pred             cEEEEecCccCChHHHHHHHH---h-c----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          255 DVYDLELTKVTDNSELRALLL---Q-T----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       255 ~i~~l~l~~~~~~~~L~~l~~---~-~----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      .++.++.+.......++..+.   . .    ..+.+|+|||+|.+.+                                 
T Consensus        70 ~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~---------------------------------  116 (319)
T PRK00440         70 NFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS---------------------------------  116 (319)
T ss_pred             ceEEeccccccchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH---------------------------------
Confidence            344444333322222222221   1 1    2356999999998721                                 


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                                      .....|+..++...    ....+|+++|.+..+.+++.+  |+. .++|+.++.++...+++.+
T Consensus       117 ----------------~~~~~L~~~le~~~----~~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~~ei~~~l~~~  173 (319)
T PRK00440        117 ----------------DAQQALRRTMEMYS----QNTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKKEAVAERLRYI  173 (319)
T ss_pred             ----------------HHHHHHHHHHhcCC----CCCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCHHHHHHHHHHH
Confidence                            01234566665432    335677888988888888887  665 4899999999888888776


Q ss_pred             hCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHH
Q 009640          407 LGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVV  453 (530)
Q Consensus       407 l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~  453 (530)
                      +....               ..+++..+..++....+|+..++..+.
T Consensus       174 ~~~~~---------------~~i~~~al~~l~~~~~gd~r~~~~~l~  205 (319)
T PRK00440        174 AENEG---------------IEITDDALEAIYYVSEGDMRKAINALQ  205 (319)
T ss_pred             HHHcC---------------CCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            64322               234555555555555555555555443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.52  E-value=3.1e-13  Score=149.31  Aligned_cols=157  Identities=16%  Similarity=0.296  Sum_probs=117.3

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc---------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD---------  255 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~---------  255 (530)
                      ...++|.+|++|+|++.+++.|...+..   +         ..+.+||||||||||||++|+++|+.+++.         
T Consensus        15 a~KyRP~~f~dliGq~~~v~~L~~~~~~---g---------ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~   82 (598)
T PRK09111         15 ARKYRPQTFDDLIGQEAMVRTLTNAFET---G---------RIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPT   82 (598)
T ss_pred             HhhhCCCCHHHhcCcHHHHHHHHHHHHc---C---------CCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCc
Confidence            4457899999999999988877765531   1         124589999999999999999999988543         


Q ss_pred             --------------------EEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCcccc
Q 009640          256 --------------------VYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTA  309 (530)
Q Consensus       256 --------------------i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~  309 (530)
                                          ++.++..+..+-.+++.++..+      ...-||||||+|.+-                 
T Consensus        83 ~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls-----------------  145 (598)
T PRK09111         83 IDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLS-----------------  145 (598)
T ss_pred             cccCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCC-----------------
Confidence                                2333333333456677776544      245799999999871                 


Q ss_pred             ccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEE
Q 009640          310 KTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHV  389 (530)
Q Consensus       310 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I  389 (530)
                                                      ....+.||..|+..    .+..++|++|+.++++.+.+++  |+ ..+
T Consensus       146 --------------------------------~~a~naLLKtLEeP----p~~~~fIl~tte~~kll~tI~S--Rc-q~~  186 (598)
T PRK09111        146 --------------------------------TAAFNALLKTLEEP----PPHVKFIFATTEIRKVPVTVLS--RC-QRF  186 (598)
T ss_pred             --------------------------------HHHHHHHHHHHHhC----CCCeEEEEEeCChhhhhHHHHh--he-eEE
Confidence                                            22467888888753    3567888899999999999887  66 569


Q ss_pred             EeCCCCHHHHHHHHHHhhCC
Q 009640          390 SLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       390 ~~~~p~~~~r~~i~~~~l~~  409 (530)
                      .|..++.++....+...+..
T Consensus       187 ~f~~l~~~el~~~L~~i~~k  206 (598)
T PRK09111        187 DLRRIEADVLAAHLSRIAAK  206 (598)
T ss_pred             EecCCCHHHHHHHHHHHHHH
Confidence            99999999988888877654

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.52  E-value=4.8e-13  Score=143.93  Aligned_cols=154  Identities=15%  Similarity=0.215  Sum_probs=111.2

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      .++|.+|++|+|++.+++.+...+..    .        ..+..||||||||||||++|+++|+.+..            
T Consensus        10 kyRP~~~~diiGq~~~v~~L~~~i~~----~--------~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~   77 (451)
T PRK06305         10 KYRPQTFSEILGQDAVVAVLKNALRF----N--------RAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQ   77 (451)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHc----C--------CCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcc
Confidence            35789999999999987766665532    1        12467999999999999999999998743            


Q ss_pred             -------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          255 -------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       255 -------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                                   +++.++.....+-..++.+....      ..+.||||||+|.+-                       
T Consensus        78 c~~C~~i~~~~~~d~~~i~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt-----------------------  134 (451)
T PRK06305         78 CASCKEISSGTSLDVLEIDGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLT-----------------------  134 (451)
T ss_pred             cHHHHHHhcCCCCceEEeeccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhC-----------------------
Confidence                         34444433223334555443222      467899999999871                       


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                                ....+.||..|+..    .+..++|++||.+.+|.+++.+  |+. .++|..++
T Consensus       135 --------------------------~~~~n~LLk~lEep----~~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~l~  181 (451)
T PRK06305        135 --------------------------KEAFNSLLKTLEEP----PQHVKFFLATTEIHKIPGTILS--RCQ-KMHLKRIP  181 (451)
T ss_pred             --------------------------HHHHHHHHHHhhcC----CCCceEEEEeCChHhcchHHHH--hce-EEeCCCCC
Confidence                                      11346788888753    3567888889999999999998  664 58999999


Q ss_pred             HHHHHHHHHHhhC
Q 009640          396 PHAFKVLAKNYLG  408 (530)
Q Consensus       396 ~~~r~~i~~~~l~  408 (530)
                      .++....+...+.
T Consensus       182 ~~el~~~L~~~~~  194 (451)
T PRK06305        182 EETIIDKLALIAK  194 (451)
T ss_pred             HHHHHHHHHHHHH
Confidence            9988877766543

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.52  E-value=2.2e-13  Score=153.38  Aligned_cols=197  Identities=19%  Similarity=0.213  Sum_probs=128.2

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +|  ....+|.+|++++|++++.... ..+...+....         ...+|||||||||||++|+++|+.++.+++.++
T Consensus        17 PL--aek~RP~tldd~vGQe~ii~~~-~~L~~~i~~~~---------~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~ln   84 (725)
T PRK13341         17 PL--ADRLRPRTLEEFVGQDHILGEG-RLLRRAIKADR---------VGSLILYGPPGVGKTTLARIIANHTRAHFSSLN   84 (725)
T ss_pred             Ch--HHhcCCCcHHHhcCcHHHhhhh-HHHHHHHhcCC---------CceEEEECCCCCCHHHHHHHHHHHhcCcceeeh
Confidence            46  3456799999999998876431 12223332221         247899999999999999999999998888877


Q ss_pred             cCccCChHHHHHHHHh-------cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCC
Q 009640          261 LTKVTDNSELRALLLQ-------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNN  333 (530)
Q Consensus       261 l~~~~~~~~L~~l~~~-------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~  333 (530)
                      .... +..+++..+..       ...+.||||||||.+-.                                        
T Consensus        85 a~~~-~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~----------------------------------------  123 (725)
T PRK13341         85 AVLA-GVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNK----------------------------------------  123 (725)
T ss_pred             hhhh-hhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCH----------------------------------------
Confidence            6532 22334433332       24568999999998721                                        


Q ss_pred             CCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEe--CCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          334 NNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTT--NHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       334 ~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TT--N~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                               .....|+..++.      ..+++|++|  |....++++|++  |. ..+.|+.++.+++..+++.++....
T Consensus       124 ---------~qQdaLL~~lE~------g~IiLI~aTTenp~~~l~~aL~S--R~-~v~~l~pLs~edi~~IL~~~l~~~~  185 (725)
T PRK13341        124 ---------AQQDALLPWVEN------GTITLIGATTENPYFEVNKALVS--RS-RLFRLKSLSDEDLHQLLKRALQDKE  185 (725)
T ss_pred             ---------HHHHHHHHHhcC------ceEEEEEecCCChHhhhhhHhhc--cc-cceecCCCCHHHHHHHHHHHHHHHH
Confidence                     112346665542      345666654  334578999998  53 4589999999999999998765211


Q ss_pred             ccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHH
Q 009640          412 HHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAM  456 (530)
Q Consensus       412 ~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l  456 (530)
                              ..+......+++..+..++..+.+|.+.++..+..+.
T Consensus       186 --------~~~g~~~v~I~deaL~~La~~s~GD~R~lln~Le~a~  222 (725)
T PRK13341        186 --------RGYGDRKVDLEPEAEKHLVDVANGDARSLLNALELAV  222 (725)
T ss_pred             --------hhcCCcccCCCHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence                    0010112456676666666666677777766655544

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.52  E-value=4.6e-13  Score=147.27  Aligned_cols=154  Identities=17%  Similarity=0.290  Sum_probs=114.2

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      ..+|.+|++|+|++.+++.+...+..    ..        .+..||||||||||||++|+++|+.+..            
T Consensus         9 kyRP~~f~diiGqe~iv~~L~~~i~~----~~--------i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C   76 (563)
T PRK06647          9 KRRPRDFNSLEGQDFVVETLKHSIES----NK--------IANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGEC   76 (563)
T ss_pred             HhCCCCHHHccCcHHHHHHHHHHHHc----CC--------CCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccc
Confidence            35899999999999988877765542    11        2457999999999999999999998853            


Q ss_pred             ------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          255 ------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       255 ------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                  +++.++...-..-.+++.+...+      ...-|++|||+|.+-                        
T Consensus        77 ~~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls------------------------  132 (563)
T PRK06647         77 SSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLS------------------------  132 (563)
T ss_pred             hHHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcC------------------------
Confidence                        34444433222345666665432      355799999999871                        


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                               ....+.||..++..    ....++|++|+.+.+|.++|++  |+. .++|..++.
T Consensus       133 -------------------------~~a~naLLK~LEep----p~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~  180 (563)
T PRK06647        133 -------------------------NSAFNALLKTIEEP----PPYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSL  180 (563)
T ss_pred             -------------------------HHHHHHHHHhhccC----CCCEEEEEecCChHHhHHHHHH--hce-EEEecCCCH
Confidence                                     22467888888843    4568888998889999999998  764 589999999


Q ss_pred             HHHHHHHHHhhC
Q 009640          397 HAFKVLAKNYLG  408 (530)
Q Consensus       397 ~~r~~i~~~~l~  408 (530)
                      ++...+++..+.
T Consensus       181 ~el~~~L~~i~~  192 (563)
T PRK06647        181 EKIYNMLKKVCL  192 (563)
T ss_pred             HHHHHHHHHHHH
Confidence            998888876653

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.51  E-value=1.3e-12  Score=137.03  Aligned_cols=158  Identities=15%  Similarity=0.195  Sum_probs=108.4

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---------CcEEEEecCc
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---------YDVYDLELTK  263 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---------~~i~~l~l~~  263 (530)
                      .+.+.+.++..+.|...+...+.+..         +..+++|||||||||++++++++++.         ..++.+++..
T Consensus        14 p~~l~gRe~e~~~l~~~l~~~~~~~~---------~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~   84 (365)
T TIGR02928        14 PDRIVHRDEQIEELAKALRPILRGSR---------PSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQI   84 (365)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCC---------CCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCC
Confidence            35788988888888888877665322         35799999999999999999998763         4566666554


Q ss_pred             cCChH-------------------------H-HHHHHH---hcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          264 VTDNS-------------------------E-LRALLL---QTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       264 ~~~~~-------------------------~-L~~l~~---~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                      ..+..                         + +..++.   ....+.||+|||+|.+..                     
T Consensus        85 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~---------------------  143 (365)
T TIGR02928        85 LDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVG---------------------  143 (365)
T ss_pred             CCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhcc---------------------
Confidence            33211                         1 112222   234578999999999831                     


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC---CCChhhhcCCcee-EEEE
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD---SVDPALIRCGRMD-VHVS  390 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~---~LDpALlRpGR~d-~~I~  390 (530)
                                             .  ....+..|+...+-. ...+..+++|++||.++   .+++.+.+  ||. ..|+
T Consensus       144 -----------------------~--~~~~L~~l~~~~~~~-~~~~~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~  195 (365)
T TIGR02928       144 -----------------------D--DDDLLYQLSRARSNG-DLDNAKVGVIGISNDLKFRENLDPRVKS--SLCEEEII  195 (365)
T ss_pred             -----------------------C--CcHHHHhHhcccccc-CCCCCeEEEEEEECCcchHhhcCHHHhc--cCCcceee
Confidence                                   0  112345555442111 11135678899999875   58888887  664 6799


Q ss_pred             eCCCCHHHHHHHHHHhhC
Q 009640          391 LGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       391 ~~~p~~~~r~~i~~~~l~  408 (530)
                      |++++.++...|++..+.
T Consensus       196 f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       196 FPPYDAEELRDILENRAE  213 (365)
T ss_pred             eCCCCHHHHHHHHHHHHH
Confidence            999999999999988774

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=3e-13  Score=143.62  Aligned_cols=154  Identities=12%  Similarity=0.251  Sum_probs=109.7

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      ..+|.+|++|+|++.+++.+...+.    ...        .+..||||||||||||++|+++|+.+..            
T Consensus         9 k~RP~~~~eiiGq~~~~~~L~~~~~----~~~--------~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~   76 (397)
T PRK14955          9 KYRPKKFADITAQEHITRTIQNSLR----MGR--------VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQE   76 (397)
T ss_pred             hcCCCcHhhccChHHHHHHHHHHHH----hCC--------cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCccccccc
Confidence            4688999999999998887766443    111        2457999999999999999999999854            


Q ss_pred             --------------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccc
Q 009640          255 --------------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTT  308 (530)
Q Consensus       255 --------------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~  308 (530)
                                          +++.++......-.+++.+....      ...-||||||+|.+-                
T Consensus        77 ~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~----------------  140 (397)
T PRK14955         77 VTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLS----------------  140 (397)
T ss_pred             CCCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCC----------------
Confidence                                23333332223345666665444      245799999999871                


Q ss_pred             cccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEE
Q 009640          309 AKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVH  388 (530)
Q Consensus       309 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~  388 (530)
                                                       ....+.||..++..    .+..++|++|+.+.++-+++.+  |.. .
T Consensus       141 ---------------------------------~~~~~~LLk~LEep----~~~t~~Il~t~~~~kl~~tl~s--R~~-~  180 (397)
T PRK14955        141 ---------------------------------IAAFNAFLKTLEEP----PPHAIFIFATTELHKIPATIAS--RCQ-R  180 (397)
T ss_pred             ---------------------------------HHHHHHHHHHHhcC----CCCeEEEEEeCChHHhHHHHHH--HHH-H
Confidence                                             11345678877633    3456778888888899999887  654 5


Q ss_pred             EEeCCCCHHHHHHHHHHhhC
Q 009640          389 VSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       389 I~~~~p~~~~r~~i~~~~l~  408 (530)
                      ++|..++.++....+...+.
T Consensus       181 v~f~~l~~~ei~~~l~~~~~  200 (397)
T PRK14955        181 FNFKRIPLEEIQQQLQGICE  200 (397)
T ss_pred             hhcCCCCHHHHHHHHHHHHH
Confidence            88999998888877776653

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.50  E-value=2.9e-13  Score=132.28  Aligned_cols=158  Identities=16%  Similarity=0.230  Sum_probs=100.6

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      +...+.+|+++..  ...+.+++.+..++..         ...+.++|+||||||||++++++++++   +.+++.+++.
T Consensus         7 ~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~---------~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~   75 (226)
T TIGR03420         7 GLPDDPTFDNFYA--GGNAELLAALRQLAAG---------KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLA   75 (226)
T ss_pred             CCCCchhhcCcCc--CCcHHHHHHHHHHHhc---------CCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHH
Confidence            3456678888873  2334455555555432         124689999999999999999999987   4677777766


Q ss_pred             ccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchh
Q 009640          263 KVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGR  342 (530)
Q Consensus       263 ~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (530)
                      .+..  ....++.......+|+|||+|.+-                                            ......
T Consensus        76 ~~~~--~~~~~~~~~~~~~lLvIDdi~~l~--------------------------------------------~~~~~~  109 (226)
T TIGR03420        76 ELAQ--ADPEVLEGLEQADLVCLDDVEAIA--------------------------------------------GQPEWQ  109 (226)
T ss_pred             HHHH--hHHHHHhhcccCCEEEEeChhhhc--------------------------------------------CChHHH
Confidence            6532  223444445566799999999861                                            010012


Q ss_pred             hhHHHHhhhccCCccCCCCCeEEEEEeC-CCCCCC---hhhhcCCce--eEEEEeCCCCHHHHHHHHHHhhC
Q 009640          343 VTLSGLLNFTDGLWSCCSEEKIIVFTTN-HRDSVD---PALIRCGRM--DVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       343 ~~ls~LLn~lDgl~s~~~~~~ivI~TTN-~~~~LD---pALlRpGR~--d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                         ..|...++....  .+. .+|+|+| .+..++   +.|.+  |+  ..+|.++.|+.+++..+++.+..
T Consensus       110 ---~~L~~~l~~~~~--~~~-~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~~~l~~~~~  173 (226)
T TIGR03420       110 ---EALFHLYNRVRE--AGG-RLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKIAALQSRAA  173 (226)
T ss_pred             ---HHHHHHHHHHHH--cCC-eEEEECCCChHHCCcccHHHHH--HHhcCeeEecCCCCHHHHHHHHHHHHH
Confidence               233333333222  123 4555555 444432   77887  55  58899999999999999877653

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.50  E-value=4e-13  Score=154.47  Aligned_cols=158  Identities=15%  Similarity=0.184  Sum_probs=110.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEE
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVY  257 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~  257 (530)
                      ..+..++.++|.++..+.+++.+    .++         .+.+.+|+||||||||++++++|..+          +..++
T Consensus       181 ~r~~~ld~~iGr~~ei~~~i~~l----~r~---------~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~  247 (852)
T TIGR03345       181 AREGKIDPVLGRDDEIRQMIDIL----LRR---------RQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLL  247 (852)
T ss_pred             hcCCCCCcccCCHHHHHHHHHHH----hcC---------CcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEE
Confidence            35678899999888655444433    221         14689999999999999999999986          36678


Q ss_pred             EEecCccC--------ChHHHHHHHHhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          258 DLELTKVT--------DNSELRALLLQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       258 ~l~l~~~~--------~~~~L~~l~~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      .++++.+.        -...++.+|...   ..++||||||||.+.+..+                              
T Consensus       248 ~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~------------------------------  297 (852)
T TIGR03345       248 SLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGG------------------------------  297 (852)
T ss_pred             EeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCC------------------------------
Confidence            77776543        124678888765   4689999999999852110                              


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHH
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKV  401 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~  401 (530)
                                 .......-+-|+..+.      .+.+.+|+||+..+     .+||||.|  ||. .|.++.|+.++...
T Consensus       298 -----------~~~~~d~~n~Lkp~l~------~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf~-~i~v~eps~~~~~~  357 (852)
T TIGR03345       298 -----------QAGQGDAANLLKPALA------RGELRTIAATTWAEYKKYFEKDPALTR--RFQ-VVKVEEPDEETAIR  357 (852)
T ss_pred             -----------ccccccHHHHhhHHhh------CCCeEEEEecCHHHHhhhhhccHHHHH--hCe-EEEeCCCCHHHHHH
Confidence                       0000011122333332      46788999888754     48999999  996 79999999999999


Q ss_pred             HHHHhhC
Q 009640          402 LAKNYLG  408 (530)
Q Consensus       402 i~~~~l~  408 (530)
                      |++.+..
T Consensus       358 iL~~~~~  364 (852)
T TIGR03345       358 MLRGLAP  364 (852)
T ss_pred             HHHHHHH
Confidence            9765543

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.49  E-value=7.5e-13  Score=147.11  Aligned_cols=155  Identities=19%  Similarity=0.299  Sum_probs=114.4

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++++|++++++.|...+..    ..        ...+||||||||||||++|+++|+.++.           
T Consensus         8 ~kyRP~~f~~liGq~~i~~~L~~~l~~----~r--------l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~C   75 (620)
T PRK14948          8 HKYRPQRFDELVGQEAIATTLKNALIS----NR--------IAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPC   75 (620)
T ss_pred             HHhCCCcHhhccChHHHHHHHHHHHHc----CC--------CCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCC
Confidence            456889999999999988877665542    11        1358999999999999999999999854           


Q ss_pred             ---------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCcccccccc
Q 009640          255 ---------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKR  313 (530)
Q Consensus       255 ---------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r  313 (530)
                                     +++.++......-..++.++..+      ...-||||||+|.+-                     
T Consensus        76 g~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt---------------------  134 (620)
T PRK14948         76 GKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLS---------------------  134 (620)
T ss_pred             cccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccC---------------------
Confidence                           34455544334456777777654      234699999999871                     


Q ss_pred             chhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCC
Q 009640          314 SSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGT  393 (530)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~  393 (530)
                                                  ....+.||..|+..    ....++|++|+.++.|-++|++  |+ ..++|..
T Consensus       135 ----------------------------~~a~naLLK~LEeP----p~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~  179 (620)
T PRK14948        135 ----------------------------TAAFNALLKTLEEP----PPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRR  179 (620)
T ss_pred             ----------------------------HHHHHHHHHHHhcC----CcCeEEEEEeCChhhhhHHHHh--he-eEEEecC
Confidence                                        22457889999843    3567888888999999999987  65 4588888


Q ss_pred             CCHHHHHHHHHHhhC
Q 009640          394 CGPHAFKVLAKNYLG  408 (530)
Q Consensus       394 p~~~~r~~i~~~~l~  408 (530)
                      ++.++....+.....
T Consensus       180 l~~~ei~~~L~~ia~  194 (620)
T PRK14948        180 IPLEAMVQHLSEIAE  194 (620)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            888777666655443

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.48  E-value=1.4e-12  Score=143.17  Aligned_cols=215  Identities=17%  Similarity=0.216  Sum_probs=119.8

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc--------
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL--------  252 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l--------  252 (530)
                      +|  ....+|.+|++++|++...+.+...+    ..         +.+.++|||||||||||++|+++.+++        
T Consensus        54 ~~--~~~~rp~~f~~iiGqs~~i~~l~~al----~~---------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~  118 (531)
T TIGR02902        54 PL--SEKTRPKSFDEIIGQEEGIKALKAAL----CG---------PNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPF  118 (531)
T ss_pred             hH--HHhhCcCCHHHeeCcHHHHHHHHHHH----hC---------CCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCc
Confidence            56  44578899999999998877776432    11         124689999999999999999998753        


Q ss_pred             --CCcEEEEecCccC-ChHHHH-HHH--------------H------------hcCCCeEEEEcCccchhhhhhhhhhcc
Q 009640          253 --CYDVYDLELTKVT-DNSELR-ALL--------------L------------QTTNRSIIVIEDIDCSVDLTADRMLKS  302 (530)
Q Consensus       253 --~~~i~~l~l~~~~-~~~~L~-~l~--------------~------------~~~~~sII~IDeID~~~~~~~~r~~~~  302 (530)
                        +.+++.++++... ++..+. .++              .            ......+|||||||.+-......--+ 
T Consensus       119 ~~~~~fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~~q~~LL~-  197 (531)
T TIGR02902       119 KEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLLK-  197 (531)
T ss_pred             CCCCCEEEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCHHHHHHHHH-
Confidence              3567888765321 111111 011              0            01234799999999872111110000 


Q ss_pred             cCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhc-cCCccCCCCCeEEEEEeCCCCCCChhhhc
Q 009640          303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFT-DGLWSCCSEEKIIVFTTNHRDSVDPALIR  381 (530)
Q Consensus       303 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~l-Dgl~s~~~~~~ivI~TTN~~~~LDpALlR  381 (530)
                                   .+++....+...  --.   ..+.   .+-+.+.... .++.   .+-++|++|||.|+.|+|+|++
T Consensus       198 -------------~Le~~~~~~~~~--~~~---~~~~---~~~~~~~~~~~~~~~---~d~rlI~ATt~~p~~L~paLrs  253 (531)
T TIGR02902       198 -------------VLEDRKVFLDSA--YYN---SENP---NIPSHIHDIFQNGLP---ADFRLIGATTRNPEEIPPALRS  253 (531)
T ss_pred             -------------HHHhCeeeeccc--ccc---ccCc---ccccchhhhcccCcc---cceEEEEEecCCcccCChHHhh
Confidence                         000000000000  000   0000   0000000000 1222   2447777888999999999999


Q ss_pred             CCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009640          382 CGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       382 pGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~  440 (530)
                        |+. .|.|+.++.+++..|+++++.........+.++.++..  ..+..++.+++..
T Consensus       254 --R~~-~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y--~~n~Rel~nll~~  307 (531)
T TIGR02902       254 --RCV-EIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKY--ASNGREAVNIVQL  307 (531)
T ss_pred             --hhh-eeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHh--hhhHHHHHHHHHH
Confidence              874 68899999999999999988654433122233333321  1245666666543

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.48  E-value=6.3e-13  Score=133.47  Aligned_cols=143  Identities=19%  Similarity=0.193  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHH------------
Q 009640          204 KQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELR------------  271 (530)
Q Consensus       204 ~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~------------  271 (530)
                      +.+.+.+..++..           .+.+||+||||||||++|+++|..++.+++.++++.-.+..++.            
T Consensus         8 ~~l~~~~l~~l~~-----------g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~   76 (262)
T TIGR02640         8 KRVTSRALRYLKS-----------GYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVH   76 (262)
T ss_pred             HHHHHHHHHHHhc-----------CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHH
Confidence            4455555555543           25799999999999999999999999999988766532222211            


Q ss_pred             ---------------------HHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCC
Q 009640          272 ---------------------ALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCG  330 (530)
Q Consensus       272 ---------------------~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~  330 (530)
                                           .++.....+.+|+|||||.+-                                      
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~g~l~~A~~~g~~lllDEi~r~~--------------------------------------  118 (262)
T TIGR02640        77 DQFIHNVVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSK--------------------------------------  118 (262)
T ss_pred             HHHHHHhhhhhcccceeecCchHHHHHHcCCEEEEcchhhCC--------------------------------------
Confidence                                 011122456799999999861                                      


Q ss_pred             CCCCCCCCcchhhhHHHHhhhccCCc-cC-----------CCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCC
Q 009640          331 NNNNNNGEESGRVTLSGLLNFTDGLW-SC-----------CSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGT  393 (530)
Q Consensus       331 ~~~~~~~~~~~~~~ls~LLn~lDgl~-s~-----------~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~  393 (530)
                                 ..+.+.|+..|+.-. ..           ...+..||+|+|...     .+++||++  || ..+++++
T Consensus       119 -----------~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~--R~-~~i~i~~  184 (262)
T TIGR02640       119 -----------PETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLD--RL-ITIFMDY  184 (262)
T ss_pred             -----------HHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHHh--hc-EEEECCC
Confidence                       123445555554211 00           012456889999763     67999999  98 6799999


Q ss_pred             CCHHHHHHHHHHhhCC
Q 009640          394 CGPHAFKVLAKNYLGI  409 (530)
Q Consensus       394 p~~~~r~~i~~~~l~~  409 (530)
                      |+.++-..|++..++.
T Consensus       185 P~~~~e~~Il~~~~~~  200 (262)
T TIGR02640       185 PDIDTETAILRAKTDV  200 (262)
T ss_pred             CCHHHHHHHHHHhhCC
Confidence            9999999999988754

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).

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.48  E-value=1.5e-12  Score=144.25  Aligned_cols=154  Identities=13%  Similarity=0.249  Sum_probs=111.0

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      .++|.+|++++|++.+++.+...+.    ..        ..+.+|||+||||||||++|+++|+.+..            
T Consensus         9 kyRP~~f~eivGQe~i~~~L~~~i~----~~--------ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~   76 (620)
T PRK14954          9 KYRPSKFADITAQEHITHTIQNSLR----MD--------RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQE   76 (620)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHH----cC--------CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccc
Confidence            3588999999999998887666432    21        22457999999999999999999999865            


Q ss_pred             --------------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccc
Q 009640          255 --------------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTT  308 (530)
Q Consensus       255 --------------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~  308 (530)
                                          +++.++.....+-.+++.+....      ...-||||||+|.+-                
T Consensus        77 ~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt----------------  140 (620)
T PRK14954         77 VTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLS----------------  140 (620)
T ss_pred             cCCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcC----------------
Confidence                                22223322223345677665544      346799999999871                


Q ss_pred             cccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEE
Q 009640          309 AKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVH  388 (530)
Q Consensus       309 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~  388 (530)
                                                       ....+.||..|+..    .+..++|++|+.+.+|-+++.+  |. ..
T Consensus       141 ---------------------------------~~a~naLLK~LEeP----p~~tv~IL~t~~~~kLl~TI~S--Rc-~~  180 (620)
T PRK14954        141 ---------------------------------TAAFNAFLKTLEEP----PPHAIFIFATTELHKIPATIAS--RC-QR  180 (620)
T ss_pred             ---------------------------------HHHHHHHHHHHhCC----CCCeEEEEEeCChhhhhHHHHh--hc-eE
Confidence                                             11356788888754    3457788888888999999987  54 56


Q ss_pred             EEeCCCCHHHHHHHHHHhhC
Q 009640          389 VSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       389 I~~~~p~~~~r~~i~~~~l~  408 (530)
                      |+|..++.++....+...+.
T Consensus       181 vef~~l~~~ei~~~L~~i~~  200 (620)
T PRK14954        181 FNFKRIPLDEIQSQLQMICR  200 (620)
T ss_pred             EecCCCCHHHHHHHHHHHHH
Confidence            99999999888877766554

>PRK08727 hypothetical protein; Validated

Probab=99.48  E-value=1.3e-12  Score=128.99  Aligned_cols=186  Identities=20%  Similarity=0.260  Sum_probs=116.5

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      ++.....+|++++..+.-   ....+.....        | .+...++||||||||||+|+.|+|+++   +..+..+++
T Consensus        10 ~~~~~~~~f~~f~~~~~n---~~~~~~~~~~--------~-~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~   77 (233)
T PRK08727         10 LRYPSDQRFDSYIAAPDG---LLAQLQALAA--------G-QSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPL   77 (233)
T ss_pred             CCCCCcCChhhccCCcHH---HHHHHHHHHh--------c-cCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeH
Confidence            445667789998766542   1222222111        1 123469999999999999999998876   455556665


Q ss_pred             CccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          262 TKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       262 ~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                      ....  ..+.+.+....+..+|+|||||.+..                                            ....
T Consensus        78 ~~~~--~~~~~~~~~l~~~dlLiIDDi~~l~~--------------------------------------------~~~~  111 (233)
T PRK08727         78 QAAA--GRLRDALEALEGRSLVALDGLESIAG--------------------------------------------QRED  111 (233)
T ss_pred             HHhh--hhHHHHHHHHhcCCEEEEeCcccccC--------------------------------------------ChHH
Confidence            4432  34556666677788999999998721                                            1112


Q ss_pred             hhhHHHHhhhccCCccCCCCCeEEEEEeC-CCCCC---ChhhhcCCce--eEEEEeCCCCHHHHHHHHHHhhCCcCccch
Q 009640          342 RVTLSGLLNFTDGLWSCCSEEKIIVFTTN-HRDSV---DPALIRCGRM--DVHVSLGTCGPHAFKVLAKNYLGIESHHAL  415 (530)
Q Consensus       342 ~~~ls~LLn~lDgl~s~~~~~~ivI~TTN-~~~~L---DpALlRpGR~--d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~  415 (530)
                      ...+-.++|.+.   .   .+.-||+|+| .|..+   +|+|.+  ||  ...+.++.|+.+++..+++......     
T Consensus       112 ~~~lf~l~n~~~---~---~~~~vI~ts~~~p~~l~~~~~dL~S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~-----  178 (233)
T PRK08727        112 EVALFDFHNRAR---A---AGITLLYTARQMPDGLALVLPDLRS--RLAQCIRIGLPVLDDVARAAVLRERAQRR-----  178 (233)
T ss_pred             HHHHHHHHHHHH---H---cCCeEEEECCCChhhhhhhhHHHHH--HHhcCceEEecCCCHHHHHHHHHHHHHHc-----
Confidence            233444555442   1   2233555555 66655   799998  86  5789999999999999998754321     


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHH
Q 009640          416 FDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKE  451 (530)
Q Consensus       416 ~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~  451 (530)
                                ...+++..+..++.+..+|...++..
T Consensus       179 ----------~l~l~~e~~~~La~~~~rd~r~~l~~  204 (233)
T PRK08727        179 ----------GLALDEAAIDWLLTHGERELAGLVAL  204 (233)
T ss_pred             ----------CCCCCHHHHHHHHHhCCCCHHHHHHH
Confidence                      23355555555555555566666443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.47  E-value=5.9e-13  Score=153.42  Aligned_cols=157  Identities=17%  Similarity=0.240  Sum_probs=112.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEE
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVY  257 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~  257 (530)
                      ..+..++.++|.++..+.+++.+    .++         .+.+.+|+||||||||++++++|..+          ++.++
T Consensus       172 ~r~~~l~~vigr~~ei~~~i~iL----~r~---------~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~  238 (857)
T PRK10865        172 AEQGKLDPVIGRDEEIRRTIQVL----QRR---------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVL  238 (857)
T ss_pred             HhcCCCCcCCCCHHHHHHHHHHH----hcC---------CcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEE
Confidence            34667889999887655554433    222         14689999999999999999999988          78888


Q ss_pred             EEecCccCC--------hHHHHHHHHhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          258 DLELTKVTD--------NSELRALLLQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       258 ~l~l~~~~~--------~~~L~~l~~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      .++++.+..        +..++.+|...   ..++||||||||.+.+...                              
T Consensus       239 ~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~------------------------------  288 (857)
T PRK10865        239 ALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGK------------------------------  288 (857)
T ss_pred             EEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCC------------------------------
Confidence            888776521        23577777653   5689999999999852110                              


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHh-hhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHH
Q 009640          327 STCGNNNNNNGEESGRVTLSGLL-NFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFK  400 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LL-n~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~  400 (530)
                               ..   .....+.+| ..+   .   .+++.+|+||+..+     .+|+||.|  ||+ .|.++.|+.+++.
T Consensus       289 ---------~~---~~~d~~~~lkp~l---~---~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~  347 (857)
T PRK10865        289 ---------AD---GAMDAGNMLKPAL---A---RGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTI  347 (857)
T ss_pred             ---------Cc---cchhHHHHhcchh---h---cCCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHH
Confidence                     00   001112222 222   1   46789999999887     48999999  998 5899999999999


Q ss_pred             HHHHHhhC
Q 009640          401 VLAKNYLG  408 (530)
Q Consensus       401 ~i~~~~l~  408 (530)
                      .|++.+..
T Consensus       348 ~iL~~l~~  355 (857)
T PRK10865        348 AILRGLKE  355 (857)
T ss_pred             HHHHHHhh
Confidence            99987654

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.47  E-value=2e-12  Score=127.77  Aligned_cols=157  Identities=18%  Similarity=0.184  Sum_probs=97.3

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---CcEEEEecC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---YDVYDLELT  262 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~  262 (530)
                      ...+..+|+++.-..  -+.+...+..+...+.         .+.++||||||||||+|+.|+|+++.   ..+..+++.
T Consensus        14 ~~~~~~~fd~f~~~~--n~~a~~~l~~~~~~~~---------~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~   82 (235)
T PRK08084         14 YLPDDETFASFYPGD--NDSLLAALQNALRQEH---------SGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLD   82 (235)
T ss_pred             CCCCcCCccccccCc--cHHHHHHHHHHHhCCC---------CCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHH
Confidence            355677899886431  2234455555443221         35799999999999999999999874   445555554


Q ss_pred             ccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchh
Q 009640          263 KVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGR  342 (530)
Q Consensus       263 ~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (530)
                      ....  ...+++....+-.+|+|||||.+-                                            ......
T Consensus        83 ~~~~--~~~~~~~~~~~~dlliiDdi~~~~--------------------------------------------~~~~~~  116 (235)
T PRK08084         83 KRAW--FVPEVLEGMEQLSLVCIDNIECIA--------------------------------------------GDELWE  116 (235)
T ss_pred             HHhh--hhHHHHHHhhhCCEEEEeChhhhc--------------------------------------------CCHHHH
Confidence            3221  122233333334689999999872                                            111123


Q ss_pred             hhHHHHhhhccCCccCCCCC-eEEEEEeCCCCC---CChhhhcCCcee--EEEEeCCCCHHHHHHHHHHh
Q 009640          343 VTLSGLLNFTDGLWSCCSEE-KIIVFTTNHRDS---VDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       343 ~~ls~LLn~lDgl~s~~~~~-~ivI~TTN~~~~---LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~  406 (530)
                      ..+-.++|.+   ..  .+. .+|+.+++.|..   +.|.|.+  |+.  ..+.+..|+.+++..+++..
T Consensus       117 ~~lf~l~n~~---~e--~g~~~li~ts~~~p~~l~~~~~~L~S--Rl~~g~~~~l~~~~~~~~~~~l~~~  179 (235)
T PRK08084        117 MAIFDLYNRI---LE--SGRTRLLITGDRPPRQLNLGLPDLAS--RLDWGQIYKLQPLSDEEKLQALQLR  179 (235)
T ss_pred             HHHHHHHHHH---HH--cCCCeEEEeCCCChHHcCcccHHHHH--HHhCCceeeecCCCHHHHHHHHHHH
Confidence            3344444443   21  123 455545555555   5799999  775  88999999999999998753

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

Probab=99.47  E-value=4.1e-13  Score=151.87  Aligned_cols=153  Identities=20%  Similarity=0.294  Sum_probs=104.1

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecC
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELT  262 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~  262 (530)
                      ++.++|.++..+.+++.+..    +         .+.++||+||||||||++++++|...          +..+|.+++.
T Consensus       185 ~~~liGR~~ei~~~i~iL~r----~---------~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~  251 (758)
T PRK11034        185 IDPLIGREKELERAIQVLCR----R---------RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG  251 (758)
T ss_pred             CCcCcCCCHHHHHHHHHHhc----c---------CCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHH
Confidence            45667766655555553322    1         24678999999999999999999874          5667777655


Q ss_pred             ccC--------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          263 KVT--------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       263 ~~~--------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      .+.        .+..++.++...  ..++||||||||.+++...                                    
T Consensus       252 ~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~------------------------------------  295 (758)
T PRK11034        252 SLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGA------------------------------------  295 (758)
T ss_pred             HHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCC------------------------------------
Confidence            432        134466666543  5689999999999863110                                    


Q ss_pred             CCCCCCcchhhhHHHHhh-hccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          333 NNNNGEESGRVTLSGLLN-FTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn-~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                          ... ....+..+|. .+.      .+++.+|++||.++     .+||||.|  ||+ .|+++.|+.+++..|++.+
T Consensus       296 ----~~~-g~~d~~nlLkp~L~------~g~i~vIgATt~~E~~~~~~~D~AL~r--RFq-~I~v~ePs~~~~~~IL~~~  361 (758)
T PRK11034        296 ----ASG-GQVDAANLIKPLLS------SGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGL  361 (758)
T ss_pred             ----CCC-cHHHHHHHHHHHHh------CCCeEEEecCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHH
Confidence                000 1111222222 221      46788999999875     57999999  996 6999999999999999876


Q ss_pred             hC
Q 009640          407 LG  408 (530)
Q Consensus       407 l~  408 (530)
                      ..
T Consensus       362 ~~  363 (758)
T PRK11034        362 KP  363 (758)
T ss_pred             HH
Confidence            53

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.46  E-value=1.5e-12  Score=144.71  Aligned_cols=156  Identities=15%  Similarity=0.269  Sum_probs=112.9

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------  254 (530)
                      ..++|.+|++|+|++.+++.|...+..    ..        ....||||||||||||++++++|+.++.           
T Consensus         8 ~kyRP~~~~eiiGq~~~~~~L~~~i~~----~~--------i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~   75 (585)
T PRK14950          8 RKWRSQTFAELVGQEHVVQTLRNAIAE----GR--------VAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCG   75 (585)
T ss_pred             HHhCCCCHHHhcCCHHHHHHHHHHHHh----CC--------CceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence            456899999999999988877665532    11        1346899999999999999999998742           


Q ss_pred             --------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          255 --------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       255 --------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                    +++.++.+...+..+++.+....      ...-||||||+|.+-                      
T Consensus        76 ~c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~----------------------  133 (585)
T PRK14950         76 TCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLS----------------------  133 (585)
T ss_pred             cCHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCC----------------------
Confidence                          34444443334455666665432      345799999999871                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ...++.||..|+..    ....+||++|+..+.+.+.+.+  |+ ..++|..+
T Consensus       134 ---------------------------~~a~naLLk~LEep----p~~tv~Il~t~~~~kll~tI~S--R~-~~i~f~~l  179 (585)
T PRK14950        134 ---------------------------TAAFNALLKTLEEP----PPHAIFILATTEVHKVPATILS--RC-QRFDFHRH  179 (585)
T ss_pred             ---------------------------HHHHHHHHHHHhcC----CCCeEEEEEeCChhhhhHHHHh--cc-ceeeCCCC
Confidence                                       12456788888754    3457888888888889888887  65 35889999


Q ss_pred             CHHHHHHHHHHhhCC
Q 009640          395 GPHAFKVLAKNYLGI  409 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~  409 (530)
                      +..+...++...+..
T Consensus       180 ~~~el~~~L~~~a~~  194 (585)
T PRK14950        180 SVADMAAHLRKIAAA  194 (585)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            998888877766543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.45  E-value=7.1e-12  Score=132.86  Aligned_cols=158  Identities=16%  Similarity=0.191  Sum_probs=107.4

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEecCccCC
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLELTKVTD  266 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l~~~~~  266 (530)
                      ..+.+.+-++..++|...+...+.+..         +..+++|||||||||++++.+++++     +..++.+++....+
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~~---------~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~   98 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSR---------PLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRT   98 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCCC---------CCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCC
Confidence            446677777777777777766554321         3578999999999999999999987     46677777654322


Q ss_pred             h-----------------------HHHHHH----HHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhh
Q 009640          267 N-----------------------SELRAL----LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKE  319 (530)
Q Consensus       267 ~-----------------------~~L~~l----~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~  319 (530)
                      .                       .++...    +.....+.||+|||+|.+..                          
T Consensus        99 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~--------------------------  152 (394)
T PRK00411         99 RYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFE--------------------------  152 (394)
T ss_pred             HHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhc--------------------------
Confidence            1                       111111    11224568999999998730                          


Q ss_pred             hccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC---CCCChhhhcCCce-eEEEEeCCCC
Q 009640          320 MGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR---DSVDPALIRCGRM-DVHVSLGTCG  395 (530)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~---~~LDpALlRpGR~-d~~I~~~~p~  395 (530)
                                         ......+..|++.++...   +.++.+|+++|..   +.++|.+.+  |+ ...|+|++++
T Consensus       153 -------------------~~~~~~l~~l~~~~~~~~---~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~  208 (394)
T PRK00411        153 -------------------KEGNDVLYSLLRAHEEYP---GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYT  208 (394)
T ss_pred             -------------------cCCchHHHHHHHhhhccC---CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCC
Confidence                               001235667777665442   2367788888876   357888776  55 3679999999


Q ss_pred             HHHHHHHHHHhhC
Q 009640          396 PHAFKVLAKNYLG  408 (530)
Q Consensus       396 ~~~r~~i~~~~l~  408 (530)
                      .++...+++..+.
T Consensus       209 ~~e~~~il~~r~~  221 (394)
T PRK00411        209 ADEIFDILKDRVE  221 (394)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988764

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.45  E-value=3.2e-12  Score=142.17  Aligned_cols=157  Identities=17%  Similarity=0.311  Sum_probs=118.0

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----------  253 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----------  253 (530)
                      ...++|.+|++|+|++.+++.+...+..    .        ..+..||||||+|+|||++++++|+.+.           
T Consensus         8 ~~kyRP~~f~~viGq~~~~~~L~~~i~~----~--------~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~C   75 (614)
T PRK14971          8 ARKYRPSTFESVVGQEALTTTLKNAIAT----N--------KLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEAC   75 (614)
T ss_pred             HHHHCCCCHHHhcCcHHHHHHHHHHHHc----C--------CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCC
Confidence            4456889999999999988877765531    1        1246799999999999999999999874           


Q ss_pred             --------------CcEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCcccccccc
Q 009640          254 --------------YDVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKR  313 (530)
Q Consensus       254 --------------~~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r  313 (530)
                                    .+++.++.....+-.+++.++..+      ...-|++|||+|.+-                     
T Consensus        76 g~C~sC~~~~~~~~~n~~~ld~~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls---------------------  134 (614)
T PRK14971         76 NECESCVAFNEQRSYNIHELDAASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLS---------------------  134 (614)
T ss_pred             CcchHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCC---------------------
Confidence                          455666555444456788777654      234599999999871                     


Q ss_pred             chhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCC
Q 009640          314 SSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGT  393 (530)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~  393 (530)
                                                  ....+.||..|+..    .+..++|++|+.+.+|-++|++  |+ ..++|..
T Consensus       135 ----------------------------~~a~naLLK~LEep----p~~tifIL~tt~~~kIl~tI~S--Rc-~iv~f~~  179 (614)
T PRK14971        135 ----------------------------QAAFNAFLKTLEEP----PSYAIFILATTEKHKILPTILS--RC-QIFDFNR  179 (614)
T ss_pred             ----------------------------HHHHHHHHHHHhCC----CCCeEEEEEeCCchhchHHHHh--hh-heeecCC
Confidence                                        12456888888854    3557788888888999999998  65 4499999


Q ss_pred             CCHHHHHHHHHHhhCC
Q 009640          394 CGPHAFKVLAKNYLGI  409 (530)
Q Consensus       394 p~~~~r~~i~~~~l~~  409 (530)
                      ++.++....+...+..
T Consensus       180 ls~~ei~~~L~~ia~~  195 (614)
T PRK14971        180 IQVADIVNHLQYVASK  195 (614)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999888887766543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.44  E-value=3e-12  Score=125.54  Aligned_cols=153  Identities=15%  Similarity=0.210  Sum_probs=96.2

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      .+...+.+|+++.....  +.+...+..+..        +....++++|+||||||||+|++++++++   +..++.++.
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            45567788999873321  223333444332        12234689999999999999999999986   566777765


Q ss_pred             CccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          262 TKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       262 ~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                      ....      ..+.......+|+|||+|.+-                                              ...
T Consensus        79 ~~~~------~~~~~~~~~~~liiDdi~~l~----------------------------------------------~~~  106 (227)
T PRK08903         79 ASPL------LAFDFDPEAELYAVDDVERLD----------------------------------------------DAQ  106 (227)
T ss_pred             HHhH------HHHhhcccCCEEEEeChhhcC----------------------------------------------chH
Confidence            5432      122334567899999999861                                              001


Q ss_pred             hhhHHHHhhhccCCccCCCCCeEEEEEeCCCC---CCChhhhcCCce--eEEEEeCCCCHHHHHHHHHHh
Q 009640          342 RVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD---SVDPALIRCGRM--DVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       342 ~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~---~LDpALlRpGR~--d~~I~~~~p~~~~r~~i~~~~  406 (530)
                      .   ..|+..++....  ....++|+|++.+.   .+.+.|.+  |+  ...|+++.|+...+..++..+
T Consensus       107 ~---~~L~~~~~~~~~--~~~~~vl~~~~~~~~~~~l~~~L~s--r~~~~~~i~l~pl~~~~~~~~l~~~  169 (227)
T PRK08903        107 Q---IALFNLFNRVRA--HGQGALLVAGPAAPLALPLREDLRT--RLGWGLVYELKPLSDADKIAALKAA  169 (227)
T ss_pred             H---HHHHHHHHHHHH--cCCcEEEEeCCCCHHhCCCCHHHHH--HHhcCeEEEecCCCHHHHHHHHHHH
Confidence            2   233444433322  23345666666432   35677876  66  579999999998887777654

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.44  E-value=7.3e-13  Score=143.04  Aligned_cols=167  Identities=19%  Similarity=0.306  Sum_probs=105.2

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEE
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDL  259 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l  259 (530)
                      ....+..+|++++..+.-.. ....+..+...+      |..+ ++++||||||||||+|+.|+|+++     +..++.+
T Consensus       113 ~~l~~~~tfd~fv~g~~n~~-a~~~~~~~~~~~------~~~~-~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi  184 (450)
T PRK00149        113 SPLNPKYTFDNFVVGKSNRL-AHAAALAVAENP------GKAY-NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYV  184 (450)
T ss_pred             cCCCCCCcccccccCCCcHH-HHHHHHHHHhCc------CccC-CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEE
Confidence            34556779999754333222 333344444332      2222 579999999999999999999998     4567777


Q ss_pred             ecCccCCh-------HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          260 ELTKVTDN-------SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       260 ~l~~~~~~-------~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      +...+...       .....+.....+..+|+|||||.+.+                                       
T Consensus       185 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~---------------------------------------  225 (450)
T PRK00149        185 TSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAG---------------------------------------  225 (450)
T ss_pred             EHHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcC---------------------------------------
Confidence            76554211       11122333345688999999998721                                       


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC---CChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhh
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l  407 (530)
                           ..   .+...|+..++.+...  +..+||.++..|..   ++++|.+  ||.  ..+++..|+.++|..|++..+
T Consensus       226 -----~~---~~~~~l~~~~n~l~~~--~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~  293 (450)
T PRK00149        226 -----KE---RTQEEFFHTFNALHEA--GKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKA  293 (450)
T ss_pred             -----CH---HHHHHHHHHHHHHHHC--CCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHH
Confidence                 11   1223444444444331  23344444445544   6789998  885  689999999999999999887


Q ss_pred             CCc
Q 009640          408 GIE  410 (530)
Q Consensus       408 ~~~  410 (530)
                      ...
T Consensus       294 ~~~  296 (450)
T PRK00149        294 EEE  296 (450)
T ss_pred             HHc
Confidence            643

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.44  E-value=9.6e-13  Score=140.27  Aligned_cols=194  Identities=16%  Similarity=0.227  Sum_probs=113.9

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEe
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLE  260 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~  260 (530)
                      +..+..+|++++..+.-. .....+..+...+      |.. ..+++||||||||||+|+.|+|+++     +..++.++
T Consensus       102 ~l~~~~tfd~fi~g~~n~-~a~~~~~~~~~~~------~~~-~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       102 PLNPKYTFDNFVVGKSNR-LAHAAALAVAENP------GKA-YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CCCCCCcccccccCCcHH-HHHHHHHHHHhCc------Ccc-CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE
Confidence            345667899954323222 2333344444432      111 2578999999999999999999988     56777777


Q ss_pred             cCccCCh-------HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCC
Q 009640          261 LTKVTDN-------SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNN  333 (530)
Q Consensus       261 l~~~~~~-------~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~  333 (530)
                      ...+...       ..+..+........+|+|||||.+.+                                        
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~----------------------------------------  213 (405)
T TIGR00362       174 SEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAG----------------------------------------  213 (405)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcC----------------------------------------
Confidence            6543210       01112222334578999999998721                                        


Q ss_pred             CCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC---CChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhC
Q 009640          334 NNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       334 ~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                          ..   .+...|+..++.+..  .+..+||.+++.|..   +++.|.+  ||.  ..++++.|+.++|..|++..+.
T Consensus       214 ----~~---~~~~~l~~~~n~~~~--~~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~pd~~~r~~il~~~~~  282 (405)
T TIGR00362       214 ----KE---RTQEEFFHTFNALHE--NGKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVDIEPPDLETRLAILQKKAE  282 (405)
T ss_pred             ----CH---HHHHHHHHHHHHHHH--CCCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEEeCCCCHHHHHHHHHHHHH
Confidence                11   112234444444433  123444444445544   5688888  886  5899999999999999998876


Q ss_pred             CcCccchHHHHHHHHHhCCCCCHHHHHHHHH
Q 009640          409 IESHHALFDVVESCIRAGGALTPAQIGEVLL  439 (530)
Q Consensus       409 ~~~~~~~~~~i~~l~~~~~~~spadi~~~l~  439 (530)
                      ........+.++-++. ...-+..++...+.
T Consensus       283 ~~~~~l~~e~l~~ia~-~~~~~~r~l~~~l~  312 (405)
T TIGR00362       283 EEGLELPDEVLEFIAK-NIRSNVRELEGALN  312 (405)
T ss_pred             HcCCCCCHHHHHHHHH-hcCCCHHHHHHHHH
Confidence            5443322333444443 23344555555443

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.43  E-value=2.2e-12  Score=149.04  Aligned_cols=158  Identities=16%  Similarity=0.192  Sum_probs=109.9

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEE
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVY  257 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~  257 (530)
                      ..+..++.++|.++..+.+++.+    .++         .+...+|+||||||||+++.++|..+          +++++
T Consensus       167 ~~~~~~~~~igr~~ei~~~~~~l----~r~---------~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~  233 (852)
T TIGR03346       167 AREGKLDPVIGRDEEIRRTIQVL----SRR---------TKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLL  233 (852)
T ss_pred             hhCCCCCcCCCcHHHHHHHHHHH----hcC---------CCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEE
Confidence            35667888999887655544433    222         24688999999999999999999986          67888


Q ss_pred             EEecCccC--------ChHHHHHHHHhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          258 DLELTKVT--------DNSELRALLLQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       258 ~l~l~~~~--------~~~~L~~l~~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      .+++..+.        .+..++.+|...   ..++||||||||.+++...                              
T Consensus       234 ~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~------------------------------  283 (852)
T TIGR03346       234 ALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGK------------------------------  283 (852)
T ss_pred             EeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCC------------------------------
Confidence            88776542        123577777654   4689999999999852100                              


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHH
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKV  401 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~  401 (530)
                                 ........+-|...+    .  .+.+.+|++||..+     .+|+||.|  ||.. |.++.|+.+++..
T Consensus       284 -----------~~~~~d~~~~Lk~~l----~--~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~~-i~v~~p~~~~~~~  343 (852)
T TIGR03346       284 -----------AEGAMDAGNMLKPAL----A--RGELHCIGATTLDEYRKYIEKDAALER--RFQP-VFVDEPTVEDTIS  343 (852)
T ss_pred             -----------CcchhHHHHHhchhh----h--cCceEEEEeCcHHHHHHHhhcCHHHHh--cCCE-EEeCCCCHHHHHH
Confidence                       000111112222222    1  46788899888764     47999999  9975 8999999999999


Q ss_pred             HHHHhhC
Q 009640          402 LAKNYLG  408 (530)
Q Consensus       402 i~~~~l~  408 (530)
                      |++.+..
T Consensus       344 iL~~~~~  350 (852)
T TIGR03346       344 ILRGLKE  350 (852)
T ss_pred             HHHHHHH
Confidence            9987643

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.

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.43  E-value=3.2e-12  Score=135.63  Aligned_cols=98  Identities=24%  Similarity=0.258  Sum_probs=68.3

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhh--hcC-CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC-----
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHR--VGR-AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD-----  266 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~--~g~-~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~-----  266 (530)
                      .|+|++++|+.+...+....++-.....  -.. ..+.++||+||||||||++|+++|..++.+++.++.+.+..     
T Consensus        72 ~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~gyvG  151 (412)
T PRK05342         72 YVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVG  151 (412)
T ss_pred             HeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccCCccc
Confidence            3799999999887766543322111000  011 23578999999999999999999999999999998876532     


Q ss_pred             ---hHHHHHHHHh------cCCCeEEEEcCccchh
Q 009640          267 ---NSELRALLLQ------TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       267 ---~~~L~~l~~~------~~~~sII~IDeID~~~  292 (530)
                         ...+..++..      ...++||||||||.+.
T Consensus       152 ~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~  186 (412)
T PRK05342        152 EDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIA  186 (412)
T ss_pred             chHHHHHHHHHHhccccHHHcCCcEEEEechhhhc
Confidence               1223444332      2468999999999983

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

Probab=99.42  E-value=1.2e-12  Score=132.00  Aligned_cols=150  Identities=20%  Similarity=0.294  Sum_probs=104.7

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc---EEEEecCc
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD---VYDLELTK  263 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~---i~~l~l~~  263 (530)
                      .-+|.++++.+|++++.-+ ...+..++...+         -..++||||||||||+||+.||+...-+   |+.++.++
T Consensus       131 rmRPktL~dyvGQ~hlv~q-~gllrs~ieq~~---------ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~  200 (554)
T KOG2028|consen  131 RMRPKTLDDYVGQSHLVGQ-DGLLRSLIEQNR---------IPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATN  200 (554)
T ss_pred             hcCcchHHHhcchhhhcCc-chHHHHHHHcCC---------CCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccc
Confidence            3578899999998887554 344444444332         3579999999999999999999988655   66666555


Q ss_pred             cCChHHHHHHHHhc-------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          264 VTDNSELRALLLQT-------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       264 ~~~~~~L~~l~~~~-------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      . +-.++|.+|.++       ..+.|||||||+.+-.                                           
T Consensus       201 a-~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNk-------------------------------------------  236 (554)
T KOG2028|consen  201 A-KTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNK-------------------------------------------  236 (554)
T ss_pred             c-chHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhh-------------------------------------------
Confidence            4 345788888875       4789999999998721                                           


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEE-Ee-CCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVF-TT-NHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~-TT-N~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                            .....||-.++      .+.+++|+ || |..-.|..||+.  |+- .+.+.....++...|+.+
T Consensus       237 ------sQQD~fLP~VE------~G~I~lIGATTENPSFqln~aLlS--RC~-VfvLekL~~n~v~~iL~r  292 (554)
T KOG2028|consen  237 ------SQQDTFLPHVE------NGDITLIGATTENPSFQLNAALLS--RCR-VFVLEKLPVNAVVTILMR  292 (554)
T ss_pred             ------hhhhcccceec------cCceEEEecccCCCccchhHHHHh--ccc-eeEeccCCHHHHHHHHHH
Confidence                  01112444443      35577777 44 445689999998  553 356777778888888766

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.42  E-value=7.3e-12  Score=120.44  Aligned_cols=173  Identities=19%  Similarity=0.284  Sum_probs=138.5

Q ss_pred             ccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEE
Q 009640          182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYD  258 (530)
Q Consensus       182 w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~  258 (530)
                      ...++..++..+.+|+|.+.+|+.+.+....|+....         ...+||||..|||||||++|+-+++   +..++.
T Consensus        48 L~pv~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~p---------ANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVE  118 (287)
T COG2607          48 LEPVPDPDPIDLADLVGVDRQKEALVRNTEQFAEGLP---------ANNVLLWGARGTGKSSLVKALLNEYADEGLRLVE  118 (287)
T ss_pred             ccCCCCCCCcCHHHHhCchHHHHHHHHHHHHHHcCCc---------ccceEEecCCCCChHHHHHHHHHHHHhcCCeEEE
Confidence            4567888889999999999999999999999998543         3789999999999999999999987   667788


Q ss_pred             EecCccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          259 LELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       259 l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                      |+-.++.+-..|..++...+.+-|||+||+--  +                                           .+
T Consensus       119 V~k~dl~~Lp~l~~~Lr~~~~kFIlFcDDLSF--e-------------------------------------------~g  153 (287)
T COG2607         119 VDKEDLATLPDLVELLRARPEKFILFCDDLSF--E-------------------------------------------EG  153 (287)
T ss_pred             EcHHHHhhHHHHHHHHhcCCceEEEEecCCCC--C-------------------------------------------CC
Confidence            87777777778888888889999999999842  1                                           01


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhh--------------------cCCceeEEEEeCCCCHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALI--------------------RCGRMDVHVSLGTCGPHA  398 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALl--------------------RpGR~d~~I~~~~p~~~~  398 (530)
                         ......|-..|||--.....+++|.+|+|+-.-|+.-+.                    =..||...+.|..|+.++
T Consensus       154 ---d~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~  230 (287)
T COG2607         154 ---DDAYKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDE  230 (287)
T ss_pred             ---chHHHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHH
Confidence               113345667778766666789999999999766653221                    123999999999999999


Q ss_pred             HHHHHHHhhCCcC
Q 009640          399 FKVLAKNYLGIES  411 (530)
Q Consensus       399 r~~i~~~~l~~~~  411 (530)
                      ...|+.+|.....
T Consensus       231 YL~~V~~~a~~~~  243 (287)
T COG2607         231 YLKIVDHYAKHFG  243 (287)
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999875433

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

Probab=99.40  E-value=4.9e-12  Score=143.14  Aligned_cols=159  Identities=14%  Similarity=0.251  Sum_probs=112.0

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALL  274 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~  274 (530)
                      .|+|+++.++.|.+.+.....+-.   .-+ .+...+||+||||||||.+|+++|..++.+++.++++.......+.+++
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---HEH-KPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLI  534 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhcccc---CCC-CCcceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHc
Confidence            368899988888888865532110   001 1123699999999999999999999999999999887764322222222


Q ss_pred             ---------------Hh---cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          275 ---------------LQ---TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       275 ---------------~~---~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                                     ..   ....|||+|||||.+-                                            
T Consensus       535 G~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~--------------------------------------------  570 (758)
T PRK11034        535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAH--------------------------------------------  570 (758)
T ss_pred             CCCCCcccccccchHHHHHHhCCCcEEEeccHhhhh--------------------------------------------
Confidence                           11   2356999999999871                                            


Q ss_pred             CCcchhhhHHHHhhhccCC-ccCC------CCCeEEEEEeCCC-------------------------CCCChhhhcCCc
Q 009640          337 GEESGRVTLSGLLNFTDGL-WSCC------SEEKIIVFTTNHR-------------------------DSVDPALIRCGR  384 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl-~s~~------~~~~ivI~TTN~~-------------------------~~LDpALlRpGR  384 (530)
                           ....+.||+.||.- -...      -.+.|||+|||.-                         ..+.|.|+.  |
T Consensus       571 -----~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--R  643 (758)
T PRK11034        571 -----PDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--R  643 (758)
T ss_pred             -----HHHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--c
Confidence                 22566777777632 1100      1357899999932                         135677887  9


Q ss_pred             eeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          385 MDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       385 ~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      +|..|.|++.+.+....|+..++.
T Consensus       644 id~ii~f~~L~~~~l~~I~~~~l~  667 (758)
T PRK11034        644 LDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_pred             CCEEEEcCCCCHHHHHHHHHHHHH
Confidence            999999999999999999987764

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.39  E-value=5.3e-12  Score=145.54  Aligned_cols=151  Identities=19%  Similarity=0.258  Sum_probs=107.0

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEec
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLEL  261 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l  261 (530)
                      .++.++|.++..+.+++.+.    +         ..++++||+||||||||+++.++|..+          +..++.+++
T Consensus       177 ~~~~~igr~~ei~~~~~~L~----r---------~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~  243 (821)
T CHL00095        177 NLDPVIGREKEIERVIQILG----R---------RTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDI  243 (821)
T ss_pred             CCCCCCCcHHHHHHHHHHHc----c---------cccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeH
Confidence            35677887776666666442    2         225789999999999999999999987          478999987


Q ss_pred             CccC------C--hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          262 TKVT------D--NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       262 ~~~~------~--~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      +.+.      +  +..++.++..+  ..++||||||||.+++..+                                   
T Consensus       244 ~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~-----------------------------------  288 (821)
T CHL00095        244 GLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGA-----------------------------------  288 (821)
T ss_pred             HHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCC-----------------------------------
Confidence            6542      1  34678888765  4689999999999863110                                   


Q ss_pred             CCCCCCCcchhhhHHHHh-hhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          332 NNNNNGEESGRVTLSGLL-NFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LL-n~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                          ..   .....+.+| ..+.      .+++.+|++||..+     ..||+|.|  ||.. |.++.|+.++...|++.
T Consensus       289 ----~~---g~~~~a~lLkp~l~------rg~l~~IgaTt~~ey~~~ie~D~aL~r--Rf~~-I~v~ep~~~e~~aILr~  352 (821)
T CHL00095        289 ----AE---GAIDAANILKPALA------RGELQCIGATTLDEYRKHIEKDPALER--RFQP-VYVGEPSVEETIEILFG  352 (821)
T ss_pred             ----CC---CcccHHHHhHHHHh------CCCcEEEEeCCHHHHHHHHhcCHHHHh--cceE-EecCCCCHHHHHHHHHH
Confidence                00   011222333 2222      46688888888764     47999999  9975 89999999998888765


Q ss_pred             h
Q 009640          406 Y  406 (530)
Q Consensus       406 ~  406 (530)
                      .
T Consensus       353 l  353 (821)
T CHL00095        353 L  353 (821)
T ss_pred             H
Confidence            4

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.38  E-value=8.3e-12  Score=127.48  Aligned_cols=162  Identities=12%  Similarity=0.109  Sum_probs=105.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHH------------------HHHh-cCCCeEEEEcCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRA------------------LLLQ-TTNRSIIVIEDI  288 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~------------------l~~~-~~~~sII~IDeI  288 (530)
                      .+.+||.||||||||++++++|..++.+++.++++......++..                  .|.. ...+.+|++|||
T Consensus        64 ~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~~g~illlDEi  143 (327)
T TIGR01650        64 DRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQHNVALCFDEY  143 (327)
T ss_pred             CCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHhCCeEEEechh
Confidence            468999999999999999999999999999998766533222111                  1111 246789999999


Q ss_pred             cchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc--------CCc--cC
Q 009640          289 DCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD--------GLW--SC  358 (530)
Q Consensus       289 D~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD--------gl~--s~  358 (530)
                      |.+-                                                 ..+++.|...||        +..  -.
T Consensus       144 n~a~-------------------------------------------------p~~~~~L~~lLE~~~~l~i~~~~~~i~  174 (327)
T TIGR01650       144 DAGR-------------------------------------------------PDVMFVIQRVLEAGGKLTLLDQNRVIR  174 (327)
T ss_pred             hccC-------------------------------------------------HHHHHHHHHHhccCCeEEECCCceEec
Confidence            9761                                                 112233333332        100  00


Q ss_pred             CCCCeEEEEEeCCCC------------CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCc---cchHHHHHHHH
Q 009640          359 CSEEKIIVFTTNHRD------------SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESH---HALFDVVESCI  423 (530)
Q Consensus       359 ~~~~~ivI~TTN~~~------------~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~---~~~~~~i~~l~  423 (530)
                      +.....||+|+|..+            .|++|++.  ||-..+.++||+.++-..|+.........   ....+.+-+++
T Consensus       175 ~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~~~~~~~~~~~i~~~mV~la  252 (327)
T TIGR01650       175 AHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMD--RWSIVTTLNYLEHDNEAAIVLAKAKGFDDTEGKDIINAMVRVA  252 (327)
T ss_pred             CCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHh--heeeEeeCCCCCHHHHHHHHHhhccCCCccchHHHHHHHHHHH
Confidence            123567899999865            46899999  99999999999999999998765422111   11222222232


Q ss_pred             Hh----------CCCCCHHHHHHHHHH
Q 009640          424 RA----------GGALTPAQIGEVLLR  440 (530)
Q Consensus       424 ~~----------~~~~spadi~~~l~~  440 (530)
                      ..          ..++||..+..+...
T Consensus       253 ~~tR~~~~~~~i~~~~SpR~li~w~~~  279 (327)
T TIGR01650       253 DMTRNAFINGDISTVMSPRTVITWAEN  279 (327)
T ss_pred             HHHHhhhccCCccccccHHHHHHHHHH
Confidence            21          346788777666544

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.38  E-value=6.2e-12  Score=137.68  Aligned_cols=168  Identities=17%  Similarity=0.232  Sum_probs=104.0

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEe
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLE  260 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~  260 (530)
                      .+....+|++++..+.-.. ....+......+      +. +.+.++|||++|||||+|+.|||+++     ++.++.++
T Consensus       280 ~L~~~~TFDnFvvG~sN~~-A~aaa~avae~~------~~-~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit  351 (617)
T PRK14086        280 RLNPKYTFDTFVIGASNRF-AHAAAVAVAEAP------AK-AYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS  351 (617)
T ss_pred             CCCCCCCHhhhcCCCccHH-HHHHHHHHHhCc------cc-cCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee
Confidence            3456678999875443221 222222222221      11 23469999999999999999999987     46777777


Q ss_pred             cCccCCh-------HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCC
Q 009640          261 LTKVTDN-------SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNN  333 (530)
Q Consensus       261 l~~~~~~-------~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~  333 (530)
                      ...+...       ..+..+.....+..+|+||||+.+.+                                        
T Consensus       352 aeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~g----------------------------------------  391 (617)
T PRK14086        352 SEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLED----------------------------------------  391 (617)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccC----------------------------------------
Confidence            6554211       11112222335679999999998731                                        


Q ss_pred             CCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC----CCCChhhhcCCce--eEEEEeCCCCHHHHHHHHHHhh
Q 009640          334 NNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR----DSVDPALIRCGRM--DVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       334 ~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~----~~LDpALlRpGR~--d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                          ....+   ..|++.++.+..   .+.-||+|+|.+    ..|++.|.+  ||  ...+.+..||.+.|..|++..+
T Consensus       392 ----ke~tq---eeLF~l~N~l~e---~gk~IIITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~PD~EtR~aIL~kka  459 (617)
T PRK14086        392 ----KESTQ---EEFFHTFNTLHN---ANKQIVLSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPPELETRIAILRKKA  459 (617)
T ss_pred             ----CHHHH---HHHHHHHHHHHh---cCCCEEEecCCChHhhhhccHHHHh--hhhcCceEEcCCCCHHHHHHHHHHHH
Confidence                11112   233444443332   223355577764    357899999  76  6778999999999999999887


Q ss_pred             CCcCcc
Q 009640          408 GIESHH  413 (530)
Q Consensus       408 ~~~~~~  413 (530)
                      ......
T Consensus       460 ~~r~l~  465 (617)
T PRK14086        460 VQEQLN  465 (617)
T ss_pred             HhcCCC
Confidence            654433

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.38  E-value=9.4e-12  Score=131.56  Aligned_cols=98  Identities=28%  Similarity=0.306  Sum_probs=66.0

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhh----HhhhcCC-CCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC---
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEF----YHRVGRA-WKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD---  266 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~----y~~~g~~-~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~---  266 (530)
                      .|+|+++.++.+...+....++-..    -..-+.+ .+.++||+||||||||++|+++|..++.++..++.+.+..   
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            3589999999887766433322110    0000111 1467999999999999999999999999998887665421   


Q ss_pred             -----hHHHHHHHHh------cCCCeEEEEcCccchh
Q 009640          267 -----NSELRALLLQ------TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       267 -----~~~L~~l~~~------~~~~sII~IDeID~~~  292 (530)
                           ...+..++..      ...++||||||||.+.
T Consensus       158 vG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~  194 (413)
T TIGR00382       158 VGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKIS  194 (413)
T ss_pred             ccccHHHHHHHHHHhCcccHHhcccceEEecccchhc
Confidence                 1224444432      2467899999999873

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.37  E-value=3.6e-12  Score=136.90  Aligned_cols=165  Identities=19%  Similarity=0.303  Sum_probs=101.1

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEe
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLE  260 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~  260 (530)
                      +..+..+|++++..+.-.. ....+..+...+..        ..+++||||||||||+|+.|+|+++     +..++.++
T Consensus        97 ~l~~~~tFdnFv~g~~n~~-a~~~~~~~~~~~~~--------~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~  167 (440)
T PRK14088         97 PLNPDYTFENFVVGPGNSF-AYHAALEVAKNPGR--------YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT  167 (440)
T ss_pred             CCCCCCcccccccCCchHH-HHHHHHHHHhCcCC--------CCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE
Confidence            4456778999875444332 23334444443321        3569999999999999999999987     45677776


Q ss_pred             cCccCCh-------HHHHHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          261 LTKVTDN-------SELRALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       261 l~~~~~~-------~~L~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      ...+...       ..+..+.... .++.+|+|||+|.+.+                                       
T Consensus       168 ~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~---------------------------------------  208 (440)
T PRK14088        168 SEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIG---------------------------------------  208 (440)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcC---------------------------------------
Confidence            5443110       1111222222 2588999999998742                                       


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEe-CCCCC---CChhhhcCCce--eEEEEeCCCCHHHHHHHHHHh
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTT-NHRDS---VDPALIRCGRM--DVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TT-N~~~~---LDpALlRpGR~--d~~I~~~~p~~~~r~~i~~~~  406 (530)
                           ...   +...|+..++.+..  .+. .+|+|| +.|..   +++.|.+  ||  ...+.+..||.+.|..|++..
T Consensus       209 -----~~~---~q~elf~~~n~l~~--~~k-~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~i~~pd~e~r~~IL~~~  275 (440)
T PRK14088        209 -----KTG---VQTELFHTFNELHD--SGK-QIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKKIARKM  275 (440)
T ss_pred             -----cHH---HHHHHHHHHHHHHH--cCC-eEEEECCCCHHHHHHHHHHHhh--HHhcCceEeeCCCCHHHHHHHHHHH
Confidence                 000   11233344443333  123 455555 45554   4577887  55  578899999999999999988


Q ss_pred             hCCcC
Q 009640          407 LGIES  411 (530)
Q Consensus       407 l~~~~  411 (530)
                      +....
T Consensus       276 ~~~~~  280 (440)
T PRK14088        276 LEIEH  280 (440)
T ss_pred             HHhcC
Confidence            76443

>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=99.36  E-value=8.5e-12  Score=121.98  Aligned_cols=164  Identities=19%  Similarity=0.256  Sum_probs=97.7

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEecCc
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLELTK  263 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l~~  263 (530)
                      +..||++++-.+.-+ .....+......+.      . ....++||||+|+|||+|+.||++++     +..+..++...
T Consensus         3 ~~~tFdnfv~g~~N~-~a~~~~~~ia~~~~------~-~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~   74 (219)
T PF00308_consen    3 PKYTFDNFVVGESNE-LAYAAAKAIAENPG------E-RYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEE   74 (219)
T ss_dssp             TT-SCCCS--TTTTH-HHHHHHHHHHHSTT------T-SSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHH
T ss_pred             CCCccccCCcCCcHH-HHHHHHHHHHhcCC------C-CCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHH
Confidence            567899986444322 23333444444432      1 12468999999999999999999986     56677777655


Q ss_pred             cCC-------hHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          264 VTD-------NSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       264 ~~~-------~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      +..       ...+..+......-.+|+|||||.+.+                                           
T Consensus        75 f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~-------------------------------------------  111 (219)
T PF00308_consen   75 FIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAG-------------------------------------------  111 (219)
T ss_dssp             HHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTT-------------------------------------------
T ss_pred             HHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcC-------------------------------------------
Confidence            421       122334445557789999999998731                                           


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC---CChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                       .   ..+...|.+.++.+..  .+..+||.+...|..   ++|.|..  ||.  ..+.+..|+.+.|..|++.......
T Consensus       112 -~---~~~q~~lf~l~n~~~~--~~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~pd~~~r~~il~~~a~~~~  183 (219)
T PF00308_consen  112 -K---QRTQEELFHLFNRLIE--SGKQLILTSDRPPSELSGLLPDLRS--RLSWGLVVELQPPDDEDRRRILQKKAKERG  183 (219)
T ss_dssp             -H---HHHHHHHHHHHHHHHH--TTSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEEEE----HHHHHHHHHHHHHHTT
T ss_pred             -c---hHHHHHHHHHHHHHHh--hCCeEEEEeCCCCccccccChhhhh--hHhhcchhhcCCCCHHHHHHHHHHHHHHhC
Confidence             1   1123344444444333  244555555566665   4678888  764  6899999999999999988765433

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.

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.35  E-value=3e-11  Score=131.17  Aligned_cols=220  Identities=17%  Similarity=0.246  Sum_probs=138.0

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHH---cC--------------hhhHh----hhcCCCCceEEEECCCC
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFA---NG--------------KEFYH----RVGRAWKRGYLLYGPPG  238 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l---~~--------------~~~y~----~~g~~~~rG~LL~GPPG  238 (530)
                      ..|  |..+.|..|.+|.+++.+-+.++.+|..|=   .+              ++.+.    ..+.|.++-+||+||||
T Consensus       259 kLW--Vdky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppG  336 (877)
T KOG1969|consen  259 KLW--VDKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPG  336 (877)
T ss_pred             cee--ecccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCC
Confidence            368  889999999999999999999999887652   11              11111    13577788899999999


Q ss_pred             CChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhc----------CCCeEEEEcCccchhhhhhhhhhcccCCccc
Q 009640          239 SGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQT----------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTT  308 (530)
Q Consensus       239 TGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~----------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~  308 (530)
                      -||||||+.||++.||.+++++.++-.+...+++.+..+          ++|..|||||||-.....             
T Consensus       337 lGKTTLAHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~~~~-------------  403 (877)
T KOG1969|consen  337 LGKTTLAHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAPRAA-------------  403 (877)
T ss_pred             CChhHHHHHHHHhcCceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCcHHH-------------
Confidence            999999999999999999999999988777666554432          579999999999652100             


Q ss_pred             cccccchhhhhhccccc---cccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCce
Q 009640          309 AKTKRSSSIKEMGSRIA---SSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRM  385 (530)
Q Consensus       309 ~~~~r~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~  385 (530)
                              ++-+.+-+.   .++.+...  ..+...+.--+.+|            .|-||+.+|.  ..-|||.----+
T Consensus       404 --------Vdvilslv~a~~k~~~Gkq~--~~~~~rkkkr~~~L------------~RPIICICNd--LYaPaLR~Lr~~  459 (877)
T KOG1969|consen  404 --------VDVILSLVKATNKQATGKQA--KKDKKRKKKRSKLL------------TRPIICICND--LYAPALRPLRPF  459 (877)
T ss_pred             --------HHHHHHHHHhhcchhhcCcc--cchhhhhhhccccc------------cCCEEEEecC--ccchhhhhcccc
Confidence                    000000000   00011100  00001111112222            1458888884  456888632268


Q ss_pred             eEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHH
Q 009640          386 DVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVV  453 (530)
Q Consensus       386 d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~  453 (530)
                      -..|+|..|......+-++.....+...               .-+..|..+|..+.+|.+.|++.|.
T Consensus       460 A~ii~f~~p~~s~Lv~RL~~IC~rE~mr---------------~d~~aL~~L~el~~~DIRsCINtLQ  512 (877)
T KOG1969|consen  460 AEIIAFVPPSQSRLVERLNEICHRENMR---------------ADSKALNALCELTQNDIRSCINTLQ  512 (877)
T ss_pred             eEEEEecCCChhHHHHHHHHHHhhhcCC---------------CCHHHHHHHHHHhcchHHHHHHHHH
Confidence            8899999998876655444444333322               3333444555555566666666543

>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=99.35  E-value=1.3e-11  Score=110.15  Aligned_cols=115  Identities=26%  Similarity=0.382  Sum_probs=79.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHH-----------HHHHhcCCCeEEEEcCccchhh
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELR-----------ALLLQTTNRSIIVIEDIDCSVD  293 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~-----------~l~~~~~~~sII~IDeID~~~~  293 (530)
                      .++++++||||||||++++++++.+   +.+++.++...........           ........+.+|+|||++.+..
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~~~   98 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSR   98 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhhhH
Confidence            4689999999999999999999999   8899998877664332222           1122335789999999997610


Q ss_pred             hhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccC--CCCCeEEEEEeCC
Q 009640          294 LTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSC--CSEEKIIVFTTNH  371 (530)
Q Consensus       294 ~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~--~~~~~ivI~TTN~  371 (530)
                                                                       .....++..+......  ...+..+|++||.
T Consensus        99 -------------------------------------------------~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~  129 (151)
T cd00009          99 -------------------------------------------------GAQNALLRVLETLNDLRIDRENVRVIGATNR  129 (151)
T ss_pred             -------------------------------------------------HHHHHHHHHHHhcCceeccCCCeEEEEecCc
Confidence                                                             0112333333332210  0246778889988


Q ss_pred             CC--CCChhhhcCCceeEEEEeCC
Q 009640          372 RD--SVDPALIRCGRMDVHVSLGT  393 (530)
Q Consensus       372 ~~--~LDpALlRpGR~d~~I~~~~  393 (530)
                      ..  .+++.+..  |++.+|.+++
T Consensus       130 ~~~~~~~~~~~~--r~~~~i~~~~  151 (151)
T cd00009         130 PLLGDLDRALYD--RLDIRIVIPL  151 (151)
T ss_pred             cccCCcChhHHh--hhccEeecCC
Confidence            77  78888888  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.

>PRK05642 DNA replication initiation factor; Validated

Probab=99.35  E-value=2.1e-11  Score=120.40  Aligned_cols=160  Identities=18%  Similarity=0.225  Sum_probs=100.2

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCC-CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAW-KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~-~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +...+..+|++++...  .......+..+.....       .| .++++||||+|||||+|+.|+|+++   +..++.++
T Consensus        10 ~~~~~~~tfdnF~~~~--~~~a~~~~~~~~~~~~-------~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~   80 (234)
T PRK05642         10 VRLRDDATFANYYPGA--NAAALGYVERLCEADA-------GWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLP   80 (234)
T ss_pred             CCCCCcccccccCcCC--hHHHHHHHHHHhhccc-------cCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEee
Confidence            4456677899987332  2344555544433211       12 3678999999999999999999875   56777777


Q ss_pred             cCccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          261 LTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       261 l~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                      ..++...  ...++....+-.+|+||||+.+.                                            ....
T Consensus        81 ~~~~~~~--~~~~~~~~~~~d~LiiDDi~~~~--------------------------------------------~~~~  114 (234)
T PRK05642         81 LAELLDR--GPELLDNLEQYELVCLDDLDVIA--------------------------------------------GKAD  114 (234)
T ss_pred             HHHHHhh--hHHHHHhhhhCCEEEEechhhhc--------------------------------------------CChH
Confidence            6655321  12333333444689999999762                                            1111


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC---CChhhhcCCce--eEEEEeCCCCHHHHHHHHHHh
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRM--DVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~--d~~I~~~~p~~~~r~~i~~~~  406 (530)
                      ....+-.++|.   +..  .+..+||.++..|..   +.|.|.+  |+  ...+.+..|+.+++..+++..
T Consensus       115 ~~~~Lf~l~n~---~~~--~g~~ilits~~~p~~l~~~~~~L~S--Rl~~gl~~~l~~~~~e~~~~il~~k  178 (234)
T PRK05642        115 WEEALFHLFNR---LRD--SGRRLLLAASKSPRELPIKLPDLKS--RLTLALVFQMRGLSDEDKLRALQLR  178 (234)
T ss_pred             HHHHHHHHHHH---HHh--cCCEEEEeCCCCHHHcCccCccHHH--HHhcCeeeecCCCCHHHHHHHHHHH
Confidence            22234444443   332  234455544445543   3689998  77  477889999999999998854

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.35  E-value=1.3e-11  Score=132.61  Aligned_cols=167  Identities=20%  Similarity=0.274  Sum_probs=101.2

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      ..+..+|++++..+.-+. ....+..+...+..  .-|.+ .++++||||||+|||+|++|+|+++   +..++.++...
T Consensus       104 l~~~~tFdnFv~g~~N~~-a~~~a~~~a~~~~~--~~~~~-~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~  179 (445)
T PRK12422        104 LDPLMTFANFLVTPENDL-PHRILQEFTKVSEQ--GKGFP-FNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSEL  179 (445)
T ss_pred             CCccccccceeeCCcHHH-HHHHHHHHHhcccc--ccCCC-CceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHH
Confidence            456678999864333221 12223333221100  00111 2679999999999999999999987   57777776544


Q ss_pred             cCCh-------HHHHHHHHh-cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          264 VTDN-------SELRALLLQ-TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       264 ~~~~-------~~L~~l~~~-~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                      +...       ..+. .|.. ..+..+|+||||+.+.+                                          
T Consensus       180 f~~~~~~~l~~~~~~-~f~~~~~~~dvLiIDDiq~l~~------------------------------------------  216 (445)
T PRK12422        180 FTEHLVSAIRSGEMQ-RFRQFYRNVDALFIEDIEVFSG------------------------------------------  216 (445)
T ss_pred             HHHHHHHHHhcchHH-HHHHHcccCCEEEEcchhhhcC------------------------------------------
Confidence            3210       1111 1222 35678999999998621                                          


Q ss_pred             CCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCC-C---CCCChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhCC
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNH-R---DSVDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~-~---~~LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                        ....+..+-.++|.+   ..   .+..+|+|+|. |   ..++++|.+  ||.  ..+.+..|+.++|..|++.....
T Consensus       217 --k~~~qeelf~l~N~l---~~---~~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~~iL~~k~~~  286 (445)
T PRK12422        217 --KGATQEEFFHTFNSL---HT---EGKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLRSFLERKAEA  286 (445)
T ss_pred             --ChhhHHHHHHHHHHH---HH---CCCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHHHHHHHHHHH
Confidence              111222333444433   22   22356666665 4   357899999  885  89999999999999999887654


Q ss_pred             c
Q 009640          410 E  410 (530)
Q Consensus       410 ~  410 (530)
                      .
T Consensus       287 ~  287 (445)
T PRK12422        287 L  287 (445)
T ss_pred             c
Confidence            3

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.34  E-value=2e-11  Score=116.29  Aligned_cols=123  Identities=21%  Similarity=0.294  Sum_probs=90.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC------------------------cEEEEecCcc-CChHHHHHHHHhc-----
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY------------------------DVYDLELTKV-TDNSELRALLLQT-----  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~------------------------~i~~l~l~~~-~~~~~L~~l~~~~-----  277 (530)
                      +..||||||||+|||++++++|+.+..                        +++.+....- .+-..++.++..+     
T Consensus        14 ~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~~~   93 (188)
T TIGR00678        14 AHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTPQ   93 (188)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccCcc
Confidence            467999999999999999999998743                        2333332211 2335566555443     


Q ss_pred             -CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCc
Q 009640          278 -TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLW  356 (530)
Q Consensus       278 -~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~  356 (530)
                       ..+.||||||+|.+-                                                 ....+.||..|+.. 
T Consensus        94 ~~~~kviiide~~~l~-------------------------------------------------~~~~~~Ll~~le~~-  123 (188)
T TIGR00678        94 ESGRRVVIIEDAERMN-------------------------------------------------EAAANALLKTLEEP-  123 (188)
T ss_pred             cCCeEEEEEechhhhC-------------------------------------------------HHHHHHHHHHhcCC-
Confidence             346799999999872                                                 12345688888753 


Q ss_pred             cCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          357 SCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       357 s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                         ....++|++||.+..|++++.+  |+ ..++|.+|+.++...++...
T Consensus       124 ---~~~~~~il~~~~~~~l~~~i~s--r~-~~~~~~~~~~~~~~~~l~~~  167 (188)
T TIGR00678       124 ---PPNTLFILITPSPEKLLPTIRS--RC-QVLPFPPLSEEALLQWLIRQ  167 (188)
T ss_pred             ---CCCeEEEEEECChHhChHHHHh--hc-EEeeCCCCCHHHHHHHHHHc
Confidence               3457788888888999999998  66 47999999999988887765

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.

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

Probab=99.33  E-value=2.8e-11  Score=138.04  Aligned_cols=155  Identities=14%  Similarity=0.251  Sum_probs=109.2

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCc-eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKR-GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSE  269 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~r-G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~  269 (530)
                      +.|+|+++.++.|...+....        .|..   -+. .+||+||||||||+||+++|..++.+++.++++.+.....
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~--------~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~  525 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSR--------AGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHT  525 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHh--------cCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhccc
Confidence            446788887777777665432        2221   123 4899999999999999999999999999998776533211


Q ss_pred             -------------------HHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCC
Q 009640          270 -------------------LRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCG  330 (530)
Q Consensus       270 -------------------L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~  330 (530)
                                         +...+. ....+||+|||||.+-                                      
T Consensus       526 ~~~lig~~~gyvg~~~~~~l~~~~~-~~p~~VvllDEieka~--------------------------------------  566 (731)
T TIGR02639       526 VSRLIGAPPGYVGFEQGGLLTEAVR-KHPHCVLLLDEIEKAH--------------------------------------  566 (731)
T ss_pred             HHHHhcCCCCCcccchhhHHHHHHH-hCCCeEEEEechhhcC--------------------------------------
Confidence                               222222 2456999999999761                                      


Q ss_pred             CCCCCCCCcchhhhHHHHhhhccCCccCC-------CCCeEEEEEeCCCC-------------------------CCChh
Q 009640          331 NNNNNNGEESGRVTLSGLLNFTDGLWSCC-------SEEKIIVFTTNHRD-------------------------SVDPA  378 (530)
Q Consensus       331 ~~~~~~~~~~~~~~ls~LLn~lDgl~s~~-------~~~~ivI~TTN~~~-------------------------~LDpA  378 (530)
                                 ....+.||..||.-.-..       -.+.+||+|||...                         .+.|.
T Consensus       567 -----------~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pe  635 (731)
T TIGR02639       567 -----------PDIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPE  635 (731)
T ss_pred             -----------HHHHHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChH
Confidence                       224566777776431100       13468999998742                         25677


Q ss_pred             hhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          379 LIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       379 LlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      |+.  |||..|.|.+.+.++...|++.++.
T Consensus       636 f~~--Rid~Vi~F~pLs~e~l~~Iv~~~L~  663 (731)
T TIGR02639       636 FRN--RLDAIIHFNPLSEEVLEKIVQKFVD  663 (731)
T ss_pred             HHh--cCCeEEEcCCCCHHHHHHHHHHHHH
Confidence            776  9999999999999999999998865

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.32  E-value=6.6e-11  Score=122.27  Aligned_cols=156  Identities=19%  Similarity=0.284  Sum_probs=102.1

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-------CCcEEEEe-
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-------CYDVYDLE-  260 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-------~~~i~~l~-  260 (530)
                      .|.+|++|+|++++++.+.-.+..             +...++||+||||||||++++++|+-+       +.++-... 
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            567899999999988876542211             112479999999999999999999998       22111100 


Q ss_pred             -----c--------------------C----ccCChHHHHHHHHh-----------cCCCeEEEEcCccchhhhhhhhhh
Q 009640          261 -----L--------------------T----KVTDNSELRALLLQ-----------TTNRSIIVIEDIDCSVDLTADRML  300 (530)
Q Consensus       261 -----l--------------------~----~~~~~~~L~~l~~~-----------~~~~sII~IDeID~~~~~~~~r~~  300 (530)
                           +                    +    .+.+.-++...+..           .....+||||||+.+         
T Consensus        70 ~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl---------  140 (334)
T PRK13407         70 EDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLL---------  140 (334)
T ss_pred             cCCcccccccCCcccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhC---------
Confidence                 0                    0    00111112222111           123468999999986         


Q ss_pred             cccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc---------CCccCCCCCeEEEEEeCC
Q 009640          301 KSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD---------GLWSCCSEEKIIVFTTNH  371 (530)
Q Consensus       301 ~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD---------gl~s~~~~~~ivI~TTN~  371 (530)
                                                              ...+.+.|++.|+         |.........++|+|+|.
T Consensus       141 ----------------------------------------~~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP  180 (334)
T PRK13407        141 ----------------------------------------EDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNP  180 (334)
T ss_pred             ----------------------------------------CHHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCc
Confidence                                                    1234556666664         322222345678888886


Q ss_pred             CC-CCChhhhcCCceeEEEEeCCCCH-HHHHHHHHHhhC
Q 009640          372 RD-SVDPALIRCGRMDVHVSLGTCGP-HAFKVLAKNYLG  408 (530)
Q Consensus       372 ~~-~LDpALlRpGR~d~~I~~~~p~~-~~r~~i~~~~l~  408 (530)
                      .+ .++++|+.  ||...|.+++|.. +++.+|+.....
T Consensus       181 ~e~~l~~aLld--RF~~~v~v~~~~~~~e~~~il~~~~~  217 (334)
T PRK13407        181 EEGELRPQLLD--RFGLSVEVRSPRDVETRVEVIRRRDA  217 (334)
T ss_pred             ccCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHhhc
Confidence            55 69999999  9999999999987 899999987654

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.32  E-value=3.8e-11  Score=133.59  Aligned_cols=156  Identities=17%  Similarity=0.282  Sum_probs=105.2

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecCc
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELTK  263 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~~  263 (530)
                      +.|.+-++..++|...|...+....        ....+++|||||||||++++.+..+|          .+.++.+++..
T Consensus       755 D~LPhREeEIeeLasfL~paIkgsg--------pnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~  826 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQSG--------SNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMN  826 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhcCC--------CCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCc
Confidence            6677777778888877776665321        12335699999999999999998877          25667787754


Q ss_pred             cCCh-----------------------HHHHHHHHhc----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          264 VTDN-----------------------SELRALLLQT----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       264 ~~~~-----------------------~~L~~l~~~~----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                      +.+.                       ..+..+|...    ....||||||||.+..                       
T Consensus       827 Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~k-----------------------  883 (1164)
T PTZ00112        827 VVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLIT-----------------------  883 (1164)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCc-----------------------
Confidence            4322                       1233444432    2357999999999841                       


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCC---CCCCChhhhcCCceeE-EEEeC
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNH---RDSVDPALIRCGRMDV-HVSLG  392 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~---~~~LDpALlRpGR~d~-~I~~~  392 (530)
                                           .  .+..|-.|++...   . .+..++||+++|.   ++.|+|.+..  ||.. .|.|+
T Consensus       884 ---------------------K--~QDVLYnLFR~~~---~-s~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~  934 (1164)
T PTZ00112        884 ---------------------K--TQKVLFTLFDWPT---K-INSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFS  934 (1164)
T ss_pred             ---------------------c--HHHHHHHHHHHhh---c-cCCeEEEEEecCchhcchhhhhhhhh--ccccccccCC
Confidence                                 0  1223444444322   1 1356788898886   6678898887  6643 48899


Q ss_pred             CCCHHHHHHHHHHhhCC
Q 009640          393 TCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       393 ~p~~~~r~~i~~~~l~~  409 (530)
                      +++.+++..|++.-+..
T Consensus       935 PYTaEQL~dILk~RAe~  951 (1164)
T PTZ00112        935 PYKGDEIEKIIKERLEN  951 (1164)
T ss_pred             CCCHHHHHHHHHHHHHh
Confidence            99999999999877653

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.32  E-value=1.7e-11  Score=131.89  Aligned_cols=157  Identities=16%  Similarity=0.322  Sum_probs=119.6

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc------------
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD------------  255 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~------------  255 (530)
                      ++|.+|++++|++.+.+.|...+..   ++         ...+|||.||-||||||+|+.+|.-+++.            
T Consensus        10 yRP~~F~evvGQe~v~~~L~nal~~---~r---------i~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~   77 (515)
T COG2812          10 YRPKTFDDVVGQEHVVKTLSNALEN---GR---------IAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCI   77 (515)
T ss_pred             hCcccHHHhcccHHHHHHHHHHHHh---Cc---------chhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhh
Confidence            4889999999999988887776543   11         13589999999999999999999988543            


Q ss_pred             ------------EEEEecCccCChHHHHHHHHhc-C-----CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhh
Q 009640          256 ------------VYDLELTKVTDNSELRALLLQT-T-----NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSI  317 (530)
Q Consensus       256 ------------i~~l~l~~~~~~~~L~~l~~~~-~-----~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~  317 (530)
                                  ++.++..+-.+-+++|.+..+. .     +.-|++|||++.+                          
T Consensus        78 ~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHML--------------------------  131 (515)
T COG2812          78 SCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHML--------------------------  131 (515)
T ss_pred             hhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhh--------------------------
Confidence                        2222222223456788888776 2     3459999999987                          


Q ss_pred             hhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHH
Q 009640          318 KEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPH  397 (530)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~  397 (530)
                                             +....++||..++.-    ...+++|++|..+.++++.+++  |+ .+..|..-+.+
T Consensus       132 -----------------------S~~afNALLKTLEEP----P~hV~FIlATTe~~Kip~TIlS--Rc-q~f~fkri~~~  181 (515)
T COG2812         132 -----------------------SKQAFNALLKTLEEP----PSHVKFILATTEPQKIPNTILS--RC-QRFDFKRLDLE  181 (515)
T ss_pred             -----------------------hHHHHHHHhcccccC----ccCeEEEEecCCcCcCchhhhh--cc-ccccccCCCHH
Confidence                                   344678999999843    5679999999999999999996  54 34678888888


Q ss_pred             HHHHHHHHhhCCcCc
Q 009640          398 AFKVLAKNYLGIESH  412 (530)
Q Consensus       398 ~r~~i~~~~l~~~~~  412 (530)
                      +....+...+..+..
T Consensus       182 ~I~~~L~~i~~~E~I  196 (515)
T COG2812         182 EIAKHLAAILDKEGI  196 (515)
T ss_pred             HHHHHHHHHHHhcCC
Confidence            888888888875443

>PRK06620 hypothetical protein; Validated

Probab=99.31  E-value=7.7e-11  Score=114.80  Aligned_cols=150  Identities=17%  Similarity=0.253  Sum_probs=94.2

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcC-CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGR-AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~-~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      ++..+..+|++++..+.-.. ....+..+...      .+. |..+.++||||||||||||++|+|+..+..+..  ...
T Consensus         7 ~~~~~~~tfd~Fvvg~~N~~-a~~~~~~~~~~------~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~--~~~   77 (214)
T PRK06620          7 FTTSSKYHPDEFIVSSSNDQ-AYNIIKNWQCG------FGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYIIK--DIF   77 (214)
T ss_pred             CCCCCCCCchhhEecccHHH-HHHHHHHHHHc------cccCCCcceEEEECCCCCCHHHHHHHHHhccCCEEcc--hhh
Confidence            34456668999866553222 33334443321      122 224689999999999999999999998753322  111


Q ss_pred             cCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhh
Q 009640          264 VTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRV  343 (530)
Q Consensus       264 ~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  343 (530)
                      .  ..   ..+   ....+|+|||||.+                                                 ...
T Consensus        78 ~--~~---~~~---~~~d~lliDdi~~~-------------------------------------------------~~~  100 (214)
T PRK06620         78 F--NE---EIL---EKYNAFIIEDIENW-------------------------------------------------QEP  100 (214)
T ss_pred             h--ch---hHH---hcCCEEEEeccccc-------------------------------------------------hHH
Confidence            1  11   111   24479999999954                                                 012


Q ss_pred             hHHHHhhhccCCccCCCCCeEEEEEeCCCCC--CChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhC
Q 009640          344 TLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS--VDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       344 ~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~--LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      .+..++|.+.   .  .+..+||.++..|..  + |+|++  |+.  ..+.+..|+.+.+..+++..+.
T Consensus       101 ~lf~l~N~~~---e--~g~~ilits~~~p~~l~l-~~L~S--Rl~~gl~~~l~~pd~~~~~~~l~k~~~  161 (214)
T PRK06620        101 ALLHIFNIIN---E--KQKYLLLTSSDKSRNFTL-PDLSS--RIKSVLSILLNSPDDELIKILIFKHFS  161 (214)
T ss_pred             HHHHHHHHHH---h--cCCEEEEEcCCCccccch-HHHHH--HHhCCceEeeCCCCHHHHHHHHHHHHH
Confidence            3455555553   2  244566666655554  5 88998  775  4699999999999999877644

>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=99.31  E-value=3.4e-12  Score=115.31  Aligned_cols=62  Identities=27%  Similarity=0.443  Sum_probs=48.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHh---------------cCCCeEEEEcCccch
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQ---------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~---------------~~~~sII~IDeID~~  291 (530)
                      ++||+||||||||+|++.+|..++.+++.+.++...+..+|.....-               ...++|+|||||+.+
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~a   77 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINRA   77 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG-
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcccC
Confidence            58999999999999999999999999999999887666655432110               125789999999975

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.

>PHA02244 ATPase-like protein

Probab=99.30  E-value=3.7e-11  Score=124.07  Aligned_cols=132  Identities=20%  Similarity=0.313  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHH----------H--
Q 009640          204 KQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSEL----------R--  271 (530)
Q Consensus       204 ~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L----------~--  271 (530)
                      ......+..++...           ..+||+||||||||++|++||..++.+++.++..  .+...+          .  
T Consensus       106 ~~~~~ri~r~l~~~-----------~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l--~d~~~L~G~i~~~g~~~dg  172 (383)
T PHA02244        106 HYETADIAKIVNAN-----------IPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAI--MDEFELKGFIDANGKFHET  172 (383)
T ss_pred             HHHHHHHHHHHhcC-----------CCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecC--hHHHhhcccccccccccch
Confidence            33444555665543           4799999999999999999999999999988732  111111          1  


Q ss_pred             HHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHh--
Q 009640          272 ALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLL--  349 (530)
Q Consensus       272 ~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LL--  349 (530)
                      .++.......+|+|||||.+-+                                              .....|+.++  
T Consensus       173 pLl~A~~~GgvLiLDEId~a~p----------------------------------------------~vq~~L~~lLd~  206 (383)
T PHA02244        173 PFYEAFKKGGLFFIDEIDASIP----------------------------------------------EALIIINSAIAN  206 (383)
T ss_pred             HHHHHhhcCCEEEEeCcCcCCH----------------------------------------------HHHHHHHHHhcc
Confidence            2233346778999999997621                                              0111122222  


Q ss_pred             ---hhccCCccCCCCCeEEEEEeCCC-----------CCCChhhhcCCceeEEEEeCCCCHHH
Q 009640          350 ---NFTDGLWSCCSEEKIIVFTTNHR-----------DSVDPALIRCGRMDVHVSLGTCGPHA  398 (530)
Q Consensus       350 ---n~lDgl~s~~~~~~ivI~TTN~~-----------~~LDpALlRpGR~d~~I~~~~p~~~~  398 (530)
                         ..+++... ...+..+|+|+|.+           ..|++|++.  || .+|+|+||+..+
T Consensus       207 r~l~l~g~~i~-~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllD--RF-v~I~~dyp~~~E  265 (383)
T PHA02244        207 KFFDFADERVT-AHEDFRVISAGNTLGKGADHIYVARNKIDGATLD--RF-APIEFDYDEKIE  265 (383)
T ss_pred             CeEEecCcEEe-cCCCEEEEEeeCCCccCcccccCCCcccCHHHHh--hc-EEeeCCCCcHHH
Confidence               22222221 23567889999973           578999999  99 579999998433

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.30  E-value=1.2e-10  Score=121.36  Aligned_cols=151  Identities=18%  Similarity=0.242  Sum_probs=105.9

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc------------
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD------------  255 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~------------  255 (530)
                      .||..|+.|+|++++++.+...+..    .        ..+..+||+||+|+|||+++.++|+.+...            
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            5899999999999988777664431    1        113479999999999999999999988441            


Q ss_pred             ------------------EEEEecC---------ccCChHHHHHHH---Hhc---CCCeEEEEcCccchhhhhhhhhhcc
Q 009640          256 ------------------VYDLELT---------KVTDNSELRALL---LQT---TNRSIIVIEDIDCSVDLTADRMLKS  302 (530)
Q Consensus       256 ------------------i~~l~l~---------~~~~~~~L~~l~---~~~---~~~sII~IDeID~~~~~~~~r~~~~  302 (530)
                                        ++.+...         ...+-.+++.+.   ...   ...-||+|||+|.+           
T Consensus        85 ~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l-----------  153 (351)
T PRK09112         85 PDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDM-----------  153 (351)
T ss_pred             CCCCCHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhc-----------
Confidence                              1111100         001123344432   222   24568888888876           


Q ss_pred             cCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcC
Q 009640          303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRC  382 (530)
Q Consensus       303 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRp  382 (530)
                                                            +....+.||..++..    ....++|+.|+.++.|.|.+++ 
T Consensus       154 --------------------------------------~~~aanaLLk~LEEp----p~~~~fiLit~~~~~llptIrS-  190 (351)
T PRK09112        154 --------------------------------------NRNAANAILKTLEEP----PARALFILISHSSGRLLPTIRS-  190 (351)
T ss_pred             --------------------------------------CHHHHHHHHHHHhcC----CCCceEEEEECChhhccHHHHh-
Confidence                                                  123456788888763    2456777778889999999987 


Q ss_pred             CceeEEEEeCCCCHHHHHHHHHHh
Q 009640          383 GRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       383 GR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                       |+ .++.|+.|+.++...++...
T Consensus       191 -Rc-~~i~l~pl~~~~~~~~L~~~  212 (351)
T PRK09112        191 -RC-QPISLKPLDDDELKKALSHL  212 (351)
T ss_pred             -hc-cEEEecCCCHHHHHHHHHHh
Confidence             77 68999999999999988873

>PRK08181 transposase; Validated

Probab=99.28  E-value=3.6e-11  Score=120.75  Aligned_cols=125  Identities=18%  Similarity=0.284  Sum_probs=83.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhhhhccccCCCCCCCCCccccCCCCCCCcccccC--ChhhhHHHHHH---HHHHHcChh
Q 009640          144 TLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLAL--EPQLKKQITED---LTAFANGKE  218 (530)
Q Consensus       144 ~vl~~yl~~v~~~~~~~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~~~~f~~l~~--~~~~k~~i~~~---l~~~l~~~~  218 (530)
                      .-..+||..+++.+.+.++.++..++...+.++.            ..+|+++..  .+.+.+.....   +..|+..  
T Consensus        40 ~~~~e~L~~ll~~E~~~R~~~~~~r~lk~A~~p~------------~~tle~fd~~~~~~~~~~~~~~L~~~~~~~~~--  105 (269)
T PRK08181         40 WPAARFLAAIAEHELAERARRRIERHLAEAHLPP------------GKTLDSFDFEAVPMVSKAQVMAIAAGDSWLAK--  105 (269)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC------------CCCHhhCCccCCCCCCHHHHHHHHHHHHHHhc--
Confidence            3457899999999888888888888888865432            234444421  12222222222   2234432  


Q ss_pred             hHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC-------hHHHHHHHHhcCCCeEEEEcCc
Q 009640          219 FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD-------NSELRALLLQTTNRSIIVIEDI  288 (530)
Q Consensus       219 ~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~-------~~~L~~l~~~~~~~sII~IDeI  288 (530)
                               ..+++|+||||||||+|+.|+|+++   |+.++.++...+..       +..+.+.+....++.+|+|||+
T Consensus       106 ---------~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDl  176 (269)
T PRK08181        106 ---------GANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDL  176 (269)
T ss_pred             ---------CceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEecc
Confidence                     3689999999999999999999876   66676666544321       1234455666678899999999


Q ss_pred             cch
Q 009640          289 DCS  291 (530)
Q Consensus       289 D~~  291 (530)
                      +..
T Consensus       177 g~~  179 (269)
T PRK08181        177 AYV  179 (269)
T ss_pred             ccc
Confidence            975

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.28  E-value=2.2e-10  Score=118.06  Aligned_cols=148  Identities=14%  Similarity=0.236  Sum_probs=108.9

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC--------cEEEEecC-
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY--------DVYDLELT-  262 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~--------~i~~l~l~-  262 (530)
                      +|++++|++.+++.+...+..    .        ..+..||||||+|+|||++|.++|..+..        +++.+... 
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~----~--------~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~   69 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIK----N--------RFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN   69 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHc----C--------CCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecccc
Confidence            589999999988887765521    1        22468999999999999999999997622        44444331 


Q ss_pred             -ccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          263 -KVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       263 -~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                       ...+-..++.+....      ...-|++|||+|.+-                                           
T Consensus        70 ~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~-------------------------------------------  106 (313)
T PRK05564         70 KKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMT-------------------------------------------  106 (313)
T ss_pred             CCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcC-------------------------------------------
Confidence             112345677776533      345799999999871                                           


Q ss_pred             CCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                            ....+.||..|+..    .++.++|++|+.++.|-|.+.+  |. ..++|..|+.++....+...+
T Consensus       107 ------~~a~naLLK~LEep----p~~t~~il~~~~~~~ll~TI~S--Rc-~~~~~~~~~~~~~~~~l~~~~  165 (313)
T PRK05564        107 ------EQAQNAFLKTIEEP----PKGVFIILLCENLEQILDTIKS--RC-QIYKLNRLSKEEIEKFISYKY  165 (313)
T ss_pred             ------HHHHHHHHHHhcCC----CCCeEEEEEeCChHhCcHHHHh--hc-eeeeCCCcCHHHHHHHHHHHh
Confidence                  22356899998853    4667888888999999999998  66 479999999999887776654

>PRK06526 transposase; Provisional

Probab=99.28  E-value=1e-11  Score=123.86  Aligned_cols=126  Identities=15%  Similarity=0.242  Sum_probs=78.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhccccCCCCCCCCCccccCCCCCCCcccccC--ChhhhHHHHHHHHHHHcChhhHhh
Q 009640          145 LLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLAL--EPQLKKQITEDLTAFANGKEFYHR  222 (530)
Q Consensus       145 vl~~yl~~v~~~~~~~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~~~~f~~l~~--~~~~k~~i~~~l~~~l~~~~~y~~  222 (530)
                      -..+||..+++.+.+.++.++..+..+.+.++.            ..+|+++..  .+.+.+..+..+    ..-+|.. 
T Consensus        34 ~~~e~l~~ll~~E~~~R~~~~~~~~lk~a~~p~------------~~~le~fd~~~~~~~~~~~~~~l----~~~~fi~-   96 (254)
T PRK06526         34 SHEEFLAACLQREVAARESHGGEGRIRAARFPA------------RKSLEEFDFDHQRSLKRDTIAHL----GTLDFVT-   96 (254)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC------------CCChhhccCccCCCcchHHHHHH----hcCchhh-
Confidence            356899999999999999998888888876543            122222211  111222222211    1122221 


Q ss_pred             hcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC-------ChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          223 VGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT-------DNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       223 ~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~-------~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                          .+.+++|+||||||||+|+.+|+.++   |+.++......+.       ....+.+.+.....+.+|||||++..
T Consensus        97 ----~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~  171 (254)
T PRK06526         97 ----GKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYI  171 (254)
T ss_pred             ----cCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccC
Confidence                14689999999999999999999987   5555544443321       11123444555667899999999975

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.27  E-value=8.9e-11  Score=121.63  Aligned_cols=156  Identities=17%  Similarity=0.287  Sum_probs=103.3

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-------cEE----
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-------DVY----  257 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-------~i~----  257 (530)
                      ...+|.+|+|++++|..+...+..             |...|+||.||+|||||+++++++..+..       +|.    
T Consensus        12 ~~~pf~~ivGq~~~k~al~~~~~~-------------p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~   78 (350)
T CHL00081         12 PVFPFTAIVGQEEMKLALILNVID-------------PKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPS   78 (350)
T ss_pred             CCCCHHHHhChHHHHHHHHHhccC-------------CCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCC
Confidence            455799999999999888765543             22368999999999999999999888731       111    


Q ss_pred             ------------------------EEecCcc---CChH------HHHHHHHh-----------cCCCeEEEEcCccchhh
Q 009640          258 ------------------------DLELTKV---TDNS------ELRALLLQ-----------TTNRSIIVIEDIDCSVD  293 (530)
Q Consensus       258 ------------------------~l~l~~~---~~~~------~L~~l~~~-----------~~~~sII~IDeID~~~~  293 (530)
                                              .+.+..+   .+++      ++.+.|..           .....+|+||||+.+- 
T Consensus        79 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~-  157 (350)
T CHL00081         79 DPELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLD-  157 (350)
T ss_pred             ChhhhchhhhhhhcccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCC-
Confidence                                    0000000   0111      12222221           1235799999999872 


Q ss_pred             hhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc---------CCccCCCCCeE
Q 009640          294 LTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD---------GLWSCCSEEKI  364 (530)
Q Consensus       294 ~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD---------gl~s~~~~~~i  364 (530)
                                                                      ..+.+.||+.|+         |.........+
T Consensus       158 ------------------------------------------------~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfi  189 (350)
T CHL00081        158 ------------------------------------------------DHLVDILLDSAASGWNTVEREGISIRHPARFV  189 (350)
T ss_pred             ------------------------------------------------HHHHHHHHHHHHhCCeEEeeCCeeeecCCCEE
Confidence                                                            223445666553         33222234566


Q ss_pred             EEEEeCCCC-CCChhhhcCCceeEEEEeCCCC-HHHHHHHHHHhhC
Q 009640          365 IVFTTNHRD-SVDPALIRCGRMDVHVSLGTCG-PHAFKVLAKNYLG  408 (530)
Q Consensus       365 vI~TTN~~~-~LDpALlRpGR~d~~I~~~~p~-~~~r~~i~~~~l~  408 (530)
                      +|+|.|..+ .|.++|+.  ||..+|.+.+|+ .+.+.+|++....
T Consensus       190 viaT~np~eg~l~~~Lld--Rf~l~i~l~~~~~~~~e~~il~~~~~  233 (350)
T CHL00081        190 LVGSGNPEEGELRPQLLD--RFGMHAEIRTVKDPELRVKIVEQRTS  233 (350)
T ss_pred             EEeccCcccCCCCHHHHH--HhCceeecCCCCChHHHHHHHHhhhc
Confidence            777777655 69999999  999999999998 6999999987654

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=3.3e-10  Score=118.79  Aligned_cols=153  Identities=17%  Similarity=0.251  Sum_probs=111.0

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-------------
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-------------  254 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-------------  254 (530)
                      .+|+++++|+|++++++.+...+..    .        ..+.+|||+||+|+||+++|.++|+.+-.             
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            5899999999999988887765432    1        12458999999999999999999998721             


Q ss_pred             ---------------------cEEEEecC--c-------cCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhh
Q 009640          255 ---------------------DVYDLELT--K-------VTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADR  298 (530)
Q Consensus       255 ---------------------~i~~l~l~--~-------~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r  298 (530)
                                           +++.+...  +       ...-.+++.+....      ..+-||+|||+|.+       
T Consensus        81 ~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m-------  153 (365)
T PRK07471         81 TSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEM-------  153 (365)
T ss_pred             ccccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhc-------
Confidence                                 22333221  1       01224455554332      35679999999976       


Q ss_pred             hhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChh
Q 009640          299 MLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPA  378 (530)
Q Consensus       299 ~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpA  378 (530)
                                                                +....+.||..++..    ....++|++|+.++.+.|.
T Consensus       154 ------------------------------------------~~~aanaLLK~LEep----p~~~~~IL~t~~~~~llpt  187 (365)
T PRK07471        154 ------------------------------------------NANAANALLKVLEEP----PARSLFLLVSHAPARLLPT  187 (365)
T ss_pred             ------------------------------------------CHHHHHHHHHHHhcC----CCCeEEEEEECCchhchHH
Confidence                                                      233567888888753    3467888999999999999


Q ss_pred             hhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          379 LIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       379 LlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      +++  |+ ..|.|+.|+.++...++.....
T Consensus       188 i~S--Rc-~~i~l~~l~~~~i~~~L~~~~~  214 (365)
T PRK07471        188 IRS--RC-RKLRLRPLAPEDVIDALAAAGP  214 (365)
T ss_pred             hhc--cc-eEEECCCCCHHHHHHHHHHhcc
Confidence            887  75 5689999999999988887654

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.27  E-value=8.2e-11  Score=126.71  Aligned_cols=160  Identities=17%  Similarity=0.312  Sum_probs=102.6

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEecCcc
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLELTKV  264 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l~~~  264 (530)
                      +.+|++++..+.-. .....+..+...+      |..+ ++++||||+|||||+|++|+++++     +..++.++...+
T Consensus       111 ~~tFdnFv~g~~n~-~A~~aa~~~a~~~------~~~~-npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f  182 (450)
T PRK14087        111 ENTFENFVIGSSNE-QAFIAVQTVSKNP------GISY-NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEF  182 (450)
T ss_pred             ccchhcccCCCcHH-HHHHHHHHHHhCc------Cccc-CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHH
Confidence            46888886544322 2334444444333      2222 579999999999999999999976     467777766544


Q ss_pred             CCh---------HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          265 TDN---------SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       265 ~~~---------~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                      ...         ..+..+........+|+||||+.+.                                           
T Consensus       183 ~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~-------------------------------------------  219 (450)
T PRK14087        183 ARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLS-------------------------------------------  219 (450)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHhccCCEEEEecccccc-------------------------------------------
Confidence            211         1233333344677899999999762                                           


Q ss_pred             CCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCC-CC---CCChhhhcCCce--eEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNH-RD---SVDPALIRCGRM--DVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~-~~---~LDpALlRpGR~--d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                       ........+-.++|.+.   .   .+..+|+|+|. |+   .+++.|.+  ||  ...+.+..|+.++|..|+++.+..
T Consensus       220 -~k~~~~e~lf~l~N~~~---~---~~k~iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~~L~~pd~e~r~~iL~~~~~~  290 (450)
T PRK14087        220 -YKEKTNEIFFTIFNNFI---E---NDKQLFFSSDKSPELLNGFDNRLIT--RFNMGLSIAIQKLDNKTATAIIKKEIKN  290 (450)
T ss_pred             -CCHHHHHHHHHHHHHHH---H---cCCcEEEECCCCHHHHhhccHHHHH--HHhCCceeccCCcCHHHHHHHHHHHHHh
Confidence             11112334445555543   2   22246666665 43   45789998  77  478889999999999999988754

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.26  E-value=2.2e-10  Score=120.13  Aligned_cols=69  Identities=19%  Similarity=0.252  Sum_probs=50.6

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhc-CCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVG-RAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g-~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      -|+|+++.|+.+...+.....+......++ -..++++||+||||||||++++++|..++.+++.++.+.
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~   82 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATK   82 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeEEEeecce
Confidence            378899999988776664322211111111 123589999999999999999999999999999998653

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.26  E-value=3.9e-11  Score=118.79  Aligned_cols=122  Identities=20%  Similarity=0.308  Sum_probs=80.4

Q ss_pred             HHHHHHHHhhhhccccCCCCCCCCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECC
Q 009640          157 AEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGP  236 (530)
Q Consensus       157 ~~~~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GP  236 (530)
                      +.++.+++++.++.+...      .|.-.+..+..+|+++....+..+.+...+..|.....   .    ...+++|+||
T Consensus        41 ~~~i~~~~~q~~~~~~~~------~s~i~~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~~---~----~~~~~~l~G~  107 (244)
T PRK07952         41 SAALERENRAMKMQRTFN------RSGIRPLHQNCSFENYRVECEGQMNALSKARQYVEEFD---G----NIASFIFSGK  107 (244)
T ss_pred             HHHHHHHHHHHHHHHHHH------HcCCCccccCCccccccCCCchHHHHHHHHHHHHHhhc---c----CCceEEEECC
Confidence            445666666666554421      12223345677999987655545556666666664321   0    1258999999


Q ss_pred             CCCChhHHHHHHHHHc---CCcEEEEecCccCC---------hHHHHHHHHhcCCCeEEEEcCccch
Q 009640          237 PGSGKSSLIAAMANYL---CYDVYDLELTKVTD---------NSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       237 PGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~---------~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      ||||||+|+.|||+++   +..++.++..++..         +....+++.......+|+|||+++.
T Consensus       108 ~GtGKThLa~aia~~l~~~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~~~dlLvIDDig~~  174 (244)
T PRK07952        108 PGTGKNHLAAAICNELLLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEIGVQ  174 (244)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhccCCEEEEeCCCCC
Confidence            9999999999999998   66777776655421         1223455666678899999999985

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.25  E-value=2.1e-10  Score=127.94  Aligned_cols=180  Identities=17%  Similarity=0.271  Sum_probs=101.0

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEE
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVY  257 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~  257 (530)
                      .+|.+|++++|++...+.+...+.             .+.+..++|+||||||||++|+++++..          +.+++
T Consensus       148 ~rp~~~~~iiGqs~~~~~l~~~ia-------------~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv  214 (615)
T TIGR02903       148 LRPRAFSEIVGQERAIKALLAKVA-------------SPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFV  214 (615)
T ss_pred             cCcCcHHhceeCcHHHHHHHHHHh-------------cCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeE
Confidence            468899999999887776654431             1224579999999999999999998776          34577


Q ss_pred             EEecCccCC-hHHH----------------HHHHHh------------cCCCeEEEEcCccchhhhhhhhhhcccCCccc
Q 009640          258 DLELTKVTD-NSEL----------------RALLLQ------------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTT  308 (530)
Q Consensus       258 ~l~l~~~~~-~~~L----------------~~l~~~------------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~  308 (530)
                      .++...+.. ...+                ++.+..            .....+|||||++.+-......-..       
T Consensus       215 ~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~-------  287 (615)
T TIGR02903       215 EVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLK-------  287 (615)
T ss_pred             EEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHH-------
Confidence            776654321 1111                111111            1235699999999862111100000       


Q ss_pred             cccccchhhhhhccccccccCCCCCCCCCCcchhhhHHH-HhhhccCCccCCCCCeEEEE-EeCCCCCCChhhhcCCcee
Q 009640          309 AKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSG-LLNFTDGLWSCCSEEKIIVF-TTNHRDSVDPALIRCGRMD  386 (530)
Q Consensus       309 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~-LLn~lDgl~s~~~~~~ivI~-TTN~~~~LDpALlRpGR~d  386 (530)
                             .+++ + .+..  .++..    +. ....... +-..++...   ...+++|+ ||+.++.++++|++  ||.
T Consensus       288 -------~Le~-~-~v~~--~~~~~----~~-~~~~~~~~ik~~~~~~~---~~~~VLI~aTt~~~~~l~~aLrS--R~~  346 (615)
T TIGR02903       288 -------VLED-K-RVEF--SSSYY----DP-DDPNVPKYIKKLFEEGA---PADFVLIGATTRDPEEINPALRS--RCA  346 (615)
T ss_pred             -------HHhh-C-eEEe--eccee----cc-CCcccchhhhhhcccCc---cceEEEEEeccccccccCHHHHh--cee
Confidence                   0000 0 0000  00000    00 0000001 111111111   22345554 66778899999998  887


Q ss_pred             EEEEeCCCCHHHHHHHHHHhhCC
Q 009640          387 VHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       387 ~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                       .++|++.+.++...|++.++..
T Consensus       347 -~i~~~pls~edi~~Il~~~a~~  368 (615)
T TIGR02903       347 -EVFFEPLTPEDIALIVLNAAEK  368 (615)
T ss_pred             -EEEeCCCCHHHHHHHHHHHHHH
Confidence             4789999999999999987653

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.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.25  E-value=7.5e-11  Score=122.34  Aligned_cols=130  Identities=23%  Similarity=0.250  Sum_probs=91.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHH------HHH--Hh----cCC----C--eEEEEcCcc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELR------ALL--LQ----TTN----R--SIIVIEDID  289 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~------~l~--~~----~~~----~--sII~IDeID  289 (530)
                      .+.+||-||||||||+|++++|..++.+++.+.++.-...+++.      ...  ..    ...    .  +|+++|||+
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            46899999999999999999999999999999988654433321      111  00    111    1  499999999


Q ss_pred             chhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC-------Cc-cCCCC
Q 009640          290 CSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG-------LW-SCCSE  361 (530)
Q Consensus       290 ~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg-------l~-s~~~~  361 (530)
                      ..                                                 ...+.+.||..|+.       .. -.-..
T Consensus       123 ra-------------------------------------------------~p~~q~aLl~~l~e~~vtv~~~~~~~~~~  153 (329)
T COG0714         123 RA-------------------------------------------------PPEVQNALLEALEERQVTVPGLTTIRLPP  153 (329)
T ss_pred             cC-------------------------------------------------CHHHHHHHHHHHhCcEEEECCcCCcCCCC
Confidence            75                                                 12355666666654       11 11134


Q ss_pred             CeEEEEEeC-----CCCCCChhhhcCCceeEEEEeCCC-CHHHHHHHHHHhhC
Q 009640          362 EKIIVFTTN-----HRDSVDPALIRCGRMDVHVSLGTC-GPHAFKVLAKNYLG  408 (530)
Q Consensus       362 ~~ivI~TTN-----~~~~LDpALlRpGR~d~~I~~~~p-~~~~r~~i~~~~l~  408 (530)
                      ..+||+|+|     ....|++|+++  ||-..++++|| ...+...+.....+
T Consensus       154 ~f~viaT~Np~e~~g~~~l~eA~ld--Rf~~~~~v~yp~~~~e~~~i~~~~~~  204 (329)
T COG0714         154 PFIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEERIILARVGG  204 (329)
T ss_pred             CCEEEEccCccccCCCcCCCHHHHh--hEEEEEecCCCCchHHHHHHHHhCcc
Confidence            567888889     45578999999  99999999999 55556666555554

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.23  E-value=8e-11  Score=123.38  Aligned_cols=70  Identities=17%  Similarity=0.220  Sum_probs=50.9

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCC-CCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRA-WKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~-~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      .|+|+++.|+.+...+.....+.........+ .+.++||+||||||||++++++|..++.+++.++.+.+
T Consensus        16 ~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~f   86 (443)
T PRK05201         16 YIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKF   86 (443)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchhh
Confidence            37899999999988775432211111111111 25789999999999999999999999999999986543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.22  E-value=2.1e-10  Score=132.14  Aligned_cols=156  Identities=17%  Similarity=0.271  Sum_probs=106.7

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcC-CCCce-EEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGR-AWKRG-YLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNS  268 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~-~~~rG-~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~  268 (530)
                      +.|+|+++..+.|.+.+.....+      +.. ..+.| +||+||||||||.||+++|..+   ...++.++++.+....
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            46788999888888888665321      111 12345 8999999999999999999998   4467777776653221


Q ss_pred             H-------------------HHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccC
Q 009640          269 E-------------------LRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTC  329 (530)
Q Consensus       269 ~-------------------L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~  329 (530)
                      .                   |...+.+ ...|||+|||||.+-                                     
T Consensus       640 ~~~~l~g~~~gyvg~~~~g~L~~~v~~-~p~svvllDEieka~-------------------------------------  681 (852)
T TIGR03345       640 TVSRLKGSPPGYVGYGEGGVLTEAVRR-KPYSVVLLDEVEKAH-------------------------------------  681 (852)
T ss_pred             hhccccCCCCCcccccccchHHHHHHh-CCCcEEEEechhhcC-------------------------------------
Confidence            1                   2233332 567999999999751                                     


Q ss_pred             CCCCCCCCCcchhhhHHHHhhhccCCccCC-------CCCeEEEEEeCCCC-----------------------------
Q 009640          330 GNNNNNNGEESGRVTLSGLLNFTDGLWSCC-------SEEKIIVFTTNHRD-----------------------------  373 (530)
Q Consensus       330 ~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~-------~~~~ivI~TTN~~~-----------------------------  373 (530)
                                  ....+.|+..+|.-.-..       -.+.+||+|||...                             
T Consensus       682 ------------~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  749 (852)
T TIGR03345       682 ------------PDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLK  749 (852)
T ss_pred             ------------HHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHH
Confidence                        224556666665321000       13578999999521                             


Q ss_pred             CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          374 SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       374 ~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      .+.|+|+.  |++ .|.|.+.+.++...|+...+.
T Consensus       750 ~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv~~~L~  781 (852)
T TIGR03345       750 VFKPAFLG--RMT-VIPYLPLDDDVLAAIVRLKLD  781 (852)
T ss_pred             hccHHHhc--cee-EEEeCCCCHHHHHHHHHHHHH
Confidence            14577777  998 789999999999999988764

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=99.20  E-value=4.4e-10  Score=129.81  Aligned_cols=161  Identities=17%  Similarity=0.312  Sum_probs=108.1

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHH
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSE  269 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~  269 (530)
                      ++.|+|++...+.|...+......-.   .-+.| ...+||+||||||||++|++||+.+   +..++.++++.+.....
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~---~~~~p-~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~  642 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLS---DPNRP-IGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHS  642 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhccc---CCCCC-CceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhh
Confidence            55688988888888887765432100   00001 1258999999999999999999987   45677777766543322


Q ss_pred             HHHHH---------------Hh---cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          270 LRALL---------------LQ---TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       270 L~~l~---------------~~---~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      ..+++               ..   ....+||+|||||.+-                                       
T Consensus       643 ~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~---------------------------------------  683 (857)
T PRK10865        643 VSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAH---------------------------------------  683 (857)
T ss_pred             HHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCC---------------------------------------
Confidence            32222               11   1234899999999761                                       


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCc-cC------CCCCeEEEEEeCCC-------------------------CCCChhh
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLW-SC------CSEEKIIVFTTNHR-------------------------DSVDPAL  379 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~-s~------~~~~~ivI~TTN~~-------------------------~~LDpAL  379 (530)
                                ....+.|++.+|.-. ..      .-.+.+||+|||..                         ..+.|+|
T Consensus       684 ----------~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEL  753 (857)
T PRK10865        684 ----------PDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEF  753 (857)
T ss_pred             ----------HHHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHH
Confidence                      224566777665211 00      01235889999973                         1345788


Q ss_pred             hcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          380 IRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       380 lRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      +.  |+|..|.|.+++.+....|++.++.
T Consensus       754 ln--Rld~iivF~PL~~edl~~Iv~~~L~  780 (857)
T PRK10865        754 IN--RIDEVVVFHPLGEQHIASIAQIQLQ  780 (857)
T ss_pred             HH--hCCeeEecCCCCHHHHHHHHHHHHH
Confidence            88  9999999999999999999988874

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.19  E-value=5.1e-10  Score=129.62  Aligned_cols=160  Identities=18%  Similarity=0.308  Sum_probs=108.0

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSEL  270 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L  270 (530)
                      ..|+|++...+.|.+.+......-.   . ...+...+||+||||||||++|++||..+   +.+++.++++.......+
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~---~-~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~  640 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLS---D-PNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSV  640 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCC---C-CCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchH
Confidence            5688899888888887776432100   0 00112358999999999999999999988   467888887765433222


Q ss_pred             HHH---------------HH---hcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          271 RAL---------------LL---QTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       271 ~~l---------------~~---~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      .++               |.   .....+||+|||||.+                                         
T Consensus       641 ~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka-----------------------------------------  679 (852)
T TIGR03346       641 ARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKA-----------------------------------------  679 (852)
T ss_pred             HHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccC-----------------------------------------
Confidence            222               11   1234589999999976                                         


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCc--cC-----CCCCeEEEEEeCCCCC-------------------------CChhhh
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLW--SC-----CSEEKIIVFTTNHRDS-------------------------VDPALI  380 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~--s~-----~~~~~ivI~TTN~~~~-------------------------LDpALl  380 (530)
                              .....+.||+.+|.-.  ..     .-.+.|||+|||....                         +.|.|+
T Consensus       680 --------~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~  751 (852)
T TIGR03346       680 --------HPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFL  751 (852)
T ss_pred             --------CHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHh
Confidence                    1234566777774221  00     0134689999998321                         345666


Q ss_pred             cCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          381 RCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       381 RpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      .  |+|..|.|.+++.+....|+..++.
T Consensus       752 ~--Rid~IivF~PL~~e~l~~I~~l~L~  777 (852)
T TIGR03346       752 N--RIDEIVVFHPLGREQIARIVEIQLG  777 (852)
T ss_pred             c--CcCeEEecCCcCHHHHHHHHHHHHH
Confidence            6  9999999999999999999987764

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.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.19  E-value=4.4e-10  Score=116.40  Aligned_cols=153  Identities=20%  Similarity=0.293  Sum_probs=101.0

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-------CcE--------
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-------YDV--------  256 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-------~~i--------  256 (530)
                      .|..|+|++++|..+.-.+..+             ...++||.||||||||++++++++.+.       .++        
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            5889999999988776544321             135799999999999999999998772       111        


Q ss_pred             -------------------------EEEecC----ccCChHHHHHHHH-----------hcCCCeEEEEcCccchhhhhh
Q 009640          257 -------------------------YDLELT----KVTDNSELRALLL-----------QTTNRSIIVIEDIDCSVDLTA  296 (530)
Q Consensus       257 -------------------------~~l~l~----~~~~~~~L~~l~~-----------~~~~~sII~IDeID~~~~~~~  296 (530)
                                               .++.++    .+.+.-++.+.+.           ......+||||||+.+-    
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                                     111110    1111223333221           11345799999999861    


Q ss_pred             hhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc---------CCccCCCCCeEEEE
Q 009640          297 DRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD---------GLWSCCSEEKIIVF  367 (530)
Q Consensus       297 ~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD---------gl~s~~~~~~ivI~  367 (530)
                                                                   ..+.+.|++.|+         |.........++|+
T Consensus       145 ---------------------------------------------~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~ivia  179 (337)
T TIGR02030       145 ---------------------------------------------DHLVDVLLDVAASGWNVVEREGISIRHPARFVLVG  179 (337)
T ss_pred             ---------------------------------------------HHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEe
Confidence                                                         223445555553         33222234567777


