Citrus Sinensis ID: 012525

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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-
Protein Sequence
MSGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQERYKWDHGGDTFRKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNNNTNKRLKKLSSGGSGKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKTLWP
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccHHHHcccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccEEEEEEEccccccccccccccccccccccccccccccEEEEccEEEEEccccccHHHHHHHHHHHHcccEEccccccccccccccHHHHHHHHHHHHHccccHHHHccccEEEEccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHccccccccccccccccHHHHccHccccccccccccccEEEEEEEEEEccccccccEEEEcccccccccccEEEEccccccccccccccccccccccEEEccccccEEEEEccccccccccEEEEEccccccccccccccHcccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHccHHcccccccccccEcccccccccccccccccHcccccHHHHHHHHHHHEEcHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEHcccccEEEEccccccHHHHHHHHHHHHcccEEEEEHHHHcccccccccccHHHHHHHHHccccHHHHHHcEEEEEcHHHHcccccccccccccccHHHHHHHHHHHHccEEEEEccccccccccccccEEEEccccccc
Coil and Loop (DISEMBL)
msgiwrwkrqlsdiasssmlpssrtrftplvagpvnylsnnsigraagghrrqpffigiqerykwdhggDTFRKIRaeancprcskhmdllfsnpsnlsppvpapavdgsggyqavnicpncksayyfrphriaplqgsFVEISISAnnhnnnntNKRLKklssggsgklsFWDTLRsyggelpplpsgdvtsnskgngngnglavhlppgppfapgveavrkmgpsngggsggngggggssgggggggsrwggsnlgedlptpkeicKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHanlkkgsgaepktaaavdnddnveleksnvllmgptgsgkTLLAKTLARHVNVPFVIADattltqagyvgeDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKvsrdnlyiktsgldsktlwp
Flexible Loop (DISEMBL)
msgiwrwkrqlsdiasssmlpssrtRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQERYKWDHGGDTFRKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISAnnhnnnntnkrlkklssggsGKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHanlkkgsgaepKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAEslnisrdvsgeGVQQALLKMLEGTETKTfaavskvsrdnlyiktsgldsktlwp
Low Complexity Region (SEG)
MSGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQERYKWDHGGDTFRKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISAnnhnnnntnKRlkklssggsgklsFWDTLRSYGGELPPLPSGDVTsnskgngngngLAVHLPPGPPFAPGVEAVRKMgpsngggsggngggggssgggggggsrwggsnlgEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKTLWP
Disordered region (IsUnstruct)
****WRW*******************FTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQERYKWDHGGDTFRKIRAEANCPRCSKHMDLLF*****************SGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISI**************************FWDTL*****************************************************************************************EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANL**************************VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI********VQQALLKMLEGTETKTFAAVSKVSRDNLYIK***********
Disordered Region (DISOPRED)
**G*W**KRQLSDIASSSM*******F*PLVAGPVNYLSNNSIGRAAGG*RRQ***********************AEANCPRCSKHMDLLFS*********************AVNICPNCKSAYYFRPHRIAPLQGSFVEIS***********************************************************************************************************************PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANL*****************DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK**************IKTSGLDSKTLWP
Disordered Region (DISEMBL)
MSGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQERYKWDHGGDTFRKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNNNTNKRLKKLSSGGSGKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKTLWP
Disordered Region (DISPRO)
*SGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQERYKWDHGGDTFRKIRAEANCPRCSKHMDLLFSNP***************GGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISA********************GKLSFWDTLRSYGGELPPLPS***************LAVHLPPGPPFAPGVEAVRKMGPSNG*****************************EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHA*******************DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK*ESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKTLWP
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQERYKWDHGGDTFRKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNNNTNKRLKKLSSGGSGKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKTLWP
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	461	2.2.26 [Sep-21-2011]
B0JL96	444	ATP-dependent Clp proteas	yes	no	0.357	0.371	0.635	5e-58
Q2JW64	448	ATP-dependent Clp proteas	yes	no	0.353	0.363	0.654	6e-58
B7KBH7	447	ATP-dependent Clp proteas	yes	no	0.360	0.371	0.649	8e-58
Q8XYP6	424	ATP-dependent Clp proteas	yes	no	0.360	0.391	0.615	1e-57
B2UFQ3	424	ATP-dependent Clp proteas	yes	no	0.360	0.391	0.615	1e-57
A5WC69	425	ATP-dependent Clp proteas	yes	no	0.370	0.402	0.653	1e-57
Q472D2	425	ATP-dependent Clp proteas	yes	no	0.338	0.367	0.645	2e-57
Q21KA8	431	ATP-dependent Clp proteas	yes	no	0.349	0.373	0.637	2e-57
Q47FB7	420	ATP-dependent Clp proteas	yes	no	0.340	0.373	0.639	2e-57
Q63V40	423	ATP-dependent Clp proteas	yes	no	0.338	0.368	0.639	2e-57