Q ss_pred             EeCCCC-CCChhhhcCCceeEEEEeCCCCH-HHHHHHHHHhhC
Q 009640          368 TTNHRD-SVDPALIRCGRMDVHVSLGTCGP-HAFKVLAKNYLG  408 (530)
Q Consensus       368 TTN~~~-~LDpALlRpGR~d~~I~~~~p~~-~~r~~i~~~~l~  408 (530)
                      |+|..+ .|+++|+.  ||..+|.+++|+. +++..|+++...
T Consensus       180 t~np~eg~l~~~Lld--Rf~l~i~l~~p~~~eer~eIL~~~~~  220 (337)
T TIGR02030       180 SGNPEEGELRPQLLD--RFGLHAEIRTVRDVELRVEIVERRTE  220 (337)
T ss_pred             ccccccCCCCHHHHh--hcceEEECCCCCCHHHHHHHHHhhhh
Confidence            888655 69999999  9999999999976 888999987544

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.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.18  E-value=1.2e-10  Score=111.42  Aligned_cols=195  Identities=15%  Similarity=0.277  Sum_probs=123.8

Q ss_pred             CCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-C----
Q 009640          179 DSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-C----  253 (530)
Q Consensus       179 ~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-~----  253 (530)
                      +..|  +..++|..+.+++|.++..+.+.    -+.....         -..+++.||||||||+-+.++|++| |    
T Consensus        14 ~l~w--VeKYrP~~l~dIVGNe~tv~rl~----via~~gn---------mP~liisGpPG~GKTTsi~~LAr~LLG~~~k   78 (333)
T KOG0991|consen   14 QLPW--VEKYRPSVLQDIVGNEDTVERLS----VIAKEGN---------MPNLIISGPPGTGKTTSILCLARELLGDSYK   78 (333)
T ss_pred             cchH--HHhhCchHHHHhhCCHHHHHHHH----HHHHcCC---------CCceEeeCCCCCchhhHHHHHHHHHhChhhh
Confidence            3458  88999999999999998655443    2332221         2479999999999999999999987 3    


Q ss_pred             CcEEEEecCccCChHHHH---HHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccc
Q 009640          254 YDVYDLELTKVTDNSELR---ALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRI  324 (530)
Q Consensus       254 ~~i~~l~l~~~~~~~~L~---~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~  324 (530)
                      --+..++.++-.+-.-+|   +.|.+.      ...-||++||.|++-.  +                            
T Consensus        79 e~vLELNASdeRGIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~--g----------------------------  128 (333)
T KOG0991|consen   79 EAVLELNASDERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTA--G----------------------------  128 (333)
T ss_pred             hHhhhccCccccccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhh--H----------------------------
Confidence            234566666655444443   345543      1335999999998721  0                            


Q ss_pred             ccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          325 ASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       325 ~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                                         ....|-..|+=..+    ..-+.+++|..+++-+.+.+  |+-.                -
T Consensus       129 -------------------AQQAlRRtMEiyS~----ttRFalaCN~s~KIiEPIQS--RCAi----------------L  167 (333)
T KOG0991|consen  129 -------------------AQQALRRTMEIYSN----TTRFALACNQSEKIIEPIQS--RCAI----------------L  167 (333)
T ss_pred             -------------------HHHHHHHHHHHHcc----cchhhhhhcchhhhhhhHHh--hhHh----------------h
Confidence                               11223333332222    23477788988887666655  3311                1


Q ss_pred             HhhCCcCccchHHHHHHHHH-hCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHhh
Q 009640          405 NYLGIESHHALFDVVESCIR-AGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKI  460 (530)
Q Consensus       405 ~~l~~~~~~~~~~~i~~l~~-~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~~  460 (530)
                      +|-...+.. ....+.+.++ +...||+.-+..++..+.+|++.|++.+........
T Consensus       168 Rysklsd~q-iL~Rl~~v~k~Ekv~yt~dgLeaiifta~GDMRQalNnLQst~~g~g  223 (333)
T KOG0991|consen  168 RYSKLSDQQ-ILKRLLEVAKAEKVNYTDDGLEAIIFTAQGDMRQALNNLQSTVNGFG  223 (333)
T ss_pred             hhcccCHHH-HHHHHHHHHHHhCCCCCcchHHHhhhhccchHHHHHHHHHHHhcccc
Confidence            122222222 2222333322 468899999999999999999999999887765443

>PRK09087 hypothetical protein; Validated

Probab=99.18  E-value=5.2e-10  Score=109.87  Aligned_cols=152  Identities=15%  Similarity=0.121  Sum_probs=90.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++++..+.-.. +...+..+.   .       ...+.++||||+|+|||||++++|+..+..+++..  .+
T Consensus        12 ~~~~~~~~~~~Fi~~~~N~~-a~~~l~~~~---~-------~~~~~l~l~G~~GsGKThLl~~~~~~~~~~~i~~~--~~   78 (226)
T PRK09087         12 FSHDPAYGRDDLLVTESNRA-AVSLVDHWP---N-------WPSPVVVLAGPVGSGKTHLASIWREKSDALLIHPN--EI   78 (226)
T ss_pred             CCCCCCCChhceeecCchHH-HHHHHHhcc---c-------CCCCeEEEECCCCCCHHHHHHHHHHhcCCEEecHH--Hc
Confidence            34456678999875332221 222222211   1       01234899999999999999999998776655442  21


Q ss_pred             CChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhh
Q 009640          265 TDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVT  344 (530)
Q Consensus       265 ~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (530)
                      . ..-+    .... ..+|+|||+|.+-                                            .   .+..
T Consensus        79 ~-~~~~----~~~~-~~~l~iDDi~~~~--------------------------------------------~---~~~~  105 (226)
T PRK09087         79 G-SDAA----NAAA-EGPVLIEDIDAGG--------------------------------------------F---DETG  105 (226)
T ss_pred             c-hHHH----Hhhh-cCeEEEECCCCCC--------------------------------------------C---CHHH
Confidence            1 1111    1111 2588899999751                                            0   1122


Q ss_pred             HHHHhhhccCCccCCCCCeEEEEEeCCCCC---CChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhCC
Q 009640          345 LSGLLNFTDGLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       345 ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      +-.++|.+   ..  .+..+||.++..|..   ..|.|+.  |+.  ..+++..|+.+.+..+++..+..
T Consensus       106 lf~l~n~~---~~--~g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l~~pd~e~~~~iL~~~~~~  168 (226)
T PRK09087        106 LFHLINSV---RQ--AGTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEIGEPDDALLSQVIFKLFAD  168 (226)
T ss_pred             HHHHHHHH---Hh--CCCeEEEECCCChHHhccccccHHH--HHhCCceeecCCCCHHHHHHHHHHHHHH
Confidence            34444443   32  133444444444442   3688988  775  88999999999999999988754

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.17  E-value=3.8e-10  Score=125.13  Aligned_cols=206  Identities=20%  Similarity=0.267  Sum_probs=127.9

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEE-
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD-  258 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~-  258 (530)
                      ..|  +..+.|.++++|+++++..+.+...+.....        +....+.++|+||||||||++++++|++++.+++. 
T Consensus        72 ~pW--~eKyrP~~ldel~~~~~ki~~l~~~l~~~~~--------~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew  141 (637)
T TIGR00602        72 EPW--VEKYKPETQHELAVHKKKIEEVETWLKAQVL--------ENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEW  141 (637)
T ss_pred             Cch--HHHhCCCCHHHhcCcHHHHHHHHHHHHhccc--------ccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHH
Confidence            368  7789999999999999888776665543221        12223459999999999999999999999876533 


Q ss_pred             EecC--------------------cc-CChHHHHHHHHhc------------CCCeEEEEcCccchhhhhhhhhhcccCC
Q 009640          259 LELT--------------------KV-TDNSELRALLLQT------------TNRSIIVIEDIDCSVDLTADRMLKSSNT  305 (530)
Q Consensus       259 l~l~--------------------~~-~~~~~L~~l~~~~------------~~~sII~IDeID~~~~~~~~r~~~~~~~  305 (530)
                      ++..                    .+ .....+..++..+            ..+.||||||||.++.            
T Consensus       142 ~npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~------------  209 (637)
T TIGR00602       142 SNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFY------------  209 (637)
T ss_pred             hhhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhch------------
Confidence            1110                    00 1223344444432            3567999999998741            


Q ss_pred             ccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhh--hccCCccCCCCCeEEEEEeC-CCC---------
Q 009640          306 STTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLN--FTDGLWSCCSEEKIIVFTTN-HRD---------  373 (530)
Q Consensus       306 ~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn--~lDgl~s~~~~~~ivI~TTN-~~~---------  373 (530)
                                                       . ....+..+|.  ..+      .....+|+++| .+.         
T Consensus       210 ---------------------------------r-~~~~lq~lLr~~~~e------~~~~pLI~I~TE~~~~~~~~~~~~  249 (637)
T TIGR00602       210 ---------------------------------R-DTRALHEILRWKYVS------IGRCPLVFIITESLEGDNNQRRLL  249 (637)
T ss_pred             ---------------------------------h-hHHHHHHHHHHHhhc------CCCceEEEEecCCccccccccccc
Confidence                                             0 0113344444  221      12233444333 221         


Q ss_pred             -----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHH
Q 009640          374 -----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLA  448 (530)
Q Consensus       374 -----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~a  448 (530)
                           .|.++++..-|+ .+|.|.+.+....+..++..+..+... ..       ....--++..|..++..+.+|.+.|
T Consensus       250 f~~~~lL~~eLls~~rv-~~I~FnPia~t~l~K~L~rIl~~E~~~-~~-------~~~~~p~~~~l~~I~~~s~GDiRsA  320 (637)
T TIGR00602       250 FPAETIMNKEILEEPRV-SNISFNPIAPTIMKKFLNRIVTIEAKK-NG-------EKIKVPKKTSVELLCQGCSGDIRSA  320 (637)
T ss_pred             cchhcccCHhHhcccce-eEEEeCCCCHHHHHHHHHHHHHhhhhc-cc-------cccccCCHHHHHHHHHhCCChHHHH
Confidence                 134788843355 379999999999888887776543211 00       0001125677888888888999999


Q ss_pred             HHHHHHHH
Q 009640          449 MKEVVSAM  456 (530)
Q Consensus       449 l~~l~~~l  456 (530)
                      +..|.-+.
T Consensus       321 In~LQf~~  328 (637)
T TIGR00602       321 INSLQFSS  328 (637)
T ss_pred             HHHHHHHH
Confidence            98887553

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

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.15  E-value=7e-10  Score=128.06  Aligned_cols=159  Identities=16%  Similarity=0.272  Sum_probs=105.4

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHH-
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSE-  269 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~-  269 (530)
                      +.|+|+++..+.|...+......-   ..-+.| ...+||+||||||||+||+++|..+   ..+++.++++++..... 
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl---~~~~~p-~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGL---KNPNRP-IASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTV  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcc---cCCCCC-ceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccH
Confidence            557888888888877765432110   000111 1248999999999999999999988   35677777766532222 


Q ss_pred             ------------------HHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          270 ------------------LRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       270 ------------------L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                                        |...+. ....+||+|||||.+-                                       
T Consensus       585 ~~l~g~~~gyvg~~~~~~l~~~~~-~~p~~VvllDeieka~---------------------------------------  624 (821)
T CHL00095        585 SKLIGSPPGYVGYNEGGQLTEAVR-KKPYTVVLFDEIEKAH---------------------------------------  624 (821)
T ss_pred             HHhcCCCCcccCcCccchHHHHHH-hCCCeEEEECChhhCC---------------------------------------
Confidence                              222222 1345999999999861                                       


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCcc--C-----CCCCeEEEEEeCCCCC------------------------------
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWS--C-----CSEEKIIVFTTNHRDS------------------------------  374 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s--~-----~~~~~ivI~TTN~~~~------------------------------  374 (530)
                                ....+.||..+|.-.-  .     .-.+.|||+|||....                              
T Consensus       625 ----------~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~  694 (821)
T CHL00095        625 ----------PDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLV  694 (821)
T ss_pred             ----------HHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHH
Confidence                      2345667777763210  0     0145789999995321                              


Q ss_pred             -------CChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          375 -------VDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       375 -------LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                             +.|.|+.  |+|..|.|.+.+.++...|+...+.
T Consensus       695 ~~~~~~~f~pefln--Rid~ii~F~pL~~~~l~~Iv~~~l~  733 (821)
T CHL00095        695 NEELKQFFRPEFLN--RLDEIIVFRQLTKNDVWEIAEIMLK  733 (821)
T ss_pred             HHHHHHhcCHHHhc--cCCeEEEeCCCCHHHHHHHHHHHHH
Confidence                   2345666  9999999999999999999988764

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.14  E-value=1.4e-09  Score=112.55  Aligned_cols=124  Identities=21%  Similarity=0.303  Sum_probs=95.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC------------------------cEEEEecCc---cCChHHHHHHHHhc---
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY------------------------DVYDLELTK---VTDNSELRALLLQT---  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~------------------------~i~~l~l~~---~~~~~~L~~l~~~~---  277 (530)
                      +.+|||+||+|+||+++|.++|+.+..                        |++.+....   ...-+++|.+....   
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~~~~~  101 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSFVVQT  101 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHHHhhc
Confidence            458999999999999999999998843                        556665432   22445677765543   


Q ss_pred             ---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC
Q 009640          278 ---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG  354 (530)
Q Consensus       278 ---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg  354 (530)
                         ...-|++||++|.+                                                 +....+.||+.|+.
T Consensus       102 ~~~~~~kv~iI~~a~~m-------------------------------------------------~~~aaNaLLK~LEE  132 (328)
T PRK05707        102 AQLGGRKVVLIEPAEAM-------------------------------------------------NRNAANALLKSLEE  132 (328)
T ss_pred             cccCCCeEEEECChhhC-------------------------------------------------CHHHHHHHHHHHhC
Confidence               24568899999987                                                 12356789999985


Q ss_pred             CccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          355 LWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       355 l~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                      -    .++.++|++|+.++.|.|.+++  |+.. |.|+.|+.++....+....
T Consensus       133 P----p~~~~fiL~t~~~~~ll~TI~S--Rc~~-~~~~~~~~~~~~~~L~~~~  178 (328)
T PRK05707        133 P----SGDTVLLLISHQPSRLLPTIKS--RCQQ-QACPLPSNEESLQWLQQAL  178 (328)
T ss_pred             C----CCCeEEEEEECChhhCcHHHHh--hcee-eeCCCcCHHHHHHHHHHhc
Confidence            3    3578899999999999999998  8755 8999999998887776554

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=99.13  E-value=2.9e-09  Score=111.57  Aligned_cols=154  Identities=18%  Similarity=0.277  Sum_probs=109.5

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc-----EEEEecCccCChH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD-----VYDLELTKVTDNS  268 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~-----i~~l~l~~~~~~~  268 (530)
                      +.+..-++..+++...+..++.+..         |..+++|||||||||..++-++.++...     ++.+++....+..
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~---------p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~   87 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGER---------PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPY   87 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCC---------CccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHH
Confidence            3477788888888888877776543         3469999999999999999999998444     7777766553322


Q ss_pred             H-------------------------HHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccc
Q 009640          269 E-------------------------LRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSR  323 (530)
Q Consensus       269 ~-------------------------L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~  323 (530)
                      .                         +.+.+.......||++||+|.+++                              
T Consensus        88 ~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~------------------------------  137 (366)
T COG1474          88 QVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVD------------------------------  137 (366)
T ss_pred             HHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhcc------------------------------
Confidence            2                         122222234568999999999852                              


Q ss_pred             cccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC---CCCChhhhcCCce-eEEEEeCCCCHHHH
Q 009640          324 IASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR---DSVDPALIRCGRM-DVHVSLGTCGPHAF  399 (530)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~---~~LDpALlRpGR~-d~~I~~~~p~~~~r  399 (530)
                                    ..  ..+|-.|+..-+-.    ...+++|+.+|..   +.|||.+.+  ++ ..+|.|++.+.++.
T Consensus       138 --------------~~--~~~LY~L~r~~~~~----~~~v~vi~i~n~~~~~~~ld~rv~s--~l~~~~I~F~pY~a~el  195 (366)
T COG1474         138 --------------KD--GEVLYSLLRAPGEN----KVKVSIIAVSNDDKFLDYLDPRVKS--SLGPSEIVFPPYTAEEL  195 (366)
T ss_pred             --------------cc--chHHHHHHhhcccc----ceeEEEEEEeccHHHHHHhhhhhhh--ccCcceeeeCCCCHHHH
Confidence                          00  14555666554433    3457888888875   578998887  44 35699999999999


Q ss_pred             HHHHHHhhC
Q 009640          400 KVLAKNYLG  408 (530)
Q Consensus       400 ~~i~~~~l~  408 (530)
                      ..|+..-..
T Consensus       196 ~~Il~~R~~  204 (366)
T COG1474         196 YDILRERVE  204 (366)
T ss_pred             HHHHHHHHH
Confidence            999987654

>PRK08116 hypothetical protein; Validated

Probab=99.12  E-value=2.5e-10  Score=114.94  Aligned_cols=150  Identities=17%  Similarity=0.243  Sum_probs=88.6

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD  266 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~  266 (530)
                      ..+|+++...+... .+......|.++-   .... ...+|++||||||||||+|+.|||+++   +..++.++...+..
T Consensus        81 ~~tFdnf~~~~~~~-~a~~~a~~y~~~~---~~~~-~~~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~  155 (268)
T PRK08116         81 NSTFENFLFDKGSE-KAYKIARKYVKKF---EEMK-KENVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLN  155 (268)
T ss_pred             hcchhcccCChHHH-HHHHHHHHHHHHH---Hhhc-cCCceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHH
Confidence            34677765444432 2333344444321   1111 123689999999999999999999997   67777777554311


Q ss_pred             ----------hHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          267 ----------NSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       267 ----------~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                                ......++....+..+|+|||+...-                                            
T Consensus       156 ~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~--------------------------------------------  191 (268)
T PRK08116        156 RIKSTYKSSGKEDENEIIRSLVNADLLILDDLGAER--------------------------------------------  191 (268)
T ss_pred             HHHHHHhccccccHHHHHHHhcCCCEEEEecccCCC--------------------------------------------
Confidence                      01122344445667899999996420                                            


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC-CC----CChhhhcCCce---eEEEEeCCCCH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR-DS----VDPALIRCGRM---DVHVSLGTCGP  396 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~-~~----LDpALlRpGR~---d~~I~~~~p~~  396 (530)
                      .   .......|.+.||....   .+..+|+|||.+ +.    +++++..  |+   ...|.|.-+|.
T Consensus       192 ~---t~~~~~~l~~iin~r~~---~~~~~IiTsN~~~~eL~~~~~~ri~s--Rl~e~~~~v~~~g~d~  251 (268)
T PRK08116        192 D---TEWAREKVYNIIDSRYR---KGLPTIVTTNLSLEELKNQYGKRIYD--RILEMCTPVENEGKSY  251 (268)
T ss_pred             C---CHHHHHHHHHHHHHHHH---CCCCEEEECCCCHHHHHHHHhHHHHH--HHHHcCEEEEeeCcCh
Confidence            0   11233455666664432   345688899975 22    5777776  64   45567766665

>PRK12377 putative replication protein; Provisional

Probab=99.08  E-value=1.2e-09  Score=108.47  Aligned_cols=96  Identities=18%  Similarity=0.293  Sum_probs=61.2

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~  265 (530)
                      ...+|+++....+-.+.+...+..|...-.   .    ...+++|+||||||||+|+.|||+++   +..+..+...++.
T Consensus        69 ~~~tFdnf~~~~~~~~~a~~~a~~~a~~~~---~----~~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~  141 (248)
T PRK12377         69 RKCSFANYQVQNDGQRYALSQAKSIADELM---T----GCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVM  141 (248)
T ss_pred             ccCCcCCcccCChhHHHHHHHHHHHHHHHH---h----cCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHH
Confidence            444788775433333333333433332211   0    13689999999999999999999998   5666666654432


Q ss_pred             C--------hHHHHHHHHhcCCCeEEEEcCccch
Q 009640          266 D--------NSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       266 ~--------~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      .        .....+++.......+|+||||...
T Consensus       142 ~~l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~  175 (248)
T PRK12377        142 SRLHESYDNGQSGEKFLQELCKVDLLVLDEIGIQ  175 (248)
T ss_pred             HHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            1        1123355666788999999999864

>PRK09183 transposase/IS protein; Provisional

Probab=99.08  E-value=4.2e-10  Score=112.79  Aligned_cols=128  Identities=13%  Similarity=0.161  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhccccCCCCCCCCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhc
Q 009640          145 LLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVG  224 (530)
Q Consensus       145 vl~~yl~~v~~~~~~~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g  224 (530)
                      -..+||..+++.+...++.++..+..+.+.++..       ..-....|+...+.   .+..+..+..    -.+     
T Consensus        38 ~~~e~l~~ll~~E~~~R~~~~~~~~~k~a~~p~~-------~~l~~fd~~~~~~~---~~~~i~~L~~----~~~-----   98 (259)
T PRK09183         38 SYMDFLEHLLHEEKLARHQRKQAMYTRMAAFPAV-------KTFEEYDFTFATGA---PQKQLQSLRS----LSF-----   98 (259)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC-------CcHhhcccccCCCC---CHHHHHHHhc----CCc-----
Confidence            3568999999998888888888888877655431       00011111211121   1122222221    111     


Q ss_pred             CCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC-------hHHHHHHHHh-cCCCeEEEEcCccch
Q 009640          225 RAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD-------NSELRALLLQ-TTNRSIIVIEDIDCS  291 (530)
Q Consensus       225 ~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~-------~~~L~~l~~~-~~~~sII~IDeID~~  291 (530)
                      +....+++|+||||||||+|+.|+|+.+   |+.+..++...+..       ...+...+.. ...+.+++|||++..
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~~dlLiiDdlg~~  176 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYL  176 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcCCCEEEEcccccC
Confidence            1113579999999999999999998775   66666665443321       1123344544 467789999999864

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.07  E-value=2e-09  Score=114.19  Aligned_cols=27  Identities=37%  Similarity=0.614  Sum_probs=24.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      ++.++|+||||||||++|+++|+.++.
T Consensus       194 ~~~iil~GppGtGKT~lA~~la~~l~~  220 (459)
T PRK11331        194 KKNIILQGPPGVGKTFVARRLAYLLTG  220 (459)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhcC
Confidence            468999999999999999999998853

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.06  E-value=1.1e-09  Score=96.51  Aligned_cols=65  Identities=26%  Similarity=0.417  Sum_probs=48.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCc---EEEEecCccC--------------------ChHHHHHHHHhc--CCCeE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYD---VYDLELTKVT--------------------DNSELRALLLQT--TNRSI  282 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~---i~~l~l~~~~--------------------~~~~L~~l~~~~--~~~sI  282 (530)
                      ...++|+||||||||++++++|..+...   ++.++.....                    ....+..++..+  ..+.|
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            3579999999999999999999999775   7777655432                    122344444444  34699


Q ss_pred             EEEcCccchh
Q 009640          283 IVIEDIDCSV  292 (530)
Q Consensus       283 I~IDeID~~~  292 (530)
                      |+|||++.+.
T Consensus        82 iiiDei~~~~   91 (148)
T smart00382       82 LILDEITSLL   91 (148)
T ss_pred             EEEECCcccC
Confidence            9999999874

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=99.05  E-value=6.4e-09  Score=107.02  Aligned_cols=147  Identities=18%  Similarity=0.240  Sum_probs=104.6

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----------------
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----------------  254 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----------------  254 (530)
                      .|++|+|++++++.+...+..    .        ..+..||||||+|+||+++|.++|+.+-.                 
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            488999999988877775532    1        11458999999999999999999998722                 


Q ss_pred             -cEEEEecCcc-----------------------CChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccC
Q 009640          255 -DVYDLELTKV-----------------------TDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSN  304 (530)
Q Consensus       255 -~i~~l~l~~~-----------------------~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~  304 (530)
                       |++.+.....                       ..-..++.+....      ...-|++||++|.+-            
T Consensus        70 PDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~------------  137 (314)
T PRK07399         70 PDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMN------------  137 (314)
T ss_pred             CCEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcC------------
Confidence             2233322110                       0112445553322      346799999998861            


Q ss_pred             CccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCc
Q 009640          305 TSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGR  384 (530)
Q Consensus       305 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR  384 (530)
                                                           ....+.||..|+..    + ..++|++|+.++.|-|.+++  |
T Consensus       138 -------------------------------------~~aaNaLLK~LEEP----p-~~~fILi~~~~~~Ll~TI~S--R  173 (314)
T PRK07399        138 -------------------------------------EAAANALLKTLEEP----G-NGTLILIAPSPESLLPTIVS--R  173 (314)
T ss_pred             -------------------------------------HHHHHHHHHHHhCC----C-CCeEEEEECChHhCcHHHHh--h
Confidence                                                 22456899999854    2 34688889999999999998  7


Q ss_pred             eeEEEEeCCCCHHHHHHHHHHhh
Q 009640          385 MDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       385 ~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                      . ..|.|+.++.++...++....
T Consensus       174 c-q~i~f~~l~~~~~~~~L~~~~  195 (314)
T PRK07399        174 C-QIIPFYRLSDEQLEQVLKRLG  195 (314)
T ss_pred             c-eEEecCCCCHHHHHHHHHHhh
Confidence            5 669999999999988888764

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.05  E-value=7.4e-09  Score=107.11  Aligned_cols=65  Identities=23%  Similarity=0.283  Sum_probs=52.8

Q ss_pred             CCCcc-cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-------cEEEEec
Q 009640          190 PSTFE-TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-------DVYDLEL  261 (530)
Q Consensus       190 ~~~f~-~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-------~i~~l~l  261 (530)
                      -.-|+ ++.|+++.++++.+.+.....+.       ...++.++|+||||||||||+.++|+.++.       .+|.+..
T Consensus        46 y~~F~~~~~G~~~~i~~lv~~l~~~a~g~-------~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~  118 (361)
T smart00763       46 YRFFDHDFFGMEEAIERFVNYFKSAAQGL-------EERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKW  118 (361)
T ss_pred             ccccchhccCcHHHHHHHHHHHHHHHhcC-------CCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEe
Confidence            33567 89999999999988777665321       123578999999999999999999999976       8999977

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK04132 replication factor C small subunit; Provisional

Probab=99.04  E-value=3.3e-09  Score=120.69  Aligned_cols=154  Identities=14%  Similarity=0.150  Sum_probs=115.1

Q ss_pred             EEEEC--CCCCChhHHHHHHHHHc-----CCcEEEEecCccCChHHHHHHHHhc----C----CCeEEEEcCccchhhhh
Q 009640          231 YLLYG--PPGSGKSSLIAAMANYL-----CYDVYDLELTKVTDNSELRALLLQT----T----NRSIIVIEDIDCSVDLT  295 (530)
Q Consensus       231 ~LL~G--PPGTGKTsLa~AiA~~l-----~~~i~~l~l~~~~~~~~L~~l~~~~----~----~~sII~IDeID~~~~~~  295 (530)
                      .+..|  |++.||||+|.|+|+++     +.+++.++.++..+-..+++++...    +    +.-||+|||+|.+-   
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            45568  99999999999999998     6689999999877777888776542    1    23699999999971   


Q ss_pred             hhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCC
Q 009640          296 ADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSV  375 (530)
Q Consensus       296 ~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~L  375 (530)
                                                                    ....+.|+..|+..    .....+|++||.++.+
T Consensus       644 ----------------------------------------------~~AQnALLk~lEep----~~~~~FILi~N~~~kI  673 (846)
T PRK04132        644 ----------------------------------------------QDAQQALRRTMEMF----SSNVRFILSCNYSSKI  673 (846)
T ss_pred             ----------------------------------------------HHHHHHHHHHhhCC----CCCeEEEEEeCChhhC
Confidence                                                          12356788888854    3457899999999999


Q ss_pred             ChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHH
Q 009640          376 DPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSA  455 (530)
Q Consensus       376 DpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~  455 (530)
                      .|+|++  |+ ..+.|+.|+.++....++..+..+               ...+++..+..++..+.+|+..|+..+...
T Consensus       674 i~tIrS--RC-~~i~F~~ls~~~i~~~L~~I~~~E---------------gi~i~~e~L~~Ia~~s~GDlR~AIn~Lq~~  735 (846)
T PRK04132        674 IEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENE---------------GLELTEEGLQAILYIAEGDMRRAINILQAA  735 (846)
T ss_pred             chHHhh--hc-eEEeCCCCCHHHHHHHHHHHHHhc---------------CCCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            999998  75 668999999887776665543221               233566666777777777777777766544

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.04  E-value=2.8e-09  Score=109.53  Aligned_cols=119  Identities=19%  Similarity=0.302  Sum_probs=88.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC------------------------CcEEEEecCccCC----hHHHHHHHHhc----
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC------------------------YDVYDLELTKVTD----NSELRALLLQT----  277 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~------------------------~~i~~l~l~~~~~----~~~L~~l~~~~----  277 (530)
                      .+|||||||||||++|.++|+.+.                        .+++.++.+....    ...++++....    
T Consensus        26 alL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~~~  105 (325)
T COG0470          26 ALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSESP  105 (325)
T ss_pred             eeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHHhccCC
Confidence            699999999999999999999986                        5888888887755    33455554433    


Q ss_pred             --CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCC
Q 009640          278 --TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGL  355 (530)
Q Consensus       278 --~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl  355 (530)
                        ...-||+|||+|.+-                                                 ....+.|+..+.--
T Consensus       106 ~~~~~kviiidead~mt-------------------------------------------------~~A~nallk~lEep  136 (325)
T COG0470         106 LEGGYKVVIIDEADKLT-------------------------------------------------EDAANALLKTLEEP  136 (325)
T ss_pred             CCCCceEEEeCcHHHHh-------------------------------------------------HHHHHHHHHHhccC
Confidence              245799999999872                                                 12345677777633


Q ss_pred             ccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          356 WSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       356 ~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                          .....+|++||.++.+-|.+.+  |+ ..|.|..|+...+.....
T Consensus       137 ----~~~~~~il~~n~~~~il~tI~S--Rc-~~i~f~~~~~~~~i~~~e  178 (325)
T COG0470         137 ----PKNTRFILITNDPSKILPTIRS--RC-QRIRFKPPSRLEAIAWLE  178 (325)
T ss_pred             ----CCCeEEEEEcCChhhccchhhh--cc-eeeecCCchHHHHHHHhh
Confidence                3567899999999999998887  65 447887766665555444

>PRK08939 primosomal protein DnaI; Reviewed

Probab=99.04  E-value=8.4e-10  Score=113.10  Aligned_cols=97  Identities=21%  Similarity=0.330  Sum_probs=67.1

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC-
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT-  265 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~-  265 (530)
                      ..+|+++...+.-+..+......|+..-.   . | +..+|++||||||||||+|+.|||+++   |+.+..+....+. 
T Consensus       123 ~atf~~~~~~~~~~~~~~~~~~~fi~~~~---~-~-~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~  197 (306)
T PRK08939        123 QASLADIDLDDRDRLDALMAALDFLEAYP---P-G-EKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIR  197 (306)
T ss_pred             cCcHHHhcCCChHHHHHHHHHHHHHHHhh---c-c-CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHH
Confidence            46788887655445555555556664311   1 1 245799999999999999999999998   6777766655431 


Q ss_pred             ------ChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          266 ------DNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       266 ------~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                            .+..+.+.+.......+|+||||.+-
T Consensus       198 ~lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e  229 (306)
T PRK08939        198 ELKNSISDGSVKEKIDAVKEAPVLMLDDIGAE  229 (306)
T ss_pred             HHHHHHhcCcHHHHHHHhcCCCEEEEecCCCc
Confidence                  11234556666788899999999863

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.03  E-value=2.9e-09  Score=110.42  Aligned_cols=146  Identities=21%  Similarity=0.319  Sum_probs=103.0

Q ss_pred             CcccccC-ChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------------
Q 009640          192 TFETLAL-EPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------------  254 (530)
Q Consensus       192 ~f~~l~~-~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------------  254 (530)
                      .|++|.| ++.+.+.+...+.    ..        ..+..||||||+|+||+++|.++|+.+..                
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----KN--------RLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCK   70 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHH----cC--------CCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHH
Confidence            3677877 7777666655442    21        12468999999999999999999998632                


Q ss_pred             --------cEEEEecCcc-CChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhh
Q 009640          255 --------DVYDLELTKV-TDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKE  319 (530)
Q Consensus       255 --------~i~~l~l~~~-~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~  319 (530)
                              |++.+....- ..-.+++.+....      ...-|++|||+|.+-                           
T Consensus        71 ~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~---------------------------  123 (329)
T PRK08058         71 RIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMT---------------------------  123 (329)
T ss_pred             HHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhC---------------------------
Confidence                    2333332211 1234566665433      245699999999871                           


Q ss_pred             hccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHH
Q 009640          320 MGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAF  399 (530)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r  399 (530)
                                            ....+.||..|+..    ++..++|++|+.++.|-|++++  |. ..|+|..|+.++.
T Consensus       124 ----------------------~~a~NaLLK~LEEP----p~~~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~~~~  174 (329)
T PRK08058        124 ----------------------ASAANSLLKFLEEP----SGGTTAILLTENKHQILPTILS--RC-QVVEFRPLPPESL  174 (329)
T ss_pred             ----------------------HHHHHHHHHHhcCC----CCCceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCHHHH
Confidence                                  22457899999854    4567888999999999999998  65 4589999999988


Q ss_pred             HHHHHH
Q 009640          400 KVLAKN  405 (530)
Q Consensus       400 ~~i~~~  405 (530)
                      ...++.
T Consensus       175 ~~~L~~  180 (329)
T PRK08058        175 IQRLQE  180 (329)
T ss_pred             HHHHHH
Confidence            777764

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

Probab=99.02  E-value=4.6e-09  Score=117.48  Aligned_cols=161  Identities=17%  Similarity=0.286  Sum_probs=116.6

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---CcEEEEecCccCChHHH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---YDVYDLELTKVTDNSEL  270 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~~~~~~~~L  270 (530)
                      ..|+|+++..+.|.+.+..-..+=.   .-.. +...+||.||.|+|||-||+++|..|.   -.++.++++++.....+
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~---dp~r-PigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsV  566 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLG---DPNR-PIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSV  566 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCC---CCCC-CceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHH
Confidence            4578888888888887765432100   0001 123588899999999999999999996   78899999988766666


Q ss_pred             HHHHHhc------------------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          271 RALLLQT------------------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       271 ~~l~~~~------------------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      .+|+-..                  ...|||+||||+..                                         
T Consensus       567 SrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKA-----------------------------------------  605 (786)
T COG0542         567 SRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKA-----------------------------------------  605 (786)
T ss_pred             HHHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhc-----------------------------------------
Confidence            6664321                  24599999999976                                         


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCccCCCC-------CeEEEEEeCCCC----------------------------CCCh
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWSCCSE-------EKIIVFTTNHRD----------------------------SVDP  377 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s~~~~-------~~ivI~TTN~~~----------------------------~LDp  377 (530)
                              ...+++-||+.+|.-.-..+.       +.|||||||--.                            ...|
T Consensus       606 --------HpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~P  677 (786)
T COG0542         606 --------HPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRP  677 (786)
T ss_pred             --------CHHHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCH
Confidence                    234778888888743222122       358999999531                            1345


Q ss_pred             hhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          378 ALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       378 ALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      +|+.  |+|..|.|.+.+.+....|+..++..
T Consensus       678 EFLN--Rid~II~F~~L~~~~l~~Iv~~~L~~  707 (786)
T COG0542         678 EFLN--RIDEIIPFNPLSKEVLERIVDLQLNR  707 (786)
T ss_pred             HHHh--hcccEEeccCCCHHHHHHHHHHHHHH
Confidence            6676  99999999999999999999988753

>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=3.2e-10  Score=100.23  Aligned_cols=105  Identities=24%  Similarity=0.282  Sum_probs=61.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHH--HHhc-------C---CCeEEEEcCccchhhhhhh
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRAL--LLQT-------T---NRSIIVIEDIDCSVDLTAD  297 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l--~~~~-------~---~~sII~IDeID~~~~~~~~  297 (530)
                      ++||.|+||+|||++++++|..++.++..+..+.-...+++...  +...       .   -..|+++|||...      
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNra------   74 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRA------   74 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS------
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccC------
Confidence            47999999999999999999999999999987643333333221  1110       1   1369999999876      


Q ss_pred             hhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc-------CCccCCCCCeEEEEEeC
Q 009640          298 RMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD-------GLWSCCSEEKIIVFTTN  370 (530)
Q Consensus       298 r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD-------gl~s~~~~~~ivI~TTN  370 (530)
                                                                 ...+.+.||..|.       |..-...+..+||+|-|
T Consensus        75 -------------------------------------------ppktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqN  111 (131)
T PF07726_consen   75 -------------------------------------------PPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQN  111 (131)
T ss_dssp             --------------------------------------------HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-
T ss_pred             -------------------------------------------CHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecC
Confidence                                                       2346677887763       33333356678899999


Q ss_pred             CCC-----CCChhhhcCCce
Q 009640          371 HRD-----SVDPALIRCGRM  385 (530)
Q Consensus       371 ~~~-----~LDpALlRpGR~  385 (530)
                      ..+     .|++|++.  ||
T Consensus       112 p~e~~Gty~Lpea~~D--RF  129 (131)
T PF07726_consen  112 PVEQEGTYPLPEAQLD--RF  129 (131)
T ss_dssp             TT--S------HHHHT--TS
T ss_pred             ccccCceecCCHHHhc--cc
Confidence            877     68999998  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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.02  E-value=1.7e-09  Score=115.60  Aligned_cols=128  Identities=20%  Similarity=0.241  Sum_probs=80.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC--c--EEEEecCc---cCChHHHHHH-----HHh-----cCCCeEEEEcCccc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY--D--VYDLELTK---VTDNSELRAL-----LLQ-----TTNRSIIVIEDIDC  290 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~--~--i~~l~l~~---~~~~~~L~~l-----~~~-----~~~~sII~IDeID~  290 (530)
                      ...+||+||||||||++|+++|..++.  .  +..+..+.   +.+...+...     |..     .....|||+|||..
T Consensus        39 g~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~r  118 (498)
T PRK13531         39 GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWK  118 (498)
T ss_pred             CCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcCcHHHhhhhhcCchhhhcCCccccccEEeeccccc
Confidence            357999999999999999999998753  2  22332211   1111111111     111     11334999999986


Q ss_pred             hhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc-CCccC-----CCCCeE
Q 009640          291 SVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD-GLWSC-----CSEEKI  364 (530)
Q Consensus       291 ~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD-gl~s~-----~~~~~i  364 (530)
                      +                                                 +..+.+.||..|. +....     .-..++
T Consensus       119 a-------------------------------------------------sp~~QsaLLeam~Er~~t~g~~~~~lp~rf  149 (498)
T PRK13531        119 A-------------------------------------------------GPAILNTLLTAINERRFRNGAHEEKIPMRL  149 (498)
T ss_pred             C-------------------------------------------------CHHHHHHHHHHHHhCeEecCCeEEeCCCcE
Confidence            5                                                 2346778888883 22111     113367


Q ss_pred             EEEEeCCCC---CCChhhhcCCceeEEEEeCCCC-HHHHHHHHHHh
Q 009640          365 IVFTTNHRD---SVDPALIRCGRMDVHVSLGTCG-PHAFKVLAKNY  406 (530)
Q Consensus       365 vI~TTN~~~---~LDpALlRpGR~d~~I~~~~p~-~~~r~~i~~~~  406 (530)
                      +++|||...   ...+|+..  ||-.+|.++||+ .++.+.|+...
T Consensus       150 iv~ATN~LPE~g~~leAL~D--RFliri~vp~l~~~~~e~~lL~~~  193 (498)
T PRK13531        150 LVTASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQ  193 (498)
T ss_pred             EEEECCCCcccCCchHHhHh--hEEEEEECCCCCchHHHHHHHHcc
Confidence            777888422   23359999  999999999997 57778887653

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.00  E-value=2.7e-09  Score=119.83  Aligned_cols=153  Identities=19%  Similarity=0.278  Sum_probs=101.1

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-------------------
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-------------------  252 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-------------------  252 (530)
                      .|..|+|++.++..+.-...    .+.         ..|+||+||||||||+++++|++.+                   
T Consensus         2 pf~~ivGq~~~~~al~~~av----~~~---------~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~   68 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAV----DPR---------IGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPE   68 (633)
T ss_pred             CcchhcChHHHHHHHHHHhh----CCC---------CCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCcc
Confidence            57899999988876644332    211         2479999999999999999999988                   


Q ss_pred             ----------------CCcEEEEecCcc----CChHHHHHHHHh-----------cCCCeEEEEcCccchhhhhhhhhhc
Q 009640          253 ----------------CYDVYDLELTKV----TDNSELRALLLQ-----------TTNRSIIVIEDIDCSVDLTADRMLK  301 (530)
Q Consensus       253 ----------------~~~i~~l~l~~~----~~~~~L~~l~~~-----------~~~~sII~IDeID~~~~~~~~r~~~  301 (530)
                                      ..+++.+.++..    .+.-++...+..           .....|||||||+.+-         
T Consensus        69 ~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~---------  139 (633)
T TIGR02442        69 EWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLD---------  139 (633)
T ss_pred             ccChhhhhcccccccCCCCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCC---------
Confidence                            234555443321    112223333321           1244699999999871         


Q ss_pred             ccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc-C--------CccCCCCCeEEEEEeCCC
Q 009640          302 SSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD-G--------LWSCCSEEKIIVFTTNHR  372 (530)
Q Consensus       302 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD-g--------l~s~~~~~~ivI~TTN~~  372 (530)
                                                              ..+.+.||+.|+ |        .........++|+|+|..
T Consensus       140 ----------------------------------------~~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~  179 (633)
T TIGR02442       140 ----------------------------------------DHLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPE  179 (633)
T ss_pred             ----------------------------------------HHHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCC
Confidence                                                    234556676664 2        111112346788888864


Q ss_pred             -CCCChhhhcCCceeEEEEeCCCC-HHHHHHHHHHhhC
Q 009640          373 -DSVDPALIRCGRMDVHVSLGTCG-PHAFKVLAKNYLG  408 (530)
Q Consensus       373 -~~LDpALlRpGR~d~~I~~~~p~-~~~r~~i~~~~l~  408 (530)
                       ..|.++|+.  ||+.+|.++++. .+++.+++...+.
T Consensus       180 eg~l~~~L~d--R~~l~i~v~~~~~~~~~~~il~~~~~  215 (633)
T TIGR02442       180 EGDLRPQLLD--RFGLCVDVAAPRDPEERVEIIRRRLA  215 (633)
T ss_pred             CCCCCHHHHh--hcceEEEccCCCchHHHHHHHHHHHh
Confidence             368999999  999999999885 5777888876543

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.

>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=99.00  E-value=4.4e-10  Score=105.67  Aligned_cols=64  Identities=25%  Similarity=0.524  Sum_probs=51.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC----cEEEEecCccCC----hHHHHHHHHhcC------CCeEEEEcCccchh
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY----DVYDLELTKVTD----NSELRALLLQTT------NRSIIVIEDIDCSV  292 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~----~i~~l~l~~~~~----~~~L~~l~~~~~------~~sII~IDeID~~~  292 (530)
                      ..+||.||+|||||.|++++|..+..    ++..++++.+..    ...+.+++....      ...||+|||||.+.
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~   81 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAH   81 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhHHHhhcc
Confidence            56899999999999999999999996    999999999887    444555554432      33599999999973

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 ....

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

Probab=98.98  E-value=5.4e-09  Score=110.26  Aligned_cols=134  Identities=20%  Similarity=0.310  Sum_probs=95.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe-cCcc------CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhh
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE-LTKV------TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRM  299 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~-l~~~------~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~  299 (530)
                      ..+||+||||+|||+||+.||...+++|+.+- ..+.      ..-..+++.|..+  +.-|||++|||+.+++-..   
T Consensus       539 vSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD~vp---  615 (744)
T KOG0741|consen  539 VSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYVP---  615 (744)
T ss_pred             eEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhcccc---
Confidence            57999999999999999999999999998763 2222      2234588889988  4569999999999974211   


Q ss_pred             hcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEE-EEeCCCCCCC-h
Q 009640          300 LKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIV-FTTNHRDSVD-P  377 (530)
Q Consensus       300 ~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI-~TTN~~~~LD-p  377 (530)
                                                          -+..-+..++..|+..+.....  .+++++| +||...+-|. -
T Consensus       616 ------------------------------------IGPRfSN~vlQaL~VllK~~pp--kg~kLli~~TTS~~~vL~~m  657 (744)
T KOG0741|consen  616 ------------------------------------IGPRFSNLVLQALLVLLKKQPP--KGRKLLIFGTTSRREVLQEM  657 (744)
T ss_pred             ------------------------------------cCchhhHHHHHHHHHHhccCCC--CCceEEEEecccHHHHHHHc
Confidence                                                2234467788999999987765  3445554 5666555443 2


Q ss_pred             hhhcCCceeEEEEeCCCCH-HHHHHHHHH
Q 009640          378 ALIRCGRMDVHVSLGTCGP-HAFKVLAKN  405 (530)
Q Consensus       378 ALlRpGR~d~~I~~~~p~~-~~r~~i~~~  405 (530)
                      .++.  .|+-.|++|..+. ++...++..
T Consensus       658 ~i~~--~F~~~i~Vpnl~~~~~~~~vl~~  684 (744)
T KOG0741|consen  658 GILD--CFSSTIHVPNLTTGEQLLEVLEE  684 (744)
T ss_pred             CHHH--hhhheeecCccCchHHHHHHHHH
Confidence            4445  7888999987766 555555443

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=98.95  E-value=1e-08  Score=106.29  Aligned_cols=57  Identities=12%  Similarity=0.202  Sum_probs=48.5

Q ss_pred             hhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          343 VTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       343 ~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                      ..-+.||+.|+.-    ..+.++|++|++++.|.|.+++  |+ ..|.|+.|+.++....+...
T Consensus       147 ~AaNaLLKtLEEP----p~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        147 AAANALLKTLEEP----PPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             HHHHHHHHHhcCC----CcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            3568899999853    5678999999999999999998  87 68999999999988887654

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.93  E-value=1e-08  Score=102.53  Aligned_cols=94  Identities=26%  Similarity=0.453  Sum_probs=61.1

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD  266 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~  266 (530)
                      ...+.++-+.+...+.....+..+..   +|.     -..+++||||||||||+|+.|||+++   |..++.+...++..
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            33445555666555555555544442   121     25799999999999999999999998   56667766655421


Q ss_pred             -------hHHHH-HHHHhcCCCeEEEEcCccch
Q 009640          267 -------NSELR-ALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       267 -------~~~L~-~l~~~~~~~sII~IDeID~~  291 (530)
                             +.... ++.....+..+||||||-..
T Consensus       147 ~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~  179 (254)
T COG1484         147 KLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYE  179 (254)
T ss_pred             HHHHHHhcCchHHHHHHHhhcCCEEEEecccCc
Confidence                   11122 23333677889999999864

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=98.92  E-value=1.4e-08  Score=106.75  Aligned_cols=168  Identities=16%  Similarity=0.214  Sum_probs=100.6

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----CcEEEE
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----YDVYDL  259 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----~~i~~l  259 (530)
                      ....+..+|++++..+.-... ......+...+.      . ....++||||.|.|||+|++|++++..     ..++.+
T Consensus        78 ~~l~~~ytFdnFv~g~~N~~A-~aa~~~va~~~g------~-~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~  149 (408)
T COG0593          78 SGLNPKYTFDNFVVGPSNRLA-YAAAKAVAENPG------G-AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYL  149 (408)
T ss_pred             ccCCCCCchhheeeCCchHHH-HHHHHHHHhccC------C-cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEec
Confidence            445677899998766554332 222333333332      1 235789999999999999999999983     234444


Q ss_pred             ecCccCCh--HHH----HHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCC
Q 009640          260 ELTKVTDN--SEL----RALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNN  333 (530)
Q Consensus       260 ~l~~~~~~--~~L----~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~  333 (530)
                      ....+...  ..+    ..-|.+..+-.+++||||+.+.                                         
T Consensus       150 ~se~f~~~~v~a~~~~~~~~Fk~~y~~dlllIDDiq~l~-----------------------------------------  188 (408)
T COG0593         150 TSEDFTNDFVKALRDNEMEKFKEKYSLDLLLIDDIQFLA-----------------------------------------  188 (408)
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHhhccCeeeechHhHhc-----------------------------------------
Confidence            33322100  000    0112222355699999999983                                         


Q ss_pred             CCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCC---ChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhC
Q 009640          334 NNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSV---DPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       334 ~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~L---DpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                         +....+..+-.+.|.+   ..  .++.||+.+...|..|   +|.|.+  ||.  ..+.+..|+.+.|..|++....
T Consensus       189 ---gk~~~qeefFh~FN~l---~~--~~kqIvltsdr~P~~l~~~~~rL~S--R~~~Gl~~~I~~Pd~e~r~aiL~kka~  258 (408)
T COG0593         189 ---GKERTQEEFFHTFNAL---LE--NGKQIVLTSDRPPKELNGLEDRLRS--RLEWGLVVEIEPPDDETRLAILRKKAE  258 (408)
T ss_pred             ---CChhHHHHHHHHHHHH---Hh--cCCEEEEEcCCCchhhccccHHHHH--HHhceeEEeeCCCCHHHHHHHHHHHHH
Confidence               1111233333344433   32  2335555554556654   589998  764  7888999999999999988654


Q ss_pred             CcC
Q 009640          409 IES  411 (530)
Q Consensus       409 ~~~  411 (530)
                      ...
T Consensus       259 ~~~  261 (408)
T COG0593         259 DRG  261 (408)
T ss_pred             hcC
Confidence            433

>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=98.91  E-value=3e-08  Score=92.44  Aligned_cols=110  Identities=22%  Similarity=0.311  Sum_probs=79.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC-----------------------CcEEEEecCcc---CChHHHHHHHHhc----
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC-----------------------YDVYDLELTKV---TDNSELRALLLQT----  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~-----------------------~~i~~l~l~~~---~~~~~L~~l~~~~----  277 (530)
                      +..||||||+|+||+++|.++|+.+-                       .|++.++....   ..-.+++.+....    
T Consensus        19 ~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~~   98 (162)
T PF13177_consen   19 PHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLSP   98 (162)
T ss_dssp             -SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS-
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHHHHHHHHHHHH
Confidence            45799999999999999999999771                       35566655443   3456777776654    


Q ss_pred             --CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCC
Q 009640          278 --TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGL  355 (530)
Q Consensus       278 --~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl  355 (530)
                        ...-|++|||+|.+                                                 .....+.||..|+..
T Consensus        99 ~~~~~KviiI~~ad~l-------------------------------------------------~~~a~NaLLK~LEep  129 (162)
T PF13177_consen   99 SEGKYKVIIIDEADKL-------------------------------------------------TEEAQNALLKTLEEP  129 (162)
T ss_dssp             TTSSSEEEEEETGGGS--------------------------------------------------HHHHHHHHHHHHST
T ss_pred             hcCCceEEEeehHhhh-------------------------------------------------hHHHHHHHHHHhcCC
Confidence              24569999999987                                                 233568899999854


Q ss_pred             ccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCC
Q 009640          356 WSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGT  393 (530)
Q Consensus       356 ~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~  393 (530)
                          ....++|++|+.++.|-|.+++  |. ..|.|+.
T Consensus       130 ----p~~~~fiL~t~~~~~il~TI~S--Rc-~~i~~~~  160 (162)
T PF13177_consen  130 ----PENTYFILITNNPSKILPTIRS--RC-QVIRFRP  160 (162)
T ss_dssp             ----TTTEEEEEEES-GGGS-HHHHT--TS-EEEEE--
T ss_pred             ----CCCEEEEEEECChHHChHHHHh--hc-eEEecCC
Confidence                4678999999999999999998  75 3455554

...

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.91  E-value=4.1e-08  Score=107.17  Aligned_cols=71  Identities=28%  Similarity=0.471  Sum_probs=57.8

Q ss_pred             CCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          179 DSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       179 ~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      ...|  +..+.|.+.++|+......++|...+...+..        ....+-+||+||||||||++++++|+++++++..
T Consensus         6 ~~~W--~~ky~P~~~~eLavhkkKv~eV~~wl~~~~~~--------~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~E   75 (519)
T PF03215_consen    6 SEPW--VEKYAPKTLDELAVHKKKVEEVRSWLEEMFSG--------SSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQE   75 (519)
T ss_pred             cCcc--chhcCCCCHHHhhccHHHHHHHHHHHHHHhcc--------CCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEE
Confidence            3478  88899999999999988888888877764432        2334567889999999999999999999988865


Q ss_pred             E
Q 009640          259 L  259 (530)
Q Consensus       259 l  259 (530)
                      -
T Consensus        76 w   76 (519)
T PF03215_consen   76 W   76 (519)
T ss_pred             e
Confidence            3

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.88  E-value=1.3e-08  Score=102.07  Aligned_cols=194  Identities=16%  Similarity=0.215  Sum_probs=119.0

Q ss_pred             CCCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc--
Q 009640          178 YDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD--  255 (530)
Q Consensus       178 ~~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~--  255 (530)
                      +..+|  ++.++|..++++++++++...+.+    |...+.         -...|+|||||||||+.+.|.|..+-.+  
T Consensus        27 ~~~pw--vekyrP~~l~dv~~~~ei~st~~~----~~~~~~---------lPh~L~YgPPGtGktsti~a~a~~ly~~~~   91 (360)
T KOG0990|consen   27 YPQPW--VEKYRPPFLGIVIKQEPIWSTENR----YSGMPG---------LPHLLFYGPPGTGKTSTILANARDFYSPHP   91 (360)
T ss_pred             cCCCC--ccCCCCchhhhHhcCCchhhHHHH----hccCCC---------CCcccccCCCCCCCCCchhhhhhhhcCCCC
Confidence            44568  889999999999998886554444    333221         2389999999999999999999988442  


Q ss_pred             ----EEEEecCccCCh---HHHHHHHHhcC---------CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhh
Q 009640          256 ----VYDLELTKVTDN---SELRALLLQTT---------NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKE  319 (530)
Q Consensus       256 ----i~~l~l~~~~~~---~~L~~l~~~~~---------~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~  319 (530)
                          +..++++.-.+-   ..-.+.|..+.         ..-.|++||.|++-                           
T Consensus        92 ~~~m~lelnaSd~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT---------------------------  144 (360)
T KOG0990|consen   92 TTSMLLELNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMT---------------------------  144 (360)
T ss_pred             chhHHHHhhccCccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHhh---------------------------
Confidence                222333332221   12223344433         56789999999872                           


Q ss_pred             hccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHH
Q 009640          320 MGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAF  399 (530)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r  399 (530)
                                            +...++|-..+.-+.    .+.-++.-+|++.++.|++..  |+.. ..|..-+...-
T Consensus       145 ----------------------~~AQnALRRviek~t----~n~rF~ii~n~~~ki~pa~qs--Rctr-frf~pl~~~~~  195 (360)
T KOG0990|consen  145 ----------------------RDAQNALRRVIEKYT----ANTRFATISNPPQKIHPAQQS--RCTR-FRFAPLTMAQQ  195 (360)
T ss_pred             ----------------------HHHHHHHHHHHHHhc----cceEEEEeccChhhcCchhhc--cccc-CCCCCCChhhh
Confidence                                  111233334444332    344455789999999999996  5533 34555555555


Q ss_pred             HHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHH
Q 009640          400 KVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQ  457 (530)
Q Consensus       400 ~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~  457 (530)
                      .....+....+.               ..++|.-...+..-..+|..+|++.+...+.
T Consensus       196 ~~r~shi~e~e~---------------~~~~~~~~~a~~r~s~gDmr~a~n~Lqs~~~  238 (360)
T KOG0990|consen  196 TERQSHIRESEQ---------------KETNPEGYSALGRLSVGDMRVALNYLQSILK  238 (360)
T ss_pred             hhHHHHHHhcch---------------hhcCHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            555555544332               2344444444555556677777777665544

>smart00350 MCM minichromosome maintenance proteins

Probab=98.87  E-value=8.5e-09  Score=113.05  Aligned_cols=159  Identities=18%  Similarity=0.200  Sum_probs=95.1

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCC--CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe----cCccCChH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAW--KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE----LTKVTDNS  268 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~--~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~----l~~~~~~~  268 (530)
                      .+.|.+.+|..|.-.+.   ..-.....-|...  ...+||+|+||||||++++++++.+....|...    ...+.. .
T Consensus       204 ~i~G~~~~k~~l~l~l~---gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~~l~~-~  279 (509)
T smart00350      204 SIYGHEDIKKAILLLLF---GGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTA-A  279 (509)
T ss_pred             cccCcHHHHHHHHHHHh---CCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcCCccc-c
Confidence            46777777776654332   2111000111111  225999999999999999999998865544321    111100 0


Q ss_pred             HHHHH----------HHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          269 ELRAL----------LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       269 ~L~~l----------~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                      .++.-          ........+++|||+|.+-                                              
T Consensus       280 ~~~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~----------------------------------------------  313 (509)
T smart00350      280 VTRDPETREFTLEGGALVLADNGVCCIDEFDKMD----------------------------------------------  313 (509)
T ss_pred             ceEccCcceEEecCccEEecCCCEEEEechhhCC----------------------------------------------
Confidence            01110          0112356799999999872                                              


Q ss_pred             cchhhhHHHHhhhcc---------CCccCCCCCeEEEEEeCCCC-------------CCChhhhcCCceeEEEE-eCCCC
Q 009640          339 ESGRVTLSGLLNFTD---------GLWSCCSEEKIIVFTTNHRD-------------SVDPALIRCGRMDVHVS-LGTCG  395 (530)
Q Consensus       339 ~~~~~~ls~LLn~lD---------gl~s~~~~~~ivI~TTN~~~-------------~LDpALlRpGR~d~~I~-~~~p~  395 (530)
                         ..+.+.|+..|+         |....-.....||+|+|..+             .|+|+|++  |||..+. +.+|+
T Consensus       314 ---~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLs--RFdLi~~~~d~~~  388 (509)
T smart00350      314 ---DSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEENIDLPAPILS--RFDLLFVVLDEVD  388 (509)
T ss_pred             ---HHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhccCCChHHhC--ceeeEEEecCCCC
Confidence               112334444442         22211124567889999763             59999999  9997654 58999


Q ss_pred             HHHHHHHHHHhhC
Q 009640          396 PHAFKVLAKNYLG  408 (530)
Q Consensus       396 ~~~r~~i~~~~l~  408 (530)
                      .+....|+++.+.
T Consensus       389 ~~~d~~i~~~i~~  401 (509)
T smart00350      389 EERDRELAKHVVD  401 (509)
T ss_pred             hHHHHHHHHHHHH
Confidence            9999999988654

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=98.86  E-value=6.6e-08  Score=100.34  Aligned_cols=123  Identities=16%  Similarity=0.170  Sum_probs=92.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC------------------------CcEEEEecCc---cCChHHHHHHHHhc---
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC------------------------YDVYDLELTK---VTDNSELRALLLQT---  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~------------------------~~i~~l~l~~---~~~~~~L~~l~~~~---  277 (530)
                      +.+|||+||+|+||+++|.++|..+-                        -|++.+....   ..+-+.+|.+....   
T Consensus        24 ~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~  103 (334)
T PRK07993         24 HHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKSSLGVDAVREVTEKLYEH  103 (334)
T ss_pred             ceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccCCHHHHHHHHHHHhhc
Confidence            45899999999999999999999872                        2344453321   13445666665543   


Q ss_pred             ---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC
Q 009640          278 ---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG  354 (530)
Q Consensus       278 ---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg  354 (530)
                         ...-|++||++|.+                                                 ....-+.||+.|+.
T Consensus       104 ~~~g~~kV~iI~~ae~m-------------------------------------------------~~~AaNaLLKtLEE  134 (334)
T PRK07993        104 ARLGGAKVVWLPDAALL-------------------------------------------------TDAAANALLKTLEE  134 (334)
T ss_pred             cccCCceEEEEcchHhh-------------------------------------------------CHHHHHHHHHHhcC
Confidence               24569999999987                                                 12346789999985


Q ss_pred             CccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          355 LWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       355 l~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                      -    +++.++|++|++++.|-|.+++  |.- .+.|+.|+.++....+...
T Consensus       135 P----p~~t~fiL~t~~~~~lLpTIrS--RCq-~~~~~~~~~~~~~~~L~~~  179 (334)
T PRK07993        135 P----PENTWFFLACREPARLLATLRS--RCR-LHYLAPPPEQYALTWLSRE  179 (334)
T ss_pred             C----CCCeEEEEEECChhhChHHHHh--ccc-cccCCCCCHHHHHHHHHHc
Confidence            3    5678999999999999999998  775 5899999998888776543

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=98.84  E-value=1.4e-07  Score=97.10  Aligned_cols=122  Identities=15%  Similarity=0.218  Sum_probs=86.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC---------------------cEEEEe--cCcc-------CChHHHHHHHHhc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY---------------------DVYDLE--LTKV-------TDNSELRALLLQT  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~---------------------~i~~l~--l~~~-------~~~~~L~~l~~~~  277 (530)
                      +.+|||+||+|+||+++|.++|+.+-.                     |++.+.  ...-       ..-+.++.+....
T Consensus        26 ~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~~~  105 (319)
T PRK08769         26 GHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQKL  105 (319)
T ss_pred             ceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHHHHH
Confidence            458999999999999999999987622                     233332  1110       1233455554432


Q ss_pred             ------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhh
Q 009640          278 ------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF  351 (530)
Q Consensus       278 ------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~  351 (530)
                            ...-|++||++|.+                                                 +....+.||+.
T Consensus       106 ~~~p~~g~~kV~iI~~ae~m-------------------------------------------------~~~AaNaLLKt  136 (319)
T PRK08769        106 ALTPQYGIAQVVIVDPADAI-------------------------------------------------NRAACNALLKT  136 (319)
T ss_pred             hhCcccCCcEEEEeccHhhh-------------------------------------------------CHHHHHHHHHH
Confidence                  13358888888876                                                 22356789999


Q ss_pred             ccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          352 TDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       352 lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                      |+.-    ..+.++|++|+.++.|-|.+++  |+ ..|.|+.|+.++-...+..
T Consensus       137 LEEP----p~~~~fiL~~~~~~~lLpTIrS--RC-q~i~~~~~~~~~~~~~L~~  183 (319)
T PRK08769        137 LEEP----SPGRYLWLISAQPARLPATIRS--RC-QRLEFKLPPAHEALAWLLA  183 (319)
T ss_pred             hhCC----CCCCeEEEEECChhhCchHHHh--hh-eEeeCCCcCHHHHHHHHHH
Confidence            9854    4567899999999999999998  76 4588999999877776654

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.82  E-value=2.8e-08  Score=102.72  Aligned_cols=63  Identities=24%  Similarity=0.391  Sum_probs=46.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC---------hHHHHHHHHhcCCCeEEEEcCccch
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD---------NSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~---------~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      .+++||||||||||+|+.|||+++   ++.++.++...+..         ..+....+.......+|+|||+...
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e  258 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTE  258 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCC
Confidence            689999999999999999999998   67777776554311         1112222444567789999999864

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=98.81  E-value=7.4e-08  Score=107.22  Aligned_cols=128  Identities=18%  Similarity=0.225  Sum_probs=88.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC--cEEEEecCcc----CChHHHHHHHH-----------hcCCCeEEEEcCccch
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY--DVYDLELTKV----TDNSELRALLL-----------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~--~i~~l~l~~~----~~~~~L~~l~~-----------~~~~~sII~IDeID~~  291 (530)
                      .|+||.|+||||||+++++++..+..  +|..+.....    .+.-++...+.           ......+||||||+.+
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            58999999999999999999998865  3666654211    11111221111           0134479999999987


Q ss_pred             hhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc---------CCccCCCCC
Q 009640          292 VDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD---------GLWSCCSEE  362 (530)
Q Consensus       292 ~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD---------gl~s~~~~~  362 (530)
                      -                                                 ..+.+.|++.|+         |........
T Consensus        97 ~-------------------------------------------------~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~  127 (589)
T TIGR02031        97 D-------------------------------------------------DGLSNRLLQALDEGVVIVEREGISVVHPAK  127 (589)
T ss_pred             C-------------------------------------------------HHHHHHHHHHHHcCCeEEEECCCceeecCc
Confidence            1                                                 234566777664         222212234


Q ss_pred             eEEEEEeCCCC---CCChhhhcCCceeEEEEeCCC-CHHHHHHHHHHhh
Q 009640          363 KIIVFTTNHRD---SVDPALIRCGRMDVHVSLGTC-GPHAFKVLAKNYL  407 (530)
Q Consensus       363 ~ivI~TTN~~~---~LDpALlRpGR~d~~I~~~~p-~~~~r~~i~~~~l  407 (530)
                      ..||+|+|..+   .|.++|+.  ||+.+|.+.++ +..+|.+|++.++
T Consensus       128 f~lIAt~np~e~~g~L~~~Lld--Rf~l~v~~~~~~~~~er~eil~~~~  174 (589)
T TIGR02031       128 FALIATYDPAEGGGGLPDHLLD--RLALHVSLEDVASQDLRVEIVRRER  174 (589)
T ss_pred             eEEEEecCCccccCCCCHHHHH--hccCeeecCCCCCHHHHHHHHHHHH
Confidence            67888999876   79999999  99999998765 6677899998876

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=98.76  E-value=2.9e-07  Score=101.75  Aligned_cols=91  Identities=13%  Similarity=0.199  Sum_probs=69.8

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~  265 (530)
                      ...+|+.++|....-+.+++.+.......           ..+||+|++||||+++|++|....   +.+++.+++..+.
T Consensus       191 ~~~~~~~liG~s~~~~~~~~~~~~~a~~~-----------~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~  259 (534)
T TIGR01817       191 RSGKEDGIIGKSPAMRQVVDQARVVARSN-----------STVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALS  259 (534)
T ss_pred             ccCccCceEECCHHHHHHHHHHHHHhCcC-----------CCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCC
Confidence            34578999999988888888887776543           479999999999999999999885   5689999998874


Q ss_pred             ChHHHHHHH-H-----------------hcCCCeEEEEcCccch
Q 009640          266 DNSELRALL-L-----------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       266 ~~~~L~~l~-~-----------------~~~~~sII~IDeID~~  291 (530)
                      . ..+...+ -                 .......|||||||.+
T Consensus       260 ~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L  302 (534)
T TIGR01817       260 E-TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEI  302 (534)
T ss_pred             H-HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhC
Confidence            3 3333322 1                 1234578999999987

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.

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

Probab=98.76  E-value=5.2e-08  Score=109.15  Aligned_cols=154  Identities=21%  Similarity=0.298  Sum_probs=105.4

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEec
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLEL  261 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l  261 (530)
                      .++-++|-++..+.+++.|.+..             +..-+|.|+||+|||.++..+|...          +..+|.+++
T Consensus       168 klDPvIGRd~EI~r~iqIL~RR~-------------KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~  234 (786)
T COG0542         168 KLDPVIGRDEEIRRTIQILSRRT-------------KNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDL  234 (786)
T ss_pred             CCCCCcChHHHHHHHHHHHhccC-------------CCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecH
Confidence            46778887776666666554332             3456899999999999999999876          778899988


Q ss_pred             CccC--------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          262 TKVT--------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       262 ~~~~--------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      ..+.        -+..|+.++...  ..+.|||||||+.+.+..+.                                  
T Consensus       235 g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~----------------------------------  280 (786)
T COG0542         235 GSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGAT----------------------------------  280 (786)
T ss_pred             HHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcc----------------------------------
Confidence            7763        245677887765  34899999999998641110                                  


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                          .+  . ..-.+.+|.-.  +   ..++.-+|++|+..+     .=|+||-|  ||.. |.+..|+.++-..|++-.
T Consensus       281 ----~G--~-a~DAaNiLKPa--L---ARGeL~~IGATT~~EYRk~iEKD~AL~R--RFQ~-V~V~EPs~e~ti~ILrGl  345 (786)
T COG0542         281 ----EG--G-AMDAANLLKPA--L---ARGELRCIGATTLDEYRKYIEKDAALER--RFQK-VLVDEPSVEDTIAILRGL  345 (786)
T ss_pred             ----cc--c-ccchhhhhHHH--H---hcCCeEEEEeccHHHHHHHhhhchHHHh--cCce-eeCCCCCHHHHHHHHHHH
Confidence                00  0 11122233221  1   135566777665433     24999999  9955 899999999999998754


Q ss_pred             h
Q 009640          407 L  407 (530)
Q Consensus       407 l  407 (530)
                      -
T Consensus       346 k  346 (786)
T COG0542         346 K  346 (786)
T ss_pred             H
Confidence            3

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=98.76  E-value=1.1e-07  Score=98.01  Aligned_cols=123  Identities=15%  Similarity=0.167  Sum_probs=91.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC------------------------cEEEEecC--ccCChHHHHHHHHhc----
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY------------------------DVYDLELT--KVTDNSELRALLLQT----  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~------------------------~i~~l~l~--~~~~~~~L~~l~~~~----  277 (530)
                      +.+|||+||+|+||+++|.++|..+-.                        |++.+...  ...+-+++|.+....    
T Consensus        24 ~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~I~id~iR~l~~~~~~~~  103 (325)
T PRK06871         24 HHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKDIGVDQVREINEKVSQHA  103 (325)
T ss_pred             ceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCCCCHHHHHHHHHHHhhcc
Confidence            458999999999999999999998732                        23444321  112345666664443    


Q ss_pred             --CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCC
Q 009640          278 --TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGL  355 (530)
Q Consensus       278 --~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl  355 (530)
                        ...-|++||++|.+                                                 +....+.||..|+.-
T Consensus       104 ~~g~~KV~iI~~a~~m-------------------------------------------------~~~AaNaLLKtLEEP  134 (325)
T PRK06871        104 QQGGNKVVYIQGAERL-------------------------------------------------TEAAANALLKTLEEP  134 (325)
T ss_pred             ccCCceEEEEechhhh-------------------------------------------------CHHHHHHHHHHhcCC
Confidence              23458889999987                                                 233567899999853


Q ss_pred             ccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          356 WSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       356 ~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                          .+..++|++|++++.|.|.+++  |. ..+.|+.|+.++....+...
T Consensus       135 ----p~~~~fiL~t~~~~~llpTI~S--RC-~~~~~~~~~~~~~~~~L~~~  178 (325)
T PRK06871        135 ----RPNTYFLLQADLSAALLPTIYS--RC-QTWLIHPPEEQQALDWLQAQ  178 (325)
T ss_pred             ----CCCeEEEEEECChHhCchHHHh--hc-eEEeCCCCCHHHHHHHHHHH
Confidence                5678999999999999999998  76 55899999998888777654

>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=98.75  E-value=1.7e-08  Score=96.78  Aligned_cols=46  Identities=28%  Similarity=0.537  Sum_probs=35.9

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .|++|.|++.+|+.+.-...            |   ..++||+||||||||++|++++..|
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            37899999999988765442            1   3589999999999999999999877

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=98.74  E-value=3.4e-07  Score=94.98  Aligned_cols=83  Identities=16%  Similarity=0.269  Sum_probs=58.1

Q ss_pred             cCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHHH-
Q 009640          197 ALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELRA-  272 (530)
Q Consensus       197 ~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~~-  272 (530)
                      +|....-+.+.+.+......           ...+||+|+|||||+++|++|-...   +.+++.+++..+.. ..+.. 
T Consensus         2 iG~S~~m~~~~~~~~~~a~~-----------~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~-~~l~~~   69 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPL-----------DRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSE-NLLDSE   69 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCCh-HHHHHH
Confidence            34444555566666655543           3579999999999999999998766   46899999987643 23332 


Q ss_pred             HH-----------------HhcCCCeEEEEcCccch
Q 009640          273 LL-----------------LQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       273 l~-----------------~~~~~~sII~IDeID~~  291 (530)
                      +|                 ........|||||||.+
T Consensus        70 lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L  105 (329)
T TIGR02974        70 LFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATA  105 (329)
T ss_pred             HhccccccccCcccccCCchhhCCCCEEEeCChHhC
Confidence            22                 11235689999999987

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

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.73  E-value=5.8e-09  Score=98.73  Aligned_cols=63  Identities=27%  Similarity=0.556  Sum_probs=45.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC-------ChHHHHHHHHhcCCCeEEEEcCccc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT-------DNSELRALLLQTTNRSIIVIEDIDC  290 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~-------~~~~L~~l~~~~~~~sII~IDeID~  290 (530)
                      ..|++|+||||||||+||.|||+++   |+.++.++..++.       .+....+++.......+|||||+..
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~  119 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGY  119 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTS
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCccccccEecccccce
Confidence            4699999999999999999999987   7777777765541       1223444555666778999999975

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.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.72  E-value=1.2e-06  Score=87.71  Aligned_cols=24  Identities=33%  Similarity=0.449  Sum_probs=22.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -++|+||||+|||++++.+++.+.
T Consensus        45 ~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        45 FILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhcC
Confidence            478999999999999999999986

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.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.72  E-value=8.9e-08  Score=99.03  Aligned_cols=122  Identities=16%  Similarity=0.220  Sum_probs=88.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC-------------------------CcEEEEecCc----------cCChHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC-------------------------YDVYDLELTK----------VTDNSELRA  272 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~-------------------------~~i~~l~l~~----------~~~~~~L~~  272 (530)
                      +.+|||+||+|+|||++|.++|..+.                         -|++.++...          ..+-+.+|.
T Consensus        21 ~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~iR~  100 (325)
T PRK08699         21 PNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDAVRE  100 (325)
T ss_pred             ceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHHHHH
Confidence            45899999999999999999999863                         3456665422          123456676


Q ss_pred             HHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHH
Q 009640          273 LLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLS  346 (530)
Q Consensus       273 l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls  346 (530)
                      +...+      ...-|++||++|.+                                                 +....+
T Consensus       101 l~~~~~~~p~~~~~kV~iiEp~~~L-------------------------------------------------d~~a~n  131 (325)
T PRK08699        101 IIDNVYLTSVRGGLRVILIHPAESM-------------------------------------------------NLQAAN  131 (325)
T ss_pred             HHHHHhhCcccCCceEEEEechhhC-------------------------------------------------CHHHHH
Confidence            65543      24568899999987                                                 122345


Q ss_pred             HHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          347 GLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       347 ~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                      .||..|+...    .+..+|++|++++.+.|.+.+  |+ ..+.|+.|+.++....+..
T Consensus       132 aLLk~LEep~----~~~~~Ilvth~~~~ll~ti~S--Rc-~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        132 SLLKVLEEPP----PQVVFLLVSHAADKVLPTIKS--RC-RKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             HHHHHHHhCc----CCCEEEEEeCChHhChHHHHH--Hh-hhhcCCCCCHHHHHHHHHh
Confidence            6777777542    346788899999999999887  65 5688999999887766653

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=98.71  E-value=2e-07  Score=95.84  Aligned_cols=122  Identities=16%  Similarity=0.180  Sum_probs=92.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC-----------------------CcEEEEecCc---cCChHHHHHHHHhc----
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC-----------------------YDVYDLELTK---VTDNSELRALLLQT----  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~-----------------------~~i~~l~l~~---~~~~~~L~~l~~~~----  277 (530)
                      +.+|||+||.|+||+++|.++|..+-                       -|++.+....   ..+-+.++.+....    
T Consensus        25 ~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~vdqiR~l~~~~~~~~  104 (319)
T PRK06090         25 PGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGKSITVEQIRQCNRLAQESS  104 (319)
T ss_pred             ceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCCcCCHHHHHHHHHHHhhCc
Confidence            45899999999999999999999772                       2455554431   22345566654332    


Q ss_pred             --CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCC
Q 009640          278 --TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGL  355 (530)
Q Consensus       278 --~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl  355 (530)
                        ...-|++||++|.+                                                 ....-+.||+.++.-
T Consensus       105 ~~~~~kV~iI~~ae~m-------------------------------------------------~~~AaNaLLKtLEEP  135 (319)
T PRK06090        105 QLNGYRLFVIEPADAM-------------------------------------------------NESASNALLKTLEEP  135 (319)
T ss_pred             ccCCceEEEecchhhh-------------------------------------------------CHHHHHHHHHHhcCC
Confidence              23469999999987                                                 123567899999853


Q ss_pred             ccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          356 WSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       356 ~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                          ..+.++|++|+.++.|-|.+++  |. ..|.|+.|+.++....+..
T Consensus       136 ----p~~t~fiL~t~~~~~lLpTI~S--RC-q~~~~~~~~~~~~~~~L~~  178 (319)
T PRK06090        136 ----APNCLFLLVTHNQKRLLPTIVS--RC-QQWVVTPPSTAQAMQWLKG  178 (319)
T ss_pred             ----CCCeEEEEEECChhhChHHHHh--cc-eeEeCCCCCHHHHHHHHHH
Confidence                4678999999999999999998  76 4689999999988877754

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=98.70  E-value=2.6e-07  Score=95.82  Aligned_cols=88  Identities=14%  Similarity=0.193  Sum_probs=66.1

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChH
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNS  268 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~  268 (530)
                      .|++++|....-+.+.+.+.......           ..+||+|+|||||+++|++|-...   +.+++.+++..+.. .
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~~-----------~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~-~   71 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPLD-----------KPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-N   71 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCCC-----------CCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCH-H
Confidence            46778888888888888887776543           489999999999999999998765   46899999988643 3


Q ss_pred             HHHHHH-H-----------------hcCCCeEEEEcCccch
Q 009640          269 ELRALL-L-----------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       269 ~L~~l~-~-----------------~~~~~sII~IDeID~~  291 (530)
                      .+...+ .                 .......|||||||.+
T Consensus        72 ~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L  112 (326)
T PRK11608         72 LLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATA  112 (326)
T ss_pred             HHHHHHccccccccCCcccccCCchhccCCCeEEeCChhhC
Confidence            333322 1                 1234578999999987

>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=98.69  E-value=1.2e-07  Score=88.93  Aligned_cols=84  Identities=18%  Similarity=0.192  Sum_probs=58.3

Q ss_pred             cCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHHHH
Q 009640          197 ALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELRAL  273 (530)
Q Consensus       197 ~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~~l  273 (530)
                      +|....-+.+++.+......+           ..+||+|++||||+.+|++|-+..   +.+|+.++++.+..+.--..+
T Consensus         2 iG~s~~m~~~~~~~~~~a~~~-----------~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~~~~e~~L   70 (168)
T PF00158_consen    2 IGESPAMKRLREQAKRAASSD-----------LPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPEELLESEL   70 (168)
T ss_dssp             S--SHHHHHHHHHHHHHTTST-----------S-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-HHHHHHHH
T ss_pred             EeCCHHHHHHHHHHHHHhCCC-----------CCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhcchhhhhh
Confidence            455555556666666655543           589999999999999999999876   468999999988544333445


Q ss_pred             HHhc-----------------CCCeEEEEcCccch
Q 009640          274 LLQT-----------------TNRSIIVIEDIDCS  291 (530)
Q Consensus       274 ~~~~-----------------~~~sII~IDeID~~  291 (530)
                      |-..                 ....+|||||||.+
T Consensus        71 FG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L  105 (168)
T PF00158_consen   71 FGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDL  105 (168)
T ss_dssp             HEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS
T ss_pred             hccccccccccccccCCceeeccceEEeecchhhh
Confidence            5321                 24579999999998

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 ....

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

Probab=98.68  E-value=8.2e-08  Score=96.17  Aligned_cols=65  Identities=37%  Similarity=0.473  Sum_probs=53.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-------C-hHHHHHHHHhc------CCCeEEEEcCccchh
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-------D-NSELRALLLQT------TNRSIIVIEDIDCSV  292 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-------~-~~~L~~l~~~~------~~~sII~IDeID~~~  292 (530)
                      +.++||.||.|+|||.||..+|..|+.+|..-+.+.+.       + +.-|.+|+..+      ..+.||+|||||.+.
T Consensus        97 KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIa  175 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIA  175 (408)
T ss_pred             eccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhh
Confidence            56799999999999999999999999999988887763       1 23366666655      468999999999983

>PRK06921 hypothetical protein; Provisional

Probab=98.68  E-value=6.9e-08  Score=97.18  Aligned_cols=63  Identities=30%  Similarity=0.377  Sum_probs=44.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecCccCCh-----HHHHHHHHhcCCCeEEEEcCccc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELTKVTDN-----SELRALLLQTTNRSIIVIEDIDC  290 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~~~~~~-----~~L~~l~~~~~~~sII~IDeID~  290 (530)
                      ..+++|+||||||||+|+.|||+++    +..++.+....+...     ..+...+.......+|+|||++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~~~~~~~~~~~~~~~~dlLiIDDl~~  188 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKVEVLFIDDLFK  188 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHHHHHHHHHHHHHhcCCCEEEEecccc
Confidence            4689999999999999999999987    456666665433110     11223344456789999999964

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.62  E-value=3.9e-07  Score=102.89  Aligned_cols=90  Identities=17%  Similarity=0.182  Sum_probs=67.4

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCCh
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDN  267 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~  267 (530)
                      .+|++++|....-+.+.+.+.......           ..+||+|+|||||+++|++|.+..   +.+++.+++..+..+
T Consensus       322 ~~~~~l~g~s~~~~~~~~~~~~~a~~~-----------~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~~  390 (638)
T PRK11388        322 HTFDHMPQDSPQMRRLIHFGRQAAKSS-----------FPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDE  390 (638)
T ss_pred             ccccceEECCHHHHHHHHHHHHHhCcC-----------CCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCChH
Confidence            357888888777777777777666543           479999999999999999999876   468999999887543


Q ss_pred             HHHHHHHHh--------------cCCCeEEEEcCccch
Q 009640          268 SELRALLLQ--------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       268 ~~L~~l~~~--------------~~~~sII~IDeID~~  291 (530)
                      .-...+|-.              ......|||||||.+
T Consensus       391 ~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l  428 (638)
T PRK11388        391 ALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYL  428 (638)
T ss_pred             HHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhC
Confidence            222334431              134678999999987

>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=98.62  E-value=1.4e-07  Score=95.33  Aligned_cols=134  Identities=20%  Similarity=0.359  Sum_probs=78.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcE---EEEecCccCChHHHHHHHHhc-------------CCCeEEEEcCccch
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDV---YDLELTKVTDNSELRALLLQT-------------TNRSIIVIEDIDCS  291 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i---~~l~l~~~~~~~~L~~l~~~~-------------~~~sII~IDeID~~  291 (530)
                      .+.+||.||+|||||++++..-..+.-+-   ..+..+...+...+.+++...             .++.|+||||+..-
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            36899999999999999988776664333   344555544445555554332             24579999999864


Q ss_pred             hhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhh-cc--CCccCC------CCC
Q 009640          292 VDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF-TD--GLWSCC------SEE  362 (530)
Q Consensus       292 ~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~-lD--gl~s~~------~~~  362 (530)
                      -                                           .+....+..+ +||.+ ||  |.+...      =..
T Consensus       113 ~-------------------------------------------~d~ygtq~~i-ElLRQ~i~~~g~yd~~~~~~~~i~~  148 (272)
T PF12775_consen  113 Q-------------------------------------------PDKYGTQPPI-ELLRQLIDYGGFYDRKKLEWKSIED  148 (272)
T ss_dssp             ----------------------------------------------TTS--HHH-HHHHHHHHCSEEECTTTTEEEEECS
T ss_pred             C-------------------------------------------CCCCCCcCHH-HHHHHHHHhcCcccCCCcEEEEEee
Confidence            1                                           0111112222 34433 22  322211      134


Q ss_pred             eEEEEEeCCCC---CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          363 KIIVFTTNHRD---SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       363 ~ivI~TTN~~~---~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      +.+|+|+|...   .+++.|+|  .|- .+.+++|+.++...|+..++.
T Consensus       149 i~~vaa~~p~~Gr~~is~R~~r--~f~-i~~~~~p~~~sl~~If~~il~  194 (272)
T PF12775_consen  149 IQFVAAMNPTGGRNPISPRFLR--HFN-ILNIPYPSDESLNTIFSSILQ  194 (272)
T ss_dssp             EEEEEEESSTTT--SHHHHHHT--TEE-EEE----TCCHHHHHHHHHHH
T ss_pred             eEEEEecCCCCCCCCCChHHhh--heE-EEEecCCChHHHHHHHHHHHh
Confidence            66788887532   48889998  774 589999999999888877664

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.57  E-value=2.3e-06  Score=87.12  Aligned_cols=62  Identities=23%  Similarity=0.365  Sum_probs=42.7

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC--CcEEEEecC
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC--YDVYDLELT  262 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~--~~i~~l~l~  262 (530)
                      =+-++|+.+.++..-- +...++.       |+-..+|+|+.||||||||.||-+||.+||  .+|..++.+
T Consensus        38 ~dG~VGQ~~AReAaGv-Iv~mik~-------gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~isgs  101 (450)
T COG1224          38 GDGLVGQEEAREAAGV-IVKMIKQ-------GKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAISGS  101 (450)
T ss_pred             CCcccchHHHHHhhhH-HHHHHHh-------CcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCceeeccc
Confidence            3667888887765332 2233322       233468999999999999999999999996  344444433

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.57  E-value=3.2e-07  Score=95.17  Aligned_cols=64  Identities=30%  Similarity=0.453  Sum_probs=56.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC--------hHHHHHHHHhc------CCCeEEEEcCccch
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD--------NSELRALLLQT------TNRSIIVIEDIDCS  291 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~--------~~~L~~l~~~~------~~~sII~IDeID~~  291 (530)
                      +..+||.||.|+|||.|+..+|..++.+|...+++.+..        ++-|.+|+..+      .+..||||||+|.+
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi  303 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKI  303 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhh
Confidence            568999999999999999999999999999999888732        45578888776      46899999999998

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=98.56  E-value=2.6e-06  Score=96.95  Aligned_cols=90  Identities=14%  Similarity=0.252  Sum_probs=67.6

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD  266 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~  266 (530)
                      ...|++++|.....+.+.+.+..+....           ..+||+|+||||||++|++|....   +.+++.+++..+..
T Consensus       372 n~~~~~liG~S~~~~~~~~~~~~~a~~~-----------~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~  440 (686)
T PRK15429        372 DSEFGEIIGRSEAMYSVLKQVEMVAQSD-----------STVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPA  440 (686)
T ss_pred             cccccceeecCHHHHHHHHHHHHHhCCC-----------CCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCCh
Confidence            3578899999988888888888766543           489999999999999999998865   56889988877632


Q ss_pred             hHHHHH-HHH-----------------hcCCCeEEEEcCccch
Q 009640          267 NSELRA-LLL-----------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       267 ~~~L~~-l~~-----------------~~~~~sII~IDeID~~  291 (530)
                      . .+.. +|.                 ......+|||||||.+
T Consensus       441 ~-~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L  482 (686)
T PRK15429        441 G-LLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDM  482 (686)
T ss_pred             h-HhhhhhcCcccccccccccchhhHHHhcCCCeEEEechhhC
Confidence            1 1111 111                 2234689999999987

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.54  E-value=1.8e-07  Score=84.61  Aligned_cols=77  Identities=22%  Similarity=0.333  Sum_probs=52.5

Q ss_pred             CChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC---cEEEEecCccCChHHHHHHH
Q 009640          198 LEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY---DVYDLELTKVTDNSELRALL  274 (530)
Q Consensus       198 ~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~---~i~~l~l~~~~~~~~L~~l~  274 (530)
                      |....-+.+.+.+.......           ..+||+|+|||||+++|++|....+.   .++.+++....     .+++
T Consensus         2 G~S~~~~~l~~~l~~~a~~~-----------~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-----~~~l   65 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERLAKSS-----------SPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-----AELL   65 (138)
T ss_dssp             -SCHHHHHHHHHHHHHHCSS-----------S-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-----HHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCC-----------CcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-----HHHH
Confidence            33445566777776666543           58999999999999999999998764   33333333322     3455


Q ss_pred             HhcCCCeEEEEcCccch
Q 009640          275 LQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       275 ~~~~~~sII~IDeID~~  291 (530)
                      ..+ ....|+|+|||.+
T Consensus        66 ~~a-~~gtL~l~~i~~L   81 (138)
T PF14532_consen   66 EQA-KGGTLYLKNIDRL   81 (138)
T ss_dssp             HHC-TTSEEEEECGCCS
T ss_pred             HHc-CCCEEEECChHHC
Confidence            554 7788999999998

>TIGR00368 Mg chelatase-related protein

Probab=98.54  E-value=5.5e-07  Score=98.13  Aligned_cols=48  Identities=25%  Similarity=0.441  Sum_probs=36.1

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ...|+++.|+..+++.+.-.+    .           ....++|.||||||||+++++|+..+
T Consensus       188 ~~d~~dv~Gq~~~~~al~~aa----~-----------~g~~vlliG~pGsGKTtlar~l~~ll  235 (499)
T TIGR00368       188 DLDLKDIKGQQHAKRALEIAA----A-----------GGHNLLLFGPPGSGKTMLASRLQGIL  235 (499)
T ss_pred             CCCHHHhcCcHHHHhhhhhhc----c-----------CCCEEEEEecCCCCHHHHHHHHhccc
Confidence            347899999888765443322    1           12469999999999999999999865

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=98.51  E-value=9e-07  Score=92.37  Aligned_cols=157  Identities=19%  Similarity=0.248  Sum_probs=103.8

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc--------------
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD--------------  255 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~--------------  255 (530)
                      ...|.-++|++.+|..+.-.-.             .|.-.|+|+-|+.|||||++++|||..|.--              
T Consensus        13 ~~pf~aivGqd~lk~aL~l~av-------------~P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~   79 (423)
T COG1239          13 NLPFTAIVGQDPLKLALGLNAV-------------DPQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDD   79 (423)
T ss_pred             ccchhhhcCchHHHHHHhhhhc-------------ccccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCC
Confidence            4467788999998887655322             1234699999999999999999999988211              


Q ss_pred             --------------------------EEEEecCcc----CChHHHHHHHHh-----------cCCCeEEEEcCccchhhh
Q 009640          256 --------------------------VYDLELTKV----TDNSELRALLLQ-----------TTNRSIIVIEDIDCSVDL  294 (530)
Q Consensus       256 --------------------------i~~l~l~~~----~~~~~L~~l~~~-----------~~~~sII~IDeID~~~~~  294 (530)
                                                +..+.++..    .+.-++.+.+..           ..++.|++|||+..+-  
T Consensus        80 P~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~--  157 (423)
T COG1239          80 PEEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLD--  157 (423)
T ss_pred             hhhhhHHHHhhccccccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEecccccc--
Confidence                                      111111111    111123333331           1356899999998762  


Q ss_pred             hhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhh---------ccCCccCCCCCeEE
Q 009640          295 TADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF---------TDGLWSCCSEEKII  365 (530)
Q Consensus       295 ~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~---------lDgl~s~~~~~~iv  365 (530)
                                                                     ......||+.         .+|+.-...-..++
T Consensus       158 -----------------------------------------------d~lvd~LLd~aaeG~n~vereGisi~hpa~fvl  190 (423)
T COG1239         158 -----------------------------------------------DHLVDALLDVAAEGVNDVEREGISIRHPARFLL  190 (423)
T ss_pred             -----------------------------------------------HHHHHHHHHHHHhCCceeeeCceeeccCccEEE
Confidence                                                           1233344444         35555444566889


Q ss_pred             EEEeCCC-CCCChhhhcCCceeEEEEeCCC-CHHHHHHHHHHhhCCc
Q 009640          366 VFTTNHR-DSVDPALIRCGRMDVHVSLGTC-GPHAFKVLAKNYLGIE  410 (530)
Q Consensus       366 I~TTN~~-~~LDpALlRpGR~d~~I~~~~p-~~~~r~~i~~~~l~~~  410 (530)
                      |+|+|.- ..|-|-|+.  ||..+|.+.+| +.+.|.+|.++-+...
T Consensus       191 igTmNPEeGeLrpqLlD--Rfg~~v~~~~~~~~~~rv~Ii~r~~~f~  235 (423)
T COG1239         191 IGTMNPEEGELRPQLLD--RFGLEVDTHYPLDLEERVEIIRRRLAFE  235 (423)
T ss_pred             EeecCccccccchhhHh--hhcceeeccCCCCHHHHHHHHHHHHHhh
Confidence            9999975 478899999  99999999887 5678888887766543

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.50  E-value=7e-06  Score=90.45  Aligned_cols=91  Identities=19%  Similarity=0.224  Sum_probs=65.7

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~  265 (530)
                      ...+|++++|....-+.+++.+......           ...+||+|++||||+++|+++-...   +.+++.+++..+.
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            4457899999887777777777665543           2469999999999999999986654   4578999988875


Q ss_pred             ChHHHH-HHHH-----------------hcCCCeEEEEcCccch
Q 009640          266 DNSELR-ALLL-----------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       266 ~~~~L~-~l~~-----------------~~~~~sII~IDeID~~  291 (530)
                      . ..+. .+|-                 +......|||||||.+
T Consensus       268 ~-~~~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L  310 (520)
T PRK10820        268 D-DVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEM  310 (520)
T ss_pred             H-HHHHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEEeChhhC
Confidence            3 2232 2331                 1133578999999987

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=98.47  E-value=1.6e-06  Score=95.13  Aligned_cols=91  Identities=16%  Similarity=0.267  Sum_probs=69.5

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~  265 (530)
                      ...+|++++|....-+.+.+.+..+....           ..+||+|++||||+++|++|-+..   +.+++.+++..+.
T Consensus       207 ~~~~f~~iiG~S~~m~~~~~~i~~~A~~~-----------~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~  275 (526)
T TIGR02329       207 TRYRLDDLLGASAPMEQVRALVRLYARSD-----------ATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIA  275 (526)
T ss_pred             cccchhheeeCCHHHHHHHHHHHHHhCCC-----------CcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCC
Confidence            34678999999888888888887776654           489999999999999999998765   5689999988874


Q ss_pred             ChHHHHH-HHH------------------hcCCCeEEEEcCccch
Q 009640          266 DNSELRA-LLL------------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       266 ~~~~L~~-l~~------------------~~~~~sII~IDeID~~  291 (530)
                      . ..+.. +|-                  +......|||||||.+
T Consensus       276 e-~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~L  319 (526)
T TIGR02329       276 E-SLLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEM  319 (526)
T ss_pred             h-hHHHHHhcCCcccccccccccccccchhhcCCceEEecChHhC
Confidence            3 22332 222                  1124568999999987

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.

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.47  E-value=4.3e-07  Score=98.71  Aligned_cols=47  Identities=28%  Similarity=0.377  Sum_probs=33.0

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .|.++.|+..+++.+.-    -           ......++|+||||||||+|++.|+..+.
T Consensus       189 d~~~v~Gq~~~~~al~l----a-----------a~~G~~llliG~~GsGKTtLak~L~gllp  235 (506)
T PRK09862        189 DLSDVIGQEQGKRGLEI----T-----------AAGGHNLLLIGPPGTGKTMLASRINGLLP  235 (506)
T ss_pred             CeEEEECcHHHHhhhhe----e-----------ccCCcEEEEECCCCCcHHHHHHHHhccCC
Confidence            67777776655443221    1           11235699999999999999999998763

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.46  E-value=7.9e-06  Score=89.85  Aligned_cols=88  Identities=14%  Similarity=0.172  Sum_probs=66.9

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChH
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNS  268 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~  268 (530)
                      .+.+++|.....+.+.+.+......+           ..+||+|++||||+++|++|....   +.+++.+++..+.. .
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~-----------~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~-~  252 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASD-----------LNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPE-S  252 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCC-----------CcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCCh-H
Confidence            46788998888888888887765543           589999999999999999999875   46899999888753 2


Q ss_pred             HHH-HHHH-----------------hcCCCeEEEEcCccch
Q 009640          269 ELR-ALLL-----------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       269 ~L~-~l~~-----------------~~~~~sII~IDeID~~  291 (530)
                      .+. .+|-                 .......|||||||.+
T Consensus       253 ~~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L  293 (509)
T PRK05022        253 LAESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGEL  293 (509)
T ss_pred             HHHHHhcCccccccCCCcccCCcchhhcCCCEEEecChhhC
Confidence            222 2222                 1234567999999987

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.46  E-value=1.8e-07  Score=81.01  Aligned_cols=61  Identities=23%  Similarity=0.369  Sum_probs=38.7

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      +.||||||+|||+++..+|..+...+-.-....+-....-.+.+.......++++||+...
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~~q~vvi~DD~~~~   61 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQGQPVVIIDDFGQD   61 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccCCCcEEEEeecCcc
Confidence            4799999999999999999887533211111111111112234455567789999999875

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

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.45  E-value=2e-06  Score=84.90  Aligned_cols=160  Identities=17%  Similarity=0.250  Sum_probs=106.6

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-CCcEE------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-CYDVY------  257 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~------  257 (530)
                      +..+.|.+++.+....+....+....    ...+         -..+|+|||+|+||-|.+-++-+++ |.-+.      
T Consensus         4 vdkyrpksl~~l~~~~e~~~~Lksl~----~~~d---------~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~   70 (351)
T KOG2035|consen    4 VDKYRPKSLDELIYHEELANLLKSLS----STGD---------FPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIET   70 (351)
T ss_pred             hhhcCcchhhhcccHHHHHHHHHHhc----ccCC---------CCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeee
Confidence            66778999999888777666554422    2122         1479999999999999999999987 21111      


Q ss_pred             ----------------------EEecCccCCh--HHHHHHHHhc---C------C--CeEEEEcCccchhhhhhhhhhcc
Q 009640          258 ----------------------DLELTKVTDN--SELRALLLQT---T------N--RSIIVIEDIDCSVDLTADRMLKS  302 (530)
Q Consensus       258 ----------------------~l~l~~~~~~--~~L~~l~~~~---~------~--~sII~IDeID~~~~~~~~r~~~~  302 (530)
                                            .++.++.+..  .-+.+++.+.   .      +  =-+|+|-|.|.+-          
T Consensus        71 ~t~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT----------  140 (351)
T KOG2035|consen   71 RTFTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELT----------  140 (351)
T ss_pred             EEEecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhh----------
Confidence                                  1112222211  1144444432   1      1  1488999999871          


Q ss_pred             cCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcC
Q 009640          303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRC  382 (530)
Q Consensus       303 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRp  382 (530)
                                                             +....+|-..|+-+.+.|    -+|+.+|...++-+++.+ 
T Consensus       141 ---------------------------------------~dAQ~aLRRTMEkYs~~~----RlIl~cns~SriIepIrS-  176 (351)
T KOG2035|consen  141 ---------------------------------------RDAQHALRRTMEKYSSNC----RLILVCNSTSRIIEPIRS-  176 (351)
T ss_pred             ---------------------------------------HHHHHHHHHHHHHHhcCc----eEEEEecCcccchhHHhh-
Confidence                                                   112345666677665544    488899999999999997 


Q ss_pred             CceeEEEEeCCCCHHHHHHHHHHhhCCcCcc
Q 009640          383 GRMDVHVSLGTCGPHAFKVLAKNYLGIESHH  413 (530)
Q Consensus       383 GR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~  413 (530)
                       |. ..|.++.|+.++.-.++...+..+...
T Consensus       177 -RC-l~iRvpaps~eeI~~vl~~v~~kE~l~  205 (351)
T KOG2035|consen  177 -RC-LFIRVPAPSDEEITSVLSKVLKKEGLQ  205 (351)
T ss_pred             -he-eEEeCCCCCHHHHHHHHHHHHHHhccc
Confidence             65 558999999999999988887665544

>PHA02624 large T antigen; Provisional

Probab=98.44  E-value=1.1e-06  Score=96.02  Aligned_cols=123  Identities=20%  Similarity=0.237  Sum_probs=80.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhccc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSS  303 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~  303 (530)
                      |+|.++.+|||||||||||+++.+|++.++-.+..++...    +.+.-.|.-+...-+++|||+-.-.-          
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt----~ks~FwL~pl~D~~~~l~dD~t~~~~----------  492 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQPA----------  492 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCc----chhHHHhhhhhhceEEEeeecccccc----------
Confidence            6788899999999999999999999999966666665332    23334455556667999999864210          


Q ss_pred             CCccccccccchhhhhhccccccccCCCCCCCCCC-cchhhhHHHHhhhccCCccCCC-----CC-----eEEEEEeCCC
Q 009640          304 NTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE-ESGRVTLSGLLNFTDGLWSCCS-----EE-----KIIVFTTNHR  372 (530)
Q Consensus       304 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ls~LLn~lDgl~s~~~-----~~-----~ivI~TTN~~  372 (530)
                                                 .+.  .-. +..-..+..|-|.|||--.-+-     ..     --.|.|||. 
T Consensus       493 ---------------------------~~~--~Lp~G~~~dNl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlliT~Ne-  542 (647)
T PHA02624        493 ---------------------------DNK--DLPSGQGMNNLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIVTMNE-  542 (647)
T ss_pred             ---------------------------ccc--cCCcccccchhhHHHhhcCCCCccccchhccCchhccCCCeEEeecC-
Confidence                                       000  000 0011235678899998721110     00     135678886 


Q ss_pred             CCCChhhhcCCceeEEEEeC
Q 009640          373 DSVDPALIRCGRMDVHVSLG  392 (530)
Q Consensus       373 ~~LDpALlRpGR~d~~I~~~  392 (530)
                      ..||..|.-  ||-+.|.|.
T Consensus       543 y~iP~T~~~--Rf~~~~~F~  560 (647)
T PHA02624        543 YLIPQTVKA--RFAKVLDFK  560 (647)
T ss_pred             cccchhHHH--HHHHhcccc
Confidence            577888887  998888886

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.43  E-value=2.6e-06  Score=93.53  Aligned_cols=89  Identities=16%  Similarity=0.225  Sum_probs=68.3

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHH-----------cCCcEEEE
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY-----------LCYDVYDL  259 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~-----------l~~~i~~l  259 (530)
                      .+|++++|....-+.+.+.+..+....           ..+||+|+|||||+++|++|-+.           .+.+|+.+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~A~s~-----------~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~i  284 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLYARSS-----------AAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAV  284 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCCC-----------CcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEe
Confidence            568999999888888888887766543           48999999999999999999887           46789999


Q ss_pred             ecCccCChHHHHH-HHH------------------hcCCCeEEEEcCccch
Q 009640          260 ELTKVTDNSELRA-LLL------------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       260 ~l~~~~~~~~L~~-l~~------------------~~~~~sII~IDeID~~  291 (530)
                      ++..+.. ..+.. +|-                  +......|||||||.+
T Consensus       285 nCaal~e-~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~L  334 (538)
T PRK15424        285 NCGAIAE-SLLEAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEM  334 (538)
T ss_pred             ecccCCh-hhHHHHhcCCccccccCccccccCCchhccCCCEEEEcChHhC
Confidence            9988753 22322 222                  1223568999999987

>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=98.42  E-value=4e-06  Score=82.57  Aligned_cols=64  Identities=22%  Similarity=0.289  Sum_probs=55.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhc-CCCeEEEEcCccch
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQT-TNRSIIVIEDIDCS  291 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~-~~~sII~IDeID~~  291 (530)
                      ..|-.++||+|||||.+++++|..+|..++..+.++-.+-..+.++|..+ ...+.+++||++.+
T Consensus        32 ~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~~~~l~ril~G~~~~GaW~cfdefnrl   96 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMDYQSLSRILKGLAQSGAWLCFDEFNRL   96 (231)
T ss_dssp             TTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-HHHHHHHHHHHHHHT-EEEEETCCCS
T ss_pred             CCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccccHHHHHHHHHHHhhcCchhhhhhhhhh
Confidence            35778999999999999999999999999999999998999999999876 67899999999987

>PF13173 AAA_14: AAA domain

Probab=98.41  E-value=7.3e-07  Score=79.57  Aligned_cols=63  Identities=24%  Similarity=0.446  Sum_probs=47.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC--CcEEEEecCccCChH----HHHHHHHhc--CCCeEEEEcCccch
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC--YDVYDLELTKVTDNS----ELRALLLQT--TNRSIIVIEDIDCS  291 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~--~~i~~l~l~~~~~~~----~L~~l~~~~--~~~sII~IDeID~~  291 (530)
                      +-++|+||.|+|||++++.++..+.  .++..+++.......    ++.+.+.+.  ..+.+||||||..+
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEiq~~   73 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLADPDLLEYFLELIKPGKKYIFIDEIQYL   73 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHhhhhhHHHHHHhhccCCcEEEEehhhhh
Confidence            4689999999999999999999886  777788776653221    133444443  36799999999976

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=98.39  E-value=1.1e-05  Score=88.57  Aligned_cols=130  Identities=15%  Similarity=0.234  Sum_probs=84.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecCccCChHH----------------------HHHHHH--
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELTKVTDNSE----------------------LRALLL--  275 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~~~~~~~~----------------------L~~l~~--  275 (530)
                      .+.+.|-||||||.++..+-++|          .++++.++...+....+                      |..-|.  
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            57788999999999999999877          46677777655533222                      222233  


Q ss_pred             -hcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC
Q 009640          276 -QTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG  354 (530)
Q Consensus       276 -~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg  354 (530)
                       .-..++||+|||+|.++.                                              .++.   -|-|++|=
T Consensus       504 k~~~~~~VvLiDElD~Lvt----------------------------------------------r~Qd---VlYn~fdW  534 (767)
T KOG1514|consen  504 KPKRSTTVVLIDELDILVT----------------------------------------------RSQD---VLYNIFDW  534 (767)
T ss_pred             CCCCCCEEEEeccHHHHhc----------------------------------------------ccHH---HHHHHhcC
Confidence             114679999999999851                                              0122   35555552


Q ss_pred             CccCCCCCeEEEEEeCCCCCCChhhhc---CCcee-EEEEeCCCCHHHHHHHHHHhhCCc
Q 009640          355 LWSCCSEEKIIVFTTNHRDSVDPALIR---CGRMD-VHVSLGTCGPHAFKVLAKNYLGIE  410 (530)
Q Consensus       355 l~s~~~~~~ivI~TTN~~~~LDpALlR---pGR~d-~~I~~~~p~~~~r~~i~~~~l~~~  410 (530)
                      ... .+...+||+..|.. +|++.++-   .-|++ ..|.|.+.+.++..+|+..-|...
T Consensus       535 pt~-~~sKLvvi~IaNTm-dlPEr~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~  592 (767)
T KOG1514|consen  535 PTL-KNSKLVVIAIANTM-DLPERLLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGL  592 (767)
T ss_pred             CcC-CCCceEEEEecccc-cCHHHHhccchhhhccceeeecCCCCHHHHHHHHHHhhcch
Confidence            222 13445666666654 34444442   13665 568899999999999998877655

>PHA00729 NTP-binding motif containing protein

Probab=98.36  E-value=3.8e-06  Score=81.96  Aligned_cols=135  Identities=15%  Similarity=0.176  Sum_probs=73.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc----------cCChHHHHHHHH----hcCCCeEEEEcCccchhhhh
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK----------VTDNSELRALLL----QTTNRSIIVIEDIDCSVDLT  295 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~----------~~~~~~L~~l~~----~~~~~sII~IDeID~~~~~~  295 (530)
                      .++|+|+||||||+||.+||+.++.++..+....          +.+..++...+.    ......+|+|||+-.-+.. 
T Consensus        19 nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~-   97 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSK-   97 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhcc-
Confidence            7999999999999999999999875444432111          112233333332    2233468999997543200 


Q ss_pred             hhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCC
Q 009640          296 ADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSV  375 (530)
Q Consensus       296 ~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~L  375 (530)
                      .                                   ..    +.........+-+.+.   +   .-.++++++..++.|
T Consensus        98 ~-----------------------------------~w----h~~~~~~yf~L~~aLr---S---R~~l~il~~ls~edL  132 (226)
T PHA00729         98 Y-----------------------------------VW----YEDYMKTFYKIYALIR---T---RVSAVIFTTPSPEDL  132 (226)
T ss_pred             c-----------------------------------ch----hhhccchHHHHHHHHH---h---hCcEEEEecCCHHHH
Confidence            0                                   00    0000011122333332   1   224688888888888


Q ss_pred             ChhhhcCCceeEEEEeC-CCCHHHHHHHHHHhhCCc
Q 009640          376 DPALIRCGRMDVHVSLG-TCGPHAFKVLAKNYLGIE  410 (530)
Q Consensus       376 DpALlRpGR~d~~I~~~-~p~~~~r~~i~~~~l~~~  410 (530)
                      -..|...|-....|.=. --...++..|.+.+....
T Consensus       133 ~~~Lr~Rg~~~~kI~en~~~~~~~~~~~~~~~~~~~  168 (226)
T PHA00729        133 AFYLREKGWYQIRVTMVNRKTMTARATLYSKDFGRN  168 (226)
T ss_pred             HHHHHhCCCcHHHhhhcccCcccchhhHHHHHHhhc
Confidence            88887756555444432 222345566776666544

>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=98.34  E-value=5.2e-06  Score=80.41  Aligned_cols=133  Identities=28%  Similarity=0.350  Sum_probs=70.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEE----EEecCccC--------------------------------------
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVY----DLELTKVT--------------------------------------  265 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~----~l~l~~~~--------------------------------------  265 (530)
                      ...++||||.|+|||+|++.+.+.+.-.-+    ........                                      
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            368999999999999999999999843221    11111000                                      


Q ss_pred             --ChHHHHHHHHh---cCCCeEEEEcCccchh-hhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          266 --DNSELRALLLQ---TTNRSIIVIEDIDCSV-DLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       266 --~~~~L~~l~~~---~~~~sII~IDeID~~~-~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                        ....+..++..   ...+.||+|||+|.+. .                                            ..
T Consensus       100 ~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~--------------------------------------------~~  135 (234)
T PF01637_consen  100 EDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIA--------------------------------------------SE  135 (234)
T ss_dssp             GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBC--------------------------------------------TT
T ss_pred             hhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhc--------------------------------------------cc
Confidence              01112222222   2345999999999883 1                                            01


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC------CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD------SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~------~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      .....+..|.+.++....  ...+.+|+++....      .-.+.+.  +|+.. +.+++.+.++...++...+..
T Consensus       136 ~~~~~~~~l~~~~~~~~~--~~~~~~v~~~S~~~~~~~~~~~~~~~~--~~~~~-~~l~~l~~~e~~~~~~~~~~~  206 (234)
T PF01637_consen  136 EDKDFLKSLRSLLDSLLS--QQNVSIVITGSSDSLMEEFLDDKSPLF--GRFSH-IELKPLSKEEAREFLKELFKE  206 (234)
T ss_dssp             TTHHHHHHHHHHHHH------TTEEEEEEESSHHHHHHTT-TTSTTT--T---E-EEE----HHHHHHHHHHHHHC
T ss_pred             chHHHHHHHHHHHhhccc--cCCceEEEECCchHHHHHhhcccCccc--cccce-EEEeeCCHHHHHHHHHHHHHH
Confidence            123455667777776443  24454555444321      1122233  48877 999999999999999886543

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.34  E-value=1.2e-06  Score=77.56  Aligned_cols=64  Identities=34%  Similarity=0.544  Sum_probs=42.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc--------CCcEEEEecCccCCh---------------------HHHHHHHHhc-
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL--------CYDVYDLELTKVTDN---------------------SELRALLLQT-  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l--------~~~i~~l~l~~~~~~---------------------~~L~~l~~~~-  277 (530)
                      .+.++++||||+|||+++..++..+        ..+++.+++....+.                     .++.+.+.+. 
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            3568999999999999999999988        677777765544322                     2222222222 


Q ss_pred             --CCCeEEEEcCccch
Q 009640          278 --TNRSIIVIEDIDCS  291 (530)
Q Consensus       278 --~~~sII~IDeID~~  291 (530)
                        ....+|+|||+|.+
T Consensus        84 ~~~~~~~lviDe~~~l   99 (131)
T PF13401_consen   84 DRRRVVLLVIDEADHL   99 (131)
T ss_dssp             HHCTEEEEEEETTHHH
T ss_pred             HhcCCeEEEEeChHhc
Confidence              22359999999986

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.33  E-value=9.2e-06  Score=82.16  Aligned_cols=89  Identities=15%  Similarity=0.216  Sum_probs=56.0

Q ss_pred             cCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---------CCcEEEEecCccCCh
Q 009640          197 ALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---------CYDVYDLELTKVTDN  267 (530)
Q Consensus       197 ~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---------~~~i~~l~l~~~~~~  267 (530)
                      ++.+..++ +.+.++..+..|..      .-..++||+|++|.|||++++..+...         ..+++.+.....-+.
T Consensus        37 IgY~~A~~-~L~~L~~Ll~~P~~------~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~  109 (302)
T PF05621_consen   37 IGYPRAKE-ALDRLEELLEYPKR------HRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDE  109 (302)
T ss_pred             ecCHHHHH-HHHHHHHHHhCCcc------cCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCCh
Confidence            34444444 55557777766642      224689999999999999999998754         235556654333222


Q ss_pred             HHHHHH------------------------HHhcCCCeEEEEcCccchh
Q 009640          268 SELRAL------------------------LLQTTNRSIIVIEDIDCSV  292 (530)
Q Consensus       268 ~~L~~l------------------------~~~~~~~sII~IDeID~~~  292 (530)
                      ..+-..                        +.+..+.-+|+|||++.++
T Consensus       110 ~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lL  158 (302)
T PF05621_consen  110 RRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLL  158 (302)
T ss_pred             HHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHh
Confidence            221111                        2223466799999999985

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.32  E-value=1.2e-05  Score=80.03  Aligned_cols=52  Identities=25%  Similarity=0.399  Sum_probs=37.4

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-++|+...++.- -.+...++.+..       ..|++||.||||||||.||-||+.+||
T Consensus        38 ~g~vGQ~~AReAa-giivdlik~Kkm-------aGravLlaGppgtGKTAlAlaisqELG   89 (456)
T KOG1942|consen   38 AGFVGQENAREAA-GIIVDLIKSKKM-------AGRAVLLAGPPGTGKTALALAISQELG   89 (456)
T ss_pred             cccccchhhhhhh-hHHHHHHHhhhc-------cCcEEEEecCCCCchhHHHHHHHHHhC
Confidence            4567877776542 223344444432       247999999999999999999999995

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.32  E-value=3.1e-06  Score=96.56  Aligned_cols=128  Identities=19%  Similarity=0.266  Sum_probs=77.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcE-------EEEecCccCC-hHHH-HHHH-----HhcCCCeEEEEcCccchhhh
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDV-------YDLELTKVTD-NSEL-RALL-----LQTTNRSIIVIEDIDCSVDL  294 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i-------~~l~l~~~~~-~~~L-~~l~-----~~~~~~sII~IDeID~~~~~  294 (530)
                      -.+||.|+||||||.+++++++......       ..+.++.... .... ....     .......+++|||+|.+-  
T Consensus       493 ihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~vgLTa~~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkms--  570 (915)
T PTZ00111        493 INVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSVGLTASIKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCH--  570 (915)
T ss_pred             ceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccccccchhhhcccccCcccccCCcEEEcCCCeEEecchhhCC--
Confidence            3699999999999999999998654332       2333322110 0000 0000     111346799999999871  


Q ss_pred             hhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc---------CCccCCCCCeEE
Q 009640          295 TADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD---------GLWSCCSEEKII  365 (530)
Q Consensus       295 ~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD---------gl~s~~~~~~iv  365 (530)
                                                                     ....+.|+..|+         |+...-..+..|
T Consensus       571 -----------------------------------------------~~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rV  603 (915)
T PTZ00111        571 -----------------------------------------------NESRLSLYEVMEQQTVTIAKAGIVATLKAETAI  603 (915)
T ss_pred             -----------------------------------------------HHHHHHHHHHHhCCEEEEecCCcceecCCCeEE
Confidence                                                           112234444442         222111345678


Q ss_pred             EEEeCCCC-------------CCChhhhcCCceeEE-EEeCCCCHHHHHHHHHHhh
Q 009640          366 VFTTNHRD-------------SVDPALIRCGRMDVH-VSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       366 I~TTN~~~-------------~LDpALlRpGR~d~~-I~~~~p~~~~r~~i~~~~l  407 (530)
                      |+|+|..+             .|+|+|+.  |||.. +.++.|+.+.=+.|..+.+
T Consensus       604 IAAaNP~~gryd~~~s~~eni~Lp~~LLS--RFDLIf~l~D~~d~~~D~~lA~hI~  657 (915)
T PTZ00111        604 LASCNPINSRYNKNKAVIENINISPSLFT--RFDLIYLVLDHIDQDTDQLISLSIA  657 (915)
T ss_pred             EEEcCCcccccCcccCcccccCCChHHhh--hhcEEEEecCCCChHHHHHHHHHHH
Confidence            99999852             47899999  99965 5568888877666655544

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.32  E-value=5.9e-05  Score=77.13  Aligned_cols=122  Identities=15%  Similarity=0.219  Sum_probs=88.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC-------------cEEEEec-CccCChHHHHHHHHhc-------CCCeEEEEc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY-------------DVYDLEL-TKVTDNSELRALLLQT-------TNRSIIVIE  286 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~-------------~i~~l~l-~~~~~~~~L~~l~~~~-------~~~sII~ID  286 (530)
                      ...|||||++|+||+.++.++|+.+-.             ++..++. ....+-.+++.+....       ..+-|++||
T Consensus        18 ~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir~l~~~~~~~~~~~~~~KvvII~   97 (299)
T PRK07132         18 SHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFLSAINKLYFSSFVQSQKKILIIK   97 (299)
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHHHHHHHhccCCcccCCceEEEEe
Confidence            468999999999999999999988711             2233331 1112335676665544       256799999


Q ss_pred             CccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEE
Q 009640          287 DIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIV  366 (530)
Q Consensus       287 eID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI  366 (530)
                      ++|.+-                                                 ....+.||..|+..    ++..++|
T Consensus        98 ~~e~m~-------------------------------------------------~~a~NaLLK~LEEP----p~~t~~i  124 (299)
T PRK07132         98 NIEKTS-------------------------------------------------NSLLNALLKTIEEP----PKDTYFL  124 (299)
T ss_pred             cccccC-------------------------------------------------HHHHHHHHHHhhCC----CCCeEEE
Confidence            998861                                                 22456899999864    4668888


Q ss_pred             EEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          367 FTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       367 ~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                      ++|+.+++|-|.+.+  |. ..++|.+++.++....+..
T Consensus       125 l~~~~~~kll~TI~S--Rc-~~~~f~~l~~~~l~~~l~~  160 (299)
T PRK07132        125 LTTKNINKVLPTIVS--RC-QVFNVKEPDQQKILAKLLS  160 (299)
T ss_pred             EEeCChHhChHHHHh--Ce-EEEECCCCCHHHHHHHHHH
Confidence            888899999999987  54 4489999998888766654

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.27  E-value=1.5e-05  Score=80.72  Aligned_cols=111  Identities=16%  Similarity=0.218  Sum_probs=78.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC----------------cEEEEecCc---cCChHHHHHHHHhc------CCCeE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY----------------DVYDLELTK---VTDNSELRALLLQT------TNRSI  282 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~----------------~i~~l~l~~---~~~~~~L~~l~~~~------~~~sI  282 (530)
                      +..|||+||+|+||+.+|.++|..+-.                |++.+....   ..+-..++.+....      ...-|
T Consensus        19 ~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~kv   98 (290)
T PRK05917         19 PSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYKI   98 (290)
T ss_pred             CeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCceE
Confidence            458999999999999999999988732                344443221   12344555554443      23458


Q ss_pred             EEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCC
Q 009640          283 IVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEE  362 (530)
Q Consensus       283 I~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~  362 (530)
                      ++||++|.+                                                 +...-+.||+.|+.-    .++
T Consensus        99 ~ii~~ad~m-------------------------------------------------t~~AaNaLLK~LEEP----p~~  125 (290)
T PRK05917         99 YIIHEADRM-------------------------------------------------TLDAISAFLKVLEDP----PQH  125 (290)
T ss_pred             EEEechhhc-------------------------------------------------CHHHHHHHHHHhhcC----CCC
Confidence            889999987                                                 123457899999863    467


Q ss_pred             eEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          363 KIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       363 ~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                      .++|++|+.++.|.|.+++  |+ ..+.|+.+
T Consensus       126 ~~fiL~~~~~~~ll~TI~S--Rc-q~~~~~~~  154 (290)
T PRK05917        126 GVIILTSAKPQRLPPTIRS--RS-LSIHIPME  154 (290)
T ss_pred             eEEEEEeCChhhCcHHHHh--cc-eEEEccch
Confidence            8999999999999999997  66 33566643

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.26  E-value=2.2e-05  Score=84.04  Aligned_cols=73  Identities=27%  Similarity=0.405  Sum_probs=56.0

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..|  +....|.+.++|+.......+|..++..+.....      ....+-+||.||+||||||.++-||.++|+.+..=
T Consensus        70 elW--~eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~~~~------~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew  141 (634)
T KOG1970|consen   70 ELW--VEKYKPRTLEELAVHKKKISEVKQWLKQVAEFTP------KLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIEW  141 (634)
T ss_pred             chh--HHhcCcccHHHHhhhHHhHHHHHHHHHHHHHhcc------CCCceEEEEeCCCCCCchhHHHHHHHhhCceeeee
Confidence            468  8889999999999988877777777763322111      11235688999999999999999999999988754


Q ss_pred             e
Q 009640          260 E  260 (530)
Q Consensus       260 ~  260 (530)
                      .
T Consensus       142 ~  142 (634)
T KOG1970|consen  142 S  142 (634)
T ss_pred             c
Confidence            3

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=98.24  E-value=7.8e-06  Score=93.71  Aligned_cols=175  Identities=22%  Similarity=0.292  Sum_probs=112.1

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHc-ChhhHhhhcCCC-Cc-eEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFAN-GKEFYHRVGRAW-KR-GYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~-~~~~y~~~g~~~-~r-G~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      .|  ...+.|.....+.+....-..+.+.+..+-+ .+--|...+-.. .. .+|++||||.|||+.+.++|..++++++
T Consensus       309 ~~--~~k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g~~v~  386 (871)
T KOG1968|consen  309 GW--TEKYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELGFKVV  386 (871)
T ss_pred             cc--ccccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhccccee
Confidence            46  4456666667787777766677777766622 122222221111 12 3699999999999999999999999999


Q ss_pred             EEecCccCChHHHHHHHHhc-------------------CC-CeEEEEcCccchhhhhhhhhhcccCCccccccccchhh
Q 009640          258 DLELTKVTDNSELRALLLQT-------------------TN-RSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSI  317 (530)
Q Consensus       258 ~l~l~~~~~~~~L~~l~~~~-------------------~~-~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~  317 (530)
                      ..+.+...+...+...+..+                   .. --||++||+|-+++  .+|+                  
T Consensus       387 E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~--~dRg------------------  446 (871)
T KOG1968|consen  387 EKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG--EDRG------------------  446 (871)
T ss_pred             ecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc--hhhh------------------
Confidence            99999887766665544332                   11 23999999998752  1211                  


Q ss_pred             hhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHH
Q 009640          318 KEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPH  397 (530)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~  397 (530)
                                             .-.-++.|.+.         ..+=||+|+|...-.....+.  |-+.-|+|+.|+.+
T Consensus       447 -----------------------~v~~l~~l~~k---------s~~Piv~~cndr~~p~sr~~~--~~~~~l~f~kP~~~  492 (871)
T KOG1968|consen  447 -----------------------GVSKLSSLCKK---------SSRPLVCTCNDRNLPKSRALS--RACSDLRFSKPSSE  492 (871)
T ss_pred             -----------------------hHHHHHHHHHh---------ccCCeEEEecCCCCccccchh--hhcceeeecCCcHH
Confidence                                   11123344441         234578888876655543333  44477899999999


Q ss_pred             HHHHHHHHhhCCcC
Q 009640          398 AFKVLAKNYLGIES  411 (530)
Q Consensus       398 ~r~~i~~~~l~~~~  411 (530)
                      +...-+..++..+.
T Consensus       493 ~i~~ri~si~~se~  506 (871)
T KOG1968|consen  493 LIRSRIMSICKSEG  506 (871)
T ss_pred             HHHhhhhhhhcccc
Confidence            88777766665443

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.24  E-value=1.7e-05  Score=78.95  Aligned_cols=112  Identities=14%  Similarity=0.166  Sum_probs=77.4

Q ss_pred             CCceEEEECCCCCChhHHHHHHHHHcC----------------------CcEEEEecCc-cCChHHHHHHHHhc---C--
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMANYLC----------------------YDVYDLELTK-VTDNSELRALLLQT---T--  278 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~~l~----------------------~~i~~l~l~~-~~~~~~L~~l~~~~---~--  278 (530)
                      .+..|||+||+|+||..+|.++|..+-                      -|++.+.... ...-.+++++....   +  
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            356899999999999999999998772                      1223221111 12234455444322   1  


Q ss_pred             --CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCc
Q 009640          279 --NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLW  356 (530)
Q Consensus       279 --~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~  356 (530)
                        ..-|++|+++|.+                                                 .....+.||..++.- 
T Consensus        86 ~~~~KV~II~~ae~m-------------------------------------------------~~~AaNaLLK~LEEP-  115 (261)
T PRK05818         86 SNGKKIYIIYGIEKL-------------------------------------------------NKQSANSLLKLIEEP-  115 (261)
T ss_pred             cCCCEEEEeccHhhh-------------------------------------------------CHHHHHHHHHhhcCC-
Confidence              2468888888876                                                 233568899999853 


Q ss_pred             cCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          357 SCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       357 s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                         ..+.++|++|+.++.|-|.+++  |.-. +.|+.+
T Consensus       116 ---p~~t~fiLit~~~~~lLpTI~S--RCq~-~~~~~~  147 (261)
T PRK05818        116 ---PKNTYGIFTTRNENNILNTILS--RCVQ-YVVLSK  147 (261)
T ss_pred             ---CCCeEEEEEECChHhCchHhhh--heee-eecCCh
Confidence               5678999999999999999998  7643 556555

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

Probab=98.24  E-value=5.3e-06  Score=94.49  Aligned_cols=92  Identities=21%  Similarity=0.321  Sum_probs=62.3

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcC-CCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC----
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGR-AWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT----  265 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~-~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~----  265 (530)
                      +.|+|+++....|-+.+.....+      ++. .+.--+||.||.|+|||-||+|+|.++   .-.++.++++++.    
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            34677888777777777665532      111 133458999999999999999999998   4457778877632    


Q ss_pred             ---------ChHHHHHHHHhc--CCCeEEEEcCccch
Q 009640          266 ---------DNSELRALLLQT--TNRSIIVIEDIDCS  291 (530)
Q Consensus       266 ---------~~~~L~~l~~~~--~~~sII~IDeID~~  291 (530)
                               +....-.+....  ..-|||+|||||..
T Consensus       636 ligsp~gyvG~e~gg~LteavrrrP~sVVLfdeIEkA  672 (898)
T KOG1051|consen  636 LIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKA  672 (898)
T ss_pred             ccCCCcccccchhHHHHHHHHhcCCceEEEEechhhc
Confidence                     122222333332  34599999999975

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.21  E-value=4.7e-05  Score=82.53  Aligned_cols=86  Identities=13%  Similarity=0.198  Sum_probs=59.4

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSEL  270 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L  270 (530)
                      ..+++....-.++...+......           ...+++.|.+||||+++++++....   +.+++.+++..+. ...+
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~~-----------~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~-~~~~  201 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSRS-----------DITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIP-KDLI  201 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhCc-----------CCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCC-HHHH
Confidence            34666666666666666553322           2478999999999999999998875   4688999988763 2333


Q ss_pred             HHHH-H-----------------hcCCCeEEEEcCccch
Q 009640          271 RALL-L-----------------QTTNRSIIVIEDIDCS  291 (530)
Q Consensus       271 ~~l~-~-----------------~~~~~sII~IDeID~~  291 (530)
                      ...+ -                 .......|||||||.+
T Consensus       202 ~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l  240 (463)
T TIGR01818       202 ESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDM  240 (463)
T ss_pred             HHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhC
Confidence            3333 1                 1134678999999987

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.

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=98.21  E-value=3.6e-06  Score=89.17  Aligned_cols=48  Identities=29%  Similarity=0.480  Sum_probs=39.6

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ...|.||.|++..|+.+.-..               +-..++||+||||||||++|.-|..-|
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAA---------------AGgHnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAA---------------AGGHNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHH---------------hcCCcEEEecCCCCchHHhhhhhcccC
Confidence            457999999999999776533               224689999999999999999887766

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

Probab=98.20  E-value=1.9e-05  Score=80.03  Aligned_cols=68  Identities=19%  Similarity=0.252  Sum_probs=48.0

Q ss_pred             ccCChhhhHHHHHHHHHHHcChhhHhhh-cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          196 LALEPQLKKQITEDLTAFANGKEFYHRV-GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       196 l~~~~~~k~~i~~~l~~~l~~~~~y~~~-g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      ++|+.+.|+.+--.+..-..+...-..+ .--.|+++|+.||.|+|||-+|+.+|+..+.+|+.++.+.
T Consensus        17 IIGQ~~AKkaVAIALRNR~RR~qL~~~lr~EV~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATK   85 (444)
T COG1220          17 IIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATK   85 (444)
T ss_pred             hcCcHHHHHHHHHHHHHHHHHHhcCHHHhhccCccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeee
Confidence            6888888887765554322111111111 1123679999999999999999999999999999887553

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.20  E-value=5.9e-05  Score=81.97  Aligned_cols=87  Identities=11%  Similarity=0.170  Sum_probs=60.1

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHH
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSE  269 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~  269 (530)
                      +.++.+.....+.+.+.+......           ...+|+.|++||||+++|+++....   +.+++.+++..+.. ..
T Consensus       137 ~~~lig~s~~~~~l~~~~~~~~~~-----------~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~-~~  204 (469)
T PRK10923        137 TTDIIGEAPAMQDVFRIIGRLSRS-----------SISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPK-DL  204 (469)
T ss_pred             cccceecCHHHHHHHHHHHHHhcc-----------CCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCH-HH
Confidence            456677665555565555443322           3579999999999999999999886   46899999988733 33


Q ss_pred             HHHHH-Hh-----------------cCCCeEEEEcCccch
Q 009640          270 LRALL-LQ-----------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       270 L~~l~-~~-----------------~~~~sII~IDeID~~  291 (530)
                      +...+ ..                 ......|||||||.+
T Consensus       205 ~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l  244 (469)
T PRK10923        205 IESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDM  244 (469)
T ss_pred             HHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccC
Confidence            33332 21                 124568999999987

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.20  E-value=8.6e-06  Score=85.68  Aligned_cols=92  Identities=15%  Similarity=0.218  Sum_probs=68.9

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecCcc
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELTKV  264 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~~~  264 (530)
                      ....+++++|....-+++++.+..+-.           -...+|++|++||||+.+|++|....    ..+++.+++..+
T Consensus        73 ~~~~~~~LIG~~~~~~~~~eqik~~ap-----------~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~  141 (403)
T COG1221          73 KSEALDDLIGESPSLQELREQIKAYAP-----------SGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAY  141 (403)
T ss_pred             cchhhhhhhccCHHHHHHHHHHHhhCC-----------CCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHh
Confidence            445678888887777777777766322           23579999999999999999997443    568999999998


Q ss_pred             CChHHHHHHHHhc-----------------CCCeEEEEcCccch
Q 009640          265 TDNSELRALLLQT-----------------TNRSIIVIEDIDCS  291 (530)
Q Consensus       265 ~~~~~L~~l~~~~-----------------~~~sII~IDeID~~  291 (530)
                      ..+-....+|--.                 ....+||+|||..+
T Consensus       142 ~en~~~~eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~L  185 (403)
T COG1221         142 SENLQEAELFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRL  185 (403)
T ss_pred             CcCHHHHHHhccccceeecccCCcCchheecCCCEEehhhhhhC
Confidence            7776666665411                 23579999999987

>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=98.20  E-value=2.3e-06  Score=89.71  Aligned_cols=99  Identities=16%  Similarity=0.344  Sum_probs=62.5

Q ss_pred             CCCCceEEEECCCCCChhHHHHHHHHHcCCc------EEEEe------cCccC-ChHHHHHHHHhcCCC-eEEEEcCccc
Q 009640          225 RAWKRGYLLYGPPGSGKSSLIAAMANYLCYD------VYDLE------LTKVT-DNSELRALLLQTTNR-SIIVIEDIDC  290 (530)
Q Consensus       225 ~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~------i~~l~------l~~~~-~~~~L~~l~~~~~~~-sII~IDeID~  290 (530)
                      .+.++|++||||+|+|||+|.-...+.+...      +...-      +..+. ....+..+.....+. .||+|||+..
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            4568999999999999999999998887441      11110      00011 112233333343333 4999999985


Q ss_pred             hhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeC
Q 009640          291 SVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTN  370 (530)
Q Consensus       291 ~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN  370 (530)
                      -                                              +-.....+..|++.+   +   ..++++|+|+|
T Consensus       139 ~----------------------------------------------DiaDAmil~rLf~~l---~---~~gvvlVaTSN  166 (362)
T PF03969_consen  139 T----------------------------------------------DIADAMILKRLFEAL---F---KRGVVLVATSN  166 (362)
T ss_pred             c----------------------------------------------chhHHHHHHHHHHHH---H---HCCCEEEecCC
Confidence            3                                              222456777777765   2   36789999999


Q ss_pred             C-CCCC
Q 009640          371 H-RDSV  375 (530)
Q Consensus       371 ~-~~~L  375 (530)
                      + |+.|
T Consensus       167 ~~P~~L  172 (362)
T PF03969_consen  167 RPPEDL  172 (362)
T ss_pred             CChHHH
Confidence            7 4444

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

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.19  E-value=4.7e-05  Score=82.33  Aligned_cols=86  Identities=15%  Similarity=0.198  Sum_probs=57.9

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSEL  270 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L  270 (530)
                      ..+.+....-..+.+.+......           ...+|++|++||||+++++++....   +.+++.+++..+.. ..+
T Consensus       143 ~~ii~~S~~~~~~~~~~~~~a~~-----------~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~-~~~  210 (457)
T PRK11361        143 GHILTNSPAMMDICKDTAKIALS-----------QASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPE-SLL  210 (457)
T ss_pred             cceecccHHHhHHHHHHHHHcCC-----------CcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCH-HHH
Confidence            34555544444555555444433           2479999999999999999998765   57899999887743 333


Q ss_pred             HHH-HHh-----------------cCCCeEEEEcCccch
Q 009640          271 RAL-LLQ-----------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       271 ~~l-~~~-----------------~~~~sII~IDeID~~  291 (530)
                      ... |-.                 .....+|||||||.+
T Consensus       211 ~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l  249 (457)
T PRK11361        211 ESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEM  249 (457)
T ss_pred             HHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhC
Confidence            332 221                 123578999999997

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.17  E-value=6.5e-05  Score=81.04  Aligned_cols=87  Identities=16%  Similarity=0.227  Sum_probs=58.5

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHH
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSE  269 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~  269 (530)
                      +..+.+.....+.+...+......           ...++++|++||||+++|+++....   +.+++.+++..+.. ..
T Consensus       138 ~~~lig~s~~~~~l~~~i~~~a~~-----------~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~-~~  205 (445)
T TIGR02915       138 LRGLITSSPGMQKICRTIEKIAPS-----------DITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPE-NL  205 (445)
T ss_pred             ccceeecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCCh-HH
Confidence            344555555555555555443322           3578999999999999999998776   46789999888743 33


Q ss_pred             HHHHHHh------------------cCCCeEEEEcCccch
Q 009640          270 LRALLLQ------------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       270 L~~l~~~------------------~~~~sII~IDeID~~  291 (530)
                      +...+..                  ......|||||||.+
T Consensus       206 ~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l  245 (445)
T TIGR02915       206 LESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDL  245 (445)
T ss_pred             HHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhC
Confidence            3333211                  134578999999987

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).

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.17  E-value=4.4e-05  Score=77.58  Aligned_cols=118  Identities=20%  Similarity=0.236  Sum_probs=81.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC------------------------CcEEEEecCc-cCChHHHHHHHHhc-----
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC------------------------YDVYDLELTK-VTDNSELRALLLQT-----  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~------------------------~~i~~l~l~~-~~~~~~L~~l~~~~-----  277 (530)
                      +.+|||+||  +||+++|.++|..+-                        -|++.+.... ...-..+|.+....     
T Consensus        24 ~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~~p~  101 (290)
T PRK07276         24 NHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSGY  101 (290)
T ss_pred             ceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhhCcc
Confidence            458999996  689999999998662                        2333333221 12345666665443     


Q ss_pred             -CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCc
Q 009640          278 -TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLW  356 (530)
Q Consensus       278 -~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~  356 (530)
                       ...-|++||++|.+-                                                 ...-+.||+.|+.- 
T Consensus       102 ~~~~kV~II~~ad~m~-------------------------------------------------~~AaNaLLKtLEEP-  131 (290)
T PRK07276        102 EGKQQVFIIKDADKMH-------------------------------------------------VNAANSLLKVIEEP-  131 (290)
T ss_pred             cCCcEEEEeehhhhcC-------------------------------------------------HHHHHHHHHHhcCC-
Confidence             245699999999871                                                 23467899999853 


Q ss_pred             cCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          357 SCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       357 s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                         +.+.++|++|+.++.|-|.+++  |. .+|.|+. +.+....++.
T Consensus       132 ---p~~t~~iL~t~~~~~lLpTI~S--Rc-q~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        132 ---QSEIYIFLLTNDENKVLPTIKS--RT-QIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             ---CCCeEEEEEECChhhCchHHHH--cc-eeeeCCC-cHHHHHHHHH
Confidence               4568999999999999999998  76 5578865 5555555554

>PF05729 NACHT: NACHT domain

Probab=98.16  E-value=1.7e-05  Score=72.75  Aligned_cols=24  Identities=46%  Similarity=0.717  Sum_probs=21.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |-++++|+||+|||++++.++..+
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~   24 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQL   24 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHH
Confidence            357899999999999999999877

>PHA02774 E1; Provisional

Probab=98.16  E-value=2.1e-05  Score=85.83  Aligned_cols=58  Identities=24%  Similarity=0.436  Sum_probs=43.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEE-EecCccCChHHHHHHHHhcCCCeEEEEcCc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD-LELTKVTDNSELRALLLQTTNRSIIVIEDI  288 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~-l~l~~~~~~~~L~~l~~~~~~~sII~IDeI  288 (530)
                      |.|.++.++||||||||||+++.+|++.++..++. ++..+   .    -.|..+....|++|||+
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            45667899999999999999999999999765544 44321   1    11344455679999999

>PLN03210 Resistant to P

Probab=98.15  E-value=4.7e-05  Score=91.65  Aligned_cols=60  Identities=17%  Similarity=0.197  Sum_probs=42.2

Q ss_pred             ccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          184 SVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       184 ~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .+...++..+++++|.+...+++...+..           +....+-+-++||+|.||||||+++++.+..
T Consensus       174 ~l~~~~~~~~~~~vG~~~~l~~l~~lL~l-----------~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~  233 (1153)
T PLN03210        174 KLNLTPSNDFEDFVGIEDHIAKMSSLLHL-----------ESEEVRMVGIWGSSGIGKTTIARALFSRLSR  233 (1153)
T ss_pred             hhccccCcccccccchHHHHHHHHHHHcc-----------ccCceEEEEEEcCCCCchHHHHHHHHHHHhh
Confidence            34444566788888887776666654421           1122456889999999999999999988743

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=98.14  E-value=6.8e-05  Score=79.10  Aligned_cols=185  Identities=17%  Similarity=0.172  Sum_probs=113.2

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEecCccCCh-
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLELTKVTDN-  267 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l~~~~~~-  267 (530)
                      .++.|-+.....+.+.+...+....         ...+.+.|-||||||.+..-+-..+     ....+.++.+++... 
T Consensus       150 ~~l~gRe~e~~~v~~F~~~hle~~t---------~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~  220 (529)
T KOG2227|consen  150 GTLKGRELEMDIVREFFSLHLELNT---------SGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEAS  220 (529)
T ss_pred             CCccchHHHHHHHHHHHHhhhhccc---------CcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchH
Confidence            4566666666666665555554332         4678899999999999887665444     234466776654221 


Q ss_pred             --------------------HHHHHHHHhc----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccc
Q 009640          268 --------------------SELRALLLQT----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSR  323 (530)
Q Consensus       268 --------------------~~L~~l~~~~----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~  323 (530)
                                          .++...|.+.    ..+-|||+||+|.++.  .                           
T Consensus       221 aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~t--r---------------------------  271 (529)
T KOG2227|consen  221 AIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLIT--R---------------------------  271 (529)
T ss_pred             HHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhh--c---------------------------
Confidence                                1122233322    3467999999999841  0                           


Q ss_pred             cccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhc----CCceeEEEEeCCCCHHHH
Q 009640          324 IASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIR----CGRMDVHVSLGTCGPHAF  399 (530)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlR----pGR~d~~I~~~~p~~~~r  399 (530)
                                       ++.++-.|. +++.+   .+..+|+|+..|..+.-|..|.|    .+.-...+.|++.+.++.
T Consensus       272 -----------------~~~vLy~lF-ewp~l---p~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI  330 (529)
T KOG2227|consen  272 -----------------SQTVLYTLF-EWPKL---PNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQI  330 (529)
T ss_pred             -----------------ccceeeeeh-hcccC---CcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHH
Confidence                             111221221 22322   24678889999998887766653    355567899999999999


Q ss_pred             HHHHHHhhCCcCccchHH-HHHHHHHhCCCCCHHHHHHHH
Q 009640          400 KVLAKNYLGIESHHALFD-VVESCIRAGGALTPAQIGEVL  438 (530)
Q Consensus       400 ~~i~~~~l~~~~~~~~~~-~i~~l~~~~~~~spadi~~~l  438 (530)
                      ..|++.-+.........+ .++-+|..-.+.|+ |+..+|
T Consensus       331 ~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SG-DlRkaL  369 (529)
T KOG2227|consen  331 VEILQQRLSEESTSIFLNAAIELCARKVAAPSG-DLRKAL  369 (529)
T ss_pred             HHHHHHHHhcccccccchHHHHHHHHHhccCch-hHHHHH
Confidence            999998887654432333 45555554444554 444443

>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=98.08  E-value=3.6e-05  Score=77.72  Aligned_cols=147  Identities=22%  Similarity=0.235  Sum_probs=77.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHH--c--CCcE-EEEecCccCC------------------------hHHHHHHHHhc-
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANY--L--CYDV-YDLELTKVTD------------------------NSELRALLLQT-  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~--l--~~~i-~~l~l~~~~~------------------------~~~L~~l~~~~-  277 (530)
                      .+-+.|+|++|+|||+||..+++.  .  .++. +-+++....+                        ...+...+.+. 
T Consensus        19 ~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L   98 (287)
T PF00931_consen   19 VRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELL   98 (287)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHH
T ss_pred             eEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhh
Confidence            456889999999999999999977  3  2332 2333332211                        11222222222 


Q ss_pred             -CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCc
Q 009640          278 -TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLW  356 (530)
Q Consensus       278 -~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~  356 (530)
                       ..+++|||||++...                                                   .+..+...+-   
T Consensus        99 ~~~~~LlVlDdv~~~~---------------------------------------------------~~~~l~~~~~---  124 (287)
T PF00931_consen   99 KDKRCLLVLDDVWDEE---------------------------------------------------DLEELREPLP---  124 (287)
T ss_dssp             CCTSEEEEEEEE-SHH---------------------------------------------------HH-------H---
T ss_pred             ccccceeeeeeecccc---------------------------------------------------cccccccccc---
Confidence             458999999998641                                                   1111222111   


Q ss_pred             cCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC---ccchHHHHHHHHHhCCCCCHHH
Q 009640          357 SCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES---HHALFDVVESCIRAGGALTPAQ  433 (530)
Q Consensus       357 s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~---~~~~~~~i~~l~~~~~~~spad  433 (530)
                       .+..+.-||.||....-.. .+   +.-+..|+++..+.++-..++..+.+...   .....+...+++.. -+-.|-.
T Consensus       125 -~~~~~~kilvTTR~~~v~~-~~---~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~-c~glPLa  198 (287)
T PF00931_consen  125 -SFSSGSKILVTTRDRSVAG-SL---GGTDKVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEK-CGGLPLA  198 (287)
T ss_dssp             -CHHSS-EEEEEESCGGGGT-TH---HSCEEEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHH-TTT-HHH
T ss_pred             -ccccccccccccccccccc-cc---cccccccccccccccccccccccccccccccccccccccccccccc-ccccccc
Confidence             1112334666776532211 11   11267899999999999999999987544   12123344555553 3445544


Q ss_pred             H
Q 009640          434 I  434 (530)
Q Consensus       434 i  434 (530)
                      |
T Consensus       199 l  199 (287)
T PF00931_consen  199 L  199 (287)
T ss_dssp             H
T ss_pred             c
Confidence            4

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=98.06  E-value=3.9e-05  Score=69.81  Aligned_cols=30  Identities=33%  Similarity=0.556  Sum_probs=24.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      ++++||||+|||+++.+++..+   +..+..++
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~   34 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVD   34 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEE
Confidence            6899999999999999999887   34444443

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.

>PRK15115 response regulator GlrR; Provisional

Probab=97.99  E-value=0.00019  Score=77.34  Aligned_cols=62  Identities=19%  Similarity=0.285  Sum_probs=46.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHHH-HHH-----------------hcCCCeEEEEcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELRA-LLL-----------------QTTNRSIIVIED  287 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~~-l~~-----------------~~~~~sII~IDe  287 (530)
                      ..++++|++||||+++|+++....   +.+++.+++..+.. ..+.. +|.                 .......|||||
T Consensus       158 ~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~  236 (444)
T PRK15115        158 VSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPE-QLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDE  236 (444)
T ss_pred             CeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCH-HHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEc
Confidence            478999999999999999998875   47899999887633 23332 221                 123457899999


Q ss_pred             ccch
Q 009640          288 IDCS  291 (530)
Q Consensus       288 ID~~  291 (530)
                      ||.+
T Consensus       237 i~~l  240 (444)
T PRK15115        237 IGDM  240 (444)
T ss_pred             cccC
Confidence            9987

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=97.97  E-value=3.5e-05  Score=85.58  Aligned_cols=120  Identities=18%  Similarity=0.148  Sum_probs=83.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC--cEEEEecCc----cCChHHHHHHHHh-----------cCCCeEEEEcCccch
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY--DVYDLELTK----VTDNSELRALLLQ-----------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~--~i~~l~l~~----~~~~~~L~~l~~~-----------~~~~sII~IDeID~~  291 (530)
                      .|+||-|++|||||+++++++..+..  ++..+.++.    +.+.-+|...+..           .....||||||+..+
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            69999999999999999999999854  666654432    1223334444332           123579999999876


Q ss_pred             hhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc---------CCccCCCCC
Q 009640          292 VDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD---------GLWSCCSEE  362 (530)
Q Consensus       292 ~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD---------gl~s~~~~~  362 (530)
                                                                       ...+++.|+..|+         |........
T Consensus       106 -------------------------------------------------~~~~~~aLleame~G~vtIeR~G~s~~~Pa~  136 (584)
T PRK13406        106 -------------------------------------------------EPGTAARLAAALDTGEVRLERDGLALRLPAR  136 (584)
T ss_pred             -------------------------------------------------CHHHHHHHHHHHhCCcEEEEECCcEEecCCC
Confidence                                                             2346777887774         333322344


Q ss_pred             eEEEEEeCCC---CCCChhhhcCCceeEEEEeCCCCHHHH
Q 009640          363 KIIVFTTNHR---DSVDPALIRCGRMDVHVSLGTCGPHAF  399 (530)
Q Consensus       363 ~ivI~TTN~~---~~LDpALlRpGR~d~~I~~~~p~~~~r  399 (530)
                      .++|+|-|..   +.|.++|+.  ||+.+|.+++|+..+.
T Consensus       137 F~LIat~~~~~~~~~L~~~lLD--Rf~l~v~v~~~~~~~~  174 (584)
T PRK13406        137 FGLVALDEGAEEDERAPAALAD--RLAFHLDLDGLALRDA  174 (584)
T ss_pred             cEEEecCCChhcccCCCHHhHh--heEEEEEcCCCChHHh
Confidence            5677764433   469999999  9999999999987643

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=97.96  E-value=2.1e-05  Score=85.85  Aligned_cols=96  Identities=26%  Similarity=0.350  Sum_probs=57.6

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhc-CCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEec-------Cc-cC
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVG-RAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL-------TK-VT  265 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g-~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l-------~~-~~  265 (530)
                      +|.+.+++|+.+.-.|  |-....-+..-| ..---++||+|-||||||.|.+.+++.+-.-+|.---       +. +.
T Consensus       430 sIye~edvKkglLLqL--fGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVt  507 (804)
T KOG0478|consen  430 SIYELEDVKKGLLLQL--FGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVT  507 (804)
T ss_pred             hhhcccchhhhHHHHH--hcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEE
Confidence            4556677777664322  333333233322 1112359999999999999999999988666664321       11 11


Q ss_pred             ChHHHHHHHHhc-----CCCeEEEEcCccchh
Q 009640          266 DNSELRALLLQT-----TNRSIIVIEDIDCSV  292 (530)
Q Consensus       266 ~~~~L~~l~~~~-----~~~sII~IDeID~~~  292 (530)
                      .+.+-++++.+.     ....|..|||+|.+-
T Consensus       508 rd~dtkqlVLesGALVLSD~GiCCIDEFDKM~  539 (804)
T KOG0478|consen  508 KDPDTRQLVLESGALVLSDNGICCIDEFDKMS  539 (804)
T ss_pred             ecCccceeeeecCcEEEcCCceEEchhhhhhh
Confidence            122333444433     567899999999983

>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=97.95  E-value=2.3e-05  Score=81.01  Aligned_cols=77  Identities=18%  Similarity=0.260  Sum_probs=51.9

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC--CcEEEEecCccCC----
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC--YDVYDLELTKVTD----  266 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~--~~i~~l~l~~~~~----  266 (530)
                      .+-++|+.+.++..--.+ ..++...       -..|++||.||||||||.||-|||.+||  .+|..++.+++.+    
T Consensus        23 ~~GlVGQ~~AReAagiiv-~mIk~~K-------~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~isgSEiyS~e~k   94 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIV-DMIKEGK-------IAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVSISGSEIYSSEVK   94 (398)
T ss_dssp             ETTEES-HHHHHHHHHHH-HHHHTT---------TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEEEEGGGG-BTTC-
T ss_pred             cccccChHHHHHHHHHHH-HHHhccc-------ccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeEcccceeeecccC
Confidence            467899999888765433 3333222       2358999999999999999999999997  7888888887743    


Q ss_pred             -hHHHHHHHHhc
Q 009640          267 -NSELRALLLQT  277 (530)
Q Consensus       267 -~~~L~~l~~~~  277 (530)
                       ...|.+.|.++
T Consensus        95 KTE~L~qa~Rra  106 (398)
T PF06068_consen   95 KTEALTQAFRRA  106 (398)
T ss_dssp             HHHHHHHHHHCS
T ss_pred             chHHHHHHHHHh
Confidence             23366666653

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.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=97.85  E-value=4.6e-05  Score=73.02  Aligned_cols=33  Identities=12%  Similarity=0.074  Sum_probs=24.6

Q ss_pred             CCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          360 SEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       360 ~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                      ..+.-||++|-++..||+.+++  .++.++++..+
T Consensus       114 h~g~diiliTQ~~~~id~~ir~--lve~~~~~~k~  146 (193)
T PF05707_consen  114 HYGWDIILITQSPSQIDKFIRD--LVEYHYHCRKL  146 (193)
T ss_dssp             CTT-EEEEEES-GGGB-HHHHC--CEEEEEEEEE-
T ss_pred             cCCcEEEEEeCCHHHHhHHHHH--HHheEEEEEee
Confidence            3557799999999999998887  99999988644

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.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.83  E-value=0.00013  Score=85.86  Aligned_cols=125  Identities=21%  Similarity=0.343  Sum_probs=85.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHH--------------------hcCCCeEEEEcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLL--------------------QTTNRSIIVIED  287 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~--------------------~~~~~sII~IDe  287 (530)
                      .+++||-|.||.|||+|+.|+|+..|-.++.+++++-   ++|..+|-                    .+....-|++||
T Consensus      1543 ~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQ---TdL~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVlLDE 1619 (4600)
T COG5271        1543 GKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQ---TDLCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVLLDE 1619 (4600)
T ss_pred             CCceeecCCCCccHHHHHHHHHHHhcCceEEeecccc---chHHHHhCCCCCcccCceeEecccHHHHHhhcCCEEEeeh
Confidence            4689999999999999999999999999999999874   33444432                    234567888999


Q ss_pred             ccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC-----------Cc
Q 009640          288 IDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG-----------LW  356 (530)
Q Consensus       288 ID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg-----------l~  356 (530)
                      +.-.                                                 ++.++.||-.++|.           ..
T Consensus      1620 iNLa-------------------------------------------------SQSVlEGLNacLDhR~eayIPEld~~f 1650 (4600)
T COG5271        1620 INLA-------------------------------------------------SQSVLEGLNACLDHRREAYIPELDKTF 1650 (4600)
T ss_pred             hhhh-------------------------------------------------HHHHHHHHHHHHhhcccccccccccee
Confidence            8754                                                 23355555555552           22


Q ss_pred             cCCCCCeEEEEEeCCCC------CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          357 SCCSEEKIIVFTTNHRD------SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       357 s~~~~~~ivI~TTN~~~------~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      + |..+..|.+|-|.-+      -||..++.  ||.+ |.|...+......|+..++.
T Consensus      1651 ~-~HpnfrVFAaqNPq~qggGRKgLPkSF~n--RFsv-V~~d~lt~dDi~~Ia~~~yp 1704 (4600)
T COG5271        1651 D-VHPNFRVFAAQNPQDQGGGRKGLPKSFLN--RFSV-VKMDGLTTDDITHIANKMYP 1704 (4600)
T ss_pred             e-ccCCeeeeeecCchhcCCCcccCCHHHhh--hhhe-EEecccccchHHHHHHhhCC
Confidence            2 334444555555433      58999998  8865 67776666666666655544

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.82  E-value=5.7e-05  Score=75.70  Aligned_cols=92  Identities=15%  Similarity=0.144  Sum_probs=62.2

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEec-------CccCC
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL-------TKVTD  266 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l-------~~~~~  266 (530)
                      ..|.|+.-+++.|...+..|+.++..-      .|--+-|||+|||||+..++-||+.+-.....-+.       ...-.
T Consensus        82 ~~lfGQHla~~~Vv~alk~~~~n~~p~------KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~  155 (344)
T KOG2170|consen   82 RALFGQHLAKQLVVNALKSHWANPNPR------KPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPH  155 (344)
T ss_pred             HHhhchHHHHHHHHHHHHHHhcCCCCC------CCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCC
Confidence            346889999999999999999876410      12234579999999999999999987322221110       00111


Q ss_pred             -------hHHHHHHHHh---cCCCeEEEEcCccch
Q 009640          267 -------NSELRALLLQ---TTNRSIIVIEDIDCS  291 (530)
Q Consensus       267 -------~~~L~~l~~~---~~~~sII~IDeID~~  291 (530)
                             ..+|+..+..   ..++||.++||+|.+
T Consensus       156 ~~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKm  190 (344)
T KOG2170|consen  156 ASKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKL  190 (344)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCceEEechhhhc
Confidence                   1234444443   368899999999987

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=97.80  E-value=0.00062  Score=73.22  Aligned_cols=62  Identities=18%  Similarity=0.252  Sum_probs=47.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHHHHHHh------------------cCCCeEEEEcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELRALLLQ------------------TTNRSIIVIED  287 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~~l~~~------------------~~~~sII~IDe  287 (530)
                      ..++++|.+||||+++++++....   +.+++.+++..... ..+...+..                  ...+.+|||||
T Consensus       163 ~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~lde  241 (441)
T PRK10365        163 ATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNE-SLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDE  241 (441)
T ss_pred             CeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCH-HHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEec
Confidence            579999999999999999998765   46899999887643 344443321                  12467899999


Q ss_pred             ccch
Q 009640          288 IDCS  291 (530)
Q Consensus       288 ID~~  291 (530)
                      ||.+
T Consensus       242 i~~l  245 (441)
T PRK10365        242 IGDI  245 (441)
T ss_pred             cccC
Confidence            9997

>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=97.80  E-value=1.8e-05  Score=69.29  Aligned_cols=30  Identities=40%  Similarity=0.770  Sum_probs=27.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      |++.||||+||||+++.+|..+++.+++++
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d   31 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMD   31 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEec
Confidence            689999999999999999999998877664

...

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

Probab=97.80  E-value=0.00011  Score=79.01  Aligned_cols=93  Identities=17%  Similarity=0.255  Sum_probs=67.9

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      ...+.+|++|++....-.++++....+...           ...+|+.|.+||||..+|++|-+..   +-+|+.+++..
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A~t-----------dstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaA  306 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRIAKT-----------DSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAA  306 (560)
T ss_pred             cccccchhhhccCCHHHHHHHHHHHhhcCC-----------CCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEeccc
Confidence            346678999999888777777766655544           3589999999999999999998876   67999999987


Q ss_pred             cCChHHHH-HHH-------Hhc-----------CCCeEEEEcCccch
Q 009640          264 VTDNSELR-ALL-------LQT-----------TNRSIIVIEDIDCS  291 (530)
Q Consensus       264 ~~~~~~L~-~l~-------~~~-----------~~~sII~IDeID~~  291 (530)
                      +-. .-|. .||       ..+           ....-||+|||-.+
T Consensus       307 iPe-~LlESELFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgem  352 (560)
T COG3829         307 IPE-TLLESELFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEM  352 (560)
T ss_pred             CCH-HHHHHHHhCcCCccccccccCCCCcceeeccCCeEEehhhccC
Confidence            732 1222 222       111           23357999999876

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=97.74  E-value=1.4e-05  Score=83.12  Aligned_cols=129  Identities=22%  Similarity=0.275  Sum_probs=71.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc----c-----CCh--H--HHHH-HHHhcCCCeEEEEcCccchhhh
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK----V-----TDN--S--ELRA-LLLQTTNRSIIVIEDIDCSVDL  294 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~----~-----~~~--~--~L~~-l~~~~~~~sII~IDeID~~~~~  294 (530)
                      -.+||.|.||||||.|.+.+++.....+|..--+.    +     .+.  .  -+.. .+. .....|++|||+|.+-+ 
T Consensus        58 ihiLlvGdpg~gKS~ll~~~~~~~pr~v~~~g~~~s~~gLta~~~~d~~~~~~~leaGalv-lad~GiccIDe~dk~~~-  135 (331)
T PF00493_consen   58 IHILLVGDPGTGKSQLLKYVAKLAPRSVYTSGKGSSAAGLTASVSRDPVTGEWVLEAGALV-LADGGICCIDEFDKMKE-  135 (331)
T ss_dssp             --EEEECSCHHCHHHHHHCCCCT-SSEEEEECCGSTCCCCCEEECCCGGTSSECEEE-HHH-HCTTSEEEECTTTT--C-
T ss_pred             cceeeccchhhhHHHHHHHHHhhCCceEEECCCCcccCCccceeccccccceeEEeCCchh-cccCceeeecccccccc-
Confidence            36999999999999999999887766666542111    0     110  0  0110 111 24679999999998711 


Q ss_pred             hhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC---------CccCCCCCeEE
Q 009640          295 TADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG---------LWSCCSEEKII  365 (530)
Q Consensus       295 ~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg---------l~s~~~~~~iv  365 (530)
                                                                      .....|+..|+.         +...-.-+.-|
T Consensus       136 ------------------------------------------------~~~~~l~eaMEqq~isi~kagi~~~l~ar~sv  167 (331)
T PF00493_consen  136 ------------------------------------------------DDRDALHEAMEQQTISIAKAGIVTTLNARCSV  167 (331)
T ss_dssp             ------------------------------------------------HHHHHHHHHHHCSCEEECTSSSEEEEE---EE
T ss_pred             ------------------------------------------------hHHHHHHHHHHcCeeccchhhhcccccchhhh
Confidence                                                            012233333321         11111233468


Q ss_pred             EEEeCCCC-------------CCChhhhcCCceeEEEEe-CCCCHHHHHHHHHHhhCC
Q 009640          366 VFTTNHRD-------------SVDPALIRCGRMDVHVSL-GTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       366 I~TTN~~~-------------~LDpALlRpGR~d~~I~~-~~p~~~~r~~i~~~~l~~  409 (530)
                      ++++|...             .++++|+.  |||..+.+ ..|+.+.=..|.++.+..
T Consensus       168 laa~NP~~g~~~~~~~~~~ni~l~~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~  223 (331)
T PF00493_consen  168 LAAANPKFGRYDPNKSLSENINLPPPLLS--RFDLIFLLRDKPDEEEDERLAEHILDS  223 (331)
T ss_dssp             EEEE--TT--S-TTS-CGCCT-S-CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTT
T ss_pred             HHHHhhhhhhcchhhhhHHhcccchhhHh--hcCEEEEeccccccccccccceEEEec
Confidence            88999876             48889999  99988765 677877777777777654

; 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.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.73  E-value=4.5e-05  Score=83.20  Aligned_cols=66  Identities=29%  Similarity=0.337  Sum_probs=50.4

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-CCcEEEEec
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-CYDVYDLEL  261 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~~l~l  261 (530)
                      +-.-|+++.|.+++++.|++.+..-...-.       ..++-++|.||||+|||+|+++||+.+ .+++|.+..
T Consensus        71 ry~fF~d~yGlee~ieriv~~l~~Aa~gl~-------~~~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~kg  137 (644)
T PRK15455         71 RYPAFEEFYGMEEAIEQIVSYFRHAAQGLE-------EKKQILYLLGPVGGGKSSLAERLKSLMERVPIYVLKA  137 (644)
T ss_pred             cccchhcccCcHHHHHHHHHHHHHHHHhcC-------CCCceEEEecCCCCCchHHHHHHHHHHHhCcceeecC
Confidence            344589999999999999987754433211       124578899999999999999999988 567887754

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=97.72  E-value=8.4e-05  Score=80.77  Aligned_cols=163  Identities=17%  Similarity=0.290  Sum_probs=98.5

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCC--ceEEEECCCCCChhHHHHHHHHHcCCcEEEEec-Ccc-----
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWK--RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL-TKV-----  264 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~--rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l-~~~-----  264 (530)
                      |-.|.|.+.+|..|.-.+   +.+-..+..-|.+.+  -.+++.|.||||||-+.++.++.+-..+|..-- ++-     
T Consensus       344 ~PsIyGhe~VK~GilL~L---fGGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsPR~vYtsGkaSSaAGLTa  420 (764)
T KOG0480|consen  344 FPSIYGHELVKAGILLSL---FGGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSPRSVYTSGKASSAAGLTA  420 (764)
T ss_pred             CccccchHHHHhhHHHHH---hCCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccCCcceEecCcccccccceE
Confidence            566788888888775432   222222222233332  249999999999999999999999888886521 111     


Q ss_pred             --CChHHHHHHHHhc-----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          265 --TDNSELRALLLQT-----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       265 --~~~~~L~~l~~~~-----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                        ..+++--....++     ....|..|||+|.+= ...                                         
T Consensus       421 aVvkD~esgdf~iEAGALmLADnGICCIDEFDKMd-~~d-----------------------------------------  458 (764)
T KOG0480|consen  421 AVVKDEESGDFTIEAGALMLADNGICCIDEFDKMD-VKD-----------------------------------------  458 (764)
T ss_pred             EEEecCCCCceeeecCcEEEccCceEEechhcccC-hHh-----------------------------------------
Confidence              0111111111122     467899999999871 100                                         


Q ss_pred             CcchhhhHHHHhhhcc---------CCccCCCCCeEEEEEeCCCC-------------CCChhhhcCCcee-EEEEeCCC
Q 009640          338 EESGRVTLSGLLNFTD---------GLWSCCSEEKIIVFTTNHRD-------------SVDPALIRCGRMD-VHVSLGTC  394 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lD---------gl~s~~~~~~ivI~TTN~~~-------------~LDpALlRpGR~d-~~I~~~~p  394 (530)
                          +   ..++..|+         |+...-+.+--||+++|...             .+++++++  ||| ..|.+..|
T Consensus       459 ----q---vAihEAMEQQtISIaKAGv~aTLnARtSIlAAANPv~GhYdR~ktl~eNi~msApimS--RFDL~FiLlD~~  529 (764)
T KOG0480|consen  459 ----Q---VAIHEAMEQQTISIAKAGVVATLNARTSILAAANPVGGHYDRKKTLRENINMSAPIMS--RFDLFFILLDDC  529 (764)
T ss_pred             ----H---HHHHHHHHhheehheecceEEeecchhhhhhhcCCcCCccccccchhhhcCCCchhhh--hhcEEEEEecCC
Confidence                0   01111111         11111122334777887653             47899999  999 56778999


Q ss_pred             CHHHHHHHHHHhhCC
Q 009640          395 GPHAFKVLAKNYLGI  409 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~  409 (530)
                      ++..=..|.++.+..
T Consensus       530 nE~~D~~ia~hIld~  544 (764)
T KOG0480|consen  530 NEVVDYAIARHILDL  544 (764)
T ss_pred             chHHHHHHHHHHHHH
Confidence            998888888877754

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

Probab=97.71  E-value=0.0011  Score=71.26  Aligned_cols=89  Identities=16%  Similarity=0.155  Sum_probs=66.1

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChH
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNS  268 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~  268 (530)
                      .+..++|....-+++.+.+.....+.           ..+|++|.+||||-.+|++|-...   +-+|+.+++..+..+-
T Consensus       139 ~~~~liG~S~am~~l~~~i~kvA~s~-----------a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~l  207 (464)
T COG2204         139 LGGELVGESPAMQQLRRLIAKVAPSD-----------ASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENL  207 (464)
T ss_pred             ccCCceecCHHHHHHHHHHHHHhCCC-----------CCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHHH
Confidence            35677888887788888777665543           589999999999999999998877   4599999998874332


Q ss_pred             HHHHHHHh-----------------cCCCeEEEEcCccch
Q 009640          269 ELRALLLQ-----------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       269 ~L~~l~~~-----------------~~~~sII~IDeID~~  291 (530)
                      -=..+|-.                 ......||||||..+
T Consensus       208 ~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~m  247 (464)
T COG2204         208 LESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEM  247 (464)
T ss_pred             HHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccC
Confidence            22234431                 124578999999876

>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=97.70  E-value=0.00026  Score=66.71  Aligned_cols=30  Identities=23%  Similarity=0.225  Sum_probs=23.3

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +|++||||||||+|+..++...   |..+..++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s   34 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVT   34 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            6899999999999998887654   45555444

A related protein is found in archaea.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.70  E-value=0.00015  Score=70.03  Aligned_cols=40  Identities=28%  Similarity=0.390  Sum_probs=31.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      |+|...-++++||||||||+++..+|...   +..+..++...
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            67777789999999999999999888654   55677776654

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

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.68  E-value=4.1e-05  Score=71.12  Aligned_cols=35  Identities=31%  Similarity=0.386  Sum_probs=31.1

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +.+..++|+||||||||++++++|..+++.+++.+
T Consensus         2 ~~~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d   36 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD   36 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            34568999999999999999999999999998753

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.68  E-value=0.00012  Score=76.93  Aligned_cols=63  Identities=25%  Similarity=0.372  Sum_probs=42.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc----C-CcEEEEecCcc----------------------CChHHHHHHHHhcCCC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL----C-YDVYDLELTKV----------------------TDNSELRALLLQTTNR  280 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l----~-~~i~~l~l~~~----------------------~~~~~L~~l~~~~~~~  280 (530)
                      ..-++|.||+|+||||++..||..+    + ..+..+.....                      .+..++...+.+....
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            3568999999999999999999864    2 23433332221                      2233455566666777


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      .+|+||....
T Consensus       217 DlVLIDTaG~  226 (374)
T PRK14722        217 HMVLIDTIGM  226 (374)
T ss_pred             CEEEEcCCCC
Confidence            8888888764

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.67  E-value=7.5e-05  Score=66.16  Aligned_cols=53  Identities=13%  Similarity=0.049  Sum_probs=42.7

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ..|.|++-+++.|.+.+..++.++..      ..|--+.||||||||||.+++-||+.+
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            45789999999999999999977531      112245589999999999999999986

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

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.63  E-value=0.00051  Score=66.02  Aligned_cols=63  Identities=24%  Similarity=0.470  Sum_probs=39.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCCh----------HHHHHHHHh-----------cCCCeEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDN----------SELRALLLQ-----------TTNRSIIV  284 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~----------~~L~~l~~~-----------~~~~sII~  284 (530)
                      +-.++.||||||||+++++++..+   +..++-+..+.-...          ..+..++..           ..+..+||
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            567889999999999999988766   667777765542111          112222221           12347999


Q ss_pred             EcCccch
Q 009640          285 IEDIDCS  291 (530)
Q Consensus       285 IDeID~~  291 (530)
                      |||+-.+
T Consensus        99 VDEasmv  105 (196)
T PF13604_consen   99 VDEASMV  105 (196)
T ss_dssp             ESSGGG-
T ss_pred             Eeccccc
Confidence            9999876

>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.62  E-value=0.002  Score=61.28  Aligned_cols=129  Identities=16%  Similarity=0.253  Sum_probs=89.1

Q ss_pred             cChHHHHHHHHhhccCCCCCccccceeecccC----------------------CCCceEEEeCCCCeEeecccCeEEEE
Q 009640           59 VNDLYRHVNLYLNSVNPAGSSTCRRLTLSRSR----------------------SSNRISFTVAPNHTVHDSFSGHSLSW  116 (530)
Q Consensus        59 ~n~~~~a~~~yl~~~~~~~~~~~~~l~~~~~~----------------------~~~~~~~~~~~~~~~~d~f~g~~~~w  116 (530)
                      ..++|+.+-.||+.......  .+++.+....                      +...+.+.+.+| ...+.|+|..++.
T Consensus        34 ~D~~Y~~lm~Wls~q~~~~~--~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~G-~h~F~y~G~~~~~  110 (187)
T PF08740_consen   34 DDEAYDWLMRWLSSQPFSKR--SRHLSATTRSNSSWDDDESDDEDSWDTNTSDDKKKPIRFTPSPG-THWFWYKGRWFWF  110 (187)
T ss_pred             CCHHHHHHHHHHhhCCcccc--cceeEEEeecccccccccccccchhccccccCCcCCeEEEeCCC-CEEEEECCEEEEE
Confidence            47899999999998743331  1555554311                      355677888888 8899999999999


Q ss_pred             EEEeecccccc---cccceEEEecccchhhhhHHHHHHHHHHHHHHHHHHHhhhhccccCCCCCCCCCccccCCCCCCCc
Q 009640          117 THHVDTVQDSV---EEKRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFTNNGHGSYDSGWVSVPFRHPSTF  193 (530)
Q Consensus       117 ~~~~~~~~~~~---~~~~~~~l~~~~~~~~~vl~~yl~~v~~~~~~~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~~~~f  193 (530)
                      .+.........   .....++|++-.+++ .+|+.+|.++.+.  ..+.......+|...+.+   ..|..+...+++++
T Consensus       111 ~R~~~~~~~~~~~~~~~e~l~l~~lg~s~-~~l~~ll~ear~~--~~~~~~~~t~Iy~~~~~~---~~W~~~~~r~~Rpl  184 (187)
T PF08740_consen  111 SRQRESNSYNSWTGAPDETLTLSCLGRSP-KPLKDLLEEAREY--YLKKQKGKTTIYRADGSE---YRWRRVASRPKRPL  184 (187)
T ss_pred             EEEeccccccccCCCCceEEEEEEecCCH-HHHHHHHHHHHHH--HHHhcCCcEEEEeCCCCC---CCCcCCCCcCCCCC
Confidence            88773322111   125678888888776 5788888876664  334445556677774332   26999988999998


Q ss_pred             ccc
Q 009640          194 ETL  196 (530)
Q Consensus       194 ~~l  196 (530)
                      ++|
T Consensus       185 sTV  187 (187)
T PF08740_consen  185 STV  187 (187)
T ss_pred             CCC
Confidence            875

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) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.60  E-value=0.00053  Score=63.03  Aligned_cols=24  Identities=33%  Similarity=0.616  Sum_probs=22.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      --+.+.||||+|||+++.-+|+.|
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHH
Confidence            468899999999999999999888

>PRK07261 topology modulation protein; Provisional

Probab=97.60  E-value=0.00025  Score=66.61  Aligned_cols=30  Identities=30%  Similarity=0.429  Sum_probs=26.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +++.|+||+|||||++.|+..++.+++.++
T Consensus         3 i~i~G~~GsGKSTla~~l~~~~~~~~i~~D   32 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKLSQHYNCPVLHLD   32 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCeEecC
Confidence            789999999999999999999988877654

>PRK08118 topology modulation protein; Reviewed

Probab=97.57  E-value=0.00013  Score=68.42  Aligned_cols=57  Identities=23%  Similarity=0.257  Sum_probs=39.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc------cCChHHHHHHHHhc-CCCeEEEEcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK------VTDNSELRALLLQT-TNRSIIVIED  287 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~------~~~~~~L~~l~~~~-~~~sII~IDe  287 (530)
                      -+++.||||+|||||++.|++.++.++++++.--      ..+..+...++... ..++. |||-
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~~~~~~~~~~~~~~~w-VidG   66 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVPKEEQITVQNELVKEDEW-IIDG   66 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcCCCHHHHHHHHHHHhcCCCE-EEeC
Confidence            5899999999999999999999999998887321      12333455554443 34554 4443

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.50  E-value=8.8e-05  Score=72.46  Aligned_cols=22  Identities=45%  Similarity=0.878  Sum_probs=20.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      .-+|+||+|||||||+|+.+++
T Consensus        13 ~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             cEEEEECCCCCCHHHHHHhcCC
Confidence            4599999999999999999984

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.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.49  E-value=0.00069  Score=71.78  Aligned_cols=62  Identities=15%  Similarity=0.266  Sum_probs=39.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH-cCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY-LCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~-l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      .++++.||||||||+++.+++.+ ............+..+-. .+.+.......+|+|||+--+
T Consensus       210 ~Nli~lGp~GTGKThla~~l~~~~a~~sG~f~T~a~Lf~~L~-~~~lg~v~~~DlLI~DEvgyl  272 (449)
T TIGR02688       210 YNLIELGPKGTGKSYIYNNLSPYVILISGGTITVAKLFYNIS-TRQIGLVGRWDVVAFDEVATL  272 (449)
T ss_pred             CcEEEECCCCCCHHHHHHHHhHHHHHHcCCcCcHHHHHHHHH-HHHHhhhccCCEEEEEcCCCC
Confidence            48999999999999999999888 322221111111111111 133444567899999999875

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.

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=97.44  E-value=0.00017  Score=80.70  Aligned_cols=94  Identities=23%  Similarity=0.302  Sum_probs=56.6

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCc---eEEEECCCCCChhHHHHHHHHHcCCcEEEEecC-cc-----
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKR---GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT-KV-----  264 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~r---G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~-~~-----  264 (530)
                      -.|.|.+.+|+.|.-.+  |-..+....+ | .|-|   ++||.|-||||||.|.+.+++.+-..+|.---+ +.     
T Consensus       286 PsIyG~e~VKkAilLqL--fgGv~k~~~~-g-~~iRGDInILLvGDPgtaKSqlLk~v~~~aPr~vytsgkgss~~GLTA  361 (682)
T COG1241         286 PSIYGHEDVKKAILLQL--FGGVKKNLPD-G-TRIRGDIHILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSSAAGLTA  361 (682)
T ss_pred             ccccCcHHHHHHHHHHh--cCCCcccCCC-C-cccccceeEEEcCCCchhHHHHHHHHHhhCCceEEEccccccccCcee
Confidence            45778888888775433  2221111110 1 1223   489999999999999999999998777754211 11     


Q ss_pred             -C-ChHHHHHHHHhc-----CCCeEEEEcCccch
Q 009640          265 -T-DNSELRALLLQT-----TNRSIIVIEDIDCS  291 (530)
Q Consensus       265 -~-~~~~L~~l~~~~-----~~~sII~IDeID~~  291 (530)
                       . .+...-++..++     ..+.|++|||+|.+
T Consensus       362 av~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm  395 (682)
T COG1241         362 AVVRDKVTGEWVLEAGALVLADGGVCCIDEFDKM  395 (682)
T ss_pred             EEEEccCCCeEEEeCCEEEEecCCEEEEEeccCC
Confidence             0 011011122222     57899999999986

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.43  E-value=0.0017  Score=68.80  Aligned_cols=26  Identities=42%  Similarity=0.686  Sum_probs=23.0

Q ss_pred             CCceEEEECCCCCChhHHHHHHHHHc
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +++-++|+||+|+||||+++-+|..+
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~  198 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIY  198 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45678999999999999999999876

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.42  E-value=0.00077  Score=66.37  Aligned_cols=38  Identities=26%  Similarity=0.293  Sum_probs=30.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      |+|...-++++||||||||+|+.+++...   +..++.++.
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            67778889999999999999999997653   556655543

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=97.42  E-value=0.0064  Score=59.86  Aligned_cols=125  Identities=12%  Similarity=0.094  Sum_probs=92.2

Q ss_pred             ceEEEECCCC-CChhHHHHHHHHHcC---------CcEEEEecCc-------cCChHHHHHHHHhc------CCCeEEEE
Q 009640          229 RGYLLYGPPG-SGKSSLIAAMANYLC---------YDVYDLELTK-------VTDNSELRALLLQT------TNRSIIVI  285 (530)
Q Consensus       229 rG~LL~GPPG-TGKTsLa~AiA~~l~---------~~i~~l~l~~-------~~~~~~L~~l~~~~------~~~sII~I  285 (530)
                      ..|||.|..+ +||.-++.-++..+.         -|++.+....       ..+-..+|++....      ...-|++|
T Consensus        16 hAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~~~p~~g~~KViII   95 (263)
T PRK06581         16 NSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLSKTSAISGYKVAII   95 (263)
T ss_pred             heeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHhhCcccCCcEEEEE
Confidence            5899999998 999999888777662         3566664331       23445666665433      24569999


Q ss_pred             cCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEE
Q 009640          286 EDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKII  365 (530)
Q Consensus       286 DeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~iv  365 (530)
                      +++|.+-                                                 ....+.||..++.-    ....++
T Consensus        96 ~~ae~mt-------------------------------------------------~~AANALLKtLEEP----P~~t~f  122 (263)
T PRK06581         96 YSAELMN-------------------------------------------------LNAANSCLKILEDA----PKNSYI  122 (263)
T ss_pred             echHHhC-------------------------------------------------HHHHHHHHHhhcCC----CCCeEE
Confidence            9999872                                                 23467899999853    467888


Q ss_pred             EEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          366 VFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       366 I~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      |++|..++.|.|.+++  |+ .++.|..|....-.+++..++..
T Consensus       123 ILit~~~~~LLpTIrS--RC-q~i~~~~p~~~~~~e~~~~~~~p  163 (263)
T PRK06581        123 FLITSRAASIISTIRS--RC-FKINVRSSILHAYNELYSQFIQP  163 (263)
T ss_pred             EEEeCChhhCchhHhh--ce-EEEeCCCCCHHHHHHHHHHhccc
Confidence            9999999999999998  76 56889999988877777666654

>PRK13947 shikimate kinase; Provisional

Probab=97.41  E-value=0.00014  Score=67.67  Aligned_cols=31  Identities=26%  Similarity=0.429  Sum_probs=29.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .++|.|+||||||++++.+|+.+++++++.+
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            5899999999999999999999999999875

>PRK03839 putative kinase; Provisional

Probab=97.40  E-value=0.00013  Score=68.78  Aligned_cols=30  Identities=33%  Similarity=0.589  Sum_probs=27.8

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      ++|.|+||+||||+++.+|+.+++++++++
T Consensus         3 I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            789999999999999999999999988763

>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=97.40  E-value=0.00033  Score=70.54  Aligned_cols=92  Identities=25%  Similarity=0.417  Sum_probs=58.7

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC---cEEEEec-Cc
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY---DVYDLEL-TK  263 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~---~i~~l~l-~~  263 (530)
                      ..+.+++++...+...+.+.+.+...+..           ...+|+.||+|+||||++.++..++..   .++.++- .+
T Consensus        98 ~~~~sle~l~~~~~~~~~~~~~l~~~v~~-----------~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E  166 (270)
T PF00437_consen   98 SKPFSLEDLGESGSIPEEIAEFLRSAVRG-----------RGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPE  166 (270)
T ss_dssp             SS--CHCCCCHTHHCHHHHHHHHHHCHHT-----------TEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-
T ss_pred             cccccHhhccCchhhHHHHHHHHhhcccc-----------ceEEEEECCCccccchHHHHHhhhccccccceEEeccccc
Confidence            35557888877776666666555443322           357999999999999999999998843   4444431 11


Q ss_pred             c-------------CChHHHHHHHHhc--CCCeEEEEcCccc
Q 009640          264 V-------------TDNSELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       264 ~-------------~~~~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                      +             .....+.+++..+  ..|.+|+|.||-.
T Consensus       167 ~~l~~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR~  208 (270)
T PF00437_consen  167 LRLPGPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIGEIRD  208 (270)
T ss_dssp             S--SCSSEEEEEEETTTBSHHHHHHHHTTS--SEEEESCE-S
T ss_pred             eeecccceEEEEeecCcccHHHHHHHHhcCCCCcccccccCC
Confidence            1             1233466666655  6899999999974

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=97.40  E-value=0.0089  Score=62.21  Aligned_cols=36  Identities=22%  Similarity=0.335  Sum_probs=29.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV  264 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~  264 (530)
                      .-+.++||..+|||||..++.+.+   ++..+.+++..+
T Consensus        32 ~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~   70 (331)
T PF14516_consen   32 SYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQL   70 (331)
T ss_pred             CEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecC
Confidence            457889999999999999988766   777777776554

>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=97.40  E-value=0.00015  Score=66.09  Aligned_cols=31  Identities=29%  Similarity=0.411  Sum_probs=28.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .++|+||||+|||++++++|..+++.+++.+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d   31 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD   31 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            3789999999999999999999999998765

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.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.37  E-value=0.00096  Score=67.18  Aligned_cols=85  Identities=22%  Similarity=0.361  Sum_probs=52.3

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCce-EEEECCCCCChhHHHHHHHHHcC---CcEEEEe------
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRG-YLLYGPPGSGKSSLIAAMANYLC---YDVYDLE------  260 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG-~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~------  260 (530)
                      .++++++..++..+.+.+.+    ..           ++| +++.||+|+||||+++++..++.   ..++.++      
T Consensus        57 ~~l~~lg~~~~~~~~l~~~~----~~-----------~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~  121 (264)
T cd01129          57 LDLEKLGLKPENLEIFRKLL----EK-----------PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQ  121 (264)
T ss_pred             CCHHHcCCCHHHHHHHHHHH----hc-----------CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceec
Confidence            45788887777655543322    21           234 78999999999999999988774   3344442      


Q ss_pred             cCcc-----CC--hHHHHHHHHhc--CCCeEEEEcCccc
Q 009640          261 LTKV-----TD--NSELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       261 l~~~-----~~--~~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                      +..+     ..  ...+..++..+  ..|.+|+|.||-.
T Consensus       122 ~~~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR~  160 (264)
T cd01129         122 IPGINQVQVNEKAGLTFARGLRAILRQDPDIIMVGEIRD  160 (264)
T ss_pred             CCCceEEEeCCcCCcCHHHHHHHHhccCCCEEEeccCCC
Confidence            1111     00  11233444433  5799999999953

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.36  E-value=0.00093  Score=65.90  Aligned_cols=37  Identities=27%  Similarity=0.239  Sum_probs=26.6

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      |++...-+++.||||||||+++..++..+   +..+..+.
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            46666779999999999999976555433   44555444

>PRK00625 shikimate kinase; Provisional

Probab=97.34  E-value=0.00018  Score=67.86  Aligned_cols=31  Identities=32%  Similarity=0.564  Sum_probs=29.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .++|.|+||+|||++++.+|+.+++++++++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhh
Confidence            4789999999999999999999999999975

>cd01394 radB RadB

Probab=97.33  E-value=0.00094  Score=64.88  Aligned_cols=38  Identities=26%  Similarity=0.401  Sum_probs=29.8

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      |++..+-++++||||||||+++..+|.++   +..+..++.
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~   55 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDT   55 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEC
Confidence            56666669999999999999999998765   456655643

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

>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=97.33  E-value=0.00017  Score=64.87  Aligned_cols=26  Identities=50%  Similarity=0.723  Sum_probs=23.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      +++.||||+||||+++.++..++..+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~~~   27 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGAVV   27 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCEE
Confidence            68999999999999999999998333

...

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.32  E-value=0.00019  Score=64.97  Aligned_cols=33  Identities=27%  Similarity=0.518  Sum_probs=29.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      ...+|+.|-||||||+++.++|..+++..+.++
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~~i~is   39 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLEYIEIS   39 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCceEehh
Confidence            457999999999999999999999999988763

>PRK13949 shikimate kinase; Provisional

Probab=97.31  E-value=0.0002  Score=67.15  Aligned_cols=32  Identities=34%  Similarity=0.436  Sum_probs=29.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +.++|.||||+|||++++.+|+.+++++++++
T Consensus         2 ~~I~liG~~GsGKstl~~~La~~l~~~~id~D   33 (169)
T PRK13949          2 ARIFLVGYMGAGKTTLGKALARELGLSFIDLD   33 (169)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCCeeccc
Confidence            36899999999999999999999999999875

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.31  E-value=0.00076  Score=65.72  Aligned_cols=63  Identities=24%  Similarity=0.309  Sum_probs=39.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHH-----HcCCcE---------EEEecCccCC-----------hHH---HHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN-----YLCYDV---------YDLELTKVTD-----------NSE---LRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~-----~l~~~i---------~~l~l~~~~~-----------~~~---L~~l~~~~~~~  280 (530)
                      +.++|.||.|+|||++.+.++.     ..|..+         ++-..+.+..           ..+   +..++..+..+
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     233222         1111111111           122   33334456889


Q ss_pred             eEEEEcCccch
Q 009640          281 SIIVIEDIDCS  291 (530)
Q Consensus       281 sII~IDeID~~  291 (530)
                      ++++|||+..-
T Consensus       110 slvllDE~~~g  120 (213)
T cd03281         110 SLVLIDEFGKG  120 (213)
T ss_pred             cEEEeccccCC
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

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=97.30  E-value=0.00079  Score=79.02  Aligned_cols=139  Identities=20%  Similarity=0.214  Sum_probs=89.1

Q ss_pred             CCCceEEEECCCCCChhH-HHHHHHHHcCCcEEEEecCccCChHHHHHHHHh-c------------CCC----eEEEEcC
Q 009640          226 AWKRGYLLYGPPGSGKSS-LIAAMANYLCYDVYDLELTKVTDNSELRALLLQ-T------------TNR----SIIVIED  287 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTs-La~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~-~------------~~~----sII~IDe  287 (530)
                      .-.|+|+++||||+|||+ |.-++-+++-+++..++.+.-.........+.+ +            ++|    -|+|.||
T Consensus      1492 nt~R~~i~cGppGSgK~mlM~~sLrs~~~~ev~~~Nfs~~t~T~s~ls~Ler~t~yy~~tg~~~l~PK~~vK~lVLFcDe 1571 (3164)
T COG5245        1492 NTLRSYIYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMTPSKLSVLERETEYYPNTGVVRLYPKPVVKDLVLFCDE 1571 (3164)
T ss_pred             hccceEEEECCCCCccchhcchhhhhhhheeeeEEeeccccCCHHHHHHHHhhceeeccCCeEEEccCcchhheEEEeec
Confidence            346899999999999999 567899999999999998776544434444443 2            122    4899999


Q ss_pred             ccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCC------CC
Q 009640          288 IDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCC------SE  361 (530)
Q Consensus       288 ID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~------~~  361 (530)
                      |. + + .++.                                     ...+..-.-+..|+ +=.|+|+..      -.
T Consensus      1572 In-L-p-~~~~-------------------------------------y~~~~vI~FlR~l~-e~QGfw~s~~~~wvTI~ 1610 (3164)
T COG5245        1572 IN-L-P-YGFE-------------------------------------YYPPTVIVFLRPLV-ERQGFWSSIAVSWVTIC 1610 (3164)
T ss_pred             cC-C-c-cccc-------------------------------------cCCCceEEeeHHHH-HhcccccchhhhHhhhc
Confidence            98 2 1 0000                                     00011111111222 224566532      24


Q ss_pred             CeEEEEEeCCCCCC-----ChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          362 EKIIVFTTNHRDSV-----DPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       362 ~~ivI~TTN~~~~L-----DpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      ++++.+++|.+.+.     ...++|  | ...|++.||.-.....|...++.
T Consensus      1611 ~i~l~Gacnp~td~gRv~~~eRf~r--~-~v~vf~~ype~~SL~~Iyea~l~ 1659 (3164)
T COG5245        1611 GIILYGACNPGTDEGRVKYYERFIR--K-PVFVFCCYPELASLRNIYEAVLM 1659 (3164)
T ss_pred             ceEEEccCCCCCCcccCccHHHHhc--C-ceEEEecCcchhhHHHHHHHHHH
Confidence            57888999987643     355665  2 46688999999999999887774

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.30  E-value=0.0058  Score=62.49  Aligned_cols=153  Identities=20%  Similarity=0.190  Sum_probs=95.2

Q ss_pred             ccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHH---HHHcCCcEEEEecCccC-C-----
Q 009640          196 LALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAM---ANYLCYDVYDLELTKVT-D-----  266 (530)
Q Consensus       196 l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~Ai---A~~l~~~i~~l~l~~~~-~-----  266 (530)
                      +.|..+..+.+.+.+..-.-..+         ...+++.||.|+|||.++...   +.+.|-+++.+.+.... +     
T Consensus        26 l~g~~~~~~~l~~~lkqt~~~gE---------snsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~al   96 (408)
T KOG2228|consen   26 LFGVQDEQKHLSELLKQTILHGE---------SNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIAL   96 (408)
T ss_pred             eeehHHHHHHHHHHHHHHHHhcC---------CCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHHH
Confidence            45555556666666665554433         468999999999999987633   34778888888765431 1     


Q ss_pred             ---------------------hHHHHHHHHhc-------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhh
Q 009640          267 ---------------------NSELRALLLQT-------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIK  318 (530)
Q Consensus       267 ---------------------~~~L~~l~~~~-------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~  318 (530)
                                           ...+.+++...       ..+-|.++||||-..+                         
T Consensus        97 ~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~-------------------------  151 (408)
T KOG2228|consen   97 KGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAP-------------------------  151 (408)
T ss_pred             HHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhcccc-------------------------
Confidence                                 11233333221       2345667789998631                         


Q ss_pred             hhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC---CChhhhcCCceeEE-EEeCCC
Q 009640          319 EMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRMDVH-VSLGTC  394 (530)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~d~~-I~~~~p  394 (530)
                                          . ++.+  -|-|.+|-..++ ...+.||+.|.+-+.   |...+.+  ||... |+|..+
T Consensus       152 --------------------h-~rQt--llYnlfDisqs~-r~Piciig~Ttrld~lE~LEKRVKS--RFshr~I~m~~~  205 (408)
T KOG2228|consen  152 --------------------H-SRQT--LLYNLFDISQSA-RAPICIIGVTTRLDILELLEKRVKS--RFSHRVIFMLPS  205 (408)
T ss_pred             --------------------c-hhhH--HHHHHHHHHhhc-CCCeEEEEeeccccHHHHHHHHHHh--hcccceeeccCC
Confidence                                1 1222  245555544432 456778887776654   4456666  99765 777543


Q ss_pred             -CHHHHHHHHHHhhC
Q 009640          395 -GPHAFKVLAKNYLG  408 (530)
Q Consensus       395 -~~~~r~~i~~~~l~  408 (530)
                       ...+...+++..+.
T Consensus       206 ~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  206 LPLGDYVDLYRKLLS  220 (408)
T ss_pred             CChHHHHHHHHHHhc
Confidence             67889999999884

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.29  E-value=0.0011  Score=63.82  Aligned_cols=63  Identities=16%  Similarity=0.317  Sum_probs=41.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH-----cCCcEE-------------EEecC-cc---C-----ChHHHHHHHHhcC--C
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY-----LCYDVY-------------DLELT-KV---T-----DNSELRALLLQTT--N  279 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~-----l~~~i~-------------~l~l~-~~---~-----~~~~L~~l~~~~~--~  279 (530)
                      +-++|.||+|+||||+++.|+..     .|.++-             .+... ++   .     ....+..++....  .
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~l~~~~s~~~~e~~~~~~iL~~~~~~~  105 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKGE  105 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcccceEEEeccchhccccccChHHHHHHHHHHHHHhccCCC
Confidence            57899999999999999999853     344321             11000 00   0     1134566677777  8


Q ss_pred             CeEEEEcCccch
Q 009640          280 RSIIVIEDIDCS  291 (530)
Q Consensus       280 ~sII~IDeID~~  291 (530)
                      |++|++||.-.-
T Consensus       106 p~llllDEp~~g  117 (199)
T cd03283         106 PVLFLLDEIFKG  117 (199)
T ss_pred             CeEEEEecccCC
Confidence            999999997653

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

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=97.28  E-value=0.0013  Score=69.42  Aligned_cols=24  Identities=38%  Similarity=0.409  Sum_probs=21.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ..+|+.||+|+||||+++|++.++
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i  173 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHC  173 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            357899999999999999999887

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).

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.28  E-value=0.0016  Score=66.23  Aligned_cols=61  Identities=26%  Similarity=0.358  Sum_probs=41.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc----C-CcEEEEecCcc----------------------CChHHHHHHHHhcCCC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL----C-YDVYDLELTKV----------------------TDNSELRALLLQTTNR  280 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l----~-~~i~~l~l~~~----------------------~~~~~L~~l~~~~~~~  280 (530)
                      ++-++|.||+|+||||++..+|.++    + ..+..+.....                      .+..++.+.+......
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~~~~  273 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRLRDK  273 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHccCC
Confidence            3468899999999999999999876    3 55555544331                      2334556666666667


Q ss_pred             eEEEEcCc
Q 009640          281 SIIVIEDI  288 (530)
Q Consensus       281 sII~IDeI  288 (530)
                      .+||||..
T Consensus       274 d~vliDt~  281 (282)
T TIGR03499       274 DLILIDTA  281 (282)
T ss_pred             CEEEEeCC
Confidence            78888753

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.27  E-value=0.00054  Score=76.87  Aligned_cols=54  Identities=24%  Similarity=0.287  Sum_probs=43.4

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      ...+|..|+++.++++.++.|...+..               ++.+||+||||||||++++++|..+..
T Consensus        23 ~~~~~~~~~~vigq~~a~~~L~~~~~~---------------~~~~l~~G~~G~GKttla~~l~~~l~~   76 (637)
T PRK13765         23 IEVPERLIDQVIGQEHAVEVIKKAAKQ---------------RRHVMMIGSPGTGKSMLAKAMAELLPK   76 (637)
T ss_pred             cccCcccHHHcCChHHHHHHHHHHHHh---------------CCeEEEECCCCCcHHHHHHHHHHHcCh
Confidence            345678999999999988766554431               247999999999999999999998863

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.27  E-value=0.0022  Score=68.42  Aligned_cols=62  Identities=23%  Similarity=0.397  Sum_probs=41.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc-CChHHHHHH---HHhcC--CCeEEEEcCccch
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV-TDNSELRAL---LLQTT--NRSIIVIEDIDCS  291 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~-~~~~~L~~l---~~~~~--~~sII~IDeID~~  291 (530)
                      -++++||-+||||++++-+...+.-.++.++..+. .+..++.+.   +....  .++.||||||.++
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~~~l~d~~~~~~~~~~~~~~yifLDEIq~v  106 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLDEIQNV  106 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcchhhHHHHHHHHHHhhccCCceEEEecccCc
Confidence            78999999999999998888877554333333332 233333322   22332  5589999999986

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=97.26  E-value=0.00055  Score=76.75  Aligned_cols=52  Identities=31%  Similarity=0.374  Sum_probs=41.7

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +...+++++|+++.++.+...+..               +++++|+||||||||++++++|+.++.+
T Consensus        13 ~~~~~~~viG~~~a~~~l~~a~~~---------------~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        13 PERLIDQVIGQEEAVEIIKKAAKQ---------------KRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             chhhHhhccCHHHHHHHHHHHHHc---------------CCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            446789999999887766554431               2489999999999999999999999755

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.25  E-value=0.00097  Score=65.18  Aligned_cols=39  Identities=28%  Similarity=0.392  Sum_probs=31.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      |++...-++++||||||||+++..+|...   +..++.++..
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            56666678999999999999999998755   6666666655

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.25  E-value=0.00097  Score=67.31  Aligned_cols=26  Identities=31%  Similarity=0.549  Sum_probs=23.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .++++.||||+|||||.++++..+..
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~~  137 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILST  137 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccCC
Confidence            58899999999999999999998843

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.

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

Probab=97.23  E-value=0.0012  Score=64.32  Aligned_cols=29  Identities=31%  Similarity=0.306  Sum_probs=24.6

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |++...-+.|+||||+|||+|+..+|...
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~   43 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEA   43 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHh
Confidence            56666779999999999999999988654

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.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.23  E-value=0.00065  Score=63.85  Aligned_cols=63  Identities=21%  Similarity=0.238  Sum_probs=45.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChH-----------------------HHHHHHHh-cCCCeEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS-----------------------ELRALLLQ-TTNRSIIVI  285 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~-----------------------~L~~l~~~-~~~~sII~I  285 (530)
                      -+|+.||||+|||++|..+|..++.+++.+......+.+                       +|..++.. ..++.+|+|
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            379999999999999999999988777777655443332                       24444444 345668888


Q ss_pred             cCccchh
Q 009640          286 EDIDCSV  292 (530)
Q Consensus       286 DeID~~~  292 (530)
                      |-+-.++
T Consensus        83 D~Lt~~~   89 (170)
T PRK05800         83 DCLTTWV   89 (170)
T ss_pred             hhHHHHH
Confidence            8777663

>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=97.22  E-value=0.001  Score=61.14  Aligned_cols=65  Identities=23%  Similarity=0.388  Sum_probs=41.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEecC--cc-----------------CChHHHHHH-HHh--cCCCeEEEEc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT--KV-----------------TDNSELRAL-LLQ--TTNRSIIVIE  286 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~--~~-----------------~~~~~L~~l-~~~--~~~~sII~ID  286 (530)
                      .-+.|.||+|+|||+|+++|+..+..+--.+.+.  .+                 -+..+.+++ +..  +..|.++++|
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~r~~l~~~l~~~~~i~ilD  105 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARALLLNPDLLLLD  105 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCCccEEEECCEEcccCCHHHHHhceEEEeeCCHHHHHHHHHHHHHhcCCCEEEEe
Confidence            4588999999999999999999874321111111  00                 112233333 222  2689999999


Q ss_pred             Cccchhh
Q 009640          287 DIDCSVD  293 (530)
Q Consensus       287 eID~~~~  293 (530)
                      |...-+|
T Consensus       106 Ep~~~lD  112 (157)
T cd00267         106 EPTSGLD  112 (157)
T ss_pred             CCCcCCC
Confidence            9987653

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.

>PRK04296 thymidine kinase; Provisional

Probab=97.22  E-value=0.0023  Score=61.18  Aligned_cols=30  Identities=27%  Similarity=0.262  Sum_probs=23.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l  259 (530)
                      -.|++||||+|||+++..++..+   +..++.+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            36889999999999998888766   5555555

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.21  E-value=0.00029  Score=66.34  Aligned_cols=29  Identities=24%  Similarity=0.456  Sum_probs=25.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +++.||||+||||+++.+|..+++..+++
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is~   30 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLSA   30 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            68999999999999999999998765553

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.

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.18  E-value=0.00029  Score=65.84  Aligned_cols=32  Identities=31%  Similarity=0.372  Sum_probs=30.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +.+.|.|++|+||||+.+++|+.|+++|+|.+
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D   34 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTD   34 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccch
Confidence            46899999999999999999999999999985

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.18  E-value=0.00024  Score=66.51  Aligned_cols=37  Identities=35%  Similarity=0.509  Sum_probs=25.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCc---EEEEecCcc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYD---VYDLELTKV  264 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~---i~~l~l~~~  264 (530)
                      ++.++|+||||+|||++++++...+...   ++.+++...
T Consensus        24 ~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen   24 PRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             ---EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            4789999999999999999998877444   666666554

>PRK14532 adenylate kinase; Provisional

Probab=97.17  E-value=0.00034  Score=66.41  Aligned_cols=30  Identities=20%  Similarity=0.396  Sum_probs=26.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .++|.||||+||||+++.+|..+++..++.
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            378999999999999999999999877654

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.17  E-value=0.00035  Score=63.68  Aligned_cols=28  Identities=36%  Similarity=0.441  Sum_probs=24.8

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      ++|.||||+||||+++.++..++..+++
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~   29 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFID   29 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEe
Confidence            6899999999999999999998776654

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.17  E-value=0.0099  Score=58.83  Aligned_cols=46  Identities=11%  Similarity=0.131  Sum_probs=35.8

Q ss_pred             CCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          361 EEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       361 ~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      -++-+|+++...-.|||.++.  -++..+-+. -+......|++++...
T Consensus       127 ~~is~i~l~Q~~~~lp~~iR~--n~~y~i~~~-~s~~dl~~i~~~~~~~  172 (241)
T PF04665_consen  127 YNISIIFLSQSYFHLPPNIRS--NIDYFIIFN-NSKRDLENIYRNMNIK  172 (241)
T ss_pred             cceEEEEEeeecccCCHHHhh--cceEEEEec-CcHHHHHHHHHhcccc
Confidence            346788889888999999866  888888776 4677777888877654

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK14531 adenylate kinase; Provisional

Probab=97.16  E-value=0.0004  Score=65.83  Aligned_cols=31  Identities=26%  Similarity=0.441  Sum_probs=27.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +-+++.||||+||||+++.+|..+|+..+++
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            4589999999999999999999999887654

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.16  E-value=0.0014  Score=67.12  Aligned_cols=62  Identities=26%  Similarity=0.384  Sum_probs=41.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC-----CcEEEEecC-c----------c---CChHHHHHHHHhc--CCCeEEEEc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC-----YDVYDLELT-K----------V---TDNSELRALLLQT--TNRSIIVIE  286 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~-----~~i~~l~l~-~----------~---~~~~~L~~l~~~~--~~~sII~ID  286 (530)
                      ++++|+.||+|+||||+++|+++++.     ..++.++-. +          +   .....+.+++..+  ..|.+|++.
T Consensus       132 ~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v~~~~~~~~~~~~~~l~~aLR~~pD~iivG  211 (299)
T TIGR02782       132 RKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQLRTSDDAISMTRLLKATLRLRPDRIIVG  211 (299)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEEEEEecCCCCCHHHHHHHHhcCCCCEEEEe
Confidence            46899999999999999999999872     334333210 0          0   0111455555544  679999999


Q ss_pred             Ccc
Q 009640          287 DID  289 (530)
Q Consensus       287 eID  289 (530)
                      ||=
T Consensus       212 EiR  214 (299)
T TIGR02782       212 EVR  214 (299)
T ss_pred             ccC
Confidence            985

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.

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.16  E-value=0.00067  Score=69.70  Aligned_cols=29  Identities=31%  Similarity=0.380  Sum_probs=24.8

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      ..++|+.||||-|.|||+|....-..+..
T Consensus        63 ~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~   91 (367)
T COG1485          63 GPVRGLYLWGGVGRGKTMLMDLFYESLPG   91 (367)
T ss_pred             CCCceEEEECCCCccHHHHHHHHHhhCCc
Confidence            45789999999999999999888777643

>PRK13948 shikimate kinase; Provisional

Probab=97.16  E-value=0.00046  Score=65.59  Aligned_cols=34  Identities=24%  Similarity=0.145  Sum_probs=31.6

Q ss_pred             CCceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .++.++|.|+||+||||+++.+|..+++++++.+
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D   42 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALMLHFIDTD   42 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCCCEEECC
Confidence            3578999999999999999999999999999886

>TIGR02012 tigrfam_recA protein RecA

Probab=97.15  E-value=0.00084  Score=69.25  Aligned_cols=69  Identities=20%  Similarity=0.264  Sum_probs=43.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc---------------------cCChHHHHHH---HHh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK---------------------VTDNSELRAL---LLQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~---------------------~~~~~~L~~l---~~~  276 (530)
                      |+|..+-+++|||||||||+|+..++...   +..+..++...                     ..+..+...+   +.+
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            56666779999999999999987665544   44444443211                     1111112222   223


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||-+-++.
T Consensus       131 ~~~~~lIVIDSv~al~  146 (321)
T TIGR02012       131 SGAVDIIVVDSVAALV  146 (321)
T ss_pred             ccCCcEEEEcchhhhc
Confidence            3578899999998874

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.

>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=97.15  E-value=0.00038  Score=62.70  Aligned_cols=30  Identities=33%  Similarity=0.457  Sum_probs=28.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +.+.|+||||||++++.+|..+++++++.+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            578999999999999999999999999886

>PRK06217 hypothetical protein; Validated

Probab=97.13  E-value=0.00041  Score=65.70  Aligned_cols=31  Identities=32%  Similarity=0.380  Sum_probs=28.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -++|.|+||+||||+++++|..+++++++++
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcC
Confidence            4899999999999999999999999887764

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.12  E-value=0.017  Score=67.81  Aligned_cols=32  Identities=31%  Similarity=0.314  Sum_probs=26.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      +-++++||+|.|||+++...+...+ ++.-+++
T Consensus        33 ~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l   64 (903)
T PRK04841         33 RLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSL   64 (903)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC-CeEEEec
Confidence            5689999999999999999887776 6555544

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.11  E-value=0.0016  Score=63.92  Aligned_cols=28  Identities=29%  Similarity=0.284  Sum_probs=23.6

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      |++...-+.|+||||||||+|+..+|..
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~   42 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVT   42 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4566667899999999999999998754

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 .

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.09  E-value=0.00041  Score=64.15  Aligned_cols=28  Identities=36%  Similarity=0.603  Sum_probs=24.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      ++|.||||+||||+++++++.++..+++
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v~   28 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFIE   28 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEEe
Confidence            4789999999999999999999866544

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.

>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=97.08  E-value=0.00046  Score=65.47  Aligned_cols=29  Identities=34%  Similarity=0.510  Sum_probs=26.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+|||++++.||..+++.++++
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~   30 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHIST   30 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            68999999999999999999998776664

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.08  E-value=0.011  Score=62.08  Aligned_cols=24  Identities=29%  Similarity=0.510  Sum_probs=21.5

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCC
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .|+.||||||||+|++.+|+.+..
T Consensus       136 ~LIvG~pGtGKTTLl~~la~~i~~  159 (380)
T PRK12608        136 GLIVAPPRAGKTVLLQQIAAAVAA  159 (380)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            599999999999999999998743

>PRK13946 shikimate kinase; Provisional

Probab=97.07  E-value=0.00048  Score=65.41  Aligned_cols=33  Identities=33%  Similarity=0.432  Sum_probs=30.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      ++.++|.|+||+|||++++.+|..+|+++++.+
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D   42 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDAD   42 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcC
Confidence            467999999999999999999999999999876

>TIGR00767 rho transcription termination factor Rho

Probab=97.07  E-value=0.0083  Score=63.45  Aligned_cols=24  Identities=29%  Similarity=0.537  Sum_probs=21.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+++.||||||||+|+.+|++...
T Consensus       170 ~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       170 RGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             EEEEECCCCCChhHHHHHHHHhhc
Confidence            389999999999999999999864

Members of this family differ in the specificity of RNA binding.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.07  E-value=0.0015  Score=58.82  Aligned_cols=27  Identities=30%  Similarity=0.412  Sum_probs=24.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      .-++|.|+.|+|||++++++++.++..
T Consensus        23 ~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        23 TVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            458899999999999999999999753

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.07  E-value=0.00073  Score=73.11  Aligned_cols=69  Identities=26%  Similarity=0.323  Sum_probs=45.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC--------------------ChHHHHHHHHhc--C
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT--------------------DNSELRALLLQT--T  278 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~--------------------~~~~L~~l~~~~--~  278 (530)
                      |++...-+||+||||+|||+|+..+|...   +..++.++..+-.                    ...++..++...  .
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            56666778999999999999999998765   5666666543210                    011122222222  4


Q ss_pred             CCeEEEEcCccchh
Q 009640          279 NRSIIVIEDIDCSV  292 (530)
Q Consensus       279 ~~sII~IDeID~~~  292 (530)
                      .|.+||||.|..+.
T Consensus       156 ~~~lVVIDSIq~l~  169 (446)
T PRK11823        156 KPDLVVIDSIQTMY  169 (446)
T ss_pred             CCCEEEEechhhhc
Confidence            67889999988763

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

Probab=97.06  E-value=0.0011  Score=68.48  Aligned_cols=69  Identities=19%  Similarity=0.241  Sum_probs=44.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc---------------------cCChHHHHHHH---Hh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK---------------------VTDNSELRALL---LQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~---------------------~~~~~~L~~l~---~~  276 (530)
                      |+|..+-+++|||||||||+|+-.+|...   +..+..++...                     ..+..++..++   .+
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            46666678999999999999998776543   44555443321                     11122222222   23


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||-+-++.
T Consensus       131 s~~~~lIVIDSvaal~  146 (325)
T cd00983         131 SGAVDLIVVDSVAALV  146 (325)
T ss_pred             ccCCCEEEEcchHhhc
Confidence            3578899999998874

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.06  E-value=0.00058  Score=64.19  Aligned_cols=34  Identities=38%  Similarity=0.623  Sum_probs=30.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      ++.++|.||||+|||++++.+|+.+++++++.+.
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~~~~vd~D~   37 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQ   37 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcCCcEEECCc
Confidence            3579999999999999999999999999988753

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=97.03  E-value=0.00048  Score=66.57  Aligned_cols=22  Identities=41%  Similarity=0.827  Sum_probs=18.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .++.||||||||+++.+++..+
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            7899999999999888877776

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.03  E-value=0.0052  Score=64.74  Aligned_cols=24  Identities=33%  Similarity=0.573  Sum_probs=21.5

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCC
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .|++||||||||+|+++|++....
T Consensus       172 ~lIvgppGvGKTTLaK~Ian~I~~  195 (416)
T PRK09376        172 GLIVAPPKAGKTVLLQNIANSITT  195 (416)
T ss_pred             EEEeCCCCCChhHHHHHHHHHHHh
Confidence            688899999999999999997744

>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=97.03  E-value=0.0014  Score=51.86  Aligned_cols=29  Identities=34%  Similarity=0.408  Sum_probs=23.3

Q ss_pred             EEEECCCCCChhHHHHHHHHHc-CCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL-CYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l-~~~i~~l  259 (530)
                      +.+.|+||+|||+++++++..+ +.++..+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l~~~~~~~i   31 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQLGGRSVVVL   31 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCEEEE
Confidence            5688999999999999999997 3444444

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.

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.01  E-value=0.0013  Score=63.44  Aligned_cols=60  Identities=20%  Similarity=0.307  Sum_probs=38.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      |....--++|.|+.|+|||++++.|+.+.    |.-.+....+...    ...+...-||.|||++.+
T Consensus        48 g~k~d~~lvl~G~QG~GKStf~~~L~~~~----~~d~~~~~~~kd~----~~~l~~~~iveldEl~~~  107 (198)
T PF05272_consen   48 GCKNDTVLVLVGKQGIGKSTFFRKLGPEY----FSDSINDFDDKDF----LEQLQGKWIVELDELDGL  107 (198)
T ss_pred             CCcCceeeeEecCCcccHHHHHHHHhHHh----ccCccccCCCcHH----HHHHHHhHheeHHHHhhc
Confidence            33344567899999999999999997762    2212222222222    223344578999999986

>PF13245 AAA_19: Part of AAA domain

Probab=97.00  E-value=0.0011  Score=53.76  Aligned_cols=33  Identities=39%  Similarity=0.610  Sum_probs=20.9

Q ss_pred             eEEEECCCCCChhH-HHHHHHHHc------CCcEEEEecC
Q 009640          230 GYLLYGPPGSGKSS-LIAAMANYL------CYDVYDLELT  262 (530)
Q Consensus       230 G~LL~GPPGTGKTs-La~AiA~~l------~~~i~~l~l~  262 (530)
                      -+++.||||||||+ ++..++..+      +..+..+..+
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            35569999999995 455555555      3445555443

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=96.98  E-value=0.00079  Score=62.78  Aligned_cols=31  Identities=32%  Similarity=0.497  Sum_probs=28.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .++|.|+||+|||++++.+|..+++++++.+
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~lg~~~~d~D   34 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQALGYRFVDTD   34 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEEcc
Confidence            5789999999999999999999999999875

>PRK08233 hypothetical protein; Provisional

Probab=96.97  E-value=0.0052  Score=57.50  Aligned_cols=24  Identities=21%  Similarity=0.272  Sum_probs=21.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.+.|+||+||||++.++|..++
T Consensus         5 iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCC
Confidence            356789999999999999999885

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.96  E-value=0.00051  Score=63.89  Aligned_cols=29  Identities=31%  Similarity=0.586  Sum_probs=26.5

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +++.|.|||||||++..++ .+|++++.++
T Consensus         3 I~ITGTPGvGKTT~~~~L~-~lg~~~i~l~   31 (180)
T COG1936           3 IAITGTPGVGKTTVCKLLR-ELGYKVIELN   31 (180)
T ss_pred             EEEeCCCCCchHHHHHHHH-HhCCceeeHH
Confidence            6899999999999999999 9999988764

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.96  E-value=0.0012  Score=69.68  Aligned_cols=69  Identities=23%  Similarity=0.308  Sum_probs=44.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC--------------------ChHHHHHHHHh--cC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT--------------------DNSELRALLLQ--TT  278 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~--------------------~~~~L~~l~~~--~~  278 (530)
                      |++...-+||+||||+|||+|+..+|..+   +..++.++..+-.                    ....+..++..  ..
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            45666678999999999999999998765   3456555432210                    11122223222  25


Q ss_pred             CCeEEEEcCccchh
Q 009640          279 NRSIIVIEDIDCSV  292 (530)
Q Consensus       279 ~~sII~IDeID~~~  292 (530)
                      +|.+|+||.|..+.
T Consensus       158 ~~~lVVIDSIq~l~  171 (372)
T cd01121         158 KPDLVIIDSIQTVY  171 (372)
T ss_pred             CCcEEEEcchHHhh
Confidence            78999999998763

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.94  E-value=0.013  Score=63.06  Aligned_cols=35  Identities=29%  Similarity=0.325  Sum_probs=26.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEecC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLELT  262 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l~  262 (530)
                      .+-++|.||+|+||||++..||..+     +..+.-++..
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D  260 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLD  260 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECC
Confidence            3468899999999999999998765     2455555443

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.94  E-value=0.00076  Score=62.03  Aligned_cols=29  Identities=28%  Similarity=0.452  Sum_probs=26.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +-+.|||||||||+++-+|.++|+++++-
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vsa   31 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVSA   31 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceeec
Confidence            45789999999999999999999998873

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.94  E-value=0.00082  Score=63.31  Aligned_cols=31  Identities=19%  Similarity=0.355  Sum_probs=26.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+++.||||+||||+++.+|..+|+..++.
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~g~~~~~~   34 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKYGFTHLST   34 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            3578899999999999999999998765543

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.

>PRK13764 ATPase; Provisional

Probab=96.93  E-value=0.0025  Score=70.86  Aligned_cols=62  Identities=26%  Similarity=0.455  Sum_probs=40.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC---cEEEEe------cCc-cC-------ChHHHHHHHHhcCCCeEEEEcCccc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY---DVYDLE------LTK-VT-------DNSELRALLLQTTNRSIIVIEDIDC  290 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~---~i~~l~------l~~-~~-------~~~~L~~l~~~~~~~sII~IDeID~  290 (530)
                      +.++|+.||||+||||+++|++.++..   .+..++      +.. +.       +...+.+.+. ...|.+|++||+=.
T Consensus       257 ~~~ILIsG~TGSGKTTll~AL~~~i~~~~riV~TiEDp~El~~~~~i~q~~~~~~~~~~~~~~lL-R~rPD~IivGEiRd  335 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQVPPEITQYSKLEGSMEETADILL-LVRPDYTIYDEMRK  335 (602)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhhCCCEEEEECCCccccCCCcceEEeeccccHHHHHHHHH-hhCCCEEEECCCCC
Confidence            468999999999999999999998853   332332      111 10       1111222221 36799999999864

>PRK14530 adenylate kinase; Provisional

Probab=96.92  E-value=0.00089  Score=65.13  Aligned_cols=30  Identities=27%  Similarity=0.426  Sum_probs=27.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .++|.||||+||||+++.||..+++++++.
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            589999999999999999999999887755

>PRK05973 replicative DNA helicase; Provisional

Probab=96.92  E-value=0.0037  Score=61.80  Aligned_cols=39  Identities=23%  Similarity=0.018  Sum_probs=28.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      |++...-+|+.|+||+|||+|+-.+|...   |.+++.+++.
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSlE  101 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLE  101 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence            45556679999999999999988776654   6666555443

>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=96.92  E-value=0.0018  Score=66.95  Aligned_cols=64  Identities=33%  Similarity=0.419  Sum_probs=48.6

Q ss_pred             cc-cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-CCcEEEEecCc
Q 009640          193 FE-TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-CYDVYDLELTK  263 (530)
Q Consensus       193 f~-~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~~l~l~~  263 (530)
                      |+ ++.|.++..++|++++..-..+-+       .-++-+||.||+|+|||||+..+.+.+ .+.+|.+..+-
T Consensus        59 f~~~~~G~~~~i~~lV~~fk~AA~g~~-------~~krIl~L~GPvg~GKSsl~~~Lk~~le~y~~Y~l~~~P  124 (358)
T PF08298_consen   59 FEDEFYGMEETIERLVNYFKSAAQGLE-------ERKRILLLLGPVGGGKSSLAELLKRGLEEYPIYTLKGCP  124 (358)
T ss_pred             ccccccCcHHHHHHHHHHHHHHHhccC-------ccceEEEEECCCCCCHHHHHHHHHHHhheEEEEEecCCc
Confidence            55 789999988888887665443222       335778999999999999999999888 56777775443

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=96.90  E-value=0.0017  Score=66.93  Aligned_cols=57  Identities=25%  Similarity=0.332  Sum_probs=41.7

Q ss_pred             ChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          199 EPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       199 ~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .++.++.+.+.+...+....     -......+.|.|+||+|||++++.+|..+|+++++++
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            45555556665555443222     1344567999999999999999999999999999754

>PRK13695 putative NTPase; Provisional

Probab=96.89  E-value=0.0078  Score=56.38  Aligned_cols=22  Identities=41%  Similarity=0.777  Sum_probs=20.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ++|.|+||+|||||+..+++.+
T Consensus         3 i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          3 IGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999988775

>PRK02496 adk adenylate kinase; Provisional

Probab=96.89  E-value=0.00092  Score=63.22  Aligned_cols=29  Identities=28%  Similarity=0.524  Sum_probs=26.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +++.||||+|||++++.+|..+++..+++
T Consensus         4 i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          4 LIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            78999999999999999999999877664

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.88  E-value=0.0017  Score=56.60  Aligned_cols=24  Identities=38%  Similarity=0.368  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ++++++||||+|||+++.+.+..+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~   24 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILEL   24 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHH
Confidence            368999999999999888777666

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

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.88  E-value=0.004  Score=61.33  Aligned_cols=22  Identities=36%  Similarity=0.649  Sum_probs=20.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +-+.||+|||||||.+.||...
T Consensus        32 vsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          32 VAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7789999999999999999977

>PRK06547 hypothetical protein; Provisional

Probab=96.88  E-value=0.0015  Score=61.49  Aligned_cols=33  Identities=30%  Similarity=0.460  Sum_probs=28.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +.-+++.||||+|||++++.+|..++..+++++
T Consensus        15 ~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         15 MITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            457889999999999999999999988777654

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=96.87  E-value=0.0011  Score=69.88  Aligned_cols=52  Identities=29%  Similarity=0.505  Sum_probs=41.1

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..++++....+.+++.+.+.                  .+|+|+.||||.||||+|+|+|.++......+
T Consensus       243 k~~ledY~L~dkl~eRL~er------------------aeGILIAG~PGaGKsTFaqAlAefy~~~GkiV  294 (604)
T COG1855         243 KLSLEDYGLSDKLKERLEER------------------AEGILIAGAPGAGKSTFAQALAEFYASQGKIV  294 (604)
T ss_pred             EechhhcCCCHHHHHHHHhh------------------hcceEEecCCCCChhHHHHHHHHHHHhcCcEE
Confidence            34678888888887776652                  37999999999999999999999985544433

>PRK06762 hypothetical protein; Provisional

Probab=96.87  E-value=0.0012  Score=61.22  Aligned_cols=32  Identities=19%  Similarity=0.289  Sum_probs=26.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .-++|.|+||+||||+++.++..++..++.++
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~   34 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERLGRGTLLVS   34 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEEec
Confidence            45789999999999999999999965555553

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.87  E-value=0.0051  Score=57.84  Aligned_cols=24  Identities=38%  Similarity=0.559  Sum_probs=21.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||+|+|||||+++||...
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~~   52 (178)
T cd03247          29 EKIALLGRSGSGKSTLLQLLTGDL   52 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhccC
Confidence            458899999999999999999976

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.87  E-value=0.003  Score=65.34  Aligned_cols=62  Identities=23%  Similarity=0.348  Sum_probs=41.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEec-Ccc------------CChHHHHHHHHhc--CCCeEEEEcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLEL-TKV------------TDNSELRALLLQT--TNRSIIVIED  287 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l-~~~------------~~~~~L~~l~~~~--~~~sII~IDe  287 (530)
                      +.++|+.||+|+||||+++|++.+.     +..++.++- .++            .+.-.+.+++..+  ..|.+|++-|
T Consensus       144 ~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El~~~~~n~v~l~~~~~~~~~~lv~~aLR~~PD~IivGE  223 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEIQCAAENAVALHTSDTVDMARLLKSTMRLRPDRIIVGE  223 (323)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCcccccCCCCEEEeccCCCcCHHHHHHHHhCCCCCEEEEee
Confidence            4689999999999999999999886     233444431 110            1112344555444  6899999999


Q ss_pred             cc
Q 009640          288 ID  289 (530)
Q Consensus       288 ID  289 (530)
                      |=
T Consensus       224 iR  225 (323)
T PRK13833        224 VR  225 (323)
T ss_pred             cC
Confidence            84

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.87  E-value=0.0027  Score=58.98  Aligned_cols=24  Identities=29%  Similarity=0.469  Sum_probs=21.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||+|+|||||++.|+...
T Consensus        27 e~~~l~G~nGsGKSTLl~~i~G~~   50 (163)
T cd03216          27 EVHALLGENGAGKSTLMKILSGLY   50 (163)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            458899999999999999999876

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.86  E-value=0.0022  Score=61.71  Aligned_cols=24  Identities=50%  Similarity=0.775  Sum_probs=21.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+++.||+|+||||++.+++.++.
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            368899999999999999998884

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>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=96.86  E-value=0.0041  Score=56.59  Aligned_cols=64  Identities=23%  Similarity=0.299  Sum_probs=41.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc---EE-----EEecCccCChHHHHHH-HHh--cCCCeEEEEcCccchh
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD---VY-----DLELTKVTDNSELRAL-LLQ--TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~---i~-----~l~l~~~~~~~~L~~l-~~~--~~~~sII~IDeID~~~  292 (530)
                      .-+.|.||+|+|||||+++|+..+...   ++     .+....--+..+.+++ +..  +.+|.|+++||-..-+
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~~i~~~~~lS~G~~~rv~laral~~~p~illlDEP~~~L  101 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQLSGGEKMRLALAKLLLENPNLLLLDEPTNHL  101 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCeEEEEEEccCCHHHHHHHHHHHHHhcCCCEEEEeCCccCC
Confidence            458899999999999999999987321   10     1111000223344443 222  3789999999988754

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.

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

Probab=96.85  E-value=0.0057  Score=65.53  Aligned_cols=91  Identities=12%  Similarity=0.171  Sum_probs=67.2

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD  266 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~  266 (530)
                      ...+..++|....-.++.+.++....+.           ..+||.|..||||..+|+||-...   ..+++.+++..+-.
T Consensus       219 ~~~~~~iIG~S~am~~ll~~i~~VA~Sd-----------~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPe  287 (550)
T COG3604         219 VLEVGGIIGRSPAMRQLLKEIEVVAKSD-----------STVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPE  287 (550)
T ss_pred             hcccccceecCHHHHHHHHHHHHHhcCC-----------CeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccch
Confidence            4467788998888888888777665543           589999999999999999998876   67899999887732


Q ss_pred             hHHHHHHH-------Hhc----------CCCeEEEEcCccch
Q 009640          267 NSELRALL-------LQT----------TNRSIIVIEDIDCS  291 (530)
Q Consensus       267 ~~~L~~l~-------~~~----------~~~sII~IDeID~~  291 (530)
                      +--=..+|       ..+          ....-||+|||--+
T Consensus       288 sLlESELFGHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGel  329 (550)
T COG3604         288 SLLESELFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGEL  329 (550)
T ss_pred             HHHHHHHhcccccccccchhccCcceeecCCCeEechhhccC
Confidence            21112222       222          34578999999876

>PRK14528 adenylate kinase; Provisional

Probab=96.85  E-value=0.001  Score=63.26  Aligned_cols=30  Identities=23%  Similarity=0.490  Sum_probs=26.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -+++.||||+||||+++.+|..+++..+++
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~~~~~is~   32 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERLSIPQIST   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCeeeC
Confidence            489999999999999999999999887664

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.84  E-value=0.0011  Score=65.44  Aligned_cols=30  Identities=20%  Similarity=0.469  Sum_probs=27.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.||||+||||+++.+|..+++..+++
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g~~~is~   37 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKENLKHINM   37 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            389999999999999999999999887765

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.82  E-value=0.0029  Score=60.11  Aligned_cols=26  Identities=31%  Similarity=0.663  Sum_probs=23.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      ...+++.||+|+||||++++++..+.
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            35789999999999999999999874

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.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.81  E-value=0.0059  Score=57.07  Aligned_cols=24  Identities=33%  Similarity=0.594  Sum_probs=21.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||+|+|||||+++||..+
T Consensus        29 ~~~~l~G~nGsGKstLl~~i~G~~   52 (171)
T cd03228          29 EKVAIVGPSGSGKSTLLKLLLRLY   52 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC
Confidence            458899999999999999999986

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.81  E-value=0.014  Score=61.75  Aligned_cols=49  Identities=27%  Similarity=0.396  Sum_probs=35.3

Q ss_pred             hhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          200 PQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .++++.+.+.+..++..+..+.    ..++-++|.||+|+||||++..||..+
T Consensus       217 ~~~~~~l~~~l~~~l~~~~~~~----~~~~vI~LVGptGvGKTTTiaKLA~~L  265 (436)
T PRK11889        217 EEVIEYILEDMRSHFNTENVFE----KEVQTIALIGPTGVGKTTTLAKMAWQF  265 (436)
T ss_pred             HHHHHHHHHHHHHHhccccccc----cCCcEEEEECCCCCcHHHHHHHHHHHH
Confidence            4566667777766665442221    124678999999999999999999877

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.79  E-value=0.005  Score=62.11  Aligned_cols=89  Identities=26%  Similarity=0.462  Sum_probs=55.1

Q ss_pred             ccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCce-EEEECCCCCChhHHHHHHHHHcCC----cE
Q 009640          182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRG-YLLYGPPGSGKSSLIAAMANYLCY----DV  256 (530)
Q Consensus       182 w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG-~LL~GPPGTGKTsLa~AiA~~l~~----~i  256 (530)
                      +..+| ....+|+.+..++-+.+ +.       .           .++| +|+.||.|+||||..+||-++.+.    ++
T Consensus        98 lR~Ip-~~i~~~e~LglP~i~~~-~~-------~-----------~~~GLILVTGpTGSGKSTTlAamId~iN~~~~~HI  157 (353)
T COG2805          98 LRLIP-SKIPTLEELGLPPIVRE-LA-------E-----------SPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHI  157 (353)
T ss_pred             EeccC-ccCCCHHHcCCCHHHHH-HH-------h-----------CCCceEEEeCCCCCcHHHHHHHHHHHHhccCCcce
Confidence            44444 45668999988775444 21       1           1467 566899999999999999999854    45


Q ss_pred             EEEec-Ccc--CCh-------------HHHHHHHHhc--CCCeEEEEcCccc
Q 009640          257 YDLEL-TKV--TDN-------------SELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       257 ~~l~l-~~~--~~~-------------~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                      +.++- -++  .+.             ......|..+  ..|.||++-|+=.
T Consensus       158 lTIEDPIE~vh~skkslI~QREvG~dT~sF~~aLraALReDPDVIlvGEmRD  209 (353)
T COG2805         158 LTIEDPIEYVHESKKSLINQREVGRDTLSFANALRAALREDPDVILVGEMRD  209 (353)
T ss_pred             EEecCchHhhhcchHhhhhHHHhcccHHHHHHHHHHHhhcCCCEEEEecccc
Confidence            54431 111  111             1122223333  5799999998853

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=96.79  E-value=0.0046  Score=59.43  Aligned_cols=21  Identities=24%  Similarity=0.534  Sum_probs=19.6

Q ss_pred             ceEEEECCCCCChhHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMA  249 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA  249 (530)
                      +-++|.||.|+|||+|.+.|+
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

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.78  E-value=0.0043  Score=58.24  Aligned_cols=62  Identities=23%  Similarity=0.236  Sum_probs=44.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC-----------------------hHHHHHHHHhcCCCeEEEEcC
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD-----------------------NSELRALLLQTTNRSIIVIED  287 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~-----------------------~~~L~~l~~~~~~~sII~IDe  287 (530)
                      +|+.||||+|||++|..+|...+.+++.+......+                       ..+|.+.+...+.+.+|+||-
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            589999999999999999988777777775544322                       123444454444567888888


Q ss_pred             ccchh
Q 009640          288 IDCSV  292 (530)
Q Consensus       288 ID~~~  292 (530)
                      +...+
T Consensus        82 lt~~~   86 (169)
T cd00544          82 LTLWV   86 (169)
T ss_pred             HhHHH
Confidence            77663

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.

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=96.77  E-value=0.0055  Score=58.95  Aligned_cols=64  Identities=23%  Similarity=0.356  Sum_probs=40.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHH-H----cCCcE--------------EEEecCcc-C--------ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN-Y----LCYDV--------------YDLELTKV-T--------DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~-~----l~~~i--------------~~l~l~~~-~--------~~~~L~~l~~~~~~~  280 (530)
                      .-++|.||.|+|||++.+.|+. .    .|..+              +.+..... .        ....+..++.....|
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            4589999999999999999993 2    22211              11111100 0        112344445556899


Q ss_pred             eEEEEcCccchh
Q 009640          281 SIIVIEDIDCSV  292 (530)
Q Consensus       281 sII~IDeID~~~  292 (530)
                      .++++||.-.-+
T Consensus       110 ~llllDEp~~gl  121 (202)
T cd03243         110 SLVLIDELGRGT  121 (202)
T ss_pred             eEEEEecCCCCC
Confidence            999999997643

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

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.76  E-value=0.0013  Score=64.03  Aligned_cols=29  Identities=28%  Similarity=0.457  Sum_probs=26.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++++||||+|||++++.||..+++..+++
T Consensus         3 I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            79999999999999999999999777664

>TIGR01351 adk adenylate kinases

Probab=96.76  E-value=0.0013  Score=63.78  Aligned_cols=29  Identities=31%  Similarity=0.486  Sum_probs=26.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +++.||||+||||+++.+|..+++..+++
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            68999999999999999999998877663

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.

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

Probab=96.74  E-value=0.0039  Score=59.99  Aligned_cols=37  Identities=30%  Similarity=0.330  Sum_probs=28.5

Q ss_pred             ChhhHhhhc--CCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          216 GKEFYHRVG--RAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       216 ~~~~y~~~g--~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.+.-+++|  +|.+.=+|+.|+.|||||-|...+|--+
T Consensus        14 ndelDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~   52 (235)
T COG2874          14 NDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGF   52 (235)
T ss_pred             cHHHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHH
Confidence            445555554  6776668899999999999999998644

>PLN02200 adenylate kinase family protein

Probab=96.74  E-value=0.0017  Score=64.31  Aligned_cols=31  Identities=19%  Similarity=0.316  Sum_probs=26.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      +.-+++.||||+||||+++.+|..+|+..+.
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~~g~~his   73 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVETFGFKHLS   73 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCeEEE
Confidence            3457889999999999999999999876443

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=96.73  E-value=0.0038  Score=66.63  Aligned_cols=200  Identities=17%  Similarity=0.192  Sum_probs=108.8

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCC--CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc--cC-ChHH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAW--KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK--VT-DNSE  269 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~--~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~--~~-~~~~  269 (530)
                      +|.|.+++|+.+.-.+.   ..++.--.-|...  .-+++|.|.||.-||-|.+.|.+-.-..+|.---.+  +. +..-
T Consensus       343 EIyGheDVKKaLLLlLV---Ggvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlapRgvYTTGrGSSGVGLTAAV  419 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLV---GGVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAPRGVYTTGRGSSGVGLTAAV  419 (721)
T ss_pred             hhccchHHHHHHHHHhh---CCCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcCcccceecCCCCCccccchhh
Confidence            46788888887655443   2222111122222  124899999999999999999998877777653211  11 1111


Q ss_pred             HHHHHH----------hcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          270 LRALLL----------QTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       270 L~~l~~----------~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                      ++.-..          -.....|..|||+|.+-+  .+|..-                -|    +.           +..
T Consensus       420 mkDpvTgEM~LEGGALVLAD~GICCIDEfDKM~e--~DRtAI----------------HE----VM-----------EQQ  466 (721)
T KOG0482|consen  420 MKDPVTGEMVLEGGALVLADGGICCIDEFDKMDE--SDRTAI----------------HE----VM-----------EQQ  466 (721)
T ss_pred             hcCCCCCeeEeccceEEEccCceEeehhhhhhhh--hhhHHH----------------HH----HH-----------Hhh
Confidence            111110          014567999999999832  122110                00    00           000


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-------------CCChhhhcCCceeEEEEe-CCCCHHHHHHHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-------------SVDPALIRCGRMDVHVSL-GTCGPHAFKVLAKN  405 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-------------~LDpALlRpGR~d~~I~~-~~p~~~~r~~i~~~  405 (530)
                      .-.....+++..+.       .+.-|+++.|...             .|++||++  |||....+ ..||.+.=..|+++
T Consensus       467 TISIaKAGI~TtLN-------AR~sILaAANPayGRYnprrs~e~NI~LPaALLS--RFDll~Li~D~pdrd~D~~LA~H  537 (721)
T KOG0482|consen  467 TISIAKAGINTTLN-------ARTSILAAANPAYGRYNPRRSPEQNINLPAALLS--RFDLLWLIQDRPDRDNDLRLAQH  537 (721)
T ss_pred             hhhhhhhccccchh-------hhHHhhhhcCccccccCcccChhHhcCCcHHHHH--hhhhhhhhccCCcccchHHHHHH
Confidence            01111122222221       2233666776532             58999999  99975554 78999888888887


Q ss_pred             hhCCcCcc---------chHHHHH---HHHHhCCCCCHHHHHHHHH
Q 009640          406 YLGIESHH---------ALFDVVE---SCIRAGGALTPAQIGEVLL  439 (530)
Q Consensus       406 ~l~~~~~~---------~~~~~i~---~l~~~~~~~spadi~~~l~  439 (530)
                      ..-...|.         ...+.+.   .+++.-.-+.|.++.+.+.
T Consensus       538 iTyVH~H~~qp~~~fepl~~~~mR~yI~~ak~~~P~vp~~l~dyi~  583 (721)
T KOG0482|consen  538 ITYVHQHEEQPPLDFEPLDPNLMRRYISLAKRKNPVVPEALADYIT  583 (721)
T ss_pred             hHhhhccCCCCCccCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH
Confidence            76543222         0122233   3344456677778777664

>PRK04182 cytidylate kinase; Provisional

Probab=96.73  E-value=0.0014  Score=61.17  Aligned_cols=29  Identities=31%  Similarity=0.509  Sum_probs=26.8

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.|+||+|||++++++|..+++++++.
T Consensus         3 I~i~G~~GsGKstia~~la~~lg~~~id~   31 (180)
T PRK04182          3 ITISGPPGSGKTTVARLLAEKLGLKHVSA   31 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCcEecH
Confidence            68999999999999999999999988873

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.72  E-value=0.0071  Score=62.56  Aligned_cols=62  Identities=27%  Similarity=0.442  Sum_probs=40.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEec-Ccc------------CChHHHHHHHHhc--CCCeEEEEcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLEL-TKV------------TDNSELRALLLQT--TNRSIIVIED  287 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l-~~~------------~~~~~L~~l~~~~--~~~sII~IDe  287 (530)
                      +..+++.||+|+||||+++|++.+.     ...++.++- .++            ...-.+.+++..+  ..|..|++.|
T Consensus       148 ~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El~~~~~~~v~~~~~~~~~~~~ll~~aLR~~PD~IivGE  227 (319)
T PRK13894        148 HRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYVQYHTSIDVNMTALLKTTLRMRPDRILVGE  227 (319)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCccccCCCCEEEEecCCCCCHHHHHHHHhcCCCCEEEEec
Confidence            4689999999999999999999874     122332210 000            1112345555544  6899999999


Q ss_pred             cc
Q 009640          288 ID  289 (530)
Q Consensus       288 ID  289 (530)
                      |-
T Consensus       228 iR  229 (319)
T PRK13894        228 VR  229 (319)
T ss_pred             cC
Confidence            86

>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=96.72  E-value=0.0012  Score=57.88  Aligned_cols=22  Identities=36%  Similarity=0.590  Sum_probs=20.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ++|.|+|||||||+++.++..+
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            5899999999999999999998

...

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=96.71  E-value=0.0025  Score=59.20  Aligned_cols=23  Identities=35%  Similarity=0.608  Sum_probs=21.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.||+|||||+|.+++|+..
T Consensus        31 ~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          31 FIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             eEEEeCCCCccHHHHHHHHHhcc
Confidence            48999999999999999999965

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.71  E-value=0.0042  Score=60.13  Aligned_cols=62  Identities=23%  Similarity=0.253  Sum_probs=38.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH-----cCCcEEEE--------------ecCc-cC--------ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY-----LCYDVYDL--------------ELTK-VT--------DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~-----l~~~i~~l--------------~l~~-~~--------~~~~L~~l~~~~~~~  280 (530)
                      +-++|.||.|+|||++++.++..     +|..+-..              ...+ +.        ...++..++..+..|
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~~~~la~~G~~vpa~~~~l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~~il~~~~~~  109 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADGD  109 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCcchhhcCccChhheeEecCCccccchhhhHHHHHHHHHHHHHHhcCCC
Confidence            56899999999999999998732     23322100              0000 00        011344445556789


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      +++++||+..
T Consensus       110 ~lvllDE~~~  119 (204)
T cd03282         110 SLVLIDELGR  119 (204)
T ss_pred             cEEEeccccC
Confidence            9999999865

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

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=96.68  E-value=0.021  Score=60.59  Aligned_cols=87  Identities=23%  Similarity=0.382  Sum_probs=56.0

Q ss_pred             EEEEeCCCC---CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCc--------------------cchHHHHHH
Q 009640          365 IVFTTNHRD---SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESH--------------------HALFDVVES  421 (530)
Q Consensus       365 vI~TTN~~~---~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~--------------------~~~~~~i~~  421 (530)
                      |||.|+.+.   .|..||  |.|.-+.|.++.++.+.-+..+...|.....                    ......++.
T Consensus       186 VIFlT~dv~~~k~LskaL--Pn~vf~tI~L~Das~~~Ak~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~  263 (431)
T PF10443_consen  186 VIFLTDDVSYSKPLSKAL--PNRVFKTISLSDASPESAKQYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDE  263 (431)
T ss_pred             EEEECCCCchhhhHHHhC--CCCceeEEeecCCCHHHHHHHHHHHhcccccccccccccccccccccccccccchHHHHH
Confidence            555554443   455565  4488899999999999999999888865311                    013344555


Q ss_pred             HHHh-CCCCCHHHHHHHHHH--hccCHHHHHHHHHHH
Q 009640          422 CIRA-GGALTPAQIGEVLLR--NRGNVDLAMKEVVSA  455 (530)
Q Consensus       422 l~~~-~~~~spadi~~~l~~--~~~d~~~al~~l~~~  455 (530)
                      ++.. +..+|  ||+.++.+  ....|..|++++++.
T Consensus       264 ~i~~LGGRlt--DLe~lvrRiksGe~p~~Av~~iI~q  298 (431)
T PF10443_consen  264 CIEPLGGRLT--DLEFLVRRIKSGESPEEAVEEIISQ  298 (431)
T ss_pred             HHHHcCCcHH--HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            5542 33344  56666654  446899999988854

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 [].

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.67  E-value=0.0015  Score=61.30  Aligned_cols=31  Identities=29%  Similarity=0.357  Sum_probs=26.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +-++|.||||+||||++++++..++..++.+
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~~~~~~~   33 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLAEPWLHF   33 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhCCCcccc
Confidence            4589999999999999999999987766544

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK14527 adenylate kinase; Provisional

Probab=96.67  E-value=0.0012  Score=62.83  Aligned_cols=31  Identities=26%  Similarity=0.479  Sum_probs=26.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++++||||+||||+++.+|..++...++.
T Consensus         7 ~~i~i~G~pGsGKsT~a~~La~~~~~~~is~   37 (191)
T PRK14527          7 KVVIFLGPPGAGKGTQAERLAQELGLKKLST   37 (191)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCCCCc
Confidence            4589999999999999999999998765543

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=96.66  E-value=0.0013  Score=60.82  Aligned_cols=26  Identities=38%  Similarity=0.644  Sum_probs=20.7

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      +.|.|+||||||||++++|.. |+.++
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            689999999999999999999 77755

>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=96.65  E-value=0.0029  Score=63.87  Aligned_cols=61  Identities=23%  Similarity=0.389  Sum_probs=34.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc----------CChHHHHHHHHh----c-CCCeEEEEcCccch
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV----------TDNSELRALLLQ----T-TNRSIIVIEDIDCS  291 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~----------~~~~~L~~l~~~----~-~~~sII~IDeID~~  291 (530)
                      ++|+|.||+|||++++.|+.++   +..+..++...+          ..+..++..+..    . ....||++|+.--+
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls~~~iVI~Dd~nYi   82 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALSKDTIVILDDNNYI   82 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHTT-SEEEE-S---S
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhccCeEEEEeCCchH
Confidence            6899999999999999999986   566666652221          123334444332    2 56789999998865

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK09354 recA recombinase A; Provisional

Probab=96.64  E-value=0.0039  Score=65.01  Aligned_cols=69  Identities=19%  Similarity=0.256  Sum_probs=42.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc---------------------cCChHHHHHH---HHh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK---------------------VTDNSELRAL---LLQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~---------------------~~~~~~L~~l---~~~  276 (530)
                      |+|..+-+++|||||||||+|+..++...   +.....++...                     ..+..+...+   +.+
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            46666778999999999999998765433   44444333221                     1111122122   223


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||=|-++.
T Consensus       136 s~~~~lIVIDSvaaL~  151 (349)
T PRK09354        136 SGAVDLIVVDSVAALV  151 (349)
T ss_pred             cCCCCEEEEeChhhhc
Confidence            3578899999988874

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.63  E-value=0.0085  Score=56.11  Aligned_cols=23  Identities=39%  Similarity=0.657  Sum_probs=21.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||+|+|||+|+++||..+
T Consensus        30 ~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          30 SLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHhcc
Confidence            48899999999999999999976

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

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.61  E-value=0.0019  Score=59.76  Aligned_cols=29  Identities=31%  Similarity=0.588  Sum_probs=26.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +.++|+||+|||++++.+|+.+++++++.
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~~~   31 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLISA   31 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCceecH
Confidence            67999999999999999999999998764

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.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=96.60  E-value=0.0086  Score=55.54  Aligned_cols=25  Identities=32%  Similarity=0.444  Sum_probs=19.5

Q ss_pred             ceEEEECCCCCChhH-HHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSS-LIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTs-La~AiA~~l~  253 (530)
                      +.+++.||+|||||. ++..+...+.
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~   50 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALK   50 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhc
Confidence            578999999999999 5555555543

>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=96.60  E-value=0.0017  Score=59.35  Aligned_cols=27  Identities=30%  Similarity=0.502  Sum_probs=23.4

Q ss_pred             EECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          233 LYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       233 L~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      |.||||+|||++++.||..+++..+++
T Consensus         1 i~G~PgsGK~t~~~~la~~~~~~~is~   27 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYGLVHISV   27 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHTSEEEEH
T ss_pred             CcCCCCCChHHHHHHHHHhcCcceech
Confidence            579999999999999999998765553

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 ....

>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=96.60  E-value=0.0021  Score=61.94  Aligned_cols=32  Identities=38%  Similarity=0.575  Sum_probs=25.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      -|+++||+|||||.++-++|+.+|.+++.++-
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            47999999999999999999999999988863

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>TIGR01069 mutS2 MutS2 family protein

Probab=96.59  E-value=0.023  Score=65.61  Aligned_cols=63  Identities=17%  Similarity=0.365  Sum_probs=40.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-----CCc----------EEEEecCccCC--------------hHHHHHHHHhcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-----CYD----------VYDLELTKVTD--------------NSELRALLLQTTN  279 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-----~~~----------i~~l~l~~~~~--------------~~~L~~l~~~~~~  279 (530)
                      +.++|.||.|+|||++.+.++...     |..          +++--.+.+.+              ...+..++..+..
T Consensus       323 ~~liItGpNg~GKSTlLK~i~~~~l~aq~G~~Vpa~~~~~~~~~d~i~~~i~~~~si~~~LStfS~~m~~~~~il~~~~~  402 (771)
T TIGR01069       323 RVLAITGPNTGGKTVTLKTLGLLALMFQSGIPIPANEHSEIPYFEEIFADIGDEQSIEQNLSTFSGHMKNISAILSKTTE  402 (771)
T ss_pred             eEEEEECCCCCCchHHHHHHHHHHHHHHhCCCccCCccccccchhheeeecChHhHHhhhhhHHHHHHHHHHHHHHhcCC
Confidence            578999999999999999998762     211          11111111111              1123444555678


Q ss_pred             CeEEEEcCccch
Q 009640          280 RSIIVIEDIDCS  291 (530)
Q Consensus       280 ~sII~IDeID~~  291 (530)
                      |++|+|||+-.-
T Consensus       403 ~sLvLlDE~g~G  414 (771)
T TIGR01069       403 NSLVLFDELGAG  414 (771)
T ss_pred             CcEEEecCCCCC
Confidence            999999999753

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.

>PRK04040 adenylate kinase; Provisional

Probab=96.58  E-value=0.0022  Score=61.24  Aligned_cols=29  Identities=24%  Similarity=0.492  Sum_probs=25.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc--CCcEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL--CYDVY  257 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l--~~~i~  257 (530)
                      .-++++|+|||||||+++.++..+  ++.++
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~~   33 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLKEDYKIV   33 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhccCCeEE
Confidence            457899999999999999999999  56554

>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=96.57  E-value=0.0062  Score=61.43  Aligned_cols=84  Identities=24%  Similarity=0.353  Sum_probs=56.3

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh----HHH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN----SEL  270 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~----~~L  270 (530)
                      +++.-+++.+.|.. +.+-+..|          ....||.|.+||||.|+++-.|.-.+++++.+..+.-.+.    .+|
T Consensus         9 ~lVlf~~ai~hi~r-i~RvL~~~----------~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~y~~~~f~~dL   77 (268)
T PF12780_consen    9 NLVLFDEAIEHIAR-ISRVLSQP----------RGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITKGYSIKDFKEDL   77 (268)
T ss_dssp             -----HHHHHHHHH-HHHHHCST----------TEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTSTTTHHHHHHHHH
T ss_pred             ceeeHHHHHHHHHH-HHHHHcCC----------CCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeCCcCHHHHHHHH
Confidence            45556666666555 44444443          2468999999999999999999999999999987764332    457


Q ss_pred             HHHHHhc---CCCeEEEEcCcc
Q 009640          271 RALLLQT---TNRSIIVIEDID  289 (530)
Q Consensus       271 ~~l~~~~---~~~sII~IDeID  289 (530)
                      +.++.++   ..|.+++|+|-+
T Consensus        78 k~~~~~ag~~~~~~vfll~d~q   99 (268)
T PF12780_consen   78 KKALQKAGIKGKPTVFLLTDSQ   99 (268)
T ss_dssp             HHHHHHHHCS-S-EEEEEECCC
T ss_pred             HHHHHHHhccCCCeEEEecCcc
Confidence            7777665   578999998854

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.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.57  E-value=0.0065  Score=57.69  Aligned_cols=62  Identities=16%  Similarity=0.322  Sum_probs=39.2

Q ss_pred             EEEECCCCCChhHHHHHHHH-----HcCCcE---------E-----EEecCccC---------ChHHHHHHHHhcCCCeE
Q 009640          231 YLLYGPPGSGKSSLIAAMAN-----YLCYDV---------Y-----DLELTKVT---------DNSELRALLLQTTNRSI  282 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~-----~l~~~i---------~-----~l~l~~~~---------~~~~L~~l~~~~~~~sI  282 (530)
                      ++|+||.|.|||++++.++-     ..|..+         +     .+...+..         .-..+..++..+..|++
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            68999999999999999983     223222         1     11111100         11234455666679999


Q ss_pred             EEEcCccchh
Q 009640          283 IVIEDIDCSV  292 (530)
Q Consensus       283 I~IDeID~~~  292 (530)
                      +++||+-.-+
T Consensus        82 lllDEp~~g~   91 (185)
T smart00534       82 VLLDELGRGT   91 (185)
T ss_pred             EEEecCCCCC
Confidence            9999998643

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=96.57  E-value=0.0098  Score=61.07  Aligned_cols=82  Identities=17%  Similarity=0.297  Sum_probs=50.5

Q ss_pred             ChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEE----EecCccCChHHHHHHH
Q 009640          199 EPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD----LELTKVTDNSELRALL  274 (530)
Q Consensus       199 ~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~----l~l~~~~~~~~L~~l~  274 (530)
                      ++++++-+.+.+-.-+...       .+...-++|+|+.|+|||+++..|...+|-....    +.+....++   +--+
T Consensus        54 d~~~~~~l~~~lg~~L~~~-------~~~~~~~~l~G~g~nGKStl~~~l~~l~G~~~~~~~~~~~~~~~~~~---~f~~  123 (304)
T TIGR01613        54 DNELIEYLQRVIGYSLTGN-------YTEQKLFFLYGNGGNGKSTFQNLLSNLLGDYATTAVASLKMNEFQEH---RFGL  123 (304)
T ss_pred             CHHHHHHHHHHHhHHhcCC-------CCceEEEEEECCCCCcHHHHHHHHHHHhChhhccCCcchhhhhccCC---Cchh
Confidence            4445555555554444332       2446789999999999999999999888754321    112221110   1112


Q ss_pred             HhcCCCeEEEEcCccc
Q 009640          275 LQTTNRSIIVIEDIDC  290 (530)
Q Consensus       275 ~~~~~~sII~IDeID~  290 (530)
                      .....+.+++++|++.
T Consensus       124 a~l~gk~l~~~~E~~~  139 (304)
T TIGR01613       124 ARLEGKRAVIGDEVQK  139 (304)
T ss_pred             hhhcCCEEEEecCCCC
Confidence            3345678999999874

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.56  E-value=0.052  Score=55.94  Aligned_cols=22  Identities=9%  Similarity=0.120  Sum_probs=18.0

Q ss_pred             EEEeCCCCHHHHHHHHHHhhCC
Q 009640          388 HVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       388 ~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      .|+++..+.++.+.++..|...
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~  279 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADS  279 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHC
Confidence            5788888999999998888753

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).

>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=96.56  E-value=0.0043  Score=58.63  Aligned_cols=22  Identities=32%  Similarity=0.341  Sum_probs=19.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      .-+.|.||.|+|||||.+++..
T Consensus        22 ~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          22 VLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             CEEEEECCCCCCHHHHHHHHhh
Confidence            3478999999999999999964

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.

>PRK01184 hypothetical protein; Provisional

Probab=96.55  E-value=0.0021  Score=60.65  Aligned_cols=29  Identities=28%  Similarity=0.300  Sum_probs=24.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.||||+||||+++ ++.++++.+++.
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            46889999999999876 889999887665

>PF13479 AAA_24: AAA domain

Probab=96.53  E-value=0.0018  Score=63.09  Aligned_cols=62  Identities=34%  Similarity=0.518  Sum_probs=39.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecC-------------ccCChHHHHHHHHhc----CCCeEEEEcCccchh
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT-------------KVTDNSELRALLLQT----TNRSIIVIEDIDCSV  292 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~-------------~~~~~~~L~~l~~~~----~~~sII~IDeID~~~  292 (530)
                      -+|||||||+|||+++..+-+-+   +++++-.             .+.+-.++.+.+...    ..=..||||-|+.+.
T Consensus         5 ~~lIyG~~G~GKTt~a~~~~k~l---~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y~tiVIDsis~~~   81 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASLPKPL---FIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEEDEADYDTIVIDSISWLE   81 (213)
T ss_pred             EEEEECCCCCCHHHHHHhCCCeE---EEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhccCCCCEEEEECHHHHH
Confidence            58999999999999999883322   2233222             112344566655332    345699999999875


Q ss_pred             hh
Q 009640          293 DL  294 (530)
Q Consensus       293 ~~  294 (530)
                      .+
T Consensus        82 ~~   83 (213)
T PF13479_consen   82 DM   83 (213)
T ss_pred             HH
Confidence            43

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=96.53  E-value=0.005  Score=57.14  Aligned_cols=64  Identities=25%  Similarity=0.444  Sum_probs=40.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC---------------CcEEEEe----cCc--cC-ChH---HHHHHHHhcC--CCe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC---------------YDVYDLE----LTK--VT-DNS---ELRALLLQTT--NRS  281 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~---------------~~i~~l~----l~~--~~-~~~---~L~~l~~~~~--~~s  281 (530)
                      +-.++.||.|+|||+++++++-.+.               ..+-..+    ...  +. ...   .+...+...+  .|+
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            4788999999999999999865442               2222222    111  11 122   2344454443  899


Q ss_pred             EEEEcCccchh
Q 009640          282 IIVIEDIDCSV  292 (530)
Q Consensus       282 II~IDeID~~~  292 (530)
                      +++|||+..-+
T Consensus       102 llllDEp~~gl  112 (162)
T cd03227         102 LYILDEIDRGL  112 (162)
T ss_pred             EEEEeCCCCCC
Confidence            99999998754

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.

>PRK10436 hypothetical protein; Provisional

Probab=96.52  E-value=0.0091  Score=64.79  Aligned_cols=85  Identities=24%  Similarity=0.409  Sum_probs=53.9

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCce-EEEECCCCCChhHHHHHHHHHcC---CcEEEEe------
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRG-YLLYGPPGSGKSSLIAAMANYLC---YDVYDLE------  260 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG-~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~------  260 (530)
                      .+++++++.+...+.+.+.+    ..           +.| +|+.||+|+||||++.|+-++++   .+++.++      
T Consensus       195 ~~L~~LG~~~~~~~~l~~~~----~~-----------~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE~~  259 (462)
T PRK10436        195 LDLETLGMTPAQLAQFRQAL----QQ-----------PQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVEIP  259 (462)
T ss_pred             CCHHHcCcCHHHHHHHHHHH----Hh-----------cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCcccc
Confidence            47888888777655554433    11           345 67889999999999988877774   3455443      


Q ss_pred             cCcc-----C--ChHHHHHHHHhc--CCCeEEEEcCccc
Q 009640          261 LTKV-----T--DNSELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       261 l~~~-----~--~~~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                      +..+     .  ........+..+  ..|.||+|.||--
T Consensus       260 l~gi~Q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEIRD  298 (462)
T PRK10436        260 LAGINQTQIHPKAGLTFQRVLRALLRQDPDVIMVGEIRD  298 (462)
T ss_pred             CCCcceEeeCCccCcCHHHHHHHHhcCCCCEEEECCCCC
Confidence            1111     1  111244444443  6899999999863

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=96.52  E-value=0.005  Score=59.89  Aligned_cols=27  Identities=33%  Similarity=0.587  Sum_probs=23.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -..|+.|||||||||+.+-||.-+...
T Consensus       138 lntLiigpP~~GKTTlLRdiaR~~s~g  164 (308)
T COG3854         138 LNTLIIGPPQVGKTTLLRDIARLLSDG  164 (308)
T ss_pred             eeeEEecCCCCChHHHHHHHHHHhhcc
Confidence            467899999999999999999987443

>PRK14526 adenylate kinase; Provisional

Probab=96.51  E-value=0.0025  Score=62.04  Aligned_cols=28  Identities=36%  Similarity=0.678  Sum_probs=25.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      ++|.||||+||||+++.+|..+++..++
T Consensus         3 i~l~G~pGsGKsT~a~~La~~~~~~~is   30 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNELNYYHIS   30 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            7899999999999999999999876654

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.51  E-value=0.0097  Score=58.39  Aligned_cols=62  Identities=27%  Similarity=0.400  Sum_probs=41.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHH-Hc----CCc---------EEEEecCccC--------------ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN-YL----CYD---------VYDLELTKVT--------------DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~-~l----~~~---------i~~l~l~~~~--------------~~~~L~~l~~~~~~~  280 (530)
                      +-++|.||.|+|||++.+.++. .+    |..         +++-=.+.+.              .-.++..++..+..+
T Consensus        32 ~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~~  111 (222)
T cd03287          32 YCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTSR  111 (222)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCccccccccchHHHHHHHHHHHHHhCCCC
Confidence            4689999999999999999987 22    211         1100011110              123466667788899


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      ++++|||+..
T Consensus       112 sLvllDE~~~  121 (222)
T cd03287         112 SLVILDELGR  121 (222)
T ss_pred             eEEEEccCCC
Confidence            9999999975

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

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.50  E-value=0.0026  Score=60.28  Aligned_cols=29  Identities=41%  Similarity=0.715  Sum_probs=24.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+++.||||+||||+|+.||+.++  +..++
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~--i~hls   30 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLG--LPHLD   30 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC--CcEEc
Confidence            478999999999999999999954  44444

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.50  E-value=0.013  Score=65.32  Aligned_cols=85  Identities=26%  Similarity=0.376  Sum_probs=53.1

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCce-EEEECCCCCChhHHHHHHHHHcC---CcEEEEe------
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRG-YLLYGPPGSGKSSLIAAMANYLC---YDVYDLE------  260 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG-~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~------  260 (530)
                      .+++++++.++..+.+.+.+.    .           +.| +|+.||+|+||||+..++.++++   .+++.++      
T Consensus       293 ~~l~~lg~~~~~~~~l~~~~~----~-----------~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~  357 (564)
T TIGR02538       293 LDIDKLGFEPDQKALFLEAIH----K-----------PQGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEIN  357 (564)
T ss_pred             CCHHHcCCCHHHHHHHHHHHH----h-----------cCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceec
Confidence            467888887776555544332    1           345 67899999999999999888874   3344432      


Q ss_pred             cCcc-----C--ChHHHHHHHHhc--CCCeEEEEcCccc
Q 009640          261 LTKV-----T--DNSELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       261 l~~~-----~--~~~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                      +..+     .  ........+..+  ..|.||+|.||-.
T Consensus       358 ~~~~~q~~v~~~~g~~~~~~l~~~LR~dPDvI~vGEiRd  396 (564)
T TIGR02538       358 LPGINQVNVNPKIGLTFAAALRSFLRQDPDIIMVGEIRD  396 (564)
T ss_pred             CCCceEEEeccccCCCHHHHHHHHhccCCCEEEeCCCCC
Confidence            1111     0  011233444433  6899999999863

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.

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=96.49  E-value=0.025  Score=58.41  Aligned_cols=96  Identities=19%  Similarity=0.228  Sum_probs=65.5

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      +...+...|+.+++....-+.+++.-..+.--           --.+|+.|..||||-.+|+|.-...   ..+|.-+++
T Consensus       195 ~~~~~~~~F~~~v~~S~~mk~~v~qA~k~Aml-----------DAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNC  263 (511)
T COG3283         195 VAAQDVSGFEQIVAVSPKMKHVVEQAQKLAML-----------DAPLLITGETGTGKDLLAKACHLASPRHSKPFLALNC  263 (511)
T ss_pred             cccccccchHHHhhccHHHHHHHHHHHHhhcc-----------CCCeEEecCCCchHHHHHHHHhhcCcccCCCeeEeec
Confidence            45556778999988776655555544333221           2468999999999999999865544   678999999


Q ss_pred             CccCChHHHHHHHHhc------------CCCeEEEEcCccch
Q 009640          262 TKVTDNSELRALLLQT------------TNRSIIVIEDIDCS  291 (530)
Q Consensus       262 ~~~~~~~~L~~l~~~~------------~~~sII~IDeID~~  291 (530)
                      ..+-.+..-..+|-.+            .+..-+|+|||-.+
T Consensus       264 A~lPe~~aEsElFG~apg~~gk~GffE~AngGTVlLDeIgEm  305 (511)
T COG3283         264 ASLPEDAAESELFGHAPGDEGKKGFFEQANGGTVLLDEIGEM  305 (511)
T ss_pred             CCCchhHhHHHHhcCCCCCCCccchhhhccCCeEEeehhhhc
Confidence            8875544444454433            23456788988765

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=96.48  E-value=0.012  Score=52.26  Aligned_cols=63  Identities=29%  Similarity=0.353  Sum_probs=44.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC--------------------cEEEEecCccCChHHHHHH--HHhcCCCeEEEEc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY--------------------DVYDLELTKVTDNSELRAL--LLQTTNRSIIVIE  286 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~--------------------~i~~l~l~~~~~~~~L~~l--~~~~~~~sII~ID  286 (530)
                      .-++|+|+=|+|||++++++|..+|.                    ++|.+++-.+.+..++-.+  +......+|++||
T Consensus        16 ~vi~L~GdLGaGKTtf~r~l~~~lg~~~~V~SPTF~l~~~Y~~~~~~l~H~DLYRl~~~~e~~~~g~~e~~~~~~i~~IE   95 (123)
T PF02367_consen   16 DVILLSGDLGAGKTTFVRGLARALGIDEEVTSPTFSLVNEYEGGNIPLYHFDLYRLEDPEELEDLGLEEYLFEDGICVIE   95 (123)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTT--S----TTTTSEEEEEETTEEEEEEE-TT-SSTHHHHHCTTTTCSSSSEEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHcCCCCCcCCCCeEEEEEecCCCceEEEeeccccCCHHHHHHCCchhhhCCCCEEEEE
Confidence            45899999999999999999999964                    3344455555555554443  2334678999998


Q ss_pred             Cccch
Q 009640          287 DIDCS  291 (530)
Q Consensus       287 eID~~  291 (530)
                      =-+.+
T Consensus        96 W~e~~  100 (123)
T PF02367_consen   96 WPERL  100 (123)
T ss_dssp             SGGGG
T ss_pred             Ccccc
Confidence            66665

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.