>sp|B0JL96|CLPX_MICAN ATP-dependent Clp protease ATP-binding subunit ClpX OS=Microcystis aeruginosa (strain NIES-843) GN=clpX PE=3 SV=1

 Score =  225 bits (574), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 110/173 (63%), Positives = 141/173 (81%), Gaps = 8/173 (4%)

Query: 259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
           E +P P+EI K LD +VIGQ +AKKVLSVAVYNHYKR+     +K  G  P        +
Sbjct: 74  EQIPKPREIKKHLDDYVIGQNEAKKVLSVAVYNHYKRLKDIQTQKAGGGSP--------E 125

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
           D++EL+KSN+LL+GPTGSGKTLLA+TLA+ ++VPF +ADATTLT+AGYVGEDVE+IL +L
Sbjct: 126 DSIELQKSNILLIGPTGSGKTLLAQTLAKILDVPFAVADATTLTEAGYVGEDVENILLRL 185

Query: 379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           L  A+ +VE AQ+G++YIDE+DKI +K+E+ +I+RDVSGEGVQQALLKMLEGT
Sbjct: 186 LQVADLDVEEAQRGIIYIDEIDKIARKSENTSITRDVSGEGVQQALLKMLEGT 238

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.
Microcystis aeruginosa (strain NIES-843) (taxid: 449447)

>sp|Q2JW64|CLPX_SYNJA ATP-dependent Clp protease ATP-binding subunit ClpX OS=Synechococcus sp. (strain JA-3-3Ab) GN=clpX PE=3 SV=1

 Score =  225 bits (573), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 112/171 (65%), Positives = 143/171 (83%), Gaps = 8/171 (4%)

Query: 261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDN 320
           LP P+EI + LD++VIGQEKAKKVLSVAVYNHYKR+        + A P +  A + D+ 
Sbjct: 79  LPKPREIMRYLDQYVIGQEKAKKVLSVAVYNHYKRL-------AAKANPNSLGAAELDE- 130

Query: 321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLA 380
           VEL+KSN+L++GPTGSGKTLLA+TLAR ++VPF +ADATTLT+AGYVGEDVE+IL +LL 
Sbjct: 131 VELQKSNILVIGPTGSGKTLLAETLARMLDVPFAVADATTLTEAGYVGEDVENILLRLLQ 190

Query: 381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
            A+ +VE AQ+G++YIDE+DKI +K+E+ +I+RDVSGEGVQQALLKMLEGT
Sbjct: 191 VADMDVEEAQRGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKMLEGT 241

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Synechococcus sp. (strain JA-3-3Ab) (taxid: 321327)

>sp|B7KBH7|CLPX_CYAP7 ATP-dependent Clp protease ATP-binding subunit ClpX OS=Cyanothece sp. (strain PCC 7424) GN=clpX PE=3 SV=1

 Score =  224 bits (572), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 115/177 (64%), Positives = 146/177 (82%), Gaps = 11/177 (6%)

Query: 256 NLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKK-GSGAEPKTAAA 314
           +LG+ +P P+EI K LD++VIGQ +AKKVLSVAVYNHYKR+     K+ G+GA       
Sbjct: 76  SLGQ-IPKPREIKKYLDEYVIGQNEAKKVLSVAVYNHYKRLSDIQAKRTGTGA------- 127

Query: 315 VDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESI 374
              DD VEL+KSN+LLMGPTGSGKTLLA+TLA+ ++VPF +ADATTLT+AGYVGEDVE+I
Sbjct: 128 --TDDPVELQKSNILLMGPTGSGKTLLAQTLAKILDVPFAVADATTLTEAGYVGEDVENI 185

Query: 375 LYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           L +LL  A+ +VE AQ+G++YIDE+DKI +K+E+ +I+RDVSGEGVQQALLKMLEGT
Sbjct: 186 LLRLLQVADLDVEEAQRGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKMLEGT 242

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Cyanothece sp. (strain PCC 7424) (taxid: 65393)

>sp|Q8XYP6|CLPX_RALSO ATP-dependent Clp protease ATP-binding subunit ClpX OS=Ralstonia solanacearum (strain GMI1000) GN=clpX PE=3 SV=1

 Score =  224 bits (571), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 112/182 (61%), Positives = 143/182 (78%), Gaps = 16/182 (8%)

Query: 250 SRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEP 309
            + GG  +  DLPTP EI + LD++VIGQE+AKK+L+VAVYNHYKR+ H   K       
Sbjct: 56  EKEGGLAVKSDLPTPHEIRQSLDQYVIGQEQAKKILAVAVYNHYKRLKHLGKK------- 108

Query: 310 KTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGE 369
                    D+VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPFVIADATTLT+AGYVGE
Sbjct: 109 ---------DDVELSKSNILLIGPTGSGKTLLAQTLARLLNVPFVIADATTLTEAGYVGE 159