>PRK10646 ADP-binding protein; Provisional

Probab=96.48  E-value=0.019  Score=52.89  Aligned_cols=62  Identities=26%  Similarity=0.383  Sum_probs=43.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC--------------------cEEEEecCccCChHHHHHH-HHhc-CCCeEEEEcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY--------------------DVYDLELTKVTDNSELRAL-LLQT-TNRSIIVIED  287 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~--------------------~i~~l~l~~~~~~~~L~~l-~~~~-~~~sII~IDe  287 (530)
                      -++|.|+=|+|||++++++|+.+|.                    ++|.+++-.+.+..++..+ |.+. ....|++||=
T Consensus        30 vi~L~GdLGaGKTtf~rgl~~~Lg~~~~V~SPTFtlv~~Y~~~~~~l~H~DlYRL~~~~el~~lG~~e~~~~~~i~~IEW  109 (153)
T PRK10646         30 VIYLYGDLGAGKTTFSRGFLQALGHQGNVKSPTYTLVEPYTLDNLMVYHFDLYRLADPEELEFMGIRDYFANDAICLVEW  109 (153)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCCCCCCCCEeeEEEeeCCCCCEEEEeeccCCCHHHHHHcchHHhhcCCCEEEEEC
Confidence            4899999999999999999999974                    2344455455555555444 3333 4568888886


Q ss_pred             ccch
Q 009640          288 IDCS  291 (530)
Q Consensus       288 ID~~  291 (530)
                      .|.+
T Consensus       110 ~e~~  113 (153)
T PRK10646        110 PQQG  113 (153)
T ss_pred             Ccch
Confidence            5543

>PLN02199 shikimate kinase

Probab=96.47  E-value=0.0053  Score=62.35  Aligned_cols=33  Identities=33%  Similarity=0.524  Sum_probs=30.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .+.++|.|++|+|||++++.+|+.+++++++.+
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD  134 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCD  134 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEehH
Confidence            358999999999999999999999999999975

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

Probab=96.46  E-value=0.017  Score=66.53  Aligned_cols=127  Identities=20%  Similarity=0.278  Sum_probs=80.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecCccC--------ChHHHHHHHHh---cCCCeEEEEc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELTKVT--------DNSELRALLLQ---TTNRSIIVIE  286 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~~~~--------~~~~L~~l~~~---~~~~sII~ID  286 (530)
                      +++-+|.|.||.|||.++.-+|+..          +..++.+++..+.        -+..+..++..   .....||+||
T Consensus       208 k~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfig  287 (898)
T KOG1051|consen  208 KNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLG  287 (898)
T ss_pred             CCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEec
Confidence            3677999999999999999999866          3455666655432        13456666664   3577899999


Q ss_pred             CccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEE
Q 009640          287 DIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIV  366 (530)
Q Consensus       287 eID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI  366 (530)
                      |++.+.+...                                          .....-...+|..+-+     .++.-+|
T Consensus       288 elh~lvg~g~------------------------------------------~~~~~d~~nlLkp~L~-----rg~l~~I  320 (898)
T KOG1051|consen  288 ELHWLVGSGS------------------------------------------NYGAIDAANLLKPLLA-----RGGLWCI  320 (898)
T ss_pred             ceeeeecCCC------------------------------------------cchHHHHHHhhHHHHh-----cCCeEEE
Confidence            9999853110                                          0112223334433211     2336688


Q ss_pred             EEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          367 FTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       367 ~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                      +||..-+     .=||||-|  ||+. +.++.|+.+.-..|+.
T Consensus       321 GatT~e~Y~k~iekdPalEr--rw~l-~~v~~pS~~~~~~iL~  360 (898)
T KOG1051|consen  321 GATTLETYRKCIEKDPALER--RWQL-VLVPIPSVENLSLILP  360 (898)
T ss_pred             ecccHHHHHHHHhhCcchhh--Ccce-eEeccCcccchhhhhh
Confidence            8665433     34999999  9987 5688888765444443

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

Probab=96.45  E-value=0.0069  Score=60.68  Aligned_cols=51  Identities=22%  Similarity=0.194  Sum_probs=38.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHHHHHHh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELRALLLQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~~l~~~  276 (530)
                      |+|..+-+|++|+||||||+++...+...   |.+++.++...  +..++.+.+.+
T Consensus        19 G~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e--~~~~l~~~~~~   72 (260)
T COG0467          19 GLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEE--SPEELLENARS   72 (260)
T ss_pred             CCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecC--CHHHHHHHHHH
Confidence            57777889999999999999998887655   66788877665  35556555543

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=96.45  E-value=0.0064  Score=57.52  Aligned_cols=64  Identities=16%  Similarity=0.237  Sum_probs=39.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc---EE----EEe--cCcc-CChHHHHHH-HHh--cCCCeEEEEcCccchh
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD---VY----DLE--LTKV-TDNSELRAL-LLQ--TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~---i~----~l~--l~~~-~~~~~L~~l-~~~--~~~~sII~IDeID~~~  292 (530)
                      .-+.|.||.|+|||||++.|+..+..+   +.    .+.  .... .+..+-+++ +..  +..|.++++||--.-+
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~~~p~lllLDEPts~L  102 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAYL  102 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHhcCCCEEEEECCcccC
Confidence            357899999999999999999976321   11    111  0110 122222332 222  2689999999988755

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.44  E-value=0.0036  Score=67.41  Aligned_cols=86  Identities=23%  Similarity=0.325  Sum_probs=54.3

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCce-EEEECCCCCChhHHHHHHHHHcCCcEE---EEe-----
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRG-YLLYGPPGSGKSSLIAAMANYLCYDVY---DLE-----  260 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG-~LL~GPPGTGKTsLa~AiA~~l~~~i~---~l~-----  260 (530)
                      .-+|+++++.+...+.+...+..               +.| +|+.||.|+||||...++-++++.+..   .++     
T Consensus       234 ~l~l~~Lg~~~~~~~~~~~~~~~---------------p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~  298 (500)
T COG2804         234 ILDLEKLGMSPFQLARLLRLLNR---------------PQGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEY  298 (500)
T ss_pred             cCCHHHhCCCHHHHHHHHHHHhC---------------CCeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeee
Confidence            34678888888777666554421               457 556799999999999999999865443   332     


Q ss_pred             -cCcc---CChH----HHHHHHHhc--CCCeEEEEcCccc
Q 009640          261 -LTKV---TDNS----ELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       261 -l~~~---~~~~----~L~~l~~~~--~~~sII~IDeID~  290 (530)
                       +..+   .-|.    ...+.+...  ..|.||.+.||--
T Consensus       299 ~~~gI~Q~qVN~k~gltfa~~LRa~LRqDPDvImVGEIRD  338 (500)
T COG2804         299 QLPGINQVQVNPKIGLTFARALRAILRQDPDVIMVGEIRD  338 (500)
T ss_pred             ecCCcceeecccccCCCHHHHHHHHhccCCCeEEEeccCC
Confidence             1111   1111    122222222  6799999999963

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.43  E-value=0.0028  Score=64.70  Aligned_cols=30  Identities=30%  Similarity=0.238  Sum_probs=25.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-CCcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-CYDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~~  258 (530)
                      .-++|.|||||||||+++.++..+ +..+++
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l~   33 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVN   33 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEEe
Confidence            357899999999999999999998 555444

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.42  E-value=0.013  Score=64.25  Aligned_cols=86  Identities=24%  Similarity=0.364  Sum_probs=53.8

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCce-EEEECCCCCChhHHHHHHHHHcC---CcEEEEec----
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRG-YLLYGPPGSGKSSLIAAMANYLC---YDVYDLEL----  261 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG-~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l----  261 (530)
                      +.++++++..++..+.+...+    ..           +.| +|+.||+|+||||++.++.+++.   .+++.++-    
T Consensus       218 ~~~l~~Lg~~~~~~~~l~~~~----~~-----------~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~  282 (486)
T TIGR02533       218 RLDLETLGMSPELLSRFERLI----RR-----------PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEY  282 (486)
T ss_pred             CCCHHHcCCCHHHHHHHHHHH----hc-----------CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeee
Confidence            457788887777655544432    22           356 68899999999999999888774   34554431    


Q ss_pred             --Ccc-----CC--hHHHHHHHHhc--CCCeEEEEcCccc
Q 009640          262 --TKV-----TD--NSELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       262 --~~~-----~~--~~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                        ..+     ..  .......+..+  ..|.||+|.||-.
T Consensus       283 ~~~~~~q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEiRd  322 (486)
T TIGR02533       283 QIEGIGQIQVNPKIGLTFAAGLRAILRQDPDIIMVGEIRD  322 (486)
T ss_pred             ecCCCceEEEccccCccHHHHHHHHHhcCCCEEEEeCCCC
Confidence              111     00  01223333333  6899999999864

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.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.41  E-value=0.0038  Score=57.20  Aligned_cols=29  Identities=41%  Similarity=0.517  Sum_probs=24.7

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l  259 (530)
                      +++.|+||+|||++++.++..+   +.+.+.+
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i   33 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVL   33 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            5789999999999999999998   5555554

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK06696 uridine kinase; Validated

Probab=96.37  E-value=0.01  Score=58.10  Aligned_cols=38  Identities=16%  Similarity=0.207  Sum_probs=31.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTD  266 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~  266 (530)
                      .-+.+.|+||+||||+++.||..+   +..++.+++.++..
T Consensus        23 ~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~~   63 (223)
T PRK06696         23 LRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFHN   63 (223)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeccccccC
Confidence            457789999999999999999999   66777776666543

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=96.37  E-value=0.0065  Score=63.46  Aligned_cols=61  Identities=25%  Similarity=0.438  Sum_probs=41.8

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDC  290 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~  290 (530)
                      |+|.+..+++||||.||||+++-.+-+.++-.++..  .+  +.+  .=.|.....--|-+|||+-.
T Consensus       258 g~PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViSf--~N--s~S--hFWLqPL~d~Ki~llDDAT~  318 (432)
T PF00519_consen  258 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISF--VN--SKS--HFWLQPLADAKIALLDDATY  318 (432)
T ss_dssp             TBTTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-G--GG--TTS--CGGGGGGCT-SSEEEEEE-H
T ss_pred             CCCcccEEEEECCCCCchhHHHHHHHHHhCCEEEEe--cC--CCC--cccccchhcCcEEEEcCCcc
Confidence            678899999999999999999999999998876653  11  111  11233334446778888753

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.36  E-value=0.0092  Score=61.47  Aligned_cols=26  Identities=19%  Similarity=0.553  Sum_probs=23.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      ...+++.||+|+||||++++++.++.
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~~~  169 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDEIP  169 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHccCC
Confidence            46899999999999999999998873

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.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.34  E-value=0.017  Score=63.66  Aligned_cols=39  Identities=18%  Similarity=0.086  Sum_probs=29.2

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      |+|..+-+|++|+||||||+|+..++...    |..++.+++.
T Consensus        27 G~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~e   69 (509)
T PRK09302         27 GLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFE   69 (509)
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEcc
Confidence            56777789999999999999998776432    4556555443

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.31  E-value=0.0096  Score=62.28  Aligned_cols=61  Identities=28%  Similarity=0.453  Sum_probs=39.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC----CcEEEEecC---------------ccC-ChHHHHHHHHhc--CCCeEEEEc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC----YDVYDLELT---------------KVT-DNSELRALLLQT--TNRSIIVIE  286 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~----~~i~~l~l~---------------~~~-~~~~L~~l~~~~--~~~sII~ID  286 (530)
                      .-+|+.||+|+||||+++++.+++.    ..++.++-.               ++. ....+.+.+..+  ..|.+|+++
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~~~~~~~i~q~evg~~~~~~~~~l~~~lr~~pd~i~vg  202 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVHRNKRSLINQREVGLDTLSFANALRAALREDPDVILIG  202 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhccCccceEEccccCCCCcCHHHHHHHhhccCCCEEEEe
Confidence            3578999999999999999998774    234433210               000 111244444443  689999999


Q ss_pred             Ccc
Q 009640          287 DID  289 (530)
Q Consensus       287 eID  289 (530)
                      |+-
T Consensus       203 Eir  205 (343)
T TIGR01420       203 EMR  205 (343)
T ss_pred             CCC
Confidence            995

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.

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

Probab=96.31  E-value=0.0045  Score=60.51  Aligned_cols=39  Identities=28%  Similarity=0.334  Sum_probs=29.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      |+|...-+|+.||||||||+|+..++...    |..++.++..
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~e   57 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFE   57 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESS
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEec
Confidence            67777889999999999999998766433    7777777654

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 ....

>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=96.30  E-value=0.0067  Score=62.75  Aligned_cols=148  Identities=21%  Similarity=0.227  Sum_probs=77.3

Q ss_pred             hhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCC
Q 009640          201 QLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNR  280 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~  280 (530)
                      ...+.|.+.|.....+        +|.+|.+||-||-.|||||||+|+-+.++-....++...    +.|.--|--+-..
T Consensus       136 ~~~~~i~~iL~~lv~N--------~PKkRy~lFkGPvNsGKTTlAAAlLdL~gG~~LNvN~p~----dkl~FELG~AiDQ  203 (417)
T PF06431_consen  136 NFDDVILEILKCLVEN--------IPKKRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQ  203 (417)
T ss_dssp             THHHHHHHHHHHHHHT--------BTTB-EEEEE-STTSSHHHHHHHHHHHH-EEEE-TSS-T----TTHHHHHCCCTT-
T ss_pred             chHHHHHHHHHHHhcC--------CCcceeEEEecCcCCchHHHHHHHHHhcCCceeecCCCh----hhcchhhheeece
Confidence            3344555555555543        466899999999999999999999999987766665543    2333334445566


Q ss_pred             eEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccC--
Q 009640          281 SIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSC--  358 (530)
Q Consensus       281 sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~--  358 (530)
                      -.++|||+---.      ..          .+ .                     =..+..-..|..|-.-|||--.-  
T Consensus       204 fmVvFEDVKGq~------~~----------~~-~---------------------Lp~G~G~~NLDNLRD~LDG~V~VNL  245 (417)
T PF06431_consen  204 FMVVFEDVKGQP------SD----------NK-D---------------------LPPGQGMNNLDNLRDYLDGAVKVNL  245 (417)
T ss_dssp             SEEEEEEE--SS------TT----------TT-T-------------------------SHHHHHHTTHHHHH-SS-EEE
T ss_pred             EEEEEEecCCCc------CC----------CC-C---------------------CCCCCCcccchhhhhhccCceeech
Confidence            788888875210      00          00 0                     00111223455566667765321  


Q ss_pred             ---CCCCe-----EEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHH
Q 009640          359 ---CSEEK-----IIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVL  402 (530)
Q Consensus       359 ---~~~~~-----ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i  402 (530)
                         ....+     --|.|.|. ..||..+.-  ||-+.+.|. |...-++.|
T Consensus       246 ErKH~NK~sQiFPPgIvTmNe-Y~iP~Tv~v--Rf~~~~~F~-~k~~l~~~L  293 (417)
T PF06431_consen  246 ERKHQNKRSQIFPPGIVTMNE-YKIPQTVKV--RFCKVLDFR-PKPNLRKSL  293 (417)
T ss_dssp             ECSSSEEEEE----EEEEESS--B--HHHHT--TEEEEEE-----HHHHHHH
T ss_pred             hhhhcccccccCCCceEeecc-ccCCcceee--eeEeeEecc-ccHHHHHHH
Confidence               01111     24678886 578888888  999999886 344444443

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.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.29  E-value=0.0042  Score=61.80  Aligned_cols=30  Identities=40%  Similarity=0.525  Sum_probs=25.3

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      ++|.|+||+||||+++++|..+   +.+++.++
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~   34 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILG   34 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEc
Confidence            6899999999999999999988   45665554

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.

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=96.29  E-value=0.0037  Score=57.13  Aligned_cols=34  Identities=29%  Similarity=0.362  Sum_probs=30.0

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      |.+-.+++.|+.||||||++++++.+|+.+|++-
T Consensus        10 ~~k~~i~vmGvsGsGKSTigk~L~~~l~~~F~dg   43 (191)
T KOG3354|consen   10 PFKYVIVVMGVSGSGKSTIGKALSEELGLKFIDG   43 (191)
T ss_pred             CCceeEEEEecCCCChhhHHHHHHHHhCCccccc
Confidence            4455788899999999999999999999998875

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=96.29  E-value=0.18  Score=50.09  Aligned_cols=56  Identities=16%  Similarity=0.128  Sum_probs=36.1

Q ss_pred             ceeEEEEeCCCCHHHHHHHHHHhhCCcCcc-ch--HHHHHHHHHhCCCCCHHHHHHHHHH
Q 009640          384 RMDVHVSLGTCGPHAFKVLAKNYLGIESHH-AL--FDVVESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       384 R~d~~I~~~~p~~~~r~~i~~~~l~~~~~~-~~--~~~i~~l~~~~~~~spadi~~~l~~  440 (530)
                      |++..|++++.+.++-...++..|+....+ .+  .+.+..+...+.+ .|.-|.+++..
T Consensus       190 R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg-~P~lin~~~~~  248 (269)
T COG3267         190 RIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQG-IPRLINNLATL  248 (269)
T ss_pred             eEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhcc-chHHHHHHHHH
Confidence            899999999999998888888777643211 12  2233333333344 78788877754

>PHA00350 putative assembly protein

Probab=96.28  E-value=0.016  Score=61.43  Aligned_cols=62  Identities=18%  Similarity=0.188  Sum_probs=37.4

Q ss_pred             EEEECCCCCChhHHHHH--H--HHHcCCcEEEEecCccCCh--------------------------HHHHHHHHhcCCC
Q 009640          231 YLLYGPPGSGKSSLIAA--M--ANYLCYDVYDLELTKVTDN--------------------------SELRALLLQTTNR  280 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~A--i--A~~l~~~i~~l~l~~~~~~--------------------------~~L~~l~~~~~~~  280 (530)
                      +|++|+||+|||..+-.  |  |-..|..++. ++..+.-+                          ..+...+.-.+..
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            68999999999998775  3  2233655542 33221100                          0111122224577


Q ss_pred             eEEEEcCccchhh
Q 009640          281 SIIVIEDIDCSVD  293 (530)
Q Consensus       281 sII~IDeID~~~~  293 (530)
                      ++|||||+..+++
T Consensus        83 aLIViDEaq~~~p   95 (399)
T PHA00350         83 ALYVIDEAQMIFP   95 (399)
T ss_pred             CEEEEECchhhcC
Confidence            9999999999975

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=96.28  E-value=0.014  Score=57.04  Aligned_cols=62  Identities=24%  Similarity=0.390  Sum_probs=41.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-----CC---------cEEEEecCccC--------------ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-----CY---------DVYDLELTKVT--------------DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-----~~---------~i~~l~l~~~~--------------~~~~L~~l~~~~~~~  280 (530)
                      +-++|.||.|.|||++.+.++...     |.         .+++--.+.+.              .-.++..++..+..|
T Consensus        31 ~~~~itG~n~~gKs~~l~~i~~~~~la~~G~~vpa~~~~i~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~~  110 (218)
T cd03286          31 RILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATPD  110 (218)
T ss_pred             cEEEEECCCCCchHHHHHHHHHHHHHHHcCCccCccccEeccccEEEEecCcccccccCcchHHHHHHHHHHHHHhCCCC
Confidence            568999999999999998887642     21         11111111110              123456678888999


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      ++|+|||+-.
T Consensus       111 sLvLlDE~~~  120 (218)
T cd03286         111 SLVILDELGR  120 (218)
T ss_pred             eEEEEecccC
Confidence            9999999865

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

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.28  E-value=0.0036  Score=59.40  Aligned_cols=29  Identities=38%  Similarity=0.453  Sum_probs=25.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      -+.|.||+|+||||+++.||..++.+++.
T Consensus         4 ~i~l~G~sGsGKsTl~~~l~~~~~~~~~~   32 (186)
T PRK10078          4 LIWLMGPSGSGKDSLLAALRQREQTQLLV   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHhccCCCeEEE
Confidence            57899999999999999999988766544

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.28  E-value=0.028  Score=52.36  Aligned_cols=24  Identities=46%  Similarity=0.725  Sum_probs=21.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||.|+|||||++.|+..+
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G~~   51 (166)
T cd03223          28 DRLLITGPSGTGKSSLFRALAGLW   51 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            458899999999999999999986

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.27  E-value=0.0099  Score=61.88  Aligned_cols=63  Identities=14%  Similarity=0.253  Sum_probs=41.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC--cEEEEe------cCcc--------------CChHHHHHHHHhc--CCCeEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY--DVYDLE------LTKV--------------TDNSELRALLLQT--TNRSII  283 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~--~i~~l~------l~~~--------------~~~~~L~~l~~~~--~~~sII  283 (530)
                      +.++|+.||+|+||||+++|++.+...  .++.++      +...              ...-.+.+++..+  .+|.+|
T Consensus       160 ~~nili~G~tgSGKTTll~aL~~~ip~~~ri~tiEd~~El~l~~~~n~~~~~~~~~~~~~~~~~~~~ll~~~LR~~PD~I  239 (332)
T PRK13900        160 KKNIIISGGTSTGKTTFTNAALREIPAIERLITVEDAREIVLSNHPNRVHLLASKGGQGRAKVTTQDLIEACLRLRPDRI  239 (332)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHhhCCCCCeEEEecCCCccccccCCCEEEEEecCCCCCcCcCcHHHHHHHHhccCCCeE
Confidence            468999999999999999999998842  333331      1000              0011244555544  579999


Q ss_pred             EEcCccc
Q 009640          284 VIEDIDC  290 (530)
Q Consensus       284 ~IDeID~  290 (530)
                      ++.|+-.
T Consensus       240 ivGEiR~  246 (332)
T PRK13900        240 IVGELRG  246 (332)
T ss_pred             EEEecCC
Confidence            9999863

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=96.27  E-value=0.017  Score=66.70  Aligned_cols=63  Identities=13%  Similarity=0.309  Sum_probs=39.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH-----cCCc----------EEEEecCccCC--------------hHHHHHHHHhcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY-----LCYD----------VYDLELTKVTD--------------NSELRALLLQTTN  279 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~-----l~~~----------i~~l~l~~~~~--------------~~~L~~l~~~~~~  279 (530)
                      +.++|.||.+.|||++.+.++-.     +|..          +++--++.+.+              ...+..++..+..
T Consensus       328 ~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~Il~~~~~  407 (782)
T PRK00409        328 TVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKADK  407 (782)
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccceEEEecCCccchhhchhHHHHHHHHHHHHHHhCCc
Confidence            57899999999999999988643     2322          22111111111              1223444555678


Q ss_pred             CeEEEEcCccch
Q 009640          280 RSIIVIEDIDCS  291 (530)
Q Consensus       280 ~sII~IDeID~~  291 (530)
                      |++|+|||+-.-
T Consensus       408 ~sLvLlDE~~~G  419 (782)
T PRK00409        408 NSLVLFDELGAG  419 (782)
T ss_pred             CcEEEecCCCCC
Confidence            999999999763

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=96.26  E-value=0.015  Score=55.06  Aligned_cols=33  Identities=27%  Similarity=0.590  Sum_probs=25.0

Q ss_pred             HhhhcCCCCce--EEEECCCCCChhHHHHHHHHHc
Q 009640          220 YHRVGRAWKRG--YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       220 y~~~g~~~~rG--~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |..+.+.+..|  +.+.||.|+|||||.+.+|.-+
T Consensus        18 f~~L~f~l~~Ge~~~i~G~NG~GKTtLLRilaGLl   52 (209)
T COG4133          18 FSDLSFTLNAGEALQITGPNGAGKTTLLRILAGLL   52 (209)
T ss_pred             ecceeEEEcCCCEEEEECCCCCcHHHHHHHHHccc
Confidence            33444444334  6788999999999999999987

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.25  E-value=0.0045  Score=59.56  Aligned_cols=28  Identities=29%  Similarity=0.386  Sum_probs=24.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      .-+++.|+||+||||+++.+|..++...
T Consensus         4 ~~i~i~G~~G~GKst~a~~l~~~~~~~~   31 (197)
T PRK12339          4 TIHFIGGIPGVGKTSISGYIARHRAIDI   31 (197)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            4688999999999999999999988654

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.24  E-value=0.0054  Score=61.56  Aligned_cols=39  Identities=18%  Similarity=0.100  Sum_probs=30.8

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      |+|...-+|++||||||||+|+..+|...   +..+..+++.
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            67777789999999999999999876643   5666666654

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.19  E-value=0.027  Score=64.68  Aligned_cols=63  Identities=19%  Similarity=0.257  Sum_probs=39.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---C--CcEEEEecCcc----------CChHHHHHHHHhc------------CCCe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---C--YDVYDLELTKV----------TDNSELRALLLQT------------TNRS  281 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~--~~i~~l~l~~~----------~~~~~L~~l~~~~------------~~~s  281 (530)
                      +-.+|.|+||||||++++++...+   +  ..++-+-.+.-          .....+.++|...            ....
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~g~~a~Tih~lL~~~~~~~~~~~~~~~~~~~  418 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLEDPIDCD  418 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHhcCCccccHHHHhhccCCccchhhhhccccCC
Confidence            467899999999999999987765   3  44554433321          0112244444321            2357


Q ss_pred             EEEEcCccch
Q 009640          282 IIVIEDIDCS  291 (530)
Q Consensus       282 II~IDeID~~  291 (530)
                      +|+|||+-.+
T Consensus       419 llIvDEaSMv  428 (720)
T TIGR01448       419 LLIVDESSMM  428 (720)
T ss_pred             EEEEeccccC
Confidence            9999998765

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms

Probab=96.18  E-value=0.015  Score=54.97  Aligned_cols=24  Identities=38%  Similarity=0.524  Sum_probs=20.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      --.++||.|+|||++..||+--++
T Consensus        24 ~~~i~G~NGsGKSnil~Ai~~~~~   47 (178)
T cd03239          24 FNAIVGPNGSGKSNIVDAICFVLG   47 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcC
Confidence            356899999999999999977663

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.18  E-value=0.021  Score=61.50  Aligned_cols=60  Identities=22%  Similarity=0.222  Sum_probs=38.6

Q ss_pred             hhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          201 QLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      .+.+.+.+.+...+.......... ..+.-++|+||||+||||++..+|..+   +..+.-+..
T Consensus        69 ~~~~~v~~~L~~~l~~~~~~~~~~-~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~  131 (437)
T PRK00771         69 HVIKIVYEELVKLLGEETEPLVLP-LKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAA  131 (437)
T ss_pred             HHHHHHHHHHHHHhCCCccccccC-CCCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecC
Confidence            445566666666654322111111 235678999999999999999999887   444544443

>PRK14529 adenylate kinase; Provisional

Probab=96.17  E-value=0.0035  Score=61.51  Aligned_cols=29  Identities=28%  Similarity=0.397  Sum_probs=26.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.||..+++..++.
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~~~~is~   31 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYDLAHIES   31 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCccc
Confidence            78999999999999999999999887643

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=96.17  E-value=0.015  Score=60.74  Aligned_cols=24  Identities=33%  Similarity=0.610  Sum_probs=20.4

Q ss_pred             CCceEEEECCCCCChhHHHHHHHH
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      .|+|++|||.-|||||+|.--.-.
T Consensus       113 ~PkGlYlYG~VGcGKTmLMDlFy~  136 (467)
T KOG2383|consen  113 PPKGLYLYGSVGCGKTMLMDLFYD  136 (467)
T ss_pred             CCceEEEecccCcchhHHHHHHhh
Confidence            379999999999999999866543

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=96.15  E-value=0.012  Score=57.47  Aligned_cols=62  Identities=26%  Similarity=0.363  Sum_probs=39.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHH-----HcCCcE---------EEEecCccC-------Ch-------HHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN-----YLCYDV---------YDLELTKVT-------DN-------SELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~-----~l~~~i---------~~l~l~~~~-------~~-------~~L~~l~~~~~~~  280 (530)
                      +-++|.||.|+|||++.+.+|.     ..+..+         ++--.+.+.       ..       ..+..++..+..|
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~~~~l~~~g~~vp~~~~~i~~~~~i~~~~~~~~~ls~g~s~f~~e~~~l~~~l~~~~~~  110 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVALIALLAQIGSFVPASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATER  110 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHhccCCeeccccceecceeeEeccCCchhhhccCcchHHHHHHHHHHHHHhCCCC
Confidence            4678999999999999999874     222221         110011111       00       1355566677899


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      ++|+|||.-.
T Consensus       111 ~llllDEp~~  120 (216)
T cd03284         111 SLVLLDEIGR  120 (216)
T ss_pred             eEEEEecCCC
Confidence            9999999853

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

>TIGR00376 DNA helicase, putative

Probab=96.15  E-value=0.01  Score=67.07  Aligned_cols=35  Identities=26%  Similarity=0.468  Sum_probs=27.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      ..+|++||||||||+++.++...+   +..+..+..+.
T Consensus       174 ~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~sn  211 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSN  211 (637)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCcH
Confidence            357899999999999999888765   66666665443

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>PLN02674 adenylate kinase

Probab=96.15  E-value=0.0056  Score=60.83  Aligned_cols=31  Identities=29%  Similarity=0.565  Sum_probs=26.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..++|.||||+||||+++.||..+++..++.
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~~~~~his~   62 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDEYCLCHLAT   62 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHcCCcEEch
Confidence            4689999999999999999999998765543

>TIGR00416 sms DNA repair protein RadA

Probab=96.14  E-value=0.012  Score=63.89  Aligned_cols=69  Identities=23%  Similarity=0.239  Sum_probs=44.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC--------------------ChHHHHHHHHh--cC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT--------------------DNSELRALLLQ--TT  278 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~--------------------~~~~L~~l~~~--~~  278 (530)
                      |++...-+||+|+||+|||+|+..+|..+   +.+++.++..+-.                    ...++..+...  ..
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            56666679999999999999999987765   3455555432210                    01112222222  25


Q ss_pred             CCeEEEEcCccchh
Q 009640          279 NRSIIVIEDIDCSV  292 (530)
Q Consensus       279 ~~sII~IDeID~~~  292 (530)
                      ++.+||||.|-.+.
T Consensus       170 ~~~~vVIDSIq~l~  183 (454)
T TIGR00416       170 NPQACVIDSIQTLY  183 (454)
T ss_pred             CCcEEEEecchhhc
Confidence            78999999988763

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)).

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.12  E-value=0.008  Score=59.42  Aligned_cols=48  Identities=23%  Similarity=0.221  Sum_probs=34.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH---cCCcEEEEecCccCChHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY---LCYDVYDLELTKVTDNSELRAL  273 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~---l~~~i~~l~l~~~~~~~~L~~l  273 (530)
                      |+|....+|++||||||||+|+..++.+   -|..++.+++..  +..++.+-
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~ee--~~~~i~~~   67 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALEE--HPVQVRRN   67 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEeeC--CHHHHHHH
Confidence            6777788999999999999999876544   266777776543  33444443

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.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.09  E-value=0.01  Score=62.20  Aligned_cols=24  Identities=33%  Similarity=0.488  Sum_probs=22.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.|.||||||.|+-.+|..+
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            457899999999999999999998

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>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=96.08  E-value=0.005  Score=57.76  Aligned_cols=22  Identities=36%  Similarity=0.779  Sum_probs=20.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ++|.|+||+||||+++.++.++
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            7899999999999999999988

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.07  E-value=0.024  Score=62.07  Aligned_cols=26  Identities=35%  Similarity=0.509  Sum_probs=22.1

Q ss_pred             CCceEEEECCCCCChhHHHHHHHHHc
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +..-+.|.||+|+||||++..||..+
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            34568899999999999999998765

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=96.04  E-value=0.0063  Score=57.44  Aligned_cols=29  Identities=34%  Similarity=0.391  Sum_probs=26.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +.|+|+||+||||+++.+++ +|+.+++.+
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            57899999999999999999 898888765

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.04  E-value=0.068  Score=49.63  Aligned_cols=28  Identities=25%  Similarity=0.260  Sum_probs=22.5

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~  258 (530)
                      +.+|+++|+||||+|.++|-..   |..+..
T Consensus         5 i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~   35 (159)
T cd00561           5 IQVYTGNGKGKTTAALGLALRALGHGYRVGV   35 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence            5689999999999999998765   555555

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.04  E-value=0.0099  Score=62.49  Aligned_cols=24  Identities=42%  Similarity=0.563  Sum_probs=21.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.||+|+||||++++|++++
T Consensus       135 glilI~GpTGSGKTTtL~aLl~~i  158 (358)
T TIGR02524       135 GIVFITGATGSGKSTLLAAIIREL  158 (358)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            458889999999999999999887

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.

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=96.02  E-value=0.0046  Score=60.36  Aligned_cols=22  Identities=41%  Similarity=0.606  Sum_probs=20.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ++++|+||+|||++++.++...
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc
Confidence            4789999999999999999984

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PLN02459 probable adenylate kinase

Probab=96.00  E-value=0.008  Score=60.20  Aligned_cols=30  Identities=20%  Similarity=0.412  Sum_probs=26.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .++|.||||+||||+++.+|..+++..+..
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~~~~is~   60 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLGVPHIAT   60 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeC
Confidence            478899999999999999999998776654

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=95.99  E-value=0.014  Score=58.31  Aligned_cols=26  Identities=31%  Similarity=0.579  Sum_probs=23.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .-+++.||||+|||+|++.|++.+..
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccc
Confidence            35899999999999999999998865

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.

>PRK12338 hypothetical protein; Provisional

Probab=95.99  E-value=0.0067  Score=62.46  Aligned_cols=29  Identities=24%  Similarity=0.260  Sum_probs=25.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      +.-+++.|+|||||||+++++|..++...
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l~~~~   32 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTLNIKH   32 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHCCCeE
Confidence            35688999999999999999999998754

>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=95.99  E-value=0.0068  Score=67.31  Aligned_cols=31  Identities=19%  Similarity=0.289  Sum_probs=29.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+.|.|+||+||||+.+.+|+.|+++++|++
T Consensus         8 ~i~LiG~~GaGKttvg~~LA~~L~~~fiD~D   38 (542)
T PRK14021          8 QAVIIGMMGAGKTRVGKEVAQMMRLPFADAD   38 (542)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            4788999999999999999999999999996

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.99  E-value=0.0057  Score=57.43  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=22.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+++.||||+||||++++||..++.
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCc
Confidence            4689999999999999999998764

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=95.98  E-value=0.015  Score=61.45  Aligned_cols=28  Identities=39%  Similarity=0.681  Sum_probs=24.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +..+.+.||.|||||+++++|...+...
T Consensus        22 ~~~~fv~G~~GtGKs~l~~~i~~~~~~~   49 (364)
T PF05970_consen   22 GLNFFVTGPAGTGKSFLIKAIIDYLRSR   49 (364)
T ss_pred             CcEEEEEcCCCCChhHHHHHHHHHhccc
Confidence            4577899999999999999999988543

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=95.97  E-value=0.014  Score=55.05  Aligned_cols=24  Identities=38%  Similarity=0.616  Sum_probs=21.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||+|+|||||++.|+..+
T Consensus        26 ~~~~l~G~nGsGKStLl~~i~G~~   49 (180)
T cd03214          26 EIVGILGPNGAGKSTLLKTLAGLL   49 (180)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            358899999999999999999976

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=95.96  E-value=0.0078  Score=46.70  Aligned_cols=23  Identities=48%  Similarity=0.723  Sum_probs=20.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -.+|+||.|+||||+..||.--+
T Consensus        25 ~tli~G~nGsGKSTllDAi~~~L   47 (62)
T PF13555_consen   25 VTLITGPNGSGKSTLLDAIQTVL   47 (62)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            38999999999999999997665

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=95.93  E-value=0.0068  Score=57.23  Aligned_cols=26  Identities=35%  Similarity=0.548  Sum_probs=23.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.+.||+|+||||++++++..++..
T Consensus         5 ~i~l~G~sGsGKSTl~~~la~~l~~~   30 (176)
T PRK09825          5 SYILMGVSGSGKSLIGSKIAALFSAK   30 (176)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCE
Confidence            47899999999999999999998764

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=95.93  E-value=0.019  Score=59.08  Aligned_cols=52  Identities=13%  Similarity=0.118  Sum_probs=35.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcC---------CcEEEEecCccCChHHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLC---------YDVYDLELTKVTDNSELRALLL  275 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---------~~i~~l~l~~~~~~~~L~~l~~  275 (530)
                      |++...-++++||||||||+|+..+|....         -.++.++...--....+.+++.
T Consensus        91 Gi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~~~~~  151 (310)
T TIGR02236        91 GIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQMAE  151 (310)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHHHHHH
Confidence            566666789999999999999998886642         2556665544323445555543

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.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=95.91  E-value=0.0074  Score=56.56  Aligned_cols=25  Identities=28%  Similarity=0.341  Sum_probs=22.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-++|.|+||+||||+++++++.+.
T Consensus         8 ~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          8 YVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            4678899999999999999999885

>PF00488 MutS_V: MutS domain V C-terminus

Probab=95.91  E-value=0.04  Score=54.52  Aligned_cols=62  Identities=23%  Similarity=0.442  Sum_probs=40.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-----CCcE----EEEec-----Cc------cC--------ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-----CYDV----YDLEL-----TK------VT--------DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i----~~l~l-----~~------~~--------~~~~L~~l~~~~~~~  280 (530)
                      +.++|.||...|||++++++|--.     |..+    ..+.+     +.      +.        .-.++..++..++.+
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            678999999999999999887643     3211    11111     11      10        113466778888899


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      ++|+|||+-.
T Consensus       124 sLvliDE~g~  133 (235)
T PF00488_consen  124 SLVLIDELGR  133 (235)
T ss_dssp             EEEEEESTTT
T ss_pred             eeeecccccC
Confidence            9999999975

; 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 ....

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=95.90  E-value=0.034  Score=65.48  Aligned_cols=62  Identities=21%  Similarity=0.345  Sum_probs=40.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHH---cCCcEEEEecCccC----------ChHHHHHHHHh-------cCCCeEEEEcCcc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY---LCYDVYDLELTKVT----------DNSELRALLLQ-------TTNRSIIVIEDID  289 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~---l~~~i~~l~l~~~~----------~~~~L~~l~~~-------~~~~sII~IDeID  289 (530)
                      -++|.|+||||||++++++...   .|+.++-+-++...          ....+..++..       .....||||||+-
T Consensus       364 v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTGkAA~~L~e~tGi~a~TI~sll~~~~~~~~~l~~~~vlIVDEAS  443 (988)
T PRK13889        364 LGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIAAENLEGGSGIASRTIASLEHGWGQGRDLLTSRDVLVIDEAG  443 (988)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcHHHHHHHhhccCcchhhHHHHHhhhcccccccccCcEEEEECcc
Confidence            3679999999999998877654   37777766544320          11234444432       2355799999997


Q ss_pred             ch
Q 009640          290 CS  291 (530)
Q Consensus       290 ~~  291 (530)
                      .+
T Consensus       444 Mv  445 (988)
T PRK13889        444 MV  445 (988)
T ss_pred             cC
Confidence            65

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.88  E-value=0.017  Score=63.28  Aligned_cols=49  Identities=14%  Similarity=0.127  Sum_probs=36.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH----cCCcEEEEecCccCChHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY----LCYDVYDLELTKVTDNSELRALL  274 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~----l~~~i~~l~l~~~~~~~~L~~l~  274 (530)
                      |+|..+.+|+.||||||||+|+..++..    .+.+.+.+.+.  .+..++.+..
T Consensus        17 Glp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e--E~~~~l~~~~   69 (484)
T TIGR02655        17 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE--ESPQDIIKNA   69 (484)
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe--cCHHHHHHHH
Confidence            6788889999999999999999987543    26788777764  3444444443

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.87  E-value=0.018  Score=63.08  Aligned_cols=37  Identities=19%  Similarity=0.146  Sum_probs=28.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      |++...-+|+.||||||||+|+..++...   |..+..++
T Consensus       259 G~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s  298 (484)
T TIGR02655       259 GFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFA  298 (484)
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            56777779999999999999998887755   44444443

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.

>PRK13808 adenylate kinase; Provisional

Probab=95.85  E-value=0.0075  Score=62.47  Aligned_cols=29  Identities=24%  Similarity=0.447  Sum_probs=26.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|+||||+|||+++..||..+++..+++
T Consensus         3 Iiv~GpPGSGK~T~a~~LA~~ygl~~is~   31 (333)
T PRK13808          3 LILLGPPGAGKGTQAQRLVQQYGIVQLST   31 (333)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceecc
Confidence            79999999999999999999998866554

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=95.84  E-value=0.022  Score=59.49  Aligned_cols=62  Identities=23%  Similarity=0.393  Sum_probs=40.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCC--cEEEEe------cC--c---c-------C--ChHHHHHHHHhc--CCCeEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCY--DVYDLE------LT--K---V-------T--DNSELRALLLQT--TNRSII  283 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~--~i~~l~------l~--~---~-------~--~~~~L~~l~~~~--~~~sII  283 (530)
                      +..+++.|++|+|||+++++++.++.-  .++.++      +.  .   +       .  ..-.+.+++..+  ..|.+|
T Consensus       178 ~~~ili~G~tGsGKTTll~al~~~i~~~~riv~iEd~~El~~~~~~~~~l~~r~~~~~g~~~~t~~~ll~~aLR~~PD~I  257 (340)
T TIGR03819       178 RLAFLISGGTGSGKTTLLSALLALVAPDERIVLVEDAAELRPDHPHVVRLEARPANVEGAGAVTLTDLVRQALRMRPDRI  257 (340)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHccCCCCCcEEEECCcceecCCCCCeeeEEeccccccCcCccCHHHHHHHHhccCCCeE
Confidence            468999999999999999999988742  122111      10  0   0       0  112345555544  579999


Q ss_pred             EEcCcc
Q 009640          284 VIEDID  289 (530)
Q Consensus       284 ~IDeID  289 (530)
                      ++-||=
T Consensus       258 ivGEiR  263 (340)
T TIGR03819       258 VVGEVR  263 (340)
T ss_pred             EEeCcC
Confidence            999985

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=95.84  E-value=0.0084  Score=65.53  Aligned_cols=63  Identities=21%  Similarity=0.329  Sum_probs=42.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecC--cc------CChHHHHHHHHhc-----CCCeEEEEcCccchh
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT--KV------TDNSELRALLLQT-----TNRSIIVIEDIDCSV  292 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~--~~------~~~~~L~~l~~~~-----~~~sII~IDeID~~~  292 (530)
                      .+||.|-||||||-+.+.+++....-++.--..  .+      ..+.--+.+-.++     ..+.|.+|||+|.+-
T Consensus       484 nvLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGASavGLTa~v~KdPvtrEWTLEaGALVLADkGvClIDEFDKMn  559 (854)
T KOG0477|consen  484 NVLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGASAVGLTAYVRKDPVTREWTLEAGALVLADKGVCLIDEFDKMN  559 (854)
T ss_pred             eEEEecCCCccHHHHHHHHHhcCcceeEeccCCccccceeEEEeeCCccceeeeccCeEEEccCceEEeehhhhhc
Confidence            399999999999999999999887777654321  11      1111112222222     568899999999983

>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=95.84  E-value=0.012  Score=54.45  Aligned_cols=33  Identities=36%  Similarity=0.418  Sum_probs=27.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      -+.|.|.||+|||++|+++...|   +.++|.++..
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            47889999999999999999887   6777777643

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 ....

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=95.82  E-value=0.0069  Score=56.36  Aligned_cols=26  Identities=35%  Similarity=0.425  Sum_probs=22.4

Q ss_pred             ECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          234 YGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       234 ~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .||||+||||+++++|..++..+++-
T Consensus         1 ~G~sGsGKSTla~~la~~l~~~~~~~   26 (163)
T PRK11545          1 MGVSGSGKSAVASEVAHQLHAAFLDG   26 (163)
T ss_pred             CCCCCCcHHHHHHHHHHHhCCeEEeC
Confidence            39999999999999999998765554

>PRK04328 hypothetical protein; Provisional

Probab=95.80  E-value=0.013  Score=58.34  Aligned_cols=49  Identities=22%  Similarity=0.233  Sum_probs=34.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH---cCCcEEEEecCccCChHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY---LCYDVYDLELTKVTDNSELRALL  274 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~---l~~~i~~l~l~~~~~~~~L~~l~  274 (530)
                      |+|...-+|++||||||||+|+..++.+   -|...+.++..+  +...+.+.+
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~ee--~~~~i~~~~   70 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVALEE--HPVQVRRNM   70 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEeeC--CHHHHHHHH
Confidence            5777778999999999999999876644   266777776544  334444443

>PRK06761 hypothetical protein; Provisional

Probab=95.80  E-value=0.0097  Score=60.37  Aligned_cols=33  Identities=27%  Similarity=0.437  Sum_probs=28.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      +-+++.||||+||||+++.++..+....+++..
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~g~~v~~   36 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQNGIEVEL   36 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcCceEEEE
Confidence            358899999999999999999999876666654

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.80  E-value=0.0062  Score=57.09  Aligned_cols=26  Identities=31%  Similarity=0.356  Sum_probs=22.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -++|.||+|+|||++++.|++.+...
T Consensus         3 ii~l~G~~GsGKsTl~~~L~~~~~~~   28 (180)
T TIGR03263         3 LIVISGPSGVGKSTLVKALLEEDPNL   28 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHccCccc
Confidence            47899999999999999999977543

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.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=95.78  E-value=0.025  Score=64.66  Aligned_cols=69  Identities=17%  Similarity=0.201  Sum_probs=42.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH---cCCcEEEEecCc---------------------cCChHHHHHHHH---h
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY---LCYDVYDLELTK---------------------VTDNSELRALLL---Q  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~---l~~~i~~l~l~~---------------------~~~~~~L~~l~~---~  276 (530)
                      |++..+-++++||||||||+|+..++..   .+..+..++...                     ..+...+..++.   +
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            4666677999999999999999654332   244444333221                     112222222222   2


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||-|..++
T Consensus       136 ~~~~~LVVIDSI~aL~  151 (790)
T PRK09519        136 SGALDIVVIDSVAALV  151 (790)
T ss_pred             cCCCeEEEEcchhhhc
Confidence            3578999999999875

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.77  E-value=0.013  Score=54.81  Aligned_cols=24  Identities=29%  Similarity=0.448  Sum_probs=21.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.|+||+|||++++++|..+
T Consensus         5 ~~i~~~G~~GsGKST~a~~la~~l   28 (175)
T PRK00889          5 VTVWFTGLSGAGKTTIARALAEKL   28 (175)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            357889999999999999999987

>COG3378 Phage associated DNA primase [General function prediction only]

Probab=95.76  E-value=0.057  Score=59.14  Aligned_cols=65  Identities=22%  Similarity=0.373  Sum_probs=43.3

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCCc-EEEEecCccCChHHHHHHHHhcCCCeEEEEcCccc
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCYD-VYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDC  290 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~-i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~  290 (530)
                      .|...+.||||-|+|||+++..|.+-+|.. +..+.++.+.....=+.-+......++|..+|.+.
T Consensus       228 ~~~k~~~l~G~G~nGKstf~~li~~llG~~n~~s~~~~~~~~~~~~~~~~A~Lvg~~~v~~~E~~k  293 (517)
T COG3378         228 SEQKLFWLYGPGGNGKSTFVDLISNLLGRYNVTSAPLTDLEADDRHPFGLAALVGKRLVTVSETEK  293 (517)
T ss_pred             cceeEEEEEcCCCCChHHHHHHHHHHhccchhccccHHHhhhhccCcchHHHhhCceEEEecCccc
Confidence            467889999999999999999999999753 44444444432111112233345667777777765

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.75  E-value=0.023  Score=59.41  Aligned_cols=26  Identities=31%  Similarity=0.567  Sum_probs=23.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +..+|+.||+|+||||+++|++.++.
T Consensus       162 ~~nilI~G~tGSGKTTll~aLl~~i~  187 (344)
T PRK13851        162 RLTMLLCGPTGSGKTTMSKTLISAIP  187 (344)
T ss_pred             CCeEEEECCCCccHHHHHHHHHcccC
Confidence            46899999999999999999999874

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=95.74  E-value=0.0085  Score=59.43  Aligned_cols=30  Identities=37%  Similarity=0.734  Sum_probs=22.2

Q ss_pred             EECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          233 LYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       233 L~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      +.||||+||||+++++...+   +.+++.+++-
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~~~~~~vNLD   33 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNGRDVYIVNLD   33 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT-S-EEEEE--
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCceEEEcc
Confidence            36999999999999999988   5666666653

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.71  E-value=0.0055  Score=58.66  Aligned_cols=66  Identities=24%  Similarity=0.371  Sum_probs=42.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEE---EEec---------Ccc----------CChHHHHHHHHhcCCCeEEEEcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVY---DLEL---------TKV----------TDNSELRALLLQTTNRSIIVIED  287 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~---~l~l---------~~~----------~~~~~L~~l~~~~~~~sII~IDe  287 (530)
                      =++|.|+||+|||++++-+|..|.-.+.   .+..         .++          ...+..+ ++..+-+.-+++.|+
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L~~~i~~vi~l~kdy~~~i~~DEslpi~ke~yres~~ks~~r-lldSalkn~~VIvDd   81 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLRGILWDESLPILKEVYRESFLKSVER-LLDSALKNYLVIVDD   81 (261)
T ss_pred             eEEEecCCCCCchHHHHHHHHHHHHhhhhccccchhhhhheecccccchHHHHHHHHHHHHHHH-HHHHHhcceEEEEec
Confidence            3689999999999999999999944333   2221         000          0111222 555555677899999


Q ss_pred             ccchhhhhh
Q 009640          288 IDCSVDLTA  296 (530)
Q Consensus       288 ID~~~~~~~  296 (530)
                      ..-.-+.+.
T Consensus        82 tNYyksmRr   90 (261)
T COG4088          82 TNYYKSMRR   90 (261)
T ss_pred             ccHHHHHHH
Confidence            887644433

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=95.71  E-value=0.023  Score=57.13  Aligned_cols=64  Identities=19%  Similarity=0.360  Sum_probs=52.4

Q ss_pred             CceEEEECCCCCChhHHHHHHH------HHcCCcEEEEecCccCChHHHHHHHHhc-----------------CCCeEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMA------NYLCYDVYDLELTKVTDNSELRALLLQT-----------------TNRSIIV  284 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA------~~l~~~i~~l~l~~~~~~~~L~~l~~~~-----------------~~~sII~  284 (530)
                      +..+||.||.|.|||.|++.|-      +.+.-.++.+++..+.++..+..+|-..                 ....++|
T Consensus       208 r~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadggmlf  287 (531)
T COG4650         208 RAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGMLF  287 (531)
T ss_pred             cCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCceEe
Confidence            4579999999999999999874      3467789999999998888888877532                 2457999


Q ss_pred             EcCccch
Q 009640          285 IEDIDCS  291 (530)
Q Consensus       285 IDeID~~  291 (530)
                      +|||..+
T Consensus       288 ldeigel  294 (531)
T COG4650         288 LDEIGEL  294 (531)
T ss_pred             hHhhhhc
Confidence            9999876

>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=95.70  E-value=0.011  Score=56.78  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=27.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc-CCcEEEEecCcc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL-CYDVYDLELTKV  264 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~~l~l~~~  264 (530)
                      |.-+++.|+||+|||+++..+...+ +-+++.++...+
T Consensus        15 P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~   52 (199)
T PF06414_consen   15 PTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEF   52 (199)
T ss_dssp             -EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGG
T ss_pred             CEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHH
Confidence            5678999999999999999999888 667777765544

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.70  E-value=0.015  Score=57.31  Aligned_cols=40  Identities=18%  Similarity=0.172  Sum_probs=32.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecCc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELTK  263 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~~  263 (530)
                      |+++..-++|.||||+|||+++..+|..+    +.+++.+++..
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            66666679999999999999998887654    77777776654

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.

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.69  E-value=0.012  Score=56.53  Aligned_cols=26  Identities=35%  Similarity=0.437  Sum_probs=23.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      ..-+.|.||+|+|||+|++.|+..+.
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            35688999999999999999999876

>PLN02165 adenylate isopentenyltransferase

Probab=95.69  E-value=0.01  Score=61.41  Aligned_cols=32  Identities=25%  Similarity=0.429  Sum_probs=28.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .-+.|.||+|+|||+|+.+||..++..+++.+
T Consensus        44 ~iivIiGPTGSGKStLA~~LA~~l~~eIIsaD   75 (334)
T PLN02165         44 KVVVIMGATGSGKSRLSVDLATRFPSEIINSD   75 (334)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHcCCceecCC
Confidence            35889999999999999999999998777654

>PRK06851 hypothetical protein; Provisional

Probab=95.69  E-value=0.009  Score=62.74  Aligned_cols=27  Identities=33%  Similarity=0.603  Sum_probs=24.0

Q ss_pred             CCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      ..+-++|.||||||||+|++.++..+.
T Consensus        29 ~~~~~il~G~pGtGKStl~~~i~~~~~   55 (367)
T PRK06851         29 ANRIFILKGGPGTGKSTLMKKIGEEFL   55 (367)
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            356799999999999999999998883

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.68  E-value=0.017  Score=59.78  Aligned_cols=51  Identities=22%  Similarity=0.304  Sum_probs=33.1

Q ss_pred             hhhHHHHHHHHHHHcC-hhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          201 QLKKQITEDLTAFANG-KEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~-~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .+++.+.+.+...+.. ...+. .....+.-++|.||||+||||+++.+|..+
T Consensus        87 ~~~~~l~~~l~~~l~~~~~~~~-~~~~~~~vi~lvGpnGsGKTTt~~kLA~~l  138 (318)
T PRK10416         87 ELKELLKEELAEILEPVEKPLN-IEEKKPFVILVVGVNGVGKTTTIGKLAHKY  138 (318)
T ss_pred             HHHHHHHHHHHHHhCcCCcccc-ccCCCCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            3555566666666542 11111 111224568889999999999999999987

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=95.66  E-value=0.026  Score=58.28  Aligned_cols=52  Identities=15%  Similarity=0.137  Sum_probs=35.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---------CCcEEEEecCccCChHHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---------CYDVYDLELTKVTDNSELRALLL  275 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---------~~~i~~l~l~~~~~~~~L~~l~~  275 (530)
                      |++...-++++||||||||+++..+|-..         +..++.++...--....+.+...
T Consensus        98 Gi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~~~  158 (317)
T PRK04301         98 GIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAE  158 (317)
T ss_pred             CccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHHHH
Confidence            56766778999999999999999888653         23556665544323444554443

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.66  E-value=0.01  Score=58.04  Aligned_cols=38  Identities=21%  Similarity=0.108  Sum_probs=28.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      |++...-++++||||||||+|+..++...   +..+..++.
T Consensus        16 Gi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~   56 (229)
T TIGR03881        16 GIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTT   56 (229)
T ss_pred             CCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEc
Confidence            56666779999999999999999877543   444444443

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.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.65  E-value=0.015  Score=56.04  Aligned_cols=33  Identities=18%  Similarity=0.157  Sum_probs=25.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC-CcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC-YDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~-~~i~~l~l  261 (530)
                      .-+.+.||||+|||||+++|+..++ ..+..++.
T Consensus         7 ~iI~I~G~sGsGKTTl~~~l~~~l~~~~~~~i~~   40 (209)
T PRK05480          7 IIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQ   40 (209)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCceEEEeC
Confidence            4578899999999999999999983 33444443

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=95.64  E-value=0.011  Score=56.79  Aligned_cols=31  Identities=26%  Similarity=0.189  Sum_probs=27.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+.++||||+|||++++.++..+|+.+++.+
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~~g~~~i~~D   33 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQKGIPILDAD   33 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCeEeeCc
Confidence            3789999999999999999998899988764

>PTZ00202 tuzin; Provisional

Probab=95.64  E-value=0.036  Score=59.25  Aligned_cols=77  Identities=17%  Similarity=0.184  Sum_probs=52.0

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS  268 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~  268 (530)
                      -|....+++|-+....++...+..          .....++-..|.||+|||||+|++.++..++...|.+++..  ...
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~----------~d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNprg--~eE  324 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRR----------LDTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVRG--TED  324 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhc----------cCCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCCC--HHH
Confidence            344456777777766666554432          11122356789999999999999999999998888888772  234


Q ss_pred             HHHHHHHhc
Q 009640          269 ELRALLLQT  277 (530)
Q Consensus       269 ~L~~l~~~~  277 (530)
                      -|+.++...
T Consensus       325 lLr~LL~AL  333 (550)
T PTZ00202        325 TLRSVVKAL  333 (550)
T ss_pred             HHHHHHHHc
Confidence            455555544

>TIGR00017 cmk cytidylate kinase

Probab=95.63  E-value=0.012  Score=57.57  Aligned_cols=30  Identities=37%  Similarity=0.514  Sum_probs=26.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -+.+.||+|+||||+++.+|..+++.+++-
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~~~~~~~~~   33 (217)
T TIGR00017         4 IIAIDGPSGAGKSTVAKAVAEKLGYAYLDS   33 (217)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceeeC
Confidence            467899999999999999999999887764

This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.

>PRK13975 thymidylate kinase; Provisional

Probab=95.61  E-value=0.017  Score=54.89  Aligned_cols=26  Identities=27%  Similarity=0.202  Sum_probs=23.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||+|+||||+++.+|..++..
T Consensus         4 ~I~ieG~~GsGKtT~~~~L~~~l~~~   29 (196)
T PRK13975          4 FIVFEGIDGSGKTTQAKLLAEKLNAF   29 (196)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            47889999999999999999999864

>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]

Probab=95.61  E-value=0.019  Score=61.51  Aligned_cols=62  Identities=24%  Similarity=0.398  Sum_probs=39.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc--------cCChHHHHHHHHh-----cCCCeEEEEcCccch
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK--------VTDNSELRALLLQ-----TTNRSIIVIEDIDCS  291 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~--------~~~~~~L~~l~~~-----~~~~sII~IDeID~~  291 (530)
                      ++||-|.|||-||-|.+-+-.-.-.-+|.---.+        +..+..-+....+     .....|+.|||+|.+
T Consensus       366 NVLLLGDPgtAKSQlLKFvEkvsPIaVYTSGKGSSAAGLTASV~RD~~tReFylEGGAMVLADgGVvCIDEFDKM  440 (729)
T KOG0481|consen  366 NVLLLGDPGTAKSQLLKFVEKVSPIAVYTSGKGSSAAGLTASVIRDPSTREFYLEGGAMVLADGGVVCIDEFDKM  440 (729)
T ss_pred             eEEEecCCchhHHHHHHHHHhcCceEEEecCCCcccccceeeEEecCCcceEEEecceEEEecCCEEEeehhhcc
Confidence            4899999999999999998877766666542111        0011111111111     145689999999987

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.60  E-value=0.014  Score=55.17  Aligned_cols=34  Identities=26%  Similarity=0.388  Sum_probs=26.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcC---CcEEEEecCcc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLC---YDVYDLELTKV  264 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~~~  264 (530)
                      +.+.|+||+|||++++.|+..++   .++..+++.++
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~~~~~~~i~~Ddf   38 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDY   38 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEehhhc
Confidence            57899999999999999999984   45555554443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.57  E-value=0.092  Score=51.84  Aligned_cols=21  Identities=43%  Similarity=0.545  Sum_probs=18.4

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+|+||||+|||+|+..+|-.
T Consensus         4 ~ll~g~~G~GKS~lal~la~~   24 (239)
T cd01125           4 SALVAPGGTGKSSLLLVLALA   24 (239)
T ss_pred             eEEEcCCCCCHHHHHHHHHHH
Confidence            379999999999999988764

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.55  E-value=0.012  Score=56.10  Aligned_cols=25  Identities=24%  Similarity=0.438  Sum_probs=22.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ++-++|.||||+|||+|++++....
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcC
Confidence            4568899999999999999998876

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	530
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		1e-06
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		3e-06
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		3e-06
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		3e-06
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		4e-06
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		4e-06
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		4e-06
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		5e-06
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-05
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-05
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		1e-05
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		1e-05
2ce7_A	476	Edta Treated Length = 476		4e-05
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		8e-05
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		2e-04
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		2e-04
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-04
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		2e-04
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		2e-04
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		2e-04
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		4e-04

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 89/204 (43%), Gaps = 45/204 (22%)
Query: 191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN 250
           ST++ +    +  K+I E +       E +  +G A  +G +LYGPPG+GK+ L  A+A+
Sbjct: 145 STYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAH 204
Query: 251 YL-C--YDVYDLELTK--VTDNSEL-RALLLQTTNR--SIIVIEDIDCSVDLTADRMLXX 302
           +  C    V   EL +  + + S + R L +       SII +++ID             
Sbjct: 205 HTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDS------------ 252
Query: 303 XXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEE 362
                            +GS     + G      G+   + T+  LLN  DG  +  S+ 
Sbjct: 253 -----------------IGSTRVEGSGG------GDSEVQRTMLELLNQLDGFET--SKN 287
Query: 363 KIIVFTTNHRDSVDPALIRCGRMD 386
             I+  TN  D +DPAL+R GR+D
Sbjct: 288 IKIIMATNRLDILDPALLRPGRID 311

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 81/219 (36%), Gaps = 75/219 (34%)
Query: 182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGK 241
            V +P RHP+ F+ + ++P                            RG LLYGPPG+GK
Sbjct: 219 MVELPLRHPALFKAIGVKP---------------------------PRGILLYGPPGTGK 251
Query: 242 SSLIAAMANYLCYDVYDLE----LTKVTDNSE--LRALLLQTTNRS--IIVIEDIDCSVD 293
           + +  A+AN      + +     ++K+   SE  LR    +    +  II I+++D    
Sbjct: 252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELD---- 307
Query: 294 LTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTD 353
                                            +         GE   R+ +S LL   D
Sbjct: 308 ---------------------------------AIAPKREKTHGEVERRI-VSQLLTLMD 333
Query: 354 GLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
           GL        I++  TN  +S+DPAL R GR D  V +G
Sbjct: 334 GLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIG 370

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 81/219 (36%), Gaps = 75/219 (34%)
Query: 182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGK 241
            V +P RHP+ F+ + ++P                            RG LLYGPPG+GK
Sbjct: 219 MVELPLRHPALFKAIGVKP---------------------------PRGILLYGPPGTGK 251
Query: 242 SSLIAAMANYLCYDVYDLE----LTKVTDNSE--LRALLLQTTNRS--IIVIEDIDCSVD 293
           + +  A+AN      + +     ++K+   SE  LR    +    +  II I+++D    
Sbjct: 252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELD---- 307
Query: 294 LTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTD 353
                                            +         GE   R+ +S LL   D
Sbjct: 308 ---------------------------------AIAPKREKTHGEVERRI-VSQLLTLMD 333
Query: 354 GLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
           GL        I++  TN  +S+DPAL R GR D  V +G
Sbjct: 334 GLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIG 370

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 81/219 (36%), Gaps = 75/219 (34%)
Query: 182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGK 241
            V +P RHP+ F+ + ++P                            RG LLYGPPG+GK
Sbjct: 219 MVELPLRHPALFKAIGVKP---------------------------PRGILLYGPPGTGK 251
Query: 242 SSLIAAMANYLCYDVYDLE----LTKVTDNSE--LRALLLQTTNRS--IIVIEDIDCSVD 293
           + +  A+AN      + +     ++K+   SE  LR    +    +  II I+++D    
Sbjct: 252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELD---- 307
Query: 294 LTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTD 353
                                            +         GE   R+ +S LL   D
Sbjct: 308 ---------------------------------AIAPKREKTHGEVERRI-VSQLLTLMD 333
Query: 354 GLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
           GL        I++  TN  +S+DPAL R GR D  V +G
Sbjct: 334 GLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIG 370

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 81/219 (36%), Gaps = 75/219 (34%)
Query: 182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGK 241
            V +P RHP+ F+ + ++P                            RG LLYGPPG+GK
Sbjct: 219 MVELPLRHPALFKAIGVKP---------------------------PRGILLYGPPGTGK 251
Query: 242 SSLIAAMANYLCYDVYDLE----LTKVTDNSE--LRALLLQTTNRS--IIVIEDIDCSVD 293
           + +  A+AN      + +     ++K+   SE  LR    +    +  II I+++D    
Sbjct: 252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELD---- 307
Query: 294 LTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTD 353
                                            +         GE   R+ +S LL   D
Sbjct: 308 ---------------------------------AIAPKREKTHGEVERRI-VSQLLTLMD 333
Query: 354 GLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
           GL        I++  TN  +S+DPAL R GR D  V +G
Sbjct: 334 GLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIG 370

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 81/219 (36%), Gaps = 75/219 (34%)
Query: 182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGK 241
            V +P RHP+ F+ + ++P                            RG LLYGPPG+GK
Sbjct: 219 MVELPLRHPALFKAIGVKP---------------------------PRGILLYGPPGTGK 251
Query: 242 SSLIAAMANYLCYDVYDLE----LTKVTDNSE--LRALLLQTTNRS--IIVIEDIDCSVD 293
           + +  A+AN      + +     ++K+   SE  LR    +    +  II I+++D    
Sbjct: 252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELD---- 307
Query: 294 LTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTD 353
                                            +         GE   R+ +S LL   D
Sbjct: 308 ---------------------------------AIAPKREKTHGEVERRI-VSQLLTLMD 333
Query: 354 GLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
           GL        I++  TN  +S+DPAL R GR D  V +G
Sbjct: 334 GLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIG 370

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 81/219 (36%), Gaps = 75/219 (34%)
Query: 182 WVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGK 241
            V +P RHP+ F+ + ++P                            RG LLYGPPG+GK
Sbjct: 219 MVELPLRHPALFKAIGVKP---------------------------PRGILLYGPPGTGK 251
Query: 242 SSLIAAMANYLCYDVYDLE----LTKVTDNSE--LRALLLQTTNRS--IIVIEDIDCSVD 293
           + +  A+AN      + +     ++K+   SE  LR    +    +  II I+++D    
Sbjct: 252 TLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELD---- 307
Query: 294 LTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTD 353
                                            +         GE   R+ +S LL   D
Sbjct: 308 ---------------------------------AIAPKREKTHGEVERRI-VSQLLTLMD 333
Query: 354 GLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
           GL        I++  TN  +S+DPAL R GR D  V +G
Sbjct: 334 GLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIG 370

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 50/210 (23%), Positives = 85/210 (40%), Gaps = 46/210 (21%)
Query: 191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN 250
           +TF  +A   + K+++ E L  +      + ++G    +G L+ GPPG+GK+ L  A+A 
Sbjct: 9   TTFADVAGCDEAKEEVAE-LVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG 67
Query: 251 YLCYDVYDL------ELTKVTDNSELRALLLQTTNRS--IIVIEDIDCSVDLTADRMLXX 302
                 + +      E+      S +R +  Q    +  II I++ID             
Sbjct: 68  EAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDA------------ 115
Query: 303 XXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEE 362
                            +G +  +   G      G +    TL+ +L   DG     +E 
Sbjct: 116 -----------------VGRQRGAGLGG------GHDEREQTLNQMLVEMDGFEG--NEG 150
Query: 363 KIIVFTTNHRDSVDPALIRCGRMDVHVSLG 392
            I++  TN  D +DPAL+R GR D  V +G
Sbjct: 151 IIVIAATNRPDVLDPALLRPGRFDRQVVVG 180

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 82/201 (40%), Gaps = 46/201 (22%)
Query: 197 ALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN-----Y 251
            LE Q++ +I E +       E Y  +G    +G +LYG PG+GK+ L  A+AN     +
Sbjct: 186 GLESQIQ-EIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATF 244
Query: 252 LCYDVYDLELTKVTDNSELRALLLQTTNR---SIIVIEDIDCSVDLTADRMLXXXXXXXX 308
           L     +L    + D   L   + +       SI+ I++ID                   
Sbjct: 245 LRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDA------------------ 286
Query: 309 XXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFT 368
                      +G++   S  G      GE   + T+  LLN  DG       +  ++  
Sbjct: 287 -----------IGTKRYDSNSG------GEREIQRTMLELLNQLDGFDDRGDVK--VIMA 327
Query: 369 TNHRDSVDPALIRCGRMDVHV 389
           TN  +++DPALIR GR+D  +
Sbjct: 328 TNKIETLDPALIRPGRIDRKI 348

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/187 (26%), Positives = 75/187 (40%), Gaps = 55/187 (29%)
Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAM-----ANYL------CYDVYDLELTKVTD 266
           E + RVG    +G LLYGPPG+GK+ L  A+     AN++        D Y  E  ++  
Sbjct: 205 EIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARI-- 262
Query: 267 NSELRALLLQTTNRS--IIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXEMGSRI 324
              +R +          II ++++D                               G R 
Sbjct: 263 ---IREMFAYAKEHEPCIIFMDEVDAI----------------------------GGRRF 291
Query: 325 ASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGR 384
           +  T         +   + TL  LL   DG +    + KII+  TN  D++DPAL+R GR
Sbjct: 292 SEGTSA-------DREIQRTLMELLTQMDG-FDNLGQTKIIM-ATNRPDTLDPALLRPGR 342
Query: 385 MDVHVSL 391
           +D  V +
Sbjct: 343 LDRKVEI 349

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 54/212 (25%), Positives = 80/212 (37%), Gaps = 72/212 (33%)
Query: 183 VSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKS 242
           V +P +HP  FE + +EP                            +G LLYGPPG+GK+
Sbjct: 33  VELPLKHPELFEKVGIEPP---------------------------KGILLYGPPGTGKT 65
Query: 243 SLIAAMA---NYLCYDVYDLELTK--VTDNSELRALLLQTTNR---SIIVIEDIDCSVDL 294
            L  A+A   N     V   EL K  + + + L   + +       SII I++ID     
Sbjct: 66  LLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDA---- 121
Query: 295 TADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDG 354
                                    + ++   +  G      G+   + TL  LL   DG
Sbjct: 122 -------------------------IAAKRTDALTG------GDREVQRTLMQLLAEMDG 150
Query: 355 LWSCCSEEKIIVFTTNHRDSVDPALIRCGRMD 386
            +    + KII   TN  D +DPA++R GR D
Sbjct: 151 -FDARGDVKII-GATNRPDILDPAILRPGRFD 180

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 82/206 (39%), Gaps = 46/206 (22%)
Query: 193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL 252
           F+ +A   + K+++ E +  F    E Y  +G    +G LL GPPG+GK+ L  A+A   
Sbjct: 10  FKDMAGNEEAKEEVVE-IVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA 68
Query: 253 CYDVYDL------ELTKVTDNSELRALLLQTTNR--SIIVIEDIDCSVDLTADRMLXXXX 304
               + +      E+      S +R L      +  SII I++ID               
Sbjct: 69  HVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDA-------------- 114
Query: 305 XXXXXXXXXXXXXXEMG-SRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEK 363
                          +G SR A           G +    TL+ LL   DG  S  +   
Sbjct: 115 ---------------IGKSRAAGGVV------SGNDEREQTLNQLLAEMDGFGSENA-PV 152
Query: 364 IIVFTTNHRDSVDPALIRCGRMDVHV 389
           I++  TN  + +DPAL+R GR D  V
Sbjct: 153 IVLAATNRPEILDPALMRPGRFDRQV 178

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 48/190 (25%), Positives = 76/190 (40%), Gaps = 45/190 (23%)
Query: 208 EDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSL---IAAMANYLCYDVYD---LEL 261
           +++  F      ++R+G    +G LL GPPG+GK+ L   +A  AN   + +     +EL
Sbjct: 29  KEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVEL 88
Query: 262 TKVTDNSELRALLLQTTNRS--IIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXE 319
                 + +R L  Q    +  I+ I++ID                              
Sbjct: 89  FVGVGAARVRDLFAQAKAHAPCIVFIDEIDA----------------------------- 119
Query: 320 MGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPAL 379
           +G    +   G      G +    TL+ LL   DG  S   E  I++  TN  D +DPAL
Sbjct: 120 VGRHRGAGLGG------GHDEREQTLNQLLVEMDGFDS--KEGIIVMAATNRPDILDPAL 171
Query: 380 IRCGRMDVHV 389
           +R GR D  +
Sbjct: 172 LRPGRFDKKI 181

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 30/48 (62%)
Query: 203 KKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN 250
           K++I E +       + Y ++G    RG LLYGPPG+GK+ L+ A+AN
Sbjct: 181 KQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVAN 228

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 75/191 (39%), Gaps = 47/191 (24%)
Query: 210 LTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN-----YLCYDVYD-LELTK 263
           +  F      +H +G    +G LL GPPG GK+ L  A+A      ++     D +E+  
Sbjct: 46  IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFV 105
Query: 264 VTDNSELRALLLQTTNRS---IIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXEM 320
               + +R  L +T  R    I+ I++ID                              +
Sbjct: 106 GVGAARVRD-LFETAKRHAPCIVFIDEIDA-----------------------------V 135
Query: 321 GSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALI 380
           G +  S   G      G +    TL+ LL   DG     +   +++  TN  D +DPAL+
Sbjct: 136 GRKRGSGVGG------GNDEREQTLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALL 187
Query: 381 RCGRMDVHVSL 391
           R GR D  +++
Sbjct: 188 RPGRFDRQIAI 198

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 75/191 (39%), Gaps = 47/191 (24%)
Query: 210 LTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN-----YLCYDVYD-LELTK 263
           +  F      +H +G    +G LL GPPG GK+ L  A+A      ++     D +E+  
Sbjct: 55  IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFV 114
Query: 264 VTDNSELRALLLQTTNRS---IIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXEM 320
               + +R  L +T  R    I+ I++ID                              +
Sbjct: 115 GVGAARVRD-LFETAKRHAPCIVFIDEIDA-----------------------------V 144
Query: 321 GSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALI 380
           G +  S   G      G +    TL+ LL   DG     +   +++  TN  D +DPAL+
Sbjct: 145 GRKRGSGVGG------GNDEREQTLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALL 196
Query: 381 RCGRMDVHVSL 391
           R GR D  +++
Sbjct: 197 RPGRFDRQIAI 207

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 47/190 (24%), Positives = 75/190 (39%), Gaps = 45/190 (23%)
Query: 208 EDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSL---IAAMANYLCYDVYD---LEL 261
           +++  F      ++R+G    +G LL GPPG+G + L   +A  AN   + +     +EL
Sbjct: 29  KEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGATLLARAVAGEANVPFFHISGSDFVEL 88
Query: 262 TKVTDNSELRALLLQTTNRS--IIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXE 319
                 + +R L  Q    +  I+ I++ID                              
Sbjct: 89  FVGVGAARVRDLFAQAKAHAPCIVFIDEIDA----------------------------- 119
Query: 320 MGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPAL 379
           +G    +   G      G +    TL+ LL   DG  S   E  I++  TN  D +DPAL
Sbjct: 120 VGRHRGAGLGG------GHDEREQTLNQLLVEMDGFDS--KEGIIVMAATNRPDILDPAL 171
Query: 380 IRCGRMDVHV 389
           +R GR D  +
Sbjct: 172 LRPGRFDKKI 181

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 75/191 (39%), Gaps = 47/191 (24%)
Query: 210 LTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN-----YLCYDVYD-LELTK 263
           +  F      +H +G    +G LL GPPG GK+ L  A+A      ++     D +E+  
Sbjct: 31  IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFV 90
Query: 264 VTDNSELRALLLQTTNR---SIIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXEM 320
               + +R  L +T  R    I+ I++ID                              +
Sbjct: 91  GVGAARVRD-LFETAKRHAPCIVFIDEIDA-----------------------------V 120
Query: 321 GSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALI 380
           G +  S   G      G +    TL+ LL   DG     +   +++  TN  D +DPAL+
Sbjct: 121 GRKRGSGVGG------GNDEREQTLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALL 172
Query: 381 RCGRMDVHVSL 391
           R GR D  +++
Sbjct: 173 RPGRFDRQIAI 183

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/181 (24%), Positives = 73/181 (40%), Gaps = 47/181 (25%)
Query: 220 YHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN-----YLCYDVYD-LELTKVTDNSELRAL 273
           +H +G    +G LL GPPG GK+ L  A+A      ++     D +E+      + +R  
Sbjct: 65  FHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRD- 123
Query: 274 LLQTTNR---SIIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTCG 330
           L +T  R    I+ I++ID                              +G +  S   G
Sbjct: 124 LFETAKRHAPCIVFIDEIDA-----------------------------VGRKRGSGVGG 154
Query: 331 XXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVS 390
                 G +    TL+ LL   DG     +   +++  TN  D +DPAL+R GR D  ++
Sbjct: 155 ------GNDEREQTLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQIA 206
Query: 391 L 391
           +
Sbjct: 207 I 207

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 80/180 (44%), Gaps = 44/180 (24%)
Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN-----YLCYDVYD-LELTKVTDNSELR 271
           E + ++G    +G LL GPPG GK+ L  A+A      +L     + +E+      + +R
Sbjct: 29  ERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGLGAARVR 88
Query: 272 ALLLQTTNRS--IIVIEDIDCSVDLTADRMLXXXXXXXXXXXXXXXXXXEMGSRIASSTC 329
           +L  +   R+  I+ I++ID                              +G + +++  
Sbjct: 89  SLFKEARARAPCIVYIDEIDA-----------------------------VGKKRSTTMS 119
Query: 330 GXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHV 389
           G       EE    TL+ LL   DG+ +  ++  I++ +TN  D +D AL+R GR+D HV
Sbjct: 120 GFSNTE--EEQ---TLNQLLVEMDGMGT--TDHVIVLASTNRADILDGALMRPGRLDRHV 172

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 53/221 (23%), Positives = 91/221 (41%), Gaps = 53/221 (23%)
Query: 197 ALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDV 256
           ALE  +++++T  + A     + +  +G     G LL GPPG GK+ L  A+AN    + 
Sbjct: 14  ALE-DIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNF 72
Query: 257 YDLE----LTKVTDNSE--LRALLLQTTNRS--IIVIEDIDCSVDLTADRMLXXXXXXXX 308
             ++    L      SE  +R +  +  N +  +I  +++D      +DR          
Sbjct: 73  ISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDR---------- 122
Query: 309 XXXXXXXXXXEMGSRIASSTCGXXXXXXGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFT 368
                     E G+ +                 RV ++ LL   DGL +   ++  I+  
Sbjct: 123 ----------ETGASV-----------------RV-VNQLLTEMDGLEA--RQQVFIMAA 152
Query: 369 TNHRDSVDPALIRCGRMDVHVSLGTCGP----HAFKVLAKN 405
           TN  D +DPA++R GR+D  + +G   P       K + KN
Sbjct: 153 TNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKN 193

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	530
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-16
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	6e-15
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-04
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	3e-13
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	4e-08
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	6e-08
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	4e-06
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	5e-06
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	6e-06
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	6e-06
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	6e-06
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	3e-05
2qgz_A	308	Helicase loader, putative primosome component; str	6e-05
2chq_A	319	Replication factor C small subunit; DNA-binding pr	8e-05
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	9e-05
2chg_A	226	Replication factor C small subunit; DNA-binding pr	9e-05
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	1e-04
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	1e-04
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	2e-04
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	3e-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 = 81.8 bits (201), Expect = 2e-16
 Identities = 75/484 (15%), Positives = 138/484 (28%), Gaps = 143/484 (29%)

Query: 118 HHVDT------------VQDSVEE-KRSFTLK-LPKRHRQTLLSAYLDHVTSRAEEFERV 163
           HH+D             +    +    +F  K +    +  L    +DH+       + V
Sbjct: 5   HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHII---MSKDAV 61

Query: 164 SRERRLFT---NNGHGSY----------DSGWVSVPFRHPSTFETLALEPQLKKQITEDL 210
           S   RLF    +                +  ++  P +     E        +  I +  
Sbjct: 62  SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT----EQRQPSMMTRMYIEQRD 117

Query: 211 TAFANGKEF--YHRVGRAWK--------------RGYLLYGPPGSGKSSLIAAMAN---- 250
             + + + F  Y+ V R                 +  L+ G  GSGK+ +   +      
Sbjct: 118 RLYNDNQVFAKYN-VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKV 176

Query: 251 --YLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTT 308
              + + ++ L L        +  +L +   +       ID +    +D    SSN    
Sbjct: 177 QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ-------IDPNWTSRSDH---SSNIKL- 225

Query: 309 AKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWS----------C 358
               R  SI+    R+  S    N               LL     + +          C
Sbjct: 226 ----RIHSIQAELRRLLKSKPYEN--------------CLL-VLLNVQNAKAWNAFNLSC 266

Query: 359 CSEEKIIVFTTNHR---DSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHAL 415
               KI++ TT  +   D +  A      +D H S+         +L K YL        
Sbjct: 267 ----KILL-TTRFKQVTDFLSAATTTHISLD-HHSMTLTPDEVKSLLLK-YLDCR----P 315

Query: 416 FDV-VESCIRAGGALTPAQIGEVLLRNRGNV-----DLAMKEVVSAMQAKI--LSGREVM 467
            D+  E           + I E  +R+          +   ++ + +++ +  L   E  
Sbjct: 316 QDLPREVL--TTNPRRLSIIAE-SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372

Query: 468 EC-DELVITRSPESVVVVRSPEN-----WDSSPGGKYGNRSKKRKEGTKANFLVRLRSLT 521
           +  D L +   P S  +   P       W             K       N L +  SL 
Sbjct: 373 KMFDRLSVF--PPSAHI---PTILLSLIW---------FDVIKSDVMVVVNKLHK-YSLV 417

Query: 522 KSDS 525
           +   
Sbjct: 418 EKQP 421

>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 = 61.4 bits (148), Expect = 5e-10
 Identities = 46/308 (14%), Positives = 96/308 (31%), Gaps = 80/308 (25%)

Query: 2   EILSQMWSLLGLLTVLQNVLPSQLLSL---LHSFYESLQDLFSPYSYFEIPEFNGYCGV- 57
            +L  +  LL  +            ++   +HS    L+ L     Y         C + 
Sbjct: 197 TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY---EN----CLLV 249

Query: 58  --DVNDLYRHVNLYLNSVNPAGSSTCRRLTLSRSRSSNRISFTVAPNHTVHDSFSGHSLS 115
             +V +  +  N +  S        C+ L  +R +    ++  ++   T H S   HS++
Sbjct: 250 LLNVQNA-KAWNAFNLS--------CKILLTTRFKQ---VTDFLSAATTTHISLDHHSMT 297

Query: 116 WTHHVDTVQDSVEEKRSFTLK--------LPKRHRQT------LLSAYLDHVTSRAEEFE 161
            T          +E +S  LK        LP+    T      +++  +    +  + ++
Sbjct: 298 LTP---------DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK 348

Query: 162 RVSRERRLFTNNGHGSYDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAF-ANGKEFY 220
            V+ ++   T     S +                  LEP   +++ + L+ F  +     
Sbjct: 349 HVNCDK--LTTIIESSLN-----------------VLEPAEYRKMFDRLSVFPPSAHIPT 389

Query: 221 HRVGRAWKRGYLLYGPPGS-----GKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLL 275
             +   W    ++            K SL+          +  + L          AL  
Sbjct: 390 ILLSLIW--FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL-- 445

Query: 276 QTTNRSII 283
              +RSI+
Sbjct: 446 ---HRSIV 450

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.5 bits (112), Expect = 1e-05
 Identities = 58/317 (18%), Positives = 103/317 (32%), Gaps = 82/317 (25%)

Query: 1   MEILSQMWSLLGLLTVLQNVLPSQLLS---LLHS-FYESLQDLFSPYSYFEIPEFNGYCG 56
             +L + +     L      LP ++L+      S   ES++D  + +  ++         
Sbjct: 304 KSLLLK-Y-----LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK--------H 349

Query: 57  VDVNDLYRHVNLYLNSVNPAGSSTCRRL--TLSRSRSSNRISFTVAPNHTVHDSFSGHSL 114
           V+ + L   +   LN + PA     R++   LS    S  I     P   +       SL
Sbjct: 350 VNCDKLTTIIESSLNVLEPA---EYRKMFDRLSVFPPSAHI-----PTILL-------SL 394

Query: 115 SWTHHV-DTVQDSVEE--KRSFTLKLPKRHRQTLLSAYLDHVTSRAEEFERVSRERRLFT 171
            W   +   V   V +  K S   K PK    ++ S YL+    + +     +  R +  
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLE---LKVKLENEYALHRSIVD 451

Query: 172 N-NGHGSYDSGWVSVPF----------RHPSTFETLALEPQLKKQITEDLTAFANGKEFY 220
           + N   ++DS  +  P+           H    E       L + +  D   F   K   
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIE-HPERMTLFRMVFLDF-RFLEQK--I 507

Query: 221 HRVGRAWK-RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSE-----LRALL 274
                AW   G +L         + +  +  Y  Y         + DN       + A+L
Sbjct: 508 RHDSTAWNASGSIL---------NTLQQLKFYKPY---------ICDNDPKYERLVNAIL 549

Query: 275 --LQTTNRSIIVIEDID 289
             L     ++I  +  D
Sbjct: 550 DFLPKIEENLICSKYTD 566

>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 = 70.6 bits (173), Expect = 3e-13
 Identities = 49/183 (26%), Positives = 72/183 (39%), Gaps = 48/183 (26%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE----LTKVTDNSE--LR 271
             +  +G    RG LLYGPPG+GK+ +  A+AN      + +     ++K+   SE  LR
Sbjct: 228 ALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLR 287

Query: 272 ALLLQTTNR--SIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTC 329
               +      +II I+++D                      KR  +  E+  RI S   
Sbjct: 288 KAFEEAEKNAPAIIFIDELDAIA------------------PKREKTHGEVERRIVSQ-- 327

Query: 330 GNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHV 389
                             LL   DGL        I++  TN  +S+DPAL R GR D  V
Sbjct: 328 ------------------LLTLMDGLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREV 367

Query: 390 SLG 392
            +G
Sbjct: 368 DIG 370

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score = 53.8 bits (130), Expect = 4e-08
 Identities = 50/184 (27%), Positives = 72/184 (39%), Gaps = 57/184 (30%)

Query: 217 KEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSEL------ 270
            E + +VG    +G LLYGPPG+GK+ L  A+A        +    +V   SEL      
Sbjct: 40  PELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET-----NATFIRVV-GSELVKKFIG 93

Query: 271 ------RAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGS 322
                 + +  L +    SII I++ID                          +I     
Sbjct: 94  EGASLVKDIFKLAKEKAPSIIFIDEID--------------------------AIA--AK 125

Query: 323 RIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRC 382
           R  + T G+       E  R TL  LL   DG  +    +  I+  TN  D +DPA++R 
Sbjct: 126 RTDALTGGDR------EVQR-TLMQLLAEMDGFDA--RGDVKIIGATNRPDILDPAILRP 176

Query: 383 GRMD 386
           GR D
Sbjct: 177 GRFD 180

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score = 53.3 bits (128), Expect = 6e-08
 Identities = 27/192 (14%), Positives = 52/192 (27%), Gaps = 53/192 (27%)

Query: 217 KEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSEL------ 270
           K F             ++G  G GKS     +   +      +    ++   EL      
Sbjct: 25  KNFLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKM-----GINPIMMS-AGELESGNAG 78

Query: 271 -----------RALLLQTTNR-SIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIK 318
                       A  +        + I D+D            +  T             
Sbjct: 79  EPAKLIRQRYREAAEIIRKGNMCCLFINDLDA---GAGRMGGTTQYTVNN---------- 125

Query: 319 EMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKI-IVFTTNHRDSVDP 377
               ++ ++T  N  +N                  G+++     ++ I+ T N   ++  
Sbjct: 126 ----QMVNATLMNIADNPTNVQ-----------LPGMYNKQENARVPIIVTGNDFSTLYA 170

Query: 378 ALIRCGRMDVHV 389
            LIR GRM+   
Sbjct: 171 PLIRDGRMEKFY 182

>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 = 47.8 bits (114), Expect = 4e-06
 Identities = 25/171 (14%), Positives = 55/171 (32%), Gaps = 52/171 (30%)

Query: 229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL----ELTKVTDNSELRAL--LLQTTNR-- 280
              LL GPP SGK++L A +A    +    +    ++   ++ ++ +A+  +     +  
Sbjct: 65  VSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQ 124

Query: 281 -SIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE 339
            S +V++DI+                                 R+       +    G  
Sbjct: 125 LSCVVVDDIE---------------------------------RLL------DYVPIGPR 145

Query: 340 SGRVTLSGLLNFTDGLWSCCSEEKIIVF-TTNHRDSVDPALIRCGRMDVHV 389
              + L  LL             K+++  TT+ +D +   +         +
Sbjct: 146 FSNLVLQALLVLLKKAPP--QGRKLLIIGTTSRKDVLQ-EMEMLNAFSTTI 193

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 46.6 bits (111), Expect = 5e-06
 Identities = 21/107 (19%), Positives = 40/107 (37%), Gaps = 15/107 (14%)

Query: 192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
           +   + L    + +       F    E   +      +G  L+G  G GK+ L+AA+AN 
Sbjct: 23  SLSDVDLNDDGRIKAIRFAERFVAEYEPGKK-----MKGLYLHGSFGVGKTYLLAAIANE 77

Query: 252 LC--------YDVYDL--ELTKVTDNSELRALLLQTTNRSIIVIEDI 288
           L           V +L  EL     +  +   L       +++++D+
Sbjct: 78  LAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDL 124

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score = 47.3 bits (113), Expect = 6e-06
 Identities = 46/186 (24%), Positives = 72/186 (38%), Gaps = 54/186 (29%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA-----NYLCYDVYDLELTKVTDNSE--L 270
           E +  +    K G LL+GPPG+GK+ L  A+A      +L      L  +K   + E  +
Sbjct: 45  ELFTGLRAPAK-GLLLFGPPGNGKTLLARAVATECSATFLNISAASL-TSKYVGDGEKLV 102

Query: 271 RAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST 328
           RAL  + +    SII I+++D                                     S 
Sbjct: 103 RALFAVARHMQPSIIFIDEVD-------------------------------------SL 125

Query: 329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVF-TTNHRDSVDPALIRCGRMD- 386
               +++  E S R+  +  L   DGL      ++I+V   TN    +D A +R  R   
Sbjct: 126 LSERSSSEHEASRRL-KTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTK 182

Query: 387 -VHVSL 391
            V+VSL
Sbjct: 183 RVYVSL 188

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score = 47.5 bits (113), Expect = 6e-06
 Identities = 41/185 (22%), Positives = 67/185 (36%), Gaps = 53/185 (28%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA-----NYLCYDVYDLELTKVTDNSE--L 270
           E +  +    + G LL+GPPG+GK+ L  A+A      +       L  +K     E  +
Sbjct: 139 ELFTGLRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASL-TSKYVGEGEKLV 196

Query: 271 RAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST 328
           RAL  + +    SII I+ +D                                     S 
Sbjct: 197 RALFAVARELQPSIIFIDQVD-------------------------------------SL 219

Query: 329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMD-- 386
                    + S R+  +  L   DG+ S   +  +++  TN    +D A++R  R    
Sbjct: 220 LCERREGEHDASRRLK-TEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKR 276

Query: 387 VHVSL 391
           V+VSL
Sbjct: 277 VYVSL 281

>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 = 6e-06
 Identities = 36/185 (19%), Positives = 65/185 (35%), Gaps = 53/185 (28%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA-----NYLCYDVYDLELTKVTDNSE--L 270
           + +  +    K G LL+GPPG+GK+ +   +A      +       L  +K     E  +
Sbjct: 108 DIFTGLRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSL-TSKWVGEGEKMV 165

Query: 271 RAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST 328
           RAL  + +    ++I I++ID                                     S 
Sbjct: 166 RALFAVARCQQPAVIFIDEID-------------------------------------SL 188

Query: 329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMD-- 386
                +   E S R+  +  L   DG  +   +  ++V  TN    +D A  R  R+   
Sbjct: 189 LSQRGDGEHESSRRI-KTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKR 245

Query: 387 VHVSL 391
           +++ L
Sbjct: 246 LYIPL 250

>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 = 45.3 bits (107), Expect = 3e-05
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 201 QLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE 260
           +LK  +     +  N  +   + G    R  +LYGPPG GK++    +A  L YD+  LE
Sbjct: 50  KLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI--LE 107

Query: 261 L 261
            
Sbjct: 108 Q 108

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 44.1 bits (104), Expect = 6e-05
 Identities = 22/108 (20%), Positives = 43/108 (39%), Gaps = 17/108 (15%)

Query: 192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
               + +    + +      AF+   +F  +   A ++G  LYG  G GKS L+AAMA+ 
Sbjct: 122 HLSDIDVNNASRME------AFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE 175

Query: 252 L---------CYDVYDL--ELTKVTDNSELRALLLQTTNRSIIVIEDI 288
           L                  ++     N  ++  +    N  +++++DI
Sbjct: 176 LSEKKGVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDI 223

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score = 43.9 bits (104), Expect = 8e-05
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 16/75 (21%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA 249
           P T + +  + ++ ++    L  +   K   H          L  GPPG+GK++   A+A
Sbjct: 13  PRTLDEVVGQDEVIQR----LKGYVERKNIPH---------LLFSGPPGTGKTATAIALA 59

Query: 250 NYLCYDVYD---LEL 261
             L  + +    +E+
Sbjct: 60  RDLFGENWRDNFIEM 74

>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* Length = 180

 Score = 42.4 bits (100), Expect = 9e-05
 Identities = 23/113 (20%), Positives = 40/113 (35%), Gaps = 18/113 (15%)

Query: 187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIA 246
           + + +  +T    P+   Q      A    + F H       +G    G PG GK+ L  
Sbjct: 4   YWN-ANLDTY--HPKNVSQNR----ALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAV 56

Query: 247 AMANYL---------CYDVYDL--ELTKVTDNSELRALLLQTTNRSIIVIEDI 288
           A    +          +D  DL   L  + D  +    L    N  ++V++D+
Sbjct: 57  ATLKAIYEKKGIRGYFFDTKDLIFRLKHLMDEGKDTKFLKTVLNSPVLVLDDL 109

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score = 43.0 bits (102), Expect = 9e-05
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 16/75 (21%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA 249
           P T + +  + ++ ++    L  +   K   H          L  GPPG+GK++   A+A
Sbjct: 13  PRTLDEVVGQDEVIQR----LKGYVERKNIPH---------LLFSGPPGTGKTATAIALA 59

Query: 250 NYLCYDVYD---LEL 261
             L  + +    +E+
Sbjct: 60  RDLFGENWRDNFIEM 74

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 51/216 (23%), Positives = 84/216 (38%), Gaps = 64/216 (29%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA------NYLCYDVYDLELTKVTDNSE-- 269
             +      W+ G LL+GPPG+GKS L  A+A       +      DL ++K    SE  
Sbjct: 36  HLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDL-VSKWLGESEKL 93

Query: 270 LRAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS 327
           ++ L  L +    SII I++ID                                     S
Sbjct: 94  VKNLFQLARENKPSIIFIDEID-------------------------------------S 116

Query: 328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVF-TTNHRDSVDPALIRCGRMD 386
            CG+ + N  E + R+  +  L    G+      + I+V   TN    +D A+ R  R +
Sbjct: 117 LCGSRSENESEAARRI-KTEFLVQMQGVGV--DNDGILVLGATNIPWVLDSAIRR--RFE 171

Query: 387 --VHVSLGTCGP--HAFKVLAKNYLGIESHHALFDV 418
             +++ L    P  HA   + K +LG  + ++L + 
Sbjct: 172 KRIYIPL----PEPHARAAMFKLHLG-TTQNSLTEA 202

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 17/75 (22%), Positives = 28/75 (37%), Gaps = 16/75 (21%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA 249
           P   + +  +  + K+    L  +       H          L  GPPG GK++   A+A
Sbjct: 21  PQRLDDIVGQEHIVKR----LKHYVKTGSMPH---------LLFAGPPGVGKTTAALALA 67

Query: 250 NYLCYDVYD---LEL 261
             L  + +    LEL
Sbjct: 68  RELFGENWRHNFLEL 82

>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 = 42.6 bits (100), Expect = 2e-04
 Identities = 48/212 (22%), Positives = 81/212 (38%), Gaps = 56/212 (26%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA------NYLCYDVYDLELTKVTDNSE-- 269
             +      W+ G LL+GPPG+GKS L  A+A       +      DL ++K    SE  
Sbjct: 158 HLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDL-VSKWLGESEKL 215

Query: 270 LRAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS 327
           ++ L  L +    SII I++ID                                     S
Sbjct: 216 VKNLFQLARENKPSIIFIDEID-------------------------------------S 238

Query: 328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVF-TTNHRDSVDPALIRCGRMD 386
            CG+ + N  E + R+  +  L    G+      + I+V   TN    +D A+ R  R +
Sbjct: 239 LCGSRSENESEAARRI-KTEFLVQMQGVGV--DNDGILVLGATNIPWVLDSAIRR--RFE 293

Query: 387 VHVSLGTCGPHAFKVLAKNYLGIESHHALFDV 418
             + +     HA   + + +LG  + ++L + 
Sbjct: 294 KRIYIPLPEAHARAAMFRLHLG-STQNSLTEA 324

>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 = 42.3 bits (100), Expect = 3e-04
 Identities = 40/186 (21%), Positives = 67/186 (36%), Gaps = 56/186 (30%)

Query: 218 EFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA-----NYLCYDVYDLELTKVTDNSE--L 270
             +    +    G LLYGPPG+GKS L  A+A      +      DL ++K    SE  +
Sbjct: 42  HLFKGNRKPTS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDL-VSKWMGESEKLV 99

Query: 271 RAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASST 328
           + L  + +    SII I+ +D                                     + 
Sbjct: 100 KQLFAMARENKPSIIFIDQVD-------------------------------------AL 122

Query: 329 CGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVF-TTNHRDSVDPALIRCGRMD- 386
            G       E S R+  + LL   +G+      + ++V   TN    +D A+ R  R + 
Sbjct: 123 TGTRGEGESEASRRI-KTELLVQMNGV--GNDSQGVLVLGATNIPWQLDSAIRR--RFER 177

Query: 387 -VHVSL 391
            +++ L
Sbjct: 178 RIYIPL 183

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	530
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	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
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.97
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.97
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.97
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.97
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.97
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.97
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.96
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.96
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.96
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.96
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.96
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.95
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.95
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.95
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.94
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.94
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.94
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.94
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.93
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.92
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.91
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.82
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.82
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.79
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.78
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.77
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.77
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.75
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.73
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.73
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.72
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.71
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.7
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.7
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.69
3pvs_A	447	Replication-associated recombination protein A; ma	99.68
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.66
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.65
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.65
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.65
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.65
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.64
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.64
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.64
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.63
3bos_A	242	Putative DNA replication factor; P-loop containing	99.63
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.62
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.62
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.61
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.6
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.6
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.59
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.58
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.58
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.57
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.56
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.55
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.55
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.52
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.52
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.5
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.5
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.49
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.49
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.49
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.48
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.41
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.41
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.39
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.35
3co5_A	143	Putative two-component system transcriptional RES	99.34
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.33
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.32
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.31
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.28
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.27
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.09
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	99.09
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.99
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.98
2qgz_A	308	Helicase loader, putative primosome component; str	98.98
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.97
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.87
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.77
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.75
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.73
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.71
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.68
2fna_A	357	Conserved hypothetical protein; structural genomic	98.66
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.62
3f8t_A	506	Predicted ATPase involved in replication control,	98.41
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.41
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.4
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.32
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.27
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.2
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.1
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.84
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.66
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.61
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.56
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.43
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.43
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.42
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.4
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.39
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.38
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.37
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.36
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.35
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.34
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.32
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.26
2krk_A	86	26S protease regulatory subunit 8; structural geno	97.26
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.23
3kw6_A	78	26S protease regulatory subunit 8; structural geno	97.23
1via_A	175	Shikimate kinase; structural genomics, transferase	97.22
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.21
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.2
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.18
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.18
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.15
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.14
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.13
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.13
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.12
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.08
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.07
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.06
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.05
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.01
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.01
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.99
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	96.99
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.98
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.98
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.96
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.96
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.96
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.95
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.94
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.93
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	96.93
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.93
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.92
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	96.92
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	96.91
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.9
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.9
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	96.88
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.87
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.87
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.86
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.86
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.84
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.82
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.78
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.77
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	96.76
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.76
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.72
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	96.71
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.71
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.71
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.7
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.66
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.65
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.64
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.62
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.62
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.6
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.6
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.59
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.58
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.58
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.58
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.58
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.57
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.57
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.54
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.54
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.53
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.53
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.53
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.48
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.47
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.45
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.44
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.42
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.41
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.4
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.29
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.28
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.28
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.23
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.23
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.22
3io5_A	333	Recombination and repair protein; storage dimer, i	96.22
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	96.17
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	96.12
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.09
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.09
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.08
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	96.08
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.08
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.06
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.01
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.98
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.98
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	95.97
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	95.95
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	95.93
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.82
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	95.81
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	95.78
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	95.78
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.78
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.76
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.75
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.73
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	95.67
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.65
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.63
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.63
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.58
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.54
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.54
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	95.54
3b6e_A	216	Interferon-induced helicase C domain-containing P;	95.53
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.48
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.48
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.47
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.46
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.45
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.45
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	95.44
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.43
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	95.43
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.41
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.36
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	95.28
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.22
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	95.21
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.2
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.17
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	95.16
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.15
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.13
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.12
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	95.11
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	95.06
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.06
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.06
2og2_A	359	Putative signal recognition particle receptor; nuc	95.05
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.01
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	95.01
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	94.99
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	94.97
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	94.91
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.91
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	94.9
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	94.85
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	94.82
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	94.81
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.81
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.8
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.76
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	94.75
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	94.73
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	94.69
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.67
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.56
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	94.56
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	94.53
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	94.49
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	94.48
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	94.44
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.41
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.4
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.36
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.34
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.32
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	94.31
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.29
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	94.24
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.23
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	94.2
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	94.2
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	94.12
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.12
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.07
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.06
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	94.06
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	94.05
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	94.04
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	94.04
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.02
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.0
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	93.98
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.95
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	93.94
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	93.93
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.91
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	93.9
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.89
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	93.82
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	93.73
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	93.72
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	93.71
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	93.69
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.66
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	93.64
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	93.62
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.58
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.57
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	93.54
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	93.51
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.48
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.45
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	93.41
2xxa_A	433	Signal recognition particle protein; protein trans	93.41
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.37
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.35
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	93.33
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.29
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.28
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	93.27
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	93.21
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	93.18
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.18
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.15
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.14
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	93.1
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.05
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.03
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	92.99
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	92.97
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	92.95
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	92.93
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	92.93
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	92.9
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	92.89
3ice_A	422	Transcription termination factor RHO; transcriptio	92.75
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	92.74
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.72
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	92.7
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	92.69
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	92.62
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	92.62
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	92.61
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	92.6
2wji_A	165	Ferrous iron transport protein B homolog; membrane	92.59
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	92.58
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	92.55
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	92.55
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	92.53
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	92.5
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	92.5
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.5
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	92.48
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	92.48
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	92.45
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.43
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	92.43
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	92.42
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	92.37
1sgw_A	214	Putative ABC transporter; structural genomics, P p	92.35
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	92.34
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	92.33
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	92.32
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	92.3
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.29
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	92.28
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.25
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	92.24
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	92.21
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	92.2
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	92.18
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	92.17
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	92.16
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	92.12
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	92.07
1g6h_A	257	High-affinity branched-chain amino acid transport	92.05
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.04
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.02
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	91.98
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	91.98
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	91.97
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	91.92
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	91.92
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	91.9
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	91.9
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	91.89
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	91.85
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	91.81
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	91.8
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	91.79
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.76
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	91.75
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	91.71
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.71
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	91.71
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	91.71
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	91.71
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	91.7
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.7
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.7
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	91.68
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	91.66
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	91.65
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	91.64
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	91.58
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	91.58
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	91.57
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	91.56
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	91.52
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	91.5
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	91.5
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	91.47
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	91.47
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	91.46
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	91.46
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.46
2ghi_A	260	Transport protein; multidrug resistance protein, M	91.45
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	91.45
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	91.44
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.41
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	91.41
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	91.41
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	91.37
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	91.37
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	91.36
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	91.35
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.34
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	91.34
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.31
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	91.28
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	91.27
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	91.24
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	91.22
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	91.22
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	91.13
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.13
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	91.12
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	91.1
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	91.09
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	91.08
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	91.08
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	91.05
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	91.02
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	91.01
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	91.0
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	90.99
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	90.95
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	90.93
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	90.93
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	90.91
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	90.89
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	90.89
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	90.88
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	90.87
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	90.86
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	90.84
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	90.84
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	90.79
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	90.78
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	90.71
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	90.7
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	90.7
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	90.69
2hf9_A	226	Probable hydrogenase nickel incorporation protein	90.68
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	90.67
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	90.63
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	90.63
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	90.6
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	90.56
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	90.51
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	90.46
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	90.46
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	90.33
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	90.33
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	90.29
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	90.25
2fh5_B	214	SR-beta, signal recognition particle receptor beta	90.25
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	90.25
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	90.24
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	90.19
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	90.15
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	90.15
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	90.09
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	90.07

>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=1.9e-43  Score=369.12  Aligned_cols=219  Identities=23%  Similarity=0.297  Sum_probs=188.0

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++|+|.+++|++|.+.+..++.+|+.|.++|+++++|+|||||||||||+||+|+|++++.+++.++.+.+
T Consensus       139 ~~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l  218 (405)
T 4b4t_J          139 VEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAEL  218 (405)
T ss_dssp             EECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGG
T ss_pred             ccCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHh
Confidence            44567889999999999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      ++..++.+|..+  .+||||||||||+++..+.+                  .                 ..+
T Consensus       219 ~sk~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~------------------~-----------------~~~  263 (405)
T 4b4t_J          219 VQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVE------------------G-----------------SGG  263 (405)
T ss_dssp             SCSSTTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSC------------------S-----------------SSG
T ss_pred             hccccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCC------------------C-----------------CCC
Confidence            4      356689999876  78999999999998521100                  0                 001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .+.....++++||+.|||+.+  ..+++||+|||+|+.|||||+||||||++|+|++||.++|..||+.++.........
T Consensus       264 ~~~~~~~~l~~lL~~lDg~~~--~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dv  341 (405)
T 4b4t_J          264 GDSEVQRTMLELLNQLDGFET--SKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGI  341 (405)
T ss_dssp             GGGHHHHHHHHHHHHHHTTTC--CCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSC
T ss_pred             CcHHHHHHHHHHHHhhhccCC--CCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccC
Confidence            223456789999999999987  478999999999999999999999999999999999999999999999765433122


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                       .++.++..+.|||+|||.++|..+
T Consensus       342 -dl~~lA~~t~G~SGADi~~l~~eA  365 (405)
T 4b4t_J          342 -NLRKVAEKMNGCSGADVKGVCTEA  365 (405)
T ss_dssp             -CHHHHHHHCCSCCHHHHHHHHHHH
T ss_pred             -CHHHHHHHCCCCCHHHHHHHHHHH
Confidence             377888889999999999999754

>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=6.8e-43  Score=365.95  Aligned_cols=219  Identities=23%  Similarity=0.296  Sum_probs=187.9

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++|+|.+++|++|.+.+..|+.+|++|.++|++|++|+|||||||||||+||+|+|++++.+++.++.+++
T Consensus       173 ~~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s~l  252 (437)
T 4b4t_I          173 MDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSEL  252 (437)
T ss_dssp             EESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESGGG
T ss_pred             eccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHHHh
Confidence            44567889999999999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      ++..++.+|..+  .+||||||||||+++.                  +|...                 ...
T Consensus       253 ~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~------------------~R~~~-----------------~~~  297 (437)
T 4b4t_I          253 IQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGT------------------KRYDS-----------------NSG  297 (437)
T ss_dssp             CCSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSC------------------CCSCS-----------------SCS
T ss_pred             hhccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcc------------------cCCCC-----------------CCC
Confidence            4      345688888866  7899999999999852                  11100                 002


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .+.....++++||+.|||+.+  .++++||+|||+|+.|||||+||||||++|+|++||.++|..||+.|+.........
T Consensus       298 ~~~~~~~~l~~LL~~lDg~~~--~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dv  375 (437)
T 4b4t_I          298 GEREIQRTMLELLNQLDGFDD--RGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDV  375 (437)
T ss_dssp             SCCHHHHHHHHHHHHHHHCCC--SSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCC
T ss_pred             ccHHHHHHHHHHHHHhhCcCC--CCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcC
Confidence            233456789999999999976  578999999999999999999999999999999999999999999999865433122


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                       .++.++..+.|||+|||+++|..+
T Consensus       376 -dl~~LA~~T~GfSGADI~~l~~eA  399 (437)
T 4b4t_I          376 -NLETLVTTKDDLSGADIQAMCTEA  399 (437)
T ss_dssp             -CHHHHHHHCCSCCHHHHHHHHHHH
T ss_pred             -CHHHHHHhCCCCCHHHHHHHHHHH
Confidence             367888889999999999999754

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=4.9e-43  Score=370.87  Aligned_cols=220  Identities=21%  Similarity=0.286  Sum_probs=186.8

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...++.+|++|+|.+++|++|.+.+..|+.+|+.|.++|+++++|+|||||||||||+||+|+|++++.+++.++.+.+
T Consensus       172 ~~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s~l  251 (434)
T 4b4t_M          172 VDEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQL  251 (434)
T ss_dssp             EESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGG
T ss_pred             cCCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehhhh
Confidence            44568889999999999999999999999999999999999999999999999999999999999999999999998887


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      +...++.+|..+  .+||||||||||+++..                  |...                 ...
T Consensus       252 ~~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~------------------R~~~-----------------~~~  296 (434)
T 4b4t_M          252 VQMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTK------------------RFDS-----------------EKS  296 (434)
T ss_dssp             CSSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCC------------------CSSG-----------------GGG
T ss_pred             hhcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhc------------------cCCC-----------------CCC
Confidence            4      345688888766  68999999999998531                  1100                 001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .......+++.||+.|||+.+  .++++||+|||+|+.|||||+||||||++|+|++|+.++|..||+.|+.........
T Consensus       297 ~~~~~~~~~~~lL~~ldg~~~--~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dv  374 (434)
T 4b4t_M          297 GDREVQRTMLELLNQLDGFSS--DDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDI  374 (434)
T ss_dssp             TTHHHHHHHHHHHHHHTTSCS--SCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCC
T ss_pred             CchHHHHHHHHHHHHhhccCC--CCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcC
Confidence            223356788999999999987  478999999999999999999999999999999999999999999998654332111


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                       .++.++..+.|||+|||.++|..+.
T Consensus       375 -dl~~lA~~t~G~sGADi~~l~~eA~  399 (434)
T 4b4t_M          375 -NWQELARSTDEFNGAQLKAVTVEAG  399 (434)
T ss_dssp             -CHHHHHHHCSSCCHHHHHHHHHHHH
T ss_pred             -CHHHHHHhCCCCCHHHHHHHHHHHH
Confidence             2677888899999999999997543

>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=6.9e-42  Score=361.79  Aligned_cols=219  Identities=23%  Similarity=0.312  Sum_probs=187.0

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++|+|.+++|+.|.+.+..|+.+|++|.++|++|++|+|||||||||||+||+|+|++++.+++.++.+.+
T Consensus       163 ~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l  242 (428)
T 4b4t_K          163 ENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEF  242 (428)
T ss_dssp             EESSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGT
T ss_pred             CCCCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchh
Confidence            34567789999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      +...++.+|..+  .+||||||||||+++..                  |...                 ...
T Consensus       243 ~~~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~------------------R~~~-----------------~~~  287 (428)
T 4b4t_K          243 VHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATK------------------RFDA-----------------QTG  287 (428)
T ss_dssp             CCSSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCS------------------CSSS-----------------CSC
T ss_pred             hccccchhHHHHHHHHHHHHHcCCCeeechhhhhhhcc------------------ccCC-----------------CCC
Confidence            3      345688999876  78999999999998521                  1100                 002


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeC-CCCHHHHHHHHHHhhCCcCccch
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLG-TCGPHAFKVLAKNYLGIESHHAL  415 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~-~p~~~~r~~i~~~~l~~~~~~~~  415 (530)
                      .+.....++++||+.|||+.+  ..+++||+|||+|+.|||||+||||||++|+|| +|+.++|..||+.++...... .
T Consensus       288 ~~~~~~r~l~~lL~~ldg~~~--~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~-~  364 (428)
T 4b4t_K          288 SDREVQRILIELLTQMDGFDQ--STNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLA-P  364 (428)
T ss_dssp             CCCHHHHHHHHHHHHHHHSCS--SCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBC-T
T ss_pred             CChHHHHHHHHHHHHhhCCCC--CCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCC-c
Confidence            234456789999999999987  467999999999999999999999999999996 899999999999998654332 1


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          416 FDVVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       416 ~~~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      ...++.++..+.|||+|||.++|..+
T Consensus       365 ~~dl~~lA~~t~G~sgadi~~l~~eA  390 (428)
T 4b4t_K          365 EADLDSLIIRNDSLSGAVIAAIMQEA  390 (428)
T ss_dssp             TCCHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             ccCHHHHHHHCCCCCHHHHHHHHHHH
Confidence            11367888889999999999999754

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.6e-42  Score=362.02  Aligned_cols=218  Identities=23%  Similarity=0.311  Sum_probs=186.5

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT  265 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~  265 (530)
                      ...+..+|++|+|.+++|++|.+.+..++.+|+.|.++|+++++|+|||||||||||+||+|+|++++.+++.++.+.+.
T Consensus       173 ~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s~l~  252 (437)
T 4b4t_L          173 FEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIV  252 (437)
T ss_dssp             EESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGTC
T ss_pred             ccCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehhhhc
Confidence            34678899999999999999999999999999999999999999999999999999999999999999999999988774


Q ss_pred             ------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          266 ------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       266 ------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                            +...++.+|..+  .+||||||||||+++.                  +|...                 ....
T Consensus       253 sk~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~------------------~R~~~-----------------~~~~  297 (437)
T 4b4t_L          253 DKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGG------------------RRFSE-----------------GTSA  297 (437)
T ss_dssp             CSSSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSC------------------CCSSS-----------------CCSS
T ss_pred             cccchHHHHHHHHHHHHHHhcCCceeeeeccccccc------------------ccccC-----------------CCCc
Confidence                  245688888766  7899999999999852                  11100                 0012


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD  417 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~  417 (530)
                      +.....+++.||+.|||+.+  .++++||+|||+|+.|||||+||||||++|+|++||.++|..||+.|+......... 
T Consensus       298 ~~~~~~~l~~lL~~lDg~~~--~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~-  374 (437)
T 4b4t_L          298 DREIQRTLMELLTQMDGFDN--LGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEF-  374 (437)
T ss_dssp             TTHHHHHHHHHHHHHHSSSC--TTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCC-
T ss_pred             chHHHHHHHHHHHHhhcccC--CCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCccc-
Confidence            33456789999999999987  478999999999999999999999999999999999999999999998754433122 


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      .++.++..+.|||+|||.++|..+
T Consensus       375 dl~~lA~~t~G~sGADi~~l~~eA  398 (437)
T 4b4t_L          375 DFEAAVKMSDGFNGADIRNCATEA  398 (437)
T ss_dssp             CHHHHHHTCCSCCHHHHHHHHHHH
T ss_pred             CHHHHHHhCCCCCHHHHHHHHHHH
Confidence            267888889999999999999644

>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=2.2e-41  Score=357.75  Aligned_cols=219  Identities=22%  Similarity=0.234  Sum_probs=187.2

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...+..+|++|+|.+++|++|.+.+..++.+|+.|.++|+++++|+|||||||||||+||+|+|++++.+++.++.+.+
T Consensus       200 v~e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s~L  279 (467)
T 4b4t_H          200 VEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSEL  279 (467)
T ss_dssp             EESSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGGGG
T ss_pred             ecCCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhHHh
Confidence            44567889999999999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      ++..++.+|..+  .+||||||||||+++..                  |...                 ..+
T Consensus       280 ~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~------------------R~~~-----------------~~~  324 (467)
T 4b4t_H          280 VQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGA------------------RFDD-----------------GAG  324 (467)
T ss_dssp             CCCSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBC------------------CSSS-----------------SCG
T ss_pred             hcccCCHHHHHHHHHHHHHHhcCCceEeeccccccccc------------------ccCc-----------------CCC
Confidence            4      345688888876  79999999999998521                  1100                 001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .......+++.||+.|||+.+  .++++||+|||+|+.|||||+||||||++|+|++|+.++|..||+.++.........
T Consensus       325 ~~~~~~~~l~~lL~~lDg~~~--~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dv  402 (467)
T 4b4t_H          325 GDNEVQRTMLELITQLDGFDP--RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGI  402 (467)
T ss_dssp             GGGHHHHHHHHHHHHHHSSCC--TTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSC
T ss_pred             ccHHHHHHHHHHHHHhhccCC--CCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCC
Confidence            223456788999999999976  578999999999999999999999999999999999999999999999865443112


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                       .++.++..+.|||+|||.++|..+
T Consensus       403 -dl~~LA~~T~GfSGADI~~l~~eA  426 (467)
T 4b4t_H          403 -RWELISRLCPNSTGAELRSVCTEA  426 (467)
T ss_dssp             -CHHHHHHHCCSCCHHHHHHHHHHH
T ss_pred             -CHHHHHHHCCCCCHHHHHHHHHHH
Confidence             367788889999999999999654

>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=6.1e-39  Score=361.52  Aligned_cols=278  Identities=18%  Similarity=0.240  Sum_probs=177.7

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc-
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV-  264 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~-  264 (530)
                      ...+..+|++++|.+++|++|.+.+..++.+++.|.+.|..+++|+|||||||||||++|+|+|++++.+++.++.+++ 
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            3456789999999999999999999999999999999999999999999999999999999999999999999987665 


Q ss_pred             -----CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          265 -----TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       265 -----~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                           .++..++++|..+  .+||||||||||+++..++...                                   ...
T Consensus       549 s~~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~-----------------------------------~~~  593 (806)
T 3cf2_A          549 TMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNI-----------------------------------GDG  593 (806)
T ss_dssp             TTTCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC---------------------------------------------
T ss_pred             ccccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCC-----------------------------------CCC
Confidence                 3577899999887  6899999999999863221100                                   012


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD  417 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~  417 (530)
                      +.....++++||++|||+.+  ..+++||+|||+|+.|||||+||||||++|+|++|+.++|..||+.++...... ...
T Consensus       594 ~~~~~rv~~~lL~~mdg~~~--~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~-~~~  670 (806)
T 3cf2_A          594 GGAADRVINQILTEMDGMST--KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDV  670 (806)
T ss_dssp             ----CHHHHHHHHHHHSSCS--SSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--C-CC-
T ss_pred             chHHHHHHHHHHHHHhCCCC--CCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCC-CCC
Confidence            34456789999999999987  467999999999999999999999999999999999999999999999765443 222


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHH--------------------hhhccccccccccccccCC
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQA--------------------KILSGREVMECDELVITRS  477 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~--------------------~~~~~~~~~~~~~~~~~~~  477 (530)
                      .++.++..+.|||+|||.++|..+.   ..|+++.++....                    ..++..++..+...++|+-
T Consensus       671 dl~~la~~t~g~SGadi~~l~~~A~---~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~pSv  747 (806)
T 3cf2_A          671 DLEFLAKMTNGFSGADLTEICQRAC---KLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSV  747 (806)
T ss_dssp             ---------------CHHHHHHHHH---HHHHHHHHC-----------------------CCC----CCTTTC-------
T ss_pred             CHHHHHHhCCCCCHHHHHHHHHHHH---HHHHHHHHHhhhhhhhhhccCccccccccccccCccCHHHHHHHHHhCCCCC
Confidence            4778888899999999999997655   5555554432110                    1245566667766666643


Q ss_pred             CCcccccCCCCcccCCCCCCCCCCccccc
Q 009640          478 PESVVVVRSPENWDSSPGGKYGNRSKKRK  506 (530)
Q Consensus       478 ~~~~~~~~~~~~w~~~~g~~~~~~~~~~~  506 (530)
                        +......+++|....+...|++..+-.
T Consensus       748 --s~~~l~~y~~~~~~f~~~~~~g~~~~~  774 (806)
T 3cf2_A          748 --SDNDIRKYEMFAQTLQQSRGFGSFRFP  774 (806)
T ss_dssp             ----------CCCC---------------
T ss_pred             --CHHHHHHHHHHHHHHhcccCccccccC
Confidence              346677899999887776666554433

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=2.9e-37  Score=347.86  Aligned_cols=266  Identities=21%  Similarity=0.239  Sum_probs=220.1

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC--
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT--  265 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~--  265 (530)
                      .+..+|++|+|.++++++|.+.+..++.+|+.|.++|+.+++|+|||||||||||+||+|+|++++.+++.++..++.  
T Consensus       198 ~~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l~sk  277 (806)
T 3cf2_A          198 LNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK  277 (806)
T ss_dssp             SSSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHHHSS
T ss_pred             CCCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHhhcc
Confidence            456799999999999999999999999999999999999999999999999999999999999999999999976652  


Q ss_pred             ----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          266 ----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       266 ----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                          ++..++.+|..+  .+||||||||||+++..                  |..                    ..+.
T Consensus       278 ~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~------------------r~~--------------------~~~~  319 (806)
T 3cf2_A          278 LAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPK------------------REK--------------------THGE  319 (806)
T ss_dssp             CTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCT------------------TTT--------------------CCCT
T ss_pred             cchHHHHHHHHHHHHHHHcCCeEEEEehhcccccc------------------cCC--------------------CCCh
Confidence                356689999877  68999999999998521                  110                    1234


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ..+.++++||..|||+.+  ..+++||+|||+++.|||||+||||||++|+++.|+.++|.+|++.++...... ....+
T Consensus       320 ~~~riv~~LL~~mdg~~~--~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~-~dvdl  396 (806)
T 3cf2_A          320 VERRIVSQLLTLMDGLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDL  396 (806)
T ss_dssp             THHHHHHHHHTHHHHCCG--GGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEEC-TTCCH
T ss_pred             HHHHHHHHHHHHHhcccc--cCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCC-cccCH
Confidence            467789999999999987  367999999999999999999999999999999999999999999999765443 22237


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHH------------HHHhhhccccccccccccccCCCCcccccCCC
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSA------------MQAKILSGREVMECDELVITRSPESVVVVRSP  487 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~------------l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  487 (530)
                      ..++..+.+|+++||..+|..+.   ..|+++....            +....++..++..+...+.|..........+.
T Consensus       397 ~~lA~~T~GfsgaDL~~Lv~eA~---~~A~~r~~~~i~~~~~~~~~e~~~~~~v~~~Df~~Al~~~~ps~~r~~~~~~p~  473 (806)
T 3cf2_A          397 EQVANETHGHVGADLAALCSEAA---LQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQ  473 (806)
T ss_dssp             HHHHHHCCSCCHHHHHHHHHHHH---HHHHHHHHHHGGGTCCCCSHHHHHHCEECTTHHHHHHSSSSCCCCCCCCCBCCC
T ss_pred             HHHHHhcCCCCHHHHHHHHHHHH---HHHHHhccccccccccccchhhhccceeeHHHHHHHHHhCCCcccccccccCCC
Confidence            78888899999999999997654   4444443322            22334556667777777778877777778889


Q ss_pred             CcccCCCCCC
Q 009640          488 ENWDSSPGGK  497 (530)
Q Consensus       488 ~~w~~~~g~~  497 (530)
                      +.|++++|..
T Consensus       474 v~w~diggl~  483 (806)
T 3cf2_A          474 VTWEDIGGLE  483 (806)
T ss_dssp             CCSTTCCSCH
T ss_pred             CCHHHhCCHH
Confidence            9999998874

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.97  E-value=2e-31  Score=267.63  Aligned_cols=214  Identities=20%  Similarity=0.295  Sum_probs=167.6

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC--
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD--  266 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~--  266 (530)
                      +..+|++|+|.+++|+.|.+.+..++.+++.|..+|...++|+||+||||||||+|+++||++++..++.++...+.+  
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            567899999999999999999999999999999999999999999999999999999999999999999998776632  


Q ss_pred             ----hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          267 ----NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       267 ----~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                          ...++.+|..+  ..|+|+|+||||.+...++.                                      .....
T Consensus        85 ~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~--------------------------------------~~~~~  126 (274)
T 2x8a_A           85 VGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSD--------------------------------------RETGA  126 (274)
T ss_dssp             THHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC-----------------------------------------------
T ss_pred             hhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCC--------------------------------------CcchH
Confidence                23567778764  68999999999987421100                                      00011


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCc-c-chHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESH-H-ALFDV  418 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~-~-~~~~~  418 (530)
                      ....++.+++.|||...  ...++++++||+|+.||||++||||||++|++++|+.++|..|++.++..... . .....
T Consensus       127 ~~~~~~~~l~~Lsgg~~--~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~  204 (274)
T 2x8a_A          127 SVRVVNQLLTEMDGLEA--RQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVN  204 (274)
T ss_dssp             CTTHHHHHHHHHHTCCS--TTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCC
T ss_pred             HHHHHHHHHHhhhcccc--cCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccC
Confidence            23467899999999875  46688999999999999999999999999999999999999999999853211 1 01123


Q ss_pred             HHHHHHh--CCCCCHHHHHHHHHHhc
Q 009640          419 VESCIRA--GGALTPAQIGEVLLRNR  442 (530)
Q Consensus       419 i~~l~~~--~~~~spadi~~~l~~~~  442 (530)
                      ++.++..  +.|||+|||..+|..+.
T Consensus       205 ~~~la~~~~~~g~sgadl~~l~~~a~  230 (274)
T 2x8a_A          205 LEAIAGDLRCDCYTGADLSALVREAS  230 (274)
T ss_dssp             HHHHHTCSGGGSCCHHHHHHHHHHHH
T ss_pred             HHHHHHhhccCCcCHHHHHHHHHHHH
Confidence            5667764  35999999999997554

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.97  E-value=3.6e-31  Score=271.69  Aligned_cols=221  Identities=22%  Similarity=0.246  Sum_probs=181.9

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-CCcEEEEecCccC-
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-CYDVYDLELTKVT-  265 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~~l~l~~~~-  265 (530)
                      .++.+|++|+|.+++|+.|.+.+..++..++.|... ..+++|+|||||||||||+||+++|+++ +.+++.++.+.+. 
T Consensus         6 ~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~-~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~~   84 (322)
T 1xwi_A            6 RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGK-RTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVS   84 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTT-CCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSCC
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCC-CCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHHh
Confidence            467789999999999999999999999999998753 4556899999999999999999999999 8999999887653 


Q ss_pred             -----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          266 -----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       266 -----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                           ....++.+|..+  .+|+||||||||.+...+                  .                    ....
T Consensus        85 ~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~------------------~--------------------~~~~  126 (322)
T 1xwi_A           85 KWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSR------------------S--------------------ENES  126 (322)
T ss_dssp             SSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCS------------------S--------------------SCCT
T ss_pred             hhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhcccc------------------c--------------------cccc
Confidence                 345677887765  689999999999984200                  0                    0122


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV  418 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~  418 (530)
                      ......++.||+.+||+... ..+++||+|||+++.||++|+|  ||+..|++++|+.++|..|++.++...........
T Consensus       127 ~~~~~~~~~ll~~ld~~~~~-~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~  203 (322)
T 1xwi_A          127 EAARRIKTEFLVQMQGVGVD-NDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEAD  203 (322)
T ss_dssp             THHHHHHHHHHHHHHCSSSC-CTTEEEEEEESCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHH
T ss_pred             hHHHHHHHHHHHHHhccccc-CCCEEEEEecCCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHH
Confidence            34566789999999998642 4679999999999999999999  99999999999999999999999976554423456


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHH
Q 009640          419 VESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVV  453 (530)
Q Consensus       419 i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~  453 (530)
                      ++.++..+.|||++||..+|..+.   ..|++.+.
T Consensus       204 l~~la~~t~G~sgadl~~l~~~A~---~~a~r~~~  235 (322)
T 1xwi_A          204 FRELGRKTDGYSGADISIIVRDAL---MQPVRKVQ  235 (322)
T ss_dssp             HHHHHHTCTTCCHHHHHHHHHHHH---THHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHH---HHHHHHHH
Confidence            888999999999999999997654   44454443

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=99.97  E-value=9.9e-31  Score=265.70  Aligned_cols=218  Identities=19%  Similarity=0.292  Sum_probs=179.2

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc--
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV--  264 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~--  264 (530)
                      ..++.+|++|+|.+++++.|.+.+..++..++.|..+|.+.++|+|||||||||||++|+++|++++.+++.++...+  
T Consensus         8 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~~   87 (301)
T 3cf0_A            8 EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLT   87 (301)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHHH
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHHh
Confidence            356778999999999999999999999999999999999999999999999999999999999999999999986654  


Q ss_pred             ----CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          265 ----TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       265 ----~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                          .....++.+|..+  ..|+||||||||.+...++...                                   ....
T Consensus        88 ~~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~-----------------------------------~~~~  132 (301)
T 3cf0_A           88 MWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNI-----------------------------------GDGG  132 (301)
T ss_dssp             HHHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTT-----------------------------------CCSS
T ss_pred             hhcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCc-----------------------------------CCcc
Confidence                2345577788766  5799999999999853111000                                   0112


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV  418 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~  418 (530)
                      ......++.||+.|||+..  ..+++||+|||+++.||++++|||||+..|+++.|+.++|..|++.++...... ....
T Consensus       133 ~~~~~~~~~lL~~l~~~~~--~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~-~~~~  209 (301)
T 3cf0_A          133 GAADRVINQILTEMDGMST--KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVD  209 (301)
T ss_dssp             CSCCHHHHHHHHHHHSSCT--TSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-SSCC
T ss_pred             hHHHHHHHHHHHHhhcccC--CCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCC-ccch
Confidence            2344578899999999865  467999999999999999999999999999999999999999999999754322 1112


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          419 VESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       419 i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ++.++..+.+|+++||.++|.++.
T Consensus       210 ~~~la~~~~g~sg~dl~~l~~~a~  233 (301)
T 3cf0_A          210 LEFLAKMTNGFSGADLTEICQRAC  233 (301)
T ss_dssp             HHHHHHTCSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHH
Confidence            456667789999999999997654

>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=4.3e-31  Score=285.19  Aligned_cols=265  Identities=21%  Similarity=0.248  Sum_probs=200.0

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC---
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT---  265 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~---  265 (530)
                      .+.+|++|+|.+..++.|.+.+..++..++.|..+|.+.++|+|||||||||||++|+++|++++.+++.+++..+.   
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            45689999999999999999999999999999999999999999999999999999999999999999999976542   


Q ss_pred             ---ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          266 ---DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       266 ---~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                         ....++.+|..+  ..|+||||||||.+...                  +.                    ......
T Consensus       279 ~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~------------------~~--------------------~~~~~~  320 (489)
T 3hu3_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPK------------------RE--------------------KTHGEV  320 (489)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBC------------------TT--------------------SCCCHH
T ss_pred             cchhHHHHHHHHHHHHhcCCcEEEecchhhhccc------------------cc--------------------cccchH
Confidence               234577778766  67899999999998420                  00                    012234


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE  420 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~  420 (530)
                      ...+++.||+.||++..  ...++||+|||+++.||++|+|+|||+..|+++.|+.++|..|++.++...... ....+.
T Consensus       321 ~~~~~~~LL~~ld~~~~--~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~-~~~~l~  397 (489)
T 3hu3_A          321 ERRIVSQLLTLMDGLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLE  397 (489)
T ss_dssp             HHHHHHHHHHHHHHSCT--TSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBC-TTCCHH
T ss_pred             HHHHHHHHHHHhhcccc--CCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCc-chhhHH
Confidence            56788999999998865  467999999999999999999999999999999999999999999998754333 222367


Q ss_pred             HHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHH------------HHHHhhhccccccccccccccCCCCcccccCCCC
Q 009640          421 SCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS------------AMQAKILSGREVMECDELVITRSPESVVVVRSPE  488 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~------------~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  488 (530)
                      .++..+.+|+++||..+|..+.   ..|++....            .+....++..++..+...+.|+..+.+....+.+
T Consensus       398 ~la~~t~g~s~~dL~~L~~~A~---~~a~r~~~~~i~~~~~~~~~~~~~~~~vt~edf~~Al~~~~ps~~re~~~e~p~v  474 (489)
T 3hu3_A          398 QVANETHGHVGADLAALCSEAA---LQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQV  474 (489)
T ss_dssp             HHHHTCTTCCHHHHHHHHHHHH---HHHHHTTTTTCCTTCSSCCHHHHHHCCBCHHHHHHHHTSHHHHHHHGGGC-----
T ss_pred             HHHHHccCCcHHHHHHHHHHHH---HHHHHhccccccccccccchhhcccCcCCHHHHHHHHHhCCchhhhcccccCCCC
Confidence            7888899999999999987543   333332211            1223345566677777777777777778889999


Q ss_pred             cccCCCCCC
Q 009640          489 NWDSSPGGK  497 (530)
Q Consensus       489 ~w~~~~g~~  497 (530)
                      .|+|+||-+
T Consensus       475 ~W~dig~~~  483 (489)
T 3hu3_A          475 TWEDIGGRS  483 (489)
T ss_dssp             ---------
T ss_pred             CHHHcCCCc
Confidence            999998864

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=99.97  E-value=4e-31  Score=271.06  Aligned_cols=225  Identities=18%  Similarity=0.200  Sum_probs=183.3

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...++.+|++|+|.+++++.|.+.+..++..++.|...+ ..++|+|||||||||||++|+++|++++.+++.++.+.+
T Consensus         9 ~~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l   87 (322)
T 3eie_A            9 LSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNR-KPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDL   87 (322)
T ss_dssp             EEECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTC-CCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHH
T ss_pred             eecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCC-CCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHH
Confidence            5567888999999999999999999999999999988744 456899999999999999999999999999999987664


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      ....++.+|..+  .+|+||||||||.+...++.                                      .
T Consensus        88 ~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~--------------------------------------~  129 (322)
T 3eie_A           88 VSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGE--------------------------------------G  129 (322)
T ss_dssp             HTTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------------------------------------------
T ss_pred             hhcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCC--------------------------------------C
Confidence            2      234567777665  68999999999998421100                                      1


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      .........+.||+.++++... ..+++||+|||+++.||++|+|  ||+..|++++|+.++|..|++.++.........
T Consensus       130 ~~~~~~~~~~~ll~~l~~~~~~-~~~v~vi~atn~~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~  206 (322)
T 3eie_A          130 ESEASRRIKTELLVQMNGVGND-SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTK  206 (322)
T ss_dssp             --CCTHHHHHHHHHHHGGGGTS-CCCEEEEEEESCGGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCH
T ss_pred             cchHHHHHHHHHHHHhcccccc-CCceEEEEecCChhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCH
Confidence            2234566789999999998643 4679999999999999999999  999999999999999999999999866544344


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHH
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS  454 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~  454 (530)
                      ..++.++..+.+|+++||..+|..+.   ..|++....
T Consensus       207 ~~l~~la~~t~g~sg~di~~l~~~a~---~~a~r~~~~  241 (322)
T 3eie_A          207 EDYRTLGAMTEGYSGSDIAVVVKDAL---MQPIRKIQS  241 (322)
T ss_dssp             HHHHHHHHTTTTCCHHHHHHHHHHHT---THHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHH---HHHHHHHhh
Confidence            56888898899999999999997665   445554443

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=99.97  E-value=2.4e-30  Score=269.02  Aligned_cols=221  Identities=19%  Similarity=0.205  Sum_probs=177.0

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc--
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV--  264 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~--  264 (530)
                      ..++.+|++|+|.+++++.|.+.+..++..++.|.. +...++|+|||||||||||++|+++|++++.+++.++...+  
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            456778999999999999999999999999999987 55667899999999999999999999999999999987654  


Q ss_pred             ----CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          265 ----TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       265 ----~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                          .....++.+|..+  ..|+||||||||.+...+.   .                                   ...
T Consensus       123 ~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~---~-----------------------------------~~~  164 (355)
T 2qp9_X          123 KWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRG---E-----------------------------------GES  164 (355)
T ss_dssp             CC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC--------------------------------------------C
T ss_pred             hhcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCC---C-----------------------------------Ccc
Confidence                1345577777665  5899999999999842100   0                                   122


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHH
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDV  418 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~  418 (530)
                      ......++.||..|||+... ..+++||+|||+++.||++|+|  ||+..|++++|+.++|..|++.++...........
T Consensus       165 ~~~~~~~~~ll~~l~~~~~~-~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~  241 (355)
T 2qp9_X          165 EASRRIKTELLVQMNGVGND-SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKED  241 (355)
T ss_dssp             THHHHHHHHHHHHHHHCC----CCEEEEEEESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHH
T ss_pred             hHHHHHHHHHHHHhhccccc-CCCeEEEeecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHH
Confidence            34566788999999988642 4678999999999999999999  99999999999999999999999986554323456


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHH
Q 009640          419 VESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEV  452 (530)
Q Consensus       419 i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l  452 (530)
                      ++.++..+.||+++||..+|..+.   ..|++..
T Consensus       242 l~~la~~t~G~sg~dl~~l~~~A~---~~a~~~~  272 (355)
T 2qp9_X          242 YRTLGAMTEGYSGSDIAVVVKDAL---MQPIRKI  272 (355)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHH---HHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHH---HHHHHHH
Confidence            788888899999999999997654   4444443

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=99.96  E-value=1.8e-29  Score=269.94  Aligned_cols=223  Identities=21%  Similarity=0.223  Sum_probs=179.2

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-CCcEEEEecCcc
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-CYDVYDLELTKV  264 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~~l~l~~~  264 (530)
                      ...++.+|++|+|.+++++.|.+.+..++..++.|... ..+++|+|||||||||||+||+++|+++ +.+++.++.+.+
T Consensus       126 ~~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~-~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~l  204 (444)
T 2zan_A          126 IERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGK-RTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDL  204 (444)
T ss_dssp             CCCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGG-GCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC--
T ss_pred             ccCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhcc-CCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHHH
Confidence            34577899999999999999999999999999988753 4556899999999999999999999999 899999988765


Q ss_pred             CC------hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 TD------NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~~------~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .+      ...++.+|..+  ..|+||||||||.+...+                  .                    ..
T Consensus       205 ~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~------------------~--------------------~~  246 (444)
T 2zan_A          205 VSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSR------------------S--------------------EN  246 (444)
T ss_dssp             -------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCS------------------S--------------------CC
T ss_pred             HhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCC------------------C--------------------Cc
Confidence            32      23467777654  689999999999984200                  0                    01


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      ........++.||+.|||+... ..+++||+|||+++.|||+|+|  ||+..|++++|+.++|..|++.++.........
T Consensus       247 ~~~~~~~~~~~lL~~l~~~~~~-~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~  323 (444)
T 2zan_A          247 ESEAARRIKTEFLVQMQGVGVD-NDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTE  323 (444)
T ss_dssp             CCGGGHHHHHHHHTTTTCSSCC-CSSCEEEEEESCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCH
T ss_pred             cccHHHHHHHHHHHHHhCcccC-CCCEEEEecCCCccccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCH
Confidence            2334567889999999998642 4679999999999999999999  999999999999999999999999765543234


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHH
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVV  453 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~  453 (530)
                      ..++.++..+.||+++||..+|..+.   ..|++.+.
T Consensus       324 ~~l~~la~~t~G~sgadl~~l~~~a~---~~a~r~~~  357 (444)
T 2zan_A          324 ADFQELGRKTDGYSGADISIIVRDAL---MQPVRKVQ  357 (444)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHH---THHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHH---HHHHHHHH
Confidence            56788888899999999999997654   44555443

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=99.96  E-value=4.1e-29  Score=268.05  Aligned_cols=214  Identities=23%  Similarity=0.318  Sum_probs=174.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC--
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT--  265 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~--  265 (530)
                      .+..+|++|+|.+++++++.+.+ .++..+..|.++|...++|+||+||||||||+|++++|++++.+++.++.+.+.  
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v-~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~~   88 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVV-EFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVEL   88 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHH-HHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTTC
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHH-HHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHHH
Confidence            35668999999999999999865 467788899999999999999999999999999999999999999999987763  


Q ss_pred             ----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          266 ----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       266 ----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                          +...++.+|..+  .+||||||||||.+...++.                  .                 ..+.+.
T Consensus        89 ~~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~------------------~-----------------~~g~~~  133 (476)
T 2ce7_A           89 FVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGA------------------G-----------------LGGGHD  133 (476)
T ss_dssp             CTTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC--------------------------------------------C
T ss_pred             HhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhccc------------------c-----------------cCcCcH
Confidence                235577888776  68999999999998421100                  0                 001234


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ....+++.||+.|||+.+  ..+++||+|||+++.|||+++||||||..|.++.|+.++|..|++.++......... .+
T Consensus       134 ~~~~~l~~LL~~ld~~~~--~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v-~l  210 (476)
T 2ce7_A          134 EREQTLNQLLVEMDGFDS--KEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDV-NL  210 (476)
T ss_dssp             HHHHHHHHHHHHHHHSCG--GGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC-CH
T ss_pred             HHHHHHHHHHHHHhccCC--CCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchh-hH
Confidence            456789999999998865  467999999999999999999999999999999999999999999998754322111 25


Q ss_pred             HHHHHhCCCCCHHHHHHHHHH
Q 009640          420 ESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~  440 (530)
                      ..++..+.|++++||.++|..
T Consensus       211 ~~la~~t~G~sgadL~~lv~~  231 (476)
T 2ce7_A          211 EIIAKRTPGFVGADLENLVNE  231 (476)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHH
T ss_pred             HHHHHhcCCCcHHHHHHHHHH
Confidence            567888999999999998865

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.96  E-value=2e-29  Score=252.71  Aligned_cols=220  Identities=23%  Similarity=0.256  Sum_probs=179.4

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...++.+|++++|.+++++.|.+.+..++..++.|..+|...++++|||||||||||++++++|+.++.+++.++...+
T Consensus         8 ~~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~   87 (285)
T 3h4m_A            8 VDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSEL   87 (285)
T ss_dssp             EESSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGG
T ss_pred             ccCCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHH
Confidence            34456788999999999999999999999999999999999999999999999999999999999999999999988776


Q ss_pred             CC------hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 TD------NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~~------~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      ..      ...+..+|..+  ..|+||||||||.+...+.+                  .                 ...
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~------------------~-----------------~~~  132 (285)
T 3h4m_A           88 VKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTD------------------A-----------------LTG  132 (285)
T ss_dssp             CCCSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSS------------------S-----------------CCG
T ss_pred             HHhccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCcc------------------c-----------------cCC
Confidence            32      23466666654  67899999999998521000                  0                 001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      ........+..+++.++++..  ..+++||+|||.++.||++++|+|||+..|+++.|+.++|..|++.++...... ..
T Consensus       133 ~~~~~~~~l~~ll~~~~~~~~--~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~-~~  209 (285)
T 3h4m_A          133 GDREVQRTLMQLLAEMDGFDA--RGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLA-ED  209 (285)
T ss_dssp             GGGHHHHHHHHHHHHHHTTCS--SSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBC-TT
T ss_pred             ccHHHHHHHHHHHHHhhCCCC--CCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCC-Cc
Confidence            123345678889999988765  467999999999999999999999999999999999999999999998754433 22


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      ..++.++..+.+++++||..++..+.
T Consensus       210 ~~~~~l~~~~~g~~~~~i~~l~~~a~  235 (285)
T 3h4m_A          210 VNLEEIAKMTEGCVGAELKAICTEAG  235 (285)
T ss_dssp             CCHHHHHHHCTTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            23567777789999999999986543

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.96  E-value=2.5e-28  Score=241.63  Aligned_cols=217  Identities=23%  Similarity=0.308  Sum_probs=169.2

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT  265 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~  265 (530)
                      +..++.+|++++|.+++++.+.+.+ .++..++.|.++|...++|+|||||||||||++++++|+.++.+++.++...+.
T Consensus         4 ~~~~~~~~~~i~G~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~~   82 (257)
T 1lv7_A            4 EDQIKTTFADVAGCDEAKEEVAELV-EYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFV   82 (257)
T ss_dssp             ECSSCCCGGGSCSCHHHHHHTHHHH-HHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSST
T ss_pred             ccCCCCCHHHhcCcHHHHHHHHHHH-HHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHHH
Confidence            3456789999999999999998865 557888889999999999999999999999999999999999999999877653


Q ss_pred             ------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          266 ------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       266 ------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                            ....++.+|..+  ..|+|+||||||.+....+                  ..                 ....
T Consensus        83 ~~~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~------------------~~-----------------~~~~  127 (257)
T 1lv7_A           83 EMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG------------------AG-----------------LGGG  127 (257)
T ss_dssp             TSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCS------------------TT-----------------SCCT
T ss_pred             HHhhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCC------------------CC-----------------cCCC
Confidence                  345677788765  5689999999999842000                  00                 0011


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD  417 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~  417 (530)
                      .......+..+|+.+|++..  ...++||+|||+++.+|++++|||||+..|+++.|+.++|..|++.++...... ...
T Consensus       128 ~~~~~~~~~~ll~~l~~~~~--~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~-~~~  204 (257)
T 1lv7_A          128 HDEREQTLNQMLVEMDGFEG--NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDI  204 (257)
T ss_dssp             TCHHHHHHHHHHHHHHTCCS--SSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TTC
T ss_pred             chHHHHHHHHHHHHhhCccc--CCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCC-ccc
Confidence            22334678899999999865  467999999999999999999999999999999999999999999998654322 111


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      .+..++..+.||+++||.+++..+
T Consensus       205 ~~~~la~~~~G~~~~dl~~l~~~a  228 (257)
T 1lv7_A          205 DAAIIARGTPGFSGADLANLVNEA  228 (257)
T ss_dssp             CHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             cHHHHHHHcCCCCHHHHHHHHHHH
Confidence            244566778999999999998654

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=99.96  E-value=5.3e-28  Score=238.76  Aligned_cols=215  Identities=22%  Similarity=0.287  Sum_probs=161.0

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC---
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD---  266 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~---  266 (530)
                      +.+|++++|.+++++.|.+.+. ++..++.|...|.+.++++|||||||||||++|+++|++++.+++.++.+.+..   
T Consensus         2 ~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~   80 (262)
T 2qz4_A            2 GVSFKDVAGMHEAKLEVREFVD-YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIG   80 (262)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHH-HHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSST
T ss_pred             CCCHHHhCCHHHHHHHHHHHHH-HHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhcc
Confidence            5689999999999999988654 578888999999999999999999999999999999999999999999877632   


Q ss_pred             ---hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          267 ---NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       267 ---~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                         ...++.+|..+  ..|+||||||||.+...+....                                  ........
T Consensus        81 ~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~----------------------------------~~~~~~~~  126 (262)
T 2qz4_A           81 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTM----------------------------------SGFSNTEE  126 (262)
T ss_dssp             THHHHHHHHHHHHHHHTCSEEEEEECC-----------------------------------------------------
T ss_pred             ChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccc----------------------------------cCccchhH
Confidence               34566777665  5699999999999842110000                                  00012234


Q ss_pred             hhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH-HHH
Q 009640          342 RVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD-VVE  420 (530)
Q Consensus       342 ~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~-~i~  420 (530)
                      ...+..|++.++++..  ...++||+|||.++.||++++|+|||+..|++++|+.++|..|++.++.........+ .+.
T Consensus       127 ~~~l~~ll~~~~~~~~--~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~  204 (262)
T 2qz4_A          127 EQTLNQLLVEMDGMGT--TDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQ  204 (262)
T ss_dssp             CHHHHHHHHHHHTCCT--TCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHH
T ss_pred             HHHHHHHHHHhhCcCC--CCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHH
Confidence            5678899999998765  4679999999999999999999999999999999999999999999986443331222 346


Q ss_pred             HHHHhCCCCCHHHHHHHHHHh
Q 009640          421 SCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~  441 (530)
                      .++..+.+++++||.+++..+
T Consensus       205 ~l~~~~~g~~~~~l~~l~~~a  225 (262)
T 2qz4_A          205 RLAELTPGFSGADIANICNEA  225 (262)
T ss_dssp             HHHHTCTTCCHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHH
Confidence            777788999999999998754

>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=99.95  E-value=5.7e-28  Score=251.23  Aligned_cols=263  Identities=20%  Similarity=0.245  Sum_probs=194.0

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC-
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD-  266 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~-  266 (530)
                      .++.+|++|+|.+++++.|.+.+..++..++.|...+ ..++++|||||||||||++|+++|++++.+++.++.+.+.. 
T Consensus        78 ~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~  156 (357)
T 3d8b_A           78 GPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSK  156 (357)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-SCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGCCS
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhcc-CCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhhcc
Confidence            3577899999999999999999999999999888776 45689999999999999999999999999999999877632 


Q ss_pred             -----hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          267 -----NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       267 -----~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                           ...++.+|..+  ..|+||||||||.+...+..                                      ....
T Consensus       157 ~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~--------------------------------------~~~~  198 (357)
T 3d8b_A          157 WVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGD--------------------------------------GEHE  198 (357)
T ss_dssp             STTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC--------------------------------------------C
T ss_pred             ccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCC--------------------------------------Ccch
Confidence                 23456666654  67999999999998521000                                      1223


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      .....++.||..++|+.......++||+|||.++.||++++|  ||+..|+++.|+.++|..+++.++.........+.+
T Consensus       199 ~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l  276 (357)
T 3d8b_A          199 SSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEI  276 (357)
T ss_dssp             HHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHH
T ss_pred             HHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHH
Confidence            456678899999999875445678999999999999999999  999999999999999999999988654433234567


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHH-------HHHhhhccccccccccccccCCCCcccccCCCCcccC
Q 009640          420 ESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSA-------MQAKILSGREVMECDELVITRSPESVVVVRSPENWDS  492 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~-------l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~  492 (530)
                      +.++..+.+|+++||..+|..+.   ..+++.+...       .+...++..++..+...+.|+...  .....+++|..
T Consensus       277 ~~la~~t~G~s~~dl~~l~~~a~---~~~ir~l~~~~~~~~~~~~~~~i~~~d~~~al~~~~ps~~~--~~~~~~~~~~~  351 (357)
T 3d8b_A          277 EQIVQQSDAFSGADMTQLCREAS---LGPIRSLQTADIATITPDQVRPIAYIDFENAFRTVRPSVSP--KDLELYENWNK  351 (357)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHHH---THHHHHCCC----------CCCBCHHHHHHHHHHHGGGCCC--CCHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHH---HHHHHHhhhhhhccccccccCCcCHHHHHHHHHhcCCCCCH--HHHHHHHHHHH
Confidence            88888899999999999987544   2233322111       112234445555555555443322  34455678887


Q ss_pred             CCCC
Q 009640          493 SPGG  496 (530)
Q Consensus       493 ~~g~  496 (530)
                      .+|.
T Consensus       352 ~~g~  355 (357)
T 3d8b_A          352 TFGC  355 (357)
T ss_dssp             HHSC
T ss_pred             HhCC
Confidence            7664

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.95  E-value=2.9e-27  Score=238.54  Aligned_cols=266  Identities=17%  Similarity=0.230  Sum_probs=187.9

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...++.+|++++|.+++++.+.+.+..++..++.|..++. .++++|||||||||||++|+++|++++.+++.++.+.+
T Consensus        12 ~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~-~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l   90 (297)
T 3b9p_A           12 VEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRA-PAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASL   90 (297)
T ss_dssp             BCCSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGC-CCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTT
T ss_pred             ccCCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCC-CCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHH
Confidence            34457889999999999999999999999999998887764 45899999999999999999999999999999998765


Q ss_pred             CC------hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 TD------NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~~------~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      ..      ...++.+|..+  ..|+||||||||.+++....                                      .
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~--------------------------------------~  132 (297)
T 3b9p_A           91 TSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSS--------------------------------------S  132 (297)
T ss_dssp             SSSSCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----------------------------------------
T ss_pred             hhcccchHHHHHHHHHHHHHHcCCcEEEeccHHHhcccccc--------------------------------------C
Confidence            32      33455666544  68999999999998531100                                      1


Q ss_pred             CCcchhhhHHHHhhhccCCccC-CCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccch
Q 009640          337 GEESGRVTLSGLLNFTDGLWSC-CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHAL  415 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~-~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~  415 (530)
                      .........+.||..+|++... .+..++||+|||.++.||++++|  ||+..+++++|+.++|..|++.++........
T Consensus       133 ~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~  210 (297)
T 3b9p_A          133 EHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLD  210 (297)
T ss_dssp             --CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSC
T ss_pred             cchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCC
Confidence            1222345677899999987642 13568999999999999999999  99999999999999999999998875443323


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHH-------HhhhccccccccccccccCCCCcccccCCCC
Q 009640          416 FDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQ-------AKILSGREVMECDELVITRSPESVVVVRSPE  488 (530)
Q Consensus       416 ~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  488 (530)
                      ...++.++..+.|++++||..++..+.   ..|++++.....       ...++..++..+...+.|+.  .......++
T Consensus       211 ~~~~~~la~~~~g~~~~~l~~l~~~a~---~~a~r~~~~~~~~~~~~~~~~~i~~~d~~~a~~~~~~s~--~~~~~~~~~  285 (297)
T 3b9p_A          211 TEALRRLAKITDGYSGSDLTALAKDAA---LEPIRELNVEQVKCLDISAMRAITEQDFHSSLKRIRRSV--APQSLNSYE  285 (297)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHT---THHHHTCC--------CCCCCCCCHHHHHHHTTSCCCSS--CHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHH---HHHHHHHhhhhcccccccccCCcCHHHHHHHHHHcCCCC--CHHHHHHHH
Confidence            456778888899999999999987544   223332211110       11233444444444433322  223445667


Q ss_pred             cccCCCCC
Q 009640          489 NWDSSPGG  496 (530)
Q Consensus       489 ~w~~~~g~  496 (530)
                      +|....|.
T Consensus       286 ~~~~~~~~  293 (297)
T 3b9p_A          286 KWSQDYGD  293 (297)
T ss_dssp             HHC-----
T ss_pred             HHHHHhCC
Confidence            78877654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.95  E-value=6.8e-27  Score=252.21  Aligned_cols=214  Identities=21%  Similarity=0.292  Sum_probs=172.7

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC--
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD--  266 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~--  266 (530)
                      ++.+|++|+|.+++++++.+.+ .++..+..|.++|...++|+||+||||||||+|+++||++++.+++.++.+.+..  
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv-~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~  104 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIV-EFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF  104 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHH-HHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSC
T ss_pred             CCCCHHHcCCcHHHHHHHHHHH-HHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhh
Confidence            6789999999999999998855 5577888899999999999999999999999999999999999999999876632  


Q ss_pred             ----hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          267 ----NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       267 ----~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                          ...++.+|..+  ..|+|+||||||.+....+.                                   ........
T Consensus       105 ~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~-----------------------------------~~~~~~~e  149 (499)
T 2dhr_A          105 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGS-----------------------------------GVGGGNDE  149 (499)
T ss_dssp             TTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSS-----------------------------------STTTSSHH
T ss_pred             hhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhcc-----------------------------------CcCCCcHH
Confidence                34577788776  36899999999987310000                                   00011233


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE  420 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~  420 (530)
                      ...+++.||+.|||...  ...+++|++||+|+.|||+|+||||||.+|+++.|+.++|..|++.++...... ....+.
T Consensus       150 ~~~~l~~LL~~Ldg~~~--~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~-~dv~l~  226 (499)
T 2dhr_A          150 REQTLNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-EDVDLA  226 (499)
T ss_dssp             HHHHHHHHHHHGGGCCS--SCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCC-CSSTTH
T ss_pred             HHHHHHHHHHHhccccc--CccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCC-hHHHHH
Confidence            45678999999998875  466899999999999999999999999999999999999999999987643222 111256


Q ss_pred             HHHHhCCCCCHHHHHHHHHHh
Q 009640          421 SCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~  441 (530)
                      .++..+.|++++||.++|..+
T Consensus       227 ~lA~~t~G~~gadL~~lv~~A  247 (499)
T 2dhr_A          227 LLAKRTPGFVGADLENLLNEA  247 (499)
T ss_dssp             HHHTTSCSCCHHHHHHHHHHH
T ss_pred             HHHHhcCCCCHHHHHHHHHHH
Confidence            677789999999999998653

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.94  E-value=4.3e-26  Score=239.57  Aligned_cols=217  Identities=21%  Similarity=0.267  Sum_probs=176.5

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...++.+|++|+|.+.+++.|.+.+..++..++.|..++.+ .+++|||||||||||++|+++|++++.+++.++++.+
T Consensus       106 ~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l  184 (389)
T 3vfd_A          106 VDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAP-ARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASL  184 (389)
T ss_dssp             BCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCC-CSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC
T ss_pred             hccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCC-CceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHh
Confidence            566788999999999999999999999999999999888754 6899999999999999999999999999999998876


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      ....++.+|..+  ..|+||||||||.++.-...                                      .
T Consensus       185 ~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~--------------------------------------~  226 (389)
T 3vfd_A          185 TSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERRE--------------------------------------G  226 (389)
T ss_dssp             -------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------------------------------------------
T ss_pred             hccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCC--------------------------------------c
Confidence            3      234466666654  67899999999998521100                                      1


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      ........+..||..++|+.......++||+|||+++.||++++|  ||+..|+++.|+.++|..|++.++.........
T Consensus       227 ~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~  304 (389)
T 3vfd_A          227 EHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQ  304 (389)
T ss_dssp             --CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCH
T ss_pred             cchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCH
Confidence            223356678899999998876545678999999999999999999  999999999999999999999998765544345


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      +.++.++..+.++++++|..++..+.
T Consensus       305 ~~~~~la~~~~g~~~~~l~~L~~~a~  330 (389)
T 3vfd_A          305 KELAQLARMTDGYSGSDLTALAKDAA  330 (389)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            56788888899999999999986544

>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=99.94  E-value=6.1e-28  Score=239.96  Aligned_cols=217  Identities=24%  Similarity=0.303  Sum_probs=165.9

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC-
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD-  266 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~-  266 (530)
                      .++.+|++++|.+++++.+.+.+. ++..++.|..+|...++|+|||||||||||++|+++|++++.+++.++.+.+.. 
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            456789999999999999988654 588899999999999999999999999999999999999999999888765421 


Q ss_pred             -----hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          267 -----NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       267 -----~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                           ...++.+|..+  ..|+||||||||.+...+....                                  ....+.
T Consensus        84 ~~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~----------------------------------~~~~~~  129 (268)
T 2r62_A           84 FVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGG----------------------------------VVSGND  129 (268)
T ss_dssp             CSSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC--------------------------------------------CC
T ss_pred             hcchHHHHHHHHHHHHHhcCCeEEEEeChhhhcccccccc----------------------------------cCCCch
Confidence                 22344455544  5789999999999842110000                                  001122


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      .....++.||+.+++..+. ...++||+|||.++.||++++|+|||+..|+++.|+.++|..+++.++...... ....+
T Consensus       130 ~~~~~~~~ll~~l~~~~~~-~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-~~~~~  207 (268)
T 2r62_A          130 EREQTLNQLLAEMDGFGSE-NAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLA-NDVNL  207 (268)
T ss_dssp             CSCSSTTTTTTTTTCSSCS-CSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCC-SSCCT
T ss_pred             hHHHHHHHHHHHhhCcccC-CCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCC-CccCH
Confidence            2344677899999987642 455899999999999999999999999999999999999999999998643221 11113


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHh
Q 009640          420 ESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~  441 (530)
                      +.++..+.+++++||.+++..+
T Consensus       208 ~~la~~~~g~~g~dl~~l~~~a  229 (268)
T 2r62_A          208 QEVAKLTAGLAGADLANIINEA  229 (268)
T ss_dssp             TTTTSSSCSSCHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHH
Confidence            4456567899999999988643

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=99.94  E-value=4.3e-26  Score=225.17  Aligned_cols=218  Identities=21%  Similarity=0.262  Sum_probs=168.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +...++.+|++++|.++++.++.+.... +..+..+..++...++|++|+||||||||+|+++||+.++..++.++...+
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            3445677999999999999999886554 567788999999999999999999999999999999999999988875443


Q ss_pred             C------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          265 T------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       265 ~------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .      ....+..+|..+  ..|++++|||||.+.......                                   ...
T Consensus        86 ~~~~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~-----------------------------------~~~  130 (254)
T 1ixz_A           86 VEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSG-----------------------------------VGG  130 (254)
T ss_dssp             HHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC-------------------------------------------
T ss_pred             HHHHhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCcc-----------------------------------ccc
Confidence            1      123466777765  468999999999874211000                                   001


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchH
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALF  416 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~  416 (530)
                      ........++.+++.++|...  ...++++++||+|+.|||+++|+|||+.+|+++.|+.++|..|++.++...... ..
T Consensus       131 ~~~~~~~~~~~ll~~l~g~~~--~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-~~  207 (254)
T 1ixz_A          131 GNDEREQTLNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-ED  207 (254)
T ss_dssp             -CHHHHHHHHHHHHHHHTCCT--TCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC-TT
T ss_pred             cchHHHHHHHHHHHHHhCCCC--CCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCC-cc
Confidence            122334567899999998765  355788899999999999999999999999999999999999999887643322 11


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          417 DVVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       417 ~~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      ..+..++..+.|++++||.++|..+
T Consensus       208 ~~~~~la~~~~G~~~~dl~~~~~~a  232 (254)
T 1ixz_A          208 VDLALLAKRTPGFVGADLENLLNEA  232 (254)
T ss_dssp             CCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             cCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            1255677889999999999999644

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.93  E-value=6.4e-25  Score=220.01  Aligned_cols=217  Identities=21%  Similarity=0.275  Sum_probs=168.0

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT  265 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~  265 (530)
                      ...++.+|++++|.+++++++.+... ++..+..+..++...++|++|+||||||||+|+++||+.++..++.++...+.
T Consensus        32 ~~~~~~~~~~i~g~~~~~~~l~~l~~-~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~~  110 (278)
T 1iy2_A           32 TEAPKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFV  110 (278)
T ss_dssp             CCCCCCCGGGSSSCHHHHHHHHHHHH-HHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHH
T ss_pred             cCCCCCCHHHhCChHHHHHHHHHHHH-HHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHHH
Confidence            34477899999999999999887555 45677888999999999999999999999999999999999999888765431


Q ss_pred             ------ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          266 ------DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       266 ------~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                            ....+..+|..+  ..|++++|||||.+.......                                   ....
T Consensus       111 ~~~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~-----------------------------------~~~~  155 (278)
T 1iy2_A          111 EMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSG-----------------------------------VGGG  155 (278)
T ss_dssp             HSTTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC-------------------------------------------
T ss_pred             HHHhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccc-----------------------------------cCCc
Confidence                  123466677765  468999999999874211000                                   0001


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHH
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFD  417 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~  417 (530)
                      .......+..+++.++|...  ...++++++||+|+.|||+++|+|||+.+|+++.|+.++|..|++.++...... ...
T Consensus       156 ~~~~~~~~~~ll~~lsgg~~--~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-~~~  232 (278)
T 1iy2_A          156 NDEREQTLNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-EDV  232 (278)
T ss_dssp             CHHHHHHHHHHHHHHTTCCT--TCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBC-TTC
T ss_pred             chHHHHHHHHHHHHHhCCCC--CCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCC-ccc
Confidence            12235567889999998764  355788999999999999999999999999999999999999999988643322 111


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          418 VVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       418 ~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      .+..++..+.+++++||.++|..+
T Consensus       233 ~~~~la~~~~G~~~~dl~~l~~~a  256 (278)
T 1iy2_A          233 DLALLAKRTPGFVGADLENLLNEA  256 (278)
T ss_dssp             CHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CHHHHHHHcCCCCHHHHHHHHHHH
Confidence            255677789999999999998644

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.92  E-value=8.4e-26  Score=228.66  Aligned_cols=173  Identities=14%  Similarity=0.065  Sum_probs=124.3

Q ss_pred             hhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC------ChHHHHHHHHhc------CCCeEEEEcCcc
Q 009640          222 RVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT------DNSELRALLLQT------TNRSIIVIEDID  289 (530)
Q Consensus       222 ~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~------~~~~L~~l~~~~------~~~sII~IDeID  289 (530)
                      ..+..+++|+|||||||||||+||+++|++++.+++.++++.+.      ....++.+|..+      ..||||||||||
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            34677789999999999999999999999999999999977653      234466777655      479999999999


Q ss_pred             chhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCcc---------CCC
Q 009640          290 CSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWS---------CCS  360 (530)
Q Consensus       290 ~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s---------~~~  360 (530)
                      ++.+   ++..                                 ........+...+.|++.||+...         ...
T Consensus       110 ~~~~---~~~~---------------------------------~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~  153 (293)
T 3t15_A          110 AGAG---RMGG---------------------------------TTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQEN  153 (293)
T ss_dssp             --------------------------------------------------CHHHHHHHHHHHHHCCC-----------CC
T ss_pred             hhcC---CCCC---------------------------------CccccchHHHHHHHHHHHhccccccccccccccccC
Confidence            9852   0000                                 001122345677899999986541         113


Q ss_pred             CCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHH
Q 009640          361 EEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEV  437 (530)
Q Consensus       361 ~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~  437 (530)
                      .+++||+|||+++.||+||+||||||.+|+  .|+.++|..|++.++......  .+.+..+   +.+|++++|.-+
T Consensus       154 ~~v~vI~ttN~~~~ld~al~R~~R~d~~i~--~P~~~~r~~Il~~~~~~~~~~--~~~l~~~---~~~~~~~~l~~~  223 (293)
T 3t15_A          154 ARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTREDRIGVCTGIFRTDNVP--AEDVVKI---VDNFPGQSIDFF  223 (293)
T ss_dssp             CCCCEEEECSSCCC--CHHHHHHHEEEEEE--CCCHHHHHHHHHHHHGGGCCC--HHHHHHH---HHHSCSCCHHHH
T ss_pred             CCcEEEEecCCcccCCHHHhCCCCCceeEe--CcCHHHHHHHHHHhccCCCCC--HHHHHHH---hCCCCcccHHHH
Confidence            568999999999999999999999999998  479999999999988754433  3334444   467888888643

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.82  E-value=3e-19  Score=183.05  Aligned_cols=199  Identities=14%  Similarity=0.140  Sum_probs=147.3

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..|  .....|.+|++++|.+..++.+...+.......        ....++||+||||||||++|+++|+.++.+++.+
T Consensus        17 ~~~--~~~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~~--------~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~   86 (338)
T 3pfi_A           17 ETY--ETSLRPSNFDGYIGQESIKKNLNVFIAAAKKRN--------ECLDHILFSGPAGLGKTTLANIISYEMSANIKTT   86 (338)
T ss_dssp             --------CCCCSGGGCCSCHHHHHHHHHHHHHHHHTT--------SCCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEE
T ss_pred             hhh--hhccCCCCHHHhCChHHHHHHHHHHHHHHHhcC--------CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEe
Confidence            357  455678899999999999999888877654321        2246899999999999999999999999999999


Q ss_pred             ecCccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          260 ELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       260 ~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                      +...+.....+...+.....+++|||||||.+.                                               
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~-----------------------------------------------  119 (338)
T 3pfi_A           87 AAPMIEKSGDLAAILTNLSEGDILFIDEIHRLS-----------------------------------------------  119 (338)
T ss_dssp             EGGGCCSHHHHHHHHHTCCTTCEEEEETGGGCC-----------------------------------------------
T ss_pred             cchhccchhHHHHHHHhccCCCEEEEechhhcC-----------------------------------------------
Confidence            998888888888999888899999999999872                                               


Q ss_pred             chhhhHHHHhhhccCCcc--------------CCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWS--------------CCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s--------------~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                        ......|+..++...-              .....+++|++||....++++|++  ||+..|+|+.|+.+++..+++.
T Consensus       120 --~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~  195 (338)
T 3pfi_A          120 --PAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSELALILQK  195 (338)
T ss_dssp             --HHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHH
Confidence              1123344444442210              001247899999999999999999  9999999999999999999998


Q ss_pred             hhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009640          406 YLGIESHHALFDVVESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       406 ~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~  440 (530)
                      ++.........+.++.++. ...-.+.++.+++.+
T Consensus       196 ~~~~~~~~~~~~~~~~l~~-~~~G~~r~l~~~l~~  229 (338)
T 3pfi_A          196 AALKLNKTCEEKAALEIAK-RSRSTPRIALRLLKR  229 (338)
T ss_dssp             HHHHTTCEECHHHHHHHHH-TTTTCHHHHHHHHHH
T ss_pred             HHHhcCCCCCHHHHHHHHH-HHCcCHHHHHHHHHH
Confidence            8764433322344555555 334456666666543

>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=99.82  E-value=3.1e-22  Score=214.58  Aligned_cols=215  Identities=10%  Similarity=0.021  Sum_probs=128.5

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC--CcEEEEecCccC
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC--YDVYDLELTKVT  265 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~--~~i~~l~l~~~~  265 (530)
                      .+...|++++|++++++.+...+..+..        |..+++|+|||||||||||++|+++|++++  .+++.++.+.+.
T Consensus        31 ~~~~~~~~iiG~~~~~~~l~~~~~~~~~--------~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~  102 (456)
T 2c9o_A           31 LAKQAASGLVGQENAREACGVIVELIKS--------KKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVY  102 (456)
T ss_dssp             CBCSEETTEESCHHHHHHHHHHHHHHHT--------TCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGC
T ss_pred             ChhhchhhccCHHHHHHHHHHHHHHHHh--------CCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHH
Confidence            3455789999999999988876654432        445668999999999999999999999999  899999987763


Q ss_pred             C-----hHHHHHHHHhc-----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          266 D-----NSELRALLLQT-----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       266 ~-----~~~L~~l~~~~-----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                      +     ...++++|..+     ..||||||||||+++..+......              ...+...++..+...     
T Consensus       103 ~~~~~~~~~~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~--------------~~~~~~~~~~~~l~~-----  163 (456)
T 2c9o_A          103 STEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMG--------------GYGKTISHVIIGLKT-----  163 (456)
T ss_dssp             CSSSCHHHHHHHHHHHTEEEEEEEEEEEEEEEEEEEEEC----------------------------CEEEEEEE-----
T ss_pred             HHhhhhhHHHHHHHHHHHhhhhcCCcEEEEechhhcccccCCCCCC--------------CcchHHHHHHHHHhc-----
Confidence            2     23478888776     579999999999986322110000              000000000000000     


Q ss_pred             CCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeE--EEEeCCCC--HHHHHHHHHHhhCCcC
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDV--HVSLGTCG--PHAFKVLAKNYLGIES  411 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~--~I~~~~p~--~~~r~~i~~~~l~~~~  411 (530)
                      .+........+.++..++......++.++|++|||+++.+|+++.||||||.  .++++.|+  .++|++|++.+.    
T Consensus       164 ~~~~~~~~~~~~ll~~l~~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~----  239 (456)
T 2c9o_A          164 AKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVT----  239 (456)
T ss_dssp             TTEEEEEEECHHHHHHHHHTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEE----
T ss_pred             cccchhHhhhHHHHHHHhhccCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHH----
Confidence            0011112233456666542221224445566899999999999999999999  66677774  466777765432    


Q ss_pred             ccchHHHHHHHHHhCCCCCHHHHHHHHH
Q 009640          412 HHALFDVVESCIRAGGALTPAQIGEVLL  439 (530)
Q Consensus       412 ~~~~~~~i~~l~~~~~~~spadi~~~l~  439 (530)
                          ...++.++..+.|  ++|+..+|.
T Consensus       240 ----~~dl~~~a~~t~g--gadl~~l~~  261 (456)
T 2c9o_A          240 ----LHDLDVANARPQG--GQDILSMMG  261 (456)
T ss_dssp             ----HHHHHHTC----------------
T ss_pred             ----HHHHHHHHHhCCC--hhHHHHHHh
Confidence                1236666666677  889988884

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.79  E-value=3.1e-18  Score=173.03  Aligned_cols=169  Identities=15%  Similarity=0.242  Sum_probs=129.1

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCC---ceEEEECCCCCChhHHHHHHHHHcC-------CcEEEEecCcc
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWK---RGYLLYGPPGSGKSSLIAAMANYLC-------YDVYDLELTKV  264 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~---rG~LL~GPPGTGKTsLa~AiA~~l~-------~~i~~l~l~~~  264 (530)
                      +++|.+++++.|.+.+..+.. +..+.+.|....   .++|||||||||||++|+++|+.++       .+++.++...+
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            689999999999998876653 566666675543   4599999999999999999999983       37888887665


Q ss_pred             CC------hHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          265 TD------NSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       265 ~~------~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                      ..      ...+..+|..+ .++||||||||.++...                                        ...
T Consensus       111 ~~~~~g~~~~~~~~~~~~~-~~~vl~iDEid~l~~~~----------------------------------------~~~  149 (309)
T 3syl_A          111 VGQYIGHTAPKTKEVLKRA-MGGVLFIDEAYYLYRPD----------------------------------------NER  149 (309)
T ss_dssp             CCSSTTCHHHHHHHHHHHH-TTSEEEEETGGGSCCCC-------------------------------------------
T ss_pred             hhhcccccHHHHHHHHHhc-CCCEEEEEChhhhccCC----------------------------------------Ccc
Confidence            32      34466666665 57899999999984200                                        011


Q ss_pred             cchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          339 ESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                      ......+..|++.++..    ...++||+|||.++     .++|+|++  ||+.+|+|+.|+.+++..|++.++....
T Consensus       150 ~~~~~~~~~Ll~~l~~~----~~~~~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~  221 (309)
T 3syl_A          150 DYGQEAIEILLQVMENN----RDDLVVILAGYADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQN  221 (309)
T ss_dssp             CCTHHHHHHHHHHHHHC----TTTCEEEEEECHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTT
T ss_pred             cccHHHHHHHHHHHhcC----CCCEEEEEeCChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcC
Confidence            22455778888888843    35678889998654     36899999  9999999999999999999999986543

>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=99.78  E-value=2.1e-18  Score=175.94  Aligned_cols=198  Identities=17%  Similarity=0.146  Sum_probs=146.3

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..|  +....|.+|++++|++++++.+...+.    .        ...+..||++||||||||++++++|+.++.+++.+
T Consensus        14 ~~~--~~k~rP~~~~~ivg~~~~~~~l~~~l~----~--------~~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i   79 (324)
T 3u61_B           14 HIL--EQKYRPSTIDECILPAFDKETFKSITS----K--------GKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFV   79 (324)
T ss_dssp             SSH--HHHSCCCSTTTSCCCHHHHHHHHHHHH----T--------TCCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEE
T ss_pred             chH--HHhhCCCCHHHHhCcHHHHHHHHHHHH----c--------CCCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEE
Confidence            467  567889999999999998887776554    1        12246789999999999999999999999999999


Q ss_pred             ecCccCChHHHHHHHHhc-------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          260 ELTKVTDNSELRALLLQT-------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       260 ~l~~~~~~~~L~~l~~~~-------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      +.+... ...++..+...       ..+.||||||+|.+.+                                       
T Consensus        80 ~~~~~~-~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~---------------------------------------  119 (324)
T 3u61_B           80 NGSDCK-IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGL---------------------------------------  119 (324)
T ss_dssp             ETTTCC-HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGG---------------------------------------
T ss_pred             cccccC-HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCc---------------------------------------
Confidence            987754 55555544431       2689999999998720                                       


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCc
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESH  412 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~  412 (530)
                               ......|+..++...    ....+|+|||.+..++++|++  |+. .|.|+.|+.+++..|+..++..   
T Consensus       120 ---------~~~~~~L~~~le~~~----~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e~~~il~~~~~~---  180 (324)
T 3u61_B          120 ---------AESQRHLRSFMEAYS----SNCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDEDKIEMMKQMIRR---  180 (324)
T ss_dssp             ---------HHHHHHHHHHHHHHG----GGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHHHHHHHHHHHHH---
T ss_pred             ---------HHHHHHHHHHHHhCC----CCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHH---
Confidence                     112345666665432    456889999999999999999  885 6999999999999888776422   


Q ss_pred             cchHHHHHHH-HHhCCCCCH-HHHHHHHHHhccCHHHHHHHHHHHH
Q 009640          413 HALFDVVESC-IRAGGALTP-AQIGEVLLRNRGNVDLAMKEVVSAM  456 (530)
Q Consensus       413 ~~~~~~i~~l-~~~~~~~sp-adi~~~l~~~~~d~~~al~~l~~~l  456 (530)
                            +... ......+++ ..+..++....+|...++..+....
T Consensus       181 ------l~~~~~~~~~~~~~~~~~~~l~~~~~gd~R~a~~~L~~~~  220 (324)
T 3u61_B          181 ------LTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYS  220 (324)
T ss_dssp             ------HHHHHHHHTCCBSCHHHHHHHHHHTCSCTTHHHHHHHHHG
T ss_pred             ------HHHHHHHcCCCCCcHHHHHHHHHhCCCCHHHHHHHHHHHh
Confidence                  2222 223456666 6677776667778888877776655

>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=99.77  E-value=7.7e-20  Score=193.80  Aligned_cols=163  Identities=15%  Similarity=0.155  Sum_probs=73.2

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcC-CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-------
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGR-AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-------  265 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~-~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-------  265 (530)
                      +.|+|++++|+.|...+..+..++..+..++. .+++++||+||||||||++++++|+.++.+++.++.+.+.       
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            46899999999999888776665555554443 3568999999999999999999999999999999876542       


Q ss_pred             -ChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhh
Q 009640          266 -DNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVT  344 (530)
Q Consensus       266 -~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (530)
                       ....++.+|..+.  .++++||+|.+.+.                                         ........+
T Consensus        95 d~e~~lr~lf~~a~--~~~~~De~d~~~~~-----------------------------------------~~~~~e~rv  131 (444)
T 1g41_A           95 EVDSIIRDLTDSAM--KLVRQQEIAKNRAR-----------------------------------------AEDVAEERI  131 (444)
T ss_dssp             CTHHHHHHHHHHHH--HHHHHHHHHSCC----------------------------------------------------
T ss_pred             cHHHHHHHHHHHHH--hcchhhhhhhhhcc-----------------------------------------chhhHHHHH
Confidence             2455677766542  23447777765210                                         112334678


Q ss_pred             HHHHhhhccCCccCCCCCeEEEEE-eCCCCCCChhhhcCCceeEEEEeCCCCHH-HHHHHH
Q 009640          345 LSGLLNFTDGLWSCCSEEKIIVFT-TNHRDSVDPALIRCGRMDVHVSLGTCGPH-AFKVLA  403 (530)
Q Consensus       345 ls~LLn~lDgl~s~~~~~~ivI~T-TN~~~~LDpALlRpGR~d~~I~~~~p~~~-~r~~i~  403 (530)
                      ++.||+.|||+.+.  .. + +++ ||+++.|||||+||||||++|+++.|+.. .+.+|+
T Consensus       132 l~~LL~~~dg~~~~--~~-v-~a~~TN~~~~ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          132 LDALLPPAKNQWGE--VE-N-HDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             -------------------------------------------------------------
T ss_pred             HHHHHHHhhccccc--cc-c-ccccccCHHHHHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            99999999999763  22 3 444 99999999999999999999999999998 666665

>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=99.77  E-value=1e-17  Score=170.29  Aligned_cols=194  Identities=17%  Similarity=0.158  Sum_probs=143.7

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD  266 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~  266 (530)
                      ..+|.+|++++|.+..++.+...+.......        ....++||+||||||||++|+++|+.++.+++.++...+..
T Consensus         5 ~~~p~~~~~~ig~~~~~~~l~~~l~~~~~~~--------~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~   76 (324)
T 1hqc_A            5 ALRPKTLDEYIGQERLKQKLRVYLEAAKARK--------EPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEK   76 (324)
T ss_dssp             CCCCCSTTTCCSCHHHHHHHHHHHHHHHHHC--------SCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCCS
T ss_pred             ccCcccHHHhhCHHHHHHHHHHHHHHHHccC--------CCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccCC
Confidence            3467799999999999888888776554211        12468999999999999999999999999999999888888


Q ss_pred             hHHHHHHHHh-cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhH
Q 009640          267 NSELRALLLQ-TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTL  345 (530)
Q Consensus       267 ~~~L~~l~~~-~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  345 (530)
                      ..++...|.. ...+++|||||||.+..                                                 ...
T Consensus        77 ~~~l~~~l~~~~~~~~~l~lDEi~~l~~-------------------------------------------------~~~  107 (324)
T 1hqc_A           77 PGDLAAILANSLEEGDILFIDEIHRLSR-------------------------------------------------QAE  107 (324)
T ss_dssp             HHHHHHHHTTTCCTTCEEEETTTTSCCH-------------------------------------------------HHH
T ss_pred             hHHHHHHHHHhccCCCEEEEECCccccc-------------------------------------------------chH
Confidence            8888888887 67889999999998721                                                 112


Q ss_pred             HHHhhhccCCc--------c------CCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          346 SGLLNFTDGLW--------S------CCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       346 s~LLn~lDgl~--------s------~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                      ..|++.++...        .      .....+++|+|||.+..++++|.+  ||+..+.++.|+.+++..++..++....
T Consensus       108 ~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~  185 (324)
T 1hqc_A          108 EHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLG  185 (324)
T ss_dssp             HHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHHHHHHHHHHHhcC
Confidence            23333333211        0      001347899999999999999998  9999999999999999999998875433


Q ss_pred             ccchHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009640          412 HHALFDVVESCIRAGGALTPAQIGEVLLR  440 (530)
Q Consensus       412 ~~~~~~~i~~l~~~~~~~spadi~~~l~~  440 (530)
                      .....+.++.++..+ .-.|.++.+++..
T Consensus       186 ~~~~~~~~~~l~~~~-~G~~r~l~~~l~~  213 (324)
T 1hqc_A          186 VRITEEAALEIGRRS-RGTMRVAKRLFRR  213 (324)
T ss_dssp             CCCCHHHHHHHHHHS-CSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHc-cCCHHHHHHHHHH
Confidence            332234455555543 3456677666654

>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=99.75  E-value=2.8e-17  Score=165.39  Aligned_cols=219  Identities=16%  Similarity=0.192  Sum_probs=142.4

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhh-cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC------
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRV-GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD------  266 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~-g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~------  266 (530)
                      +.++|++++++.|...+............. +...+.++|||||||||||++++++|+.++.+++.++.+.+..      
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            357899999999988887654333222111 1123578999999999999999999999999999998876532      


Q ss_pred             --hHHHHHHHHhc-------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          267 --NSELRALLLQT-------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       267 --~~~L~~l~~~~-------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                        ...+..++...       ..++||||||||.+....                                     .....
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~-------------------------------------~~~~~  137 (310)
T 1ofh_A           95 EVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKG-------------------------------------EYSGA  137 (310)
T ss_dssp             STTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCS-------------------------------------SCCSS
T ss_pred             cHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccc-------------------------------------ccccc
Confidence              23466666543       247999999999973100                                     00001


Q ss_pred             CcchhhhHHHHhhhccCCccC------CCCCeEEEEE----eCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          338 EESGRVTLSGLLNFTDGLWSC------CSEEKIIVFT----TNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~------~~~~~ivI~T----TN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                      +.......+.|+..+++....      ....++||+|    ++.+..++|+|++  ||+.+|+|++|+.+++..|++..+
T Consensus       138 ~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~~~  215 (310)
T 1ofh_A          138 DVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPH  215 (310)
T ss_dssp             HHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSST
T ss_pred             chhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHhhH
Confidence            111223467788888864210      1245778887    5678899999999  999999999999999999998543


Q ss_pred             CCcCccchHHHHHHHHHhC---CCCCHHHHHHHHHHh--------ccCHHHHHHHHHHHH
Q 009640          408 GIESHHALFDVVESCIRAG---GALTPAQIGEVLLRN--------RGNVDLAMKEVVSAM  456 (530)
Q Consensus       408 ~~~~~~~~~~~i~~l~~~~---~~~spadi~~~l~~~--------~~d~~~al~~l~~~l  456 (530)
                      ..     ........+...   ..++++.+..+....        .+++..+.+.+...+
T Consensus       216 ~~-----~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~g~~R~l~~~l~~~~  270 (310)
T 1ofh_A          216 AS-----LTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLM  270 (310)
T ss_dssp             TC-----HHHHHHHHHHHTTCEEEECHHHHHHHHHHHHHHHHHSCCCTTHHHHHHHHHHS
T ss_pred             HH-----HHHHHHHHHHhcCCeeccCHHHHHHHHHHhhhhcccccccCcHHHHHHHHHHH
Confidence            21     222222222211   247777766666544        345555444443333

>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=99.73  E-value=1.1e-16  Score=151.69  Aligned_cols=187  Identities=16%  Similarity=0.195  Sum_probs=131.7

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEE
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDL  259 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l  259 (530)
                      ....+|.+|++++|.++.++.+.+.+..    .         ...++||+||||||||++++++++.+     ...++.+
T Consensus         8 ~~~~~p~~~~~~~g~~~~~~~l~~~l~~----~---------~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~   74 (226)
T 2chg_A            8 VEKYRPRTLDEVVGQDEVIQRLKGYVER----K---------NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEM   74 (226)
T ss_dssp             HHHTSCSSGGGCCSCHHHHHHHHHHHHT----T---------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEE
T ss_pred             HHhcCCCCHHHHcCcHHHHHHHHHHHhC----C---------CCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEe
Confidence            4456788999999998887777665532    1         12359999999999999999999986     4567888


Q ss_pred             ecCccCChHHHHHHHHh--------cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          260 ELTKVTDNSELRALLLQ--------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       260 ~l~~~~~~~~L~~l~~~--------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      +.....+...+...+..        ...+.||||||+|.+..                                      
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~--------------------------------------  116 (226)
T 2chg_A           75 NASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA--------------------------------------  116 (226)
T ss_dssp             ETTCTTCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCH--------------------------------------
T ss_pred             ccccccChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCH--------------------------------------
Confidence            87766555555444332        15689999999998721                                      


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcC
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIES  411 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~  411 (530)
                                 .....|+..++..    ....++|+|||.++.+++++.+  |+. .|+++.|+.++...++..++... 
T Consensus       117 -----------~~~~~l~~~l~~~----~~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~-  177 (226)
T 2chg_A          117 -----------DAQAALRRTMEMY----SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKE-  177 (226)
T ss_dssp             -----------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHH-
T ss_pred             -----------HHHHHHHHHHHhc----CCCCeEEEEeCChhhcCHHHHH--hCc-eeecCCCCHHHHHHHHHHHHHHc-
Confidence                       1234455555532    3467889999999999999999  887 89999999999999888765321 


Q ss_pred             ccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHH
Q 009640          412 HHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSA  455 (530)
Q Consensus       412 ~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~  455 (530)
                                    ...+++..+..+.....+++..+++.+...
T Consensus       178 --------------~~~~~~~~~~~l~~~~~g~~r~l~~~l~~~  207 (226)
T 2chg_A          178 --------------GVKITEDGLEALIYISGGDFRKAINALQGA  207 (226)
T ss_dssp             --------------TCCBCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             --------------CCCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence                          223555555555555556666555544433

>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=99.73  E-value=5.1e-17  Score=161.71  Aligned_cols=198  Identities=13%  Similarity=0.129  Sum_probs=125.1

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc-C--C----
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV-T--D----  266 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~-~--~----  266 (530)
                      ..+.+.....+.+......+.   ......+...++++|||||||||||++|+++|+.++.+++.++.... .  .    
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            345666555555555322221   11222234556899999999999999999999999999999876542 1  1    


Q ss_pred             hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhh
Q 009640          267 NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVT  344 (530)
Q Consensus       267 ~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (530)
                      ...++.+|..+  ..++||||||||.+++...                                       .........
T Consensus       110 ~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~---------------------------------------~~~~~~~~~  150 (272)
T 1d2n_A          110 CQAMKKIFDDAYKSQLSCVVVDDIERLLDYVP---------------------------------------IGPRFSNLV  150 (272)
T ss_dssp             HHHHHHHHHHHHTSSEEEEEECCHHHHTTCBT---------------------------------------TTTBCCHHH
T ss_pred             HHHHHHHHHHHHhcCCcEEEEEChhhhhccCC---------------------------------------CChhHHHHH
Confidence            13466677664  5689999999999852100                                       011223456


Q ss_pred             HHHHhhhccCCccCCCCCeEEEEEeCCCCCCCh-hhhcCCceeEEEEeCCCCH-HHHHHHHHHhhCCcCccchHHHHHHH
Q 009640          345 LSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDP-ALIRCGRMDVHVSLGTCGP-HAFKVLAKNYLGIESHHALFDVVESC  422 (530)
Q Consensus       345 ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDp-ALlRpGR~d~~I~~~~p~~-~~r~~i~~~~l~~~~~~~~~~~i~~l  422 (530)
                      +..|+..+++.... +..++||+|||.++.||+ .+.+  ||+..|++|.++. ++...++......     ..+.+..+
T Consensus       151 l~~L~~~~~~~~~~-~~~~~ii~ttn~~~~l~~~~l~~--rf~~~i~~p~l~~r~~i~~i~~~~~~~-----~~~~~~~l  222 (272)
T 1d2n_A          151 LQALLVLLKKAPPQ-GRKLLIIGTTSRKDVLQEMEMLN--AFSTTIHVPNIATGEQLLEALELLGNF-----KDKERTTI  222 (272)
T ss_dssp             HHHHHHHTTCCCST-TCEEEEEEEESCHHHHHHTTCTT--TSSEEEECCCEEEHHHHHHHHHHHTCS-----CHHHHHHH
T ss_pred             HHHHHHHhcCccCC-CCCEEEEEecCChhhcchhhhhc--ccceEEcCCCccHHHHHHHHHHhcCCC-----CHHHHHHH
Confidence            67777777776432 456789999999999988 4555  9999999987665 5555555442211     12234444


Q ss_pred             HHhCCCC----CHHHHHHHHHHh
Q 009640          423 IRAGGAL----TPAQIGEVLLRN  441 (530)
Q Consensus       423 ~~~~~~~----spadi~~~l~~~  441 (530)
                      +....++    ...++.+++..+
T Consensus       223 ~~~~~g~~~~g~ir~l~~~l~~a  245 (272)
T 1d2n_A          223 AQQVKGKKVWIGIKKLLMLIEMS  245 (272)
T ss_dssp             HHHHTTSEEEECHHHHHHHHHHH
T ss_pred             HHHhcCCCccccHHHHHHHHHHH
Confidence            4444444    445555555543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.72  E-value=2e-16  Score=163.64  Aligned_cols=157  Identities=17%  Similarity=0.187  Sum_probs=109.0

Q ss_pred             CCC-CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC--cEEEEecCccC
Q 009640          189 HPS-TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY--DVYDLELTKVT  265 (530)
Q Consensus       189 ~~~-~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~--~i~~l~l~~~~  265 (530)
                      .|. +|++++|.+..++.+...+.....        |...++++|||||||||||++|+++|+.++.  +++.++...+.
T Consensus        38 ~p~~~~~~ivG~~~~~~~l~~l~~~~~~--------~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  109 (368)
T 3uk6_A           38 EPRQASQGMVGQLAARRAAGVVLEMIRE--------GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIF  109 (368)
T ss_dssp             CBCSEETTEESCHHHHHHHHHHHHHHHT--------TCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGGGS
T ss_pred             CcCcchhhccChHHHHHHHHHHHHHHHc--------CCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchhhh
Confidence            444 499999999998876654443332        2333579999999999999999999999975  56666543210


Q ss_pred             --------------------------------------------------C-----hHHHHHHHHhc-----------CC
Q 009640          266 --------------------------------------------------D-----NSELRALLLQT-----------TN  279 (530)
Q Consensus       266 --------------------------------------------------~-----~~~L~~l~~~~-----------~~  279 (530)
                                                                        .     ...++..+...           ..
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~  189 (368)
T 3uk6_A          110 SLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEII  189 (368)
T ss_dssp             CSSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---C
T ss_pred             hcccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhcccccc
Confidence                                                              1     22344444322           12


Q ss_pred             CeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCC
Q 009640          280 RSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCC  359 (530)
Q Consensus       280 ~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~  359 (530)
                      |+||||||||.+-                                                 ....+.|+..++...   
T Consensus       190 ~~vl~IDEi~~l~-------------------------------------------------~~~~~~L~~~le~~~---  217 (368)
T 3uk6_A          190 PGVLFIDEVHMLD-------------------------------------------------IESFSFLNRALESDM---  217 (368)
T ss_dssp             BCEEEEESGGGSB-------------------------------------------------HHHHHHHHHHTTCTT---
T ss_pred             CceEEEhhccccC-------------------------------------------------hHHHHHHHHHhhCcC---
Confidence            6899999999872                                                 124556777665432   


Q ss_pred             CCCeEEEEEe-----------CCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          360 SEEKIIVFTT-----------NHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       360 ~~~~ivI~TT-----------N~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                       ..+++++|.           |.+..++++|++  ||.. |+|++|+.+++..+++.++..
T Consensus       218 -~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~~~-i~~~~~~~~e~~~il~~~~~~  274 (368)
T 3uk6_A          218 -APVLIMATNRGITRIRGTSYQSPHGIPIDLLD--RLLI-VSTTPYSEKDTKQILRIRCEE  274 (368)
T ss_dssp             -CCEEEEEESCSEEECBTSSCEEETTCCHHHHT--TEEE-EEECCCCHHHHHHHHHHHHHH
T ss_pred             -CCeeeeecccceeeeeccCCCCcccCCHHHHh--hccE-EEecCCCHHHHHHHHHHHHHH
Confidence             234433333           358899999999  9977 899999999999999987654

>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=99.71  E-value=7.1e-16  Score=147.75  Aligned_cols=158  Identities=18%  Similarity=0.286  Sum_probs=117.7

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------  254 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------  254 (530)
                      .|  .....|..|++++|.+...+.+...+..           + ..+..+||+||||||||++++++++.+..      
T Consensus        12 ~~--~~~~~p~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~   77 (250)
T 1njg_A           12 VL--ARKWRPQTFADVVGQEHVLTALANGLSL-----------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA   77 (250)
T ss_dssp             CH--HHHTCCCSGGGCCSCHHHHHHHHHHHHH-----------T-CCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCS
T ss_pred             HH--hhccCCccHHHHhCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            45  3456788899999999888877776542           1 11357999999999999999999998743      


Q ss_pred             ------------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccc
Q 009640          255 ------------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAK  310 (530)
Q Consensus       255 ------------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~  310 (530)
                                        +++.++.........++.++...      ..+.||||||+|.+-                  
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~------------------  139 (250)
T 1njg_A           78 TPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS------------------  139 (250)
T ss_dssp             SCCSCSHHHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC------------------
T ss_pred             CCCcccHHHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECccccc------------------
Confidence                              34555444333445567777654      257899999999861                  


Q ss_pred             cccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEE
Q 009640          311 TKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVS  390 (530)
Q Consensus       311 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~  390 (530)
                                                     ...+..|+..++..    ....++|+|||.++.+++++.+  |+ ..|+
T Consensus       140 -------------------------------~~~~~~l~~~l~~~----~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~  181 (250)
T 1njg_A          140 -------------------------------RHSFNALLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFH  181 (250)
T ss_dssp             -------------------------------HHHHHHHHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--TS-EEEE
T ss_pred             -------------------------------HHHHHHHHHHHhcC----CCceEEEEEeCChHhCCHHHHH--Hh-hhcc
Confidence                                           12345667776643    3568899999999999999998  64 6899


Q ss_pred             eCCCCHHHHHHHHHHhhC
Q 009640          391 LGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       391 ~~~p~~~~r~~i~~~~l~  408 (530)
                      ++.++.++...++..++.
T Consensus       182 l~~l~~~e~~~~l~~~~~  199 (250)
T 1njg_A          182 LKALDVEQIRHQLEHILN  199 (250)
T ss_dssp             CCCCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            999999999999988764

>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=1.7e-16  Score=172.50  Aligned_cols=172  Identities=19%  Similarity=0.312  Sum_probs=120.1

Q ss_pred             CCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcC-hhhHhhhcC---CCCceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          179 DSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANG-KEFYHRVGR---AWKRGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       179 ~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~-~~~y~~~g~---~~~rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      ...|  +..+.|.+|++++|.++.++.|...+..+... +..|...|.   +..+++||+||||||||++|+++|+++++
T Consensus        26 ~~lW--~ekyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~  103 (516)
T 1sxj_A           26 DKLW--TVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY  103 (516)
T ss_dssp             CCCH--HHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCCc--ccccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            3468  56688999999999999999988888765432 233333333   35689999999999999999999999999


Q ss_pred             cEEEEecCccCChHHHHHHHH-------------h-------cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          255 DVYDLELTKVTDNSELRALLL-------------Q-------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       255 ~i~~l~l~~~~~~~~L~~l~~-------------~-------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                      +++.++.+.......+...+.             .       ...++||||||+|.+..                     
T Consensus       104 ~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~---------------------  162 (516)
T 1sxj_A          104 DILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSG---------------------  162 (516)
T ss_dssp             EEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCT---------------------
T ss_pred             CEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccch---------------------
Confidence            999999888766544433322             1       14689999999998731                     


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCC--CCCCChhhhcCCceeEEEEeC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNH--RDSVDPALIRCGRMDVHVSLG  392 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~--~~~LDpALlRpGR~d~~I~~~  392 (530)
                                            .   .+..+..|++.++..      +..||++||.  ...++ ++.   |+...|.|+
T Consensus       163 ----------------------~---~~~~l~~L~~~l~~~------~~~iIli~~~~~~~~l~-~l~---~r~~~i~f~  207 (516)
T 1sxj_A          163 ----------------------G---DRGGVGQLAQFCRKT------STPLILICNERNLPKMR-PFD---RVCLDIQFR  207 (516)
T ss_dssp             ----------------------T---STTHHHHHHHHHHHC------SSCEEEEESCTTSSTTG-GGT---TTSEEEECC
T ss_pred             ----------------------h---hHHHHHHHHHHHHhc------CCCEEEEEcCCCCccch-hhH---hceEEEEeC
Confidence                                  0   112345566666521      1224444443  33443 343   445689999


Q ss_pred             CCCHHHHHHHHHHhhC
Q 009640          393 TCGPHAFKVLAKNYLG  408 (530)
Q Consensus       393 ~p~~~~r~~i~~~~l~  408 (530)
                      .|+.+++..++...+.
T Consensus       208 ~~~~~~~~~~L~~i~~  223 (516)
T 1sxj_A          208 RPDANSIKSRLMTIAI  223 (516)
T ss_dssp             CCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999998877653

>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=99.70  E-value=4.5e-16  Score=170.18  Aligned_cols=161  Identities=20%  Similarity=0.186  Sum_probs=113.5

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChH---
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS---  268 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~---  268 (530)
                      ..+++.|.+++++.+.+.+.....+...       ....+||+||||||||+|+++||+.++.++..+++..+....   
T Consensus        79 l~~di~G~~~vk~~i~~~~~l~~~~~~~-------~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~  151 (543)
T 3m6a_A           79 LDEEHHGLEKVKERILEYLAVQKLTKSL-------KGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIR  151 (543)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHHHHSSSC-------CSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC--------
T ss_pred             HHHHhccHHHHHHHHHHHHHHHHhcccC-------CCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhh
Confidence            3466899999998887655433222211       245799999999999999999999999999999877653322   


Q ss_pred             ------------HHHHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCC
Q 009640          269 ------------ELRALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNN  335 (530)
Q Consensus       269 ------------~L~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~  335 (530)
                                  .+...|..+ ....||||||||.+...                                         
T Consensus       152 g~~~~~ig~~~~~~~~~~~~a~~~~~vl~lDEid~l~~~-----------------------------------------  190 (543)
T 3m6a_A          152 GHRRTYVGAMPGRIIQGMKKAGKLNPVFLLDEIDKMSSD-----------------------------------------  190 (543)
T ss_dssp             ------------CHHHHHHTTCSSSEEEEEEESSSCC-------------------------------------------
T ss_pred             hHHHHHhccCchHHHHHHHHhhccCCEEEEhhhhhhhhh-----------------------------------------
Confidence                        233445555 24459999999997310                                         


Q ss_pred             CCCcchhhhHHHHhhhccCCccC-----------CCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          336 NGEESGRVTLSGLLNFTDGLWSC-----------CSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       336 ~~~~~~~~~ls~LLn~lDgl~s~-----------~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                          ......+.||..||.....           .-..++||+|||.++.|||+|++  ||+ .|+|+.|+.+++..|++
T Consensus       191 ----~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~  263 (543)
T 3m6a_A          191 ----FRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRD--RME-IINIAGYTEIEKLEIVK  263 (543)
T ss_dssp             -----------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHH--HEE-EEECCCCCHHHHHHHHH
T ss_pred             ----hccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHh--hcc-eeeeCCCCHHHHHHHHH
Confidence                0011345577777643311           01457899999999999999999  996 69999999999999999


Q ss_pred             Hhh
Q 009640          405 NYL  407 (530)
Q Consensus       405 ~~l  407 (530)
                      .++
T Consensus       264 ~~l  266 (543)
T 3m6a_A          264 DHL  266 (543)
T ss_dssp             HTH
T ss_pred             HHH
Confidence            987

>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=2.6e-16  Score=158.81  Aligned_cols=158  Identities=15%  Similarity=0.187  Sum_probs=116.4

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCc
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYD  255 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~  255 (530)
                      .|  +..+.|.+|++++|.++.++.+...+.    .       |.  ..+||||||||||||++++++|+.+     +.+
T Consensus         6 ~~--~~k~~p~~~~~~~g~~~~~~~l~~~l~----~-------~~--~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~   70 (319)
T 2chq_A            6 IW--VEKYRPRTLDEVVGQDEVIQRLKGYVE----R-------KN--IPHLLFSGPPGTGKTATAIALARDLFGENWRDN   70 (319)
T ss_dssp             CT--TTTTSCSSGGGSCSCHHHHHHHHTTTT----T-------TC--CCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHH
T ss_pred             cH--HHhcCCCCHHHHhCCHHHHHHHHHHHh----C-------CC--CCeEEEECcCCcCHHHHHHHHHHHhcCCcccCC
Confidence            56  667889999999999988776665442    2       11  2349999999999999999999987     445


Q ss_pred             EEEEecCccCChHHHHHH---HH-hc----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccc
Q 009640          256 VYDLELTKVTDNSELRAL---LL-QT----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS  327 (530)
Q Consensus       256 i~~l~l~~~~~~~~L~~l---~~-~~----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  327 (530)
                      ++.++.+...+...++..   +. ..    ..+.||+|||+|.+.                                   
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~-----------------------------------  115 (319)
T 2chq_A           71 FIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALT-----------------------------------  115 (319)
T ss_dssp             CEEEETTSTTCTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSC-----------------------------------
T ss_pred             eEEEeCccccChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCC-----------------------------------
Confidence            778877655332222222   22 11    358999999999872                                   


Q ss_pred             cCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       328 ~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                                    ......|+..++..    ....++|++||.+..+++++.+  |+. .|.|+.|+.+++..++..++
T Consensus       116 --------------~~~~~~L~~~le~~----~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~  174 (319)
T 2chq_A          116 --------------ADAQAALRRTMEMY----SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEIC  174 (319)
T ss_dssp             --------------HHHHHTTGGGTSSS----SSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHHHHHhc----CCCCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHHHHHHHHHHH
Confidence                          11234567777643    3567899999999999999999  775 79999999999999988776


Q ss_pred             CC
Q 009640          408 GI  409 (530)
Q Consensus       408 ~~  409 (530)
                      ..
T Consensus       175 ~~  176 (319)
T 2chq_A          175 EK  176 (319)
T ss_dssp             HT
T ss_pred             HH
Confidence            43

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.68  E-value=6.5e-16  Score=164.95  Aligned_cols=194  Identities=15%  Similarity=0.217  Sum_probs=136.2

Q ss_pred             CCCCCCCcccccCChhhh---HHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecC
Q 009640          186 PFRHPSTFETLALEPQLK---KQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT  262 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k---~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~  262 (530)
                      ....|.+|++++|++++.   ..+...+..    .       .  ..++|||||||||||+++++||+.++.+++.++..
T Consensus        18 ~r~rP~~l~~ivGq~~~~~~~~~L~~~i~~----~-------~--~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~   84 (447)
T 3pvs_A           18 ARMRPENLAQYIGQQHLLAAGKPLPRAIEA----G-------H--LHSMILWGPPGTGKTTLAEVIARYANADVERISAV   84 (447)
T ss_dssp             HHTCCCSTTTCCSCHHHHSTTSHHHHHHHH----T-------C--CCEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETT
T ss_pred             HHhCCCCHHHhCCcHHHHhchHHHHHHHHc----C-------C--CcEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEec
Confidence            346788999999999877   444444432    1       1  25899999999999999999999999999999876


Q ss_pred             ccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          263 KVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       263 ~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                      .. +..+++.++..+      ..++||||||||.+..                                           
T Consensus        85 ~~-~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~-------------------------------------------  120 (447)
T 3pvs_A           85 TS-GVKEIREAIERARQNRNAGRRTILFVDEVHRFNK-------------------------------------------  120 (447)
T ss_dssp             TC-CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC---------------------------------------------
T ss_pred             cC-CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCH-------------------------------------------
Confidence            53 445666666543      4689999999998720                                           


Q ss_pred             CCcchhhhHHHHhhhccCCccCCCCCeEEEEEe--CCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccc
Q 009640          337 GEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTT--NHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHA  414 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TT--N~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~  414 (530)
                            .....||..++.      ..+++|++|  |....++++|++  |+. .+.|+.|+.+++..++..++...... 
T Consensus       121 ------~~q~~LL~~le~------~~v~lI~att~n~~~~l~~aL~s--R~~-v~~l~~l~~edi~~il~~~l~~~~~~-  184 (447)
T 3pvs_A          121 ------SQQDAFLPHIED------GTITFIGATTENPSFELNSALLS--RAR-VYLLKSLSTEDIEQVLTQAMEDKTRG-  184 (447)
T ss_dssp             ----------CCHHHHHT------TSCEEEEEESSCGGGSSCHHHHT--TEE-EEECCCCCHHHHHHHHHHHHHCTTTS-
T ss_pred             ------HHHHHHHHHHhc------CceEEEecCCCCcccccCHHHhC--cee-EEeeCCcCHHHHHHHHHHHHHHHhhh-
Confidence                  012346666653      345666655  455689999999  876 57899999999999999887642211 


Q ss_pred             hHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHHHh
Q 009640          415 LFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAK  459 (530)
Q Consensus       415 ~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~~~  459 (530)
                      .       -.....+++..+..++....+|+..++..+..+....
T Consensus       185 ~-------~~~~~~i~~~al~~L~~~~~Gd~R~lln~Le~a~~~a  222 (447)
T 3pvs_A          185 Y-------GGQDIVLPDETRRAIAELVNGDARRALNTLEMMADMA  222 (447)
T ss_dssp             S-------TTSSEECCHHHHHHHHHHHCSCHHHHHHHHHHHHHHS
T ss_pred             h-------ccccCcCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhc
Confidence            0       0012346777777676667778877777666655443

>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=1.4e-15  Score=153.94  Aligned_cols=158  Identities=15%  Similarity=0.231  Sum_probs=115.6

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----Cc
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----YD  255 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----~~  255 (530)
                      +|  +..+.|.+|++++|.++.++.+...+..           |.  ..++|||||||||||++++++|+.+.     ..
T Consensus        14 ~~--~~k~~p~~~~~~~g~~~~~~~l~~~l~~-----------~~--~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~   78 (327)
T 1iqp_A           14 PW--VEKYRPQRLDDIVGQEHIVKRLKHYVKT-----------GS--MPHLLFAGPPGVGKTTAALALARELFGENWRHN   78 (327)
T ss_dssp             CH--HHHTCCCSTTTCCSCHHHHHHHHHHHHH-----------TC--CCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHH
T ss_pred             ch--hhccCCCCHHHhhCCHHHHHHHHHHHHc-----------CC--CCeEEEECcCCCCHHHHHHHHHHHhcCCcccCc
Confidence            67  5567899999999999988877765542           11  23599999999999999999999863     34


Q ss_pred             EEEEecCccCChHHHHHHHH---h-c----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccc
Q 009640          256 VYDLELTKVTDNSELRALLL---Q-T----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS  327 (530)
Q Consensus       256 i~~l~l~~~~~~~~L~~l~~---~-~----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  327 (530)
                      ++.++.+...+...++..+.   . .    ..+.||+|||+|.+.                                   
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~-----------------------------------  123 (327)
T 1iqp_A           79 FLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALT-----------------------------------  123 (327)
T ss_dssp             EEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSC-----------------------------------
T ss_pred             eEEeeccccCchHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCC-----------------------------------
Confidence            67777655322222222221   1 1    458899999999872                                   


Q ss_pred             cCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       328 ~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                                    ....+.|+..++..    ....++|+|||.++.+++++.+  |+. .+.|++++.++...++..++
T Consensus       124 --------------~~~~~~L~~~le~~----~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l~~~~~~~~l~~~~  182 (327)
T 1iqp_A          124 --------------QDAQQALRRTMEMF----SSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIA  182 (327)
T ss_dssp             --------------HHHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHHHHHhc----CCCCeEEEEeCCccccCHHHHh--hCc-EEEecCCCHHHHHHHHHHHH
Confidence                          11345566666532    3457888999999999999998  876 79999999999999888776


Q ss_pred             CC
Q 009640          408 GI  409 (530)
Q Consensus       408 ~~  409 (530)
                      ..
T Consensus       183 ~~  184 (327)
T 1iqp_A          183 EN  184 (327)
T ss_dssp             HT
T ss_pred             Hh
Confidence            43

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.65  E-value=2.4e-16  Score=145.92  Aligned_cols=152  Identities=17%  Similarity=0.204  Sum_probs=105.1

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEE
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYD  258 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~  258 (530)
                      .+..|++++|.++..+.+.+.+..             ..++++||+||||||||++++++|+.+          +.+++.
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            456789999988877666654321             224689999999999999999999997          678888


Q ss_pred             EecCccC----C----hHHHHHHHH---hcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccc
Q 009640          259 LELTKVT----D----NSELRALLL---QTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS  327 (530)
Q Consensus       259 l~l~~~~----~----~~~L~~l~~---~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  327 (530)
                      +++....    .    ...+..++.   ....++||+|||+|.+.+...                               
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~-------------------------------  132 (195)
T 1jbk_A           84 LDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGK-------------------------------  132 (195)
T ss_dssp             ECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT----------------------------------
T ss_pred             eeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCc-------------------------------
Confidence            8765432    1    123444544   346789999999999842100                               


Q ss_pred             cCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHH
Q 009640          328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVL  402 (530)
Q Consensus       328 ~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i  402 (530)
                                ..........|...++      ..++.+|+|||.++     .+|++|++  ||+ .|+++.|+.+++.+|
T Consensus       133 ----------~~~~~~~~~~l~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~i  193 (195)
T 1jbk_A          133 ----------ADGAMDAGNMLKPALA------RGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAI  193 (195)
T ss_dssp             -------------CCCCHHHHHHHHH------TTSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTT
T ss_pred             ----------ccchHHHHHHHHHhhc------cCCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHH
Confidence                      0001112223333332      24567888888876     78999999  998 699999999999877


Q ss_pred             H
Q 009640          403 A  403 (530)
Q Consensus       403 ~  403 (530)
                      +
T Consensus       194 l  194 (195)
T 1jbk_A          194 L  194 (195)
T ss_dssp             C
T ss_pred             h
Confidence            5

>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=2.1e-15  Score=152.40  Aligned_cols=188  Identities=13%  Similarity=0.218  Sum_probs=130.0

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CC
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CY  254 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~  254 (530)
                      ..|  .....|.+|++++|.++.++.+...+.    .       |.  ...+|||||||||||++++++|+.+     +.
T Consensus         9 ~~~--~~~~~p~~~~~~~g~~~~~~~l~~~l~----~-------~~--~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~   73 (323)
T 1sxj_B            9 LPW--VEKYRPQVLSDIVGNKETIDRLQQIAK----D-------GN--MPHMIISGMPGIGKTTSVHCLAHELLGRSYAD   73 (323)
T ss_dssp             CCH--HHHTCCSSGGGCCSCTHHHHHHHHHHH----S-------CC--CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHH
T ss_pred             CcH--HHhcCCCCHHHHHCCHHHHHHHHHHHH----c-------CC--CCeEEEECcCCCCHHHHHHHHHHHhcCCcccC
Confidence            356  455788999999999998887766543    1       11  1239999999999999999999986     45


Q ss_pred             cEEEEecCccCChHHHHHHHHhc--------C-CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccc
Q 009640          255 DVYDLELTKVTDNSELRALLLQT--------T-NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIA  325 (530)
Q Consensus       255 ~i~~l~l~~~~~~~~L~~l~~~~--------~-~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~  325 (530)
                      +++.++.+...+...++.++...        . .+.||||||+|.+..                                
T Consensus        74 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~--------------------------------  121 (323)
T 1sxj_B           74 GVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA--------------------------------  121 (323)
T ss_dssp             HEEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH--------------------------------
T ss_pred             CEEEecCccccChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCH--------------------------------
Confidence            57777776654555565554421        2 378999999998721                                


Q ss_pred             cccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          326 SSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       326 ~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                                       .....|+..++..    ....++|++||.++.+++++.+  |+. .|.|+.|+.++...++..
T Consensus       122 -----------------~~~~~L~~~le~~----~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~  177 (323)
T 1sxj_B          122 -----------------GAQQALRRTMELY----SNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDVLKRLLQ  177 (323)
T ss_dssp             -----------------HHHHTTHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHH
T ss_pred             -----------------HHHHHHHHHHhcc----CCCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHHHHHHHHH
Confidence                             1233455555432    3557888899999999999998  665 799999999999999887


Q ss_pred             hhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHH
Q 009640          406 YLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVV  453 (530)
Q Consensus       406 ~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~  453 (530)
                      ++...               ...+++..+..++..+.+++..++..+.
T Consensus       178 ~~~~~---------------~~~~~~~~~~~l~~~~~G~~r~a~~~l~  210 (323)
T 1sxj_B          178 IIKLE---------------DVKYTNDGLEAIIFTAEGDMRQAINNLQ  210 (323)
T ss_dssp             HHHHH---------------TCCBCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHc---------------CCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            65321               1234454444444444555555555443

>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=99.65  E-value=2.3e-15  Score=154.34  Aligned_cols=158  Identities=16%  Similarity=0.222  Sum_probs=115.2

Q ss_pred             CCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC------
Q 009640          180 SGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC------  253 (530)
Q Consensus       180 ~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~------  253 (530)
                      ..|  +..++|.+|++++|.+++++.+...+    ....         ..++|||||||||||++++++|+.++      
T Consensus        25 ~~~--~~k~~p~~~~~i~g~~~~~~~l~~~l----~~~~---------~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~   89 (353)
T 1sxj_D           25 QPW--VEKYRPKNLDEVTAQDHAVTVLKKTL----KSAN---------LPHMLFYGPPGTGKTSTILALTKELYGPDLMK   89 (353)
T ss_dssp             -CH--HHHTCCSSTTTCCSCCTTHHHHHHHT----TCTT---------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHT
T ss_pred             ccH--HHhcCCCCHHHhhCCHHHHHHHHHHH----hcCC---------CCEEEEECCCCCCHHHHHHHHHHHhCCCcccc
Confidence            367  55678999999999999887666543    2211         23599999999999999999999864      


Q ss_pred             CcEEEEecCccCChHHHHHHH---Hh---------------cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          254 YDVYDLELTKVTDNSELRALL---LQ---------------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       254 ~~i~~l~l~~~~~~~~L~~l~---~~---------------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                      ..+..++.+.......++..+   ..               ...+.||+|||+|.+.                       
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~-----------------------  146 (353)
T 1sxj_D           90 SRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMT-----------------------  146 (353)
T ss_dssp             TSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSC-----------------------
T ss_pred             cceEEEccccccchHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccC-----------------------
Confidence            467888877654444443332   11               1345799999999872                       


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                                ....+.|+..++...    ....+|++||+++.++|++.+  |+. .|.|+.|+
T Consensus       147 --------------------------~~~~~~Ll~~le~~~----~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~  193 (353)
T 1sxj_D          147 --------------------------ADAQSALRRTMETYS----GVTRFCLICNYVTRIIDPLAS--QCS-KFRFKALD  193 (353)
T ss_dssp             --------------------------HHHHHHHHHHHHHTT----TTEEEEEEESCGGGSCHHHHH--HSE-EEECCCCC
T ss_pred             --------------------------HHHHHHHHHHHHhcC----CCceEEEEeCchhhCcchhhc--cCc-eEEeCCCC
Confidence                                      112355666666432    346677899999999999999  886 79999999


Q ss_pred             HHHHHHHHHHhhC
Q 009640          396 PHAFKVLAKNYLG  408 (530)
Q Consensus       396 ~~~r~~i~~~~l~  408 (530)
                      .++...++...+.
T Consensus       194 ~~~~~~~l~~~~~  206 (353)
T 1sxj_D          194 ASNAIDRLRFISE  206 (353)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999998887664

>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=5e-15  Score=151.33  Aligned_cols=151  Identities=14%  Similarity=0.134  Sum_probs=107.1

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHH
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRA  272 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~  272 (530)
                      ++++.|++++++.+...+..               ..++|||||||||||++++++|+.++.+++.++.+......++..
T Consensus        26 ~~~i~g~~~~~~~l~~~l~~---------------~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~~~l~g   90 (331)
T 2r44_A           26 GKVVVGQKYMINRLLIGICT---------------GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLPSDLIG   90 (331)
T ss_dssp             TTTCCSCHHHHHHHHHHHHH---------------TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCHHHHHE
T ss_pred             ccceeCcHHHHHHHHHHHHc---------------CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCChhhcCC
Confidence            46788888888777665532               258999999999999999999999999999988754333333221


Q ss_pred             HH--H-------hcCC---CeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          273 LL--L-------QTTN---RSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       273 l~--~-------~~~~---~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                      ..  .       ....   .+||||||||.+-                                                
T Consensus        91 ~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~------------------------------------------------  122 (331)
T 2r44_A           91 TMIYNQHKGNFEVKKGPVFSNFILADEVNRSP------------------------------------------------  122 (331)
T ss_dssp             EEEEETTTTEEEEEECTTCSSEEEEETGGGSC------------------------------------------------
T ss_pred             ceeecCCCCceEeccCcccccEEEEEccccCC------------------------------------------------
Confidence            10  0       0012   3799999999862                                                


Q ss_pred             hhhhHHHHhhhcc-------CCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          341 GRVTLSGLLNFTD-------GLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       341 ~~~~ls~LLn~lD-------gl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                       ..+.+.|+..|+       |.........+||+|+|..+     .|+++|++  ||+.++++++|+.+++..|++..+.
T Consensus       123 -~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~~~~il~~~~~  199 (331)
T 2r44_A          123 -AKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKESELEVMRRVSN  199 (331)
T ss_dssp             -HHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHHHHHHHHHHHC
T ss_pred             -HHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHHHHHHHHhccc
Confidence             112344444443       22211234567788888554     38999999  9999999999999999999999876


Q ss_pred             C
Q 009640          409 I  409 (530)
Q Consensus       409 ~  409 (530)
                      .
T Consensus       200 ~  200 (331)
T 2r44_A          200 M  200 (331)
T ss_dssp             T
T ss_pred             c
Confidence            4

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.64  E-value=9.2e-16  Score=158.66  Aligned_cols=161  Identities=16%  Similarity=0.175  Sum_probs=113.4

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---------CCcEEEEec
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---------CYDVYDLEL  261 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---------~~~i~~l~l  261 (530)
                      ..+++++|.++..+.+...+...+..         ..+++++|+||||||||++++++++.+         +..++.++.
T Consensus        16 ~~p~~~~gr~~~~~~l~~~l~~~~~~---------~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~   86 (387)
T 2v1u_A           16 YVPDVLPHREAELRRLAEVLAPALRG---------EKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNA   86 (387)
T ss_dssp             CCCSCCTTCHHHHHHHHHTTGGGTSS---------CCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEET
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEEC
Confidence            34478899888877777755443322         224689999999999999999999998         788888886


Q ss_pred             CccCCh----------------------HH-HHHHHH---hcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccch
Q 009640          262 TKVTDN----------------------SE-LRALLL---QTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSS  315 (530)
Q Consensus       262 ~~~~~~----------------------~~-L~~l~~---~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~  315 (530)
                      ....+.                      .. +..++.   ....++||||||+|.+...                     
T Consensus        87 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~---------------------  145 (387)
T 2v1u_A           87 RHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKR---------------------  145 (387)
T ss_dssp             TTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHS---------------------
T ss_pred             CcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhccc---------------------
Confidence            654321                      22 222222   2245889999999998310                     


Q ss_pred             hhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC---CCCChhhhcCCceeE-EEEe
Q 009640          316 SIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR---DSVDPALIRCGRMDV-HVSL  391 (530)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~---~~LDpALlRpGR~d~-~I~~  391 (530)
                                             ......+..|++.++....  ...+++|+|||.+   +.+++++.+  |+.. .|+|
T Consensus       146 -----------------------~~~~~~l~~l~~~~~~~~~--~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l  198 (387)
T 2v1u_A          146 -----------------------PGGQDLLYRITRINQELGD--RVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVF  198 (387)
T ss_dssp             -----------------------TTHHHHHHHHHHGGGCC-------CEEEEECSCSTTSSSSCHHHHT--TTTSEECCB
T ss_pred             -----------------------CCCChHHHhHhhchhhcCC--CceEEEEEEECCCchHhhhCHHHHh--cCCCeEEee
Confidence                                   0123456667766654321  2467899999988   789999998  8874 8999


Q ss_pred             CCCCHHHHHHHHHHhhC
Q 009640          392 GTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       392 ~~p~~~~r~~i~~~~l~  408 (530)
                      ++++.++...+++..+.
T Consensus       199 ~~l~~~~~~~il~~~~~  215 (387)
T 2v1u_A          199 PPYTAPQLRDILETRAE  215 (387)
T ss_dssp             CCCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            99999999999988764

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.64  E-value=2.6e-15  Score=151.49  Aligned_cols=160  Identities=16%  Similarity=0.255  Sum_probs=113.7

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSEL  270 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L  270 (530)
                      +.++|++.+++.|...+......-..    ...+...+||+||||||||++|+++|+.+   +.+++.++++.+......
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~----~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~   92 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKD----PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV   92 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSC----TTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCC----CCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccH
Confidence            35678888888888887765421100    00112469999999999999999999998   556888888776543333


Q ss_pred             HHHH---------------Hh---cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          271 RALL---------------LQ---TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       271 ~~l~---------------~~---~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      ..++               ..   ....+||||||||.+-                                        
T Consensus        93 ~~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~----------------------------------------  132 (311)
T 4fcw_A           93 SRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAH----------------------------------------  132 (311)
T ss_dssp             HHHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSC----------------------------------------
T ss_pred             HHhcCCCCccccccccchHHHHHHhCCCeEEEEeChhhcC----------------------------------------
Confidence            3332               11   1345899999999871                                        


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCccCC-------CCCeEEEEEeCC--------------------------CCCCChhh
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWSCC-------SEEKIIVFTTNH--------------------------RDSVDPAL  379 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s~~-------~~~~ivI~TTN~--------------------------~~~LDpAL  379 (530)
                               ....+.|+..|+.-....       -.+.+||+|||.                          ...++|+|
T Consensus       133 ---------~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l  203 (311)
T 4fcw_A          133 ---------PDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEF  203 (311)
T ss_dssp             ---------HHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHH
T ss_pred             ---------HHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHH
Confidence                     124456666665322100       136789999998                          55789999


Q ss_pred             hcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          380 IRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       380 lRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      ++  ||+..+.+.+|+.+++..|++.++.
T Consensus       204 ~~--R~~~~~~~~p~~~~~~~~i~~~~l~  230 (311)
T 4fcw_A          204 LN--RLDEIVVFRPLTKEQIRQIVEIQMS  230 (311)
T ss_dssp             HT--TCSEEEECCCCCHHHHHHHHHHHTH
T ss_pred             Hh--cCCeEEEeCCCCHHHHHHHHHHHHH
Confidence            98  9999999999999999999998875

>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=99.64  E-value=8e-16  Score=159.64  Aligned_cols=176  Identities=21%  Similarity=0.239  Sum_probs=119.3

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhH-hhhcC-CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCC------
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFY-HRVGR-AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTD------  266 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y-~~~g~-~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~------  266 (530)
                      .|+|++.+++.|...+.......... ...+. ..+.++||+||||||||++|++||+.++.+++.++++.+..      
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            36899999999988886544322111 00111 24578999999999999999999999999999999876642      


Q ss_pred             --hHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCC
Q 009640          267 --NSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGE  338 (530)
Q Consensus       267 --~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  338 (530)
                        ...+..++...      ..++||||||||.+...                  +..                 .....+
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~------------------~~~-----------------~~~~~~  140 (363)
T 3hws_A           96 DVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRK------------------SDN-----------------PSITRD  140 (363)
T ss_dssp             HHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCC------------------SSC-----------------C---CH
T ss_pred             cHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhccc------------------ccc-----------------cccccc
Confidence              23355555544      35789999999987310                  000                 000111


Q ss_pred             cchhhhHHHHhhhccCCcc-----------------CCCCCeEEEEEeCCC----------CC-----------------
Q 009640          339 ESGRVTLSGLLNFTDGLWS-----------------CCSEEKIIVFTTNHR----------DS-----------------  374 (530)
Q Consensus       339 ~~~~~~ls~LLn~lDgl~s-----------------~~~~~~ivI~TTN~~----------~~-----------------  374 (530)
                      .....+.+.||..|||...                 -+..++++|+|+|..          ..                 
T Consensus       141 ~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~  220 (363)
T 3hws_A          141 VSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKA  220 (363)
T ss_dssp             HHHHHHHHHHHHHHHCC----------------CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCS
T ss_pred             cchHHHHHHHHHHhcCceeeccCccccccCCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccch
Confidence            1223478899999996421                 012445666666642          11                 


Q ss_pred             ------------------CChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          375 ------------------VDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       375 ------------------LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                                        ++|+|+.  |||..+.|.+|+.+.+..|+...+
T Consensus       221 ~~~~l~~~v~~~~l~~~~~~~~l~~--R~~~~~~~~pl~~~~~~~I~~~~~  269 (363)
T 3hws_A          221 SEGELLAQVEPEDLIKFGLIPEFIG--RLPVVATLNELSEEALIQILKEPK  269 (363)
T ss_dssp             CHHHHHHTCCHHHHHHHTCCHHHHT--TCCEEEECCCCCHHHHHHHHHSST
T ss_pred             hhHHHHHhCCHHHHHHcCCCHHHhc--ccCeeeecCCCCHHHHHHHHHHHH
Confidence                              7888888  999999999999999999988643

>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=99.63  E-value=1.5e-14  Score=148.69  Aligned_cols=195  Identities=17%  Similarity=0.180  Sum_probs=128.3

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +....+.+|+++.+++.+++.+...+..-..       .|. ....++|+||||||||||+++||+.++.++...+....
T Consensus        16 ~~~lr~~~l~~~~g~~~~~~~l~~~i~~~~~-------~~~-~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~   87 (334)
T 1in4_A           16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKM-------RGE-VLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVL   87 (334)
T ss_dssp             -CTTSCSSGGGCCSCHHHHHHHHHHHHHHHH-------HTC-CCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTC
T ss_pred             HHHcCCccHHHccCcHHHHHHHHHHHHHHHh-------cCC-CCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHh
Confidence            4556788999999988777666554433211       111 23579999999999999999999999998887776665


Q ss_pred             CChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhh
Q 009640          265 TDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVT  344 (530)
Q Consensus       265 ~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (530)
                      ....++..++.....+.|++|||+|.+.....                                                
T Consensus        88 ~~~~~l~~~~~~~~~~~v~~iDE~~~l~~~~~------------------------------------------------  119 (334)
T 1in4_A           88 VKQGDMAAILTSLERGDVLFIDEIHRLNKAVE------------------------------------------------  119 (334)
T ss_dssp             CSHHHHHHHHHHCCTTCEEEEETGGGCCHHHH------------------------------------------------
T ss_pred             cCHHHHHHHHHHccCCCEEEEcchhhcCHHHH------------------------------------------------
Confidence            56667777776666789999999998742000                                                


Q ss_pred             HHHHhhhccCCc------c--------CCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCc
Q 009640          345 LSGLLNFTDGLW------S--------CCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIE  410 (530)
Q Consensus       345 ls~LLn~lDgl~------s--------~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~  410 (530)
                       ..|+..+....      .        ..-....++.+||++..|++++++  ||...+.|++++.+++..+++......
T Consensus       120 -e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~  196 (334)
T 1in4_A          120 -ELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLM  196 (334)
T ss_dssp             -HHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHT
T ss_pred             -HHHHHHHHhcccceeeccCcccccccccCCCeEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHc
Confidence             00111110000      0        001235677899999999999999  999999999999999999998765322


Q ss_pred             CccchHHHHHHHHHhCCCCCHHHHHHHHH
Q 009640          411 SHHALFDVVESCIRAGGALTPAQIGEVLL  439 (530)
Q Consensus       411 ~~~~~~~~i~~l~~~~~~~spadi~~~l~  439 (530)
                      ......+.+..++... .=+|..+..+|.
T Consensus       197 ~~~~~~~~~~~ia~~~-~G~~R~a~~ll~  224 (334)
T 1in4_A          197 DVEIEDAAAEMIAKRS-RGTPRIAIRLTK  224 (334)
T ss_dssp             TCCBCHHHHHHHHHTS-TTCHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHhc-CCChHHHHHHHH
Confidence            1111223344444432 234455444443

>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=99.63  E-value=1.6e-15  Score=146.30  Aligned_cols=160  Identities=17%  Similarity=0.198  Sum_probs=104.8

Q ss_pred             CCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---CcEEEEecC
Q 009640          186 PFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---YDVYDLELT  262 (530)
Q Consensus       186 ~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~  262 (530)
                      ...++.+|+++++.+ ..+.+.+.+..+...+         ..+++||+||||||||++++++|+.+.   ..++.++..
T Consensus        20 ~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~---------~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~   89 (242)
T 3bos_A           20 HLPDDETFTSYYPAA-GNDELIGALKSAASGD---------GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLG   89 (242)
T ss_dssp             CCCTTCSTTTSCC---CCHHHHHHHHHHHHTC---------SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             CCCCCCChhhccCCC-CCHHHHHHHHHHHhCC---------CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHH
Confidence            344557899998732 2234445555555432         247899999999999999999999884   778888776


Q ss_pred             ccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchh
Q 009640          263 KVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGR  342 (530)
Q Consensus       263 ~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (530)
                      .+..  .+...+.....+.||||||+|.+..                                            .   .
T Consensus        90 ~~~~--~~~~~~~~~~~~~vliiDe~~~~~~--------------------------------------------~---~  120 (242)
T 3bos_A           90 IHAS--ISTALLEGLEQFDLICIDDVDAVAG--------------------------------------------H---P  120 (242)
T ss_dssp             GGGG--SCGGGGTTGGGSSEEEEETGGGGTT--------------------------------------------C---H
T ss_pred             HHHH--HHHHHHHhccCCCEEEEeccccccC--------------------------------------------C---H
Confidence            6532  1222333446789999999998721                                            0   0


Q ss_pred             hhHHHHhhhccCCccCCCCCeEEEEEeC-CCC---CCChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhC
Q 009640          343 VTLSGLLNFTDGLWSCCSEEKIIVFTTN-HRD---SVDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       343 ~~ls~LLn~lDgl~s~~~~~~ivI~TTN-~~~---~LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      .....|+..++....  .....+|+||| .+.   .+++++.+  |+.  ..|+++.|+.+++..++..++.
T Consensus       121 ~~~~~l~~~l~~~~~--~~~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~~~~l~~~~~  188 (242)
T 3bos_A          121 LWEEAIFDLYNRVAE--QKRGSLIVSASASPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEKLAALQRRAA  188 (242)
T ss_dssp             HHHHHHHHHHHHHHH--HCSCEEEEEESSCTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH--cCCCeEEEEcCCCHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHHHHHHHHHHH
Confidence            012334444443322  12232555555 443   46789998  776  8999999999999999988764

>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=99.62  E-value=1.3e-14  Score=149.84  Aligned_cols=185  Identities=17%  Similarity=0.228  Sum_probs=127.1

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC----------
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY----------  254 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~----------  254 (530)
                      ...+.|.+|++++|.++..+.+...+..           | ..+..|||+||||||||++++++|+.++.          
T Consensus         7 ~~k~rp~~~~~~vg~~~~~~~L~~~l~~-----------~-~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~   74 (373)
T 1jr3_A            7 ARKWRPQTFADVVGQEHVLTALANGLSL-----------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCG   74 (373)
T ss_dssp             HHHTCCCSTTTSCSCHHHHHHHHHHHHH-----------T-CCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCS
T ss_pred             HHhhCCCchhhccCcHHHHHHHHHHHHh-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCc
Confidence            3456888999999999988877776532           1 12357999999999999999999998854          


Q ss_pred             --------------cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccc
Q 009640          255 --------------DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRS  314 (530)
Q Consensus       255 --------------~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~  314 (530)
                                    +++.++.........++.++...      ..+.||+|||+|.+-                      
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~----------------------  132 (373)
T 1jr3_A           75 VCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS----------------------  132 (373)
T ss_dssp             SSHHHHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSC----------------------
T ss_pred             ccHHHHHHhccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhc----------------------
Confidence                          34555544322233456665543      247899999999871                      


Q ss_pred             hhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCC
Q 009640          315 SSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTC  394 (530)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p  394 (530)
                                                 ....+.|+..++..    ...+++|++||.+..+++++.+  |+ ..+.|+.|
T Consensus       133 ---------------------------~~~~~~Ll~~le~~----~~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l  178 (373)
T 1jr3_A          133 ---------------------------RHSFNALLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKAL  178 (373)
T ss_dssp             ---------------------------HHHHHHHHHHHHSC----CSSEEEEEEESCGGGSCHHHHT--TS-EEEECCCC
T ss_pred             ---------------------------HHHHHHHHHHHhcC----CCceEEEEEeCChHhCcHHHHh--he-eEeeCCCC
Confidence                                       12345677777643    3568899999999999999998  66 67999999


Q ss_pred             CHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHH
Q 009640          395 GPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVL  438 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l  438 (530)
                      +.++...++..++.........+.++.++..+. -.+.++.+++
T Consensus       179 ~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~-G~~r~~~~~l  221 (373)
T 1jr3_A          179 DVEQIRHQLEHILNEEHIAHEPRALQLLARAAE-GSLRDALSLT  221 (373)
T ss_dssp             CHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSS-SCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCC-CCHHHHHHHH
Confidence            999999999887743222212223444444332 2454544444

>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=99.62  E-value=1.1e-14  Score=151.04  Aligned_cols=151  Identities=17%  Similarity=0.272  Sum_probs=112.2

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----------CCcEEEEecC
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----------CYDVYDLELT  262 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----------~~~i~~l~l~  262 (530)
                      ++++|.++..+.+...+..++....         +++++|+||||||||++++++++.+           +..++.+++.
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~---------~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~   90 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEV---------KFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCR   90 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCC---------CCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCC---------CCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECc
Confidence            7899999999999888877665422         4689999999999999999999998           8889988865


Q ss_pred             ccC-Ch-----------------------HH-HHHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          263 KVT-DN-----------------------SE-LRALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       263 ~~~-~~-----------------------~~-L~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                      ... +.                       .. +..++... ..+.||||||+|.+..                       
T Consensus        91 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~-----------------------  147 (384)
T 2qby_B           91 EVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVK-----------------------  147 (384)
T ss_dssp             HHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHH-----------------------
T ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhcc-----------------------
Confidence            433 21                       12 22222222 2334999999999731                       


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhh-HHHHhhhccCCccCCCCCeEEEEEeCCC---CCCChhhhcCCceeEEEEeC
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVT-LSGLLNFTDGLWSCCSEEKIIVFTTNHR---DSVDPALIRCGRMDVHVSLG  392 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-ls~LLn~lDgl~s~~~~~~ivI~TTN~~---~~LDpALlRpGR~d~~I~~~  392 (530)
                                           .. .... +..|++..        .++.||+|||.+   +.+++++.+  ||+..|+|+
T Consensus       148 ---------------------~~-~~~~~l~~l~~~~--------~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~  195 (384)
T 2qby_B          148 ---------------------RR-GGDIVLYQLLRSD--------ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFK  195 (384)
T ss_dssp             ---------------------ST-TSHHHHHHHHTSS--------SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEEC
T ss_pred             ---------------------CC-CCceeHHHHhcCC--------cceEEEEEECCCchHhhhCHHHHh--cCCCeEEEC
Confidence                                 00 0123 45555543        457899999987   789999999  887799999


Q ss_pred             CCCHHHHHHHHHHhhC
Q 009640          393 TCGPHAFKVLAKNYLG  408 (530)
Q Consensus       393 ~p~~~~r~~i~~~~l~  408 (530)
                      +++.++...++..++.
T Consensus       196 ~l~~~~~~~il~~~~~  211 (384)
T 2qby_B          196 PYDAEQLKFILSKYAE  211 (384)
T ss_dssp             CCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999998764

>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=99.61  E-value=5.6e-15  Score=150.65  Aligned_cols=189  Identities=15%  Similarity=0.196  Sum_probs=118.5

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      +.+..+|++++..+..... ...+..+...+.       ....++|||||||||||+|++++|+++   +.+++.++...
T Consensus         4 l~~~~~f~~fv~g~~~~~a-~~~~~~~~~~~~-------~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~   75 (324)
T 1l8q_A            4 LNPKYTLENFIVGEGNRLA-YEVVKEALENLG-------SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADD   75 (324)
T ss_dssp             CCTTCCSSSCCCCTTTHHH-HHHHHHHHHTTT-------TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             CCCCCCcccCCCCCcHHHH-HHHHHHHHhCcC-------CCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHH
Confidence            3456789999732222222 233444444331       124689999999999999999999999   89999998765


Q ss_pred             cCChHHHH---------HHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCC
Q 009640          264 VTDNSELR---------ALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNN  334 (530)
Q Consensus       264 ~~~~~~L~---------~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~  334 (530)
                      +..  .+.         .+......+.||||||||.+.+                                         
T Consensus        76 ~~~--~~~~~~~~~~~~~~~~~~~~~~vL~iDEi~~l~~-----------------------------------------  112 (324)
T 1l8q_A           76 FAQ--AMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSG-----------------------------------------  112 (324)
T ss_dssp             HHH--HHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTT-----------------------------------------
T ss_pred             HHH--HHHHHHHcCcHHHHHHHhcCCCEEEEcCcccccC-----------------------------------------
Confidence            421  111         1112224589999999998721                                         


Q ss_pred             CCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC---CCChhhhcCCcee--EEEEeCCCCHHHHHHHHHHhhCC
Q 009640          335 NNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD---SVDPALIRCGRMD--VHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       335 ~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~---~LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                         ..   .+...|+..++.+..  .+.++|+.++|.+.   .++++|++  ||+  ..+++++ +.+++..|++.++..
T Consensus       113 ---~~---~~~~~l~~~l~~~~~--~~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~  181 (324)
T 1l8q_A          113 ---KE---RTQIEFFHIFNTLYL--LEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKE  181 (324)
T ss_dssp             ---CH---HHHHHHHHHHHHHHH--TTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHH
T ss_pred             ---Ch---HHHHHHHHHHHHHHH--CCCeEEEEecCChHHHHHhhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHh
Confidence               00   112234444333222  23456666666665   68999999  886  7899999 999999999988753


Q ss_pred             cCccchHHHHHHHHHhCCCCCHHHHHHHHH
Q 009640          410 ESHHALFDVVESCIRAGGALTPAQIGEVLL  439 (530)
Q Consensus       410 ~~~~~~~~~i~~l~~~~~~~spadi~~~l~  439 (530)
                      .......+.++.++...  -...++.+.+.
T Consensus       182 ~~~~l~~~~l~~l~~~~--g~~r~l~~~l~  209 (324)
T 1l8q_A          182 FNLELRKEVIDYLLENT--KNVREIEGKIK  209 (324)
T ss_dssp             TTCCCCHHHHHHHHHHC--SSHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHhC--CCHHHHHHHHH
Confidence            33332234455555543  45555555543

>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=99.60  E-value=1.5e-14  Score=148.74  Aligned_cols=190  Identities=13%  Similarity=0.210  Sum_probs=123.0

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-CC-----
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-CY-----  254 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-~~-----  254 (530)
                      .|  +..++|.+|++++|++++.+.+...+.   ..       |. .+. +||+|||||||||+++++|+.+ +.     
T Consensus         3 ~w--~~kyrP~~~~~~vg~~~~~~~l~~~~~---~~-------~~-~~~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i   68 (354)
T 1sxj_E            3 LW--VDKYRPKSLNALSHNEELTNFLKSLSD---QP-------RD-LPH-LLLYGPNGTGKKTRCMALLESIFGPGVYRL   68 (354)
T ss_dssp             -C--TTTTCCCSGGGCCSCHHHHHHHHTTTT---CT-------TC-CCC-EEEECSTTSSHHHHHHTHHHHHSCTTCCC-
T ss_pred             cc--hhccCCCCHHHhcCCHHHHHHHHHHHh---hC-------CC-CCe-EEEECCCCCCHHHHHHHHHHHHcCCCCCeE
Confidence            47  677899999999999887665544320   21       11 123 9999999999999999999964 21     


Q ss_pred             -----------------------cEEEEecCccC--ChHHHHHHHHh----------------cCCCeEEEEcCccchhh
Q 009640          255 -----------------------DVYDLELTKVT--DNSELRALLLQ----------------TTNRSIIVIEDIDCSVD  293 (530)
Q Consensus       255 -----------------------~i~~l~l~~~~--~~~~L~~l~~~----------------~~~~sII~IDeID~~~~  293 (530)
                                             +++.++.+...  ....++.++..                ...|.||+|||+|.+ +
T Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L-~  147 (354)
T 1sxj_E           69 KIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSL-T  147 (354)
T ss_dssp             -----------------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSS-C
T ss_pred             EecceeecccccccceeeeecccceEEecHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCcccc-C
Confidence                                   12333332221  11134444432                225779999999985 1


Q ss_pred             hhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC
Q 009640          294 LTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD  373 (530)
Q Consensus       294 ~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~  373 (530)
                                                                      ....+.|++.|+..    ..+..+|++||.++
T Consensus       148 ------------------------------------------------~~~~~~L~~~le~~----~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          148 ------------------------------------------------KDAQAALRRTMEKY----SKNIRLIMVCDSMS  175 (354)
T ss_dssp             ------------------------------------------------HHHHHHHHHHHHHS----TTTEEEEEEESCSC
T ss_pred             ------------------------------------------------HHHHHHHHHHHHhh----cCCCEEEEEeCCHH
Confidence                                                            11234566666543    24578999999999


Q ss_pred             CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCC-HHHHHHHHHHhccCHHHHHHHH
Q 009640          374 SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALT-PAQIGEVLLRNRGNVDLAMKEV  452 (530)
Q Consensus       374 ~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~s-padi~~~l~~~~~d~~~al~~l  452 (530)
                      .+.|++.+  |+ ..+.|+.|+.++...+++..+...               +..++ +..+..++..+.+++..|+..+
T Consensus       176 ~l~~~l~s--R~-~~~~~~~~~~~~~~~~l~~~~~~~---------------~~~~~~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          176 PIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNE---------------RIQLETKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             SSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHH---------------TCEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHh--hc-eEEecCCcCHHHHHHHHHHHHHHc---------------CCCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999998  77 779999999999999888765322               12344 4455555555556666666555


Q ss_pred             HHH
Q 009640          453 VSA  455 (530)
Q Consensus       453 ~~~  455 (530)
                      ...
T Consensus       238 ~~~  240 (354)
T 1sxj_E          238 ESM  240 (354)
T ss_dssp             THH
T ss_pred             HHH
Confidence            443

>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=99.60  E-value=2.4e-14  Score=146.74  Aligned_cols=156  Identities=18%  Similarity=0.221  Sum_probs=101.1

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      ..++.+|++++|.+.+++.+...+   + .+         ...++|||||||||||++|+++|+.++.            
T Consensus        17 ~~~~~~f~~i~G~~~~~~~l~~~~---~-~~---------~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~   83 (350)
T 1g8p_A           17 TRPVFPFSAIVGQEDMKLALLLTA---V-DP---------GIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSP   83 (350)
T ss_dssp             -CCCCCGGGSCSCHHHHHHHHHHH---H-CG---------GGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCS
T ss_pred             CCCCCCchhccChHHHHHHHHHHh---h-CC---------CCceEEEECCCCccHHHHHHHHHHhCcccccccccccccc
Confidence            346778999999988766533221   1 11         1357999999999999999999999863            


Q ss_pred             ---------------------cEEEEecCccCChHHH------HHHHHhc-----------CCCeEEEEcCccchhhhhh
Q 009640          255 ---------------------DVYDLELTKVTDNSEL------RALLLQT-----------TNRSIIVIEDIDCSVDLTA  296 (530)
Q Consensus       255 ---------------------~i~~l~l~~~~~~~~L------~~l~~~~-----------~~~sII~IDeID~~~~~~~  296 (530)
                                           +++.+...  .+...+      .+.+...           ..++||||||||.+-    
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~g~~~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~----  157 (350)
T 1g8p_A           84 NVEMIPDWATVLSTNVIRKPTPVVDLPLG--VSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLE----  157 (350)
T ss_dssp             SGGGSCTTCCCSCCCEEEECCCEEEECTT--CCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSC----
T ss_pred             ccccccchhhhhccccccCCCcccccCCC--cchhhheeechhhhhhcCCceeecCceeeecCCCEEEEeChhhCC----
Confidence                                 12222111  112221      2222211           137899999999872    


Q ss_pred             hhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC----Ccc-----CCCCCeEEEE
Q 009640          297 DRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG----LWS-----CCSEEKIIVF  367 (530)
Q Consensus       297 ~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg----l~s-----~~~~~~ivI~  367 (530)
                                                                   ......|+..++.    +..     .....++||+
T Consensus       158 ---------------------------------------------~~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~  192 (350)
T 1g8p_A          158 ---------------------------------------------DHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVG  192 (350)
T ss_dssp             ---------------------------------------------HHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEE
T ss_pred             ---------------------------------------------HHHHHHHHHHHhcCceEEEecceEEeeCCceEEEE
Confidence                                                         1123344544432    110     0013578899


Q ss_pred             EeCCCC-CCChhhhcCCceeEEEEeCCC-CHHHHHHHHHHhhC
Q 009640          368 TTNHRD-SVDPALIRCGRMDVHVSLGTC-GPHAFKVLAKNYLG  408 (530)
Q Consensus       368 TTN~~~-~LDpALlRpGR~d~~I~~~~p-~~~~r~~i~~~~l~  408 (530)
                      |||..+ .++++|++  ||+.++++++| +.+.+..|++..+.
T Consensus       193 ~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~~~~~~il~~~~~  233 (350)
T 1g8p_A          193 SGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRRRDT  233 (350)
T ss_dssp             EECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHHHHH
T ss_pred             EeCCCCCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHHHh
Confidence            999755 89999999  99999999999 67888888877543

>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=99.59  E-value=5.4e-14  Score=145.72  Aligned_cols=159  Identities=13%  Similarity=0.075  Sum_probs=115.0

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecCccCCh
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELTKVTDN  267 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~~~~~~  267 (530)
                      .++++++.++..+.+...+...+....       +..+.++|+||||||||++++++++.+    +..++.+++....+.
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~~~-------~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~   87 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNF   87 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTT-------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCC-------CCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCH
Confidence            447899999998888888877655422       112379999999999999999999998    567888876554321


Q ss_pred             H----------------------H----HHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhc
Q 009640          268 S----------------------E----LRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMG  321 (530)
Q Consensus       268 ~----------------------~----L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~  321 (530)
                      .                      .    +...+.....|.||+|||+|.+                              
T Consensus        88 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l------------------------------  137 (389)
T 1fnn_A           88 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL------------------------------  137 (389)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS------------------------------
T ss_pred             HHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc------------------------------
Confidence            1                      1    1122223356899999999986                              


Q ss_pred             cccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC---CCCChhhhcCCceeE-EEEeCCCCHH
Q 009640          322 SRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR---DSVDPALIRCGRMDV-HVSLGTCGPH  397 (530)
Q Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~---~~LDpALlRpGR~d~-~I~~~~p~~~  397 (530)
                                         ....+..|+..++.+......++.||++||.+   +.+++.+.+  |+.. .|+|++++.+
T Consensus       138 -------------------~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~  196 (389)
T 1fnn_A          138 -------------------APDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKD  196 (389)
T ss_dssp             -------------------CHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHH
T ss_pred             -------------------chHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHH
Confidence                               12245666676654421001467889999988   789999988  8875 8999999999


Q ss_pred             HHHHHHHHhhC
Q 009640          398 AFKVLAKNYLG  408 (530)
Q Consensus       398 ~r~~i~~~~l~  408 (530)
                      +...++...+.
T Consensus       197 ~~~~~l~~~~~  207 (389)
T 1fnn_A          197 QIFDILLDRAK  207 (389)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999988764

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.58  E-value=3e-15  Score=138.34  Aligned_cols=146  Identities=18%  Similarity=0.226  Sum_probs=99.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEE
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVY  257 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~  257 (530)
                      ..+.+|++++|.++..+.+.+.+    ..         ...+++||+||||||||++++++|+.+          +.+++
T Consensus        16 ~~~~~~~~~~g~~~~~~~l~~~l----~~---------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~   82 (187)
T 2p65_A           16 ARAGKLDPVIGRDTEIRRAIQIL----SR---------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLV   82 (187)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHH----TS---------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEE
T ss_pred             HhccccchhhcchHHHHHHHHHH----hC---------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEE
Confidence            34668899999888666665544    21         224689999999999999999999997          77788


Q ss_pred             EEecCccC----C----hHHHHHHHHh---cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          258 DLELTKVT----D----NSELRALLLQ---TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       258 ~l~l~~~~----~----~~~L~~l~~~---~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      .+++..+.    .    ...+..++..   ...+.||||||+|.+.+...                              
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~------------------------------  132 (187)
T 2p65_A           83 SLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGA------------------------------  132 (187)
T ss_dssp             EECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSS------------------------------
T ss_pred             EEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhccccc------------------------------
Confidence            87765431    1    1224444433   35789999999999731000                              


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCC
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCG  395 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~  395 (530)
                                ...........|+..++      ...+++|+|||.++     .+|++|++  ||+. |+++.|+
T Consensus       133 ----------~~~~~~~~~~~l~~~~~------~~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          133 ----------VAEGALDAGNILKPMLA------RGELRCIGATTVSEYRQFIEKDKALER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             ----------SCTTSCCTHHHHHHHHH------TTCSCEEEEECHHHHHHHTTTCHHHHH--HEEE-EECCSCC
T ss_pred             ----------ccccchHHHHHHHHHHh------cCCeeEEEecCHHHHHHHHhccHHHHH--hcCc-ccCCCCC
Confidence                      00011223344444443      24577899999875     68999999  9995 9999886

>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=99.58  E-value=2.3e-14  Score=147.86  Aligned_cols=160  Identities=15%  Similarity=0.206  Sum_probs=112.3

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc------CCcEEEEecCc
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL------CYDVYDLELTK  263 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l------~~~i~~l~l~~  263 (530)
                      ...+++++|.++..+.+.+.+...+..         ..++.++|+||||||||+|++++++.+      +..++.+++..
T Consensus        16 ~~~p~~~~gr~~e~~~l~~~l~~~~~~---------~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~   86 (386)
T 2qby_A           16 DYIPDELPHREDQIRKIASILAPLYRE---------EKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQ   86 (386)
T ss_dssp             SCCCSCCTTCHHHHHHHHHSSGGGGGT---------CCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHH
T ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHcC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCC
Confidence            344578899888777776655433322         224689999999999999999999998      88888887542


Q ss_pred             cCC----------------------hHHH-H---HHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhh
Q 009640          264 VTD----------------------NSEL-R---ALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSI  317 (530)
Q Consensus       264 ~~~----------------------~~~L-~---~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~  317 (530)
                      ..+                      ...+ .   ..+.....|.||+|||+|.+.+.                       
T Consensus        87 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~-----------------------  143 (386)
T 2qby_A           87 IDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKK-----------------------  143 (386)
T ss_dssp             HCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHS-----------------------
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhcc-----------------------
Confidence            211                      2222 2   22333345899999999998420                       


Q ss_pred             hhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC---CCCChhhhcCCcee-EEEEeCC
Q 009640          318 KEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR---DSVDPALIRCGRMD-VHVSLGT  393 (530)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~---~~LDpALlRpGR~d-~~I~~~~  393 (530)
                                            .....+..|+..++.+.   ..++.+|+|||.+   +.+++++.+  |+. ..|+|++
T Consensus       144 ----------------------~~~~~l~~l~~~~~~~~---~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~  196 (386)
T 2qby_A          144 ----------------------YNDDILYKLSRINSEVN---KSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPP  196 (386)
T ss_dssp             ----------------------SCSTHHHHHHHHHHSCC---C--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECC
T ss_pred             ----------------------CcCHHHHHHhhchhhcC---CCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCC
Confidence                                  01235667777776542   3568889999987   578889988  665 5899999


Q ss_pred             CCHHHHHHHHHHhhC
Q 009640          394 CGPHAFKVLAKNYLG  408 (530)
Q Consensus       394 p~~~~r~~i~~~~l~  408 (530)
                      ++.++...++...+.
T Consensus       197 l~~~~~~~il~~~~~  211 (386)
T 2qby_A          197 YNAEELEDILTKRAQ  211 (386)
T ss_dssp             CCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999988764

>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=99.57  E-value=8.2e-14  Score=145.07  Aligned_cols=173  Identities=21%  Similarity=0.255  Sum_probs=113.3

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhh------------------HhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEF------------------YHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~------------------y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      .|+|++++|+.|...+.....+...                  +.. ....+.++||+||||||||++|+++|+.++.++
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            4789999999998877543332211                  001 122356899999999999999999999999999


Q ss_pred             EEEecCccCC--------hHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcc
Q 009640          257 YDLELTKVTD--------NSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGS  322 (530)
Q Consensus       257 ~~l~l~~~~~--------~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~  322 (530)
                      +.++...+..        ...+..++...      ..++||||||||.+...   +..               .      
T Consensus       101 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~---~~~---------------~------  156 (376)
T 1um8_A          101 AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRL---SEN---------------R------  156 (376)
T ss_dssp             EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC-------------------------------
T ss_pred             EEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhh---cCC---------------C------
Confidence            9998876531        22345555433      26899999999997321   000               0      


Q ss_pred             ccccccCCCCCCCCCCcchhhhHHHHhhhccCCcc-----------------CCCCCeEEEEEeCCC-------------
Q 009640          323 RIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWS-----------------CCSEEKIIVFTTNHR-------------  372 (530)
Q Consensus       323 ~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s-----------------~~~~~~ivI~TTN~~-------------  372 (530)
                                 ....+.......+.||..|++..-                 ....++++|+|||..             
T Consensus       157 -----------~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~  225 (376)
T 1um8_A          157 -----------SITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQN  225 (376)
T ss_dssp             ------------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSC
T ss_pred             -----------ceecccchHHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhccc
Confidence                       000111123367788888886420                 012446788888721             


Q ss_pred             ----------------------------CCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          373 ----------------------------DSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       373 ----------------------------~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                                                  ..+.|+|+.  |++..|.|+.++.++...|+..
T Consensus       226 ~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~~p~l~~--R~~~~i~~~~l~~~~l~~i~~~  284 (376)
T 1um8_A          226 VLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIG--RLPVLSTLDSISLEAMVDILQK  284 (376)
T ss_dssp             CCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             ccCCCchhhhccchhHHHhhcCHHHHhhcCCChHHhc--CCCceeeccCCCHHHHHHHHhh
Confidence                                        135677777  9999999999999999988874

>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=145.03  Aligned_cols=158  Identities=19%  Similarity=0.309  Sum_probs=113.8

Q ss_pred             CCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----
Q 009640          179 DSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----  253 (530)
Q Consensus       179 ~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----  253 (530)
                      +.+|  +..+.|.+|+++.|++++.+.|...+.    ..+       .  .+||||||||||||++++++|+.+.     
T Consensus        12 ~~~~--~~k~rp~~~~~~~g~~~~~~~L~~~i~----~g~-------~--~~~ll~Gp~G~GKTtla~~la~~l~~~~~~   76 (340)
T 1sxj_C           12 NLPW--VEKYRPETLDEVYGQNEVITTVRKFVD----EGK-------L--PHLLFYGPPGTGKTSTIVALAREIYGKNYS   76 (340)
T ss_dssp             CCCH--HHHTCCSSGGGCCSCHHHHHHHHHHHH----TTC-------C--CCEEEECSSSSSHHHHHHHHHHHHHTTSHH
T ss_pred             CCch--HHHhCCCcHHHhcCcHHHHHHHHHHHh----cCC-------C--ceEEEECCCCCCHHHHHHHHHHHHcCCCcc
Confidence            3468  556899999999999887766655443    211       1  2399999999999999999999873     


Q ss_pred             CcEEEEecCccCChHHHHHHHH---hc-----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccc
Q 009640          254 YDVYDLELTKVTDNSELRALLL---QT-----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIA  325 (530)
Q Consensus       254 ~~i~~l~l~~~~~~~~L~~l~~---~~-----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~  325 (530)
                      ..+..++.+...+...++..+.   +.     ..+.|++|||+|.+-                                 
T Consensus        77 ~~~~~~~~~~~~~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~---------------------------------  123 (340)
T 1sxj_C           77 NMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMT---------------------------------  123 (340)
T ss_dssp             HHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSC---------------------------------
T ss_pred             ceEEEEcCcccccHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCC---------------------------------
Confidence            2466777665444455554432   21     247899999999872                                 


Q ss_pred             cccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          326 SSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       326 ~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                                      ....+.|+..++..    .....+|++||.+..+.|++++  |+. .+.|..++.++....+..
T Consensus       124 ----------------~~~~~~L~~~le~~----~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~~~~~~~l~~  180 (340)
T 1sxj_C          124 ----------------NAAQNALRRVIERY----TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQEAIERRIAN  180 (340)
T ss_dssp             ----------------HHHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHH
T ss_pred             ----------------HHHHHHHHHHHhcC----CCCeEEEEEecCccccchhHHh--hce-eEeccCCCHHHHHHHHHH
Confidence                            11234566666643    2456788899999999999999  775 689999999888888877


Q ss_pred             hh
Q 009640          406 YL  407 (530)
Q Consensus       406 ~l  407 (530)
                      .+
T Consensus       181 ~~  182 (340)
T 1sxj_C          181 VL  182 (340)
T ss_dssp             HH
T ss_pred             HH
Confidence            66

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.55  E-value=9e-14  Score=141.58  Aligned_cols=177  Identities=10%  Similarity=0.131  Sum_probs=117.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecCccCC----------------------hHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELTKVTD----------------------NSELRALLL  275 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~~~~~----------------------~~~L~~l~~  275 (530)
                      +.++|||||||||||++++++++++          .+.++.++...+.+                      ...|.++|.
T Consensus        45 ~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~  124 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYIT  124 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHHH
Confidence            5789999999999999999999999          35677777655322                      234566666


Q ss_pred             hc----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhh
Q 009640          276 QT----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF  351 (530)
Q Consensus       276 ~~----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~  351 (530)
                      ..    ..++||+|||||.+.                                                .+..+..|++.
T Consensus       125 ~~~~~~~~~~ii~lDE~d~l~------------------------------------------------~q~~L~~l~~~  156 (318)
T 3te6_A          125 NVPKAKKRKTLILIQNPENLL------------------------------------------------SEKILQYFEKW  156 (318)
T ss_dssp             HSCGGGSCEEEEEEECCSSSC------------------------------------------------CTHHHHHHHHH
T ss_pred             HhhhccCCceEEEEecHHHhh------------------------------------------------cchHHHHHHhc
Confidence            53    467899999999972                                                12345556554


Q ss_pred             ccCCccCCCCCeEEEEEeCCCCC----CChhhhcCCcee-EEEEeCCCCHHHHHHHHHHhhCCcCccchH--------H-
Q 009640          352 TDGLWSCCSEEKIIVFTTNHRDS----VDPALIRCGRMD-VHVSLGTCGPHAFKVLAKNYLGIESHHALF--------D-  417 (530)
Q Consensus       352 lDgl~s~~~~~~ivI~TTN~~~~----LDpALlRpGR~d-~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~--------~-  417 (530)
                      ..    .....++||+++|..+.    |++++.+  ||+ ..|.|++++.++...|+++-+...... .+        . 
T Consensus       157 ~~----~~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~~~~~~-~f~~~~~~~~~~  229 (318)
T 3te6_A          157 IS----SKNSKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLKSLLKP-FHVKVNDKKEMT  229 (318)
T ss_dssp             HH----CSSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHHHHCCC-EEEEECTTCCEE
T ss_pred             cc----ccCCcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHHhhhcc-cccccccccccc
Confidence            32    12356889999998865    4555666  886 689999999999999998877532110 00        0 


Q ss_pred             ---HHHHHHH--hCC-------CCCHHHHHHHHH---HhccCHHHHHHHHHHHHHHh
Q 009640          418 ---VVESCIR--AGG-------ALTPAQIGEVLL---RNRGNVDLAMKEVVSAMQAK  459 (530)
Q Consensus       418 ---~i~~l~~--~~~-------~~spadi~~~l~---~~~~d~~~al~~l~~~l~~~  459 (530)
                         .+.....  ...       .++++.|.-+..   ...+|++.||+-+..+.+..
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~i~~~ai~~~A~~vA~~~GD~R~Al~ilr~A~~~a  286 (318)
T 3te6_A          230 IYNNIREGQNQKIPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVEIS  286 (318)
T ss_dssp             ECCCC--------CTTEEEECEECCHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccCHHHHHHHHHHHHhhCChHHHHHHHHHHHHHHH
Confidence               0000000  001       357766655544   35689999999888777644

>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=99.55  E-value=3.7e-14  Score=151.12  Aligned_cols=190  Identities=17%  Similarity=0.240  Sum_probs=116.5

Q ss_pred             CCCCCCCccccc-CChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEE
Q 009640          186 PFRHPSTFETLA-LEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDL  259 (530)
Q Consensus       186 ~~~~~~~f~~l~-~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l  259 (530)
                      ++.+..+|++++ |.... . ....+..+...+.      .  ..+++||||||||||+|+++||+++     +..++.+
T Consensus        97 ~l~~~~tfd~fv~g~~n~-~-a~~~~~~~a~~~~------~--~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v  166 (440)
T 2z4s_A           97 PLNPDYTFENFVVGPGNS-F-AYHAALEVAKHPG------R--YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYI  166 (440)
T ss_dssp             CCCTTCSGGGCCCCTTTH-H-HHHHHHHHHHSTT------S--SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEE
T ss_pred             CCCCCCChhhcCCCCchH-H-HHHHHHHHHhCCC------C--CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEe
Confidence            345566899987 43332 2 2333444444332      1  4689999999999999999999998     8888888


Q ss_pred             ecCccCChHHHHH---------HHHhcC-CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccC
Q 009640          260 ELTKVTDNSELRA---------LLLQTT-NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTC  329 (530)
Q Consensus       260 ~l~~~~~~~~L~~---------l~~~~~-~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~  329 (530)
                      +...+.  .++..         +..... .+.||||||||.+.+                                    
T Consensus       167 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~------------------------------------  208 (440)
T 2z4s_A          167 TSEKFL--NDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIG------------------------------------  208 (440)
T ss_dssp             EHHHHH--HHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSS------------------------------------
T ss_pred             eHHHHH--HHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccC------------------------------------
Confidence            876542  12221         122224 789999999998731                                    


Q ss_pred             CCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC---CChhhhcCCcee--EEEEeCCCCHHHHHHHHH
Q 009640          330 GNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRMD--VHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       330 ~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~d--~~I~~~~p~~~~r~~i~~  404 (530)
                              ..   .+...|+..++.+..  .+..|||.|.+.+..   ++++|++  ||+  ..+.++.|+.+++..+++
T Consensus       209 --------~~---~~q~~l~~~l~~l~~--~~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~  273 (440)
T 2z4s_A          209 --------KT---GVQTELFHTFNELHD--SGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIAR  273 (440)
T ss_dssp             --------CH---HHHHHHHHHHHHHHT--TTCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHH
T ss_pred             --------Ch---HHHHHHHHHHHHHHH--CCCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHH
Confidence                    00   112234444433322  233445444444554   8999999  886  789999999999999998


Q ss_pred             HhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHH
Q 009640          405 NYLGIESHHALFDVVESCIRAGGALTPAQIGEVLL  439 (530)
Q Consensus       405 ~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~  439 (530)
                      ..+.........+.++.++.. ..-++.++.++|.
T Consensus       274 ~~~~~~~~~i~~e~l~~la~~-~~gn~R~l~~~L~  307 (440)
T 2z4s_A          274 KMLEIEHGELPEEVLNFVAEN-VDDNLRRLRGAII  307 (440)
T ss_dssp             HHHHHHTCCCCTTHHHHHHHH-CCSCHHHHHHHHH
T ss_pred             HHHHHcCCCCCHHHHHHHHHh-cCCCHHHHHHHHH
Confidence            877422211111224444443 2345666655554

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.52  E-value=1.8e-13  Score=146.97  Aligned_cols=148  Identities=16%  Similarity=0.187  Sum_probs=106.6

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcE
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDV  256 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i  256 (530)
                      ...+..|+.++|.++..+.+...+..             ..+.++||+||||||||++++++|+.+          +..+
T Consensus       173 ~~r~~~ld~iiGr~~~i~~l~~~l~r-------------~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~  239 (468)
T 3pxg_A          173 IAKEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRV  239 (468)
T ss_dssp             HTTSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCE
T ss_pred             HHhcCCCCCccCcHHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeE
Confidence            35677899999999887776665432             124689999999999999999999997          7788


Q ss_pred             EEEecCc-cC--ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          257 YDLELTK-VT--DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       257 ~~l~l~~-~~--~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      +.++++. ..  ....++.+|..+  ..++|||||   ...                                       
T Consensus       240 ~~l~~~~~~~g~~e~~~~~~~~~~~~~~~~iLfiD---~~~---------------------------------------  277 (468)
T 3pxg_A          240 MTLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID---AAI---------------------------------------  277 (468)
T ss_dssp             ECC----------CTTHHHHHHHHHTCCCCEEEEC---C-----------------------------------------
T ss_pred             EEeeCCccccchHHHHHHHHHHHHHhcCCeEEEEe---Cch---------------------------------------
Confidence            8887752 11  123466666654  468999999   100                                       


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                                 ...+.|+..|+      .+.+.+|++||.++     .+|++|.|  ||.. |.|++|+.+++..|++.+
T Consensus       278 -----------~a~~~L~~~L~------~g~v~vI~at~~~e~~~~~~~~~al~~--Rf~~-i~v~~p~~e~~~~iL~~~  337 (468)
T 3pxg_A          278 -----------DASNILKPSLA------RGELQCIGATTLDEYRKYIEKDAALER--RFQP-IQVDQPSVDESIQILQGL  337 (468)
T ss_dssp             -----------------CCCTT------SSSCEEEEECCTTTTHHHHTTCSHHHH--SEEE-EECCCCCHHHHHHHHHHT
T ss_pred             -----------hHHHHHHHhhc------CCCEEEEecCCHHHHHHHhhcCHHHHH--hCcc-ceeCCCCHHHHHHHHHHH
Confidence                       01233455554      35688999999988     69999999  9985 999999999999999988


Q ss_pred             hCC
Q 009640          407 LGI  409 (530)
Q Consensus       407 l~~  409 (530)
                      +..
T Consensus       338 ~~~  340 (468)
T 3pxg_A          338 RDR  340 (468)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            764

>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=99.52  E-value=2.8e-13  Score=153.66  Aligned_cols=154  Identities=14%  Similarity=0.249  Sum_probs=112.6

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCC----CCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh---
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRA----WKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN---  267 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~----~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~---  267 (530)
                      .++|+++.++.|...+.....        |..    +..++||+||||||||++|+++|+.++.+++.++++.+...   
T Consensus       459 ~v~g~~~~~~~l~~~i~~~~~--------g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~  530 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMARA--------GLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTV  530 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHT--------TCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCC
T ss_pred             hccCHHHHHHHHHHHHHHHhc--------ccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhH
Confidence            467788877777776654321        221    12369999999999999999999999999999998776321   


Q ss_pred             ----------------HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          268 ----------------SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       268 ----------------~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                                      ..+...+.. ..++||||||||.+-                                       
T Consensus       531 ~~l~g~~~g~~g~~~~~~l~~~~~~-~~~~vl~lDEi~~~~---------------------------------------  570 (758)
T 1r6b_X          531 SRLIGAPPGYVGFDQGGLLTDAVIK-HPHAVLLLDEIEKAH---------------------------------------  570 (758)
T ss_dssp             SSSCCCCSCSHHHHHTTHHHHHHHH-CSSEEEEEETGGGSC---------------------------------------
T ss_pred             hhhcCCCCCCcCccccchHHHHHHh-CCCcEEEEeCccccC---------------------------------------
Confidence                            123333333 457999999999861                                       


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCC-------CCCeEEEEEeCCCC-------------------------CCChhh
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCC-------SEEKIIVFTTNHRD-------------------------SVDPAL  379 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~-------~~~~ivI~TTN~~~-------------------------~LDpAL  379 (530)
                                ...++.|+..||.-.-..       -.+.+||+|||...                         .++|+|
T Consensus       571 ----------~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l  640 (758)
T 1r6b_X          571 ----------PDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEF  640 (758)
T ss_dssp             ----------HHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHH
T ss_pred             ----------HHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHH
Confidence                      225667777776321000       13578999999854                         678999


Q ss_pred             hcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          380 IRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       380 lRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      +.  |||..|.|++++.+++..|+..++.
T Consensus       641 ~~--R~~~~i~~~~l~~~~~~~i~~~~l~  667 (758)
T 1r6b_X          641 RN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_dssp             HT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             Hh--hCCcceeeCCCCHHHHHHHHHHHHH
Confidence            98  9999999999999999999998864

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=99.50  E-value=8.6e-13  Score=135.41  Aligned_cols=124  Identities=17%  Similarity=0.198  Sum_probs=96.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC------------------------CcEEEEecC---ccCChHHHHHHHHhc---
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC------------------------YDVYDLELT---KVTDNSELRALLLQT---  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~------------------------~~i~~l~l~---~~~~~~~L~~l~~~~---  277 (530)
                      +.+||||||||||||++|+++|+.+.                        .+++.++..   .-.+-..++.++...   
T Consensus        24 ~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~~~i~~ir~l~~~~~~~  103 (334)
T 1a5t_A           24 HHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEH  103 (334)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTSC
T ss_pred             ceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccccCCCCCHHHHHHHHHHHhhc
Confidence            45799999999999999999999874                        346666653   223445677776654   


Q ss_pred             ---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC
Q 009640          278 ---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG  354 (530)
Q Consensus       278 ---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg  354 (530)
                         ..+.|++|||+|.+-                                                 ....+.||+.++.
T Consensus       104 ~~~~~~kvviIdead~l~-------------------------------------------------~~a~naLLk~lEe  134 (334)
T 1a5t_A          104 ARLGGAKVVWVTDAALLT-------------------------------------------------DAAANALLKTLEE  134 (334)
T ss_dssp             CTTSSCEEEEESCGGGBC-------------------------------------------------HHHHHHHHHHHTS
T ss_pred             cccCCcEEEEECchhhcC-------------------------------------------------HHHHHHHHHHhcC
Confidence               246899999999871                                                 1235678888874


Q ss_pred             CccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          355 LWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       355 l~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                      -    ....++|++||.+++|.|++++  |+. .+.|+.|+.++...++....
T Consensus       135 p----~~~~~~Il~t~~~~~l~~ti~S--Rc~-~~~~~~~~~~~~~~~L~~~~  180 (334)
T 1a5t_A          135 P----PAETWFFLATREPERLLATLRS--RCR-LHYLAPPPEQYAVTWLSREV  180 (334)
T ss_dssp             C----CTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHC
T ss_pred             C----CCCeEEEEEeCChHhCcHHHhh--cce-eeeCCCCCHHHHHHHHHHhc
Confidence            3    3568899999999999999998  764 69999999999999888776

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.50  E-value=2.1e-13  Score=154.75  Aligned_cols=148  Identities=16%  Similarity=0.188  Sum_probs=107.3

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcE
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDV  256 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i  256 (530)
                      ...+..|+.++|.++..+.+...+..             ..+.++|||||||||||++|+++|+.+          +..+
T Consensus       173 ~~~~~~ld~iiG~~~~i~~l~~~l~~-------------~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~  239 (758)
T 3pxi_A          173 IAKEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRV  239 (758)
T ss_dssp             HTTSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCE
T ss_pred             HHhhCCCCCccCchHHHHHHHHHHhC-------------CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeE
Confidence            34667899999999888877665431             225689999999999999999999997          8888


Q ss_pred             EEEecCcc-C--ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          257 YDLELTKV-T--DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       257 ~~l~l~~~-~--~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      +.+++..- .  ....++.+|..+  ..++|||||   ...                                       
T Consensus       240 ~~~~~g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD---~~~---------------------------------------  277 (758)
T 3pxi_A          240 MTLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID---AAI---------------------------------------  277 (758)
T ss_dssp             ECC----------CTTHHHHHHHHHTCCCCEEEEC---C-----------------------------------------
T ss_pred             EEecccccccchHHHHHHHHHHHHHhcCCEEEEEc---Cch---------------------------------------
Confidence            88776111 1  123567777654  578999999   100                                       


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                                 ...+.|+..++      .+.+.+|+|||..+     .+||+|.|  ||. .|.|+.|+.+++..|++.+
T Consensus       278 -----------~~~~~L~~~l~------~~~v~~I~at~~~~~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~  337 (758)
T 3pxi_A          278 -----------DASNILKPSLA------RGELQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGL  337 (758)
T ss_dssp             -----------------CCCTT------SSSCEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHT
T ss_pred             -----------hHHHHHHHHHh------cCCEEEEeCCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHH
Confidence                       01233444444      35688999999988     79999999  995 5999999999999999987


Q ss_pred             hCC
Q 009640          407 LGI  409 (530)
Q Consensus       407 l~~  409 (530)
                      +..
T Consensus       338 ~~~  340 (758)
T 3pxi_A          338 RDR  340 (758)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            764

>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=99.49  E-value=9.2e-14  Score=159.73  Aligned_cols=189  Identities=14%  Similarity=0.157  Sum_probs=118.3

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEE
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVY  257 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~  257 (530)
                      ..+.+|+.++|.++..+.+.+.+    ..         ..++++||+||||||||++++++|+.+          +..++
T Consensus       164 ~r~~~ld~viGr~~~i~~l~~~l----~~---------~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~  230 (854)
T 1qvr_A          164 AAEGKLDPVIGRDEEIRRVIQIL----LR---------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIV  230 (854)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHH----HC---------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEE
T ss_pred             HhcCCCcccCCcHHHHHHHHHHH----hc---------CCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEE
Confidence            35678999999987766666544    21         124689999999999999999999998          88999


Q ss_pred             EEecCccCC--------hHHHHHHHHhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          258 DLELTKVTD--------NSELRALLLQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       258 ~l~l~~~~~--------~~~L~~l~~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      .++++.+..        ...+..++..+   ..|+||||||||.+.+....                             
T Consensus       231 ~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~-----------------------------  281 (854)
T 1qvr_A          231 SLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKA-----------------------------  281 (854)
T ss_dssp             EECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC--------------------------------------
T ss_pred             EeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCc-----------------------------
Confidence            998776632        23466666654   46899999999998421100                             


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC----CCChhhhcCCceeEEEEeCCCCHHHHHHH
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD----SVDPALIRCGRMDVHVSLGTCGPHAFKVL  402 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~----~LDpALlRpGR~d~~I~~~~p~~~~r~~i  402 (530)
                                  .......+.|...++      ..++.+|++||.++    .+|++|.|  ||+. |.|+.|+.+++..|
T Consensus       282 ------------~g~~~~~~~L~~~l~------~~~i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~i  340 (854)
T 1qvr_A          282 ------------EGAVDAGNMLKPALA------RGELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISI  340 (854)
T ss_dssp             ----------------------HHHHH------TTCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHH
T ss_pred             ------------cchHHHHHHHHHHHh------CCCeEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHH
Confidence                        001111222333332      24567888888775    48999999  9996 99999999999999


Q ss_pred             HHHhhCCc----CccchHHHHHHHHH-----hCCCCCHHHHHHHHH
Q 009640          403 AKNYLGIE----SHHALFDVVESCIR-----AGGALTPAQIGEVLL  439 (530)
Q Consensus       403 ~~~~l~~~----~~~~~~~~i~~l~~-----~~~~~spadi~~~l~  439 (530)
                      ++.++...    ......+.+..++.     .+..+.|.....++.
T Consensus       341 L~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~lld  386 (854)
T 1qvr_A          341 LRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLID  386 (854)
T ss_dssp             HHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHH
T ss_pred             HHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhcccccChHHHHHHHH
Confidence            98765421    11111222332222     245677777666654

>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=99.49  E-value=4.2e-13  Score=152.27  Aligned_cols=158  Identities=17%  Similarity=0.205  Sum_probs=111.2

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEE
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVY  257 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~  257 (530)
                      ..+..|+.++|.++..+.+++.+    ..         ..+.++||+||||||||++++++|+.+          +..++
T Consensus       180 ~~~~~~d~~iGr~~~i~~l~~~l----~~---------~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~  246 (758)
T 1r6b_X          180 ARVGGIDPLIGREKELERAIQVL----CR---------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIY  246 (758)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHH----TS---------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEE
T ss_pred             HhcCCCCCccCCHHHHHHHHHHH----hc---------cCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEE
Confidence            45678999999988777666543    22         235789999999999999999999987          66777


Q ss_pred             EEecCccC--------ChHHHHHHHHhcC--CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccc
Q 009640          258 DLELTKVT--------DNSELRALLLQTT--NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS  327 (530)
Q Consensus       258 ~l~l~~~~--------~~~~L~~l~~~~~--~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  327 (530)
                      .+++..+.        ....++.++....  .++||||||||.+++..                                
T Consensus       247 ~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~--------------------------------  294 (758)
T 1r6b_X          247 SLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAG--------------------------------  294 (758)
T ss_dssp             ECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSC--------------------------------
T ss_pred             EEcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcC--------------------------------
Confidence            77665442        1345777777653  48999999999985200                                


Q ss_pred             cCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHH
Q 009640          328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVL  402 (530)
Q Consensus       328 ~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i  402 (530)
                              ..........+.|...++      ..++.+|++||.++     .+||+|.|  ||+ .|.|+.|+.+++..|
T Consensus       295 --------~~~~~~~~~~~~L~~~l~------~~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~i  357 (758)
T 1r6b_X          295 --------AASGGQVDAANLIKPLLS------SGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQI  357 (758)
T ss_dssp             --------CSSSCHHHHHHHHSSCSS------SCCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHH
T ss_pred             --------CCCcchHHHHHHHHHHHh------CCCeEEEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHH
Confidence                    000111222233333333      35678888888653     57999999  998 699999999999999


Q ss_pred             HHHhh
Q 009640          403 AKNYL  407 (530)
Q Consensus       403 ~~~~l  407 (530)
                      ++.++
T Consensus       358 l~~l~  362 (758)
T 1r6b_X          358 INGLK  362 (758)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98665

>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=99.49  E-value=6.6e-13  Score=131.24  Aligned_cols=154  Identities=14%  Similarity=0.157  Sum_probs=97.0

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---CcEEEEecCccCCh
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---YDVYDLELTKVTDN  267 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~~~~~~  267 (530)
                      .+|++++|.....+.+.+.+......           ..++||+||||||||++|+++++.+.   .+++.++++.+...
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~~~~-----------~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~~   71 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHLAPL-----------DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNEN   71 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHHTTS-----------CSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCHH
T ss_pred             cccccceeCCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCChh
Confidence            47899999988888888877665432           36899999999999999999999985   67999998876422


Q ss_pred             HHHH-HHHH-----------------hcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccC
Q 009640          268 SELR-ALLL-----------------QTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTC  329 (530)
Q Consensus       268 ~~L~-~l~~-----------------~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~  329 (530)
                       .+. .+|.                 ....+++|||||||.+-.                                    
T Consensus        72 -~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~------------------------------------  114 (265)
T 2bjv_A           72 -LLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPM------------------------------------  114 (265)
T ss_dssp             -HHHHHHHCCC---------CCCCHHHHTTTSEEEEESGGGSCH------------------------------------
T ss_pred             -HHHHHhcCCcccccccccccccchhhhcCCcEEEEechHhcCH------------------------------------
Confidence             222 2221                 112468999999998721                                    


Q ss_pred             CCCCCCCCCcchhhhHHHHhhhccCCc-------cCCCCCeEEEEEeCCC-------CCCChhhhcCCcee-EEEEeCCC
Q 009640          330 GNNNNNNGEESGRVTLSGLLNFTDGLW-------SCCSEEKIIVFTTNHR-------DSVDPALIRCGRMD-VHVSLGTC  394 (530)
Q Consensus       330 ~~~~~~~~~~~~~~~ls~LLn~lDgl~-------s~~~~~~ivI~TTN~~-------~~LDpALlRpGR~d-~~I~~~~p  394 (530)
                                   .....|+..++.-.       ......+.||+|||.+       ..++++|.+  ||+ ..|.+|..
T Consensus       115 -------------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~--Rl~~~~i~lp~L  179 (265)
T 2bjv_A          115 -------------MVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLD--ALAFDVVQLPPL  179 (265)
T ss_dssp             -------------HHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHH--HHCSEEEECCCG
T ss_pred             -------------HHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHH--hhcCcEEeCCCh
Confidence                         12334444444210       0001346788999984       357899998  886 45666655


Q ss_pred             CH--HHHHHHHHHhh
Q 009640          395 GP--HAFKVLAKNYL  407 (530)
Q Consensus       395 ~~--~~r~~i~~~~l  407 (530)
                      +.  +....+++.++
T Consensus       180 ~~R~~di~~l~~~~l  194 (265)
T 2bjv_A          180 RERESDIMLMAEYFA  194 (265)
T ss_dssp             GGCHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHH
Confidence            43  45555655554

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.48  E-value=2.3e-13  Score=154.45  Aligned_cols=158  Identities=14%  Similarity=0.227  Sum_probs=112.7

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCC-ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCCh--
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWK-RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDN--  267 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~-rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~--  267 (530)
                      +.++|+++.++.|...+......-..     ...+ .++||+||||||||++|+++|+.+   +.+++.++++.+...  
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~-----~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~  565 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKD-----PKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHS  565 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSC-----TTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCC
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCC-----CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhcccccc
Confidence            45788898888888877665421100     0112 269999999999999999999998   788999998877532  


Q ss_pred             ---HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhh
Q 009640          268 ---SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVT  344 (530)
Q Consensus       268 ---~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (530)
                         ..+...+.. ..++||||||||.+-                                                 ...
T Consensus       566 ~~~~~l~~~~~~-~~~~vl~lDEi~~~~-------------------------------------------------~~~  595 (758)
T 3pxi_A          566 TSGGQLTEKVRR-KPYSVVLLDAIEKAH-------------------------------------------------PDV  595 (758)
T ss_dssp             CC---CHHHHHH-CSSSEEEEECGGGSC-------------------------------------------------HHH
T ss_pred             cccchhhHHHHh-CCCeEEEEeCccccC-------------------------------------------------HHH
Confidence               233333332 467899999999861                                                 235


Q ss_pred             HHHHhhhccCCccC-------CCCCeEEEEEeCCCCC------------CChhhhcCCceeEEEEeCCCCHHHHHHHHHH
Q 009640          345 LSGLLNFTDGLWSC-------CSEEKIIVFTTNHRDS------------VDPALIRCGRMDVHVSLGTCGPHAFKVLAKN  405 (530)
Q Consensus       345 ls~LLn~lDgl~s~-------~~~~~ivI~TTN~~~~------------LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~  405 (530)
                      .+.||+.||.-.-.       ...+.+||+|||.+..            ++|+|+.  |||..|.|++|+.+++..|++.
T Consensus       596 ~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~  673 (758)
T 3pxi_A          596 FNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSL  673 (758)
T ss_dssp             HHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHH
T ss_pred             HHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHH
Confidence            56677777642110       1235689999997654            7889988  9999999999999999999998


Q ss_pred             hhC
Q 009640          406 YLG  408 (530)
Q Consensus       406 ~l~  408 (530)
                      ++.
T Consensus       674 ~l~  676 (758)
T 3pxi_A          674 MSD  676 (758)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            764

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.41  E-value=2.2e-12  Score=139.21  Aligned_cols=146  Identities=16%  Similarity=0.126  Sum_probs=93.8

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC--cEEEEecCccCChHHH--
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY--DVYDLELTKVTDNSEL--  270 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~--~i~~l~l~~~~~~~~L--  270 (530)
                      .++|.+++++.+...+..               ..++||+||||||||+||+++|+.++.  .+..+.... .+.+++  
T Consensus        23 ~ivGq~~~i~~l~~al~~---------------~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~-~t~~dL~G   86 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALS---------------GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRF-STPEEVFG   86 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHH---------------TCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTT-CCHHHHHC
T ss_pred             hhHHHHHHHHHHHHHHhc---------------CCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhc-CCHHHhcC
Confidence            367777777665544321               358999999999999999999999854  333333321 111211  


Q ss_pred             ---------HHHHHhc-----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCC
Q 009640          271 ---------RALLLQT-----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNN  336 (530)
Q Consensus       271 ---------~~l~~~~-----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~  336 (530)
                               ...+...     ..++|||||||+.+-                                            
T Consensus        87 ~~~~~~~~~~g~~~~~~~g~l~~~~IL~IDEI~r~~--------------------------------------------  122 (500)
T 3nbx_X           87 PLSIQALKDEGRYERLTSGYLPEAEIVFLDEIWKAG--------------------------------------------  122 (500)
T ss_dssp             CBC----------CBCCTTSGGGCSEEEEESGGGCC--------------------------------------------
T ss_pred             cccHHHHhhchhHHhhhccCCCcceeeeHHhHhhhc--------------------------------------------
Confidence                     1122222     146799999998751                                            


Q ss_pred             CCcchhhhHHHHhhhcc-------CCccCCCCCeEEEEEeCCCCC---CChhhhcCCceeEEEEeCCCCH-HHHHHHHHH
Q 009640          337 GEESGRVTLSGLLNFTD-------GLWSCCSEEKIIVFTTNHRDS---VDPALIRCGRMDVHVSLGTCGP-HAFKVLAKN  405 (530)
Q Consensus       337 ~~~~~~~~ls~LLn~lD-------gl~s~~~~~~ivI~TTN~~~~---LDpALlRpGR~d~~I~~~~p~~-~~r~~i~~~  405 (530)
                           ..+.+.|+..|+       |.... ...+++|+|||....   +.+|+++  ||..+|++++|+. +++..|++.
T Consensus       123 -----~~~q~~LL~~lee~~v~i~G~~~~-~~~~~iI~ATN~lpe~~~~~~aLld--RF~~~i~v~~p~~~ee~~~IL~~  194 (500)
T 3nbx_X          123 -----PAILNTLLTAINERQFRNGAHVEK-IPMRLLVAASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTS  194 (500)
T ss_dssp             -----HHHHHHHHHHHHSSEEECSSSEEE-CCCCEEEEEESSCCCTTCTTHHHHT--TCCEEEECCSCCCHHHHHHHHTC
T ss_pred             -----HHHHHHHHHHHHHHhccCCCCcCC-cchhhhhhccccCCCccccHHHHHH--HHHHHHHHHHhhhhhhHHHHHhc
Confidence                 224556666664       22211 233467888886322   4469999  9999999999987 778888877


Q ss_pred             hhC
Q 009640          406 YLG  408 (530)
Q Consensus       406 ~l~  408 (530)
                      ...
T Consensus       195 ~~~  197 (500)
T 3nbx_X          195 QQD  197 (500)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            653

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.41  E-value=4.8e-13  Score=120.57  Aligned_cols=84  Identities=13%  Similarity=0.201  Sum_probs=64.7

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELR  271 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~  271 (530)
                      +++|.....+.+.+.+......           ...+||+||||||||++|+++++..   +.+++ +++..+.....+.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~-----------~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~~~~~   69 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSET-----------DIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNAPQLN   69 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTC-----------CSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTSSCHH
T ss_pred             CceeCCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcchhhh
Confidence            4667777777777777665432           3579999999999999999999987   77888 9888876655566


Q ss_pred             HHHHhcCCCeEEEEcCccch
Q 009640          272 ALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       272 ~l~~~~~~~sII~IDeID~~  291 (530)
                      .++..+ ..++|||||||.+
T Consensus        70 ~~~~~a-~~g~l~ldei~~l   88 (145)
T 3n70_A           70 DFIALA-QGGTLVLSHPEHL   88 (145)
T ss_dssp             HHHHHH-TTSCEEEECGGGS
T ss_pred             cHHHHc-CCcEEEEcChHHC
Confidence            666655 4578999999987

>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=99.39  E-value=2.2e-12  Score=148.20  Aligned_cols=159  Identities=16%  Similarity=0.270  Sum_probs=112.1

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChH--
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNS--  268 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~--  268 (530)
                      +.|+|++...+.+...+......-.   .-+ .+...+||+||||||||++|++||+.+   +.+++.++++.+....  
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~---~~~-~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~  633 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLK---DPN-RPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV  633 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCS---CSS-SCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGG
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccC---CCC-CCceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHH
Confidence            5678888888877777755432100   000 112479999999999999999999999   7889999887664321  


Q ss_pred             -----------------HHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          269 -----------------ELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       269 -----------------~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                                       .+...+.. ...+||||||||.+                                        
T Consensus       634 s~l~g~~~~~~G~~~~g~l~~~~~~-~~~~vl~lDEi~~l----------------------------------------  672 (854)
T 1qvr_A          634 SRLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKA----------------------------------------  672 (854)
T ss_dssp             GGC--------------CHHHHHHH-CSSEEEEESSGGGS----------------------------------------
T ss_pred             HHHcCCCCCCcCccccchHHHHHHh-CCCeEEEEeccccc----------------------------------------
Confidence                             12222222 45689999999986                                        


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCC-------CCCeEEEEEeCC--------------------------CCCCChh
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCC-------SEEKIIVFTTNH--------------------------RDSVDPA  378 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~-------~~~~ivI~TTN~--------------------------~~~LDpA  378 (530)
                               ...+++.||..||.-.-..       -.+.+||+|||.                          ...+.|+
T Consensus       673 ---------~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~  743 (854)
T 1qvr_A          673 ---------HPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPE  743 (854)
T ss_dssp             ---------CHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHH
T ss_pred             ---------CHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHH
Confidence                     1235667788777432100       135789999997                          2356788


Q ss_pred             hhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          379 LIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       379 LlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      |+.  |||..|.|.+|+.+....|+..++.
T Consensus       744 l~~--Rl~~~i~~~pl~~edi~~i~~~~l~  771 (854)
T 1qvr_A          744 FLN--RLDEIVVFRPLTKEQIRQIVEIQLS  771 (854)
T ss_dssp             HHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             HHH--hcCeEEeCCCCCHHHHHHHHHHHHH
Confidence            888  9999999999999999999998864

>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=99.35  E-value=3.8e-12  Score=129.14  Aligned_cols=122  Identities=17%  Similarity=0.247  Sum_probs=96.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc------CCcEEEEecCc-cCChHHHHHHHHhc------CCCeEEEEcCccchhhhh
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL------CYDVYDLELTK-VTDNSELRALLLQT------TNRSIIVIEDIDCSVDLT  295 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l------~~~i~~l~l~~-~~~~~~L~~l~~~~------~~~sII~IDeID~~~~~~  295 (530)
                      ..||||||||||||+++.++|+.+      ..+++.++... -.+-..++.++..+      ....|+||||+|.+-   
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            589999999999999999999874      45888888753 34455677776654      235799999999871   


Q ss_pred             hhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCC
Q 009640          296 ADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSV  375 (530)
Q Consensus       296 ~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~L  375 (530)
                                                                    ....+.||..|+..    .+..++|++||.+++|
T Consensus        96 ----------------------------------------------~~a~naLLk~LEep----~~~t~fIl~t~~~~kl  125 (305)
T 2gno_A           96 ----------------------------------------------QQAANAFLKALEEP----PEYAVIVLNTRRWHYL  125 (305)
T ss_dssp             ----------------------------------------------HHHHHHTHHHHHSC----CTTEEEEEEESCGGGS
T ss_pred             ----------------------------------------------HHHHHHHHHHHhCC----CCCeEEEEEECChHhC
Confidence                                                          12356788888743    3568889999999999


Q ss_pred             ChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          376 DPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       376 DpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      .|++++  |   .+.|+.|+.++...++...++
T Consensus       126 ~~tI~S--R---~~~f~~l~~~~i~~~L~~~~~  153 (305)
T 2gno_A          126 LPTIKS--R---VFRVVVNVPKEFRDLVKEKIG  153 (305)
T ss_dssp             CHHHHT--T---SEEEECCCCHHHHHHHHHHHT
T ss_pred             hHHHHc--e---eEeCCCCCHHHHHHHHHHHhC
Confidence            999999  7   789999999999998887764

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.34  E-value=5e-13  Score=120.20  Aligned_cols=83  Identities=12%  Similarity=0.055  Sum_probs=61.4

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALL  274 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~  274 (530)
                      +++|.+...+.+.+.+..+...           ..++||+||||||||++|+++++..+ +++.++++.+... .+..++
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~-----------~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~~-~~~~~~   71 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKR-----------TSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLID-MPMELL   71 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTC-----------SSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHHH-CHHHHH
T ss_pred             CceeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCChH-hhhhHH
Confidence            3567777778888888766543           35899999999999999999999988 8888877654321 134455


Q ss_pred             HhcCCCeEEEEcCccch
Q 009640          275 LQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       275 ~~~~~~sII~IDeID~~  291 (530)
                      ..+ .+++|||||||.+
T Consensus        72 ~~a-~~~~l~lDei~~l   87 (143)
T 3co5_A           72 QKA-EGGVLYVGDIAQY   87 (143)
T ss_dssp             HHT-TTSEEEEEECTTC
T ss_pred             HhC-CCCeEEEeChHHC
Confidence            544 4689999999987

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.33  E-value=1.7e-11  Score=124.24  Aligned_cols=151  Identities=13%  Similarity=0.180  Sum_probs=96.5

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELR  271 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~  271 (530)
                      +++|.....+.+.+.+......           ..++||+||||||||++|++|++..   +.+++.++++.+..+.--.
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~-----------~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~l~~~   71 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPS-----------DATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLES   71 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCST-----------TSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHHHHHH
T ss_pred             CcEECCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChHHHHH
Confidence            4677777777777777665432           3689999999999999999999976   5788899888764321111


Q ss_pred             HHHHh-----------------cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCC
Q 009640          272 ALLLQ-----------------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNN  334 (530)
Q Consensus       272 ~l~~~-----------------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~  334 (530)
                      .+|..                 ...+++|||||||.+-                                          
T Consensus        72 ~lfg~~~g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~------------------------------------------  109 (304)
T 1ojl_A           72 ELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS------------------------------------------  109 (304)
T ss_dssp             HHTCCCSSCCC---CCCCCHHHHHTTSEEEEESCTTCC------------------------------------------
T ss_pred             HhcCccccccCchhhhhcCHHHhcCCCEEEEeccccCC------------------------------------------
Confidence            22211                 1235799999999872                                          


Q ss_pred             CCCCcchhhhHHHHhhhccCCc-------cCCCCCeEEEEEeCCC-------CCCChhhhcCCcee-EEEEeCCCC--HH
Q 009640          335 NNGEESGRVTLSGLLNFTDGLW-------SCCSEEKIIVFTTNHR-------DSVDPALIRCGRMD-VHVSLGTCG--PH  397 (530)
Q Consensus       335 ~~~~~~~~~~ls~LLn~lDgl~-------s~~~~~~ivI~TTN~~-------~~LDpALlRpGR~d-~~I~~~~p~--~~  397 (530)
                             ......|+..++...       ......+.||+|||.+       ..+++.|..  ||. ..|++|+..  .+
T Consensus       110 -------~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~~~~i~lPpL~eR~e  180 (304)
T 1ojl_A          110 -------PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYY--RLNVVAIEMPSLRQRRE  180 (304)
T ss_dssp             -------HHHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHH--HHSSEEEECCCSGGGGG
T ss_pred             -------HHHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHh--hcCeeEEeccCHHHhHh
Confidence                   112334555554321       0012346788999975       246777777  774 446666554  34


Q ss_pred             HHHHHHHHhh
Q 009640          398 AFKVLAKNYL  407 (530)
Q Consensus       398 ~r~~i~~~~l  407 (530)
                      ....|+..++
T Consensus       181 di~~l~~~~l  190 (304)
T 1ojl_A          181 DIPLLADHFL  190 (304)
T ss_dssp             GHHHHHHHHH
T ss_pred             hHHHHHHHHH
Confidence            5555666654

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.32  E-value=2.9e-13  Score=149.41  Aligned_cols=127  Identities=18%  Similarity=0.268  Sum_probs=86.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEec----CccCC---hHHHH-------HHHHhcCCCeEEEEcCccchhhhh
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL----TKVTD---NSELR-------ALLLQTTNRSIIVIEDIDCSVDLT  295 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l----~~~~~---~~~L~-------~l~~~~~~~sII~IDeID~~~~~~  295 (530)
                      ++||+||||||||+||+++|+.++..++....    ..+..   .....       ..+.. ...+|+||||||.+-   
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~-A~~gil~IDEid~l~---  404 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGEYYLEAGALVL-ADGGIAVIDEIDKMR---  404 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECSSGGGTSSCSEEECHHHH-HSSSEECCTTTTCCC---
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceeeeccccccccccCCeeEe-cCCCcEEeehhhhCC---
Confidence            79999999999999999999999877665321    11100   00000       01111 246899999999871   


Q ss_pred             hhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC---------CccCCCCCeEEE
Q 009640          296 ADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG---------LWSCCSEEKIIV  366 (530)
Q Consensus       296 ~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg---------l~s~~~~~~ivI  366 (530)
                                                                    ....+.|+..|+.         ..........||
T Consensus       405 ----------------------------------------------~~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vI  438 (595)
T 3f9v_A          405 ----------------------------------------------DEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVI  438 (595)
T ss_dssp             ----------------------------------------------SHHHHHHHHHHHSSSEEEESSSSEEEECCCCEEE
T ss_pred             ----------------------------------------------HhHhhhhHHHHhCCEEEEecCCcEEEecCceEEE
Confidence                                                          1133456665542         221123457899


Q ss_pred             EEeCCCC-------------CCChhhhcCCcee-EEEEeCCCCHHHHHHHHHHhhCC
Q 009640          367 FTTNHRD-------------SVDPALIRCGRMD-VHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       367 ~TTN~~~-------------~LDpALlRpGR~d-~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      +|||.++             .|++||++  ||| ..+..++|+.+ ...|+++.+..
T Consensus       439 aatNp~~G~~~~~~~~~~ni~l~~aLl~--RFDl~~~~~~~~~~e-~~~i~~~il~~  492 (595)
T 3f9v_A          439 AAGNPKFGRYISERPVSDNINLPPTILS--RFDLIFILKDQPGEQ-DRELANYILDV  492 (595)
T ss_dssp             EEECCTTCCSCTTSCSCTTTCSCSSSGG--GCSCCEEECCTTHHH-HHHHHHHHHTT
T ss_pred             EEcCCcCCccCcccCchhccCCCHHHHh--hCeEEEEeCCCCCHH-HHHHHHHHHHH
Confidence            9999987             89999999  998 56667888888 88888888764

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.31  E-value=3.4e-11  Score=125.65  Aligned_cols=164  Identities=9%  Similarity=0.104  Sum_probs=105.8

Q ss_pred             CcccccCChhhhHHHHHHH-HHHHcChhhHhhhcCCCCceEEE--ECCCCCChhHHHHHHHHHc---------CCcEEEE
Q 009640          192 TFETLALEPQLKKQITEDL-TAFANGKEFYHRVGRAWKRGYLL--YGPPGSGKSSLIAAMANYL---------CYDVYDL  259 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l-~~~l~~~~~y~~~g~~~~rG~LL--~GPPGTGKTsLa~AiA~~l---------~~~i~~l  259 (530)
                      ..+.++|.++..+.|.+.+ ........       ..++.++|  +||||||||+|++++++.+         +..++.+
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~~~-------~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~   92 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSGAG-------LSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYV   92 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSC-------BCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcCCC-------CCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEE
Confidence            3477888888888887777 55544300       11457899  9999999999999999887         4566677


Q ss_pred             ecCccCCh----------------------HH----HHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCcccccccc
Q 009640          260 ELTKVTDN----------------------SE----LRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKR  313 (530)
Q Consensus       260 ~l~~~~~~----------------------~~----L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r  313 (530)
                      ++....+.                      ..    +...+.....|.||||||+|.+...                   
T Consensus        93 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~-------------------  153 (412)
T 1w5s_A           93 NAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSS-------------------  153 (412)
T ss_dssp             EGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSC-------------------
T ss_pred             ECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhc-------------------
Confidence            65332111                      11    2222232356899999999987310                   


Q ss_pred             chhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCC--CCeEEEEEeCCCC---CCC---hhhhcCCce
Q 009640          314 SSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCS--EEKIIVFTTNHRD---SVD---PALIRCGRM  385 (530)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~--~~~ivI~TTN~~~---~LD---pALlRpGR~  385 (530)
                                              .......+..|+..++.+.. .+  ..+.||+|||.++   .++   +.+.+  |+
T Consensus       154 ------------------------~~~~~~~l~~l~~~~~~~~~-~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~  206 (412)
T 1w5s_A          154 ------------------------PRIAAEDLYTLLRVHEEIPS-RDGVNRIGFLLVASDVRALSYMREKIPQVES--QI  206 (412)
T ss_dssp             ------------------------TTSCHHHHHHHHTHHHHSCC-TTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TC
T ss_pred             ------------------------cCcchHHHHHHHHHHHhccc-CCCCceEEEEEEeccccHHHHHhhhcchhhh--hc
Confidence                                    00112345555555543321 02  4677888888765   344   66666  56


Q ss_pred             eEEEEeCCCCHHHHHHHHHHhhC
Q 009640          386 DVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       386 d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      ...|.+++++.++...++...+.
T Consensus       207 ~~~i~l~~l~~~e~~~ll~~~~~  229 (412)
T 1w5s_A          207 GFKLHLPAYKSRELYTILEQRAE  229 (412)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHH
T ss_pred             CCeeeeCCCCHHHHHHHHHHHHH
Confidence            55699999999999999987654

>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=99.28  E-value=1.3e-11  Score=154.08  Aligned_cols=137  Identities=25%  Similarity=0.407  Sum_probs=97.3

Q ss_pred             CceEEEECCCCCChhHHH-HHHHHHcCCcEEEEecCccCChHHHHHHHHhc-----------------CCCeEEEEcCcc
Q 009640          228 KRGYLLYGPPGSGKSSLI-AAMANYLCYDVYDLELTKVTDNSELRALLLQT-----------------TNRSIIVIEDID  289 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa-~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~-----------------~~~sII~IDeID  289 (530)
                      .+++||+||||||||++| +++++..++.++.++.+...+...+.+.+...                 ..++||||||||
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            479999999999999999 55666668899999998888777777776531                 135799999999


Q ss_pred             chhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCC------CCe
Q 009640          290 CSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCS------EEK  363 (530)
Q Consensus       290 ~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~------~~~  363 (530)
                      ..-.   +                                  .   -+.......+.+++. ..|++....      .++
T Consensus      1347 mp~~---d----------------------------------~---yg~q~~lelLRq~le-~gg~yd~~~~~~~~~~~i 1385 (2695)
T 4akg_A         1347 LPKL---D----------------------------------K---YGSQNVVLFLRQLME-KQGFWKTPENKWVTIERI 1385 (2695)
T ss_dssp             CSCC---C----------------------------------S---SSCCHHHHHHHHHHH-TSSEECTTTCCEEEEESE
T ss_pred             cccc---c----------------------------------c---cCchhHHHHHHHHHh-cCCEEEcCCCcEEEecCE
Confidence            6310   0                                  0   001111223333332 224433111      247


Q ss_pred             EEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          364 IIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       364 ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      .+|+|||+|.     .|||+|+|  || ..|++++|+.+++..|+..++.
T Consensus      1386 ~lIaA~Npp~~gGR~~l~~rllR--rf-~vi~i~~P~~~~l~~I~~~il~ 1432 (2695)
T 4akg_A         1386 HIVGACNPPTDPGRIPMSERFTR--HA-AILYLGYPSGKSLSQIYEIYYK 1432 (2695)
T ss_dssp             EEEEEECCTTSTTCCCCCHHHHT--TE-EEEECCCCTTTHHHHHHHHHHH
T ss_pred             EEEEecCCCccCCCccCChhhhh--ee-eEEEeCCCCHHHHHHHHHHHHH
Confidence            8999999995     89999999  99 7799999999999999988774

>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=99.27  E-value=3.9e-12  Score=118.31  Aligned_cols=96  Identities=17%  Similarity=0.283  Sum_probs=65.9

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecCc
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELTK  263 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~~  263 (530)
                      ..+.+|+++.......+.+.+.+..+..+-      ..+...+++|+||||||||+|++++|+.+    |..++.++..+
T Consensus         4 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~------~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~   77 (180)
T 3ec2_A            4 YWNANLDTYHPKNVSQNRALLTIRVFVHNF------NPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKD   77 (180)
T ss_dssp             CTTCCSSSCCCCSHHHHHHHHHHHHHHHSC------CGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHH
T ss_pred             hhhCccccccCCCHHHHHHHHHHHHHHHhc------cccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHH
Confidence            356789999875555555666666666432      22335789999999999999999999987    66666665544


Q ss_pred             cCChHHHH---------HHHHhcCCCeEEEEcCccch
Q 009640          264 VTDNSELR---------ALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       264 ~~~~~~L~---------~l~~~~~~~sII~IDeID~~  291 (530)
                      +.  ..+.         .++.....+.+|+|||++..
T Consensus        78 ~~--~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~~  112 (180)
T 3ec2_A           78 LI--FRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGSE  112 (180)
T ss_dssp             HH--HHHHHHHHHTCCSHHHHHHHTCSEEEEETCSSS
T ss_pred             HH--HHHHHHhcCchHHHHHHHhcCCCEEEEeCCCCC
Confidence            31  1111         23333457899999999864

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.09  E-value=9.7e-11  Score=110.63  Aligned_cols=97  Identities=18%  Similarity=0.235  Sum_probs=62.8

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC-CCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA-WKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV  264 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~-~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~  264 (530)
                      .+.+|+++.+.....+.+.+.+..++....      .. .+++++|+||||||||+|++++|+++   +..++.++...+
T Consensus        20 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~   93 (202)
T 2w58_A           20 LRASLSDVDLNDDGRIKAIRFAERFVAEYE------PGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPEL   93 (202)
T ss_dssp             GCCCTTSSCCSSHHHHHHHHHHHHHHHHCC------SSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHH
T ss_pred             HcCCHhhccCCChhHHHHHHHHHHHHHHhh------hccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHH
Confidence            456899998766444555555666654221      11 12799999999999999999999988   567776665432


Q ss_pred             CC-------hHHHHHHHHhcCCCeEEEEcCccch
Q 009640          265 TD-------NSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       265 ~~-------~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      ..       ...+..++.....+.+|+|||++..
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~lilDei~~~  127 (202)
T 2w58_A           94 FRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAE  127 (202)
T ss_dssp             HHHHHHC---CCCHHHHHHHHHSSEEEEEEECCC
T ss_pred             HHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            10       0011222333334579999999864

>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=99.09  E-value=4.9e-11  Score=124.27  Aligned_cols=121  Identities=20%  Similarity=0.222  Sum_probs=86.7

Q ss_pred             hcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcc
Q 009640          223 VGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKS  302 (530)
Q Consensus       223 ~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~  302 (530)
                      ++++.++.++|+||||+|||||++++|+.++..++.++...    ......+....+..++++||++....+.. +    
T Consensus       164 ~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~~~~----~~~~~~lg~~~q~~~~l~dd~~~~~~~~r-~----  234 (377)
T 1svm_A          164 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPL----DRLNFELGVAIDQFLVVFEDVKGTGGESR-D----  234 (377)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCT----TTHHHHHGGGTTCSCEEETTCCCSTTTTT-T----
T ss_pred             cccCCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEeccc----hhHHHHHHHhcchhHHHHHHHHHHHHHHh-h----
Confidence            47788889999999999999999999999987766533221    12222344556778899999998742100 0    


Q ss_pred             cCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcC
Q 009640          303 SNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRC  382 (530)
Q Consensus       303 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRp  382 (530)
                                                       -.......+.+.+.+.+||..       .|+++|||++.+ ++++||
T Consensus       235 ---------------------------------l~~~~~~~~~~~l~~~ldG~v-------~v~~~tn~~~~l-~alf~p  273 (377)
T 1svm_A          235 ---------------------------------LPSGQGINNLDNLRDYLDGSV-------KVNLEKKHLNKR-TQIFPP  273 (377)
T ss_dssp             ---------------------------------CCCCSHHHHHHTTHHHHHCSS-------CEEECCSSSCCE-EECCCC
T ss_pred             ---------------------------------ccccCcchHHHHHHHHhcCCC-------eEeeccCchhhH-HHhhcC
Confidence                                             000011124567888888743       478899999999 799999


Q ss_pred             CceeEEEEeCC
Q 009640          383 GRMDVHVSLGT  393 (530)
Q Consensus       383 GR~d~~I~~~~  393 (530)
                      ||++..+++.+
T Consensus       274 g~ld~~~~~l~  284 (377)
T 1svm_A          274 GIVTMNEYSVP  284 (377)
T ss_dssp             EEEEECSCCCC
T ss_pred             cccChhHHhhc
Confidence            99999988866

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.99  E-value=4.7e-10  Score=106.53  Aligned_cols=62  Identities=19%  Similarity=0.328  Sum_probs=42.8

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      ++|.++++|||||||||||++|.|+|+++.-.++..  ..  +...  -.+.......||+|||+|..
T Consensus        54 ~iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~f--an--s~s~--f~l~~l~~~kIiiLDEad~~  115 (212)
T 1tue_A           54 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISF--VN--STSH--FWLEPLTDTKVAMLDDATTT  115 (212)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCC--CC--SSSC--GGGGGGTTCSSEEEEEECHH
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeE--Ee--ccch--hhhcccCCCCEEEEECCCch
Confidence            467778999999999999999999999997654332  11  1110  01223344569999999953

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=98.98  E-value=5.6e-10  Score=134.19  Aligned_cols=149  Identities=13%  Similarity=0.098  Sum_probs=91.7

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcC----------hhhHhh------hcCC----------CCce--EEEECCCCCC
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANG----------KEFYHR------VGRA----------WKRG--YLLYGPPGSG  240 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~----------~~~y~~------~g~~----------~~rG--~LL~GPPGTG  240 (530)
                      ...+|+++.+.++.|+.+++.+..++..          ++.|+.      .|+.          .|+|  +|+|||||||
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            3478999999999999999999988843          455655      2322          3345  9999999999


Q ss_pred             hhHHHHHHHHHcCCc---EEEEecCc----------------cC------ChHHHHHHHHh--cCCCeEEEEcCccchhh
Q 009640          241 KSSLIAAMANYLCYD---VYDLELTK----------------VT------DNSELRALLLQ--TTNRSIIVIEDIDCSVD  293 (530)
Q Consensus       241 KTsLa~AiA~~l~~~---i~~l~l~~----------------~~------~~~~L~~l~~~--~~~~sII~IDeID~~~~  293 (530)
                      ||+||.++|++...+   ...++...                +.      ++..|+.++..  ...||+|++|+||++.+
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            999999999977433   33343322                11      23446555543  46899999999999864


Q ss_pred             hhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC
Q 009640          294 LTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR  372 (530)
Q Consensus       294 ~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~  372 (530)
                      ....+...                            ++    .+.....+.++++|..|||+...  .+++|| +||+.
T Consensus      1175 ~~~~~g~~----------------------------~~----~~~~~~~r~~~q~l~~~~~~~~~--~~v~v~-~~n~~ 1218 (1706)
T 3cmw_A         1175 KAEIEGEI----------------------------GD----SHMGLAARMMSQAMRKLAGNLKQ--SNTLLI-FINQI 1218 (1706)
T ss_dssp             HHHHHSCT----------------------------TC----CCTTHHHHHHHHHHHHHHHHHHH--TTCEEE-EEECE
T ss_pred             cccccccc----------------------------cc----ccccHHHHHHHHHHHHHHhhhcc--CCeEEE-Eeccc
Confidence            32211000                            00    01133445789999999987652  445555 77774

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.98  E-value=3.1e-10  Score=115.21  Aligned_cols=97  Identities=22%  Similarity=0.339  Sum_probs=60.8

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC----CcEEEEecCcc
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC----YDVYDLELTKV  264 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~----~~i~~l~l~~~  264 (530)
                      .+.+|+++.........+...+..|+...      +.....+++||||||||||+|+.|+|+++.    ..+..+....+
T Consensus       119 ~~~tfd~f~~~~~~~~~~~~~~~~~i~~~------~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l  192 (308)
T 2qgz_A          119 RHIHLSDIDVNNASRMEAFSAILDFVEQY------PSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSF  192 (308)
T ss_dssp             GSCCGGGSCCCSHHHHHHHHHHHHHHHHC------SCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHH
T ss_pred             HhCCHhhCcCCChHHHHHHHHHHHHHHhc------cccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHH
Confidence            35689999876544445555565665421      111257999999999999999999999775    67766665432


Q ss_pred             C-------ChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          265 T-------DNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       265 ~-------~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      .       ....+..++.......|||||||+..
T Consensus       193 ~~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~  226 (308)
T 2qgz_A          193 AIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAE  226 (308)
T ss_dssp             HHHHHCCCC----CCTTHHHHTSSEEEEETCCC-
T ss_pred             HHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            1       11111112222335679999999764

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.97  E-value=1.9e-09  Score=119.30  Aligned_cols=56  Identities=29%  Similarity=0.266  Sum_probs=44.0

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      ....+|..|++++|++.+++.+...+.    .           ...+||+||||||||+|+++||+.+...
T Consensus        32 ~~~~rp~~l~~i~G~~~~l~~l~~~i~----~-----------g~~vll~Gp~GtGKTtlar~ia~~l~~~   87 (604)
T 3k1j_A           32 EIEVPEKLIDQVIGQEHAVEVIKTAAN----Q-----------KRHVLLIGEPGTGKSMLGQAMAELLPTE   87 (604)
T ss_dssp             GSCCCSSHHHHCCSCHHHHHHHHHHHH----T-----------TCCEEEECCTTSSHHHHHHHHHHTSCCS
T ss_pred             cccccccccceEECchhhHhhcccccc----C-----------CCEEEEEeCCCCCHHHHHHHHhccCCcc
Confidence            345678899999999887765555432    1           2589999999999999999999998543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.87  E-value=2.6e-09  Score=96.70  Aligned_cols=57  Identities=12%  Similarity=0.185  Sum_probs=46.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      ...++|+||+|+|||+|++++++.+   |..++.++...+...       .-..++.||+|||++.+
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~-------~~~~~~~lLilDE~~~~   95 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLT-------DAAFEAEYLAVDQVEKL   95 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCC-------GGGGGCSEEEEESTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHH-------HHHhCCCEEEEeCcccc
Confidence            4679999999999999999999988   777888877666443       11346899999999975

>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=98.77  E-value=2.8e-09  Score=108.03  Aligned_cols=68  Identities=19%  Similarity=0.246  Sum_probs=43.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCc--EEEEecCcc----C-ChHH-HHHHHHhc-CCCeEEEEcCccchh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD--VYDLELTKV----T-DNSE-LRALLLQT-TNRSIIVIEDIDCSV  292 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~--i~~l~l~~~----~-~~~~-L~~l~~~~-~~~sII~IDeID~~~  292 (530)
                      |++..+.+||+||||||||+|+.++|...+..  +++++..+.    . +... +..++... ..+ +||||+|+.+.
T Consensus       119 Gi~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~-LLVIDsI~aL~  195 (331)
T 2vhj_A          119 HRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHR-VIVIDSLKNVI  195 (331)
T ss_dssp             EEEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCS-EEEEECCTTTC
T ss_pred             CCCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCC-EEEEecccccc
Confidence            44555678999999999999999999876555  455521211    1 1122 22233222 223 99999999873

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.75  E-value=1.7e-08  Score=95.87  Aligned_cols=120  Identities=13%  Similarity=0.123  Sum_probs=75.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc--------C-CcEEEEecCccC---------------------ChHHHHHHHH-hc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL--------C-YDVYDLELTKVT---------------------DNSELRALLL-QT  277 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l--------~-~~i~~l~l~~~~---------------------~~~~L~~l~~-~~  277 (530)
                      --+|++|+||||||+++.+++...        | ..+|..++..+.                     ....+..++. ..
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~   85 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIKKPE   85 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTTSGG
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhhccc
Confidence            367999999999999998875443        3 666655543221                     1122333321 12


Q ss_pred             CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCcc
Q 009640          278 TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWS  357 (530)
Q Consensus       278 ~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s  357 (530)
                      ..++||||||++.+++....                                       ..+ .    ..+|..+.--  
T Consensus        86 ~~~~vliIDEAq~l~~~~~~---------------------------------------~~e-~----~rll~~l~~~--  119 (199)
T 2r2a_A           86 NIGSIVIVDEAQDVWPARSA---------------------------------------GSK-I----PENVQWLNTH--  119 (199)
T ss_dssp             GTTCEEEETTGGGTSBCCCT---------------------------------------TCC-C----CHHHHGGGGT--
T ss_pred             cCceEEEEEChhhhccCccc---------------------------------------cch-h----HHHHHHHHhc--
Confidence            34899999999998521000                                       000 0    1233333311  


Q ss_pred             CCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHH
Q 009640          358 CCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPH  397 (530)
Q Consensus       358 ~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~  397 (530)
                       ...+.-||++|+.++.||.+|..  |++.++++..|...
T Consensus       120 -r~~~~~iil~tq~~~~l~~~lr~--ri~~~~~l~~~~~~  156 (199)
T 2r2a_A          120 -RHQGIDIFVLTQGPKLLDQNLRT--LVRKHYHIASNKMG  156 (199)
T ss_dssp             -TTTTCEEEEEESCGGGBCHHHHT--TEEEEEEEEECSSC
T ss_pred             -CcCCeEEEEECCCHHHHhHHHHH--HhheEEEEcCcccC
Confidence             13456788899999999999888  99999999876543

>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=98.73  E-value=5.9e-08  Score=121.51  Aligned_cols=130  Identities=18%  Similarity=0.182  Sum_probs=97.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTS  306 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~  306 (530)
                      ..|.+++||||||||++++++|+.+|.+++.++++.-.+...+.++|..+ ...++++||||+.+-.             
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~~~lg~~~~g~~~~Gaw~~~DE~nr~~~-------------  711 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDE-------------  711 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCHHHHHHHHHHHHHHTCEEEEETTTSSCH-------------
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCChhHhhHHHHHHHhcCCEeeehhhhhcCh-------------
Confidence            36899999999999999999999999999999999988889999998876 4579999999998611             


Q ss_pred             cccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHH-------hhhc---------cCCccCCCCCeEEEEEeC
Q 009640          307 TTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGL-------LNFT---------DGLWSCCSEEKIIVFTTN  370 (530)
Q Consensus       307 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~L-------Ln~l---------Dgl~s~~~~~~ivI~TTN  370 (530)
                                                          .+++.+       ++.+         +|-.-.......|++|.|
T Consensus       712 ------------------------------------evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~N  755 (2695)
T 4akg_A          712 ------------------------------------KVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLN  755 (2695)
T ss_dssp             ------------------------------------HHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEEC
T ss_pred             ------------------------------------HHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeC
Confidence                                                112211       1111         121111123445777888


Q ss_pred             ----CCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          371 ----HRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       371 ----~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                          ....|+++|.+  || +.|.|.+||.+...+|+-.-.|.
T Consensus       756 Pgy~g~~eLP~~Lk~--~F-r~v~m~~Pd~~~i~ei~l~s~Gf  795 (2695)
T 4akg_A          756 PGYNGRSELPENLKK--SF-REFSMKSPQSGTIAEMILQIMGF  795 (2695)
T ss_dssp             CCSSSSCCCCHHHHT--TE-EEEECCCCCHHHHHHHHHHHHHC
T ss_pred             CCccCcccccHHHHh--he-EEEEeeCCCHHHHHHHHHHhcCC
Confidence                45679999998  88 67999999999988876444444

>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=98.71  E-value=8.2e-08  Score=94.90  Aligned_cols=59  Identities=17%  Similarity=0.268  Sum_probs=41.6

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccch
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~~  291 (530)
                      ++++++|||||||||||+++.|||+.+..-. .++.+.   .   ...|.....+.|++.||....
T Consensus       102 ~~~n~~~l~GppgtGKt~~a~ala~~~~l~G-~vn~~~---~---~f~l~~~~~k~i~l~Ee~~~~  160 (267)
T 1u0j_A          102 GKRNTIWLFGPATTGKTNIAEAIAHTVPFYG-CVNWTN---E---NFPFNDCVDKMVIWWEEGKMT  160 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHSSCEE-ECCTTC---S---SCTTGGGSSCSEEEECSCCEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHhhhcccc-eeeccc---c---ccccccccccEEEEeccccch
Confidence            5567999999999999999999999876522 222221   1   113455567788888888764

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.68  E-value=1.3e-07  Score=119.21  Aligned_cols=134  Identities=15%  Similarity=0.282  Sum_probs=93.4

Q ss_pred             CceEEEECCCCCChhHHHHHH-HHHcCCcEEEEecCccCChHHHHHHHHh------c------------CCCeEEEEcCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAM-ANYLCYDVYDLELTKVTDNSELRALLLQ------T------------TNRSIIVIEDI  288 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~Ai-A~~l~~~i~~l~l~~~~~~~~L~~l~~~------~------------~~~sII~IDeI  288 (530)
                      .+++||+||||||||+++... ++..++.++.++++.-.+...+...+..      .            .++.|+|||||
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            368999999999999887654 4444777888999888887777777652      0            12369999999


Q ss_pred             cchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc--CCccC------CC
Q 009640          289 DCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD--GLWSC------CS  360 (530)
Q Consensus       289 D~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD--gl~s~------~~  360 (530)
                      +.--                                           .+..+.+..+.-|...||  |.+..      .-
T Consensus      1384 Nmp~-------------------------------------------~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i 1420 (3245)
T 3vkg_A         1384 NLPS-------------------------------------------TDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKL 1420 (3245)
T ss_dssp             TCCC-------------------------------------------CCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEE
T ss_pred             CCCC-------------------------------------------ccccccccHHHHHHHHHHcCCeEECCCCeEEEe
Confidence            9530                                           011112334444444444  22211      01


Q ss_pred             CCeEEEEEeCCC-----CCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          361 EEKIIVFTTNHR-----DSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       361 ~~~ivI~TTN~~-----~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                      .++.+|+|.|.|     ..|+|+|+|  ||-. |++++|+.++...|+..++
T Consensus      1421 ~d~~~vaamnPp~~gGr~~l~~Rf~r--~F~v-i~i~~ps~esL~~If~til 1469 (3245)
T 3vkg_A         1421 DKIQFVGACNPPTDAGRVQLTHRFLR--HAPI-LLVDFPSTSSLTQIYGTFN 1469 (3245)
T ss_dssp             SSEEEEEEECCTTSTTCCCCCHHHHT--TCCE-EECCCCCHHHHHHHHHHHH
T ss_pred             cCeEEEEEcCCCCCCCCccCCHHHHh--hceE-EEeCCCCHHHHHHHHHHHH
Confidence            346788999988     469999999  9976 9999999999999987665

>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=98.66  E-value=2.4e-07  Score=94.01  Aligned_cols=55  Identities=24%  Similarity=0.183  Sum_probs=40.6

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      ..+.++|-++..+.|.+ +    ..            +.++++||+|+|||+|++.+++.++..++.+++..
T Consensus        11 ~~~~~~gR~~el~~L~~-l----~~------------~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~   65 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-L----RA------------PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRK   65 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-T----CS------------SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGG
T ss_pred             CHHHhcChHHHHHHHHH-h----cC------------CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchh
Confidence            44667776665444443 3    21            47899999999999999999999887777777653

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.62  E-value=8.9e-07  Score=89.54  Aligned_cols=54  Identities=24%  Similarity=0.154  Sum_probs=39.8

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      ..-+.++|-++..+.|.+.+..           |    +.++++||+|+|||+|++.+++.++  ++.+++
T Consensus         9 ~~~~~~~gR~~el~~L~~~l~~-----------~----~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~   62 (350)
T 2qen_A            9 TRREDIFDREEESRKLEESLEN-----------Y----PLTLLLGIRRVGKSSLLRAFLNERP--GILIDC   62 (350)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHH-----------C----SEEEEECCTTSSHHHHHHHHHHHSS--EEEEEH
T ss_pred             CChHhcCChHHHHHHHHHHHhc-----------C----CeEEEECCCcCCHHHHHHHHHHHcC--cEEEEe
Confidence            3446678877766666665432           1    5899999999999999999999886  444543

>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=98.41  E-value=1.4e-06  Score=92.21  Aligned_cols=138  Identities=15%  Similarity=0.159  Sum_probs=80.8

Q ss_pred             ccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHH-HHHcCCcEEEEecCccCChHHHHH--
Q 009640          196 LALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAM-ANYLCYDVYDLELTKVTDNSELRA--  272 (530)
Q Consensus       196 l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~Ai-A~~l~~~i~~l~l~~~~~~~~L~~--  272 (530)
                      |.|++.+|+.|.-.+..  ..+.      ....-++||.|+||| ||+|++++ ++.+....|.....  .+...|..  
T Consensus       215 I~G~e~vK~aLll~L~G--G~~k------~rgdihVLL~G~PGt-KS~Lar~i~~~i~pR~~ft~g~~--ss~~gLt~s~  283 (506)
T 3f8t_A          215 LPGAEEVGKMLALQLFS--CVGK------NSERLHVLLAGYPVV-CSEILHHVLDHLAPRGVYVDLRR--TELTDLTAVL  283 (506)
T ss_dssp             STTCHHHHHHHHHHHTT--CCSS------GGGCCCEEEESCHHH-HHHHHHHHHHHTCSSEEEEEGGG--CCHHHHSEEE
T ss_pred             cCCCHHHHHHHHHHHcC--Cccc------cCCceeEEEECCCCh-HHHHHHHHHHHhCCCeEEecCCC--CCccCceEEE
Confidence            77888887766554321  1111      011226999999999 99999999 77766655542211  11111110  


Q ss_pred             -----------HHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcch
Q 009640          273 -----------LLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG  341 (530)
Q Consensus       273 -----------l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (530)
                                 .+. .....|+|||||+.+-                                                 
T Consensus       284 r~~tG~~~~~G~l~-LAdgGvl~lDEIn~~~-------------------------------------------------  313 (506)
T 3f8t_A          284 KEDRGWALRAGAAV-LADGGILAVDHLEGAP-------------------------------------------------  313 (506)
T ss_dssp             EESSSEEEEECHHH-HTTTSEEEEECCTTCC-------------------------------------------------
T ss_pred             EcCCCcccCCCeeE-EcCCCeeehHhhhhCC-------------------------------------------------
Confidence                       011 1346899999999861                                                 


Q ss_pred             hhhHHHHhhhcc-------CCccCCCCCeEEEEEeCCCC-----------CCChhhhcCCceeEEEE-eCCCCHHH
Q 009640          342 RVTLSGLLNFTD-------GLWSCCSEEKIIVFTTNHRD-----------SVDPALIRCGRMDVHVS-LGTCGPHA  398 (530)
Q Consensus       342 ~~~ls~LLn~lD-------gl~s~~~~~~ivI~TTN~~~-----------~LDpALlRpGR~d~~I~-~~~p~~~~  398 (530)
                      ..+.+.|+..|+       |. . -.....||+|+|..+           .|+++++.  |||..+. +++|+.+.
T Consensus       314 ~~~qsaLlEaMEe~~VtI~G~-~-lparf~VIAA~NP~~~yd~~~s~~~~~Lp~alLD--RFDLi~i~~d~pd~e~  385 (506)
T 3f8t_A          314 EPHRWALMEAMDKGTVTVDGI-A-LNARCAVLAAINPGEQWPSDPPIARIDLDQDFLS--HFDLIAFLGVDPRPGE  385 (506)
T ss_dssp             HHHHHHHHHHHHHSEEEETTE-E-EECCCEEEEEECCCC--CCSCGGGGCCSCHHHHT--TCSEEEETTC------
T ss_pred             HHHHHHHHHHHhCCcEEECCE-E-cCCCeEEEEEeCcccccCCCCCccccCCChHHhh--heeeEEEecCCCChhH
Confidence            223444555443       33 1 134568999999876           88999999  9997554 57777654

>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=98.41  E-value=6.2e-06  Score=86.02  Aligned_cols=87  Identities=15%  Similarity=0.188  Sum_probs=59.3

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---CcEEEEecCccCChHHH
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---YDVYDLELTKVTDNSEL  270 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~~~~~~~~L  270 (530)
                      +.+.+....-+.+.+.+......           ...+|++|++||||+++++++.....   .+++.+++..+..+.--
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~a~~-----------~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~~  205 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKISCA-----------ECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFE  205 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHTTC-----------CSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHH
T ss_pred             hhhhhccHHhhHHHHHHHHhcCC-----------CCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHHHH
Confidence            34555555555566655553322           35789999999999999999998874   68999998876433222


Q ss_pred             HHHHHh-----------------cCCCeEEEEcCccch
Q 009640          271 RALLLQ-----------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       271 ~~l~~~-----------------~~~~sII~IDeID~~  291 (530)
                      ..+|-.                 .....+||||||+.+
T Consensus       206 ~elfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l  243 (387)
T 1ny5_A          206 AELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGEL  243 (387)
T ss_dssp             HHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGC
T ss_pred             HHhcCCCCCCCCCcccccCCceeeCCCcEEEEcChhhC
Confidence            333321                 123579999999987

>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=98.40  E-value=6.9e-06  Score=85.10  Aligned_cols=86  Identities=15%  Similarity=0.221  Sum_probs=60.2

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCc--EEEEecCccCChHHHHH
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYD--VYDLELTKVTDNSELRA  272 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~--i~~l~l~~~~~~~~L~~  272 (530)
                      .+.+.......+.+.+......           ...+|++|++||||+.+++++....+..  ++.+++..+..+.--..
T Consensus       130 ~~ig~s~~~~~~~~~~~~~a~~-----------~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~~  198 (368)
T 3dzd_A          130 EFVGEHPKILEIKRLIPKIAKS-----------KAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESE  198 (368)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHTS-----------CSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHHH
T ss_pred             cccccchHHHHHHhhhhhhhcc-----------chhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHHH
Confidence            4566666656666655444332           2469999999999999999999887554  99999988754433334


Q ss_pred             HHHh-----------------cCCCeEEEEcCccch
Q 009640          273 LLLQ-----------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       273 l~~~-----------------~~~~sII~IDeID~~  291 (530)
                      +|-.                 ......||||||+.+
T Consensus       199 lfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l  234 (368)
T 3dzd_A          199 LFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGEL  234 (368)
T ss_dssp             HHEECSCSSSSCCCCEECHHHHTTTSEEEEETGGGS
T ss_pred             hcCccccccCCcccccCChHhhcCCCeEEecChhhC
Confidence            4321                 124568999999987

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.32  E-value=3.3e-06  Score=106.77  Aligned_cols=130  Identities=15%  Similarity=0.116  Sum_probs=95.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTS  306 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~  306 (530)
                      ..|..++||+|||||.+++++|+.+|..++.++++.-.+...+.++|..+ ...+..++|||+.+-              
T Consensus       604 ~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~~~~g~i~~G~~~~GaW~cfDEfNrl~--------------  669 (3245)
T 3vkg_A          604 RMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLE--------------  669 (3245)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCHHHHHHHHHHHHHHTCEEEEETTTSSC--------------
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCHHHHHHHHhhHhhcCcEEEehhhhcCC--------------
Confidence            35778999999999999999999999999999999988888888888876 568899999999861              


Q ss_pred             cccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhh----------------cc-CCccCCCCCeEEEEEe
Q 009640          307 TTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF----------------TD-GLWSCCSEEKIIVFTT  369 (530)
Q Consensus       307 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~----------------lD-gl~s~~~~~~ivI~TT  369 (530)
                                                         ..++|.+...                ++ |-.-.-.....|++|.
T Consensus       670 -----------------------------------~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTm  714 (3245)
T 3vkg_A          670 -----------------------------------ERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTM  714 (3245)
T ss_dssp             -----------------------------------HHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECB
T ss_pred             -----------------------------------HHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEe
Confidence                                               0111111111                11 3110112345577788


Q ss_pred             CC----CCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          370 NH----RDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       370 N~----~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      |.    ...|+++|..  || +.|.|.+||.+...+|+-.-.|.
T Consensus       715 NpgY~gr~eLP~nLk~--lF-r~v~m~~Pd~~~i~ei~L~s~Gf  755 (3245)
T 3vkg_A          715 NPGYAGRSNLPDNLKK--LF-RSMAMIKPDREMIAQVMLYSQGF  755 (3245)
T ss_dssp             CCCGGGCCCSCHHHHT--TE-EEEECCSCCHHHHHHHHHHTTTC
T ss_pred             CCCccCcccChHHHHh--hc-EEEEEeCCCHHHHHHHHHHHccc
Confidence            83    4689999998  87 55999999999888876554444

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.27  E-value=8e-07  Score=108.31  Aligned_cols=69  Identities=14%  Similarity=0.189  Sum_probs=48.8

Q ss_pred             CCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc---------------------CChHHHHHHHH---hc
Q 009640          225 RAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV---------------------TDNSELRALLL---QT  277 (530)
Q Consensus       225 ~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~---------------------~~~~~L~~l~~---~~  277 (530)
                      ++..++++||||||||||+||.++|.+.   |..+..++....                     .....+.+.+.   +.
T Consensus      1424 i~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~ 1503 (2050)
T 3cmu_A         1424 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS 1503 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHHHhc
Confidence            7778899999999999999999998876   444555544322                     11122223333   23


Q ss_pred             CCCeEEEEcCccchhh
Q 009640          278 TNRSIIVIEDIDCSVD  293 (530)
Q Consensus       278 ~~~sII~IDeID~~~~  293 (530)
                      .+|++||||+|+.+++
T Consensus      1504 ~~~~lVVIDsi~al~p 1519 (2050)
T 3cmu_A         1504 GAVDVIVVDSVAALTP 1519 (2050)
T ss_dssp             TCCSEEEESCGGGCCC
T ss_pred             CCCCEEEEcChhHhcc
Confidence            7899999999998864

>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=98.20  E-value=1.3e-05  Score=81.74  Aligned_cols=122  Identities=16%  Similarity=0.148  Sum_probs=82.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CC-cEEEEecCccCChHHHHHHHHhc------CCCeEEEEcCccc-hhhhhh
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CY-DVYDLELTKVTDNSELRALLLQT------TNRSIIVIEDIDC-SVDLTA  296 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~-~i~~l~l~~~~~~~~L~~l~~~~------~~~sII~IDeID~-~~~~~~  296 (530)
                      ...||||||+|+||++.+.++++.+   +. +...+....   +.++++++..+      ..+-||+|||+|. +-    
T Consensus        18 ~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~plf~~~kvvii~~~~~kl~----   90 (343)
T 1jr3_D           18 RAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP---NTDWNAIFSLCQAMSLFASRQTLLLLLPENGPN----   90 (343)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT---TCCHHHHHHHHHHHHHCCSCEEEEEECCSSCCC----
T ss_pred             CcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC---CCCHHHHHHHhcCcCCccCCeEEEEECCCCCCC----
Confidence            4689999999999999999998865   33 222333322   23455554432      4678999999987 41    


Q ss_pred             hhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC---
Q 009640          297 DRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD---  373 (530)
Q Consensus       297 ~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~---  373 (530)
                                                                   ....+.|+..++..    .+..++|++|+.++   
T Consensus        91 ---------------------------------------------~~~~~aLl~~le~p----~~~~~~il~~~~~~~~~  121 (343)
T 1jr3_D           91 ---------------------------------------------AAINEQLLTLTGLL----HDDLLLIVRGNKLSKAQ  121 (343)
T ss_dssp             ---------------------------------------------TTHHHHHHHHHTTC----BTTEEEEEEESCCCTTT
T ss_pred             ---------------------------------------------hHHHHHHHHHHhcC----CCCeEEEEEcCCCChhh
Confidence                                                         11345677777643    24566676666543   


Q ss_pred             ---CCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          374 ---SVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       374 ---~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                         ++-+++..  |. ..+.+..++..+....++..+.
T Consensus       122 ~~~k~~~~i~s--r~-~~~~~~~l~~~~l~~~l~~~~~  156 (343)
T 1jr3_D          122 ENAAWFTALAN--RS-VQVTCQTPEQAQLPRWVAARAK  156 (343)
T ss_dssp             TTSHHHHHHTT--TC-EEEEECCCCTTHHHHHHHHHHH
T ss_pred             HhhHHHHHHHh--Cc-eEEEeeCCCHHHHHHHHHHHHH
Confidence               45667776  44 4689999999888887777663

>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=98.10  E-value=1.1e-05  Score=75.04  Aligned_cols=27  Identities=26%  Similarity=0.516  Sum_probs=23.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      -+.|.||+|+|||||++.|++.++..+
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            368899999999999999999986544

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.84  E-value=6.1e-05  Score=80.19  Aligned_cols=70  Identities=24%  Similarity=0.278  Sum_probs=40.0

Q ss_pred             CCCCccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CC
Q 009640          178 YDSGWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CY  254 (530)
Q Consensus       178 ~~~~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~  254 (530)
                      .+.+|  ++.+.|.+|+++  .+++++.+.. +..++...          ...+|+.||||||||+++.+++..+   +.
T Consensus        10 ~~~~~--~~~~~p~~~~~L--n~~Q~~av~~-~~~~i~~~----------~~~~li~G~aGTGKT~ll~~~~~~l~~~~~   74 (459)
T 3upu_A           10 HSSGL--VPRGSHMTFDDL--TEGQKNAFNI-VMKAIKEK----------KHHVTINGPAGTGATTLTKFIIEALISTGE   74 (459)
T ss_dssp             -------------CCSSCC--CHHHHHHHHH-HHHHHHSS----------SCEEEEECCTTSCHHHHHHHHHHHHHHTTC
T ss_pred             ccCCC--ccccCCCccccC--CHHHHHHHHH-HHHHHhcC----------CCEEEEEeCCCCCHHHHHHHHHHHHHhcCC
Confidence            34578  778889999886  4555554444 33444332          1378999999999999999999887   33


Q ss_pred             -cEEEEecC
Q 009640          255 -DVYDLELT  262 (530)
Q Consensus       255 -~i~~l~l~  262 (530)
                       .++.+..+
T Consensus        75 ~~il~~a~T   83 (459)
T 3upu_A           75 TGIILAAPT   83 (459)
T ss_dssp             CCEEEEESS
T ss_pred             ceEEEecCc
Confidence             45555433

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.66  E-value=0.00048  Score=75.14  Aligned_cols=47  Identities=21%  Similarity=0.197  Sum_probs=32.7

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHH
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ...++|-+...+.|.+.+..    .       ....+-++++||+|.|||+||..+++
T Consensus       123 ~~~~vGR~~~l~~L~~~L~~----~-------~~~~~~v~I~G~~GiGKTtLa~~~~~  169 (591)
T 1z6t_A          123 PVVFVTRKKLVNAIQQKLSK----L-------KGEPGWVTIHGMAGCGKSVLAAEAVR  169 (591)
T ss_dssp             CSSCCCCHHHHHHHHHHHTT----S-------TTSCEEEEEECCTTSSHHHHHHHHHC
T ss_pred             CCeecccHHHHHHHHHHHhc----c-------cCCCceEEEEcCCCCCHHHHHHHHHh
Confidence            35578877766666554421    1       01135689999999999999999864

>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=97.61  E-value=0.00023  Score=66.95  Aligned_cols=40  Identities=25%  Similarity=0.164  Sum_probs=31.2

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      |++...-++|+||||+|||+|+..+|...+..++.++...
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            4555566899999999999999999985566666666543

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.56  E-value=5.4e-05  Score=70.54  Aligned_cols=62  Identities=11%  Similarity=0.108  Sum_probs=37.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc--------cCC----------hHHHHHHHHhcC-CCeEEEEcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK--------VTD----------NSELRALLLQTT-NRSIIVIED  287 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~--------~~~----------~~~L~~l~~~~~-~~sII~IDe  287 (530)
                      -++++||||+|||+++..++..+   +..++.+....        +.+          ...+..++.... ...+|+|||
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            47899999999999997776553   55554432110        000          011222333333 467999999


Q ss_pred             ccch
Q 009640          288 IDCS  291 (530)
Q Consensus       288 ID~~  291 (530)
                      +..+
T Consensus        85 ~Q~~   88 (184)
T 2orw_A           85 VQFF   88 (184)
T ss_dssp             GGGS
T ss_pred             cccC
Confidence            9865

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.43  E-value=9.9e-05  Score=67.85  Aligned_cols=32  Identities=28%  Similarity=0.319  Sum_probs=29.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++.++|.||||+||||+++++|..+++.+++.
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~~~~i~~   36 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTKRILYDS   36 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            35789999999999999999999999998875

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.43  E-value=0.00022  Score=87.32  Aligned_cols=69  Identities=20%  Similarity=0.271  Sum_probs=52.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCCh------------------------HHHHHHHHh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDN------------------------SELRALLLQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~------------------------~~L~~l~~~  276 (530)
                      |++..+.+||+||||||||+|+.+++.+.   |...+.+++......                        ..+...+.+
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            57778889999999999999999998765   677777776653211                        123334555


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ..+|.+||||++..+.
T Consensus      1157 ~~~~dlvVIDsl~~L~ 1172 (2050)
T 3cmu_A         1157 SGAVDVIVVDSVAALT 1172 (2050)
T ss_dssp             HTCCSEEEESCGGGCC
T ss_pred             hCCCCEEEECCccccc
Confidence            6789999999999984

>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=97.42  E-value=0.00012  Score=66.78  Aligned_cols=33  Identities=21%  Similarity=0.315  Sum_probs=29.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      .-++|.||||+||||+++++|..++..+++++.
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            468999999999999999999999988887754

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.40  E-value=0.00051  Score=64.82  Aligned_cols=37  Identities=19%  Similarity=0.081  Sum_probs=27.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      |++...-++|+||||+|||+|+..+|..+   +..++.++
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            34445568999999999999999999654   44554443

>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=97.39  E-value=0.00046  Score=71.03  Aligned_cols=69  Identities=14%  Similarity=0.150  Sum_probs=45.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC---------------------ChHHHHHHHH---h
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT---------------------DNSELRALLL---Q  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~---------------------~~~~L~~l~~---~  276 (530)
                      |++..+-++|+||||+|||+|+..+|..+   +..+..++.....                     +..++..++.   .
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            45555668999999999999999999875   5566556543311                     1122222222   2


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+|+||.+-.+.
T Consensus       137 ~~~~dlvVIDSi~~l~  152 (356)
T 3hr8_A          137 SGVVDLIVVDSVAALV  152 (356)
T ss_dssp             TSCCSEEEEECTTTCC
T ss_pred             hcCCCeEEehHhhhhc
Confidence            3578899999998774

>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=97.38  E-value=0.0019  Score=76.02  Aligned_cols=51  Identities=24%  Similarity=0.252  Sum_probs=35.7

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHH
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      |.....++|-++..++|.+.+...  .         ...+-+.|+|++|.|||+||+.+++.
T Consensus       120 p~~~~~~vgR~~~~~~l~~~l~~~--~---------~~~~~v~i~G~gG~GKTtLa~~~~~~  170 (1249)
T 3sfz_A          120 PQRPVIFVTRKKLVHAIQQKLWKL--N---------GEPGWVTIYGMAGCGKSVLAAEAVRD  170 (1249)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHTT--T---------TSCEEEEEECSTTSSHHHHHHHHTCC
T ss_pred             CCCCceeccHHHHHHHHHHHHhhc--c---------CCCCEEEEEeCCCCCHHHHHHHHhcC
Confidence            344456788887777766655311  1         11356889999999999999998875

>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=97.37  E-value=0.00073  Score=71.74  Aligned_cols=92  Identities=13%  Similarity=0.172  Sum_probs=62.6

Q ss_pred             hhHHHHhhhccCCccCCCCCeEEEEEeCC-------------CCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          343 VTLSGLLNFTDGLWSCCSEEKIIVFTTNH-------------RDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       343 ~~ls~LLn~lDgl~s~~~~~~ivI~TTN~-------------~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      ...+.||..|+.-.    .. ++|++||.             ++.|+|.+++  ||.. +.|++++.++...+++..+..
T Consensus       310 ~a~~aLlk~lEe~~----~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~s--R~~~-~~~~~~~~~e~~~iL~~~~~~  381 (456)
T 2c9o_A          310 ECFTYLHRALESSI----AP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLD--RVMI-IRTMLYTPQEMKQIIKIRAQT  381 (456)
T ss_dssp             HHHHHHHHHTTSTT----CC-EEEEEECCSEEECBTTSSCEEETTCCHHHHT--TEEE-EECCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccC----CC-EEEEecCCccccccccccccccccCChhHHh--hcce-eeCCCCCHHHHHHHHHHHHHH
Confidence            35678888887432    33 56655543             7889999999  9977 699999999999998876421


Q ss_pred             cCccchHHHHHHHHHhCCCCCHHHHHHHHHHh-ccCHHHHHHHHHHHHH
Q 009640          410 ESHHALFDVVESCIRAGGALTPAQIGEVLLRN-RGNVDLAMKEVVSAMQ  457 (530)
Q Consensus       410 ~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~-~~d~~~al~~l~~~l~  457 (530)
                      .               ...+++..+..+...+ .+++..|+.-+..+..
T Consensus       382 ~---------------~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~  415 (456)
T 2c9o_A          382 E---------------GINISEEALNHLGEIGTKTTLRYSVQLLTPANL  415 (456)
T ss_dssp             H---------------TCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHHH
T ss_pred             h---------------CCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHH
Confidence            1               2345665555555544 5677777776655533

>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=97.36  E-value=0.00013  Score=67.17  Aligned_cols=33  Identities=24%  Similarity=0.306  Sum_probs=28.8

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      +.+.-++|.||||+||||+++.+|..+++.+++
T Consensus         3 ~~~~~I~l~G~~GsGKST~~~~L~~~l~~~~i~   35 (193)
T 2rhm_A            3 QTPALIIVTGHPATGKTTLSQALATGLRLPLLS   35 (193)
T ss_dssp             SCCEEEEEEESTTSSHHHHHHHHHHHHTCCEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHcCCeEec
Confidence            334568899999999999999999999988776

>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=97.35  E-value=0.00013  Score=65.78  Aligned_cols=31  Identities=26%  Similarity=0.263  Sum_probs=28.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -++|.||||+||||+++.+|..+++.+++.+
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            4789999999999999999999999988765

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.34  E-value=0.0012  Score=72.16  Aligned_cols=33  Identities=33%  Similarity=0.352  Sum_probs=26.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      +-+++.||||||||+++.+++..+   +..+.-+..
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~Ap  240 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAP  240 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecC
Confidence            568899999999999999998865   566665543

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.32  E-value=0.00016  Score=67.75  Aligned_cols=32  Identities=34%  Similarity=0.343  Sum_probs=28.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ...++|.||||+||||+++++|..+++.+++.
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~   56 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKLNVPFIDL   56 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHTCCEEEH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCCCEEcc
Confidence            35689999999999999999999999988765

>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=97.26  E-value=0.0061  Score=66.10  Aligned_cols=43  Identities=19%  Similarity=0.205  Sum_probs=32.2

Q ss_pred             CChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHH
Q 009640          198 LEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       198 ~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      |-++.+++|.+.+..--          ....+-+.++|++|.|||+||..+++
T Consensus       132 GR~~~~~~l~~~L~~~~----------~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          132 IREYHVDRVIKKLDEMC----------DLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCHHHHHHHHHHHHHHT----------TSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHhccc----------CCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            77777777777663210          11236788999999999999999997

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=97.26  E-value=9.1e-05  Score=60.33  Aligned_cols=52  Identities=8%  Similarity=-0.215  Sum_probs=40.9

Q ss_pred             EeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          390 SLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       390 ~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      +-++||.++|.+||+.++...... ....++.++..+.|||+|||.++|..+.
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~-~dvdl~~LA~~T~G~SGADL~~l~~eAa   58 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLT-RGINLRKIAELMPGASGAEVKGVCTEAG   58 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEEC-TTCCCHHHHHTCSSCCHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCC-cccCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            357899999999999999865433 1123678888899999999999997443

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=97.23  E-value=0.00035  Score=55.53  Aligned_cols=50  Identities=8%  Similarity=-0.220  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          392 GTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       392 ~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      |+|+.++|..||+.++...... ....++.++..+.|||+|||.++|..+.
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~-~~~dl~~la~~t~G~SGADi~~l~~eA~   50 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLT-RGINLRKIAELMPGASGAEVKGVCTEAG   50 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEEC-TTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCC-CccCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            6899999999999999865443 1223788888899999999999997543

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.22  E-value=0.0002  Score=65.38  Aligned_cols=30  Identities=37%  Similarity=0.382  Sum_probs=27.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .++|.||||+||||+++++|..+++.+++.
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d~   35 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLDS   35 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEcc
Confidence            588999999999999999999999888764

>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=97.21  E-value=0.00067  Score=69.62  Aligned_cols=69  Identities=19%  Similarity=0.204  Sum_probs=46.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC---------------------ChHHHHHHHH---h
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT---------------------DNSELRALLL---Q  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~---------------------~~~~L~~l~~---~  276 (530)
                      |++..+-++|+||||+|||+|+..+|..+   +..+..++.....                     +..++..++.   .
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            45555669999999999999999988654   4555555543211                     1122222222   2


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||++..++
T Consensus       137 ~~~~~lIVIDsl~~l~  152 (349)
T 2zr9_A          137 SGALDIIVIDSVAALV  152 (349)
T ss_dssp             TTCCSEEEEECGGGCC
T ss_pred             cCCCCEEEEcChHhhc
Confidence            3568999999999885

>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=97.20  E-value=0.00024  Score=65.05  Aligned_cols=32  Identities=28%  Similarity=0.389  Sum_probs=28.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++.++|.||||+||||+++++|..+++.++++
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            35699999999999999999999999888764

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.18  E-value=0.00026  Score=64.15  Aligned_cols=30  Identities=40%  Similarity=0.681  Sum_probs=26.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .-+.|.||||+||||+++.+|..++..+++
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id   34 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYD   34 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEe
Confidence            458999999999999999999999987665

>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=97.18  E-value=0.00068  Score=68.67  Aligned_cols=40  Identities=18%  Similarity=0.206  Sum_probs=30.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---------CCcEEEEecCc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---------CYDVYDLELTK  263 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---------~~~i~~l~l~~  263 (530)
                      |++...-++|+||||+|||+|+..+|...         +..++.++...
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            45666679999999999999999999875         44566665543

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.15  E-value=0.00028  Score=63.84  Aligned_cols=31  Identities=39%  Similarity=0.435  Sum_probs=28.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..++|.|+||+||||+++.+|..+++++++.
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~id~   38 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVLDT   38 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            4789999999999999999999999999875

>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=97.14  E-value=0.00021  Score=66.03  Aligned_cols=32  Identities=25%  Similarity=0.446  Sum_probs=28.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHH-cCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANY-LCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~-l~~~i~~l  259 (530)
                      ...++|.|+|||||||+++.+|.. +++.++++
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~l~g~~~id~   42 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAELDGFQHLEV   42 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTTEEEEEH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCCEEeeH
Confidence            345899999999999999999999 78887765

>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=97.13  E-value=0.00029  Score=64.63  Aligned_cols=31  Identities=35%  Similarity=0.489  Sum_probs=28.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -++|.|+||+||||+++.+|..+++.+++.+
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            4899999999999999999999999988753

>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=97.13  E-value=0.00087  Score=66.09  Aligned_cols=29  Identities=28%  Similarity=0.241  Sum_probs=23.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |++...-++|+||||+|||+|+..+|..+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            44445568999999999999999998754

>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=97.12  E-value=0.00096  Score=68.66  Aligned_cols=69  Identities=16%  Similarity=0.218  Sum_probs=48.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC---------------------ChHHHHHHHH---h
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT---------------------DNSELRALLL---Q  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~---------------------~~~~L~~l~~---~  276 (530)
                      |++..+-++|+||||+|||+|+..+|..+   +..+..++.....                     +...+..++.   .
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            46666779999999999999999988765   5566666653211                     1223333333   2


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||.+..+.
T Consensus       139 ~~~~~lVVIDsl~~l~  154 (356)
T 1u94_A          139 SGAVDVIVVDSVAALT  154 (356)
T ss_dssp             HTCCSEEEEECGGGCC
T ss_pred             ccCCCEEEEcCHHHhc
Confidence            3678999999999874

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.08  E-value=0.00029  Score=68.82  Aligned_cols=32  Identities=31%  Similarity=0.468  Sum_probs=28.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      -++|.||||+||||+++++|..+++.+++.+.
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            47899999999999999999999988877653

>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=97.07  E-value=0.00035  Score=63.19  Aligned_cols=30  Identities=23%  Similarity=0.414  Sum_probs=27.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.|+||+||||+++.+|..+++.+++.
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg~~~id~   33 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARALGYEFVDT   33 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEcc
Confidence            589999999999999999999999988764

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.06  E-value=0.00083  Score=66.94  Aligned_cols=57  Identities=28%  Similarity=0.412  Sum_probs=37.1

Q ss_pred             hhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          200 PQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      +++.+.+.+.+..++...     .....+.-++|.||||+||||++++++..++..++.++.
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            344444555555555431     112234568899999999999999999998544555543

>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=97.05  E-value=0.001  Score=68.14  Aligned_cols=29  Identities=28%  Similarity=0.340  Sum_probs=25.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |++...-++|+||||+|||+|+..+|..+
T Consensus       127 gi~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          127 GIETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            55666668999999999999999999887

>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=97.01  E-value=0.00041  Score=62.24  Aligned_cols=29  Identities=31%  Similarity=0.356  Sum_probs=26.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.||||+||||+++.+ ..+|+.++++
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            4789999999999999999 8999887764

>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=97.01  E-value=0.0032  Score=59.08  Aligned_cols=32  Identities=16%  Similarity=0.160  Sum_probs=27.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      -+++|+++|+||||.|-++|-..   |+.++.+..
T Consensus        30 ~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF   64 (196)
T 1g5t_A           30 IIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQF   64 (196)
T ss_dssp             CEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEe
Confidence            47889999999999999998765   788887754

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=96.99  E-value=0.00056  Score=63.81  Aligned_cols=31  Identities=32%  Similarity=0.477  Sum_probs=27.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.+|..+++.++++
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l~~~~i~~   51 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKLGIPQIST   51 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCcEEeh
Confidence            3588999999999999999999999887765

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=96.99  E-value=0.0077  Score=57.81  Aligned_cols=33  Identities=21%  Similarity=0.153  Sum_probs=27.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      -.+++.|+||+|||+++.++|..+   |+++..+.+
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~   42 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVV   42 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEe
Confidence            358899999999999999999876   777665544

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.98  E-value=0.00049  Score=63.25  Aligned_cols=31  Identities=23%  Similarity=0.354  Sum_probs=27.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.|+||+||||+++.+|..+++.+++.
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            4588999999999999999999999877653

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=96.98  E-value=0.00052  Score=62.92  Aligned_cols=32  Identities=22%  Similarity=0.316  Sum_probs=28.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +.-++|.|+||+||||+++.+|..+++.+++.
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~   37 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEeeH
Confidence            35689999999999999999999999877765

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.96  E-value=0.0004  Score=63.66  Aligned_cols=30  Identities=27%  Similarity=0.576  Sum_probs=26.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.||||+||||+++.+|..+++.+++.
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            478999999999999999999999776654

>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=96.96  E-value=0.002  Score=65.73  Aligned_cols=40  Identities=13%  Similarity=0.046  Sum_probs=30.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---------CCcEEEEecCc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---------CYDVYDLELTK  263 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---------~~~i~~l~l~~  263 (530)
                      |++...-++|+||||+|||+|+..+|...         +..++.++...
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            45555668999999999999999999873         44566665443

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=96.96  E-value=0.00039  Score=63.76  Aligned_cols=30  Identities=20%  Similarity=0.367  Sum_probs=25.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC-----CcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC-----YDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~-----~~i~~  258 (530)
                      .-++|.||||+||||+++.+|..++     +.+++
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~i~   38 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVS   38 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcCcceEEEe
Confidence            3588999999999999999999987     65554

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.95  E-value=0.00055  Score=61.64  Aligned_cols=30  Identities=30%  Similarity=0.339  Sum_probs=27.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.|+||+||||+++.+|..+++.+++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   31 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDV   31 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            378999999999999999999999888764

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=96.94  E-value=0.0015  Score=67.26  Aligned_cols=60  Identities=30%  Similarity=0.477  Sum_probs=39.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC----CcEEEEecC-cc---------------CChHHHHHHHHhc--CCCeEEEEcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC----YDVYDLELT-KV---------------TDNSELRALLLQT--TNRSIIVIED  287 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~----~~i~~l~l~-~~---------------~~~~~L~~l~~~~--~~~sII~IDe  287 (530)
                      -+++.||+|+||||++++|++.+.    ..++.++-. +.               .....+...+..+  ..|.||++||
T Consensus       125 ~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~~~~~~~~La~aL~~~PdvillDE  204 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGE  204 (356)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHHHHHHHTTSCCSEEEESC
T ss_pred             EEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeeeeccccCCHHHHHHHHhhhCcCEEecCC
Confidence            478899999999999999998873    344443210 00               0111233444444  7899999999


Q ss_pred             cc
Q 009640          288 ID  289 (530)
Q Consensus       288 ID  289 (530)
                      +-
T Consensus       205 p~  206 (356)
T 3jvv_A          205 MR  206 (356)
T ss_dssp             CC
T ss_pred             CC
Confidence            84

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.93  E-value=0.00057  Score=63.82  Aligned_cols=31  Identities=32%  Similarity=0.377  Sum_probs=27.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.++..+++.+++.
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~   49 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEACGYPFIEG   49 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHHTCCEEEG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCEEEeC
Confidence            4689999999999999999999998777663

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=96.93  E-value=0.00058  Score=64.42  Aligned_cols=29  Identities=21%  Similarity=0.285  Sum_probs=26.7

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.+|..+++.+++.
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            78999999999999999999999887765

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=96.93  E-value=0.0016  Score=67.23  Aligned_cols=69  Identities=14%  Similarity=0.231  Sum_probs=47.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC---------------------ChHHHHHHHHh---
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT---------------------DNSELRALLLQ---  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~---------------------~~~~L~~l~~~---  276 (530)
                      |++..+-++|+||||+|||+|+..+|..+   +..+..+++....                     +..++...+..   
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            45566679999999999999999888765   5566666543211                     11233333332   


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||.+..+.
T Consensus       150 ~~~~~lVVIDsl~~l~  165 (366)
T 1xp8_A          150 SGAIDVVVVDSVAALT  165 (366)
T ss_dssp             TTCCSEEEEECTTTCC
T ss_pred             cCCCCEEEEeChHHhc
Confidence            3568999999999874

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.92  E-value=0.00037  Score=63.28  Aligned_cols=29  Identities=28%  Similarity=0.289  Sum_probs=23.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHH-HcCCcEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN-YLCYDVY  257 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~-~l~~~i~  257 (530)
                      .-++|.||||+||||+++.++. .+++.++
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~~~~~~~i   32 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEecCCCCCHHHHHHHHHhhcCCcEEe
Confidence            4588999999999999999998 4554433

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=96.92  E-value=0.00055  Score=64.91  Aligned_cols=31  Identities=23%  Similarity=0.348  Sum_probs=27.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.+|..+++.+++.
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            3588999999999999999999999887765

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=96.91  E-value=0.0021  Score=60.07  Aligned_cols=23  Identities=43%  Similarity=0.765  Sum_probs=21.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||+|+|||||++.||..+
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            36789999999999999999987

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.90  E-value=0.00061  Score=62.85  Aligned_cols=31  Identities=23%  Similarity=0.345  Sum_probs=28.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.+|..+++.+++.
T Consensus        10 ~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   40 (196)
T 2c95_A           10 NIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   40 (196)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            4688999999999999999999999887765

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.90  E-value=0.0054  Score=58.80  Aligned_cols=61  Identities=13%  Similarity=0.213  Sum_probs=40.3

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc-------c-------------CChHHHHHHHHhc---CCCeEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK-------V-------------TDNSELRALLLQT---TNRSIIV  284 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~-------~-------------~~~~~L~~l~~~~---~~~sII~  284 (530)
                      ++++||||+||||++..++..+   +..++.+....       +             ....++...+.+.   ..+.+|+
T Consensus        15 ~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvVi   94 (223)
T 2b8t_A           15 EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIG   94 (223)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEEE
Confidence            6778999999999998888766   56666663211       1             0122444444432   3578999


Q ss_pred             EcCccch
Q 009640          285 IEDIDCS  291 (530)
Q Consensus       285 IDeID~~  291 (530)
                      |||+..+
T Consensus        95 IDEaQ~l  101 (223)
T 2b8t_A           95 IDEVQFF  101 (223)
T ss_dssp             ECSGGGS
T ss_pred             EecCccC
Confidence            9999864

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=96.88  E-value=0.00066  Score=63.96  Aligned_cols=29  Identities=21%  Similarity=0.303  Sum_probs=26.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.+|..++..+++.
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            68899999999999999999999887765

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=96.87  E-value=0.00063  Score=64.50  Aligned_cols=31  Identities=23%  Similarity=0.395  Sum_probs=27.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.+|..+++.+++.
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            4588999999999999999999999877664

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.87  E-value=0.00067  Score=62.73  Aligned_cols=31  Identities=19%  Similarity=0.363  Sum_probs=27.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.+|..+++.+++.
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   43 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKYGFTHLST   43 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            4688999999999999999999999877765

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.86  E-value=0.00065  Score=64.78  Aligned_cols=32  Identities=19%  Similarity=0.311  Sum_probs=28.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +.-++|.||||+||||+++.+|..+++.++++
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            35689999999999999999999999877764

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.86  E-value=0.00059  Score=62.30  Aligned_cols=29  Identities=21%  Similarity=0.196  Sum_probs=22.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      .-++|.|+||+||||+++.+|..++..++
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            45889999999999999999999999877

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.84  E-value=0.00071  Score=61.47  Aligned_cols=31  Identities=35%  Similarity=0.461  Sum_probs=26.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.++..+|..+++.
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            3578999999999999999999988766553

>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=96.82  E-value=0.0008  Score=64.51  Aligned_cols=31  Identities=29%  Similarity=0.533  Sum_probs=27.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.|+||+||||+++.||..+++.+++.
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            4589999999999999999999999877664

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.78  E-value=0.00085  Score=62.53  Aligned_cols=31  Identities=16%  Similarity=0.313  Sum_probs=27.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+++.+|..+++.+++.
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~   46 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   46 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeH
Confidence            4588999999999999999999999877764

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.77  E-value=0.0013  Score=63.99  Aligned_cols=34  Identities=18%  Similarity=0.207  Sum_probs=27.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      +.-++|.||||+||||+++.++..++..++.++.
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~   65 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDG   65 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEec
Confidence            4568899999999999999999999765555543

>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=96.76  E-value=0.00042  Score=56.57  Aligned_cols=47  Identities=13%  Similarity=-0.197  Sum_probs=37.1

Q ss_pred             CHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhc
Q 009640          395 GPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~  442 (530)
                      |.++|.+||+.++...... ....++.++..|.|||+|||.++|..+.
T Consensus         2 d~~~R~~Il~~~~~~~~~~-~dvdl~~lA~~t~G~SGADl~~l~~eAa   48 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVE-RGIRWELISRLCPNSTGAELRSVCTEAG   48 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBC-SCCCHHHHHHTCSSCCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCC-CccCHHHHHHHcCCCcHHHHHHHHHHHH
Confidence            5678999999999865543 2224788888999999999999997543

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.76  E-value=0.0011  Score=60.87  Aligned_cols=30  Identities=30%  Similarity=0.352  Sum_probs=27.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +.|.|+||+||||+++.++..+   |+.+++.+
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d   35 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYR   35 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            6899999999999999999998   89988875

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.72  E-value=0.00072  Score=64.17  Aligned_cols=32  Identities=16%  Similarity=0.190  Sum_probs=27.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +.-++|.||||+||||+++.+|..++..++++
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            34689999999999999999999999766553

>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=96.71  E-value=0.00096  Score=62.95  Aligned_cols=29  Identities=17%  Similarity=0.225  Sum_probs=26.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.+|..+++.+++.
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            78999999999999999999999887765

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.71  E-value=0.0012  Score=61.73  Aligned_cols=30  Identities=23%  Similarity=0.419  Sum_probs=25.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .-+.|.||||+||||++++||..+|..+++
T Consensus        30 ~~i~l~G~~GsGKSTl~~~L~~~~g~~~i~   59 (200)
T 4eun_A           30 RHVVVMGVSGSGKTTIAHGVADETGLEFAE   59 (200)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCCeEEc
Confidence            458899999999999999999999765554

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.71  E-value=0.00086  Score=61.68  Aligned_cols=32  Identities=38%  Similarity=0.450  Sum_probs=25.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..-+.|.||||+||||++++||..++...+.+
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i   40 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANLPGVPKVHF   40 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCSSSCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhccCCCeEEE
Confidence            34588999999999999999998765554443

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.70  E-value=0.0006  Score=69.93  Aligned_cols=50  Identities=20%  Similarity=0.300  Sum_probs=37.4

Q ss_pred             hhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          200 PQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      +.+.+.+.+.+...+...+         ...++|.||||+||||++++||+.++++++.
T Consensus         5 ~~L~~~il~~l~~~i~~g~---------~~~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A            5 HKLADDVLQLLDNRIEDNY---------RVCVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             HHHHHHHHHHHHHTTTTCS---------CEEEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCC---------eeEEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            4556666666665554322         2468999999999999999999999888744

>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=96.66  E-value=0.0012  Score=63.72  Aligned_cols=30  Identities=27%  Similarity=0.501  Sum_probs=26.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .-+.|.||||+||||+++.||..+|...++
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La~~lg~~~~~   57 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIAQNFGLQHLS   57 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCCCEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEec
Confidence            568899999999999999999999876554

>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=96.65  E-value=0.0016  Score=59.45  Aligned_cols=32  Identities=31%  Similarity=0.527  Sum_probs=28.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      .-+.|.|++|+||||+++.++..+   |++++.++
T Consensus         6 ~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d   40 (179)
T 2pez_A            6 CTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   40 (179)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEEC
Confidence            347789999999999999999998   88888775

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.64  E-value=0.0012  Score=63.02  Aligned_cols=29  Identities=24%  Similarity=0.419  Sum_probs=25.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.+|..+++.+++.
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            68999999999999999999998766554

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.62  E-value=0.0012  Score=66.86  Aligned_cols=34  Identities=26%  Similarity=0.481  Sum_probs=30.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      ++.++|.||+|+|||+++.++|..++..+++++.
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            3578999999999999999999999988888853

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.62  E-value=0.0031  Score=69.95  Aligned_cols=57  Identities=23%  Similarity=0.323  Sum_probs=37.6

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      .|-+-..++.++++|...+.    .+           .-.|++||||||||+++..+..++   +..+.-+..+.
T Consensus       184 ~~~~~~LN~~Q~~AV~~al~----~~-----------~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN  243 (646)
T 4b3f_X          184 TFFNTCLDTSQKEAVLFALS----QK-----------ELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSN  243 (646)
T ss_dssp             CCSSTTCCHHHHHHHHHHHH----CS-----------SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             cccCCCCCHHHHHHHHHHhc----CC-----------CceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCch
Confidence            33333567888887766542    11           246899999999999777666554   66666665543

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.60  E-value=0.0026  Score=64.08  Aligned_cols=28  Identities=21%  Similarity=0.184  Sum_probs=23.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      |++...-++|+||||+|||+|+..+|..
T Consensus        94 Gl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           94 GLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4555566899999999999999999875

>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=96.60  E-value=0.0015  Score=63.16  Aligned_cols=32  Identities=28%  Similarity=0.562  Sum_probs=28.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +.-++|.||||+||||+++.++..++..+++.
T Consensus        29 ~~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~   60 (243)
T 3tlx_A           29 DGRYIFLGAPGSGKGTQSLNLKKSHCYCHLST   60 (243)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            34689999999999999999999998877765

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.58  E-value=0.0014  Score=62.76  Aligned_cols=30  Identities=20%  Similarity=0.441  Sum_probs=26.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      ++-++|.||||+||+|.++.||..+++..+
T Consensus        29 ~kiI~llGpPGsGKgTqa~~L~~~~g~~hI   58 (217)
T 3umf_A           29 AKVIFVLGGPGSGKGTQCEKLVQKFHFNHL   58 (217)
T ss_dssp             CEEEEEECCTTCCHHHHHHHHHHHHCCEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            467889999999999999999999987654

>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=96.58  E-value=0.0031  Score=76.37  Aligned_cols=69  Identities=16%  Similarity=0.210  Sum_probs=51.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC---------------------ChHHHHHHHHh---
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT---------------------DNSELRALLLQ---  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~---------------------~~~~L~~l~~~---  276 (530)
                      |++..+.++|+||||||||+|+.++|...   +..++.++.....                     ....+.+++..   
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            67778889999999999999999988753   6677777655431                     12334444433   


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||+|..++
T Consensus       110 ~~~~~LVVIDSLt~L~  125 (1706)
T 3cmw_A          110 SGAVDVIVVDSVAALT  125 (1706)
T ss_dssp             HTCCSEEEESCSTTCC
T ss_pred             ccCCCEEEEcchhhhc
Confidence            3678999999999985

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.58  E-value=0.00086  Score=61.45  Aligned_cols=24  Identities=33%  Similarity=0.469  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -++|.||||+||||+++.++..++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999999886

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.58  E-value=0.0013  Score=60.84  Aligned_cols=28  Identities=29%  Similarity=0.703  Sum_probs=25.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      +.|.|+||+||||+++.+|..++..++.
T Consensus         3 I~i~G~~GsGKsT~~~~L~~~l~~~~~~   30 (205)
T 2jaq_A            3 IAIFGTVGAGKSTISAEISKKLGYEIFK   30 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHCCEEEC
T ss_pred             EEEECCCccCHHHHHHHHHHhcCCcEEc
Confidence            6899999999999999999999986653

>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=96.57  E-value=0.0014  Score=62.03  Aligned_cols=31  Identities=35%  Similarity=0.523  Sum_probs=27.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+.|.||||+||||+++.+|..+++++++.
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g~~~~d~   36 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQWHLLDS   36 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCcccC
Confidence            3578999999999999999999999877653

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.57  E-value=0.0024  Score=59.38  Aligned_cols=31  Identities=29%  Similarity=0.315  Sum_probs=25.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc--EEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD--VYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~--i~~l  259 (530)
                      .-++|.||||+||||+++.+|..++..  ++..
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~   37 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELKRDVYLT   37 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTTSCEEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhcCCEEEe
Confidence            357899999999999999999998773  5443

>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=96.54  E-value=0.0046  Score=65.20  Aligned_cols=58  Identities=22%  Similarity=0.281  Sum_probs=35.9

Q ss_pred             hhHHHHHHHHHHHcChh-hHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          202 LKKQITEDLTAFANGKE-FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       202 ~k~~i~~~l~~~l~~~~-~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +.+.+.+.+...+.... .+. +....++-+++.||||+||||++.++|..+   |..+.-++
T Consensus        73 ~~~~~~~~l~~ll~~~~~~~~-~~~~~~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~  134 (432)
T 2v3c_C           73 IIKIVYEELVKLLGEEAKKLE-LNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIA  134 (432)
T ss_dssp             HHHHHHHHHHHHHCCSCCCCC-CCSSSCCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEEC
T ss_pred             HHHHHHHHHHHHhCCCCcCcc-ccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            45555555666554321 010 001123568999999999999999999987   35555444

>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=96.54  E-value=0.0015  Score=61.81  Aligned_cols=28  Identities=25%  Similarity=0.487  Sum_probs=24.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      ++|.||||+||+|.++.||..+++..++
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            6789999999999999999999876544

>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=96.53  E-value=0.0014  Score=60.78  Aligned_cols=33  Identities=15%  Similarity=0.174  Sum_probs=28.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-CCcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-CYDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~~l~l  261 (530)
                      .-+.|.||||+||||+++.+|..+ +++++++..
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            357899999999999999999999 588887754

>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=96.53  E-value=0.0069  Score=58.31  Aligned_cols=33  Identities=27%  Similarity=0.189  Sum_probs=27.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT  262 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~  262 (530)
                      .+++.||+|+|||.++.+++..++..++.+..+
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~  142 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEESS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCC
Confidence            489999999999999999999887777666543

>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=96.53  E-value=0.0017  Score=60.37  Aligned_cols=31  Identities=29%  Similarity=0.245  Sum_probs=28.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+.|.||||+||||+++.+|..+++++++.+
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            5789999999999999999999999988854

>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=96.48  E-value=0.021  Score=56.97  Aligned_cols=58  Identities=16%  Similarity=0.214  Sum_probs=36.2

Q ss_pred             hhhHHHHHHHHHHHcChhhHhhhc-CCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEec
Q 009640          201 QLKKQITEDLTAFANGKEFYHRVG-RAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLEL  261 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~~~~y~~~g-~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l  261 (530)
                      .+++.+.+.+...+.....   .. ...+.-++|.||+|+||||++..+|..+    |..+.-+..
T Consensus        80 ~~~~~~~~~l~~~l~~~~~---~~~~~~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~  142 (296)
T 2px0_A           80 NVVGKLQEILCDMLPSADK---WQEPIHSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITT  142 (296)
T ss_dssp             THHHHHHHHHHTTSCCGGG---SCCCCCSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEEC
T ss_pred             HHHHHHHHHHHHHhCCccc---ccccCCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEec
Confidence            3555555555555533221   11 1124568899999999999999999876    445555443

>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=96.47  E-value=0.002  Score=62.34  Aligned_cols=31  Identities=32%  Similarity=0.356  Sum_probs=27.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+.|.||||+||||+++.||..+++.+++.
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            4688999999999999999999999887765

>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=96.45  E-value=0.0017  Score=60.51  Aligned_cols=30  Identities=30%  Similarity=0.312  Sum_probs=26.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+.|.||||+||||+++.+|. +|+.+++.+
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            378999999999999999999 888877754

>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=96.44  E-value=0.0017  Score=60.65  Aligned_cols=29  Identities=28%  Similarity=0.294  Sum_probs=25.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -+.|.||||+||||+++.+|. +|+.+++.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~id~   32 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPLVDA   32 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcccch
Confidence            467899999999999999998 88888765

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.42  E-value=0.0041  Score=59.13  Aligned_cols=28  Identities=18%  Similarity=0.181  Sum_probs=23.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      |++...-++|+||||+|||+|+..+|..
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~   47 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVT   47 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4555566899999999999999999985

>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=96.41  E-value=0.033  Score=60.41  Aligned_cols=43  Identities=2%  Similarity=0.115  Sum_probs=36.2

Q ss_pred             CCCeEEEEEeCCCC--CCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          360 SEEKIIVFTTNHRD--SVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       360 ~~~~ivI~TTN~~~--~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                      .-++-+|++|.+|.  .|+..+..  -|...|.|...+...-+.++.
T Consensus       376 a~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI~lrv~s~~Dsr~ILd  420 (574)
T 2iut_A          376 AAGIHLILATQRPSVDVITGLIKA--NIPTRIAFQVSSKIDSRTILD  420 (574)
T ss_dssp             TTTEEEEEEESCCCTTTSCHHHHH--TCCEEEEECCSCHHHHHHHHS
T ss_pred             hCCeEEEEEecCcccccccHHHHh--hhccEEEEEcCCHHHHHHhcC
Confidence            45788999999987  78888877  788899999999988887763

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.40  E-value=0.0022  Score=62.69  Aligned_cols=31  Identities=39%  Similarity=0.545  Sum_probs=28.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ..+.|.||||+||||+++.+|..+++.+++.
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~lg~~~~d~   79 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSLGYTFFDC   79 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCCcEEeC
Confidence            4689999999999999999999999998885

>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=96.29  E-value=0.0029  Score=61.82  Aligned_cols=32  Identities=34%  Similarity=0.377  Sum_probs=27.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH---cCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY---LCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~---l~~~i~~l~  260 (530)
                      .-++|.|+||+||||+++.++..   +|+.++.++
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~   39 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLG   39 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEEC
Confidence            35889999999999999999998   688877443

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=96.28  E-value=0.012  Score=54.50  Aligned_cols=24  Identities=21%  Similarity=0.301  Sum_probs=17.9

Q ss_pred             ceEEEECCCCCChhHH-HHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSL-IAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsL-a~AiA~~l  252 (530)
                      +.+++.+|+|+|||.. +.++...+
T Consensus        39 ~~~li~~~TGsGKT~~~~~~~~~~l   63 (207)
T 2gxq_A           39 KDLIGQARTGTGKTLAFALPIAERL   63 (207)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             CCEEEECCCCChHHHHHHHHHHHHH
Confidence            5799999999999986 33444443

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.28  E-value=0.00098  Score=62.32  Aligned_cols=30  Identities=23%  Similarity=0.270  Sum_probs=24.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .-+.|.|+||+||||+++.+|..++...++
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~l~~~~~~   40 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEYLKNNNVE   40 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCC
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHcCCc
Confidence            457899999999999999999987554333

>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=96.23  E-value=0.0042  Score=57.88  Aligned_cols=24  Identities=38%  Similarity=0.461  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||+|+||||+++++|..+
T Consensus        26 ~~i~l~G~sGsGKSTl~~~La~~l   49 (200)
T 3uie_A           26 CVIWVTGLSGSGKSTLACALNQML   49 (200)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            457789999999999999999998

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.23  E-value=0.0058  Score=55.59  Aligned_cols=18  Identities=39%  Similarity=0.554  Sum_probs=16.3

Q ss_pred             ceEEEECCCCCChhHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIA  246 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~  246 (530)
                      .-+.|.||+|+|||||++
T Consensus        10 ei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A           10 SLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHH
Confidence            347899999999999999

>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=96.22  E-value=0.0031  Score=58.98  Aligned_cols=31  Identities=23%  Similarity=0.278  Sum_probs=27.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+.|.|++|+||||+++.+|..+|+++++.+
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            4678999999999999999999999888853

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.22  E-value=0.011  Score=59.72  Aligned_cols=68  Identities=16%  Similarity=0.123  Sum_probs=42.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc-----CCcEEEEecCcc---------------------CChHHH-HHH---
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL-----CYDVYDLELTKV---------------------TDNSEL-RAL---  273 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i~~l~l~~~---------------------~~~~~L-~~l---  273 (530)
                      |++.. -++++||||+|||+|+..++..+     +..+..++...-                     .+..++ ..+   
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            35544 47899999999999977665543     445555553221                     112222 222   


Q ss_pred             H--HhcCCCeEEEEcCccchh
Q 009640          274 L--LQTTNRSIIVIEDIDCSV  292 (530)
Q Consensus       274 ~--~~~~~~sII~IDeID~~~  292 (530)
                      +  .+..+|.+||||=|-.+.
T Consensus       104 l~~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A          104 LDAIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             HHTCCTTCCEEEEEECSTTCB
T ss_pred             HHHhhccCceEEEEecccccc
Confidence            2  123579999999999874

>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=96.17  E-value=0.0045  Score=65.41  Aligned_cols=59  Identities=15%  Similarity=0.259  Sum_probs=45.8

Q ss_pred             hHHHHhhhccCCccC------CCCCeEEEEEe----CCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          344 TLSGLLNFTDGLWSC------CSEEKIIVFTT----NHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       344 ~ls~LLn~lDgl~s~------~~~~~ivI~TT----N~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                      +...||..|||-...      ..+++++|+|.    +.+.++-|.|+.  ||+.+|.|+..+.+++..|+.
T Consensus       278 vq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~--R~~i~i~l~~lt~~e~~~Il~  346 (444)
T 1g41_A          278 VQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILT  346 (444)
T ss_dssp             HHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             HHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhc--ccceeeeCCCCCHHHHHHHHH
Confidence            557899999984321      24668888887    244556688888  999999999999999999984

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=96.12  E-value=0.021  Score=53.56  Aligned_cols=60  Identities=13%  Similarity=0.076  Sum_probs=34.3

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcC---CCCceEEEECCCCCChhHH-HHHHHHH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGR---AWKRGYLLYGPPGSGKSSL-IAAMANY  251 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~---~~~rG~LL~GPPGTGKTsL-a~AiA~~  251 (530)
                      ...+|+++...+.+.+.+.+.   -...+..|+...+   .-.+.+++.+|+|+|||.. +.++...
T Consensus        12 ~~~~f~~l~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~   75 (224)
T 1qde_A           12 VVYKFDDMELDENLLRGVFGY---GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR   75 (224)
T ss_dssp             CCCCGGGGTCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccCChhhcCCCHHHHHHHHHC---CCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHH
Confidence            345789988777766655431   1122222322111   1135799999999999976 3344443

>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=96.09  E-value=0.0084  Score=56.37  Aligned_cols=29  Identities=28%  Similarity=0.340  Sum_probs=24.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |++...-+.|.||+|+|||||++.||..+
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            44444568999999999999999999855

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.09  E-value=0.0038  Score=60.68  Aligned_cols=31  Identities=32%  Similarity=0.499  Sum_probs=27.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+.|.||+|+||||+++.+|..+|+.+++-
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~Lg~~~~d~   58 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESLNWRLLDS   58 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCCcCCC
Confidence            3578999999999999999999999887763

>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=96.08  E-value=0.0037  Score=57.47  Aligned_cols=25  Identities=36%  Similarity=0.533  Sum_probs=21.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||||+||||+++.|+..++.
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            4788999999999999999986654

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=96.08  E-value=0.034  Score=52.01  Aligned_cols=59  Identities=19%  Similarity=0.190  Sum_probs=33.6

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHHHHHHHH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +..+|+++...+.+.+.+.+.   -...+..|+...++   -.+.+++.+|+|+|||..+...+-
T Consensus        12 ~~~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~   73 (220)
T 1t6n_A           12 HSSGFRDFLLKPELLRAIVDC---GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL   73 (220)
T ss_dssp             --CCSTTSCCCHHHHHHHHHT---TCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHH
T ss_pred             cCCCHhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHH
Confidence            445788888777766655431   11223333322111   125699999999999986554443

>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=96.08  E-value=0.0039  Score=57.61  Aligned_cols=31  Identities=35%  Similarity=0.470  Sum_probs=27.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .-+.|.|+||+||||+++.+|.. |+.+++.+
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~-g~~~id~d   39 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW-GYPVLDLD   39 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT-TCCEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC-CCEEEccc
Confidence            45889999999999999999998 88888754

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.06  E-value=0.0044  Score=58.27  Aligned_cols=31  Identities=29%  Similarity=0.339  Sum_probs=28.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+.|.|+||+|||++++.+|..+|+.+++.
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~   34 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDT   34 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecC
Confidence            3588999999999999999999999988875

>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=96.01  E-value=0.0042  Score=58.51  Aligned_cols=30  Identities=40%  Similarity=0.414  Sum_probs=26.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+.|.|++|+||||+++.+|. +|+.+++.
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-lg~~~id~   34 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-LGINVIDA   34 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-TTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-cCCEEEEc
Confidence            3578999999999999999998 88887775

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=95.98  E-value=0.0018  Score=60.46  Aligned_cols=25  Identities=28%  Similarity=0.372  Sum_probs=22.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.|+||+||||+++.+|..++
T Consensus        10 ~~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A           10 ALIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4588999999999999999999874

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.98  E-value=0.0043  Score=58.01  Aligned_cols=28  Identities=29%  Similarity=0.428  Sum_probs=24.4

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +..+-++|.||||+||||++++++..+.
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            3445688999999999999999999885

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=95.97  E-value=0.0056  Score=58.66  Aligned_cols=30  Identities=27%  Similarity=0.421  Sum_probs=27.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -+.|.|+||+||||+++.+|..+|+.+++.
T Consensus        18 ~i~i~G~~gsGKst~~~~l~~~lg~~~~d~   47 (236)
T 1q3t_A           18 QIAIDGPASSGKSTVAKIIAKDFGFTYLDT   47 (236)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCceecC
Confidence            477899999999999999999999888774

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=95.95  E-value=0.011  Score=55.52  Aligned_cols=32  Identities=25%  Similarity=0.381  Sum_probs=26.1

Q ss_pred             eEEEECCCCCChh-HHHHHHHHHc--CCcEEEEec
Q 009640          230 GYLLYGPPGSGKS-SLIAAMANYL--CYDVYDLEL  261 (530)
Q Consensus       230 G~LL~GPPGTGKT-sLa~AiA~~l--~~~i~~l~l  261 (530)
                      =+++|||.|+||| .|++++.++.  +..++.+..
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp   56 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKY   56 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEcc
Confidence            4778999999999 8999998865  667777653

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=95.93  E-value=0.0056  Score=64.16  Aligned_cols=32  Identities=25%  Similarity=0.255  Sum_probs=26.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +.-++|.||||+||||++++++..+++.+++.
T Consensus       258 ~~lIil~G~pGSGKSTla~~L~~~~~~~~i~~  289 (416)
T 3zvl_A          258 PEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNR  289 (416)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHTGGGTCEECCG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhcCcEEEcc
Confidence            35588999999999999999999998765543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.82  E-value=0.0072  Score=57.50  Aligned_cols=39  Identities=23%  Similarity=0.168  Sum_probs=29.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      |++...-++|+||||+|||+|+..+|..+   +..++.++..
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e   60 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALE   60 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            45555668999999999999988887653   5566666544

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=95.81  E-value=0.005  Score=57.88  Aligned_cols=30  Identities=17%  Similarity=0.088  Sum_probs=27.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .-+.|.||+|||||++++.+|..||+++|+
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~lg~~~~D   36 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHYNIPLYS   36 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTTCCEEC
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHhCcCEEC
Confidence            357899999999999999999999999987

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=95.78  E-value=0.0045  Score=61.35  Aligned_cols=29  Identities=28%  Similarity=0.273  Sum_probs=24.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-CCcEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-CYDVY  257 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-~~~i~  257 (530)
                      .-++|.||||+||||+++.++..+ ++.++
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i   32 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEe
Confidence            458899999999999999999974 55444

>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=95.78  E-value=0.047  Score=58.61  Aligned_cols=42  Identities=5%  Similarity=0.111  Sum_probs=34.9

Q ss_pred             CCeEEEEEeCCCC--CCChhhhcCCceeEEEEeCCCCHHHHHHHHH
Q 009640          361 EEKIIVFTTNHRD--SVDPALIRCGRMDVHVSLGTCGPHAFKVLAK  404 (530)
Q Consensus       361 ~~~ivI~TTN~~~--~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~  404 (530)
                      -++-+|++|.+|.  .++..+..  -+...|.|...+..+.+.++.
T Consensus       331 ~GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lrv~s~~dsr~ilg  374 (512)
T 2ius_A          331 AGIHLVLATQRPSVDVITGLIKA--NIPTRIAFTVSSKIDSRTILD  374 (512)
T ss_dssp             GTEEEEEEESCCCTTTSCHHHHH--HCCEEEEECCSSHHHHHHHHS
T ss_pred             CCcEEEEEecCCccccccHHHHh--hcCCeEEEEcCCHHHHHHhcC
Confidence            3677889999987  58887777  888899999999999888864

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.78  E-value=0.0045  Score=60.01  Aligned_cols=28  Identities=29%  Similarity=0.190  Sum_probs=25.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      .-+.|.||||+||||+++.+|..+++.+
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~lg~~~   50 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLLGQNE   50 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhhc
Confidence            3578999999999999999999999764

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.76  E-value=0.0062  Score=55.82  Aligned_cols=25  Identities=16%  Similarity=0.323  Sum_probs=22.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +-+.|.||+|+|||||+++|+..+.
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            4578999999999999999999864

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.75  E-value=0.0037  Score=63.61  Aligned_cols=35  Identities=26%  Similarity=0.387  Sum_probs=30.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      +-++|.||+|+|||+|+..||..++..+++.+.-.
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            35889999999999999999999998888876543

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=95.73  E-value=0.0054  Score=57.75  Aligned_cols=30  Identities=23%  Similarity=0.274  Sum_probs=25.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .++++|.||||+|||+|+.++|...+ .++.
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~-~iIs   63 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH-RLIA   63 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC-EEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC-eEEe
Confidence            46899999999999999999998876 4443

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=95.67  E-value=0.032  Score=51.51  Aligned_cols=17  Identities=35%  Similarity=0.446  Sum_probs=14.7

Q ss_pred             ceEEEECCCCCChhHHH
Q 009640          229 RGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa  245 (530)
                      +.+++.+|+|+|||..+
T Consensus        41 ~~~lv~apTGsGKT~~~   57 (206)
T 1vec_A           41 RDILARAKNGTGKSGAY   57 (206)
T ss_dssp             CCEEEECCSSSTTHHHH
T ss_pred             CCEEEECCCCCchHHHH
Confidence            57999999999999643

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.65  E-value=0.006  Score=56.54  Aligned_cols=24  Identities=25%  Similarity=0.319  Sum_probs=21.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||||+||||+++.|+..+
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            457899999999999999999987

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.63  E-value=0.0059  Score=55.97  Aligned_cols=25  Identities=36%  Similarity=0.522  Sum_probs=22.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-++|.|+||+||||+++.+|..++
T Consensus        14 ~~i~l~G~~GsGKsT~~~~L~~~l~   38 (186)
T 2yvu_A           14 IVVWLTGLPGSGKTTIATRLADLLQ   38 (186)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            4578999999999999999999874

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.63  E-value=0.0056  Score=57.15  Aligned_cols=29  Identities=24%  Similarity=0.240  Sum_probs=24.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc-CCcEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL-CYDVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l-~~~i~~  258 (530)
                      -+.|.||||+||||+++.++..+ ++.+++
T Consensus        23 ~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~   52 (207)
T 2qt1_A           23 IIGISGVTNSGKTTLAKNLQKHLPNCSVIS   52 (207)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTTSTTEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCcEEEe
Confidence            46789999999999999999987 544444

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=95.58  E-value=0.0075  Score=60.62  Aligned_cols=33  Identities=24%  Similarity=0.510  Sum_probs=28.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      ++-+++.||+|+|||+|+..+|..++..+++.+
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~~~~iis~D   42 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKILPVELISVD   42 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEECC
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhCCCcEEecc
Confidence            456889999999999999999999987776654

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.54  E-value=0.012  Score=56.07  Aligned_cols=39  Identities=23%  Similarity=0.173  Sum_probs=28.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH----cCCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY----LCYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~----l~~~i~~l~l~  262 (530)
                      |++...-++++|+||+|||+|+..+|..    .+..++.+++.
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            4555566999999999999999877643    25666666554

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.54  E-value=0.024  Score=52.75  Aligned_cols=34  Identities=21%  Similarity=0.210  Sum_probs=27.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      .-+.|.||+|+||||+++.++..+   +.+++.++..
T Consensus        23 ~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d   59 (201)
T 1rz3_A           23 LVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMD   59 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccC
Confidence            347789999999999999999876   6666665433

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=95.54  E-value=0.0099  Score=64.03  Aligned_cols=61  Identities=18%  Similarity=0.341  Sum_probs=40.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC--cEEEEecCc-cC-----------------ChHHHHHHHHhc--CCCeEEEEc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY--DVYDLELTK-VT-----------------DNSELRALLLQT--TNRSIIVIE  286 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~--~i~~l~l~~-~~-----------------~~~~L~~l~~~~--~~~sII~ID  286 (530)
                      .++++.||+|+||||++++|++.+.-  .++.++-.. +.                 ..-.+..++..+  ..|.+|++.
T Consensus       261 ~~i~I~GptGSGKTTlL~aL~~~i~~~~giitied~~E~~~~~~~~v~~~~r~~~~~~~~~~~~~l~~~LR~~PD~iivg  340 (511)
T 2oap_1          261 FSAIVVGETASGKTTTLNAIMMFIPPDAKVVSIEDTREIKLYHENWIAEVTRTGMGEGEIDMYDLLRAALRQRPDYIIVG  340 (511)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCCCSSEEEEECBCCSSSCCBCHHHHHHTTGGGCCSEEEES
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEEcCcccccCCCCCeEEEEeecccccCCcCHHHHHHHhhccCCCeEEeC
Confidence            46999999999999999999998843  344443211 10                 011244444433  579999999


Q ss_pred             Ccc
Q 009640          287 DID  289 (530)
Q Consensus       287 eID  289 (530)
                      |+-
T Consensus       341 Eir  343 (511)
T 2oap_1          341 EVR  343 (511)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            984

>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=95.53  E-value=0.021  Score=52.92  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=20.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.+++.+|+|+|||.++...+..+
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHH
Confidence            578999999999999888777653

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.48  E-value=0.015  Score=54.47  Aligned_cols=25  Identities=44%  Similarity=0.570  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.||+|+|||||++.|+..+.
T Consensus        23 ~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           23 QLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3467899999999999999999885

>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=95.48  E-value=0.0077  Score=59.60  Aligned_cols=30  Identities=33%  Similarity=0.259  Sum_probs=25.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+.|.|+||+||||+++.++ .+|+.+++.
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~lg~~~id~  105 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NLGAYIIDS  105 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HHTCEEEEH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HCCCcEEeh
Confidence            357899999999999999999 688877665

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.47  E-value=0.0076  Score=56.63  Aligned_cols=26  Identities=27%  Similarity=0.263  Sum_probs=22.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      +-+.|.||+|+||||+++.++..+..
T Consensus         9 ~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            9 LLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            45788999999999999999998753

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=95.46  E-value=0.01  Score=55.61  Aligned_cols=32  Identities=31%  Similarity=0.433  Sum_probs=25.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC----CcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC----YDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~----~~i~~l~  260 (530)
                      .-++|.|+||+||||+++.++..++    .+++.++
T Consensus        26 ~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           26 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            4578899999999999999999875    4455554

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.45  E-value=0.0071  Score=61.61  Aligned_cols=32  Identities=22%  Similarity=0.292  Sum_probs=27.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .-+++.||+|+|||+++..+|..++..+++.+
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            46789999999999999999999987666554

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=95.45  E-value=0.0098  Score=55.35  Aligned_cols=27  Identities=30%  Similarity=0.487  Sum_probs=23.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      |.++|.||+|+|||||++++.....-.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~~~   28 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYPDS   28 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCCCC
Confidence            568999999999999999998876443

>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=95.44  E-value=0.011  Score=47.13  Aligned_cols=46  Identities=7%  Similarity=0.001  Sum_probs=36.8

Q ss_pred             CHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          395 GPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       395 ~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      |.++|..||+.++...... ....++.++..+.|||+|||.++|..+
T Consensus         2 d~~~R~~Il~~~l~~~~~~-~~vdl~~la~~t~G~SGADi~~l~~eA   47 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLS-EEVDLEDYVARPDKISGADINSICQES   47 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBC-TTCCTHHHHTSSCCCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCC-cccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            6789999999999865543 222377888889999999999999754

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.43  E-value=0.0077  Score=55.74  Aligned_cols=25  Identities=32%  Similarity=0.658  Sum_probs=21.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.||+|+|||||++.|+..+.
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            3477899999999999999999864

>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=95.43  E-value=0.049  Score=54.51  Aligned_cols=58  Identities=16%  Similarity=0.032  Sum_probs=33.2

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC----CCceEEEECCCCCChhHHHHHHHHH
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA----WKRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~----~~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .+|+++...+.+.+.+.+.   -...+..++...++    ..+.+++.+|+|+|||..+...+-.
T Consensus         6 ~~f~~~~l~~~~~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~   67 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNK---GFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE   67 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHH
T ss_pred             CchhhcCCCHHHHHHHHHc---CCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHH
Confidence            4577777777665554431   11222222222211    1257999999999999876554443

>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=95.41  E-value=0.0089  Score=57.30  Aligned_cols=29  Identities=38%  Similarity=0.551  Sum_probs=24.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC--CcEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC--YDVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~--~~i~~  258 (530)
                      -+.|.||||+||||+++.++..++  .+++.
T Consensus        28 ~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~   58 (229)
T 4eaq_A           28 FITFEGPEGSGKTTVINEVYHRLVKDYDVIM   58 (229)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTTTSCEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHhcCCCcee
Confidence            367889999999999999999996  45543

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.36  E-value=0.016  Score=58.06  Aligned_cols=53  Identities=17%  Similarity=0.254  Sum_probs=35.4

Q ss_pred             hhhhHHHHHHHHHHHcChhhHhhhc--CCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          200 PQLKKQITEDLTAFANGKEFYHRVG--RAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~y~~~g--~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.+++.+.+.+...+........+.  ...+.-+.|.||+|+||||+++.||..+
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            4566777777777775432101122  2233457899999999999999999987

>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=95.28  E-value=0.05  Score=47.50  Aligned_cols=22  Identities=27%  Similarity=0.410  Sum_probs=20.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|+||+|||||+.++.+.
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            5899999999999999999864

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=95.22  E-value=0.023  Score=59.77  Aligned_cols=60  Identities=18%  Similarity=0.215  Sum_probs=38.8

Q ss_pred             hhhhHHHHHHHHHHHcChh-hHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          200 PQLKKQITEDLTAFANGKE-FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~-~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +.+.+.+.+.+...+.... .+... ...++-+++.||||+||||++..+|..+   +..+.-+.
T Consensus        69 ~~v~~~v~~eL~~~L~~~~~~~~~~-~~~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           69 EWFISIVYDELSKLFGGDKEPNVNP-TKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCCCCSC-CSSSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHHHHhcCccccccccc-cCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3456666677777665421 11111 1124568889999999999999999877   55555444

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=95.21  E-value=0.064  Score=51.16  Aligned_cols=54  Identities=13%  Similarity=0.031  Sum_probs=29.5

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcC---CCCceEEEECCCCCChhHHH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGR---AWKRGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~---~~~rG~LL~GPPGTGKTsLa  245 (530)
                      +..+|+++...+.+.+.+.+.   -...+..++..-+   ...+.+++.+|+|+|||...
T Consensus        27 ~~~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~   83 (242)
T 3fe2_A           27 PVLNFYEANFPANVMDVIARQ---NFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSY   83 (242)
T ss_dssp             CCSSTTTTTCCHHHHHHHHTT---TCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHH
T ss_pred             ccCCHhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHH
Confidence            345677777666655444320   1111222222111   01357999999999999763

>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=95.20  E-value=0.011  Score=59.94  Aligned_cols=62  Identities=18%  Similarity=0.341  Sum_probs=40.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc--EEEEecCc------cC--------ChHHHHHHHHhc--CCCeEEEEcCccc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD--VYDLELTK------VT--------DNSELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~--i~~l~l~~------~~--------~~~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                      ..+++.||+|+|||||+++|+..+..+  .+.++-..      ..        .....+..+..+  ..|.+|++||.-.
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            468999999999999999999987432  33332110      00        112233344443  6899999999864

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=95.16  E-value=0.035  Score=62.83  Aligned_cols=23  Identities=26%  Similarity=0.488  Sum_probs=18.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ..+++.||+|+|||+++..++..
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            45899999999999987777544

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.15  E-value=0.025  Score=59.58  Aligned_cols=60  Identities=27%  Similarity=0.331  Sum_probs=39.8

Q ss_pred             hhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          200 PQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +.+++.+.+.+...+..+....... ..+.-+++.||||+||||++..+|..+   |..+.-+.
T Consensus        73 ~~v~~~l~~eL~~~L~~~~~~~~~~-~~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~  135 (443)
T 3dm5_A           73 EHIIKIVYEELTKFLGTEAKPIEIK-EKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVC  135 (443)
T ss_dssp             HHHHHHHHHHHHHHTTSSCCCCCCC-SSSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             HHHHHHHHHHHHHHhcCcccccccC-CCCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            4566677777777765422111111 124568899999999999999999877   55555444

>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=95.13  E-value=0.0047  Score=57.66  Aligned_cols=25  Identities=20%  Similarity=0.364  Sum_probs=22.3

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +.|.||||+||||+++.++..++..
T Consensus         3 I~i~G~~GsGKsTl~~~L~~~l~~~   27 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSGAFRAA   27 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHHHHHEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhc
Confidence            6789999999999999999998643

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.12  E-value=0.011  Score=56.97  Aligned_cols=30  Identities=20%  Similarity=0.348  Sum_probs=25.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -+=|.||||+||||+++.||..+++..++.
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            355789999999999999999999887654

>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=95.11  E-value=0.029  Score=58.46  Aligned_cols=28  Identities=29%  Similarity=0.222  Sum_probs=23.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      |++...-++|+||||+|||+|+..+|..
T Consensus       174 GI~~Gei~~I~G~sGsGKTTLl~~la~~  201 (400)
T 3lda_A          174 GVETGSITELFGEFRTGKSQLCHTLAVT  201 (400)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcCCCcEEEEEcCCCCChHHHHHHHHHH
Confidence            5555666899999999999999977643

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.11  E-value=0.011  Score=55.01  Aligned_cols=26  Identities=35%  Similarity=0.562  Sum_probs=22.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .+-+.|.||+|+|||||++.|+..+.
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            35688999999999999999998764

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=95.06  E-value=0.067  Score=61.99  Aligned_cols=55  Identities=18%  Similarity=0.204  Sum_probs=36.1

Q ss_pred             cCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHH------cCCcEEEEecCc
Q 009640          197 ALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY------LCYDVYDLELTK  263 (530)
Q Consensus       197 ~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~------l~~~i~~l~l~~  263 (530)
                      +|-+...+.|.+.+..   ..         ..+-+.++||+|.|||+||+++++.      +...++-++++.
T Consensus       131 VGRe~eLeeL~elL~~---~d---------~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~  191 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLE---LR---------PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN  191 (1221)
T ss_dssp             CCCHHHHHHHHHHHHH---CC---------SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCC
T ss_pred             CCcHHHHHHHHHHHhc---cC---------CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCC
Confidence            5666666666665532   01         1356889999999999999999863      233345555443

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.06  E-value=0.011  Score=55.22  Aligned_cols=24  Identities=33%  Similarity=0.332  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||+|+|||||++.|+..++
T Consensus         8 ~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            8 VIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            467899999999999999999987

>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=95.06  E-value=0.014  Score=58.52  Aligned_cols=30  Identities=33%  Similarity=0.566  Sum_probs=25.6

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .++...-+.|.||+|+|||||++.|+..+.
T Consensus       122 ~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~~  151 (305)
T 2v9p_A          122 GIPKKNCLAFIGPPNTGKSMLCNSLIHFLG  151 (305)
T ss_dssp             TCTTCSEEEEECSSSSSHHHHHHHHHHHHT
T ss_pred             EecCCCEEEEECCCCCcHHHHHHHHhhhcC
Confidence            345556689999999999999999999983

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.05  E-value=0.021  Score=58.58  Aligned_cols=53  Identities=17%  Similarity=0.254  Sum_probs=35.7

Q ss_pred             hhhhHHHHHHHHHHHcChhhHhhhc--CCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          200 PQLKKQITEDLTAFANGKEFYHRVG--RAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~y~~~g--~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.+++.+.+.+...+........+.  ...+.-+.|.||.|+||||+++.||..+
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            4566677777777775432111222  2333458899999999999999999987

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=95.01  E-value=0.012  Score=59.35  Aligned_cols=32  Identities=22%  Similarity=0.270  Sum_probs=27.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +-+++.||+|+|||+|+.++|..++..+++.+
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            35788999999999999999999987665554

>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=95.01  E-value=0.045  Score=62.85  Aligned_cols=64  Identities=19%  Similarity=0.371  Sum_probs=39.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc-----CC----cEEEEec-----CccC--------------ChHHHHHHHHhcCC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL-----CY----DVYDLEL-----TKVT--------------DNSELRALLLQTTN  279 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l-----~~----~i~~l~l-----~~~~--------------~~~~L~~l~~~~~~  279 (530)
                      ..-++|.||.|+||||+++.+|...     +.    .-..+..     ..+.              ...++..++..+..
T Consensus       673 g~i~~ItGPNGaGKSTlLr~i~~i~~~aq~g~~vpa~~~~i~~~d~i~~~ig~~d~l~~~~stfs~em~~~~~il~~a~~  752 (918)
T 3thx_B          673 ERVMIITGPNMGGKSSYIKQVALITIMAQIGSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRKATS  752 (918)
T ss_dssp             CCEEEEESCCCHHHHHHHHHHHHHHHHHHHTCCBSSSEEEEECCSEEEEEC----------CCHHHHHHHHHHHHHHCCT
T ss_pred             CeEEEEECCCCCchHHHHHHHHHHHHHhhcCccccchhhhhhHHHHHHHhCChHHHHHHhHHHhhHHHHHHHHHHHhccC
Confidence            3558999999999999999987432     21    1111110     0010              01223444555789


Q ss_pred             CeEEEEcCccch
Q 009640          280 RSIIVIEDIDCS  291 (530)
Q Consensus       280 ~sII~IDeID~~  291 (530)
                      |++|++||.-.-
T Consensus       753 p~LlLLDEP~~G  764 (918)
T 3thx_B          753 QSLVILDELGRG  764 (918)
T ss_dssp             TCEEEEESTTTT
T ss_pred             CCEEEEeCCCCC
Confidence            999999999764

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=94.99  E-value=0.012  Score=56.27  Aligned_cols=30  Identities=23%  Similarity=0.150  Sum_probs=27.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .-+.+.|++|||||++++.+|..+|+++|+
T Consensus        15 ~iI~i~g~~gsGk~~i~~~la~~lg~~~~d   44 (223)
T 3hdt_A           15 LIITIEREYGSGGRIVGKKLAEELGIHFYD   44 (223)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHcCCcEEc
Confidence            357889999999999999999999999887

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=94.97  E-value=0.021  Score=57.29  Aligned_cols=58  Identities=16%  Similarity=0.075  Sum_probs=37.6

Q ss_pred             hhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          202 LKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       202 ~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +++.+.+.+...+.....+ .+....+.-+++.||+|+||||++..+|..+   +..+.-+.
T Consensus        79 ~~~~~~~~l~~~l~~~~~~-~~~~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~  139 (306)
T 1vma_A           79 ALESLKEIILEILNFDTKL-NVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAA  139 (306)
T ss_dssp             HHHHHHHHHHHHTCSCCCC-CCCSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHHHhCCCCCC-cccCCCCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEc
Confidence            5666777777766543211 1112234458899999999999999999876   44444443

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=94.91  E-value=0.071  Score=49.90  Aligned_cols=52  Identities=12%  Similarity=0.078  Sum_probs=28.3

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHHH
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsLa  245 (530)
                      .+|+++...+.+.+.+.+.   -...+..++...++   -.+.+++.+|+|+|||...
T Consensus         4 ~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~   58 (219)
T 1q0u_A            4 TQFTRFPFQPFIIEAIKTL---RFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAY   58 (219)
T ss_dssp             CCGGGSCCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHH
T ss_pred             CCHhhCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHH
Confidence            3577777666655544320   01112222221111   1257899999999999853

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=94.91  E-value=0.014  Score=57.64  Aligned_cols=38  Identities=21%  Similarity=0.092  Sum_probs=28.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEec
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLEL  261 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l  261 (530)
                      |++...-++|.||||+|||+|+..||..+    |..+..++.
T Consensus        31 ~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~   72 (296)
T 1cr0_A           31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (296)
T ss_dssp             SBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            34444568899999999999999999876    445555544

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=94.90  E-value=0.017  Score=63.56  Aligned_cols=32  Identities=31%  Similarity=0.527  Sum_probs=29.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      .-++|.|+||+||||+++++|..+   |++++.++
T Consensus        53 ~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lD   87 (630)
T 1x6v_B           53 CTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   87 (630)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEES
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEec
Confidence            347899999999999999999999   99999885

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=94.85  E-value=0.072  Score=50.35  Aligned_cols=53  Identities=15%  Similarity=0.206  Sum_probs=30.2

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSL  244 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsL  244 (530)
                      +..+|+++...+.+.+.+.+.   -...+..|+...++   ..+.+++.+|+|+|||..
T Consensus        22 ~~~~f~~l~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~   77 (230)
T 2oxc_A           22 EPADFESLLLSRPVLEGLRAA---GFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCV   77 (230)
T ss_dssp             --CCGGGGTCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             CCCCHhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHH
Confidence            445788887777766555431   11122223221111   135799999999999976

>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=94.82  E-value=0.08  Score=60.00  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=38.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-----CCcE----EEE----------ecCc-c----C----ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-----CYDV----YDL----------ELTK-V----T----DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-----~~~i----~~l----------~l~~-~----~----~~~~L~~l~~~~~~~  280 (530)
                      +-++|.||.|+||||+++.||...     |..+    ..+          ...+ +    .    ....+..++..+..|
T Consensus       608 ~i~~ItGpNGsGKSTlLr~iagl~~~~q~G~~vpa~~~~i~~~~~i~~~~~~~d~l~~~~stf~~e~~~~~~il~~a~~p  687 (800)
T 1wb9_A          608 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEY  687 (800)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCTT
T ss_pred             cEEEEECCCCCChHHHHHHHHHHHHHHhcCcccchhcccceeHHHHHhhCCHHHHHHhhhhhhhHHHHHHHHHHHhccCC
Confidence            458899999999999999998752     2111    111          1000 0    0    011234455667899


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      ++|++||.-.
T Consensus       688 sLlLLDEp~~  697 (800)
T 1wb9_A          688 SLVLMDEIGR  697 (800)
T ss_dssp             EEEEEESCCC
T ss_pred             CEEEEECCCC
Confidence            9999999954

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=94.81  E-value=0.077  Score=50.19  Aligned_cols=54  Identities=17%  Similarity=0.100  Sum_probs=31.0

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHHH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsLa  245 (530)
                      ...+|+++...+.+.+.+.+.   -...+..++...++   ..+.+++.+|+|+|||...
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~   79 (236)
T 2pl3_A           23 EITRFSDFPLSKKTLKGLQEA---QYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAF   79 (236)
T ss_dssp             GCSBGGGSCCCHHHHHHHHHT---TCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHH
T ss_pred             ccCCHhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHH
Confidence            445688887777766555431   11122222221111   1357999999999999853

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=94.81  E-value=0.024  Score=60.47  Aligned_cols=24  Identities=29%  Similarity=0.409  Sum_probs=21.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-++|.||+|+|||||++.||..+
T Consensus       294 eVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          294 FVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCcccHHHHHHHHHHHh
Confidence            347899999999999999999877

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=94.80  E-value=0.021  Score=51.50  Aligned_cols=23  Identities=30%  Similarity=0.407  Sum_probs=21.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||.|+|||||+++|+..+
T Consensus        35 ~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           35 MVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            47899999999999999999988

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=94.76  E-value=0.02  Score=53.70  Aligned_cols=25  Identities=24%  Similarity=0.380  Sum_probs=22.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +-+.|.||+|+|||||+++|+....
T Consensus        20 ~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           20 KTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECcCCCCHHHHHHHHHhhCC
Confidence            4578899999999999999998865

>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=94.75  E-value=0.033  Score=49.03  Aligned_cols=23  Identities=30%  Similarity=0.362  Sum_probs=20.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.|+||+|||||+.++.+.-
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            58999999999999999998754

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=94.73  E-value=0.18  Score=50.93  Aligned_cols=56  Identities=18%  Similarity=0.179  Sum_probs=32.1

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHHHHHH
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSLIAAM  248 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsLa~Ai  248 (530)
                      ..+|+++...+.+.+.+.+.   -...+..|+...++   ..+.+++.+|+|+|||..+...
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~   65 (391)
T 1xti_A            7 SSGFRDFLLKPELLRAIVDC---GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLA   65 (391)
T ss_dssp             --CGGGGCCCHHHHHHHHHH---SCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHH
T ss_pred             CCChhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHH
Confidence            34688887777766555431   11223333332211   1367999999999999865433

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=94.69  E-value=0.019  Score=54.41  Aligned_cols=24  Identities=33%  Similarity=0.618  Sum_probs=21.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||+|+|||||++.|+..+
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            447899999999999999999977

>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=94.67  E-value=0.24  Score=49.89  Aligned_cols=53  Identities=21%  Similarity=0.257  Sum_probs=30.2

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcC-----CCCceEEEECCCCCChhHHHH
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGR-----AWKRGYLLYGPPGSGKSSLIA  246 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~-----~~~rG~LL~GPPGTGKTsLa~  246 (530)
                      .+|+++...+.+.+.+.+.   -...+..++...+     ..++.+++.+|+|+|||..+.
T Consensus         5 ~~f~~~~l~~~l~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~   62 (395)
T 3pey_A            5 KSFDELGLAPELLKGIYAM---KFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS   62 (395)
T ss_dssp             CSSTTSCCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHH
T ss_pred             cCHhhCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHH
Confidence            4677777777665555431   1112222222111     123689999999999998654

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=94.56  E-value=0.022  Score=53.24  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.||+|+|||||+++|+..+.
T Consensus        21 ei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           21 RVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            3477999999999999999999884

>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=94.56  E-value=0.034  Score=51.39  Aligned_cols=33  Identities=24%  Similarity=0.277  Sum_probs=28.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      +|++|++|+|||++|..+|.. +.+++.+.....
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 878877766543

>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=94.53  E-value=0.018  Score=63.50  Aligned_cols=34  Identities=29%  Similarity=0.322  Sum_probs=24.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      .-+|+.||||||||+++..++..+    +..+..+..+
T Consensus       196 ~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~t  233 (624)
T 2gk6_A          196 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS  233 (624)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESS
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCc
Confidence            357899999999999988887765    3345444433

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=94.49  E-value=0.018  Score=52.92  Aligned_cols=24  Identities=38%  Similarity=0.486  Sum_probs=21.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .+|+||.||+|+|||+++.++...
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            479999999999999999999874

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=94.48  E-value=0.081  Score=60.87  Aligned_cols=63  Identities=22%  Similarity=0.323  Sum_probs=39.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH-----cCCcE----EEEec-----CccC--------------ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY-----LCYDV----YDLEL-----TKVT--------------DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~-----l~~~i----~~l~l-----~~~~--------------~~~~L~~l~~~~~~~  280 (530)
                      +-++|.||.|+||||+++.+|.-     .|..+    ..+..     +.+.              ....+..++..+..|
T Consensus       663 ~i~~ItGpNGsGKSTlLr~ial~~~~aq~G~~vpa~~~~~~~~d~i~~~ig~~d~l~~~lStf~~e~~~~a~il~~a~~~  742 (934)
T 3thx_A          663 MFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKD  742 (934)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHHHHTCCBSEEEEEEECCSEEEEECC---------CHHHHHHHHHHHHHHHCCTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHHhcCCccccccccchHHHHHHHhcCchhhHHHhHhhhHHHHHHHHHHHHhccCC
Confidence            45889999999999999998532     23211    11110     1111              012244455567899


Q ss_pred             eEEEEcCccch
Q 009640          281 SIIVIEDIDCS  291 (530)
Q Consensus       281 sII~IDeID~~  291 (530)
                      ++|++||+-.-
T Consensus       743 sLlLLDEp~~G  753 (934)
T 3thx_A          743 SLIIIDELGRG  753 (934)
T ss_dssp             CEEEEESCSCS
T ss_pred             cEEEEeCCCCC
Confidence            99999999753

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=94.44  E-value=0.17  Score=51.51  Aligned_cols=56  Identities=21%  Similarity=0.172  Sum_probs=31.1

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHHHH
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSLIA  246 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsLa~  246 (530)
                      .+..+|+++...+.+.+.+.+.   -...+..|+...++   -.+.+++.+|+|+|||..+.
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~   76 (400)
T 1s2m_A           18 TKGNTFEDFYLKRELLMGIFEA---GFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFV   76 (400)
T ss_dssp             ---CCGGGGCCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHH
T ss_pred             cccCChhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHH
Confidence            3456788888777766655431   11112222221111   13569999999999997543

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=94.41  E-value=0.019  Score=59.79  Aligned_cols=31  Identities=26%  Similarity=0.350  Sum_probs=26.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-+++.||+|+|||+|+..+|..++..+++.
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~~~iis~   33 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFNGEVINS   33 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHTEEEEEC
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCCCeEeec
Confidence            4578899999999999999999998776654

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.40  E-value=0.065  Score=53.76  Aligned_cols=39  Identities=21%  Similarity=0.149  Sum_probs=29.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      |++...-++|.|+||+|||+|+..+|...   +.++..+++.
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            45555669999999999999999998664   3455555544

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=94.36  E-value=0.021  Score=54.16  Aligned_cols=30  Identities=33%  Similarity=0.281  Sum_probs=24.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC---CcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC---YDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l  259 (530)
                      -+.|.||+|+||||+++.++..+.   ++++..
T Consensus         8 ~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~   40 (213)
T 4edh_A            8 FVTLEGPEGAGKSTNRDYLAERLRERGIEVQLT   40 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCCcccc
Confidence            366789999999999999999884   555544

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=94.34  E-value=0.026  Score=53.74  Aligned_cols=28  Identities=39%  Similarity=0.488  Sum_probs=23.4

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +...-+.|.||+|+|||||+++|+..+.
T Consensus        14 ~~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           14 AQGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            3345578999999999999999999875

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.32  E-value=0.029  Score=54.88  Aligned_cols=24  Identities=50%  Similarity=0.790  Sum_probs=21.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-++|.||+|+||||++++|+..+
T Consensus        26 ~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           26 GLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             EEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCccHHHHHHHHHHhC
Confidence            347899999999999999999876

>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=94.31  E-value=0.096  Score=45.83  Aligned_cols=21  Identities=19%  Similarity=0.341  Sum_probs=19.1

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|+||+|||+|+.++.+.
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            689999999999999999764

>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=94.29  E-value=0.027  Score=51.66  Aligned_cols=25  Identities=20%  Similarity=0.227  Sum_probs=22.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ..-+.|.||+|+|||||+.+++..+
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            4568899999999999999999875

>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=94.24  E-value=0.058  Score=54.62  Aligned_cols=53  Identities=21%  Similarity=0.270  Sum_probs=33.9

Q ss_pred             hhhhHHHHHHHHHHHcChhh--H-h-hhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          200 PQLKKQITEDLTAFANGKEF--Y-H-RVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~--y-~-~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.+++.+.+.+...+.....  + . ....+.+.-+.|.||+|+||||+++.||..+
T Consensus        97 ~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C           97 KIIEEAVKEAVSEILETSRRIDLIEEIRKAEKPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             HHHHHHHHHHHHHHSCCSSCCCHHHHHHSSCSSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCccccchhhhcccCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34555566666666653320  0 0 0112234457899999999999999999987

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=94.23  E-value=0.027  Score=58.10  Aligned_cols=26  Identities=46%  Similarity=0.689  Sum_probs=22.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      ..-+++.||+|+||||++++|++.+.
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            34588999999999999999998763

>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=94.20  E-value=0.075  Score=47.68  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=20.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.|+||+|||||+.++.+.-
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58999999999999999998643

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=94.20  E-value=0.039  Score=55.65  Aligned_cols=59  Identities=27%  Similarity=0.428  Sum_probs=37.3

Q ss_pred             hhHHHHHHHHHHHcChhhH---hhhc--CCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          202 LKKQITEDLTAFANGKEFY---HRVG--RAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       202 ~k~~i~~~l~~~l~~~~~y---~~~g--~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +++.+.+.+...+.....-   ..+.  ...++-+++.||+|+||||++..||..+   +..+.-+.
T Consensus        74 ~~~~~~~~l~~~l~~~~~~~~~~~l~~~~~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid  140 (320)
T 1zu4_A           74 IKDALVESLYQAYTDNDWTNKKYRIDFKENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAA  140 (320)
T ss_dssp             HHHHHHHHHHHHHHCSCC----CCCCCCTTSCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHHHhCcccccccccCccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            5556666666666433200   1122  2334568899999999999999999876   44554443

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=94.12  E-value=0.61  Score=46.12  Aligned_cols=54  Identities=20%  Similarity=0.212  Sum_probs=32.0

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhc-----CCCCceEEEECCCCCChhHH
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVG-----RAWKRGYLLYGPPGSGKSSL  244 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g-----~~~~rG~LL~GPPGTGKTsL  244 (530)
                      ....+|+++...+.+.+.+...   -...+..++..-     ...++.+++.+|+|||||..
T Consensus        89 ~~~~~f~~l~l~~~l~~~l~~~---g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a  147 (300)
T 3fmo_B           89 YSVKSFEELRLKPQLLQGVYAM---GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA  147 (300)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHT---TCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHH
T ss_pred             CCcCCHhhcCCCHHHHHHHHHc---CCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHH
Confidence            3456899998887766655431   111221122111     11236899999999999975

>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=94.12  E-value=0.073  Score=55.74  Aligned_cols=31  Identities=35%  Similarity=0.445  Sum_probs=24.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC---cEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY---DVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~---~i~~l~  260 (530)
                      -+++.||+|+||||++++|++.+..   +++.++
T Consensus       169 ii~I~GpnGSGKTTlL~allg~l~~~~g~I~~~e  202 (418)
T 1p9r_A          169 IILVTGPTGSGKSTTLYAGLQELNSSERNILTVE  202 (418)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHhhcCCCCCEEEEec
Confidence            3789999999999999999998843   455443

>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=94.07  E-value=0.058  Score=46.96  Aligned_cols=23  Identities=26%  Similarity=0.395  Sum_probs=20.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.|++|+|||||+.++++..
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            57999999999999999998653

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=94.06  E-value=0.055  Score=57.39  Aligned_cols=23  Identities=30%  Similarity=0.530  Sum_probs=20.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -.+|+||||+|||+|+..++...
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhhh
Confidence            37899999999999999988764

>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=94.06  E-value=0.12  Score=46.63  Aligned_cols=23  Identities=35%  Similarity=0.508  Sum_probs=20.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||+|+.++.+.
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            36899999999999999999875

>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=94.05  E-value=0.14  Score=46.69  Aligned_cols=23  Identities=26%  Similarity=0.374  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-++|.|++|+|||+|+.++.+.
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            36899999999999999999864

>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=94.04  E-value=0.069  Score=47.65  Aligned_cols=23  Identities=35%  Similarity=0.509  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|+||+|||+|+.++.+.
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            35899999999999999999864

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=94.04  E-value=0.06  Score=48.81  Aligned_cols=24  Identities=38%  Similarity=0.475  Sum_probs=21.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.|++|+|||+|+.++.+.-
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            368999999999999999998743

>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=94.02  E-value=0.037  Score=59.64  Aligned_cols=32  Identities=19%  Similarity=0.321  Sum_probs=25.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      .-++|.|+||+||||+++.+|.++   +.+...++
T Consensus        36 ~lIvlvGlpGSGKSTia~~La~~L~~~~~d~~v~s   70 (520)
T 2axn_A           36 TVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFN   70 (520)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCCeEEec
Confidence            468899999999999999999998   44444443

>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=94.00  E-value=0.07  Score=46.59  Aligned_cols=23  Identities=26%  Similarity=0.374  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|++|+|||+|+.++.+.
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            36899999999999999999864

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=93.98  E-value=0.07  Score=57.22  Aligned_cols=59  Identities=14%  Similarity=0.195  Sum_probs=37.8

Q ss_pred             hhhHHHHHHHHHHHcChhhHhhhcC--CCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          201 QLKKQITEDLTAFANGKEFYHRVGR--AWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~~~~y~~~g~--~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      .+.+.+.+.+...+.....  .+..  ..++-+++.|+||+||||++.++|..+   |..+.-++.
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            3555566666666653211  1111  224568899999999999999999877   666655554

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.95  E-value=0.049  Score=49.45  Aligned_cols=26  Identities=27%  Similarity=0.553  Sum_probs=22.3

Q ss_pred             CCceEEEECCCCCChhHHHHHHHHHc
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ...-+++.|++|+|||||+.++++.-
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

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=93.94  E-value=0.2  Score=46.90  Aligned_cols=17  Identities=18%  Similarity=0.317  Sum_probs=14.6

Q ss_pred             ceEEEECCCCCChhHHH
Q 009640          229 RGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa  245 (530)
                      +.+++.+|+|+|||...
T Consensus        58 ~~~l~~apTGsGKT~~~   74 (228)
T 3iuy_A           58 IDLIVVAQTGTGKTLSY   74 (228)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CCEEEECCCCChHHHHH
Confidence            57899999999999743

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=93.93  E-value=0.035  Score=53.35  Aligned_cols=25  Identities=24%  Similarity=0.290  Sum_probs=22.5

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +-|.||+|+||||+++.|+..+|..
T Consensus        28 igI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           28 IGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhchh
Confidence            6689999999999999999988754

>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=93.91  E-value=0.08  Score=46.92  Aligned_cols=24  Identities=29%  Similarity=0.477  Sum_probs=21.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.|++|+|||||+.++.+.-
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999998643

>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=93.90  E-value=0.043  Score=54.55  Aligned_cols=26  Identities=35%  Similarity=0.312  Sum_probs=22.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .-+.+.||+|+|||||++.|+..++.
T Consensus        32 ~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           32 LFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            34678999999999999999998853

>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=93.89  E-value=0.031  Score=50.71  Aligned_cols=24  Identities=33%  Similarity=0.288  Sum_probs=21.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -.+|+||.|+|||+++.||+..++
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            357899999999999999998875

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=93.82  E-value=0.16  Score=48.86  Aligned_cols=52  Identities=17%  Similarity=0.091  Sum_probs=29.4

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHHH
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsLa  245 (530)
                      .+|+++...+.+.+.+.+.   -...+..|+...++   ..+.+++.+|+|+|||...
T Consensus        43 ~~f~~l~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~   97 (249)
T 3ber_A           43 KTFKDLGVTDVLCEACDQL---GWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAF   97 (249)
T ss_dssp             CCTGGGTCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHH
T ss_pred             CCHHHcCCCHHHHHHHHHc---CCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHh
Confidence            4688887777655544321   01122222221111   1367999999999999853

>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=93.73  E-value=0.06  Score=49.21  Aligned_cols=32  Identities=19%  Similarity=0.235  Sum_probs=26.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +-+.+.|++|+||||++..++..+   ++.+..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik   39 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   39 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEEE
Confidence            457899999999999999999876   45555554

>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=93.72  E-value=0.091  Score=46.92  Aligned_cols=23  Identities=26%  Similarity=0.374  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|++|+|||+|+.++++.
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            46899999999999999999864

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=93.71  E-value=0.022  Score=54.15  Aligned_cols=25  Identities=20%  Similarity=0.300  Sum_probs=15.0

Q ss_pred             ceEEEECCCCCChhHHHHHHH-HHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMA-NYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA-~~l~  253 (530)
                      .-+.|.||+|+||||+++.|+ ..+.
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~~~~~~   53 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLLEKQKN   53 (231)
T ss_dssp             CEEEEECSCC----CHHHHHHC----
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCCC
Confidence            347789999999999999999 8763

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=93.69  E-value=0.45  Score=48.52  Aligned_cols=54  Identities=19%  Similarity=0.214  Sum_probs=32.1

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHHHH
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSLIA  246 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsLa~  246 (530)
                      ..+|+++...+.+.+.+...   -...+..++...++   ..+.+++.+|+|+|||....
T Consensus        36 ~~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~   92 (410)
T 2j0s_A           36 TPTFDTMGLREDLLRGIYAY---GFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFS   92 (410)
T ss_dssp             CCSGGGGCCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             CCCHhhcCCCHHHHHHHHHc---CCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHH
Confidence            34799988777766655431   11222223322211   13579999999999996544

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.66  E-value=0.081  Score=46.46  Aligned_cols=21  Identities=33%  Similarity=0.580  Sum_probs=19.5

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -+++.|+||+|||||+.++.+
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            578999999999999999986

>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=93.64  E-value=0.034  Score=63.08  Aligned_cols=23  Identities=39%  Similarity=0.608  Sum_probs=19.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.||||||||+++.+++..+
T Consensus       373 ~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          373 LSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHH
Confidence            57899999999999988887765

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=93.62  E-value=0.5  Score=49.60  Aligned_cols=53  Identities=21%  Similarity=0.242  Sum_probs=30.8

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhc-----CCCCceEEEECCCCCChhHH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVG-----RAWKRGYLLYGPPGSGKSSL  244 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g-----~~~~rG~LL~GPPGTGKTsL  244 (530)
                      ...+|+++...+.+.+.+.+   .-...+..++...     ....+.+|+.||+|+|||..
T Consensus        90 ~~~~f~~~~l~~~l~~~l~~---~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~  147 (479)
T 3fmp_B           90 SVKSFEELRLKPQLLQGVYA---MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA  147 (479)
T ss_dssp             CCCCSGGGTCCHHHHHHHHH---TTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHH
T ss_pred             CcCCHHHcCCCHHHHHHHHH---cCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHH
Confidence            34578888888776655543   0011111111111     01236799999999999976

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=93.58  E-value=0.041  Score=59.99  Aligned_cols=31  Identities=29%  Similarity=0.209  Sum_probs=27.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC----CcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC----YDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~----~~i~~l~  260 (530)
                      -++|.|+||+||||++++++..++    .+++.++
T Consensus       398 ~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD  432 (573)
T 1m8p_A          398 TIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLL  432 (573)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEE
T ss_pred             EEEeecCCCCCHHHHHHHHHHHhcccCCceEEEEC
Confidence            477899999999999999999986    6777775

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.57  E-value=0.065  Score=56.57  Aligned_cols=39  Identities=18%  Similarity=0.212  Sum_probs=29.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      |++...-++|.||||+|||+|+..+|..+    |.++..+++.
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E  241 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLE  241 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESS
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECC
Confidence            45555568999999999999999988754    4566666543

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=93.54  E-value=0.032  Score=55.44  Aligned_cols=36  Identities=14%  Similarity=0.178  Sum_probs=24.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC---CcEEEEecCccC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC---YDVYDLELTKVT  265 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~~~~  265 (530)
                      -+.|.||+|+||||+++.++..++   ..+..+++..+.
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            477899999999999999999876   445555555543

>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=93.51  E-value=0.037  Score=60.84  Aligned_cols=24  Identities=33%  Similarity=0.576  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +-+++.||||||||+++.++...+
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHH
Confidence            568999999999999998877655

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.48  E-value=0.054  Score=51.89  Aligned_cols=30  Identities=20%  Similarity=0.222  Sum_probs=21.8

Q ss_pred             EEEECCCCCChhHHHHHHHHHc-------CCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL-------CYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l-------~~~i~~l~  260 (530)
                      +.|.||+|+||||+++.++..+       +++++...
T Consensus        28 I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~r   64 (227)
T 3v9p_A           28 ITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVTR   64 (227)
T ss_dssp             EEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhhccccceeeeeec
Confidence            6778999999999999999988       56665443

>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=93.45  E-value=0.019  Score=55.82  Aligned_cols=24  Identities=17%  Similarity=0.238  Sum_probs=21.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.|++|+||||+++.||..+.
T Consensus        26 ~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           26 KISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            477899999999999999999983

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=93.41  E-value=0.089  Score=53.10  Aligned_cols=24  Identities=21%  Similarity=0.166  Sum_probs=21.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+-|.||+|+||||+++.|+..++
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            467889999999999999999875

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.41  E-value=0.13  Score=54.07  Aligned_cols=62  Identities=16%  Similarity=0.217  Sum_probs=38.8

Q ss_pred             hhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          201 QLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      .+.+.+.+.+...+.....--......++.+++.|++|+||||++..+|..+    |..+.-+++.
T Consensus        73 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D  138 (433)
T 2xxa_A           73 EFVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSAD  138 (433)
T ss_dssp             TTHHHHHHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECC
T ss_pred             HHHHHHHHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            3445566666666643210000111234678889999999999999999776    5666655543

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.37  E-value=0.05  Score=51.99  Aligned_cols=25  Identities=20%  Similarity=0.275  Sum_probs=22.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.+.|++|+||||+++.++..++
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            3478999999999999999999994

>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=93.35  E-value=0.13  Score=46.30  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=21.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      --++|.|+||+|||+|++.+.+..
T Consensus        15 ~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhc
Confidence            358999999999999999888755

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=93.33  E-value=0.045  Score=47.76  Aligned_cols=22  Identities=32%  Similarity=0.495  Sum_probs=20.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|++|+|||||+.++++.
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            5789999999999999999874

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.29  E-value=0.074  Score=55.99  Aligned_cols=39  Identities=15%  Similarity=0.066  Sum_probs=29.2

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      |++...-++|.|+||+|||+|+..+|...    +.++..+++.
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE  238 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLE  238 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            45555568999999999999999888654    4556666554

>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=93.28  E-value=0.044  Score=50.96  Aligned_cols=24  Identities=29%  Similarity=0.522  Sum_probs=21.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-++|.|+||+|||+|+.++++..
T Consensus        13 ~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           13 PSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            468999999999999999999864

>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=93.27  E-value=0.045  Score=50.30  Aligned_cols=23  Identities=30%  Similarity=0.484  Sum_probs=20.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||+|+|||||++++++..
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            57899999999999999999863

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=93.21  E-value=0.04  Score=62.53  Aligned_cols=33  Identities=27%  Similarity=0.344  Sum_probs=24.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      -+|+.||||||||+++..++..+    +..+..+..+
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            57899999999999888776544    4555555444

>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=93.18  E-value=0.026  Score=60.00  Aligned_cols=26  Identities=23%  Similarity=0.498  Sum_probs=23.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .-++|.|.||+||||+++.+|..++.
T Consensus        40 ~~IvlvGlpGsGKSTia~~La~~l~~   65 (469)
T 1bif_A           40 TLIVMVGLPARGKTYISKKLTRYLNF   65 (469)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            46899999999999999999998753

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=93.18  E-value=0.059  Score=53.94  Aligned_cols=25  Identities=36%  Similarity=0.565  Sum_probs=22.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.-+.|.||+|+||||+++.||..+
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            3457889999999999999999887

>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=93.15  E-value=0.05  Score=47.77  Aligned_cols=23  Identities=26%  Similarity=0.287  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||||+.++.+.
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            46899999999999999999874

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.14  E-value=0.046  Score=51.56  Aligned_cols=22  Identities=41%  Similarity=0.406  Sum_probs=20.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+.|.||.|+|||||+++|+..
T Consensus        24 ~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           24 IVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             EEEEECCTTSSTTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4778999999999999999986

>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=93.10  E-value=0.045  Score=50.17  Aligned_cols=23  Identities=30%  Similarity=0.484  Sum_probs=20.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||+|+|||||++.+++..
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            47899999999999999999864

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=93.05  E-value=0.13  Score=51.19  Aligned_cols=60  Identities=18%  Similarity=0.240  Sum_probs=37.8

Q ss_pred             hhhHHHHHHHHHHHcChhhHhh-hcCCC-CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          201 QLKKQITEDLTAFANGKEFYHR-VGRAW-KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~~~~y~~-~g~~~-~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      .+++.+.+.+...+....  .. +.... +.-+++.||+|+||||++..+|..+   +..+.-++..
T Consensus        71 ~~~~~~~~~l~~~~~~~~--~~~i~~~~~~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D  135 (297)
T 1j8m_F           71 WFIKIVYDELSNLFGGDK--EPKVIPDKIPYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGAD  135 (297)
T ss_dssp             HHHHHHHHHHHHHTTCSC--CCCCSCSSSSEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             HHHHHHHHHHHHHhcccc--ccccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            345556666666554321  11 11111 4457788999999999999999877   5566555543

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=93.03  E-value=0.035  Score=53.52  Aligned_cols=23  Identities=30%  Similarity=0.413  Sum_probs=21.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||||+||||+++.++..+
T Consensus        29 ~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           29 FIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             EEEEEESTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            46789999999999999999987

>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=92.99  E-value=0.05  Score=54.69  Aligned_cols=24  Identities=21%  Similarity=0.174  Sum_probs=21.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||+|+|||||++.|+..+.
T Consensus        92 ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           92 IIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCchHHHHHHHHHhhcc
Confidence            366899999999999999999874

>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=92.97  E-value=0.19  Score=46.41  Aligned_cols=23  Identities=22%  Similarity=0.395  Sum_probs=20.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --++|.|++|+|||+|+.++.+.
T Consensus        26 ~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           26 IKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            36899999999999999999853

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=92.95  E-value=0.078  Score=50.36  Aligned_cols=30  Identities=20%  Similarity=0.113  Sum_probs=25.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -+.|.||+|+||||+++.++..++.++..+
T Consensus         7 ~i~~eG~~g~GKst~~~~l~~~l~~~~~~~   36 (216)
T 3tmk_A            7 LILIEGLDRTGKTTQCNILYKKLQPNCKLL   36 (216)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHCSSEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcccceEE
Confidence            467889999999999999999998754433

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=92.93  E-value=0.075  Score=50.30  Aligned_cols=31  Identities=29%  Similarity=0.320  Sum_probs=28.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      .+-|.|.+||||||+++.++. +|+++++.+.
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            577999999999999999998 9999998764

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=92.93  E-value=1  Score=45.62  Aligned_cols=53  Identities=13%  Similarity=0.125  Sum_probs=30.5

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcC---CCCceEEEECCCCCChhHHH
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGR---AWKRGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~---~~~rG~LL~GPPGTGKTsLa  245 (530)
                      ..+|+++...+.+.+.+.+.   -...+..|+...+   ...+.+++.+|+|+|||..+
T Consensus        39 ~~~f~~~~l~~~~~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~   94 (414)
T 3eiq_A           39 VDSFDDMNLSESLLRGIYAY---GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF   94 (414)
T ss_dssp             CCCGGGGCCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHH
T ss_pred             hcCHhhCCCCHHHHHHHHHc---CCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHH
Confidence            35788887777766555431   1112222222111   11356899999999999864

>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=92.90  E-value=0.048  Score=55.76  Aligned_cols=28  Identities=25%  Similarity=0.338  Sum_probs=24.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      ..-+.|.||+|+|||||++.|+..+..+
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            3458899999999999999999997654

>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=92.89  E-value=0.058  Score=47.36  Aligned_cols=23  Identities=26%  Similarity=0.380  Sum_probs=20.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.|++|+|||||+.++.+.-
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999998643

>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=92.75  E-value=0.18  Score=52.20  Aligned_cols=23  Identities=30%  Similarity=0.567  Sum_probs=21.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.||||+|||+|+..||+..
T Consensus       176 r~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          176 RGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             EEEEECCSSSSHHHHHHHHHHHH
T ss_pred             EEEEecCCCCChhHHHHHHHHHH
Confidence            48999999999999999999865

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=92.74  E-value=0.37  Score=53.70  Aligned_cols=18  Identities=28%  Similarity=0.405  Sum_probs=16.0

Q ss_pred             CceEEEECCCCCChhHHH
Q 009640          228 KRGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa  245 (530)
                      .+.+++.||+|+|||..+
T Consensus        39 ~~~~lv~apTGsGKT~~~   56 (720)
T 2zj8_A           39 GKNALISIPTASGKTLIA   56 (720)
T ss_dssp             TCEEEEECCGGGCHHHHH
T ss_pred             CCcEEEEcCCccHHHHHH
Confidence            467999999999999876

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.72  E-value=0.065  Score=56.41  Aligned_cols=24  Identities=33%  Similarity=0.553  Sum_probs=20.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .+-.+++|+||||||+++..+++.
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            345788999999999999888753

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=92.70  E-value=0.099  Score=53.13  Aligned_cols=38  Identities=24%  Similarity=0.156  Sum_probs=28.8

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      |+....-++|.|+||+|||+|+..+|..+   +.++..+++
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSl   82 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSL   82 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            34444558999999999999999998764   566666654

>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=92.69  E-value=0.062  Score=47.74  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||||+.++.+.
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999999864

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=92.62  E-value=0.051  Score=52.42  Aligned_cols=26  Identities=31%  Similarity=0.489  Sum_probs=22.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .-+.|.||.|+|||||+++|+..+..
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            46779999999999999999997743

>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=92.62  E-value=0.06  Score=47.35  Aligned_cols=23  Identities=35%  Similarity=0.492  Sum_probs=20.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||||+.++.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35899999999999999999864

>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=92.61  E-value=0.065  Score=47.18  Aligned_cols=23  Identities=26%  Similarity=0.299  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||||+.++.+.
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35899999999999999999865

>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=92.60  E-value=0.058  Score=53.92  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=21.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+-|.||+|+|||||++.|+..++
T Consensus        82 iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           82 IISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            367899999999999999999876

>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=92.59  E-value=0.063  Score=47.72  Aligned_cols=22  Identities=32%  Similarity=0.513  Sum_probs=19.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+.|.|+||+|||||+.++++.
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            4789999999999999999863

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=92.58  E-value=0.25  Score=59.19  Aligned_cols=28  Identities=29%  Similarity=0.439  Sum_probs=23.5

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +...-+.+.||.|+|||||+++|.+++.
T Consensus       442 ~~G~~vaivG~sGsGKSTll~ll~~~~~  469 (1321)
T 4f4c_A          442 NAGQTVALVGSSGCGKSTIISLLLRYYD  469 (1321)
T ss_dssp             CTTCEEEEEECSSSCHHHHHHHHTTSSC
T ss_pred             cCCcEEEEEecCCCcHHHHHHHhccccc
Confidence            3334588999999999999999999874

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=92.55  E-value=0.18  Score=53.65  Aligned_cols=29  Identities=28%  Similarity=0.390  Sum_probs=25.5

Q ss_pred             EEEECCCCCChhHH-HHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSL-IAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsL-a~AiA~~l~~~i~~l  259 (530)
                      .++.|++|||||+| +..|++..+.+++.+
T Consensus       165 ~~Ifg~~g~GKT~Lal~~I~~~~~~dv~~V  194 (502)
T 2qe7_A          165 ELIIGDRQTGKTTIAIDTIINQKGQDVICI  194 (502)
T ss_dssp             CEEEECSSSCHHHHHHHHHHGGGSCSEEEE
T ss_pred             EEEECCCCCCchHHHHHHHHHhhcCCcEEE
Confidence            79999999999999 679999998886544

>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=92.55  E-value=0.068  Score=46.87  Aligned_cols=23  Identities=30%  Similarity=0.371  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||||+.++.+.
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999999863

>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=92.53  E-value=0.18  Score=46.41  Aligned_cols=23  Identities=17%  Similarity=0.280  Sum_probs=20.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-++|.|+||+|||+|+.++.+.
T Consensus        30 ~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           30 FKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhhC
Confidence            35899999999999999999763

>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=92.50  E-value=0.068  Score=47.55  Aligned_cols=24  Identities=29%  Similarity=0.425  Sum_probs=20.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.|++|+|||||+.++.+.-
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            468999999999999999998743

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=92.50  E-value=0.061  Score=47.79  Aligned_cols=23  Identities=48%  Similarity=0.533  Sum_probs=20.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -.+++||.|+|||+++.||.--+
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            35789999999999999998655

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.50  E-value=0.042  Score=52.37  Aligned_cols=26  Identities=27%  Similarity=0.268  Sum_probs=22.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||+++|+..+..+
T Consensus        32 ~~~iiG~nGsGKSTLl~~l~Gl~~p~   57 (224)
T 2pcj_A           32 FVSIIGASGSGKSTLLYILGLLDAPT   57 (224)
T ss_dssp             EEEEEECTTSCHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            47799999999999999999877543

>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=92.48  E-value=0.065  Score=47.42  Aligned_cols=23  Identities=39%  Similarity=0.579  Sum_probs=20.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||+|+.++.+.
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCccHHHHHHHHhcC
Confidence            35899999999999999999753

>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=92.48  E-value=0.06  Score=48.87  Aligned_cols=24  Identities=25%  Similarity=0.275  Sum_probs=20.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      --+++.|++|+|||+|+.++.+.-
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            358999999999999999997654

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=92.45  E-value=0.12  Score=54.47  Aligned_cols=31  Identities=35%  Similarity=0.438  Sum_probs=26.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+.|.||+|+|||||++.||+....+.-.+.
T Consensus       159 ~~~IvG~sGsGKSTLl~~Iag~~~~~~G~i~  189 (438)
T 2dpy_A          159 RMGLFAGSGVGKSVLLGMMARYTRADVIVVG  189 (438)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSCCSEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcccCCCeEEEE
Confidence            3789999999999999999999976654443

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=92.43  E-value=0.044  Score=52.68  Aligned_cols=27  Identities=26%  Similarity=0.338  Sum_probs=23.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      .-+.|.||.|+|||||+++|+..+.-+
T Consensus        32 e~~~iiG~nGsGKSTLl~~l~Gl~~p~   58 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTMLNIIGCLDKPT   58 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCCCCC
Confidence            347899999999999999999877543

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=92.43  E-value=0.061  Score=52.84  Aligned_cols=25  Identities=24%  Similarity=0.418  Sum_probs=21.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      .+.|.||+|+|||||+++|++....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~~   28 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQVS   28 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCC
Confidence            4678999999999999999998743

>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=92.42  E-value=0.12  Score=46.58  Aligned_cols=23  Identities=30%  Similarity=0.462  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|+||+|||+|+.++++.
T Consensus        17 ~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           17 VRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45899999999999999999864

>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=92.37  E-value=0.074  Score=46.56  Aligned_cols=22  Identities=27%  Similarity=0.430  Sum_probs=20.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|+||+|||||+.++.+.
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            5789999999999999999874

>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=92.35  E-value=0.052  Score=51.49  Aligned_cols=26  Identities=31%  Similarity=0.466  Sum_probs=22.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||+++|+..+..+
T Consensus        37 ~~~iiG~NGsGKSTLlk~l~Gl~~p~   62 (214)
T 1sgw_A           37 VVNFHGPNGIGKTTLLKTISTYLKPL   62 (214)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            47899999999999999999887543

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=92.34  E-value=0.1  Score=48.58  Aligned_cols=25  Identities=28%  Similarity=0.337  Sum_probs=22.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +-+++.|+||+|||||+.+++..+.
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            4688999999999999999998864

>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=92.33  E-value=0.21  Score=52.29  Aligned_cols=59  Identities=20%  Similarity=0.180  Sum_probs=37.4

Q ss_pred             hhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          201 QLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       201 ~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      .+.+.+.+.+...+....  ..+....+.-+++.||+|+||||++..+|..+   +..+.-+..
T Consensus        73 ~~~~~v~~~L~~~~~~~~--~~i~l~~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~  134 (425)
T 2ffh_A           73 VILATVYEALKEALGGEA--RLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (425)
T ss_dssp             HHHHHHHHHHHHHTTSSC--CCCCCCSSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEC
T ss_pred             HHHHHHHHHHHHHhCCCc--ccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeec
Confidence            345556666655554321  12222234567888999999999999999887   455555543

>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=92.32  E-value=0.11  Score=53.01  Aligned_cols=32  Identities=34%  Similarity=0.339  Sum_probs=25.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      .-+.|.|+||+|||||+.+++..+   +..+..++
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            458899999999999999999886   55544443

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=92.30  E-value=0.05  Score=52.36  Aligned_cols=24  Identities=33%  Similarity=0.426  Sum_probs=21.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||.|+|||||++.|+..+
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            357899999999999999999876

>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=92.29  E-value=0.075  Score=47.77  Aligned_cols=23  Identities=26%  Similarity=0.444  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --++|.|+||+|||+|+.++.+.
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999999863

>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=92.28  E-value=0.087  Score=56.30  Aligned_cols=39  Identities=15%  Similarity=-0.035  Sum_probs=29.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc----CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL----CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l~  262 (530)
                      |++...-++|.|+||+|||+|+..+|..+    +.++..+++.
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            45555568999999999999999998765    3456666543

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.25  E-value=0.052  Score=51.44  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=21.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      =+.|.|++|+||||.++.++..+
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            36788999999999999999988

>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=92.24  E-value=0.061  Score=48.75  Aligned_cols=21  Identities=29%  Similarity=0.637  Sum_probs=19.3

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -++|.|+||+|||||+..+++
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999999986

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=92.21  E-value=0.11  Score=54.79  Aligned_cols=39  Identities=21%  Similarity=0.149  Sum_probs=29.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      |++...-+++.|+||+|||+|+..+|...   |.++..+++.
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            45554558999999999999999888765   5566666544

>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=92.20  E-value=0.072  Score=47.26  Aligned_cols=22  Identities=27%  Similarity=0.398  Sum_probs=19.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|++|+|||+|+.++.+.
T Consensus        16 ~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=92.18  E-value=0.11  Score=52.98  Aligned_cols=31  Identities=26%  Similarity=0.372  Sum_probs=26.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -+.|.||+|+|||||++.|++.+..+...+.
T Consensus        73 ~~gIiG~nGaGKTTLl~~I~g~~~~~~g~i~  103 (347)
T 2obl_A           73 RIGIFAGSGVGKSTLLGMICNGASADIIVLA  103 (347)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSCCSEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCEEEEE
Confidence            3789999999999999999999977654443

>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=92.17  E-value=0.076  Score=46.75  Aligned_cols=21  Identities=33%  Similarity=0.570  Sum_probs=18.7

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -+++.|+||+|||+|+.++.+
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            378999999999999999963

>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=92.16  E-value=0.081  Score=46.59  Aligned_cols=23  Identities=22%  Similarity=0.388  Sum_probs=20.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|+||+|||+|+.++.+.
T Consensus         8 ~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            8 MRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999999763

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=92.12  E-value=0.071  Score=47.43  Aligned_cols=23  Identities=30%  Similarity=0.387  Sum_probs=20.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||+|+.++.+.
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEEEECcCCCCHHHHHHHHHhC
Confidence            35899999999999999999753

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=92.07  E-value=0.069  Score=48.10  Aligned_cols=23  Identities=30%  Similarity=0.465  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-++|.|++|+|||||+.++++.
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35889999999999999999873

>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=92.05  E-value=0.058  Score=52.50  Aligned_cols=26  Identities=46%  Similarity=0.726  Sum_probs=22.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||+++|+..+..+
T Consensus        35 ~~~liG~nGsGKSTLlk~l~Gl~~p~   60 (257)
T 1g6h_A           35 VTLIIGPNGSGKSTLINVITGFLKAD   60 (257)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCC
Confidence            37799999999999999999887543

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.04  E-value=0.082  Score=47.76  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=20.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||||+.++.+.
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

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.02  E-value=0.058  Score=52.70  Aligned_cols=26  Identities=23%  Similarity=0.275  Sum_probs=22.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||+++|+..+..+
T Consensus        34 ~~~liG~nGsGKSTLlk~l~Gl~~p~   59 (262)
T 1b0u_A           34 VISIIGSSGSGKSTFLRCINFLEKPS   59 (262)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            37799999999999999999987543

>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=91.98  E-value=0.086  Score=47.84  Aligned_cols=23  Identities=26%  Similarity=0.470  Sum_probs=20.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --++|.|+||+|||+|+.++.+.
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            46899999999999999999874

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=91.98  E-value=0.06  Score=51.44  Aligned_cols=25  Identities=28%  Similarity=0.397  Sum_probs=22.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.||.|+|||||+++|+..+.
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCc
Confidence            3478999999999999999999874

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=91.97  E-value=0.069  Score=51.74  Aligned_cols=22  Identities=41%  Similarity=0.496  Sum_probs=20.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+.|.||.|+|||||++.|+..
T Consensus        31 ~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           31 VHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999986

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=91.92  E-value=0.51  Score=45.56  Aligned_cols=17  Identities=35%  Similarity=0.456  Sum_probs=14.7

Q ss_pred             ceEEEECCCCCChhHHH
Q 009640          229 RGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa  245 (530)
                      +.+|+.+|+|+|||..+
T Consensus        92 ~~~lv~a~TGsGKT~~~  108 (262)
T 3ly5_A           92 RDLLAAAKTGSGKTLAF  108 (262)
T ss_dssp             CCCEECCCTTSCHHHHH
T ss_pred             CcEEEEccCCCCchHHH
Confidence            56899999999999753

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=91.92  E-value=0.14  Score=46.56  Aligned_cols=22  Identities=27%  Similarity=0.548  Sum_probs=19.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      .-+++.|++|+|||+|+.++.+
T Consensus        27 ~ki~vvG~~~~GKSsLi~~l~~   48 (192)
T 2il1_A           27 LQVIIIGSRGVGKTSLMERFTD   48 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            3589999999999999999974

>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=91.90  E-value=0.073  Score=46.73  Aligned_cols=21  Identities=43%  Similarity=0.688  Sum_probs=18.7

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -+++.|+||+|||+|+.++.+
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            478999999999999999864

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=91.90  E-value=0.077  Score=56.95  Aligned_cols=26  Identities=12%  Similarity=0.020  Sum_probs=23.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      ..+.|.|++|+||||+++++|..|+.
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            35788999999999999999999985

>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=91.89  E-value=0.062  Score=51.80  Aligned_cols=25  Identities=24%  Similarity=0.505  Sum_probs=21.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.||.|+|||||+++|+..+.
T Consensus        29 e~~~i~G~nGsGKSTLl~~l~Gl~~   53 (243)
T 1mv5_A           29 SIIAFAGPSGGGKSTIFSLLERFYQ   53 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3478999999999999999998763

>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=91.85  E-value=0.075  Score=57.21  Aligned_cols=29  Identities=24%  Similarity=0.295  Sum_probs=24.2

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |++...-++|.||||+|||+|+..+|...
T Consensus       277 ~i~~G~i~~i~G~~GsGKSTLl~~l~g~~  305 (525)
T 1tf7_A          277 GFFKDSIILATGATGTGKTLLVSRFVENA  305 (525)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            44455568999999999999999999765

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=91.81  E-value=0.056  Score=52.46  Aligned_cols=26  Identities=42%  Similarity=0.537  Sum_probs=22.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||++.|+..+..+
T Consensus        28 ~~~liG~NGsGKSTLlk~l~Gl~~p~   53 (249)
T 2qi9_C           28 ILHLVGPNGAGKSTLLARMAGMTSGK   53 (249)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCE
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCC
Confidence            47899999999999999999987654

>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=91.80  E-value=0.22  Score=57.85  Aligned_cols=21  Identities=33%  Similarity=0.449  Sum_probs=19.1

Q ss_pred             ceEEEECCCCCChhHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMA  249 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA  249 (530)
                      +-++|.||.|+||||+++.++
T Consensus       790 ~i~~ItGpNgsGKSTlLr~iG  810 (1022)
T 2o8b_B          790 YCVLVTGPNMGGKSTLMRQAG  810 (1022)
T ss_dssp             CEEEEECCTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCChHHHHHHHH
Confidence            568999999999999999984

>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=91.79  E-value=0.1  Score=47.67  Aligned_cols=23  Identities=26%  Similarity=0.489  Sum_probs=20.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||+|+.++.+.
T Consensus        29 ~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           29 VKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999999874

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=91.76  E-value=0.058  Score=52.23  Aligned_cols=26  Identities=27%  Similarity=0.382  Sum_probs=22.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||++.|+..+..+
T Consensus        37 ~~~i~G~nGsGKSTLl~~l~Gl~~p~   62 (247)
T 2ff7_A           37 VIGIVGRSGSGKSTLTKLIQRFYIPE   62 (247)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            47899999999999999999987543

>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=91.75  E-value=0.074  Score=52.09  Aligned_cols=23  Identities=43%  Similarity=0.547  Sum_probs=20.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||.|+|||||++.|+..+
T Consensus        48 ~~~l~G~NGsGKSTLlk~l~Gl~   70 (267)
T 2zu0_C           48 VHAIMGPNGSGKSTLSATLAGRE   70 (267)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTCT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999999864

>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=91.71  E-value=0.087  Score=47.54  Aligned_cols=23  Identities=22%  Similarity=0.355  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||+|+.++++.
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            45899999999999999999874

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=91.71  E-value=0.058  Score=52.81  Aligned_cols=26  Identities=31%  Similarity=0.557  Sum_probs=22.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||+++|+..+..+
T Consensus        52 i~~liG~NGsGKSTLlk~l~Gl~~p~   77 (263)
T 2olj_A           52 VVVVIGPSGSGKSTFLRCLNLLEDFD   77 (263)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEEcCCCCcHHHHHHHHHcCCCCC
Confidence            47899999999999999999987543

>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=91.71  E-value=0.087  Score=47.25  Aligned_cols=23  Identities=30%  Similarity=0.544  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|++|+|||+|+.++.+.
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            46899999999999999999864

>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=91.71  E-value=0.087  Score=46.78  Aligned_cols=23  Identities=26%  Similarity=0.380  Sum_probs=20.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|++|+|||+|+.++.+.
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            46899999999999999999875

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=91.71  E-value=0.96  Score=47.00  Aligned_cols=52  Identities=13%  Similarity=0.140  Sum_probs=30.5

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHH
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSL  244 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsL  244 (530)
                      -.+|+++...+.+.+.|.+   .-...+..++...++   -.+.+++.+|+|+|||..
T Consensus        55 ~~~f~~~~l~~~l~~~l~~---~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a  109 (434)
T 2db3_A           55 IQHFTSADLRDIIIDNVNK---SGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAA  109 (434)
T ss_dssp             CCCGGGSCCCHHHHHHHHH---TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             cCChhhcCCCHHHHHHHHH---cCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHH
Confidence            3578888777766555432   011222223222211   136799999999999983

>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=91.70  E-value=0.096  Score=47.31  Aligned_cols=23  Identities=26%  Similarity=0.395  Sum_probs=20.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+++.|++|+|||||+.++++..
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            58999999999999999998753

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.70  E-value=0.07  Score=54.63  Aligned_cols=25  Identities=32%  Similarity=0.510  Sum_probs=22.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-++|.||+|+|||||+++|+....
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            4689999999999999999998764

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=91.70  E-value=0.068  Score=51.46  Aligned_cols=26  Identities=27%  Similarity=0.405  Sum_probs=22.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||++.|+..+..+
T Consensus        34 ~~~l~G~nGsGKSTLl~~l~Gl~~p~   59 (240)
T 1ji0_A           34 IVTLIGANGAGKTTTLSAIAGLVRAQ   59 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCC
Confidence            37799999999999999999987543

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=91.68  E-value=0.071  Score=54.66  Aligned_cols=25  Identities=24%  Similarity=0.474  Sum_probs=22.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||.|+|||||+++||....-
T Consensus        32 ~~~llGpsGsGKSTLLr~iaGl~~p   56 (359)
T 3fvq_A           32 ILFIIGASGCGKTTLLRCLAGFEQP   56 (359)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEECCCCchHHHHHHHHhcCCCC
Confidence            3779999999999999999998743

>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=91.66  E-value=0.13  Score=53.81  Aligned_cols=23  Identities=35%  Similarity=0.450  Sum_probs=20.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||+|+|||||+++|++..
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            46789999999999999999854

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=91.65  E-value=0.09  Score=53.30  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=20.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.||||+|||||+++++..+
T Consensus        57 ~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           57 RVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            46789999999999999999876

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=91.64  E-value=0.06  Score=53.10  Aligned_cols=26  Identities=27%  Similarity=0.305  Sum_probs=22.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||+++|+..+..+
T Consensus        36 ~~~iiGpnGsGKSTLl~~l~Gl~~p~   61 (275)
T 3gfo_A           36 VTAILGGNGVGKSTLFQNFNGILKPS   61 (275)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCCCC
Confidence            37899999999999999999987543

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=91.58  E-value=0.11  Score=46.19  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ..-+++.|+||+|||||+.++.+
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            34689999999999999999975

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=91.58  E-value=0.22  Score=50.63  Aligned_cols=23  Identities=43%  Similarity=0.712  Sum_probs=20.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+.|.|+||+|||||+.+++..+
T Consensus        76 ~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           76 RVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            47789999999999999999865

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=91.57  E-value=0.1  Score=49.87  Aligned_cols=29  Identities=28%  Similarity=0.265  Sum_probs=23.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC----cEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY----DVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~----~i~~  258 (530)
                      -+.|.|++|+||||+++.++..++.    +++.
T Consensus        23 ~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~   55 (223)
T 3ld9_A           23 FITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVV   55 (223)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhccCceeeE
Confidence            3667899999999999999998754    5554

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=91.56  E-value=0.17  Score=53.95  Aligned_cols=29  Identities=28%  Similarity=0.430  Sum_probs=25.5

Q ss_pred             EEEECCCCCChhHH-HHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSL-IAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsL-a~AiA~~l~~~i~~l  259 (530)
                      .++.|++|||||+| +..|++..+.+++.+
T Consensus       178 ~~I~g~~g~GKT~Lal~~I~~~~~~dv~~V  207 (515)
T 2r9v_A          178 ELIIGDRQTGKTAIAIDTIINQKGQGVYCI  207 (515)
T ss_dssp             EEEEEETTSSHHHHHHHHHHTTTTTTEEEE
T ss_pred             EEEEcCCCCCccHHHHHHHHHhhcCCcEEE
Confidence            89999999999999 579999998886544

>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=91.52  E-value=0.11  Score=47.05  Aligned_cols=24  Identities=33%  Similarity=0.371  Sum_probs=20.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ..-+++.|++|+|||||+.++.+.
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            356899999999999999999753

>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=91.50  E-value=0.11  Score=46.35  Aligned_cols=23  Identities=26%  Similarity=0.426  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||+|+.++.+.
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            36899999999999999999864

>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=91.50  E-value=0.1  Score=47.17  Aligned_cols=24  Identities=29%  Similarity=0.326  Sum_probs=21.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-++|.|++|+|||+|+.++.+.-
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            368999999999999999998643

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=91.47  E-value=0.053  Score=49.54  Aligned_cols=25  Identities=32%  Similarity=0.360  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.||+|+|||||++.|+..+.
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3578999999999999999999874

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=91.47  E-value=0.083  Score=54.21  Aligned_cols=24  Identities=42%  Similarity=0.574  Sum_probs=21.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||.|+|||||+++||....
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           31 FMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCchHHHHHHHHhcCCC
Confidence            377899999999999999999874

>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=91.46  E-value=0.081  Score=47.51  Aligned_cols=22  Identities=41%  Similarity=0.635  Sum_probs=19.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+.|.|+||+|||||+.++++.
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            4789999999999999999864

>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=91.46  E-value=0.11  Score=46.51  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=19.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|+||+|||||+.++.+.
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

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.46  E-value=0.073  Score=52.57  Aligned_cols=26  Identities=31%  Similarity=0.630  Sum_probs=22.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||++.|+..+..+
T Consensus        49 ~~~liG~NGsGKSTLlk~l~Gl~~p~   74 (279)
T 2ihy_A           49 KWILYGLNGAGKTTLLNILNAYEPAT   74 (279)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCC
Confidence            37899999999999999999987543

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=91.45  E-value=0.071  Score=52.00  Aligned_cols=25  Identities=28%  Similarity=0.414  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.|.||.|+|||||+++|+..+.
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl~~   71 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRFYD   71 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhccCC
Confidence            3488999999999999999998764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=91.45  E-value=0.094  Score=46.56  Aligned_cols=22  Identities=41%  Similarity=0.593  Sum_probs=19.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      --+++.|+||+|||||+.++.+
T Consensus        10 ~~i~v~G~~~~GKssl~~~l~~   31 (181)
T 3tw8_B           10 FKLLIIGDSGVGKSSLLLRFAD   31 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHCS
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            3589999999999999999864

>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=91.44  E-value=0.11  Score=46.59  Aligned_cols=23  Identities=26%  Similarity=0.333  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|++|+|||+|+.++.+.
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            35799999999999999999864

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=91.41  E-value=0.086  Score=54.05  Aligned_cols=25  Identities=28%  Similarity=0.390  Sum_probs=22.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||+|+|||||++.||.....
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~p   55 (359)
T 2yyz_A           31 FVALLGPSGCGKTTTLLMLAGIYKP   55 (359)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEEcCCCchHHHHHHHHHCCCCC
Confidence            3778999999999999999998753

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=91.41  E-value=0.075  Score=51.80  Aligned_cols=26  Identities=23%  Similarity=0.448  Sum_probs=22.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||.|+|||||+++|+..+..+
T Consensus        43 i~~l~G~NGsGKSTLlk~l~Gl~~p~   68 (256)
T 1vpl_A           43 IFGLIGPNGAGKTTTLRIISTLIKPS   68 (256)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            47899999999999999999987543

>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=91.41  E-value=0.17  Score=48.46  Aligned_cols=32  Identities=31%  Similarity=0.518  Sum_probs=25.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc--CCcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL--CYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l--~~~i~~l~  260 (530)
                      .-+++.|.+|+||||++..+|..+  +..+.-++
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd   48 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   48 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEe
Confidence            356788999999999999999876  55555444

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=91.37  E-value=0.033  Score=44.39  Aligned_cols=44  Identities=14%  Similarity=0.047  Sum_probs=21.8

Q ss_pred             HHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHh
Q 009640          397 HAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       397 ~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~  441 (530)
                      ++|..||+.++...... ....++.++..+.|||+|||.++|..+
T Consensus         1 ~~R~~Il~~~l~~~~~~-~~vdl~~lA~~t~G~SGADi~~l~~eA   44 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLA-PEADLDSLIIRNDSLSGAVIAAIMQEA   44 (82)
T ss_dssp             -------------CEEC-TTCCSTTTTTSSCCCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCC-CcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            46889999888754332 111266778889999999999999744

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=91.37  E-value=0.18  Score=53.80  Aligned_cols=29  Identities=21%  Similarity=0.282  Sum_probs=25.0

Q ss_pred             EEEECCCCCChhHH-HHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSL-IAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsL-a~AiA~~l~~~i~~l  259 (530)
                      .++.|++|||||+| +..|++..+.+++.+
T Consensus       166 ~~Ifg~~g~GKT~Lal~~I~~~~~~dv~~V  195 (507)
T 1fx0_A          166 ELIIGDRQTGKTAVATDTILNQQGQNVICV  195 (507)
T ss_dssp             CBEEESSSSSHHHHHHHHHHTCCTTTCEEE
T ss_pred             EEEecCCCCCccHHHHHHHHHhhcCCcEEE
Confidence            79999999999999 679999988776544

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=91.36  E-value=0.094  Score=53.65  Aligned_cols=25  Identities=32%  Similarity=0.430  Sum_probs=22.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||.|+|||||+++||..+..
T Consensus        43 ~~~llGpnGsGKSTLLr~iaGl~~p   67 (355)
T 1z47_A           43 MVGLLGPSGSGKTTILRLIAGLERP   67 (355)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCC
Confidence            4779999999999999999998743

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=91.35  E-value=0.066  Score=52.04  Aligned_cols=24  Identities=25%  Similarity=0.339  Sum_probs=21.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||.|+|||||++.|+..+.
T Consensus        33 ~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           33 ILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             EEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            478999999999999999999874

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.34  E-value=0.074  Score=52.25  Aligned_cols=27  Identities=37%  Similarity=0.469  Sum_probs=23.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      .-+.|.||.|+|||||++.|+..+.-+
T Consensus        46 e~~~i~G~nGsGKSTLlk~l~Gl~~p~   72 (271)
T 2ixe_A           46 KVTALVGPNGSGKSTVAALLQNLYQPT   72 (271)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            347899999999999999999987543

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=91.34  E-value=0.087  Score=54.27  Aligned_cols=25  Identities=28%  Similarity=0.418  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||.|+|||||+++||..+.-
T Consensus        39 ~~~llGpnGsGKSTLLr~iaGl~~p   63 (372)
T 1v43_A           39 FLVLLGPSGCGKTTTLRMIAGLEEP   63 (372)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCC
Confidence            4779999999999999999998753

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=91.31  E-value=0.088  Score=54.38  Aligned_cols=25  Identities=32%  Similarity=0.507  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||+|+|||||+++||....-
T Consensus        31 ~~~llGpsGsGKSTLLr~iaGl~~p   55 (381)
T 3rlf_A           31 FVVFVGPSGCGKSTLLRMIAGLETI   55 (381)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEEcCCCchHHHHHHHHHcCCCC
Confidence            3779999999999999999998753

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=91.28  E-value=0.09  Score=54.18  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||+|+|||||+++||..+.
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~   54 (372)
T 1g29_1           31 FMILLGPSGCGKTTTLRMIAGLEE   54 (372)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCcHHHHHHHHHHcCCC
Confidence            477999999999999999999773

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=91.27  E-value=0.21  Score=56.31  Aligned_cols=24  Identities=29%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ..-++|.||.|+||||+++.+|..
T Consensus       576 g~i~~I~GpNGsGKSTlLr~iagl  599 (765)
T 1ewq_A          576 HELVLITGPNMAGKSTFLRQTALI  599 (765)
T ss_dssp             SCEEEEESCSSSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHhh
Confidence            356889999999999999999874

>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=91.24  E-value=0.094  Score=56.43  Aligned_cols=28  Identities=21%  Similarity=0.334  Sum_probs=22.0

Q ss_pred             CCCCceEEEECCCCCChhHHHHH--HHHHc
Q 009640          225 RAWKRGYLLYGPPGSGKSSLIAA--MANYL  252 (530)
Q Consensus       225 ~~~~rG~LL~GPPGTGKTsLa~A--iA~~l  252 (530)
                      ++...-++|.||+|+|||||++.  ++...
T Consensus        36 i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~   65 (525)
T 1tf7_A           36 LPIGRSTLVSGTSGTGKTLFSIQFLYNGII   65 (525)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            34456699999999999999999  44443

>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=91.22  E-value=0.12  Score=46.14  Aligned_cols=23  Identities=17%  Similarity=0.257  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|++|+|||+|+.++.+.
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            46899999999999999999864

>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=91.22  E-value=0.1  Score=47.54  Aligned_cols=23  Identities=26%  Similarity=0.443  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|+||+|||+|+.++++.
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            35899999999999999999873

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.13  E-value=0.081  Score=51.78  Aligned_cols=25  Identities=36%  Similarity=0.489  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||.|+|||||++.|+..+..
T Consensus        35 ~~~liG~nGsGKSTLl~~i~Gl~~p   59 (266)
T 2yz2_A           35 CLLVAGNTGSGKSTLLQIVAGLIEP   59 (266)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCC
Confidence            4779999999999999999998753

>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=91.12  E-value=0.099  Score=46.98  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=19.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|+||+|||||+.++.+.
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            4789999999999999999864

>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=91.10  E-value=0.12  Score=46.76  Aligned_cols=23  Identities=17%  Similarity=0.210  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|++|+|||||+.++.+.
T Consensus        21 ~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           21 FKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            36899999999999999999853

>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=91.09  E-value=0.12  Score=46.82  Aligned_cols=22  Identities=27%  Similarity=0.344  Sum_probs=20.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|++|+|||+|+.++.+.
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999864

>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=91.08  E-value=0.12  Score=46.93  Aligned_cols=22  Identities=27%  Similarity=0.448  Sum_probs=19.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|++|+|||+|+.++.+.
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            5899999999999999999864

>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=91.08  E-value=0.12  Score=47.30  Aligned_cols=24  Identities=29%  Similarity=0.447  Sum_probs=21.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.|+||+|||||+.++.+.-
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            9 LKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            468999999999999999998753

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=91.05  E-value=0.075  Score=52.02  Aligned_cols=24  Identities=38%  Similarity=0.768  Sum_probs=21.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||.|+|||||++.|+..+
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            347899999999999999999876

>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=91.02  E-value=0.12  Score=46.79  Aligned_cols=22  Identities=32%  Similarity=0.652  Sum_probs=20.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|++|+|||+|+.++.+.
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            5899999999999999999864

>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=91.01  E-value=0.11  Score=47.09  Aligned_cols=23  Identities=26%  Similarity=0.381  Sum_probs=20.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -++|.|++|+|||+|+.++.+.-
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            58999999999999999998754

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=91.00  E-value=0.28  Score=52.25  Aligned_cols=29  Identities=28%  Similarity=0.330  Sum_probs=24.8

Q ss_pred             EEEECCCCCChhHH-HHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSL-IAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsL-a~AiA~~l~~~i~~l  259 (530)
                      .++.|++|||||+| ...|++..+.+++.+
T Consensus       165 ~~Ifg~~g~GKT~l~l~~I~n~~~~dv~~V  194 (513)
T 3oaa_A          165 ELIIGDRQTGKTALAIDAIINQRDSGIKCI  194 (513)
T ss_dssp             CEEEESSSSSHHHHHHHHHHTTSSSSCEEE
T ss_pred             EEeecCCCCCcchHHHHHHHhhccCCceEE
Confidence            79999999999999 579999887776544

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=90.99  E-value=0.16  Score=47.92  Aligned_cols=21  Identities=29%  Similarity=0.461  Sum_probs=19.0

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -++|.|.+|+|||+|+..+..
T Consensus        15 KivlvGd~~VGKTsLi~r~~~   35 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMY   35 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCcCHHHHHHHHHh
Confidence            489999999999999999875

>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=90.95  E-value=0.11  Score=47.17  Aligned_cols=23  Identities=30%  Similarity=0.426  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|++|+|||+|+.++.+.
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            36899999999999999999864

>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=90.93  E-value=0.13  Score=47.13  Aligned_cols=23  Identities=26%  Similarity=0.379  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|++|+|||+|+.++.+.
T Consensus        29 ~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           29 YKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            46899999999999999999864

>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=90.93  E-value=0.25  Score=49.06  Aligned_cols=33  Identities=27%  Similarity=0.356  Sum_probs=25.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      ++-+.+.||+|+||||++..+|..+   +..+.-++
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~  133 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA  133 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            3457788999999999999999876   44554444

>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=90.91  E-value=0.094  Score=46.73  Aligned_cols=22  Identities=36%  Similarity=0.327  Sum_probs=20.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|+||+|||+|+.++++.
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

>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=90.89  E-value=0.13  Score=47.33  Aligned_cols=23  Identities=35%  Similarity=0.492  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|+||+|||+|+.++.+.
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            46899999999999999999854

>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=90.89  E-value=0.21  Score=46.86  Aligned_cols=29  Identities=38%  Similarity=0.559  Sum_probs=24.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHc--CCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL--CYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l--~~~i~~l  259 (530)
                      +.|-|+.|+||||.++.++..|  +++++..
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            5678999999999999999998  4555544

>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=90.88  E-value=0.12  Score=46.19  Aligned_cols=22  Identities=32%  Similarity=0.391  Sum_probs=19.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      .-++|.|+||+|||+|+.++.+
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            4689999999999999999985

>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=90.87  E-value=0.13  Score=46.72  Aligned_cols=22  Identities=27%  Similarity=0.229  Sum_probs=19.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -++|.|++|+|||+|+..+.+.
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

>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=90.86  E-value=0.13  Score=46.72  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=21.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      --+++.|+||+|||+|+.++.+.-
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            358999999999999999998753

>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=90.84  E-value=0.098  Score=51.24  Aligned_cols=25  Identities=36%  Similarity=0.646  Sum_probs=22.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||.|+|||||+++|+..+.-
T Consensus        39 ~~~liG~nGsGKSTLl~~l~Gl~~p   63 (266)
T 4g1u_C           39 MVAIIGPNGAGKSTLLRLLTGYLSP   63 (266)
T ss_dssp             EEEEECCTTSCHHHHHHHHTSSSCC
T ss_pred             EEEEECCCCCcHHHHHHHHhcCCCC
Confidence            4779999999999999999997743

>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=90.84  E-value=0.12  Score=47.50  Aligned_cols=23  Identities=35%  Similarity=0.492  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-++|.|+||+|||+|+.++.+.
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            46899999999999999999864

>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=90.79  E-value=0.11  Score=47.49  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --++|.|+||+|||+|+.++.+.
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            46899999999999999999764

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=90.78  E-value=0.078  Score=57.52  Aligned_cols=24  Identities=38%  Similarity=0.515  Sum_probs=22.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||+|+|||||+++||..++
T Consensus       371 iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          371 TVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             EEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHHhhc
Confidence            478899999999999999999985

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=90.71  E-value=0.12  Score=46.45  Aligned_cols=23  Identities=35%  Similarity=0.405  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|++|+|||||+.++.+.
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            46899999999999999999765

>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=90.70  E-value=0.11  Score=52.12  Aligned_cols=29  Identities=31%  Similarity=0.260  Sum_probs=23.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      .+|+||.||+|+|||+++.++.. -|..++
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            57999999999999999988754 454443

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=90.70  E-value=1.3  Score=42.28  Aligned_cols=31  Identities=23%  Similarity=0.274  Sum_probs=21.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      =+++|||.|+|||+.+-.++...   +..++.+.
T Consensus        21 l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~k   54 (234)
T 2orv_A           21 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   54 (234)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEe
Confidence            36779999999997665555433   55666554

>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=90.69  E-value=0.15  Score=51.23  Aligned_cols=27  Identities=26%  Similarity=0.295  Sum_probs=23.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      .+|+||.|++|+|||+++.++... |..
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~-g~~  170 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR-GHR  170 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc-CCc
Confidence            468999999999999999999775 443

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=90.68  E-value=0.13  Score=48.13  Aligned_cols=24  Identities=33%  Similarity=0.530  Sum_probs=21.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.|++|+|||||+..++..+
T Consensus        39 ~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           39 VAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            467888999999999999999876

>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=90.67  E-value=0.078  Score=54.12  Aligned_cols=25  Identities=24%  Similarity=0.612  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|.||.|+|||||++.||.....
T Consensus        28 ~~~llGpnGsGKSTLLr~iaGl~~p   52 (348)
T 3d31_A           28 YFVILGPTGAGKTLFLELIAGFHVP   52 (348)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSCC
T ss_pred             EEEEECCCCccHHHHHHHHHcCCCC
Confidence            4778999999999999999998753

>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=90.63  E-value=0.1  Score=50.88  Aligned_cols=23  Identities=26%  Similarity=0.543  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ..+.|.|+||+|||||+.++.+.
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            46899999999999999999764

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=90.63  E-value=0.13  Score=47.22  Aligned_cols=24  Identities=25%  Similarity=0.254  Sum_probs=21.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-++|.|+||+|||+|+.++.+.-
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCcCHHHHHHHHHhCC
Confidence            458999999999999999998743

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=90.60  E-value=1.1  Score=49.44  Aligned_cols=61  Identities=11%  Similarity=0.118  Sum_probs=39.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHH-------------HhcCCCeEEEEcCccch
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALL-------------LQTTNRSIIVIEDIDCS  291 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~-------------~~~~~~sII~IDeID~~  291 (530)
                      -++|.|++|+|||+++-.++..+...++.... +...-..|.+..             .......+|||||.=++
T Consensus       194 ~~vlta~RGRGKSa~lG~~~a~~~~~~~vtAP-~~~a~~~l~~~~~~~i~~~~Pd~~~~~~~~~dlliVDEAAaI  267 (671)
T 2zpa_A          194 VAAVTAARGRGKSALAGQLISRIAGRAIVTAP-AKASTDVLAQFAGEKFRFIAPDALLASDEQADWLVVDEAAAI  267 (671)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSSSCEEEECS-SCCSCHHHHHHHGGGCCBCCHHHHHHSCCCCSEEEEETGGGS
T ss_pred             eEEEecCCCCCHHHHHHHHHHHHHhCcEEECC-CHHHHHHHHHHhhCCeEEeCchhhhhCcccCCEEEEEchhcC
Confidence            36899999999999999888888666533332 222222333321             22234679999998776

>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=90.56  E-value=0.056  Score=49.84  Aligned_cols=22  Identities=27%  Similarity=0.394  Sum_probs=19.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+.|.|++|+|||||++++++.
T Consensus        28 ~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           28 EVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             EEEEEECTTSSHHHHHTTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999998753

>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=90.51  E-value=0.17  Score=46.16  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=19.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      --+++.|+||+|||+|+.++.+
T Consensus        30 ~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           30 MRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCS
T ss_pred             cEEEEECCCCCCHHHHHHHHHh
Confidence            4689999999999999999864

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=90.46  E-value=0.14  Score=47.85  Aligned_cols=25  Identities=44%  Similarity=0.538  Sum_probs=21.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -.+|+||.|+|||+++.||.-.++.
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            4688999999999999999877754

>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=90.46  E-value=0.11  Score=46.84  Aligned_cols=23  Identities=17%  Similarity=0.368  Sum_probs=20.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|+||+|||+|+.++.+.
T Consensus        19 ~~i~v~G~~~~GKssl~~~l~~~   41 (186)
T 1ksh_A           19 LRLLMLGLDNAGKTTILKKFNGE   41 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999999753

>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=90.33  E-value=0.27  Score=45.61  Aligned_cols=31  Identities=19%  Similarity=0.118  Sum_probs=24.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      -++++||+|+|||+.+..+|..+   +..++.+.
T Consensus        10 i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k   43 (191)
T 1xx6_A           10 VEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFK   43 (191)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE
Confidence            46789999999999998888766   66666553

>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=90.33  E-value=0.14  Score=46.42  Aligned_cols=23  Identities=30%  Similarity=0.489  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||||+.++.+.
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCcHHHHHHHHHcC
Confidence            36899999999999999999873

>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=90.29  E-value=0.091  Score=47.07  Aligned_cols=23  Identities=26%  Similarity=0.418  Sum_probs=9.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .-+++.|+||+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEECCCCC------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999998753

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=90.25  E-value=0.2  Score=54.18  Aligned_cols=32  Identities=31%  Similarity=0.322  Sum_probs=25.4

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC---CcEEEEe
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC---YDVYDLE  260 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~  260 (530)
                      .-++|.|+||+||||++++++..++   .+++.++
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            3478899999999999999999874   3455443

>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=90.25  E-value=0.16  Score=46.96  Aligned_cols=24  Identities=29%  Similarity=0.317  Sum_probs=21.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+++.|++|+|||+|+.++.+..
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            468999999999999999998743

>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=90.25  E-value=0.14  Score=47.45  Aligned_cols=23  Identities=22%  Similarity=0.355  Sum_probs=20.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      --+++.|+||+|||+|+.++++.
T Consensus        29 ~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           29 CKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            36899999999999999999874

>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=90.24  E-value=0.16  Score=45.42  Aligned_cols=22  Identities=23%  Similarity=0.510  Sum_probs=19.5

Q ss_pred             CceEEEECCCCCChhHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMA  249 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA  249 (530)
                      ..-+++.|+||+|||||+.++.
T Consensus        18 ~~~i~v~G~~~~GKssli~~l~   39 (183)
T 1moz_A           18 ELRILILGLDGAGKTTILYRLQ   39 (183)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHh
Confidence            3578999999999999998886

>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=90.19  E-value=0.14  Score=52.44  Aligned_cols=24  Identities=33%  Similarity=0.422  Sum_probs=21.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||||+|||||+.+|+....
T Consensus       217 ~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          217 ISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             EEEEECCCCccHHHHHHHHhcccc
Confidence            578999999999999999997665

>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=90.15  E-value=0.13  Score=48.80  Aligned_cols=24  Identities=25%  Similarity=0.286  Sum_probs=21.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-++|.|++|+|||||+.++.+..
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHcCCC
Confidence            468999999999999999998643

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=90.15  E-value=0.13  Score=54.55  Aligned_cols=24  Identities=25%  Similarity=0.458  Sum_probs=21.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+.|.||.|+|||||++.||+.+
T Consensus       139 e~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCcc
Confidence            348899999999999999999987

>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=90.09  E-value=0.11  Score=51.57  Aligned_cols=26  Identities=35%  Similarity=0.316  Sum_probs=22.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+.|.||+|+|||||+++|+.....+
T Consensus       171 iv~l~G~sG~GKSTll~~l~g~~~~~  196 (301)
T 1u0l_A          171 ISTMAGLSGVGKSSLLNAINPGLKLR  196 (301)
T ss_dssp             EEEEECSTTSSHHHHHHHHSTTCCCC
T ss_pred             eEEEECCCCCcHHHHHHHhccccccc
Confidence            46789999999999999999876543

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=90.07  E-value=0.077  Score=54.29  Aligned_cols=24  Identities=25%  Similarity=0.584  Sum_probs=21.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||.|+|||||++.||....
T Consensus        33 ~~~llGpnGsGKSTLLr~iaGl~~   56 (353)
T 1oxx_K           33 RFGILGPSGAGKTTFMRIIAGLDV   56 (353)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCC
Confidence            477999999999999999999774

---

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	530
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	6e-21
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	2e-20
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	2e-19
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	2e-12
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	4e-12
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	3e-09
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	8e-08
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	9e-07
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	5e-06
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	6e-06
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	1e-05
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	3e-05
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	3e-04
d1ye8a1	178	c.37.1.11 (A:1-178) Hypothetical kinase-like prote	8e-04
d1v5wa_	258	c.37.1.11 (A:) Meiotic recombination protein DMC1/	0.003
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	0.003
d1g8pa_	333	c.37.1.20 (A:) ATPase subunit of magnesium chelata	0.003
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	0.004

>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 = 89.9 bits (223), Expect = 6e-21
 Identities = 49/251 (19%), Positives = 88/251 (35%), Gaps = 47/251 (18%)

Query: 192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
           TF+ +A   + K+++ E +    N    +H +G    +G LL GPPG GK+ L  A+A  
Sbjct: 7   TFKDVAGAEEAKEELKEIVEFLKN-PSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 65

Query: 252 LCYDVYDLELTKVTDN------SELRAL--LLQTTNRSIIVIEDIDCSVDLTADRMLKSS 303
                     +   +       + +R L    +     I+ I++ID    +   R     
Sbjct: 66  ARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDA---VGRKR----- 117

Query: 304 NTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEK 363
                                       +    G +    TL+ LL   DG         
Sbjct: 118 ---------------------------GSGVGGGNDEREQTLNQLLVEMDGFEK--DTAI 148

Query: 364 IIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCI 423
           +++  TN  D +DPAL+R GR D  +++        + + + +   +      D+     
Sbjct: 149 VVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAK 208

Query: 424 RAGGALTPAQI 434
           R  G    A +
Sbjct: 209 RTPG-FVGADL 218

>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 = 88.7 bits (220), Expect = 2e-20
 Identities = 59/288 (20%), Positives = 101/288 (35%), Gaps = 58/288 (20%)

Query: 192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
           TF  +A   + K+++ E +         + ++G    +G L+ GPPG+GK+ L  A+A  
Sbjct: 10  TFADVAGCDEAKEEVAELVEYLRE-PSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68

Query: 252 LCYDVYDLELTKVTD------NSELRALLLQ--TTNRSIIVIEDIDCSVDLTADRMLKSS 303
                + +  +   +       S +R +  Q       II I++ID              
Sbjct: 69  AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEID-------------- 114

Query: 304 NTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEK 363
                   +R +                     G +    TL+ +L   DG     +E  
Sbjct: 115 ----AVGRQRGAG-----------------LGGGHDEREQTLNQMLVEMDGFEG--NEGI 151

Query: 364 IIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCI 423
           I++  TN  D +DPAL+R GR D  V +G       + + K ++         D      
Sbjct: 152 IVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIAR 211

Query: 424 RAGGALTPAQIGEV--------LLRNRGNVDLAMKEVVSAMQAKILSG 463
              G  + A +  +           N+  V   M E   A   KI+ G
Sbjct: 212 GTPG-FSGADLANLVNEAALFAARGNKRVVS--MVEFEKAKD-KIMMG 255

>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 = 86.0 bits (212), Expect = 2e-19
 Identities = 52/294 (17%), Positives = 108/294 (36%), Gaps = 53/294 (18%)

Query: 192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
           T+E +     +K+++ E +       + + + G    +G L YGPPG GK+ L  A+AN 
Sbjct: 5   TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 64

Query: 252 LCYDVYDLELTKVTD------NSELRALLLQ--TTNRSIIVIEDIDCSVDLTADRMLKSS 303
              +   ++  ++         + +R +  +       ++  +++D              
Sbjct: 65  CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDS------------- 111

Query: 304 NTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEK 363
                             +R      G N  + G  + R  ++ +L   DG+ +   +  
Sbjct: 112 ---------------IAKAR------GGNIGDGGGAADR-VINQILTEMDGMST--KKNV 147

Query: 364 IIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCI 423
            I+  TN  D +DPA++R GR+D  + +      +   + K  L         D+     
Sbjct: 148 FIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAK 207

Query: 424 RAGGALTPAQIGEV-----LLRNRGNVDLAMKEVVSAMQAKILSGREVMECDEL 472
              G  + A + E+      L  R +++  ++      +    S  EV E D +
Sbjct: 208 MTNG-FSGADLTEICQRACKLAIRESIESEIRRE--RERQTNPSAMEVEEDDPV 258

>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 = 65.4 bits (158), Expect = 2e-12
 Identities = 37/277 (13%), Positives = 76/277 (27%), Gaps = 36/277 (12%)

Query: 199 EPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYD 258
           + Q + ++ ++L     GK+            +LL G PGSGK+SL +A+      +V  
Sbjct: 8   DKQFENRLNDNLEELIQGKK-----AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIV 62

Query: 259 LELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIK 318
           +      DN   +           +  +D+   V                  + R +   
Sbjct: 63  I------DNDTFKQQHPNFDELVKLYEKDVVKHVT---------------PYSNRMTEAI 101

Query: 319 EMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF---TDGLWSCCSEEKIIVFTTNHRDSV 375
                               +    T + L      T        +    + T    +++
Sbjct: 102 ISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETM 161

Query: 376 DPALIRCGRMDVHVSLGTC---GPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPA 432
                   R     +        P   + L K  L  +      + V+         TP+
Sbjct: 162 YADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNREGVK---LYSSLETPS 218

Query: 433 QIGEVLLRNRGNVDLAMKEVVSAMQAKILSG-REVME 468
              +  L    N  ++ KE+   ++           +
Sbjct: 219 ISPKETLEKELNRKVSGKEIQPTLERIEQKMVLNKHQ 255

>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 = 64.3 bits (155), Expect = 4e-12
 Identities = 43/215 (20%), Positives = 69/215 (32%), Gaps = 44/215 (20%)

Query: 192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANY 251
            ++ +    +   QI E +         +  +G    RG LLYGPPG+GK+ +  A+AN 
Sbjct: 2   GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 61

Query: 252 LCYDVYDLELTKV------TDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNT 305
                + +   ++         S LR    +    +  +I   +                
Sbjct: 62  TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIA----------- 110

Query: 306 STTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKII 365
                 KR  +  E+  RI S                         T           I+
Sbjct: 111 -----PKREKTHGEVERRIVSQLL----------------------TLMDGLKQRAHVIV 143

Query: 366 VFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFK 400
           +  TN  +S+DPAL R GR D  V +G        
Sbjct: 144 MAATNRPNSIDPALRRFGRFDREVDIGIPDATGRL 178

>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 = 56.2 bits (135), Expect = 3e-09
 Identities = 30/200 (15%), Positives = 57/200 (28%), Gaps = 63/200 (31%)

Query: 200 PQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL 259
           P++   + + L                 KR +L  GP  SGK++L AA+         ++
Sbjct: 134 PKMDSVVYDFLKCMVYNI--------PKKRYWLFKGPIDSGKTTLAAALLELCGGKALNV 185

Query: 260 ELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKE 319
            L     N EL   +    ++ ++V ED+  +                  +++   S + 
Sbjct: 186 NLPLDRLNFELGVAI----DQFLVVFEDVKGT----------------GGESRDLPSGQG 225

Query: 320 MGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEK----------IIVFTT 369
           +                        L  L ++ DG      E+K            + T 
Sbjct: 226 I----------------------NNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTM 263

Query: 370 NHRDSVDPALIRCGRMDVHV 389
           N             R    +
Sbjct: 264 NE---YSVPKTLQARFVKQI 280

>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 = 51.3 bits (121), Expect = 8e-08
 Identities = 22/105 (20%), Positives = 41/105 (39%), Gaps = 4/105 (3%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKE----FYHRVGRAWKRGYLLYGPPGSGKSSLI 245
           P+  + +        ++   L  + N K+       + G    R  +LYGPPG GK++  
Sbjct: 10  PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA 69

Query: 246 AAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDC 290
             +A  L YD+ +   + V   + L A +    +   +V      
Sbjct: 70  HLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHN 114

>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 = 48.0 bits (113), Expect = 9e-07
 Identities = 21/100 (21%), Positives = 43/100 (43%), Gaps = 8/100 (8%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA 249
           P + +    +  +KK+++  L A     E             LL GPPG GK++L   +A
Sbjct: 5   PKSLDEFIGQENVKKKLSLALEAAKMRGEVLD--------HVLLAGPPGLGKTTLAHIIA 56

Query: 250 NYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDID 289
           + L  +++      +    ++ A+L       ++ I++I 
Sbjct: 57  SELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIH 96

>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 = 46.2 bits (109), Expect = 5e-06
 Identities = 29/229 (12%), Positives = 65/229 (28%), Gaps = 54/229 (23%)

Query: 201 QLKKQITEDLTAFANGKE---FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDV- 256
           Q  +    DLT    G           R      ++ G   SGK+ L+ A+   L     
Sbjct: 93  QGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDK 152

Query: 257 -YDLELTKVTD------NSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTA 309
              +   +         N  +  +        +IVI+ +   +                 
Sbjct: 153 YATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI----------------- 195

Query: 310 KTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTT 369
                      G+   ++T G  +              LL+    + +  S   +++ + 
Sbjct: 196 -----------GAAGGNTTSGGISR---------GAFDLLSDIGAMAA--SRGCVVIASL 233

Query: 370 N---HRDSVDPALIRCGRMDVHVSLGTCGPHA-FKVLAKNYLGIESHHA 414
           N   + D +   +    R +    + +      ++VL +   G++    
Sbjct: 234 NPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTH 282

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.6 bits (106), Expect = 6e-06
 Identities = 28/235 (11%), Positives = 60/235 (25%), Gaps = 20/235 (8%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA 249
           P +   L+   +L   +          ++  H          LLYGP G+GK +   A+ 
Sbjct: 7   PKSLNALSHNEELTNFLKS---LSDQPRDLPH---------LLLYGPNGTGKKTRCMALL 54

Query: 250 NYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTA 309
             +           V          L+    S     +I  S     DR++        A
Sbjct: 55  ESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVA 114

Query: 310 KTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTT 369
           + ++               C   N  N                       S+   ++   
Sbjct: 115 QMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQ------AALRRTMEKYSKNIRLIMVC 168

Query: 370 NHRDSVDPALIRCGRMDVHVSLGTCGPHAF--KVLAKNYLGIESHHALFDVVESC 422
           +    +   +     +    +            V+    + +E+   L  + ++ 
Sbjct: 169 DSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQAS 223

>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 = 44.6 bits (104), Expect = 1e-05
 Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 9/102 (8%)

Query: 190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMA 249
           P T +    + +LK+++   L A    KE             LL+GPPG GK++L   +A
Sbjct: 5   PKTLDEYIGQERLKQKLRVYLEAAKARKEPLE--------HLLLFGPPGLGKTTLAHVIA 56

Query: 250 NYLCYDVYDLELTKVTDNSELRALLLQTT-NRSIIVIEDIDC 290
           + L  ++       +    +L A+L  +     I+ I++I  
Sbjct: 57  HELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHR 98

>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 = 43.4 bits (101), Expect = 3e-05
 Identities = 23/188 (12%), Positives = 47/188 (25%), Gaps = 35/188 (18%)

Query: 204 KQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK 263
            ++ +D        +      R      LL GPP SGK++L  A       +   +++  
Sbjct: 19  TRVLDDGELLV---QQTKNSDRTPLVSVLLEGPPHSGKTAL--AAKIAEESNFPFIKICS 73

Query: 264 VTDNSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSR 323
                           + I           +  D +                       R
Sbjct: 74  PDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDI----------------------ER 111

Query: 324 IASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCG 383
           +            G     + L  LL            + +I+ TT+ +D +    +   
Sbjct: 112 LLDYVP------IGPRFSNLVLQALLVLLKKAPPQG-RKLLIIGTTSRKDVLQEMEML-N 163

Query: 384 RMDVHVSL 391
                + +
Sbjct: 164 AFSTTIHV 171

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 40.1 bits (92), Expect = 3e-04
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 209 DLTAFANGKEFYHR------VGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELT 262
           D +   N K+F+ R      +        L+ G   +GKSS+I    N L      L+L 
Sbjct: 4   DTSPKDNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLR 63

Query: 263 KVTDNSEL 270
           K  + + +
Sbjct: 64  KFEERNYI 71

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]} Length = 178

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]

 Score = 38.4 bits (88), Expect = 8e-04
 Identities = 18/155 (11%), Positives = 38/155 (24%), Gaps = 5/155 (3%)

Query: 232 LLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDCS 291
           ++ G PG GK++L+  +   L          +V D    +    +               
Sbjct: 4   IITGEPGVGKTTLVKKIVERLGKRAIGFWTEEVRDPETKKRTGFRIITTEGKKKIFSSK- 62

Query: 292 VDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNF 351
                       +     +     +I  +      +          +E G++ L      
Sbjct: 63  ---FFTSKKLVGSYGVNVQYFEELAIPILERAYREAKKDRRKVIIIDEIGKMELFSKKFR 119

Query: 352 TDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMD 386
                        +V T      V P +    R+ 
Sbjct: 120 DLVRQIMHDPNVNVVATI-PIRDVHPLVKEIRRLP 153

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 258

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (85), Expect = 0.003
 Identities = 20/150 (13%), Positives = 47/150 (31%), Gaps = 11/150 (7%)

Query: 231 YLLYGPPGSGKSSLIAAMA---------NYLCYDVYDLELTKVTDNSELRALLLQTTNRS 281
              +G   +GK+ L   +           Y    +  ++         LR +  +     
Sbjct: 40  TEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDH 99

Query: 282 IIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESG 341
             V++++  +   T++  ++  +       + +   K +      +    + +  GE + 
Sbjct: 100 DAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAE 159

Query: 342 RVTLSGLLNFTDGLWSCCSEEKIIVFTTNH 371
           R     L      L     E  + VF TN 
Sbjct: 160 RQQK--LAQMLSRLQKISEEYNVAVFVTNQ 187

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 37.1 bits (84), Expect = 0.003
 Identities = 28/240 (11%), Positives = 61/240 (25%), Gaps = 12/240 (5%)

Query: 229 RGYLLYGPPGSGKSSLIAAMANYL-CYDVYDLELTKVTDNSELRALLLQTTNRSIIVIED 287
               L G PG+GK+  +  +                        A++ +      I    
Sbjct: 44  PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPR 103

Query: 288 IDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSG 347
              S D     +++                  +   I S+        +   + R+ L  
Sbjct: 104 RGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVI 163

Query: 348 LLNFTDGL----WSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLA 403
           + +    L     S        V   +         I   R    ++ G+      +++A
Sbjct: 164 VGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIA 223

Query: 404 KNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQAKILSG 463
                I       D      R    +            R ++    ++V  + + ++L G
Sbjct: 224 D----ITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIA--PEDVRKSSK-EVLFG 276

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]} Length = 333

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]

 Score = 37.2 bits (85), Expect = 0.003
 Identities = 24/171 (14%), Positives = 55/171 (32%), Gaps = 7/171 (4%)

Query: 230 GYLLYGPPGSGKSSLIAAMANYLCY--DVYDLELTKVTDNSELRALLLQTTNRSIIVIED 287
           G L++G  G+GKS+ + A+A  L     V    ++            + +TN        
Sbjct: 30  GVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTPV 89

Query: 288 IDCSVDLTADRMLKSSNTSTTAKTK----RSSSIKEMGSRIASSTCGNNNNNNGEESGR- 342
           +D  + ++ DR++ + +                +             N   ++  +    
Sbjct: 90  VDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHIVDLLLD 149

Query: 343 VTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGT 393
           V  SG         S     + ++  + + +  D       R  + V + +
Sbjct: 150 VAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLS 200

>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 = 37.1 bits (85), Expect = 0.004
 Identities = 11/41 (26%), Positives = 18/41 (43%)

Query: 228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS 268
            +  L+ GP G GK+ +   +A         +E TK T+  
Sbjct: 49  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVG 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	530
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.9
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.89
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.89
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.86
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.83
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.82
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.78
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.77
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.76
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.75
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.71
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.71
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.67
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.53
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.53
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.51
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.41
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.4
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.38
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.38
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.3
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.26
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.24
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.19
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.17
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.93
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	98.87
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.87
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.84
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.19
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.15
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.05
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.92
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.85
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.73
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.72
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.7
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.68
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.63
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.62
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.61
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.6
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.5
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.46
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.43
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.42
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.38
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.37
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.35
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.33
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.32
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.28
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.23
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.2
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.19
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.17
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.17
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.17
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.14
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.1
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.1
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.08
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.03
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.01
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.9
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	96.85
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.82
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.82
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.81
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.79
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.78
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.77
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	96.76
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.68
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.62
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.57
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.55
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.49
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.48
d1okkd2	207	GTPase domain of the signal recognition particle r	96.48
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.46
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.44
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.4
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.4
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.39
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.28
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.26
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.2
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.2
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.12
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.12
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.04
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	96.03
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	95.99
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	95.96
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.94
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.94
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	95.83
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	95.73
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.59
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	95.49
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.48
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.46
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.27
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.23
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.14
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	95.09
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.97
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	94.79
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	94.75
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	94.75
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	94.73
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.66
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	94.61
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.6
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.59
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	94.58
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.52
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.51
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.47
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	94.41
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	94.35
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	94.3
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.29
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	94.25
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.17
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.1
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.07
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.07
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.03
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	93.94
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.9
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.87
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	93.86
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	93.74
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.62
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	93.59
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.56
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	93.4
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.31
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.21
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.2
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.15
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.14
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.12
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	93.05
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.0
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.99
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	92.98
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.92
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	92.89
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	92.87
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	92.82
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	92.77
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	92.74
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	92.72
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	92.7
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	92.62
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.61
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	92.44
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	92.39
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	92.36
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	92.34
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	92.33
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.28
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	92.23
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	92.14
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.13
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	92.12
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	92.09
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	92.01
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.95
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	91.9
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	91.88
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.87
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	91.66
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	91.64
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	91.62
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	91.61
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	91.61
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	91.57
d2awna2	232	Maltose transport protein MalK, N-terminal domain	91.47
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	91.37
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	91.32
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	91.26
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	91.15
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	91.02
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	91.0
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	90.8
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	90.8
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	90.76
d1g2912	240	Maltose transport protein MalK, N-terminal domain	90.72
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	90.62
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	90.53
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	90.44
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.44
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	90.38
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	90.29
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	90.27
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	90.25
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	90.21
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	90.16
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	90.15
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	90.13
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	90.04
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	89.84
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	89.75
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	89.62
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	89.52
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	89.5
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	89.46
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	89.35
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	89.26
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	89.23
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.19
d1xpua3	289	Transcription termination factor Rho, ATPase domai	89.13
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	88.99
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	88.98
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	88.94
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	88.92
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	88.36
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	87.96
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	87.36
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	86.88
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	86.59
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	86.39
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.05
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	86.03
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	86.02
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	85.79
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	85.73
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	85.62
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	85.59
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	85.5
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	85.41
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	84.94
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	84.12
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	83.7
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	83.6
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	82.96
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	82.36
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	82.15
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	81.22
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	80.42

>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=8.4e-39  Score=316.18  Aligned_cols=211  Identities=23%  Similarity=0.272  Sum_probs=181.4

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-----
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-----  265 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-----  265 (530)
                      .+|++|+|.+++|++|.+.+..++.+++.|.+.|+++++|+|||||||||||++++++|++++.+++.++.+.+.     
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            368999999999999999999999999999999999999999999999999999999999999999999987653     


Q ss_pred             -ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchh
Q 009640          266 -DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGR  342 (530)
Q Consensus       266 -~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (530)
                       +...++++|..+  .+||||+|||+|.++..+.   .                                   ..+....
T Consensus        81 ~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~---~-----------------------------------~~~~~~~  122 (258)
T d1e32a2          81 ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKRE---K-----------------------------------THGEVER  122 (258)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHH---H-----------------------------------CCCTTHH
T ss_pred             cHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCC---C-----------------------------------CCCchHH
Confidence             256688888765  8999999999999863211   0                                   1223355


Q ss_pred             hhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHH
Q 009640          343 VTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESC  422 (530)
Q Consensus       343 ~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l  422 (530)
                      .+++.+++.+++...  ..+++||+|||+++.||||++||||||++|+|++|+.++|+.|++.++...... ....++.+
T Consensus       123 ~~~~~~~~~~~~~~~--~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~l  199 (258)
T d1e32a2         123 RIVSQLLTLMDGLKQ--RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQV  199 (258)
T ss_dssp             HHHHHHHHHHHTCCC--SSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBC-TTCCHHHH
T ss_pred             HHHHHhccccccccc--cCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccc-cccchhhh
Confidence            678899999998876  577999999999999999999999999999999999999999999999765433 11237788


Q ss_pred             HHhCCCCCHHHHHHHHHHhc
Q 009640          423 IRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       423 ~~~~~~~spadi~~~l~~~~  442 (530)
                      +..+.|||++||..++..+.
T Consensus       200 a~~t~G~s~adl~~lv~~A~  219 (258)
T d1e32a2         200 ANETHGHVGADLAALCSEAA  219 (258)
T ss_dssp             HHHCTTCCHHHHHHHHHHHH
T ss_pred             hhcccCCCHHHHHHHHHHHH
Confidence            88999999999999997543

>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=1e-38  Score=314.82  Aligned_cols=215  Identities=23%  Similarity=0.316  Sum_probs=177.2

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC--
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT--  265 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~--  265 (530)
                      ..+.||+||+|.+++|++|.+.+ .|+.+++.|+++|..+++|+|||||||||||++|+++|++++.+++.++.+.+.  
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            45679999999999999998855 678899999999999999999999999999999999999999999999988873  


Q ss_pred             ----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          266 ----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       266 ----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                          ++..++++|..+  .+||||||||||.++..++.                                   .......
T Consensus        85 ~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~-----------------------------------~~~~~~~  129 (256)
T d1lv7a_          85 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGA-----------------------------------GLGGGHD  129 (256)
T ss_dssp             CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCST-----------------------------------TSCCTTC
T ss_pred             chhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCC-----------------------------------CCCCCcH
Confidence                467799998876  78999999999998521100                                   0001233


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ....+++.||+.||++.+  ..+++||+|||+|+.|||||+||||||.+|+|++|+.++|..|++.++...... ....+
T Consensus       130 ~~~~~~~~ll~~~d~~~~--~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~-~~~~~  206 (256)
T d1lv7a_         130 EREQTLNQMLVEMDGFEG--NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDIDA  206 (256)
T ss_dssp             HHHHHHHHHHHHHHTCCS--SSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCH
T ss_pred             HHHHHHHHHHHHhhCCCC--CCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcC-cccCH
Confidence            445678999999999976  467999999999999999999999999999999999999999999999765544 22346


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHh
Q 009640          420 ESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~  441 (530)
                      ..++..+.|||++||..++..+
T Consensus       207 ~~la~~t~G~s~adi~~l~~~A  228 (256)
T d1lv7a_         207 AIIARGTPGFSGADLANLVNEA  228 (256)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCHHHHHHHHHHH
Confidence            7788889999999999998643

>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=5.8e-39  Score=315.15  Aligned_cols=215  Identities=21%  Similarity=0.297  Sum_probs=178.6

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC--
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT--  265 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~--  265 (530)
                      .|+.+|++|+|.+++|++|.+ +..|+.+++.|.++|.++++|+|||||||||||++|++||++++.+++.++.+.+.  
T Consensus         3 ~p~~~~~di~G~~~~k~~l~~-~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~   81 (247)
T d1ixza_           3 APKVTFKDVAGAEEAKEELKE-IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM   81 (247)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHH-HHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHS
T ss_pred             CCCCcHHHHccHHHHHHHHHH-HHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhhc
Confidence            466799999999999999976 55678999999999999999999999999999999999999999999999987762  


Q ss_pred             ----ChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          266 ----DNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       266 ----~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                          +...++++|..+  .+||||||||||.++..++...                                   ...+.
T Consensus        82 ~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~-----------------------------------~~~~~  126 (247)
T d1ixza_          82 FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGV-----------------------------------GGGND  126 (247)
T ss_dssp             CTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC--------------------------------------------CH
T ss_pred             cccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCC-----------------------------------CCCcH
Confidence                345688888765  6899999999999853111100                                   01233


Q ss_pred             chhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHH
Q 009640          340 SGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVV  419 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i  419 (530)
                      ....+++.||+.||++..  ..+++||+|||+|+.|||+|+||||||.+|+|++|+.++|+.|++.|+...... ....+
T Consensus       127 ~~~~~~~~ll~~~d~~~~--~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~-~~~~~  203 (247)
T d1ixza_         127 EREQTLNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-EDVDL  203 (247)
T ss_dssp             HHHHHHHHHHHHHHTCCT--TCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC-TTCCH
T ss_pred             HHHHHHHHHHHHhhCCCC--CCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCc-cccCH
Confidence            355688999999999976  467899999999999999999999999999999999999999999999754433 22236


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHh
Q 009640          420 ESCIRAGGALTPAQIGEVLLRN  441 (530)
Q Consensus       420 ~~l~~~~~~~spadi~~~l~~~  441 (530)
                      ..++..+.+||++||.++|..+
T Consensus       204 ~~la~~t~g~s~~di~~lv~~A  225 (247)
T d1ixza_         204 ALLAKRTPGFVGADLENLLNEA  225 (247)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHH
Confidence            7788889999999999998543

>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=7e-38  Score=310.71  Aligned_cols=216  Identities=19%  Similarity=0.304  Sum_probs=175.5

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc----
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV----  264 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~----  264 (530)
                      |..+|++|+|.+++|++|.+.+..|+.+++.|.+.|.++++|+|||||||||||++++|+|++++.+++.++.+.+    
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            4679999999999999999999999999999999999999999999999999999999999999999999997665    


Q ss_pred             --CChHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcc
Q 009640          265 --TDNSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEES  340 (530)
Q Consensus       265 --~~~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (530)
                        .....++.+|..+  .+||||+|||||+++..+....                                   .+....
T Consensus        82 ~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~-----------------------------------~~~~~~  126 (265)
T d1r7ra3          82 FGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNI-----------------------------------GDGGGA  126 (265)
T ss_dssp             TTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCC-----------------------------------CTTHHH
T ss_pred             ccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcC-----------------------------------CCCcHH
Confidence              2346688888765  7999999999999863111000                                   011223


Q ss_pred             hhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHH
Q 009640          341 GRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVE  420 (530)
Q Consensus       341 ~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~  420 (530)
                      ...+++.||+.||++..  ..+++||+|||+++.|||||+||||||++|+|++|+.++|..||+.++...... ....++
T Consensus       127 ~~~~~~~ll~~l~~~~~--~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~-~~~~l~  203 (265)
T d1r7ra3         127 ADRVINQILTEMDGMST--KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLE  203 (265)
T ss_dssp             HHHHHHHHHHTCC--------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC-----CCCCH
T ss_pred             HHHHHHHHHHHhhCcCC--CCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCch-hhhhHH
Confidence            45578999999999976  467999999999999999999999999999999999999999999998753222 111356


Q ss_pred             HHHHhCCCCCHHHHHHHHHHhc
Q 009640          421 SCIRAGGALTPAQIGEVLLRNR  442 (530)
Q Consensus       421 ~l~~~~~~~spadi~~~l~~~~  442 (530)
                      .++..+.|||++||..+|..+.
T Consensus       204 ~la~~t~g~s~~di~~lv~~A~  225 (265)
T d1r7ra3         204 FLAKMTNGFSGADLTEICQRAC  225 (265)
T ss_dssp             HHHHHHCSSCCHHHHHHHHHHH
T ss_pred             HHHhcCCCCCHHHHHHHHHHHH
Confidence            7777789999999999986543

>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=2.2e-23  Score=203.47  Aligned_cols=167  Identities=16%  Similarity=0.183  Sum_probs=120.0

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC-------Ch
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT-------DN  267 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~-------~~  267 (530)
                      .+++..+..+.|.+.+..++....   .....+++|+|||||||||||++|++||++++.+++.++.++..       ..
T Consensus        10 ~~i~~~~~i~~i~~~~~~~~~~~~---~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~~~~~   86 (246)
T d1d2na_          10 GIIKWGDPVTRVLDDGELLVQQTK---NSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKC   86 (246)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHH---HCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHH
T ss_pred             CCcCcCHHHHHHHHHHHHHHHHHh---ccCCCCCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccccchh
Confidence            355555566677777777765322   11223458999999999999999999999999999999876531       12


Q ss_pred             HHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhH
Q 009640          268 SELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTL  345 (530)
Q Consensus       268 ~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  345 (530)
                      ..++++|..+  .+||||||||||.+++...                                       .+....+.++
T Consensus        87 ~~i~~if~~A~~~~p~il~iDEid~l~~~~~---------------------------------------~~~~~~~~~~  127 (246)
T d1d2na_          87 QAMKKIFDDAYKSQLSCVVVDDIERLLDYVP---------------------------------------IGPRFSNLVL  127 (246)
T ss_dssp             HHHHHHHHHHHTSSEEEEEECCHHHHTTCBT---------------------------------------TTTBCCHHHH
T ss_pred             hhhhhhhhhhhhcccceeehhhhhhHhhhcc---------------------------------------cccchhHHHH
Confidence            4578888776  6799999999999853110                                       1122345678


Q ss_pred             HHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCC-HHHHHHHHHH
Q 009640          346 SGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCG-PHAFKVLAKN  405 (530)
Q Consensus       346 s~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~-~~~r~~i~~~  405 (530)
                      +.|+..+|+.... +.+++||+|||+++.||++.++ +||+.+|++|.+. .+++..++..
T Consensus       128 ~~ll~~l~~~~~~-~~~v~vi~tTn~~~~ld~~~~~-~rF~~~i~~P~~~~r~~il~~l~~  186 (246)
T d1d2na_         128 QALLVLLKKAPPQ-GRKLLIIGTTSRKDVLQEMEML-NAFSTTIHVPNIATGEQLLEALEL  186 (246)
T ss_dssp             HHHHHHTTCCCST-TCEEEEEEEESCHHHHHHTTCT-TTSSEEEECCCEEEHHHHHHHHHH
T ss_pred             HHHHHHhcCCCcc-ccceeeeeccCChhhccchhhc-CccceEEecCCchhHHHHHHHHHh
Confidence            8999999998753 4568899999999999976554 6999999985443 3334344433

>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=5e-26  Score=228.91  Aligned_cols=154  Identities=12%  Similarity=0.093  Sum_probs=120.3

Q ss_pred             ChhhHhhhcCCCCceEEE-ECCCCCChhHHHHHHHHHcC--CcEEEEecCccC------ChHHHHHHHHhcCCCeEEEEc
Q 009640          216 GKEFYHRVGRAWKRGYLL-YGPPGSGKSSLIAAMANYLC--YDVYDLELTKVT------DNSELRALLLQTTNRSIIVIE  286 (530)
Q Consensus       216 ~~~~y~~~g~~~~rG~LL-~GPPGTGKTsLa~AiA~~l~--~~i~~l~l~~~~------~~~~L~~l~~~~~~~sII~ID  286 (530)
                      .+..|..+|...++|.|| |||||||||++|+|+|.+++  .+++.++.+++.      .+..++.+|..+..|||||||
T Consensus       110 ~~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~~~ilf~D  189 (321)
T d1w44a_         110 SPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVID  189 (321)
T ss_dssp             CCEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEE
T ss_pred             chHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhhccEEEee
Confidence            345566677666778665 89999999999999999986  678999988873      467899999999889999999


Q ss_pred             CccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEE
Q 009640          287 DIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIV  366 (530)
Q Consensus       287 eID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI  366 (530)
                      |||++...++.                                     .........++++||..|||+.+.  .+++||
T Consensus       190 Eid~~~~~r~~-------------------------------------~~~~~~~~r~v~~lL~e~dg~~~~--~~v~vi  230 (321)
T d1w44a_         190 SLKNVIGAAGG-------------------------------------NTTSGGISRGAFDLLSDIGAMAAS--RGCVVI  230 (321)
T ss_dssp             CCTTTC------------------------------------------------CCHHHHHHHHHHHHHHHH--HTCEEE
T ss_pred             hhhhhcccccc-------------------------------------CCCCCcchhhhhhhhhhccccccC--CCeEEE
Confidence            99998531110                                     012233456999999999999873  679999


Q ss_pred             EEeCCC---CCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          367 FTTNHR---DSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       367 ~TTN~~---~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      +|||+.   +.||++++||||||++|++++||.+.|.+|++.+..
T Consensus       231 aatN~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r~~il~~~~~  275 (321)
T d1w44a_         231 ASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGE  275 (321)
T ss_dssp             EECCCCCCCHHHHHHHHHHHHHSCSEEEEECSSTTEEEEEEECBT
T ss_pred             EeCCCcccccchhhhhhccCcccceeecCCCChHHHHHHHHHhcc
Confidence            999952   335667789999999999999999999999876653

>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=3.4e-22  Score=192.76  Aligned_cols=192  Identities=15%  Similarity=0.143  Sum_probs=136.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN  267 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~  267 (530)
                      -+|.+|++++|++++++.|...+..+....        ....++|||||||||||++|+++|++++++++.++.+.....
T Consensus         3 ~RP~~~~divGqe~~~~~l~~~i~~~~~~~--------~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~~   74 (238)
T d1in4a2           3 LRPKSLDEFIGQENVKKKLSLALEAAKMRG--------EVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQ   74 (238)
T ss_dssp             TSCSSGGGCCSCHHHHHHHHHHHHHHHHHT--------CCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSH
T ss_pred             CCCCcHHHcCChHHHHHHHHHHHHHHHhcC--------CCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCcccccH
Confidence            368899999999999999998887654322        224689999999999999999999999999999999988888


Q ss_pred             HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHH
Q 009640          268 SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSG  347 (530)
Q Consensus       268 ~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~  347 (530)
                      .++...+......++++|||+|.+.....+...                 ..++..     .       ...  ......
T Consensus        75 ~~~~~~~~~~~~~~~~~ide~~~~~~~~~~~l~-----------------~~~~~~-----~-------~~~--~~~~~~  123 (238)
T d1in4a2          75 GDMAAILTSLERGDVLFIDEIHRLNKAVEELLY-----------------SAIEDF-----Q-------IDI--MIGKGP  123 (238)
T ss_dssp             HHHHHHHHHCCTTCEEEEETGGGCCHHHHHHHH-----------------HHHHTS-----C-------CCC--------
T ss_pred             HHHHHHHHhhccCCchHHHHHHHhhhHHHhhcc-----------------cceeee-----e-------eee--eecCcc
Confidence            889999988888999999999997321111000                 000000     0       000  000000


Q ss_pred             HhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHH
Q 009640          348 LLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIR  424 (530)
Q Consensus       348 LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~  424 (530)
                      ....+. .   .....++|++||++..+++++++  ||+..+.++.|+.+++..+++.+..........+.+..++.
T Consensus       124 ~~~~~~-~---~~~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~  194 (238)
T d1in4a2         124 SAKSIR-I---DIQPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAK  194 (238)
T ss_dssp             -------------CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHH
T ss_pred             cccccc-c---CCCCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHH
Confidence            001110 0   12467899999999999999999  99999999999999999999988776555423333444444

>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=99.86  E-value=8.3e-21  Score=183.13  Aligned_cols=206  Identities=18%  Similarity=0.205  Sum_probs=137.5

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNS  268 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~  268 (530)
                      +|.+|++++|++++++.+...+..+....        ..+.++|||||||||||++|+++|+++++++..++.+......
T Consensus         4 RP~~~ddivGq~~~~~~L~~~i~~~~~~~--------~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~~   75 (239)
T d1ixsb2           4 RPKTLDEYIGQERLKQKLRVYLEAAKARK--------EPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPG   75 (239)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHHTTSS--------SCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhcC--------CCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccch
Confidence            68899999999999999988776554322        2347899999999999999999999999999999988887665


Q ss_pred             HHHHHHHhc-CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHH
Q 009640          269 ELRALLLQT-TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSG  347 (530)
Q Consensus       269 ~L~~l~~~~-~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~  347 (530)
                      .....+... ...+|++|||+|.+.....+.                 ....+.........+..      .        
T Consensus        76 ~~~~~~~~~~~~~~i~~iDe~~~~~~~~~~~-----------------l~~~~e~~~~~~~~~~~------~--------  124 (239)
T d1ixsb2          76 DLAAILANSLEEGDILFIDEIHRLSRQAEEH-----------------LYPAMEDFVMDIVIGQG------P--------  124 (239)
T ss_dssp             HHHHHHHTTCCTTCEEEEETGGGCCHHHHHH-----------------HHHHHHHSEEEEECSCT------T--------
T ss_pred             hhHHHHHhhccCCCeeeeecccccchhHHHh-----------------hhhhhhhhhhhhhhccc------h--------
Confidence            555555544 567899999999873211100                 00000000000000000      0        


Q ss_pred             HhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCC
Q 009640          348 LLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGG  427 (530)
Q Consensus       348 LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~  427 (530)
                        +.....  ......++|++||++...+++.+|  |+...+.+..|+.+.+..++...+......              
T Consensus       125 --~~~~~~--~~~~~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~--------------  184 (239)
T d1ixsb2         125 --AARTIR--LELPRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVR--------------  184 (239)
T ss_dssp             --CCCEEE--EECCCCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCC--------------
T ss_pred             --hhhhcc--cCCCCEEEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCc--------------
Confidence              000000  013456788999999999999999  888899999999999999988877654433              


Q ss_pred             CCCHHHHHHHHHHhccCHHHHHHHHHH
Q 009640          428 ALTPAQIGEVLLRNRGNVDLAMKEVVS  454 (530)
Q Consensus       428 ~~spadi~~~l~~~~~d~~~al~~l~~  454 (530)
                       +++..+..+...+.+|++.|+..+..
T Consensus       185 -~~~~~l~~ia~~s~gd~R~a~~~l~~  210 (239)
T d1ixsb2         185 -ITEEAALEIGRRSRGTMRVAKRLFRR  210 (239)
T ss_dssp             -BCHHHHHHHHHHTTSSHHHHHHHHHH
T ss_pred             -cchHHHHHHHHHcCCCHHHHHHHHHH
Confidence             34444444445555566666554443

>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=99.83  E-value=7.6e-21  Score=191.32  Aligned_cols=174  Identities=18%  Similarity=0.243  Sum_probs=126.8

Q ss_pred             ccCChhhhHHHHHHHHHHHcChhhHhhhc-CCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC--------C
Q 009640          196 LALEPQLKKQITEDLTAFANGKEFYHRVG-RAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT--------D  266 (530)
Q Consensus       196 l~~~~~~k~~i~~~l~~~l~~~~~y~~~g-~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~--------~  266 (530)
                      |+|++++|+.|...+...+.+........ ..+++|+|||||||||||+||+|||+.++.+++.++++.+.        .
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            68999999999988765544333222211 12458999999999999999999999999999999988764        2


Q ss_pred             hHHHHHHHHhcC-------CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCc
Q 009640          267 NSELRALLLQTT-------NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEE  339 (530)
Q Consensus       267 ~~~L~~l~~~~~-------~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (530)
                      ...++.+|..+.       +||||||||||.+.+                  ++...                   ..+.
T Consensus        96 ~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~------------------~~~~~-------------------~~~~  138 (309)
T d1ofha_          96 DSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICK------------------KGEYS-------------------GADV  138 (309)
T ss_dssp             THHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSC------------------CSSCC-------------------SSHH
T ss_pred             cccccccchhhhcccccccCCceEEehhhhhhhh------------------hccCc-------------------ccch
Confidence            356788887763       489999999999841                  00000                   0111


Q ss_pred             chhhhHHHHhhhccCCccCCC------CCeEEEEE----eCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          340 SGRVTLSGLLNFTDGLWSCCS------EEKIIVFT----TNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       340 ~~~~~ls~LLn~lDgl~s~~~------~~~ivI~T----TN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      ....+++.||..+||......      .++++|+|    +|.++.++|+|+.  |||..+.++.|+...+..|+..+..
T Consensus       139 ~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~~~Il~~~~~  215 (309)
T d1ofha_         139 SREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPHA  215 (309)
T ss_dssp             HHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSSTT
T ss_pred             hhhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhhh--hhheeeeccCCCHHHHHHHHHHHHH
Confidence            123467889999998653222      23456655    5678888888886  9999999999999999999876543

>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=5.4e-20  Score=178.27  Aligned_cols=205  Identities=19%  Similarity=0.291  Sum_probs=145.0

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChh----hHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKE----FYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~----~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      -|  +..+.|.+|++++|+++.+++|.+.+..+...+.    .+...|..+.+++|||||||||||++|+++|+++++++
T Consensus         3 lW--~eky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~   80 (253)
T d1sxja2           3 LW--TVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI   80 (253)
T ss_dssp             CH--HHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEE
T ss_pred             cc--ccCcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhh
Confidence            57  5568899999999999999999998887654322    23445667778999999999999999999999999999


Q ss_pred             EEEecCccCChHHHHHHHHhc--------------------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          257 YDLELTKVTDNSELRALLLQT--------------------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       257 ~~l~l~~~~~~~~L~~l~~~~--------------------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                      +.++.+...+...+...+...                    ..+.|+++||+|.+..                       
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~-----------------------  137 (253)
T d1sxja2          81 LEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSG-----------------------  137 (253)
T ss_dssp             EEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCT-----------------------
T ss_pred             hccccccchhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeecccccc-----------------------
Confidence            999999887766665543211                    2467999999998731                       


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                             ..+..+..++......    ...+++++++++...+++  +|  |+...|+|+.|+.
T Consensus       138 -----------------------~~~~~~~~~~~~~~~~----~~~ii~i~~~~~~~~~~~--l~--~~~~~i~f~~~~~  186 (253)
T d1sxja2         138 -----------------------GDRGGVGQLAQFCRKT----STPLILICNERNLPKMRP--FD--RVCLDIQFRRPDA  186 (253)
T ss_dssp             -----------------------TSTTHHHHHHHHHHHC----SSCEEEEESCTTSSTTGG--GT--TTSEEEECCCCCH
T ss_pred             -----------------------chhhhhHHHhhhhccc----cccccccccccccccccc--cc--ceeeeeeccccch
Confidence                                   0112233444433211    223445545555555654  44  6678899999999


Q ss_pred             HHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHH
Q 009640          397 HAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAM  456 (530)
Q Consensus       397 ~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l  456 (530)
                      +++..+++.++..+               ...+++.++.+++..+.+|.+.|+..+..+.
T Consensus       187 ~~i~~~l~~i~~~e---------------~i~i~~~~l~~i~~~s~GDiR~ai~~L~~~~  231 (253)
T d1sxja2         187 NSIKSRLMTIAIRE---------------KFKLDPNVIDRLIQTTRGDIRQVINLLSTIS  231 (253)
T ss_dssp             HHHHHHHHHHHHHH---------------TCCCCTTHHHHHHHHTTTCHHHHHHHHTHHH
T ss_pred             hHHHHHHHHHHHHh---------------CCCCCHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            99999988765322               2346666777777777778888877655443

>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=99.78  E-value=9.1e-19  Score=167.74  Aligned_cols=189  Identities=16%  Similarity=0.229  Sum_probs=137.0

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----Cc
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----YD  255 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----~~  255 (530)
                      +|  +..+.|.+|++|+|++++++.|...+..    ..         ...+|||||||||||++|+++|++++     .+
T Consensus        13 ~w--~~ky~P~~~~diig~~~~~~~l~~~i~~----~~---------~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~   77 (231)
T d1iqpa2          13 PW--VEKYRPQRLDDIVGQEHIVKRLKHYVKT----GS---------MPHLLFAGPPGVGKTTAALALARELFGENWRHN   77 (231)
T ss_dssp             CH--HHHTCCCSTTTCCSCHHHHHHHHHHHHH----TC---------CCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHH
T ss_pred             hH--HHHhCCCCHHHccCcHHHHHHHHHHHHc----CC---------CCeEEEECCCCCcHHHHHHHHHHHHHhcccCCC
Confidence            68  6788999999999999988887776542    11         24699999999999999999999874     57


Q ss_pred             EEEEecCccCChHHHHHHHHh--------cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccc
Q 009640          256 VYDLELTKVTDNSELRALLLQ--------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS  327 (530)
Q Consensus       256 i~~l~l~~~~~~~~L~~l~~~--------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  327 (530)
                      ++.++.++..+...++..+..        ...+.||+|||+|.+..                                  
T Consensus        78 ~~e~n~s~~~~~~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~----------------------------------  123 (231)
T d1iqpa2          78 FLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ----------------------------------  123 (231)
T ss_dssp             EEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH----------------------------------
T ss_pred             eeEEecCcccchhHHHHHHHHHHhhhhccCCCceEEeehhhhhcch----------------------------------
Confidence            778877664333333333221        24678999999998731                                  


Q ss_pred             cCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       328 ~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                                     .....|++.++.-    ....++|++||++..++++|.+  |+. .|.++.|+..+...+++..+
T Consensus       124 ---------------~~~~~ll~~l~~~----~~~~~~i~~~n~~~~i~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~  181 (231)
T d1iqpa2         124 ---------------DAQQALRRTMEMF----SSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIA  181 (231)
T ss_dssp             ---------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHH
T ss_pred             ---------------hHHHHHhhhcccC----CcceEEEeccCChhhchHhHhC--ccc-cccccccchhhHHHHHHHHH
Confidence                           1223466666532    3457889999999999999998  874 59999999999999998876


Q ss_pred             CCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHH
Q 009640          408 GIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSA  455 (530)
Q Consensus       408 ~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~  455 (530)
                      ......               ++...+..++..+.+|.+.|+..+..+
T Consensus       182 ~~e~i~---------------i~~~~l~~I~~~~~gdiR~ai~~Lq~~  214 (231)
T d1iqpa2         182 ENEGLE---------------LTEEGLQAILYIAEGDMRRAINILQAA  214 (231)
T ss_dssp             HTTTCE---------------ECHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHhCCC---------------CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            544332               455556666666667877777655443

>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=8.8e-18  Score=162.25  Aligned_cols=187  Identities=18%  Similarity=0.249  Sum_probs=140.2

Q ss_pred             CCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC------------
Q 009640          187 FRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY------------  254 (530)
Q Consensus       187 ~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~------------  254 (530)
                      .++|.+|++++|++++++.+...+.    ..        ..+.++|||||||||||++|+++|++++.            
T Consensus         5 KyrP~~~~dlig~~~~~~~L~~~i~----~~--------~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~   72 (239)
T d1njfa_           5 KWRPQTFADVVGQEHVLTALANGLS----LG--------RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVC   72 (239)
T ss_dssp             HTCCSSGGGSCSCHHHHHHHHHHHH----TT--------CCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCS
T ss_pred             hhCCCCHHHccChHHHHHHHHHHHH----cC--------CCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccc
Confidence            4688999999999988887665443    21        12467999999999999999999998843            


Q ss_pred             ------------cEEEEecCccCChHHHHHHHHhcC------CCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          255 ------------DVYDLELTKVTDNSELRALLLQTT------NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       255 ------------~i~~l~l~~~~~~~~L~~l~~~~~------~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                                  +++.++......-..++.++....      ..-||||||+|.+-                        
T Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~------------------------  128 (239)
T d1njfa_          73 DNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS------------------------  128 (239)
T ss_dssp             HHHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC------------------------
T ss_pred             hHHHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCC------------------------
Confidence                        466777665555667787776652      34599999999871                        


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCH
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~  396 (530)
                                               ....+.|+..|+..    +...++|++||.++++.+++.+  |+ ..|.|+.|+.
T Consensus       129 -------------------------~~~q~~Llk~lE~~----~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~  176 (239)
T d1njfa_         129 -------------------------RHSFNALLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDV  176 (239)
T ss_dssp             -------------------------HHHHHHHHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCH
T ss_pred             -------------------------HHHHHHHHHHHhcC----CCCeEEEEEcCCccccChhHhh--hh-cccccccCcH
Confidence                                     22345788888743    3567899999999999999998  77 5699999999


Q ss_pred             HHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHH
Q 009640          397 HAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAM  456 (530)
Q Consensus       397 ~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l  456 (530)
                      ++.+.++.+.+..+               ...+++..+..++..+.+|+..|+..+..+.
T Consensus       177 ~~i~~~l~~i~~~e---------------~~~~~~~~l~~i~~~s~Gd~R~ain~l~~~~  221 (239)
T d1njfa_         177 EQIRHQLEHILNEE---------------HIAHEPRALQLLARAAEGSLRDALSLTDQAI  221 (239)
T ss_dssp             HHHHHHHHHHHHHH---------------TCCBCHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHhhh---------------ccCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            98887766554322               3457777777777777888888887665443

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.76  E-value=3.3e-18  Score=163.21  Aligned_cols=191  Identities=13%  Similarity=0.206  Sum_probs=143.1

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC-----Cc
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC-----YD  255 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~-----~~  255 (530)
                      +|  +..+.|.+|++++|++++++.+...+.    ...         ..++|||||||||||++|+++|++++     .+
T Consensus         4 pw--~eKyrP~~~~d~ig~~~~~~~L~~~~~----~~~---------~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~   68 (224)
T d1sxjb2           4 PW--VEKYRPQVLSDIVGNKETIDRLQQIAK----DGN---------MPHMIISGMPGIGKTTSVHCLAHELLGRSYADG   68 (224)
T ss_dssp             CH--HHHTCCSSGGGCCSCTHHHHHHHHHHH----SCC---------CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHH
T ss_pred             ch--HhHhCCCCHHHhcCCHHHHHHHHHHHH----cCC---------CCeEEEECCCCCCchhhHHHHHHHHhccccccc
Confidence            57  667999999999999988777766542    211         23699999999999999999999985     45


Q ss_pred             EEEEecCccCChHHHHHHHHh---c------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcccccc
Q 009640          256 VYDLELTKVTDNSELRALLLQ---T------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIAS  326 (530)
Q Consensus       256 i~~l~l~~~~~~~~L~~l~~~---~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~  326 (530)
                      ++.++.++..+...+...+..   .      ....||+|||+|.+.+                                 
T Consensus        69 ~~~~n~~~~~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~---------------------------------  115 (224)
T d1sxjb2          69 VLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA---------------------------------  115 (224)
T ss_dssp             EEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH---------------------------------
T ss_pred             cccccccccCCceehhhHHHHHHHhhccCCCcceEEEEEecccccch---------------------------------
Confidence            888888877665555444332   2      2456999999998731                                 


Q ss_pred             ccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          327 STCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                                      .....|+..++..    ....+++++||..+.+.++|++  |+ ..|.|+.|+.++...++...
T Consensus       116 ----------------~~~~~ll~~~e~~----~~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~~i~~~l~~i  172 (224)
T d1sxjb2         116 ----------------GAQQALRRTMELY----SNSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDEDVLKRLLQI  172 (224)
T ss_dssp             ----------------HHHHTTHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHH
T ss_pred             ----------------hHHHHHhhhcccc----ccceeeeeccCchhhhhhHHHH--HH-HHhhhcccchhhhHHHHHHH
Confidence                            1123345555422    3567889999999999999999  77 46999999999988887765


Q ss_pred             hCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHH
Q 009640          407 LGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQ  457 (530)
Q Consensus       407 l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~  457 (530)
                      +..               +...+++..+..++..+.+|++.|+..+.....
T Consensus       173 ~~~---------------e~~~i~~~~l~~I~~~s~Gd~R~ai~~Lq~~~~  208 (224)
T d1sxjb2         173 IKL---------------EDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVA  208 (224)
T ss_dssp             HHH---------------HTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHh---------------cccCCCHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            432               245678888888888888999999988876554

>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=99.75  E-value=4.7e-18  Score=162.13  Aligned_cols=188  Identities=19%  Similarity=0.279  Sum_probs=135.3

Q ss_pred             CccccCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC-----c
Q 009640          181 GWVSVPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY-----D  255 (530)
Q Consensus       181 ~w~~~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~-----~  255 (530)
                      +|  +..+.|.+|++++|++++++.|...+.    ...         ..++|||||||||||++++++|++++.     .
T Consensus         3 pw--~ekyrP~~~~divg~~~~~~~L~~~i~----~~~---------~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~   67 (227)
T d1sxjc2           3 PW--VEKYRPETLDEVYGQNEVITTVRKFVD----EGK---------LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNM   67 (227)
T ss_dssp             CH--HHHTCCSSGGGCCSCHHHHHHHHHHHH----TTC---------CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHH
T ss_pred             ch--hhhhCCCCHHHccCcHHHHHHHHHHHH----cCC---------CCeEEEECCCCCChhHHHHHHHHHhhcCCCcce
Confidence            57  677899999999999988887766543    221         135999999999999999999999743     3


Q ss_pred             EEEEecCccCChHHHHHHHH---hc-----CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccc
Q 009640          256 VYDLELTKVTDNSELRALLL---QT-----TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASS  327 (530)
Q Consensus       256 i~~l~l~~~~~~~~L~~l~~---~~-----~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  327 (530)
                      ++..+.++..+.......+.   ..     ....||+|||+|.+.                                   
T Consensus        68 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~-----------------------------------  112 (227)
T d1sxjc2          68 VLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMT-----------------------------------  112 (227)
T ss_dssp             EEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSC-----------------------------------
T ss_pred             eEEecccccCCeeeeecchhhccccccccCCCeEEEEEeccccch-----------------------------------
Confidence            55666555544333222221   11     345699999999872                                   


Q ss_pred             cCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          328 TCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       328 ~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                                    ....+.|++.|+..    ....+++++||.+..+++++++  |+ ..+.|..|+.++...++.+.+
T Consensus       113 --------------~~~~~~Ll~~le~~----~~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~i~~~l~~I~  171 (227)
T d1sxjc2         113 --------------NAAQNALRRVIERY----TKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEAIERRIANVL  171 (227)
T ss_dssp             --------------HHHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHH
T ss_pred             --------------hhHHHHHHHHhhhc----ccceeeccccCcHHHhHHHHHH--HH-hhhcccccccccccccccccc
Confidence                          12345677777643    3567899999999999999998  76 568999999999888877665


Q ss_pred             CCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHH
Q 009640          408 GIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVS  454 (530)
Q Consensus       408 ~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~  454 (530)
                      ..+               ...+++.++..++..+.+|.+.|+..+..
T Consensus       172 ~~e---------------~i~i~~~~l~~i~~~s~Gd~R~ain~Lq~  203 (227)
T d1sxjc2         172 VHE---------------KLKLSPNAEKALIELSNGDMRRVLNVLQS  203 (227)
T ss_dssp             HTT---------------TCCBCHHHHHHHHHHHTTCHHHHHHHTTT
T ss_pred             ccc---------------cccCCHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            433               23467777777777778888888765543

>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=99.71  E-value=2.6e-17  Score=158.87  Aligned_cols=190  Identities=13%  Similarity=0.198  Sum_probs=120.5

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCC---cEEE---
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCY---DVYD---  258 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~---~i~~---  258 (530)
                      +..+.|.+|++++|++++++.|..    ++.....        ..++|||||||||||++|+++|+++..   ....   
T Consensus         2 ~eky~P~~~~diig~~~~~~~L~~----~~~~~~~--------~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~   69 (252)
T d1sxje2           2 VDKYRPKSLNALSHNEELTNFLKS----LSDQPRD--------LPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDV   69 (252)
T ss_dssp             TTTTCCCSGGGCCSCHHHHHHHHT----TTTCTTC--------CCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-----
T ss_pred             CcccCCCCHHHccCcHHHHHHHHH----HHHcCCC--------CCeEEEECCCCCCHHHHHHHHHHhhcCcccccccccc
Confidence            678899999999999887776654    3332221        236999999999999999999998611   1111   


Q ss_pred             -----------------------EecCccCC--hHHHHHHHH---h-------------cCCCeEEEEcCccchhhhhhh
Q 009640          259 -----------------------LELTKVTD--NSELRALLL---Q-------------TTNRSIIVIEDIDCSVDLTAD  297 (530)
Q Consensus       259 -----------------------l~l~~~~~--~~~L~~l~~---~-------------~~~~sII~IDeID~~~~~~~~  297 (530)
                                             +.......  .........   .             .....|++|||+|.+.     
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~-----  144 (252)
T d1sxje2          70 RQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLT-----  144 (252)
T ss_dssp             -------------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSC-----
T ss_pred             ccccccccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccc-----
Confidence                                   11111110  111111111   1             1234699999999862     


Q ss_pred             hhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCCh
Q 009640          298 RMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDP  377 (530)
Q Consensus       298 r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDp  377 (530)
                                                                  ......|+..++..    .....+|+|||+++.+++
T Consensus       145 --------------------------------------------~~~~~~l~~~~e~~----~~~~~~Il~tn~~~~i~~  176 (252)
T d1sxje2         145 --------------------------------------------KDAQAALRRTMEKY----SKNIRLIMVCDSMSPIIA  176 (252)
T ss_dssp             --------------------------------------------HHHHHHHHHHHHHS----TTTEEEEEEESCSCSSCH
T ss_pred             --------------------------------------------cccchhhhcccccc----cccccceeeeccccchhh
Confidence                                                        11234556665532    355778999999999999


Q ss_pred             hhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCC-HHHHHHHHHHhccCHHHHHHHHHHHH
Q 009640          378 ALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALT-PAQIGEVLLRNRGNVDLAMKEVVSAM  456 (530)
Q Consensus       378 ALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~s-padi~~~l~~~~~d~~~al~~l~~~l  456 (530)
                      +|++  |+ .+|+|+.|+.++...++...+..+...               +. ..-+..++..+.+|++.|+..+..+.
T Consensus       177 ~l~s--R~-~~i~~~~~~~~~~~~~l~~i~~~e~~~---------------~~~~~~l~~i~~~s~Gd~R~ai~~Lq~~~  238 (252)
T d1sxje2         177 PIKS--QC-LLIRCPAPSDSEISTILSDVVTNERIQ---------------LETKDILKRIAQASNGNLRVSLLMLESMA  238 (252)
T ss_dssp             HHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCE---------------ECCSHHHHHHHHHHTTCHHHHHHHHTHHH
T ss_pred             hhhc--ch-heeeecccchhhHHHHHHHHHHHcCCC---------------CCcHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            9998  88 589999999999999887765432221               22 22234445556678888887665444


Q ss_pred             H
Q 009640          457 Q  457 (530)
Q Consensus       457 ~  457 (530)
                      .
T Consensus       239 ~  239 (252)
T d1sxje2         239 L  239 (252)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.71  E-value=1.6e-16  Score=151.74  Aligned_cols=189  Identities=16%  Similarity=0.176  Sum_probs=134.0

Q ss_pred             cCCCCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc------CCcEEE
Q 009640          185 VPFRHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL------CYDVYD  258 (530)
Q Consensus       185 ~~~~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l------~~~i~~  258 (530)
                      +..+.|.+|++++|++++++.|...    +....         ...+|||||||||||++++++|+++      +...+.
T Consensus         3 ~~ky~P~~~~diig~~~~~~~l~~~----i~~~~---------~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~   69 (237)
T d1sxjd2           3 VEKYRPKNLDEVTAQDHAVTVLKKT----LKSAN---------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILE   69 (237)
T ss_dssp             HHHTCCSSTTTCCSCCTTHHHHHHH----TTCTT---------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEE
T ss_pred             chhhCCCCHHHccCcHHHHHHHHHH----HHcCC---------CCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhh
Confidence            5668999999999999988776653    33322         2359999999999999999999986      677787


Q ss_pred             EecCccCChHHHHHHHHh------------------cCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhh
Q 009640          259 LELTKVTDNSELRALLLQ------------------TTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEM  320 (530)
Q Consensus       259 l~l~~~~~~~~L~~l~~~------------------~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~  320 (530)
                      ++.+...........+..                  .....||||||+|.+..                           
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~---------------------------  122 (237)
T d1sxjd2          70 LNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA---------------------------  122 (237)
T ss_dssp             ECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH---------------------------
T ss_pred             eeccccccchHHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCH---------------------------
Confidence            777665543322211111                  12345999999998731                           


Q ss_pred             ccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHH
Q 009640          321 GSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFK  400 (530)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~  400 (530)
                                            ...+.|+..++-.    ....++|++||....+.+++.+  |+ .+|.|+.|+.++..
T Consensus       123 ----------------------~~~~~l~~~~~~~----~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~~~  173 (237)
T d1sxjd2         123 ----------------------DAQSALRRTMETY----SGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASNAI  173 (237)
T ss_dssp             ----------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHHHH
T ss_pred             ----------------------HHHHHHhhccccc----cccccccccccccccccccccc--hh-hhhccccccccccc
Confidence                                  1122344433321    2456788999999999999998  87 67999999999999


Q ss_pred             HHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHHhccCHHHHHHHHHHHHH
Q 009640          401 VLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLRNRGNVDLAMKEVVSAMQ  457 (530)
Q Consensus       401 ~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~~~~d~~~al~~l~~~l~  457 (530)
                      .+++..+..+               ...+++..+..+...+.+|.+.|+..|..+..
T Consensus       174 ~~L~~i~~~e---------------~i~i~~~~l~~ia~~s~gd~R~ai~~L~~~~~  215 (237)
T d1sxjd2         174 DRLRFISEQE---------------NVKCDDGVLERILDISAGDLRRGITLLQSASK  215 (237)
T ss_dssp             HHHHHHHHTT---------------TCCCCHHHHHHHHHHTSSCHHHHHHHHHHTHH
T ss_pred             hhhhhhhhhh---------------cCcCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            8887765432               24567777777777777888888887765544

>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=99.67  E-value=5.2e-17  Score=166.09  Aligned_cols=185  Identities=17%  Similarity=0.116  Sum_probs=115.5

Q ss_pred             ChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcC
Q 009640          199 EPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTT  278 (530)
Q Consensus       199 ~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~  278 (530)
                      .++++..+.+.+..++        .|.|.++++|||||||||||++|.++|++++.+++.+++++..+..    .+....
T Consensus       133 ~~~~~~~i~~~l~~~~--------~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~----~l~~~~  200 (362)
T d1svma_         133 LPKMDSVVYDFLKCMV--------YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNF----ELGVAI  200 (362)
T ss_dssp             STTHHHHHHHHHHHHH--------HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHH----HHGGGT
T ss_pred             ccchHHHHHHHHHHHH--------hCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHH----HHHhHH
Confidence            3445555555444433        3778899999999999999999999999999999999888764432    234456


Q ss_pred             CCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccC
Q 009640          279 NRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSC  358 (530)
Q Consensus       279 ~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~  358 (530)
                      .+.+.+|||+++.......                                      .....--..+..|.+.+||..+.
T Consensus       201 ~~~~~l~d~~~~~~~~~~~--------------------------------------~~~~~~~DeiD~l~~~~dg~~~~  242 (362)
T d1svma_         201 DQFLVVFEDVKGTGGESRD--------------------------------------LPSGQGINNLDNLRDYLDGSVKV  242 (362)
T ss_dssp             TCSCEEETTCCCSTTTTTT--------------------------------------CCCCSHHHHHHTTHHHHHCSSCE
T ss_pred             HHHHHHHHHHHHhhhhccC--------------------------------------CCCeEEEehHhhcccccCCcchh
Confidence            6777788888875310000                                      00000111234455556654322


Q ss_pred             CCCC----------eEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHH-HHHHhhCCcCccchHHHHHHHHHhCC
Q 009640          359 CSEE----------KIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKV-LAKNYLGIESHHALFDVVESCIRAGG  427 (530)
Q Consensus       359 ~~~~----------~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~-i~~~~l~~~~~~~~~~~i~~l~~~~~  427 (530)
                      +.+.          ..+|+|||+   ++++++||||||+.|++..|+...+.. ++...+.........+.   ++....
T Consensus       243 ~~~~~~~~~~~~~~~p~i~ttN~---~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~~~~~~---L~~li~  316 (362)
T d1svma_         243 NLEKKHLNKRTQIFPPGIVTMNE---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIAL---LLMLIW  316 (362)
T ss_dssp             EECCSSSCCEEECCCCEEEEECS---CCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTCTTCHHHH---HHHHHH
T ss_pred             hhhhhhhchhhhccCCceeeccc---ccccccccccCceEEeecCCCcHHHHHHHHHHHhcccCCCCCHHH---HHHHcc
Confidence            1111          247889995   577888999999999999998877753 33333333322212222   333235


Q ss_pred             CCCHHHHHHHHH
Q 009640          428 ALTPAQIGEVLL  439 (530)
Q Consensus       428 ~~spadi~~~l~  439 (530)
                      +++++|+.+.+.
T Consensus       317 ~~s~~D~~~~i~  328 (362)
T d1svma_         317 YRPVAEFAQSIQ  328 (362)
T ss_dssp             HSCGGGSCGGGH
T ss_pred             CCCHHHHHHHHH
Confidence            678888766654

>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=99.53  E-value=3.7e-13  Score=126.71  Aligned_cols=147  Identities=17%  Similarity=0.177  Sum_probs=107.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC------------------------CcEEEEecCcc---CChHHHHHHHHhc---
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC------------------------YDVYDLELTKV---TDNSELRALLLQT---  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~------------------------~~i~~l~l~~~---~~~~~L~~l~~~~---  277 (530)
                      +.++||+||||+|||++|+++|+.+.                        .+++.+....-   .....++++....   
T Consensus        24 ~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~l~~~~~~~  103 (207)
T d1a5ta2          24 HHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEH  103 (207)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTSC
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccchhhHHhhhhhhc
Confidence            45799999999999999999999762                        34555543322   2345566665543   


Q ss_pred             ---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccC
Q 009640          278 ---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDG  354 (530)
Q Consensus       278 ---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDg  354 (530)
                         ...-|++|||+|.+-                                                 ....+.||..|+.
T Consensus       104 ~~~~~~kviIide~d~l~-------------------------------------------------~~a~n~Llk~lEe  134 (207)
T d1a5ta2         104 ARLGGAKVVWVTDAALLT-------------------------------------------------DAAANALLKTLEE  134 (207)
T ss_dssp             CTTSSCEEEEESCGGGBC-------------------------------------------------HHHHHHHHHHHTS
T ss_pred             cccCccceEEechhhhhh-------------------------------------------------hhhhHHHHHHHHh
Confidence               245699999999872                                                 2356789999985


Q ss_pred             CccCCCCCeEEEEEeCCCCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHH
Q 009640          355 LWSCCSEEKIIVFTTNHRDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQI  434 (530)
Q Consensus       355 l~s~~~~~~ivI~TTN~~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi  434 (530)
                      .    ....++|++||++.+|.|++++  |+ ..|.|+.|+.++...+++.-                    ..++..++
T Consensus       135 p----~~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~~~~~~~~L~~~--------------------~~~~~~~~  187 (207)
T d1a5ta2         135 P----PAETWFFLATREPERLLATLRS--RC-RLHYLAPPPEQYAVTWLSRE--------------------VTMSQDAL  187 (207)
T ss_dssp             C----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHH--------------------CCCCHHHH
T ss_pred             h----cccceeeeeecChhhhhhhhcc--ee-EEEecCCCCHHHHHHHHHHc--------------------CCCCHHHH
Confidence            4    4678999999999999999998  87 78999999998877766432                    23445555


Q ss_pred             HHHHHHhccCHHHHHH
Q 009640          435 GEVLLRNRGNVDLAMK  450 (530)
Q Consensus       435 ~~~l~~~~~d~~~al~  450 (530)
                      ..++..+.+++..|+.
T Consensus       188 ~~i~~~s~Gs~r~al~  203 (207)
T d1a5ta2         188 LAALRLSAGSPGAALA  203 (207)
T ss_dssp             HHHHHHTTTCHHHHHH
T ss_pred             HHHHHHcCCCHHHHHH
Confidence            5555556667777765

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.53  E-value=9.1e-14  Score=134.69  Aligned_cols=218  Identities=9%  Similarity=0.034  Sum_probs=127.7

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---------CcEEEEecC
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---------YDVYDLELT  262 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---------~~i~~l~l~  262 (530)
                      .++.+.+-++..+.|...+..++.+..    ...+....++||||||||||++++++|+.+.         ..+..++..
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~----~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~   89 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGA----GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAF   89 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSS----CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCC----CCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccc
Confidence            446778888888888887766664321    0011122477899999999999999999873         333444433


Q ss_pred             ccCCh----------------------HHHHHH----HHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchh
Q 009640          263 KVTDN----------------------SELRAL----LLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSS  316 (530)
Q Consensus       263 ~~~~~----------------------~~L~~l----~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~  316 (530)
                      ...+.                      ..+.+.    ......+.++++|++|.+....                     
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~---------------------  148 (287)
T d1w5sa2          90 NAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSP---------------------  148 (287)
T ss_dssp             GCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCT---------------------
T ss_pred             cccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEecccc---------------------
Confidence            32211                      122222    2234577899999999874100                     


Q ss_pred             hhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC------CChhhhcCCceeEEEE
Q 009640          317 IKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS------VDPALIRCGRMDVHVS  390 (530)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~------LDpALlRpGR~d~~I~  390 (530)
                                         .........+..+.+.+.....  .....+|+.+|.++.      .++++.+  |++.+|+
T Consensus       149 -------------------~~~~~~~~~l~~l~~~l~~~~~--~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~  205 (287)
T d1w5sa2         149 -------------------RIAAEDLYTLLRVHEEIPSRDG--VNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLH  205 (287)
T ss_dssp             -------------------TSCHHHHHHHHTHHHHSCCTTS--CCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEE
T ss_pred             -------------------ccchhHHHHHHHHHHhcchhhc--ccceeEEeecccHHHHHHHHhhccchhc--ccceeee
Confidence                               0111122344445555544433  244566666665543      3467777  9999999


Q ss_pred             eCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHHhCCCCCHHHHHHHHHH------hccCHHHHHHHHHHHHHHhhhccc
Q 009640          391 LGTCGPHAFKVLAKNYLGIESHHALFDVVESCIRAGGALTPAQIGEVLLR------NRGNVDLAMKEVVSAMQAKILSGR  464 (530)
Q Consensus       391 ~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~~~~~~spadi~~~l~~------~~~d~~~al~~l~~~l~~~~~~~~  464 (530)
                      |+.++.++...|++..+......             ..+++..|..+...      ..++++.|++-+..++........
T Consensus       206 f~~y~~~el~~Il~~r~~~~~~~-------------~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~  272 (287)
T d1w5sa2         206 LPAYKSRELYTILEQRAELGLRD-------------TVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGR  272 (287)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHBCT-------------TSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             ccCCcHHHHHHHHhhhHHHhhcc-------------CCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCC
Confidence            99999999999998765321111             22444333333222      245778887777666655444444


Q ss_pred             cccccc
Q 009640          465 EVMECD  470 (530)
Q Consensus       465 ~~~~~~  470 (530)
                      ..++.+
T Consensus       273 ~~It~~  278 (287)
T d1w5sa2         273 DSLSED  278 (287)
T ss_dssp             SSCCHH
T ss_pred             CCCCHH
Confidence            444433

>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=99.51  E-value=3.5e-13  Score=129.71  Aligned_cols=162  Identities=14%  Similarity=0.053  Sum_probs=107.7

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC----CcEEEEecCcc
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC----YDVYDLELTKV  264 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~----~~i~~l~l~~~  264 (530)
                      +...++++++.+...+.|.+.|...+.++.       ..++++|||||||||||++++++|+.+.    ..++.++....
T Consensus        11 ~~y~p~~l~~Re~ei~~l~~~l~~~l~~~~-------~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~   83 (276)
T d1fnna2          11 PSYVPKRLPHREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIY   83 (276)
T ss_dssp             TTCCCSCCTTCHHHHHHHHHHHHHHHHSTT-------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHhCCC-------CCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhh
Confidence            334456788988888899998887776553       2357899999999999999999999973    45555554433


Q ss_pred             CCh----------------------HH----HHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhh
Q 009640          265 TDN----------------------SE----LRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIK  318 (530)
Q Consensus       265 ~~~----------------------~~----L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~  318 (530)
                      ...                      ..    +.+.+.......++++|++|.+...                        
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~------------------------  139 (276)
T d1fnna2          84 RNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPD------------------------  139 (276)
T ss_dssp             CSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHH------------------------
T ss_pred             hhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhh------------------------
Confidence            211                      11    1222233356778888998876311                        


Q ss_pred             hhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC---CCCChhhhcCCce-eEEEEeCCC
Q 009640          319 EMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR---DSVDPALIRCGRM-DVHVSLGTC  394 (530)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~---~~LDpALlRpGR~-d~~I~~~~p  394 (530)
                                            ....+..++..+...   .....++|+++|..   +.+++++.+  |+ ...|+|+.+
T Consensus       140 ----------------------~~~~~~~~~~~~~~~---~~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i~~~~~  192 (276)
T d1fnna2         140 ----------------------ILSTFIRLGQEADKL---GAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPY  192 (276)
T ss_dssp             ----------------------HHHHHHHHTTCHHHH---SSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCC
T ss_pred             ----------------------hhhhHHHHHhccccc---cccceEEeecCCchhhhhhcchhhhh--hhcchhccccch
Confidence                                  111222233322211   13557788888874   578898887  54 356899999


Q ss_pred             CHHHHHHHHHHhhC
Q 009640          395 GPHAFKVLAKNYLG  408 (530)
Q Consensus       395 ~~~~r~~i~~~~l~  408 (530)
                      +.+++..|++..+.
T Consensus       193 ~~~e~~~il~~r~~  206 (276)
T d1fnna2         193 TKDQIFDILLDRAK  206 (276)
T ss_dssp             BHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHH
Confidence            99999999987764

>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=99.41  E-value=9.8e-13  Score=124.34  Aligned_cols=162  Identities=16%  Similarity=0.240  Sum_probs=100.4

Q ss_pred             CCCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc
Q 009640          188 RHPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV  264 (530)
Q Consensus       188 ~~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~  264 (530)
                      .+..||++++..+.- +.....+..+...+.       ..-++++||||||||||+|+.|+|+++   +..++.++...+
T Consensus         4 n~~~tFdnF~vg~~N-~~a~~~~~~~~~~~~-------~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~   75 (213)
T d1l8qa2           4 NPKYTLENFIVGEGN-RLAYEVVKEALENLG-------SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF   75 (213)
T ss_dssp             CTTCCSSSCCCCTTT-HHHHHHHHHHHHTTT-------TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CCCCChhhccCCCcH-HHHHHHHHHHHhCcC-------CCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHH
Confidence            356789997543322 223333444444332       122468999999999999999999998   566777765544


Q ss_pred             CC-------hHHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCC
Q 009640          265 TD-------NSELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNG  337 (530)
Q Consensus       265 ~~-------~~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~  337 (530)
                      ..       ......++.....-.+|+|||||.+.                                            +
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~--------------------------------------------~  111 (213)
T d1l8qa2          76 AQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLS--------------------------------------------G  111 (213)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGT--------------------------------------------T
T ss_pred             HHHHHHHHHccchhhHHHHHhhccchhhhhhhhhc--------------------------------------------C
Confidence            21       01122333334567899999999983                                            1


Q ss_pred             CcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCCC---ChhhhcCCce--eEEEEeCCCCHHHHHHHHHHhhCC
Q 009640          338 EESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDSV---DPALIRCGRM--DVHVSLGTCGPHAFKVLAKNYLGI  409 (530)
Q Consensus       338 ~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~L---DpALlRpGR~--d~~I~~~~p~~~~r~~i~~~~l~~  409 (530)
                      ....+..+..++|.+   ..  .+..+||.++..|..+   .|.|.+  |+  ...+.++ |+.+++..+++.+...
T Consensus       112 ~~~~~~~lf~lin~~---~~--~~~~iiits~~~p~~l~~~~~dL~S--RL~~g~~~~i~-p~d~~~~~iL~~~a~~  180 (213)
T d1l8qa2         112 KERTQIEFFHIFNTL---YL--LEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIE-LDNKTRFKIIKEKLKE  180 (213)
T ss_dssp             CHHHHHHHHHHHHHH---HH--TTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECC-CCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHH---hh--ccceEEEecCCcchhccccchHHHH--HhhCceEEEEC-CCcHHHHHHHHHHHHH
Confidence            222344455555543   22  3455666566667544   578887  55  4677786 6778899998887643

>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=99.40  E-value=1.9e-12  Score=129.54  Aligned_cols=157  Identities=15%  Similarity=0.253  Sum_probs=111.9

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcC-CCCc-eEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCCh----
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGR-AWKR-GYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDN----  267 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~-~~~r-G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~----  267 (530)
                      ..|+|++++++.|...+......      +.. ..+. .+||.||||||||.||+++|..++.+++.++++.+...    
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~------l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~   95 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAG------LGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVS   95 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTT------CSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCS
T ss_pred             CeecChHHHHHHHHHHHHHHHcc------CCCCCCCceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhh
Confidence            35789999999999877644321      111 1123 58899999999999999999999999999998876421    


Q ss_pred             ---------------HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          268 ---------------SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       268 ---------------~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                                     ..+...+ .....+|+++||||.+-                                        
T Consensus        96 ~l~g~~~gy~g~~~~~~l~~~~-~~~~~~vvl~DeieKa~----------------------------------------  134 (315)
T d1r6bx3          96 RLIGAPPGYVGFDQGGLLTDAV-IKHPHAVLLLDEIEKAH----------------------------------------  134 (315)
T ss_dssp             SSCCCCSCSHHHHHTTHHHHHH-HHCSSEEEEEETGGGSC----------------------------------------
T ss_pred             hhcccCCCccccccCChhhHHH-HhCccchhhhccccccc----------------------------------------
Confidence                           1122222 34667999999999861                                        


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCcc-------CCCCCeEEEEEeCCCC-------------------------CCChhhh
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWS-------CCSEEKIIVFTTNHRD-------------------------SVDPALI  380 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s-------~~~~~~ivI~TTN~~~-------------------------~LDpALl  380 (530)
                               ..+.+.||..+|.-.-       ..-...|+|+|||--.                         .+.|.|+
T Consensus       135 ---------~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEfl  205 (315)
T d1r6bx3         135 ---------PDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFR  205 (315)
T ss_dssp             ---------HHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHH
T ss_pred             ---------chHhhhhHHhhccceecCCCCCccCccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHH
Confidence                     2245666666642110       0124578999999421                         2567777


Q ss_pred             cCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          381 RCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       381 RpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      .  |+|..|.|.+.+.++...|+..++.
T Consensus       206 n--Rid~ii~f~~l~~~~~~~I~~~~l~  231 (315)
T d1r6bx3         206 N--RLDNIIWFDHLSTDVIHQVVDKFIV  231 (315)
T ss_dssp             T--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             h--hhhhhhcccchhhhHHHHHHHHHHH
Confidence            7  9999999999999999999887753

>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=1.1e-12  Score=131.27  Aligned_cols=157  Identities=17%  Similarity=0.289  Sum_probs=111.4

Q ss_pred             ccccCChhhhHHHHHHHHHHHcChhhHhhhcCC-CCc-eEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCCh-
Q 009640          194 ETLALEPQLKKQITEDLTAFANGKEFYHRVGRA-WKR-GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDN-  267 (530)
Q Consensus       194 ~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~-~~r-G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~-  267 (530)
                      ..|+|++++++.|...+......      +.-+ .|. .+||+||||||||.+|+++|..+   +.+++.+++++..+. 
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~------l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~   96 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAG------LKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKH   96 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGG------CSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSG
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcC------CCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccch
Confidence            34689999999998877655321      1111 123 47888999999999999999998   778999988776432 


Q ss_pred             ------------------HHHHHHHHhcCCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccC
Q 009640          268 ------------------SELRALLLQTTNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTC  329 (530)
Q Consensus       268 ------------------~~L~~l~~~~~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~  329 (530)
                                        ..|.+.+.+ ...|||+|||||.+-                                     
T Consensus        97 ~~~~L~g~~~gyvG~~~~~~l~~~~~~-~p~~Vvl~DEieK~~-------------------------------------  138 (315)
T d1qvra3          97 AVSRLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKAH-------------------------------------  138 (315)
T ss_dssp             GGGGC--------------CHHHHHHH-CSSEEEEESSGGGSC-------------------------------------
T ss_pred             hhhhhcCCCCCCcCcccCChHHHHHHh-CCCcEEEEehHhhcC-------------------------------------
Confidence                              123333332 457999999999861                                     


Q ss_pred             CCCCCCCCCcchhhhHHHHhhhccCCccC-------CCCCeEEEEEeCC--------------------------CCCCC
Q 009640          330 GNNNNNNGEESGRVTLSGLLNFTDGLWSC-------CSEEKIIVFTTNH--------------------------RDSVD  376 (530)
Q Consensus       330 ~~~~~~~~~~~~~~~ls~LLn~lDgl~s~-------~~~~~ivI~TTN~--------------------------~~~LD  376 (530)
                                  ....+.|+..+|.-.-.       .-.+.|+|+|||-                          .+.+.
T Consensus       139 ------------~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~  206 (315)
T d1qvra3         139 ------------PDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFR  206 (315)
T ss_dssp             ------------HHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSC
T ss_pred             ------------HHHHHHHHHHhccCceeCCCCcEecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcC
Confidence                        12444555555432111       1245799999995                          35689


Q ss_pred             hhhhcCCceeEEEEeCCCCHHHHHHHHHHhhC
Q 009640          377 PALIRCGRMDVHVSLGTCGPHAFKVLAKNYLG  408 (530)
Q Consensus       377 pALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~  408 (530)
                      |.|+.  |||..|.|.+.+.++...|+...+.
T Consensus       207 pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l~  236 (315)
T d1qvra3         207 PEFLN--RLDEIVVFRPLTKEQIRQIVEIQLS  236 (315)
T ss_dssp             HHHHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             HHHHh--cCCeeeeccchhhhhhHHHHHHHHH
Confidence            99999  9999999999999999999876653

>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=99.38  E-value=6.6e-12  Score=122.27  Aligned_cols=196  Identities=20%  Similarity=0.236  Sum_probs=126.3

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecC
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELT  262 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~  262 (530)
                      ++.++|-++..+++...|    .++         .+.++||.||||+|||+++..+|...          +..++.++++
T Consensus        17 ld~~igRd~Ei~~l~~iL----~r~---------~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~   83 (268)
T d1r6bx2          17 IDPLIGREKELERAIQVL----CRR---------RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG   83 (268)
T ss_dssp             SCCCCSCHHHHHHHHHHH----TSS---------SSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC
T ss_pred             CCcccChHHHHHHHHHHH----hcC---------ccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeec
Confidence            455677666544444433    322         25789999999999999999999864          6789999887


Q ss_pred             ccCC--------hHHHHHHHHhc--CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCCC
Q 009640          263 KVTD--------NSELRALLLQT--TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNN  332 (530)
Q Consensus       263 ~~~~--------~~~L~~l~~~~--~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  332 (530)
                      .+..        +..+..++..+  ..+.|+||||++.+++..                                     
T Consensus        84 ~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g-------------------------------------  126 (268)
T d1r6bx2          84 SLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAG-------------------------------------  126 (268)
T ss_dssp             ---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSC-------------------------------------
T ss_pred             hHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCC-------------------------------------
Confidence            7632        34566777765  457899999999996311                                     


Q ss_pred             CCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCC-----CCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhh
Q 009640          333 NNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHR-----DSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYL  407 (530)
Q Consensus       333 ~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~-----~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l  407 (530)
                          ....+...+..+|.-   .-+  .+++-+|+||...     ..-||||.|  ||.+ |.+..|+.++-..|++.+.
T Consensus       127 ----~~~g~~~d~a~~Lkp---~L~--rg~i~vIgatT~eey~~~~e~d~al~r--rF~~-I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         127 ----AASGGQVDAANLIKP---LLS--SGKIRVIGSTTYQEFSNIFEKDRALAR--RFQK-IDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             ----CSSSCHHHHHHHHSS---CSS--SCCCEEEEEECHHHHHCCCCCTTSSGG--GEEE-EECCCCCHHHHHHHHHHHH
T ss_pred             ----CCCCccccHHHHhhH---HHh--CCCCeEEEeCCHHHHHHHHhhcHHHHh--hhcc-cccCCCCHHHHHHHHHHhh
Confidence                111123334444432   222  3667777777643     355999999  9965 9999999999999987643


Q ss_pred             CCcCccchHHHHHHHHHhCCCCCHHHHHHHH------HHhccCHHHHHHHHHHHHHHhhh
Q 009640          408 GIESHHALFDVVESCIRAGGALTPAQIGEVL------LRNRGNVDLAMKEVVSAMQAKIL  461 (530)
Q Consensus       408 ~~~~~~~~~~~i~~l~~~~~~~spadi~~~l------~~~~~d~~~al~~l~~~l~~~~~  461 (530)
                      ..         .+..  ....+++.-+...+      +..+.-|++|++-+.++.....+
T Consensus       195 ~~---------~e~~--h~v~~~~~al~~~v~ls~ryi~~~~~PdKAIdllDea~a~~~~  243 (268)
T d1r6bx2         195 PK---------YEAH--HDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARL  243 (268)
T ss_dssp             HH---------HHHH--HTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHHHHHH
T ss_pred             HH---------Hhcc--CCEEeChHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHh
Confidence            21         1111  12445555554443      33556799999977776654443

>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=6.4e-12  Score=126.22  Aligned_cols=150  Identities=19%  Similarity=0.260  Sum_probs=98.0

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcC---------------
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLC---------------  253 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~---------------  253 (530)
                      +...|.+|.|++++|+.+.-.+..    +.         ..++||+||||||||+||+++|.-|.               
T Consensus         2 ~~~~f~~I~Gq~~~kral~laa~~----~~---------~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~   68 (333)
T d1g8pa_           2 PVFPFSAIVGQEDMKLALLLTAVD----PG---------IGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNV   68 (333)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHC----GG---------GCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSG
T ss_pred             CCCChhhccCcHHHHHHHHHHHhc----cC---------CCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCcc
Confidence            345799999999998876543321    11         24799999999999999999998762               


Q ss_pred             ------------------CcEEEEecCccCChHHH------HHHHHhc-----------CCCeEEEEcCccchhhhhhhh
Q 009640          254 ------------------YDVYDLELTKVTDNSEL------RALLLQT-----------TNRSIIVIEDIDCSVDLTADR  298 (530)
Q Consensus       254 ------------------~~i~~l~l~~~~~~~~L------~~l~~~~-----------~~~sII~IDeID~~~~~~~~r  298 (530)
                                        .+++.....  .+...+      ...+..-           ....|+|||||+.+       
T Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~-------  139 (333)
T d1g8pa_          69 EMIPDWATVLSTNVIRKPTPVVDLPLG--VSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLL-------  139 (333)
T ss_dssp             GGSCTTCCCSCCCEEEECCCEEEECTT--CCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGS-------
T ss_pred             ccccchhhccccCcccccCceeeccCC--CCcccccCcchhhhccccCcceeeccccccccccEeecccHHHH-------
Confidence                              111221111  111121      2222110           13579999999976       


Q ss_pred             hhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhcc---------CCccCCCCCeEEEEEe
Q 009640          299 MLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTD---------GLWSCCSEEKIIVFTT  369 (530)
Q Consensus       299 ~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lD---------gl~s~~~~~~ivI~TT  369 (530)
                                                                ...+++.|+..|+         |.........++|+|+
T Consensus       140 ------------------------------------------~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~  177 (333)
T d1g8pa_         140 ------------------------------------------EDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSG  177 (333)
T ss_dssp             ------------------------------------------CHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEE
T ss_pred             ------------------------------------------HHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEec
Confidence                                                      2346778888775         3322223446788888


Q ss_pred             CCC-CCCChhhhcCCceeEEEEeCCC-CHHHHHHHHH
Q 009640          370 NHR-DSVDPALIRCGRMDVHVSLGTC-GPHAFKVLAK  404 (530)
Q Consensus       370 N~~-~~LDpALlRpGR~d~~I~~~~p-~~~~r~~i~~  404 (530)
                      |.. ..|+++++.  ||+.+|.+.+| +...+..+..
T Consensus       178 Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~~~~~~  212 (333)
T d1g8pa_         178 NPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIR  212 (333)
T ss_dssp             CSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHH
T ss_pred             Cccccccccchhh--hhcceeeccCcchhhHHHHHHH
Confidence            864 579999999  99999999988 4566655544

>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=99.26  E-value=2.2e-11  Score=123.87  Aligned_cols=203  Identities=22%  Similarity=0.237  Sum_probs=124.4

Q ss_pred             cccCChhhhHHHHHHHHHHHcChhh------------------HhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          195 TLALEPQLKKQITEDLTAFANGKEF------------------YHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       195 ~l~~~~~~k~~i~~~l~~~l~~~~~------------------y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      .|+|+++.|+.+-..+.....+-..                  .....+ ++..+||.||+|||||-||+++|..++.++
T Consensus        18 ~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~-p~~niLfiGPTGvGKTElAk~LA~~~~~~~   96 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVEL-SKSNILLIGPTGSGKTLMAQTLAKHLDIPI   96 (364)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTC-CCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             eecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccC-CCcceeeeCCCCccHHHHHHHHHhhcccce
Confidence            4799999999888777432221100                  111122 457899999999999999999999999999


Q ss_pred             EEEecCccCC--------hHHHHHHHHhc------CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhcc
Q 009640          257 YDLELTKVTD--------NSELRALLLQT------TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGS  322 (530)
Q Consensus       257 ~~l~l~~~~~--------~~~L~~l~~~~------~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~  322 (530)
                      +.++.+.+..        ...+.+++...      ...+||++||||.+.+......                       
T Consensus        97 ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~-----------------------  153 (364)
T d1um8a_          97 AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRS-----------------------  153 (364)
T ss_dssp             EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC-------------------------------
T ss_pred             eehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhcccccccc-----------------------
Confidence            9999988753        45577776654      3579999999998742110000                       


Q ss_pred             ccccccCCCCCCCCCCcchhhhHHHHhhhccCCc----cC-----CCCCeEEEEEeCC----------------------
Q 009640          323 RIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLW----SC-----CSEEKIIVFTTNH----------------------  371 (530)
Q Consensus       323 ~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~----s~-----~~~~~ivI~TTN~----------------------  371 (530)
                                  ...+.....+.+.||+.+||-.    ..     ...+.++|+|+|-                      
T Consensus       154 ------------~~~d~a~~~V~~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~  221 (364)
T d1um8a_         154 ------------ITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQN  221 (364)
T ss_dssp             ------------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSC
T ss_pred             ------------ccccccchHHHHhhhhhhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccc
Confidence                        0011223456778888888521    10     0123566666664                      


Q ss_pred             ---------------------------CCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHhhCCcCccchHHHHHHHHH
Q 009640          372 ---------------------------RDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNYLGIESHHALFDVVESCIR  424 (530)
Q Consensus       372 ---------------------------~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~l~~~~~~~~~~~i~~l~~  424 (530)
                                                 +..+.|.|+-  |+|..|.|...+.+....|+......     +......+..
T Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEf~g--Ri~~iv~f~~L~~~~l~~Il~~~~~~-----l~kq~~~~l~  294 (364)
T d1um8a_         222 VLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIG--RLPVLSTLDSISLEAMVDILQKPKNA-----LIKQYQQLFK  294 (364)
T ss_dssp             CCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTC-----HHHHHHHHHH
T ss_pred             cccccccccchhhhhhhhccccHHHHhhhhhHHHHHH--HhcchhhHhhhhHHHHHHHHHHHHHH-----HHHHHHHHHH
Confidence                                       1124555555  99999999999999999998643321     2333333332


Q ss_pred             h---CCCCCHHHHHHHHHH
Q 009640          425 A---GGALTPAQIGEVLLR  440 (530)
Q Consensus       425 ~---~~~~spadi~~~l~~  440 (530)
                      .   .-.||+.-+..+...
T Consensus       295 ~~gi~L~~td~a~~~la~~  313 (364)
T d1um8a_         295 MDEVDLIFEEEAIKEIAQL  313 (364)
T ss_dssp             TTTCEEEECHHHHHHHHHH
T ss_pred             hCCcEEEECHHHHHHHHHh
Confidence            1   234567666655543

>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=99.24  E-value=1.4e-11  Score=113.99  Aligned_cols=148  Identities=17%  Similarity=0.219  Sum_probs=95.8

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecC
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELT  262 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~  262 (530)
                      ++.++|.++..+++..    .+.++         .+.++||.||||+|||+++..+|...          +.++|.++++
T Consensus        21 ld~~igRd~Ei~~l~~----iL~r~---------~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~   87 (195)
T d1jbka_          21 LDPVIGRDEEIRRTIQ----VLQRR---------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMG   87 (195)
T ss_dssp             SCCCCSCHHHHHHHHH----HHTSS---------SSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHH
T ss_pred             CCCCcCcHHHHHHHHH----HHhcc---------CCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHH
Confidence            3556676655444443    33332         25789999999999999999999855          6889999987


Q ss_pred             ccCC--------hHHHHHHHHhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          263 KVTD--------NSELRALLLQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       263 ~~~~--------~~~L~~l~~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      .+..        +..+..++...   ..+.|||||||+.+++.....                                 
T Consensus        88 ~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~---------------------------------  134 (195)
T d1jbka_          88 ALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKAD---------------------------------  134 (195)
T ss_dssp             HHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT--------------------------------------
T ss_pred             HHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCC---------------------------------
Confidence            7621        33466677654   346899999999996311100                                 


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCC-----CCChhhhcCCceeEEEEeCCCCHHHHHHHH
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRD-----SVDPALIRCGRMDVHVSLGTCGPHAFKVLA  403 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~-----~LDpALlRpGR~d~~I~~~~p~~~~r~~i~  403 (530)
                          +..+ -...   |.-.|.      .+++.+|+||...+     .-||||.|  ||.. |.+..|+.++-..|+
T Consensus       135 ----g~~d-~~~~---Lkp~L~------rg~l~~IgatT~eey~~~~e~d~aL~r--rF~~-I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         135 ----GAMD-AGNM---LKPALA------RGELHCVGATTLDEYRQYIEKDAALER--RFQK-VFVAEPSVEDTIAIL  194 (195)
T ss_dssp             -----CCC-CHHH---HHHHHH------TTSCCEEEEECHHHHHHHTTTCHHHHT--TEEE-EECCCCCHHHHHTTC
T ss_pred             ----Cccc-HHHH---HHHHHh------CCCceEEecCCHHHHHHHHHcCHHHHh--cCCE-eecCCCCHHHHHHHh
Confidence                0011 1112   222222      35566777665432     45999999  9965 899999998876654

>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=99.19  E-value=9e-11  Score=120.08  Aligned_cols=151  Identities=17%  Similarity=0.262  Sum_probs=90.5

Q ss_pred             cccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc----------CCcEEEEecC
Q 009640          193 FETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL----------CYDVYDLELT  262 (530)
Q Consensus       193 f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l----------~~~i~~l~l~  262 (530)
                      ++-++|-++..+++++.|    .++         .+.+.||.||||+|||+++..+|...          +..++.++++
T Consensus        21 ld~~~gr~~ei~~~~~~L----~r~---------~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~   87 (387)
T d1qvra2          21 LDPVIGRDEEIRRVIQIL----LRR---------TKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMG   87 (387)
T ss_dssp             SCCCCSCHHHHHHHHHHH----HCS---------SCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-
T ss_pred             CCCCcCcHHHHHHHHHHH----hcC---------CCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHh
Confidence            455677666555555533    222         25678999999999999999999864          5789999988


Q ss_pred             ccCC--------hHHHHHHHHhc---CCCeEEEEcCccchhhhhhhhhhcccCCccccccccchhhhhhccccccccCCC
Q 009640          263 KVTD--------NSELRALLLQT---TNRSIIVIEDIDCSVDLTADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGN  331 (530)
Q Consensus       263 ~~~~--------~~~L~~l~~~~---~~~sII~IDeID~~~~~~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  331 (530)
                      .+..        +..+..++...   ..+.||||||++.+++..+..                                 
T Consensus        88 ~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~---------------------------------  134 (387)
T d1qvra2          88 SLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAE---------------------------------  134 (387)
T ss_dssp             ----------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------------------------------
T ss_pred             hhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCC---------------------------------
Confidence            7742        33466666654   357899999999997421100                                 


Q ss_pred             CCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCC-----CCCCChhhhcCCceeEEEEeCCCCHHHHHHHHHHh
Q 009640          332 NNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNH-----RDSVDPALIRCGRMDVHVSLGTCGPHAFKVLAKNY  406 (530)
Q Consensus       332 ~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~-----~~~LDpALlRpGR~d~~I~~~~p~~~~r~~i~~~~  406 (530)
                          +..+ -...|...|.         .+++-+|++|..     .++ |+||.|  ||.. |.+..|+.++-..|++..
T Consensus       135 ----g~~d-~a~~Lkp~L~---------rg~~~~I~~tT~~ey~~~e~-d~al~r--rF~~-v~v~ep~~~~~~~il~~~  196 (387)
T d1qvra2         135 ----GAVD-AGNMLKPALA---------RGELRLIGATTLDEYREIEK-DPALER--RFQP-VYVDEPTVEETISILRGL  196 (387)
T ss_dssp             --------------HHHHH---------TTCCCEEEEECHHHHHHHTT-CTTTCS--CCCC-EEECCCCHHHHHHHHHHH
T ss_pred             ----Cccc-HHHHHHHHHh---------CCCcceeeecCHHHHHHhcc-cHHHHH--hccc-ccCCCCcHHHHHHHHHHH
Confidence                0001 1112222222         244556665543     244 999999  9966 899999999999998765


Q ss_pred             h
Q 009640          407 L  407 (530)
Q Consensus       407 l  407 (530)
                      .
T Consensus       197 ~  197 (387)
T d1qvra2         197 K  197 (387)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.17  E-value=9.2e-11  Score=109.28  Aligned_cols=113  Identities=15%  Similarity=0.192  Sum_probs=87.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC------CcEEEEecCcc-CChHHHHHHHHhc------CCCeEEEEcCccchhhh
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC------YDVYDLELTKV-TDNSELRALLLQT------TNRSIIVIEDIDCSVDL  294 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~------~~i~~l~l~~~-~~~~~L~~l~~~~------~~~sII~IDeID~~~~~  294 (530)
                      ...+|||||||||||++|.++|++..      .|++.+....- .+-.++|.+...+      ...-|++|||+|.+   
T Consensus        15 ~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l---   91 (198)
T d2gnoa2          15 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERM---   91 (198)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGB---
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCcccc---
Confidence            46899999999999999999999872      46888876432 2456777765543      23459999999997   


Q ss_pred             hhhhhhcccCCccccccccchhhhhhccccccccCCCCCCCCCCcchhhhHHHHhhhccCCccCCCCCeEEEEEeCCCCC
Q 009640          295 TADRMLKSSNTSTTAKTKRSSSIKEMGSRIASSTCGNNNNNNGEESGRVTLSGLLNFTDGLWSCCSEEKIIVFTTNHRDS  374 (530)
Q Consensus       295 ~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~LLn~lDgl~s~~~~~~ivI~TTN~~~~  374 (530)
                                                                    .....+.||..|+..    +...++|++||+++.
T Consensus        92 ----------------------------------------------~~~aqNaLLK~LEEP----p~~t~fiLit~~~~~  121 (198)
T d2gnoa2          92 ----------------------------------------------TQQAANAFLKALEEP----PEYAVIVLNTRRWHY  121 (198)
T ss_dssp             ----------------------------------------------CHHHHHHTHHHHHSC----CTTEEEEEEESCGGG
T ss_pred             ----------------------------------------------chhhhhHHHHHHhCC----CCCceeeeccCChhh
Confidence                                                          233567899999853    467889999999999


Q ss_pred             CChhhhcCCceeEEEEeCCCCH
Q 009640          375 VDPALIRCGRMDVHVSLGTCGP  396 (530)
Q Consensus       375 LDpALlRpGR~d~~I~~~~p~~  396 (530)
                      |.|++++  |+ .+|.|+.|..
T Consensus       122 ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2         122 LLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             SCHHHHT--TS-EEEECCCCHH
T ss_pred             CHHHHhc--ce-EEEeCCCchH
Confidence            9999998  76 6688887753

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=98.93  E-value=7.9e-09  Score=107.28  Aligned_cols=70  Identities=19%  Similarity=0.230  Sum_probs=53.3

Q ss_pred             ccCChhhhHHHHHHHHHHHcChhhHhh-hcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccC
Q 009640          196 LALEPQLKKQITEDLTAFANGKEFYHR-VGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVT  265 (530)
Q Consensus       196 l~~~~~~k~~i~~~l~~~l~~~~~y~~-~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~  265 (530)
                      |+|+++.|+.|--.+....++-..-.. ..-..|.++||.||||||||.||+++|..++.+|+.++.+.+.
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            799999999988877644321110000 0122367999999999999999999999999999999998874

>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=98.87  E-value=3.1e-08  Score=94.91  Aligned_cols=85  Identities=14%  Similarity=0.180  Sum_probs=61.3

Q ss_pred             ccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccCChHHHHH
Q 009640          196 LALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVTDNSELRA  272 (530)
Q Consensus       196 l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~~~~~L~~  272 (530)
                      +++....-+.+.+.+..+...+           ..+||+||||||||.+|++|....   ...++.+++..+........
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~~-----------~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~   70 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCAE-----------CPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAE   70 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTCC-----------SCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHH
T ss_pred             eEecCHHHHHHHHHHHHHhCCC-----------CCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHH
Confidence            4566666677777777665543           479999999999999999998876   45678888877754444444


Q ss_pred             HHHh-----------------cCCCeEEEEcCccch
Q 009640          273 LLLQ-----------------TTNRSIIVIEDIDCS  291 (530)
Q Consensus       273 l~~~-----------------~~~~sII~IDeID~~  291 (530)
                      +|..                 ......|||||||.+
T Consensus        71 lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i~~L  106 (247)
T d1ny5a2          71 LFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGEL  106 (247)
T ss_dssp             HHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGC
T ss_pred             hcCcccCCcCCcccccCCHHHccCCCEEEEeChHhC
Confidence            4421                 123458999999987

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.87  E-value=2.3e-08  Score=95.12  Aligned_cols=56  Identities=21%  Similarity=0.135  Sum_probs=43.8

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      ..-++++|-++..+.|.+                 ...+.++||||+|+|||+|++.+++.++..++.+++..
T Consensus         9 ~~~~~f~GR~~el~~l~~-----------------~~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~   64 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKG-----------------LRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRK   64 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHH-----------------TCSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGG
T ss_pred             CChhhCCChHHHHHHHHh-----------------ccCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEecc
Confidence            445888887776555433                 12478999999999999999999999999888876543

>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=98.84  E-value=9.5e-10  Score=105.58  Aligned_cols=60  Identities=27%  Similarity=0.409  Sum_probs=47.4

Q ss_pred             hhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCcc
Q 009640          200 PQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKV  264 (530)
Q Consensus       200 ~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~  264 (530)
                      .+++..+.+.+..+.....     +...|+|||||||||||||+||+++|++++.+++.++.+.+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~-----~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~   68 (273)
T d1gvnb_           9 KQFENRLNDNLEELIQGKK-----AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTF   68 (273)
T ss_dssp             HHHHHHHHHHHHHHHTTCC-----CCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHH
T ss_pred             HHHHHHHHHHHHHHHhccc-----CCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHH
Confidence            3455666666666655432     45668899999999999999999999999999999987554

>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=98.19  E-value=3.1e-05  Score=74.55  Aligned_cols=47  Identities=17%  Similarity=0.167  Sum_probs=34.4

Q ss_pred             ccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          196 LALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       196 l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.|-+...+.|++.+...-...          .+-+.|||++|.|||+||+++++..
T Consensus        22 ~~gR~~~~~~i~~~L~~~~~~~----------~~~v~I~GmgGiGKTtLA~~v~~~~   68 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEMCDLD----------SFFLFLHGRAGSGKSVIASQALSKS   68 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHHTTSS----------SEEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             eeCcHHHHHHHHHHHHhccCCC----------ceEEEEECCCCCCHHHHHHHHHHhh
Confidence            4567777777777665432221          2457899999999999999999874

>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=98.15  E-value=6.8e-06  Score=72.83  Aligned_cols=25  Identities=28%  Similarity=0.570  Sum_probs=22.8

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      ++|.||||+|||||+++|+..+..+
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            7899999999999999999988654

>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=98.05  E-value=1.3e-06  Score=75.76  Aligned_cols=33  Identities=39%  Similarity=0.658  Sum_probs=29.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      ++.++|.|||||||||+++++|..|++++++..
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            467999999999999999999999999998654

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.92  E-value=2.2e-06  Score=75.80  Aligned_cols=33  Identities=21%  Similarity=0.148  Sum_probs=29.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .+-++|.|||||||||||++||..++.+++...
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~   39 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFNTTSAWEY   39 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCEEECCT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCCeEeee
Confidence            468999999999999999999999998877543

>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=97.85  E-value=4.2e-06  Score=73.44  Aligned_cols=30  Identities=30%  Similarity=0.448  Sum_probs=27.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.|||||||||++++||..++++++++
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            578999999999999999999999998863

>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=97.73  E-value=8.9e-06  Score=71.77  Aligned_cols=31  Identities=35%  Similarity=0.399  Sum_probs=28.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      .++|.||||+||||+++++|..+|+++++++
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            5788999999999999999999999999863

>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=97.72  E-value=1.2e-05  Score=70.48  Aligned_cols=34  Identities=21%  Similarity=0.306  Sum_probs=30.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      ++-++|.||||+||||+++++|..++..++.++.
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            3578999999999999999999999999888753

>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=97.70  E-value=7.3e-06  Score=72.16  Aligned_cols=33  Identities=36%  Similarity=0.430  Sum_probs=29.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      +-++|.|||||||||+++++|..++.+++.++.
T Consensus         5 ~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~   37 (176)
T d1zp6a1           5 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   37 (176)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEecH
Confidence            458899999999999999999999999998864

>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=97.68  E-value=1.2e-05  Score=71.35  Aligned_cols=31  Identities=23%  Similarity=0.405  Sum_probs=28.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +.++|.||||+||||+++.+|..+|+++++.
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~   33 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDT   33 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEeh
Confidence            5688999999999999999999999999985

>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=97.63  E-value=1.1e-05  Score=70.95  Aligned_cols=24  Identities=46%  Similarity=0.798  Sum_probs=22.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |.++|+||||||||+|+++++..+
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            679999999999999999999988

>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=97.62  E-value=1.5e-05  Score=69.51  Aligned_cols=29  Identities=34%  Similarity=0.587  Sum_probs=25.9

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      +-++|.|||||||||+|+++|..++..++
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            46899999999999999999999987655

>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=97.61  E-value=1.2e-05  Score=70.97  Aligned_cols=30  Identities=37%  Similarity=0.517  Sum_probs=27.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      +.|.|+||+||||+++++|..+++++++++
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            566699999999999999999999999864

>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=97.60  E-value=1.7e-05  Score=69.57  Aligned_cols=31  Identities=35%  Similarity=0.461  Sum_probs=27.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +=++|.|||||||||+++++|..++..++..
T Consensus         7 ~iivl~G~~GsGKsT~a~~La~~l~~~~~~~   37 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASEVAHQLHAAFLDG   37 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEEG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeech
Confidence            4578899999999999999999999877654

>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=97.50  E-value=3.7e-05  Score=67.38  Aligned_cols=29  Identities=31%  Similarity=0.390  Sum_probs=25.0

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCC
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      |.+..++|.||||+||||+++++|..++.
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            33445999999999999999999999864

>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=97.46  E-value=4e-05  Score=68.40  Aligned_cols=62  Identities=16%  Similarity=0.136  Sum_probs=40.8

Q ss_pred             CCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhc-CCCeEEEEcCcc
Q 009640          226 AWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQT-TNRSIIVIEDID  289 (530)
Q Consensus       226 ~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~-~~~sII~IDeID  289 (530)
                      +.+.-++|.|+||+||||+++.++..+++.++  +...+.+...+.+.+... .+...+|||...
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~~~~~~i--~~D~~~~~~~~~~~~~~~l~~g~~vIiD~t~   74 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHV--NRDTLGSWQRCVSSCQAALRQGKRVVIDNTN   74 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGGGTCEEE--EHHHHCSHHHHHHHHHHHHHTTCCEEEESCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhcCCEEE--chHHHHHHHHHHHHHHHHHHCCCCceeeCcC
Confidence            44567899999999999999999988876554  444444444444444433 333445566444

>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=97.43  E-value=0.00031  Score=67.07  Aligned_cols=60  Identities=18%  Similarity=0.253  Sum_probs=43.0

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDC  290 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~  290 (530)
                      +.+.+..+.|||||+||||+++.+|+..+|.- ..++-+  .+.-    -|.......|+++||.+.
T Consensus       100 ~~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~~-~~~~~~--~~~f----~l~~l~~k~~~~~~e~~~  159 (267)
T d1u0ja_         100 KFGKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWT--NENF----PFNDCVDKMVIWWEEGKM  159 (267)
T ss_dssp             CSTTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTT--CSSC----TTGGGSSCSEEEECSCCE
T ss_pred             CCCccEEEEEEcCCCCCHHHHHHHHHHHhcch-hhcccc--CCCc----cccccCCCEEEEEeCCCc
Confidence            34677889999999999999999999999643 222211  1111    245567788999999874

>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=97.42  E-value=1.2e-05  Score=73.43  Aligned_cols=61  Identities=20%  Similarity=0.341  Sum_probs=43.8

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCccCChHHHHHHHHhcCCCeEEEEcCccc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTKVTDNSELRALLLQTTNRSIIVIEDIDC  290 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~~~~~~~L~~l~~~~~~~sII~IDeID~  290 (530)
                      |.|.++.++|||||+||||+++.++++.++-.+  ++...-.++    =.|..+....|+++||+-.
T Consensus        49 ~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~v--is~~N~~s~----F~Lq~l~~~kv~l~dD~t~  109 (205)
T d1tuea_          49 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAV--ISFVNSTSH----FWLEPLTDTKVAMLDDATT  109 (205)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEE--CCCCCSSSC----GGGGGGTTCSSEEEEEECH
T ss_pred             CCCCceEEEEECCCCccHHHHHHHHHHHhCCEE--EeccCCCCC----cccccccCCeEEEEecccc
Confidence            567789999999999999999999999996433  232221111    2344556678889999744

>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=97.38  E-value=5.2e-05  Score=67.26  Aligned_cols=29  Identities=21%  Similarity=0.315  Sum_probs=26.5

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.||..+|+..++.
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            78999999999999999999999887764

>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=97.37  E-value=5.4e-05  Score=68.19  Aligned_cols=31  Identities=23%  Similarity=0.339  Sum_probs=27.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      |.-++|.||||+||||+|+.||.++|+..++
T Consensus         6 p~iI~i~G~pGSGKsT~a~~La~~~g~~~i~   36 (194)
T d1qf9a_           6 PNVVFVLGGPGSGKGTQCANIVRDFGWVHLS   36 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHCCceEc
Confidence            4568999999999999999999999987655

>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=97.35  E-value=3.7e-05  Score=69.17  Aligned_cols=31  Identities=16%  Similarity=0.203  Sum_probs=27.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      --++|.||||+||||+++.||..+++..++.
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~~~~~is~   34 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKYQLAHISA   34 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHCCcEEeh
Confidence            4589999999999999999999999887643

>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=97.33  E-value=6.4e-05  Score=66.97  Aligned_cols=30  Identities=33%  Similarity=0.512  Sum_probs=26.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .++|.|||||||||+++.||..+|+..+++
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            368899999999999999999999887764

>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=97.32  E-value=5.1e-05  Score=66.37  Aligned_cols=26  Identities=31%  Similarity=0.378  Sum_probs=22.9

Q ss_pred             ce--EEEECCCCCChhHHHHHHHHHcCC
Q 009640          229 RG--YLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       229 rG--~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      +|  ++|.|+||+||||+++++|..|+.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            55  778899999999999999999853

>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=97.28  E-value=8.9e-05  Score=66.51  Aligned_cols=30  Identities=30%  Similarity=0.573  Sum_probs=26.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.||||+||||+++.||..+|+..++.
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            367789999999999999999999887664

>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=97.23  E-value=8.9e-05  Score=66.86  Aligned_cols=31  Identities=16%  Similarity=0.313  Sum_probs=27.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      .-++|.||||+||||+|+.||..+|+..++.
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            4578899999999999999999998877663

>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=97.20  E-value=0.00011  Score=65.48  Aligned_cols=29  Identities=21%  Similarity=0.303  Sum_probs=26.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+|+.||..+++..++.
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            68899999999999999999999887763

>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=97.19  E-value=0.0001  Score=67.20  Aligned_cols=29  Identities=38%  Similarity=0.594  Sum_probs=26.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      -+.+.||||+||||+++.||+.+|++.++
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            57788999999999999999999988765

>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=97.17  E-value=0.00012  Score=66.04  Aligned_cols=32  Identities=22%  Similarity=0.361  Sum_probs=27.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++-++|.||||+||||+++.||..+|+..++.
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~is~   39 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   39 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeeEec
Confidence            35688999999999999999999998776553

>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=97.17  E-value=2.5e-05  Score=69.82  Aligned_cols=29  Identities=28%  Similarity=0.424  Sum_probs=24.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      -++|.|+||+||||+|+++|..++..+++
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~~~~~   49 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVCHGIP   49 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCC
Confidence            36688999999999999999998654443

>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=97.17  E-value=0.00012  Score=66.11  Aligned_cols=30  Identities=20%  Similarity=0.349  Sum_probs=26.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      -++|.||||+||||+++.||..+|+..+++
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            467889999999999999999999877654

>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=97.14  E-value=0.00013  Score=65.01  Aligned_cols=29  Identities=24%  Similarity=0.461  Sum_probs=25.7

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.||..+|...++.
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            67889999999999999999998776654

>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=97.10  E-value=0.00065  Score=62.67  Aligned_cols=37  Identities=19%  Similarity=0.156  Sum_probs=29.8

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      |+|...-++++||||+|||+|+..+|...   +..+..++
T Consensus        22 Gi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          22 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            56777789999999999999999998876   44555554

>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=97.10  E-value=0.00015  Score=64.96  Aligned_cols=29  Identities=24%  Similarity=0.417  Sum_probs=25.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      -++|.||||+||||.|+.||..+|+..++
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            47899999999999999999999877654

>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=97.08  E-value=0.00015  Score=64.28  Aligned_cols=29  Identities=17%  Similarity=0.225  Sum_probs=26.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      ++|.||||+||||+++.||..+++..++.
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            67899999999999999999999887763

>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=97.03  E-value=0.00015  Score=61.94  Aligned_cols=24  Identities=33%  Similarity=0.365  Sum_probs=20.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +-++|+||||+||||+|++++...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            457899999999999999987654

>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=97.01  E-value=0.00019  Score=65.60  Aligned_cols=28  Identities=29%  Similarity=0.478  Sum_probs=25.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      +-+.||||+||||+|+.||.++|+..++
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            4467999999999999999999998766

>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=96.90  E-value=0.00092  Score=67.38  Aligned_cols=85  Identities=18%  Similarity=0.294  Sum_probs=56.6

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCCCce-EEEECCCCCChhHHHHHHHHHcC---CcEEEEecC-c--
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAWKRG-YLLYGPPGSGKSSLIAAMANYLC---YDVYDLELT-K--  263 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~~rG-~LL~GPPGTGKTsLa~AiA~~l~---~~i~~l~l~-~--  263 (530)
                      .++++++..+...+.+.+    .+..           ++| +|+.||+|+||||++.++-+++.   .+++.++-. +  
T Consensus       135 ~~l~~LG~~~~~~~~l~~----l~~~-----------~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~  199 (401)
T d1p9ra_         135 LDLHSLGMTAHNHDNFRR----LIKR-----------PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFD  199 (401)
T ss_dssp             CCGGGSCCCHHHHHHHHH----HHTS-----------SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSC
T ss_pred             hhhhhhcccHHHHHHHHH----HHhh-----------hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccc
Confidence            468899888876665544    2332           345 67789999999999999999873   556666411 0  


Q ss_pred             ---c-------CChHHHHHHHHhc--CCCeEEEEcCccc
Q 009640          264 ---V-------TDNSELRALLLQT--TNRSIIVIEDIDC  290 (530)
Q Consensus       264 ---~-------~~~~~L~~l~~~~--~~~sII~IDeID~  290 (530)
                         +       .........+..+  ..|.||+|.||-.
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               1       0111244444443  6899999999974

>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=96.85  E-value=0.0011  Score=60.15  Aligned_cols=37  Identities=19%  Similarity=0.167  Sum_probs=27.1

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH----cCCcEEEEe
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY----LCYDVYDLE  260 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~----l~~~i~~l~  260 (530)
                      |+|...-++|+||||+|||+|+..+|..    -+..++.++
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s   62 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   62 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccc
Confidence            5677778999999999999998765532    244555554

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.82  E-value=0.0014  Score=62.42  Aligned_cols=69  Identities=19%  Similarity=0.268  Sum_probs=45.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc---------------------CChHHHHHH---HHh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV---------------------TDNSELRAL---LLQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~---------------------~~~~~L~~l---~~~  276 (530)
                      |+|..+-..|+||||||||+++..+|...   +..++.++...-                     .+.+++.++   +..
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            67777889999999999999986665443   555565553321                     112222222   333


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||-+.++.
T Consensus       136 ~~~~~liIiDSi~al~  151 (269)
T d1mo6a1         136 SGALDIVVIDSVAALV  151 (269)
T ss_dssp             TTCEEEEEEECSTTCC
T ss_pred             cCCCCEEEEecccccc
Confidence            4678899999998875

>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=96.82  E-value=0.0014  Score=62.34  Aligned_cols=69  Identities=16%  Similarity=0.280  Sum_probs=45.6

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc---------------------CChHHHHHH---HHh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV---------------------TDNSELRAL---LLQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~---------------------~~~~~L~~l---~~~  276 (530)
                      |+|..+-..+|||||||||+|+..+|...   +..++.++...-                     .+.++..++   +.+
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            55666778999999999999998877655   555666653321                     112222222   333


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||=+.++.
T Consensus       133 ~~~~~liIiDSi~al~  148 (268)
T d1xp8a1         133 SGAIDVVVVDSVAALT  148 (268)
T ss_dssp             TTCCSEEEEECTTTCC
T ss_pred             cCCCcEEEEecccccc
Confidence            4568899988888874

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=96.81  E-value=0.00048  Score=65.55  Aligned_cols=69  Identities=17%  Similarity=0.245  Sum_probs=44.9

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc---------------------CChHHHHH---HHHh
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV---------------------TDNSELRA---LLLQ  276 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~---------------------~~~~~L~~---l~~~  276 (530)
                      |+|..+-.+|+||||||||+++-.+|...   +..++.++...-                     .+.++..+   .+.+
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            56666778999999999999998777655   455555543221                     11222222   2333


Q ss_pred             cCCCeEEEEcCccchh
Q 009640          277 TTNRSIIVIEDIDCSV  292 (530)
Q Consensus       277 ~~~~sII~IDeID~~~  292 (530)
                      ...+.+||||=|.+++
T Consensus       130 ~~~~~liViDSi~al~  145 (263)
T d1u94a1         130 SGAVDVIVVDSVAALT  145 (263)
T ss_dssp             HTCCSEEEEECGGGCC
T ss_pred             cCCCCEEEEECccccc
Confidence            4678899999888764

>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=96.79  E-value=0.00049  Score=59.47  Aligned_cols=31  Identities=16%  Similarity=0.121  Sum_probs=25.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      -+.+.|+||||||||+.+|++++   |+.+..+.
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            47899999999999999999987   55554443

>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=96.78  E-value=0.00016  Score=65.14  Aligned_cols=26  Identities=23%  Similarity=0.452  Sum_probs=22.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      =++|.|+||+||||++++||.+++..
T Consensus         4 li~l~GlpgsGKSTla~~L~~~l~~~   29 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTRYLNFI   29 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            47899999999999999999988543

>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=96.77  E-value=0.0003  Score=61.58  Aligned_cols=27  Identities=19%  Similarity=0.300  Sum_probs=23.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +-+++.||||+||||+++.|+..++..
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            457899999999999999999988543

>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=96.76  E-value=0.001  Score=55.90  Aligned_cols=35  Identities=31%  Similarity=0.309  Sum_probs=28.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEEecCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDLELTK  263 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l~~  263 (530)
                      +..+|.+|+|+|||.++..++...+..++.+-.+.
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~~   43 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSV   43 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESCH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcChH
Confidence            46789999999999999877778888877775543

>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=96.68  E-value=0.0079  Score=55.75  Aligned_cols=63  Identities=21%  Similarity=0.286  Sum_probs=42.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc-----CC------------cEEEEecC----------ccC-ChHHHHHHHHhcCC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL-----CY------------DVYDLELT----------KVT-DNSELRALLLQTTN  279 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l-----~~------------~i~~l~l~----------~~~-~~~~L~~l~~~~~~  279 (530)
                      .+.++|+||...|||++++++|--.     |.            +-+.....          .+. .-.++..++..+..
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            4789999999999999999988643     21            11111111          111 12346677888899


Q ss_pred             CeEEEEcCccc
Q 009640          280 RSIIVIEDIDC  290 (530)
Q Consensus       280 ~sII~IDeID~  290 (530)
                      +|+|+|||+-+
T Consensus       121 ~sLvliDE~~~  131 (234)
T d1wb9a2         121 YSLVLMDEIGR  131 (234)
T ss_dssp             TEEEEEESCCC
T ss_pred             ccEEeeccccc
Confidence            99999999975

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.62  E-value=0.003  Score=57.75  Aligned_cols=36  Identities=22%  Similarity=0.177  Sum_probs=27.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      |.-++|.||+|+||||.+.-||..+   +..+.-+....
T Consensus         9 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt   47 (211)
T d2qy9a2           9 PFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDT   47 (211)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeccc
Confidence            3468899999999999999999877   45555554433

>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=96.57  E-value=0.0027  Score=61.98  Aligned_cols=62  Identities=16%  Similarity=0.322  Sum_probs=41.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC--CcEEEEec-Ccc-------------CChHHHHHHHHhc--CCCeEEEEcCcc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC--YDVYDLEL-TKV-------------TDNSELRALLLQT--TNRSIIVIEDID  289 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~--~~i~~l~l-~~~-------------~~~~~L~~l~~~~--~~~sII~IDeID  289 (530)
                      ++++|+.||+|+||||+++|++.+..  ..++.++- .++             ..+-.+.+++..+  ..|..|++.|+=
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            46899999999999999999999883  33444421 110             1112244444443  689999999985

>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=96.55  E-value=0.0033  Score=57.32  Aligned_cols=36  Identities=25%  Similarity=0.277  Sum_probs=27.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV  264 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~  264 (530)
                      +-++|.||+|+||||.+.-||..+   +..+.-+.+...
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            346789999999999999999877   566665554443

>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=96.49  E-value=0.0017  Score=59.84  Aligned_cols=29  Identities=28%  Similarity=0.340  Sum_probs=25.2

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |+|..+-++++||||||||+|+..+|...
T Consensus        32 Glp~G~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          32 GIETQAITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            57777779999999999999999888765

>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=96.48  E-value=0.0019  Score=56.39  Aligned_cols=61  Identities=26%  Similarity=0.372  Sum_probs=44.7

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCC--------------------cEEEEecCccCChHHHHHH-HHh-cCCCeEEEEcCc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCY--------------------DVYDLELTKVTDNSELRAL-LLQ-TTNRSIIVIEDI  288 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~--------------------~i~~l~l~~~~~~~~L~~l-~~~-~~~~sII~IDeI  288 (530)
                      ++|+|+=|+|||++++++|+.+|.                    .++.+++-.+.+..++..+ +.. ....+|++||=-
T Consensus        36 i~L~G~LGaGKTtfvr~~~~~lg~~~~V~SPTF~l~~~Y~~~~~~i~H~DlYRl~~~~El~~lg~~e~~~~~~i~~IEWp  115 (158)
T d1htwa_          36 VYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWS  115 (158)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTCCSCCCCCTTTCEEEEEETTEEEEEEECTTCSCTTHHHHSTHHHHHSSSCEEEEESG
T ss_pred             EEEecCCCccHHHHHHHHHhhcccccccCCCceEEEEeeccCCceEEEEEEeccCChhhhhhCCchhHhccCCEEEEECc
Confidence            789999999999999999999963                    3455556666666666554 333 255689999976


Q ss_pred             cch
Q 009640          289 DCS  291 (530)
Q Consensus       289 D~~  291 (530)
                      |.+
T Consensus       116 e~~  118 (158)
T d1htwa_         116 EKG  118 (158)
T ss_dssp             GGG
T ss_pred             hhh
Confidence            655

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.48  E-value=0.0031  Score=57.52  Aligned_cols=36  Identities=28%  Similarity=0.294  Sum_probs=27.3

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      ++-++|.||+|+||||.+.-||.++   |..+.-+..-.
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            4568899999999999999999877   45555444433

>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=96.46  E-value=0.00068  Score=60.29  Aligned_cols=29  Identities=17%  Similarity=0.157  Sum_probs=25.3

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |++..+-++++||||+|||+|+..+|...
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            56777789999999999999999998765

>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=96.44  E-value=0.00041  Score=60.98  Aligned_cols=28  Identities=29%  Similarity=0.349  Sum_probs=23.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      =++|.|+||+||||+++.+|..|+...+
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~~~   30 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQGI   30 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence            3678999999999999999999855433

>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=96.40  E-value=0.0028  Score=58.13  Aligned_cols=29  Identities=17%  Similarity=0.093  Sum_probs=25.7

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHc
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      |+|..+-++++||||||||+++..+|...
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            67777789999999999999999998754

>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=96.40  E-value=0.00053  Score=62.78  Aligned_cols=28  Identities=29%  Similarity=0.222  Sum_probs=24.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      |+|..+-++|+||||||||+|+..+|..
T Consensus        30 Gi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          30 GVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             SEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            5777788999999999999999888754

>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=96.39  E-value=0.0038  Score=58.43  Aligned_cols=25  Identities=32%  Similarity=0.343  Sum_probs=21.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      ..-.+|+|+||+|||+|+..+|..+
T Consensus        29 g~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          29 GTVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4557899999999999999888753

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=96.28  E-value=0.0018  Score=60.56  Aligned_cols=25  Identities=28%  Similarity=0.408  Sum_probs=22.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+-+.||+|+|||||+++|+..+.
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            4488999999999999999999873

>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=96.26  E-value=0.0071  Score=55.25  Aligned_cols=36  Identities=17%  Similarity=0.165  Sum_probs=26.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTK  263 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~  263 (530)
                      |.-++|.||+|+||||.++-||..+   +..+--+....
T Consensus        11 p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~Dt   49 (213)
T d1vmaa2          11 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADT   49 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeecc
Confidence            3457889999999999999999776   45554444433

>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=96.20  E-value=0.019  Score=48.18  Aligned_cols=21  Identities=19%  Similarity=0.341  Sum_probs=19.1

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|+||+|||||+..++..
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            689999999999999999864

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.20  E-value=0.0017  Score=59.31  Aligned_cols=32  Identities=31%  Similarity=0.388  Sum_probs=26.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc----CCcEEEEec
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL----CYDVYDLEL  261 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l----~~~i~~l~l  261 (530)
                      -++|.|.||+||||++++++..+    +.+++.++.
T Consensus        26 vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldg   61 (208)
T d1m7ga_          26 TIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDG   61 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcc
Confidence            48899999999999999999766    566666653

>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=96.12  E-value=0.0048  Score=50.87  Aligned_cols=31  Identities=19%  Similarity=0.122  Sum_probs=20.3

Q ss_pred             ceEEEECCCCCChhHHHH-HHHHHc---CCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIA-AMANYL---CYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~-AiA~~l---~~~i~~l  259 (530)
                      +.++|++|||+|||..+- ++...+   +..++.+
T Consensus         8 ~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~   42 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVL   42 (140)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEE
T ss_pred             CcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeee
Confidence            568999999999996553 433333   4444444

>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=96.12  E-value=0.0034  Score=57.39  Aligned_cols=34  Identities=21%  Similarity=0.297  Sum_probs=21.6

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEec
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLEL  261 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l  261 (530)
                      |.-++|.||+|+||||.++-||..+   +..+--+..
T Consensus        12 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~   48 (211)
T d1j8yf2          12 PYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGA   48 (211)
T ss_dssp             SEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEEC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEe
Confidence            3457889999999999999998876   445444443

>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=96.04  E-value=0.002  Score=57.36  Aligned_cols=28  Identities=29%  Similarity=0.471  Sum_probs=24.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      |.++|.||+|+|||+|++.++++....+
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            5689999999999999999999886544

>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=96.03  E-value=0.0021  Score=60.64  Aligned_cols=25  Identities=28%  Similarity=0.461  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+.+.||+|+|||||++.|+..+.
T Consensus        45 e~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHhcCC
Confidence            4588999999999999999998763

>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=95.99  E-value=0.0029  Score=59.51  Aligned_cols=25  Identities=28%  Similarity=0.505  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+-|.||+|+|||||++.|+..+.
T Consensus        42 e~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             CEEEEECCCCChHHHHHHHHhcccC
Confidence            4588999999999999999998773

>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=95.96  E-value=0.0022  Score=60.34  Aligned_cols=25  Identities=40%  Similarity=0.517  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+-|.||.|+|||||++.|+..+.
T Consensus        41 e~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcccC
Confidence            3478999999999999999998773

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.94  E-value=0.0024  Score=57.17  Aligned_cols=28  Identities=32%  Similarity=0.463  Sum_probs=24.3

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      |.+.|.||+|+|||++++.++..+.-.+
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~~~~~   28 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEHSSIF   28 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTTTE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCCce
Confidence            4588999999999999999999886554

>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=95.94  E-value=0.0068  Score=52.42  Aligned_cols=22  Identities=14%  Similarity=0.342  Sum_probs=19.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -++|.|.||+|||||+.++.+.
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999764

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.83  E-value=0.0034  Score=55.24  Aligned_cols=24  Identities=25%  Similarity=0.263  Sum_probs=21.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCC
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      +-+.||+|+||||+|++|+..++.
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcc
Confidence            558999999999999999987743

>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=95.73  E-value=0.017  Score=53.11  Aligned_cols=62  Identities=19%  Similarity=0.332  Sum_probs=41.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc-----CC----cEEEEe--------cCc---cC--------ChHHHHHHHHhcCCC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL-----CY----DVYDLE--------LTK---VT--------DNSELRALLLQTTNR  280 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l-----~~----~i~~l~--------l~~---~~--------~~~~L~~l~~~~~~~  280 (530)
                      +.++|+||...|||++++++|--.     |.    .-..+.        ...   +.        .-.++..++..+..+
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            468999999999999999887543     21    111221        111   10        013466778888999


Q ss_pred             eEEEEcCccc
Q 009640          281 SIIVIEDIDC  290 (530)
Q Consensus       281 sII~IDeID~  290 (530)
                      |+|+|||+-.
T Consensus       116 sLvliDE~~~  125 (224)
T d1ewqa2         116 SLVLLDEVGR  125 (224)
T ss_dssp             EEEEEESTTT
T ss_pred             cEEeeccccc
Confidence            9999999975

>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=95.59  E-value=0.0049  Score=53.04  Aligned_cols=22  Identities=18%  Similarity=0.418  Sum_probs=19.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|+||+|||||+..+.+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            3789999999999999998763

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.49  E-value=0.0074  Score=57.54  Aligned_cols=25  Identities=32%  Similarity=0.413  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .-+-|.||.|+|||||+++|+..+.
T Consensus        63 e~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHhCCCc
Confidence            3478999999999999999999873

>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=95.48  E-value=0.0059  Score=52.81  Aligned_cols=31  Identities=19%  Similarity=0.239  Sum_probs=25.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      -+-+.|+||+|||||+..++.+|   |+.+..+.
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            45689999999999999999987   55565553

>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=95.46  E-value=0.003  Score=57.41  Aligned_cols=30  Identities=23%  Similarity=0.190  Sum_probs=25.5

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHHcC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      |++...-++|+||||+|||+++..+|..+-
T Consensus        30 Gl~~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          30 GLESQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            466666799999999999999999997763

>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=95.27  E-value=0.0073  Score=59.62  Aligned_cols=22  Identities=32%  Similarity=0.600  Sum_probs=17.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +-.++.||||||||+++..+..
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~  185 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLA  185 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCceehHHHHHH
Confidence            4578999999999998865443

>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=95.23  E-value=0.0047  Score=54.41  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcC
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      +=++|.||||+||||+++.++....
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            3478999999999999999998874

>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=95.14  E-value=0.0072  Score=54.86  Aligned_cols=32  Identities=28%  Similarity=0.266  Sum_probs=25.3

Q ss_pred             ceEEE--ECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          229 RGYLL--YGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       229 rG~LL--~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      ||.|+  .||.|+||||+++.+++.|   |+++..+.
T Consensus         2 rG~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           2 RGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeeEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            56554  5999999999999999987   56665553

>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=95.09  E-value=0.0068  Score=53.67  Aligned_cols=30  Identities=23%  Similarity=0.290  Sum_probs=24.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      .+|+||.||+|+|||+++.++... |..++.
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            479999999999999999988765 665543

>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=94.97  E-value=0.037  Score=49.20  Aligned_cols=23  Identities=35%  Similarity=0.447  Sum_probs=17.2

Q ss_pred             ceEEEECCCCCChhHHH-HHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLI-AAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa-~AiA~~  251 (530)
                      +.+++.+|+|+|||..+ .+++..
T Consensus        41 ~~~il~apTGsGKT~~a~l~i~~~   64 (202)
T d2p6ra3          41 KNLLLAMPTAAGKTLLAEMAMVRE   64 (202)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCchhHHHHHHHHHH
Confidence            56899999999999875 334433

>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=94.79  E-value=0.071  Score=48.26  Aligned_cols=52  Identities=13%  Similarity=0.144  Sum_probs=33.2

Q ss_pred             CCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCCC---CceEEEECCCCCChhHHH
Q 009640          191 STFETLALEPQLKKQITEDLTAFANGKEFYHRVGRAW---KRGYLLYGPPGSGKSSLI  245 (530)
Q Consensus       191 ~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~~---~rG~LL~GPPGTGKTsLa  245 (530)
                      .+|+++...+.+.+.|.+ .  -+..+...+...+|.   .+.+++..|+|||||...
T Consensus        12 ~sF~~l~L~~~l~~~L~~-~--g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlay   66 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYA-Y--GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF   66 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHH-H--TCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHH
T ss_pred             CCHHHCCCCHHHHHHHHH-C--CCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhh
Confidence            489999888887776643 1  122222223322221   367999999999999743

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.75  E-value=0.012  Score=53.89  Aligned_cols=31  Identities=29%  Similarity=0.457  Sum_probs=21.2

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc---CCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL---CYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l  259 (530)
                      +.+++.+|+|+|||..+...+-++   +..++.+
T Consensus        59 ~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv   92 (237)
T d1gkub1          59 ESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVI   92 (237)
T ss_dssp             CCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEE
T ss_pred             CCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEE
Confidence            578999999999997655444333   4445444

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.75  E-value=0.0079  Score=54.14  Aligned_cols=25  Identities=32%  Similarity=0.339  Sum_probs=22.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +-+.||+|+||||++++++..++..
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~~~   29 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLGQN   29 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhchh
Confidence            4578999999999999999998754

>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=94.73  E-value=0.04  Score=47.09  Aligned_cols=21  Identities=29%  Similarity=0.447  Sum_probs=19.3

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|+||+|||+|+..+.+.
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999874

>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=94.66  E-value=0.021  Score=49.06  Aligned_cols=21  Identities=33%  Similarity=0.646  Sum_probs=19.0

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|.||+|||+|+..+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999999863

>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=94.61  E-value=0.034  Score=47.83  Aligned_cols=20  Identities=30%  Similarity=0.484  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.||+|||+|+..+.+
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999875

>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=94.60  E-value=0.014  Score=53.10  Aligned_cols=30  Identities=33%  Similarity=0.621  Sum_probs=23.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHc--CCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL--CYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l--~~~i~~l~  260 (530)
                      +++.||||+|||||+.++..++  +..+..++
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            5789999999999999998766  44555554

>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=94.59  E-value=0.018  Score=49.72  Aligned_cols=21  Identities=33%  Similarity=0.474  Sum_probs=19.1

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|.||+|||+|+..+.+.
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            689999999999999999853

>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=94.58  E-value=0.033  Score=47.65  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=19.3

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|+||+|||||+..+.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999999874

>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=94.52  E-value=0.0085  Score=56.56  Aligned_cols=35  Identities=26%  Similarity=0.483  Sum_probs=22.3

Q ss_pred             ceEEEECCCCCChhHHHHH-HHHHc---CC---cEEEEecCc
Q 009640          229 RGYLLYGPPGSGKSSLIAA-MANYL---CY---DVYDLELTK  263 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~A-iA~~l---~~---~i~~l~l~~  263 (530)
                      ..+|+.||||||||+++.. ++..+   +.   .+..+..+.
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            3589999999999986543 33322   32   455555543

>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=94.51  E-value=0.059  Score=46.21  Aligned_cols=21  Identities=33%  Similarity=0.580  Sum_probs=19.0

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -+++.|+||+|||||+.++.+
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999998855

>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=94.47  E-value=0.0097  Score=50.02  Aligned_cols=21  Identities=29%  Similarity=0.518  Sum_probs=19.2

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|+||+|||||+..+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999999874

>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=94.41  E-value=0.012  Score=51.73  Aligned_cols=28  Identities=25%  Similarity=0.306  Sum_probs=23.4

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDV  256 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i  256 (530)
                      .+|+||.||+|.|||+++.++... |..+
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~-g~~l   42 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR-GHRL   42 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeE
Confidence            479999999999999999888766 5543

>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=94.35  E-value=0.048  Score=47.16  Aligned_cols=20  Identities=40%  Similarity=0.685  Sum_probs=18.9

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +++.|+||+|||+|+.++.+
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999886

>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=94.30  E-value=0.011  Score=52.43  Aligned_cols=29  Identities=31%  Similarity=0.260  Sum_probs=23.9

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      .+|+||.||+|+|||+++.++... |..++
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~-G~~lv   43 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK-NHLFV   43 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT-TCEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCcee
Confidence            479999999999999999888653 65544

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.29  E-value=0.055  Score=51.32  Aligned_cols=32  Identities=28%  Similarity=0.293  Sum_probs=24.8

Q ss_pred             EECCCCCChhHHHHHHHHHc------CCcEEEEecCcc
Q 009640          233 LYGPPGSGKSSLIAAMANYL------CYDVYDLELTKV  264 (530)
Q Consensus       233 L~GPPGTGKTsLa~AiA~~l------~~~i~~l~l~~~  264 (530)
                      |.||||+|||||+..|...+      +..+..+++.++
T Consensus        32 i~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~Ddf   69 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDF   69 (286)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGG
T ss_pred             eECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCC
Confidence            68999999999999987765      345666666554

>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=94.25  E-value=0.11  Score=46.16  Aligned_cols=49  Identities=24%  Similarity=0.238  Sum_probs=28.9

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhH
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSS  243 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTs  243 (530)
                      +|+++...+++.+.|.+.  . ...+...+...+|   -.+.+++.+|+|||||.
T Consensus         2 sF~~l~L~~~l~~~L~~~--g-~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTl   53 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEA--G-FEKPSPIQEEAIPVAITGRDILARAKNGTGKTA   53 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHT--T-CCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHH
T ss_pred             ChHHcCCCHHHHHHHHHC--C-CCCCCHHHHHHHHHHHcCCCEEEecCCcchhhh
Confidence            688888888776665542  1 1111111111111   13579999999999995

>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=94.17  E-value=0.012  Score=52.44  Aligned_cols=23  Identities=30%  Similarity=0.353  Sum_probs=20.7

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      |.++|.|+||+|||||+.++.+.
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            47899999999999999999863

>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=94.10  E-value=0.013  Score=49.65  Aligned_cols=22  Identities=23%  Similarity=0.431  Sum_probs=19.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -++|.|+||+|||||+.++.+.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999764

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.07  E-value=0.02  Score=50.45  Aligned_cols=26  Identities=15%  Similarity=0.345  Sum_probs=22.8

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      ++.++|.||+|+|||+|++.++....
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            46789999999999999999997753

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=94.07  E-value=0.016  Score=50.98  Aligned_cols=28  Identities=39%  Similarity=0.490  Sum_probs=23.4

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +-++|++|+||||+|..+ .+.|+++++.
T Consensus         6 IgitG~~gSGKstva~~l-~~~g~~~~~~   33 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALL-RSWGYPVLDL   33 (191)
T ss_dssp             EEEEECTTSCHHHHHHHH-HHTTCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHH-HHCCCeEEEc
Confidence            447899999999999998 5688888764

>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=94.03  E-value=0.03  Score=48.43  Aligned_cols=21  Identities=29%  Similarity=0.436  Sum_probs=19.1

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -++|.|.||+|||+|+..+.+
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998876

>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=93.94  E-value=0.13  Score=46.54  Aligned_cols=52  Identities=21%  Similarity=0.300  Sum_probs=32.6

Q ss_pred             CCCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhH
Q 009640          189 HPSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSS  243 (530)
Q Consensus       189 ~~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTs  243 (530)
                      ...+|+++...+.+.+.|.+.  .| ..+-..+...+|   ..+.++...|+|||||.
T Consensus        15 ~~~sF~~l~L~~~l~~~L~~~--g~-~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          15 VTPTFDTMGLREDLLRGIYAY--GF-EKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHH--TC-CSCCHHHHHHHHHHHTTCCEEEECCTTSSHHH
T ss_pred             CCCCHHHCCCCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHCCCCeEEEcCcchhhhh
Confidence            344899999888877766541  11 222222222221   14679999999999996

>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=93.90  E-value=0.029  Score=48.42  Aligned_cols=20  Identities=35%  Similarity=0.732  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.||+|||+|+..+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999875

>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=93.87  E-value=0.017  Score=51.11  Aligned_cols=24  Identities=29%  Similarity=0.571  Sum_probs=21.5

Q ss_pred             CceEEEECCCCCChhHHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ...++|.|+||+|||||+.++.+.
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            357899999999999999999875

>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=93.86  E-value=0.17  Score=44.16  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=17.0

Q ss_pred             ceEEEECCCCCChhHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +..|+.+|.|+|||.++..++.
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEeCCCCcHHHHHHHHHH
Confidence            4578999999999986555554

>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=93.74  E-value=0.032  Score=51.99  Aligned_cols=39  Identities=21%  Similarity=0.118  Sum_probs=28.4

Q ss_pred             cCCCCceEEEECCCCCChhHHHHHHHHH----cCCcEEEEecC
Q 009640          224 GRAWKRGYLLYGPPGSGKSSLIAAMANY----LCYDVYDLELT  262 (530)
Q Consensus       224 g~~~~rG~LL~GPPGTGKTsLa~AiA~~----l~~~i~~l~l~  262 (530)
                      |..+..-++|.|+||+|||+++..+|..    .+.++..+++.
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            3444445889999999999998888743    26677766654

>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=93.62  E-value=0.018  Score=49.95  Aligned_cols=21  Identities=33%  Similarity=0.700  Sum_probs=18.9

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|+||+|||+|+..+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            688999999999999998764

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.59  E-value=0.023  Score=51.24  Aligned_cols=24  Identities=42%  Similarity=0.591  Sum_probs=21.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      =++|.||+|+|||+|++.+.....
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            378899999999999999998865

>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=93.56  E-value=0.063  Score=45.85  Aligned_cols=21  Identities=29%  Similarity=0.468  Sum_probs=19.1

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|.+|+|||+|+..+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            789999999999999998764

>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=93.40  E-value=0.014  Score=50.23  Aligned_cols=21  Identities=19%  Similarity=0.485  Sum_probs=18.7

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -++|.|+||+|||||+.++..
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            389999999999999999854

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=93.31  E-value=0.013  Score=50.83  Aligned_cols=22  Identities=18%  Similarity=0.327  Sum_probs=19.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|+||+|||||+..+.+.
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999998753

>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=93.21  E-value=0.037  Score=49.03  Aligned_cols=30  Identities=23%  Similarity=0.377  Sum_probs=25.0

Q ss_pred             EEEECCCCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +.+.|+.|+||||+++.++..|   |+++..+.
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~   35 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            4678999999999999999987   66766654

>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=93.20  E-value=0.037  Score=47.10  Aligned_cols=20  Identities=30%  Similarity=0.502  Sum_probs=18.4

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +++.|.+|+|||+|+..+.+
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68899999999999999885

>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=0.022  Score=54.13  Aligned_cols=24  Identities=25%  Similarity=0.473  Sum_probs=17.6

Q ss_pred             ceEEEECCCCCChhHHHH-HHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIA-AMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~-AiA~~l  252 (530)
                      ..+|+.||||||||+++. .+|..+
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~ll   49 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYLM   49 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEecCCccHHHHHHHHHHHHH
Confidence            458999999999997554 454443

>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=93.14  E-value=0.018  Score=49.69  Aligned_cols=21  Identities=33%  Similarity=0.599  Sum_probs=19.0

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      .+.|.|+||+|||||+.++.+
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

>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=93.12  E-value=0.016  Score=50.30  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=19.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      .++|.|+||+|||||+.+|.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999763

>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=93.05  E-value=0.34  Score=42.99  Aligned_cols=55  Identities=16%  Similarity=0.060  Sum_probs=31.6

Q ss_pred             CcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC----CCceEEEECCCCCChhHHHHHHH
Q 009640          192 TFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA----WKRGYLLYGPPGSGKSSLIAAMA  249 (530)
Q Consensus       192 ~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~----~~rG~LL~GPPGTGKTsLa~AiA  249 (530)
                      +|+++...+++.+.+.+ .  -...+...+...+|    .+..+++..|+|+|||......+
T Consensus         5 sf~~l~l~~~l~~~l~~-~--g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1           5 NFNELNLSDNILNAIRN-K--GFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             CGGGSSCCHHHHHHHHH-H--TCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHH
T ss_pred             CHHHcCCCHHHHHHHHH-C--CCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccc
Confidence            68888777776665543 1  01122112221111    13478999999999998664433

>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=93.00  E-value=0.036  Score=47.65  Aligned_cols=21  Identities=43%  Similarity=0.687  Sum_probs=18.5

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|+||+|||+|+..+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            688999999999999988653

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=92.99  E-value=0.025  Score=48.34  Aligned_cols=22  Identities=27%  Similarity=0.344  Sum_probs=19.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -++|.|+||+|||+|+..+...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4788999999999999999764

>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=92.98  E-value=0.033  Score=50.03  Aligned_cols=28  Identities=43%  Similarity=0.459  Sum_probs=23.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +-|+|++|+||||+++.+. .+|+.+++.
T Consensus         6 IgitG~igSGKStv~~~l~-~~G~~vida   33 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFA-DLGINVIDA   33 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HTTCEEEEH
T ss_pred             EEEECCCcCCHHHHHHHHH-HCCCcEEEc
Confidence            4479999999999999885 789988875

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=92.92  E-value=0.016  Score=52.16  Aligned_cols=24  Identities=33%  Similarity=0.603  Sum_probs=21.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+.|.||.|+|||||++.|++.+.
T Consensus        29 i~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          29 VVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCChHHHHHHHHhcccc
Confidence            377999999999999999998774

>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=92.89  E-value=0.024  Score=48.86  Aligned_cols=20  Identities=30%  Similarity=0.604  Sum_probs=18.9

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|+||+|||+|+..+++
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999986

>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=92.87  E-value=0.063  Score=51.48  Aligned_cols=35  Identities=17%  Similarity=0.100  Sum_probs=26.7

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC-----CcEEEEecCcc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC-----YDVYDLELTKV  264 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~-----~~i~~l~l~~~  264 (530)
                      =+-+.||+|+||||+++.|+..|.     ..+..+++..+
T Consensus        82 iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F  121 (308)
T d1sq5a_          82 IISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             EEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeee
Confidence            355789999999999999999874     44555555544

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.82  E-value=0.028  Score=48.09  Aligned_cols=20  Identities=30%  Similarity=0.454  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|+||+|||+|+..+.+
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

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.77  E-value=0.028  Score=48.34  Aligned_cols=21  Identities=29%  Similarity=0.444  Sum_probs=19.2

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|+||+|||+|+..+.+.
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999999864

>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=92.74  E-value=0.055  Score=46.31  Aligned_cols=21  Identities=29%  Similarity=0.496  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|.||+|||+|+..+.+.
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999988763

>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=92.72  E-value=0.036  Score=49.58  Aligned_cols=28  Identities=29%  Similarity=0.343  Sum_probs=24.0

Q ss_pred             EEECCCCCChhHHHHHHHHHcCCcEEEEe
Q 009640          232 LLYGPPGSGKSSLIAAMANYLCYDVYDLE  260 (530)
Q Consensus       232 LL~GPPGTGKTsLa~AiA~~l~~~i~~l~  260 (530)
                      -++|++|+||||+++.+. .+|+.+++.+
T Consensus         6 gITG~igSGKStv~~~l~-~~G~~vidaD   33 (205)
T d1jjva_           6 GLTGGIGSGKTTIANLFT-DLGVPLVDAD   33 (205)
T ss_dssp             EEECSTTSCHHHHHHHHH-TTTCCEEEHH
T ss_pred             EEECCCCCCHHHHHHHHH-HCCCeEEEch
Confidence            379999999999999886 6899988764

>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=92.70  E-value=0.026  Score=50.51  Aligned_cols=22  Identities=23%  Similarity=0.401  Sum_probs=20.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +.+.|++|+||||+++.++..|
T Consensus         5 IviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           5 IVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            5678999999999999999987

>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=92.62  E-value=0.03  Score=48.15  Aligned_cols=21  Identities=29%  Similarity=0.585  Sum_probs=19.1

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|+||+|||+|+..+.+.
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            689999999999999999863

>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=92.44  E-value=0.022  Score=50.24  Aligned_cols=29  Identities=24%  Similarity=0.277  Sum_probs=24.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      =+.+-|+.|+||||+++.|+.+++...+.
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~~~~~~   39 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKNDICLL   39 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTTTEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEE
Confidence            36678999999999999999999765544

>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=92.39  E-value=0.025  Score=49.88  Aligned_cols=21  Identities=38%  Similarity=0.499  Sum_probs=19.2

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -+.|.|+||+|||||+.+|.+
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            389999999999999999975

>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=92.36  E-value=0.25  Score=44.17  Aligned_cols=52  Identities=13%  Similarity=0.139  Sum_probs=31.4

Q ss_pred             CCCcccccCChhhhHHHHHHHHHHHcChhhHhhhcCC---CCceEEEECCCCCChhHH
Q 009640          190 PSTFETLALEPQLKKQITEDLTAFANGKEFYHRVGRA---WKRGYLLYGPPGSGKSSL  244 (530)
Q Consensus       190 ~~~f~~l~~~~~~k~~i~~~l~~~l~~~~~y~~~g~~---~~rG~LL~GPPGTGKTsL  244 (530)
                      -.+|+++...+++.+.+.+ +  =...+...+...+|   ..+.+++..|+|||||..
T Consensus         9 ~~sF~~l~l~~~l~~~L~~-~--g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a   63 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFG-Y--GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT   63 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHH-H--TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             ccChhhCCCCHHHHHHHHH-C--CCCCCCHHHHHHHHHHHcCCCEEeecccccchhhh
Confidence            3478999887777666643 1  11222222222111   236799999999999983

>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=92.34  E-value=0.035  Score=48.03  Aligned_cols=20  Identities=35%  Similarity=0.644  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +++.|+||+|||||+..+.+
T Consensus         7 i~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999876

>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=92.33  E-value=0.027  Score=49.24  Aligned_cols=20  Identities=25%  Similarity=0.536  Sum_probs=18.4

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|+||+|||+|+..+.+
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            78899999999999999875

>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=92.28  E-value=0.027  Score=47.64  Aligned_cols=20  Identities=45%  Similarity=0.747  Sum_probs=18.4

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|+||+|||||+.++.+
T Consensus         4 I~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999999974

>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=92.23  E-value=0.036  Score=47.68  Aligned_cols=20  Identities=35%  Similarity=0.645  Sum_probs=18.4

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|+||+|||||+..+.+
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            68999999999999999875

>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=92.14  E-value=0.028  Score=54.55  Aligned_cols=23  Identities=35%  Similarity=0.596  Sum_probs=20.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+=+.||||+|||||+.+++..+
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~   78 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLL   78 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHH
Confidence            35679999999999999999876

>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=92.13  E-value=0.034  Score=47.83  Aligned_cols=20  Identities=30%  Similarity=0.476  Sum_probs=18.8

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.||+|||+|+..+.+
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=92.12  E-value=0.035  Score=47.46  Aligned_cols=21  Identities=38%  Similarity=0.583  Sum_probs=18.9

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|+||+|||||+.++.+.
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999998764

>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=92.09  E-value=0.031  Score=54.10  Aligned_cols=22  Identities=41%  Similarity=0.605  Sum_probs=19.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +=+.||||+|||||+.+++.++
T Consensus        54 igitG~pGaGKSTli~~l~~~~   75 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGSLL   75 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EeeeCCCCCCHHHHHHHHHHHH
Confidence            5579999999999999999865

>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=92.01  E-value=0.039  Score=48.04  Aligned_cols=20  Identities=35%  Similarity=0.660  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.||+|||||+..+.+
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999886

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.95  E-value=0.034  Score=47.70  Aligned_cols=20  Identities=35%  Similarity=0.625  Sum_probs=18.3

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +++.|.||+|||+|+..+.+
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            68899999999999998875

>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=91.90  E-value=0.05  Score=49.78  Aligned_cols=31  Identities=32%  Similarity=0.358  Sum_probs=22.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEEEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVYDL  259 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~l  259 (530)
                      +-..|.|++|+|||||+.++........=.+
T Consensus        96 kt~~~~G~SGVGKSTLiN~L~~~~~~~T~~v  126 (225)
T d1u0la2          96 KISTMAGLSGVGKSSLLNAINPGLKLRVSEV  126 (225)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCCCC----
T ss_pred             CeEEEECCCCCCHHHHHHhhcchhhhhccCc
Confidence            4568899999999999999977665444333

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.88  E-value=0.042  Score=47.04  Aligned_cols=20  Identities=30%  Similarity=0.438  Sum_probs=18.5

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.||+|||+|+..+.+
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999875

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.87  E-value=0.043  Score=46.71  Aligned_cols=20  Identities=20%  Similarity=0.380  Sum_probs=18.7

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|++|+|||+|+..+.+
T Consensus         5 v~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999986

>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=91.66  E-value=0.057  Score=48.94  Aligned_cols=31  Identities=16%  Similarity=0.095  Sum_probs=26.1

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      |+=+.+-|+-|+||||+++.|+.+++...+.
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~~~~i~   32 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYPEWHVA   32 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCTTSEEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhhcCCc
Confidence            4557889999999999999999999765543

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.64  E-value=0.043  Score=46.93  Aligned_cols=22  Identities=27%  Similarity=0.259  Sum_probs=19.5

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -++|.|++|+|||+|+..+.+.
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999998763

>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=91.62  E-value=0.047  Score=46.84  Aligned_cols=20  Identities=30%  Similarity=0.627  Sum_probs=18.7

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +++.|+||+|||+|+..+.+
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999876

>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=91.61  E-value=0.037  Score=50.45  Aligned_cols=28  Identities=21%  Similarity=0.230  Sum_probs=23.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEE
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYD  258 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~  258 (530)
                      +-|+|+.||||||+|..++..+|+.+++
T Consensus         4 IgiTG~igSGKsTva~~l~e~~g~~~i~   31 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNYSAVKYQ   31 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEECC
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCeEEc
Confidence            5689999999999999999988865544

>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=91.61  E-value=0.072  Score=47.98  Aligned_cols=31  Identities=19%  Similarity=0.191  Sum_probs=26.8

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      +.+.|+-|+||||+++.++..|..+++.+..
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            5578999999999999999999888776653

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.57  E-value=0.037  Score=50.90  Aligned_cols=25  Identities=28%  Similarity=0.360  Sum_probs=21.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+-|.||+|+|||||++.|+.....
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~gl~~p   57 (230)
T d1l2ta_          33 FVSIMGPSGSGKSTMLNIIGCLDKP   57 (230)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             EEEEECCCCCCcchhhHhccCCCCC
Confidence            4778999999999999999987644

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.47  E-value=0.041  Score=50.60  Aligned_cols=26  Identities=31%  Similarity=0.488  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+-|.||.|+|||||++.|+..+.-+
T Consensus        28 i~~liGpsGsGKSTLl~~i~Gl~~p~   53 (232)
T d2awna2          28 FVVFVGPSGCGKSTLLRMIAGLETIT   53 (232)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCS
T ss_pred             EEEEECCCCChHHHHHHHHhcCCCCC
Confidence            47789999999999999999877433

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.37  E-value=0.043  Score=50.72  Aligned_cols=23  Identities=35%  Similarity=0.622  Sum_probs=20.2

Q ss_pred             EEECCCCCChhHHHHHHHHHcCC
Q 009640          232 LLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       232 LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -|.||.|+|||||++.|+..+.-
T Consensus        28 ~liGpnGaGKSTll~~i~Gl~~p   50 (240)
T d2onka1          28 VLLGPTGAGKSVFLELIAGIVKP   50 (240)
T ss_dssp             EEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEECCCCChHHHHHHHHHcCCCC
Confidence            47899999999999999997743

>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=91.32  E-value=0.044  Score=47.42  Aligned_cols=22  Identities=27%  Similarity=0.422  Sum_probs=19.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+.|.|.||+|||||+.++.+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999864

>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=91.26  E-value=0.053  Score=46.67  Aligned_cols=21  Identities=38%  Similarity=0.547  Sum_probs=19.0

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|+||+|||||+..+.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999988763

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=91.15  E-value=0.046  Score=50.47  Aligned_cols=25  Identities=28%  Similarity=0.418  Sum_probs=22.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+-|.||.|+|||||++.|+..+.-
T Consensus        34 ~~~liGpsGaGKSTLl~~i~Gl~~p   58 (239)
T d1v43a3          34 FLVLLGPSGCGKTTTLRMIAGLEEP   58 (239)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCC
Confidence            4778999999999999999998753

>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=91.02  E-value=0.053  Score=46.83  Aligned_cols=23  Identities=17%  Similarity=0.355  Sum_probs=19.8

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +=+++.|++|+|||+|+..+.+.
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34788999999999999998864

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=91.00  E-value=0.14  Score=47.65  Aligned_cols=16  Identities=38%  Similarity=0.534  Sum_probs=14.3

Q ss_pred             CceEEEECCCCCChhH
Q 009640          228 KRGYLLYGPPGSGKSS  243 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTs  243 (530)
                      ++..|+.+|+|+|||+
T Consensus         9 ~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TCEEEECCCTTSSTTT
T ss_pred             CCcEEEEECCCCCHHH
Confidence            4678999999999995

>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=90.80  E-value=0.036  Score=47.82  Aligned_cols=20  Identities=30%  Similarity=0.599  Sum_probs=8.3

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.||+|||+|+.++.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68899999999999998875

>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=90.80  E-value=0.063  Score=45.83  Aligned_cols=20  Identities=35%  Similarity=0.516  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.||+|||+|+..+.+
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78899999999999999876

>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=90.76  E-value=0.024  Score=47.92  Aligned_cols=21  Identities=33%  Similarity=0.610  Sum_probs=19.3

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +.|.|.||+|||||+.++.+.
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            678999999999999999875

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=90.72  E-value=0.059  Score=49.78  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+-|.||.|+|||||+++|+....
T Consensus        31 ~~~liG~sGaGKSTll~~i~gl~~   54 (240)
T d1g2912          31 FMILLGPSGCGKTTTLRMIAGLEE   54 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCChHHHHHHHHhcCCC
Confidence            367899999999999999998763

>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=90.62  E-value=0.055  Score=46.42  Aligned_cols=20  Identities=30%  Similarity=0.569  Sum_probs=18.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +.|.|.||+|||||+.++.+
T Consensus         8 I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           8 IAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEECSSSSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999975

>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=90.53  E-value=0.2  Score=44.49  Aligned_cols=31  Identities=26%  Similarity=0.185  Sum_probs=25.5

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCcEEEEec
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYDVYDLEL  261 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~i~~l~l  261 (530)
                      .+|.+|+|+|||.++.+++.+++..+..+-.
T Consensus        88 ~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p  118 (206)
T d2fz4a1          88 GCIVLPTGSGKTHVAMAAINELSTPTLIVVP  118 (206)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             cEEEeCCCCCceehHHhHHHHhcCceeEEEc
Confidence            4678899999999999999999877665543

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=90.44  E-value=0.049  Score=50.31  Aligned_cols=26  Identities=31%  Similarity=0.342  Sum_probs=22.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+-|.||+|+|||||++.|+.....+
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            36789999999999999999877543

>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=90.44  E-value=0.084  Score=52.24  Aligned_cols=35  Identities=26%  Similarity=0.299  Sum_probs=26.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      .+++++.|++|+|||+++..+...+   +..++.++..
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            3789999999999999987666443   6666666543

>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=90.38  E-value=0.043  Score=47.64  Aligned_cols=22  Identities=23%  Similarity=0.510  Sum_probs=19.0

Q ss_pred             CceEEEECCCCCChhHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMA  249 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA  249 (530)
                      .--++|.|+||+|||||+..+.
T Consensus        17 ~~KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          17 ELRILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTC
T ss_pred             eEEEEEECCCCCCHHHHHHHHh
Confidence            3458999999999999998874

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.29  E-value=0.07  Score=45.94  Aligned_cols=20  Identities=40%  Similarity=0.592  Sum_probs=18.3

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ++|.|.+|+|||+|+..+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998874

>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=90.27  E-value=0.075  Score=45.61  Aligned_cols=21  Identities=29%  Similarity=0.411  Sum_probs=18.9

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|.+|+|||+|+..+++.
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999998863

>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=90.25  E-value=0.063  Score=46.49  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=19.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+.+.|.||+|||||+.+|.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            3678899999999999999753

>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=90.21  E-value=0.045  Score=49.44  Aligned_cols=29  Identities=14%  Similarity=0.102  Sum_probs=24.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCcEE
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYDVY  257 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~i~  257 (530)
                      +=+.+-||-|+||||+++.|+..|....+
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l~~~~~   31 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLCEDWEV   31 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTTEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhcCCC
Confidence            34778999999999999999999854433

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=90.16  E-value=0.048  Score=50.02  Aligned_cols=26  Identities=27%  Similarity=0.649  Sum_probs=22.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+-|.||.|+|||||++.|+..+.-+
T Consensus        28 ~~~liGpsGaGKSTll~~l~Gl~~p~   53 (229)
T d3d31a2          28 YFVILGPTGAGKTLFLELIAGFHVPD   53 (229)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSCCS
T ss_pred             EEEEECCCCCcHHHHHHHHhcCcCCC
Confidence            37899999999999999999977443

>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=90.15  E-value=0.036  Score=47.81  Aligned_cols=21  Identities=24%  Similarity=0.445  Sum_probs=17.5

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|+||+|||+|+.++++.
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999987653

>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=90.13  E-value=0.052  Score=50.21  Aligned_cols=24  Identities=25%  Similarity=0.559  Sum_probs=21.5

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      .-+-|.||.|+|||||++.|+..+
T Consensus        29 e~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          29 SIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            347789999999999999999877

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.04  E-value=0.08  Score=45.92  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=19.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -++|.|.||+|||+|+..+...
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999998763

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.84  E-value=0.076  Score=46.66  Aligned_cols=20  Identities=40%  Similarity=0.684  Sum_probs=18.5

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +++.|+||+|||+|+..+.+
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            78899999999999998875

>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=89.75  E-value=0.16  Score=47.01  Aligned_cols=36  Identities=25%  Similarity=0.179  Sum_probs=29.9

Q ss_pred             CCceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          227 WKRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       227 ~~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      .+|-+++.|.-|+||||++.++|..+   |..+.-+++.
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            36788899999999999999999887   7777766654

>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=89.62  E-value=0.058  Score=46.26  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=19.7

Q ss_pred             CceEEEECCCCCChhHHHHHHHH
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~  250 (530)
                      ..-+.|.|+|++|||||+.+|.+
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            34589999999999999998844

>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=89.52  E-value=0.12  Score=47.92  Aligned_cols=23  Identities=30%  Similarity=0.404  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCChhHHHHHHHHH
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -.++|.|.||+|||||+.+|.+.
T Consensus        33 l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          33 LTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             cEEEEECCCCCcHHHHHHHHhCC
Confidence            46999999999999999999764

>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=89.50  E-value=0.084  Score=46.00  Aligned_cols=21  Identities=29%  Similarity=0.439  Sum_probs=19.0

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|.+|+|||+|+..+.+.
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            789999999999999998763

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=89.46  E-value=0.047  Score=50.50  Aligned_cols=24  Identities=25%  Similarity=0.584  Sum_probs=21.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+-|.||.|+|||||++.|+....
T Consensus        33 ~~~iiG~sGsGKSTll~~i~gl~~   56 (242)
T d1oxxk2          33 RFGILGPSGAGKTTFMRIIAGLDV   56 (242)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHHcCcC
Confidence            477899999999999999999763

>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=89.35  E-value=0.088  Score=45.67  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=19.4

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      =++|.|.+|+|||+|+..+.+.
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988763

>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=89.23  E-value=0.071  Score=46.21  Aligned_cols=20  Identities=35%  Similarity=0.539  Sum_probs=17.6

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +-|.|+||+|||||+.++.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            57899999999999999853

>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=89.13  E-value=0.093  Score=49.66  Aligned_cols=23  Identities=30%  Similarity=0.589  Sum_probs=20.9

Q ss_pred             EEEECCCCCChhHHHHHHHHHcC
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .++.||+|||||+|+..||+...
T Consensus        46 ~~I~g~~g~GKT~l~~~i~~~~~   68 (289)
T d1xpua3          46 GLIVAPPKAGKTMLLQNIAQSIA   68 (289)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHH
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHh
Confidence            89999999999999999998663

>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=88.99  E-value=0.029  Score=48.44  Aligned_cols=23  Identities=39%  Similarity=0.481  Sum_probs=20.3

Q ss_pred             EEEECCCCCChhHHHHHHHHHcC
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      .+|+||.|+|||+++.||.-.|+
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            47899999999999999997763

>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=88.98  E-value=0.097  Score=45.78  Aligned_cols=21  Identities=19%  Similarity=0.379  Sum_probs=18.5

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      ++|.|++|+|||+|+..+...
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999988753

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=88.94  E-value=0.077  Score=48.95  Aligned_cols=26  Identities=27%  Similarity=0.405  Sum_probs=22.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+-|.||.|+|||||+++|+..+..+
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            36789999999999999999988544

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.92  E-value=0.082  Score=49.30  Aligned_cols=24  Identities=25%  Similarity=0.333  Sum_probs=21.0

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLC  253 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~  253 (530)
                      -+-|.||.|+|||||+++|+..+.
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            367899999999999999998663

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=88.36  E-value=0.081  Score=45.67  Aligned_cols=20  Identities=55%  Similarity=0.683  Sum_probs=18.1

Q ss_pred             EEEECCCCCChhHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~  250 (530)
                      +.|.|.||+|||||+.++.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67899999999999999864

>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=87.96  E-value=0.096  Score=48.19  Aligned_cols=26  Identities=23%  Similarity=0.448  Sum_probs=22.3

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      -+-|.||.|+|||||+++|+..+.-+
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            35689999999999999999988543

>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=87.36  E-value=0.16  Score=47.91  Aligned_cols=35  Identities=14%  Similarity=0.188  Sum_probs=24.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCcc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKV  264 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~  264 (530)
                      =+-+.|++|+||||+++++++.+   +.+...++..++
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsf   43 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   43 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCC
Confidence            36789999999999999999877   455555655554

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=86.88  E-value=0.12  Score=47.93  Aligned_cols=25  Identities=48%  Similarity=0.798  Sum_probs=22.3

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +-|.||.|+|||||+++|+..+..+
T Consensus        33 ~~liG~nGaGKSTLl~~i~Gl~~p~   57 (254)
T d1g6ha_          33 TLIIGPNGSGKSTLINVITGFLKAD   57 (254)
T ss_dssp             EEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEECCCCCcHHHHHHHHHCCCcCC
Confidence            6789999999999999999987544

>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=86.59  E-value=0.26  Score=43.15  Aligned_cols=32  Identities=19%  Similarity=0.315  Sum_probs=25.8

Q ss_pred             ceEEEECC-CCCChhHHHHHHHHHc---CCcEEEEe
Q 009640          229 RGYLLYGP-PGSGKSSLIAAMANYL---CYDVYDLE  260 (530)
Q Consensus       229 rG~LL~GP-PGTGKTsLa~AiA~~l---~~~i~~l~  260 (530)
                      +-|++.|- +|+|||+++..||..|   |+.+.-++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEEC
Confidence            35788998 6999999999999877   66666654

>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=86.39  E-value=0.45  Score=44.47  Aligned_cols=22  Identities=36%  Similarity=0.587  Sum_probs=20.1

Q ss_pred             EEEECCCCCChhHHHHHHHHHc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      +++.|++|||||+|+..||+..
T Consensus        71 ~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          71 IGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEeeCCCCCCHHHHHHHHHHHH
Confidence            8999999999999999998763

>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=86.05  E-value=0.18  Score=43.75  Aligned_cols=18  Identities=44%  Similarity=0.667  Sum_probs=17.1

Q ss_pred             EEEECCCCCChhHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAM  248 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~Ai  248 (530)
                      ++|-|.+|+|||+|+..+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            689999999999999998

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.03  E-value=0.2  Score=43.22  Aligned_cols=22  Identities=36%  Similarity=0.327  Sum_probs=19.6

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|++|+|||+|+..+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999988764

>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=86.02  E-value=0.16  Score=47.51  Aligned_cols=24  Identities=38%  Similarity=0.517  Sum_probs=20.6

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCC
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+|+||.|+|||+++.||+-.++.
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            478999999999999999876643

>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=85.79  E-value=0.7  Score=42.79  Aligned_cols=50  Identities=16%  Similarity=0.060  Sum_probs=34.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHH---HcCCcEEEEecCccCChH---HHHHHHHhc
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMAN---YLCYDVYDLELTKVTDNS---ELRALLLQT  277 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~---~l~~~i~~l~l~~~~~~~---~L~~l~~~~  277 (530)
                      +..-||+|..|+|||-++...+.   .-|+.+..+-.+.+-...   .+++.|...
T Consensus       104 ~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~  159 (264)
T d1gm5a3         104 PMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKF  159 (264)
T ss_dssp             CCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCS
T ss_pred             cceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhc
Confidence            45679999999999997765543   348888888777664333   344445433

>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=85.73  E-value=0.17  Score=45.69  Aligned_cols=22  Identities=36%  Similarity=0.451  Sum_probs=19.2

Q ss_pred             eEEEECCCCCChhHHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      -+++.|..|+|||||++.+.+.
T Consensus         5 v~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHS
T ss_pred             EEEEeeCCCCCHHHHHHHHHhc
Confidence            4789999999999999888764

>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=85.62  E-value=0.15  Score=46.51  Aligned_cols=23  Identities=48%  Similarity=0.655  Sum_probs=19.8

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -+-|-||.|+|||||+++|+...
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            36788999999999999998843

>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=85.59  E-value=0.79  Score=41.59  Aligned_cols=38  Identities=24%  Similarity=0.149  Sum_probs=28.2

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecCccC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELTKVT  265 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~~~~  265 (530)
                      +...||+|.+|+|||-++-..+...   |..+..+-.+..-
T Consensus        76 ~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~L  116 (233)
T d2eyqa3          76 AMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLL  116 (233)
T ss_dssp             CCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHH
T ss_pred             ccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHh
Confidence            4678999999999999876554433   7788777665543

>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=85.50  E-value=0.057  Score=49.54  Aligned_cols=27  Identities=33%  Similarity=0.476  Sum_probs=19.1

Q ss_pred             ceEEEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGYLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +..+|.|++|+|||||+.++.......
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~~~~~  124 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPELGLR  124 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-----
T ss_pred             ceEEEECCCCccHHHHHHhhccHhHhh
Confidence            345788999999999999997655433

>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=85.41  E-value=0.22  Score=48.36  Aligned_cols=27  Identities=33%  Similarity=0.589  Sum_probs=22.0

Q ss_pred             ceE-EEECCCCCChhHHHHHHHHHcCCc
Q 009640          229 RGY-LLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       229 rG~-LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      .|+ +++||.|+|||+++.||+-.||..
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~~~lg~~   52 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAISFVLGVR   52 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHTTC-
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            354 789999999999999998777643

>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=84.94  E-value=0.6  Score=42.68  Aligned_cols=35  Identities=31%  Similarity=0.355  Sum_probs=28.0

Q ss_pred             CceEEEECCCCCChhHHHHHHHHHc---CCcEEEEecC
Q 009640          228 KRGYLLYGPPGSGKSSLIAAMANYL---CYDVYDLELT  262 (530)
Q Consensus       228 ~rG~LL~GPPGTGKTsLa~AiA~~l---~~~i~~l~l~  262 (530)
                      .+=+.+.|.=|+||||++..+|..+   |..+.-+++.
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            4557788999999999988888776   7777777665

>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=84.12  E-value=0.22  Score=48.00  Aligned_cols=25  Identities=32%  Similarity=0.182  Sum_probs=22.1

Q ss_pred             eEEEECCCCCChhHHHHHHHHHcCC
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYLCY  254 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l~~  254 (530)
                      -+.|-|+-|+||||+++.++++++.
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            3678899999999999999999854

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=83.70  E-value=0.78  Score=42.94  Aligned_cols=21  Identities=24%  Similarity=0.283  Sum_probs=18.3

Q ss_pred             EEEECCCCCChhHHHHHHHHH
Q 009640          231 YLLYGPPGSGKSSLIAAMANY  251 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~  251 (530)
                      +++.|++|+|||+++..++..
T Consensus        71 ~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          71 ELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             CEEEESTTSSHHHHHHHHHHH
T ss_pred             EEeecCCCCChHHHHHHHHHh
Confidence            789999999999998877754

>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=83.60  E-value=0.26  Score=44.13  Aligned_cols=21  Identities=38%  Similarity=0.531  Sum_probs=18.8

Q ss_pred             eEEEECCCCCChhHHHHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAAMAN  250 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~  250 (530)
                      -+||-|++|+|||+|++.+..
T Consensus         8 KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999998854

>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=82.96  E-value=1.6  Score=36.10  Aligned_cols=60  Identities=18%  Similarity=0.325  Sum_probs=38.8

Q ss_pred             EEECCCCCChhH-HHHHHHH--HcCCcEEEEecCc--------------------cCChHHHHHHHHhc---CCCeEEEE
Q 009640          232 LLYGPPGSGKSS-LIAAMAN--YLCYDVYDLELTK--------------------VTDNSELRALLLQT---TNRSIIVI  285 (530)
Q Consensus       232 LL~GPPGTGKTs-La~AiA~--~l~~~i~~l~l~~--------------------~~~~~~L~~l~~~~---~~~sII~I  285 (530)
                      +++||=.+|||+ |++.+-+  ..+..+..+....                    +....++...+...   ....+|+|
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            689999999999 7766633  3477777665331                    01233444444332   35679999


Q ss_pred             cCccch
Q 009640          286 EDIDCS  291 (530)
Q Consensus       286 DeID~~  291 (530)
                      ||+.-+
T Consensus        86 DE~QFf   91 (139)
T d2b8ta1          86 DEVQFF   91 (139)
T ss_dssp             CSGGGS
T ss_pred             chhhhc
Confidence            999865

>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=82.36  E-value=0.33  Score=41.71  Aligned_cols=23  Identities=39%  Similarity=0.444  Sum_probs=19.9

Q ss_pred             eEEEECCCCCChhHHHHHHHHHc
Q 009640          230 GYLLYGPPGSGKSSLIAAMANYL  252 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~AiA~~l  252 (530)
                      -++|-|.+|+|||+|+..+...-
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            37899999999999999997653

>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=82.15  E-value=0.21  Score=47.63  Aligned_cols=18  Identities=28%  Similarity=0.584  Sum_probs=15.5

Q ss_pred             eEEEECCCCCChhHHHHH
Q 009640          230 GYLLYGPPGSGKSSLIAA  247 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~A  247 (530)
                      -.||+|.+|||||||...
T Consensus        16 valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             EEEEEECTTSCHHHHTCB
T ss_pred             EEEEEccCCCCccccccC
Confidence            479999999999998753

>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=81.22  E-value=0.35  Score=46.50  Aligned_cols=25  Identities=20%  Similarity=0.283  Sum_probs=22.2

Q ss_pred             EEEECCCCCChhHHHHHHHHHcCCc
Q 009640          231 YLLYGPPGSGKSSLIAAMANYLCYD  255 (530)
Q Consensus       231 ~LL~GPPGTGKTsLa~AiA~~l~~~  255 (530)
                      +.+-|+-|+||||+++.++++++..
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~~~   32 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFAIT   32 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTTTS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhhc
Confidence            5678999999999999999998654

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=80.42  E-value=0.31  Score=46.26  Aligned_cols=17  Identities=29%  Similarity=0.624  Sum_probs=15.0

Q ss_pred             eEEEECCCCCChhHHHH
Q 009640          230 GYLLYGPPGSGKSSLIA  246 (530)
Q Consensus       230 G~LL~GPPGTGKTsLa~  246 (530)
                      --||+|.+|||||||..
T Consensus        16 ~alfFGLSGTGKTTLs~   32 (313)
T d2olra1          16 VAVFFGLSGTGKTTLST   32 (313)
T ss_dssp             EEEEECSTTSSHHHHHC
T ss_pred             EEEEEccCCCCccccee
Confidence            46899999999999884