Query: 370 DVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE 429
           DVE+I+ KLL    + V+ AQ+G+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++E
Sbjct: 160 DVENIIQKLLQNCNYEVDKAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIE 219

Query: 430 GT 431
           GT
Sbjct: 220 GT 221

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Ralstonia solanacearum (strain GMI1000) (taxid: 267608)

>sp|B2UFQ3|CLPX_RALPJ ATP-dependent Clp protease ATP-binding subunit ClpX OS=Ralstonia pickettii (strain 12J) GN=clpX PE=3 SV=1

 Score =  224 bits (570), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 112/182 (61%), Positives = 143/182 (78%), Gaps = 16/182 (8%)

Query: 250 SRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEP 309
            + GG  +  DLPTP EI + LD++VIGQE+AKK+L+VAVYNHYKR+ H   K       
Sbjct: 56  EKEGGLAVKSDLPTPHEIRQSLDQYVIGQEQAKKILAVAVYNHYKRLKHLGKK------- 108

Query: 310 KTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGE 369
                    D+VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPFVIADATTLT+AGYVGE
Sbjct: 109 ---------DDVELSKSNILLIGPTGSGKTLLAQTLARLLNVPFVIADATTLTEAGYVGE 159

Query: 370 DVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE 429
           DVE+I+ KLL    + V+ AQ+G+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++E
Sbjct: 160 DVENIIQKLLQNCNYEVDKAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLVE 219

Query: 430 GT 431
           GT
Sbjct: 220 GT 221

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Ralstonia pickettii (strain 12J) (taxid: 402626)

>sp|A5WC69|CLPX_PSYWF ATP-dependent Clp protease ATP-binding subunit ClpX OS=Psychrobacter sp. (strain PRwf-1) GN=clpX PE=3 SV=1

 Score =  224 bits (570), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 115/176 (65%), Positives = 144/176 (81%), Gaps = 5/176 (2%)

Query: 257 LGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVD 316
           L + LPTPKEI + LD +VIGQE AKK LSVAVYNHYKR+  A       AE K  A + 
Sbjct: 61  LTKKLPTPKEIREHLDGYVIGQETAKKALSVAVYNHYKRLKVA----AKLAEDKKQAKLG 116

Query: 317 NDD-NVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESIL 375
            DD  VEL KSN+LL+GPTGSGKTLLA+TLAR ++VPF +ADATTLT+AGYVGEDVE+I+
Sbjct: 117 ADDAMVELSKSNILLIGPTGSGKTLLAQTLARMLDVPFAMADATTLTEAGYVGEDVENIV 176

Query: 376 YKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
            KLL  A+++VE A+QG++Y+DE+DKI+KK E+++I+RDVSGEGVQQALLK++EGT
Sbjct: 177 QKLLQAADYDVEKAEQGIIYVDEIDKISKKGENMSITRDVSGEGVQQALLKLIEGT 232

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Psychrobacter sp. (strain PRwf-1) (taxid: 349106)

>sp|Q472D2|CLPX_CUPPJ ATP-dependent Clp protease ATP-binding subunit ClpX OS=Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) GN=clpX PE=3 SV=1

 Score =  224 bits (570), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 111/172 (64%), Positives = 139/172 (80%), Gaps = 16/172 (9%)

Query: 260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDD 319
           DLPTP EI + LD++VIGQE+AKK+L+VAVYNHYKR+ H   K                D
Sbjct: 66  DLPTPHEIRESLDQYVIGQEQAKKILAVAVYNHYKRLKHLGKK----------------D 109

Query: 320 NVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLL 379
           +VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPFVIADATTLT+AGYVGEDVE+I+ KLL
Sbjct: 110 DVELSKSNILLIGPTGSGKTLLAQTLARLLNVPFVIADATTLTEAGYVGEDVENIIQKLL 169

Query: 380 AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
               + VE AQ+G+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct: 170 QNCNYEVEKAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIEGT 221

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) (taxid: 264198)

>sp|Q21KA8|CLPX_SACD2 ATP-dependent Clp protease ATP-binding subunit ClpX OS=Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024) GN=clpX PE=3 SV=1

 Score =  224 bits (570), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 111/174 (63%), Positives = 144/174 (82%), Gaps = 13/174 (7%)

Query: 258 GEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDN 317
           G+ LPTP+EI + LD++VIGQ++AKKVL+VAVYNHYKR+   + KK              
Sbjct: 63  GDKLPTPQEISETLDEYVIGQKQAKKVLAVAVYNHYKRLRVGDKKKSK------------ 110

Query: 318 DDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYK 377
            D+VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPF IADATTLT+AGYVGEDVE+I+ K
Sbjct: 111 -DDVELGKSNILLVGPTGSGKTLLAETLARLLNVPFTIADATTLTEAGYVGEDVENIIQK 169

Query: 378 LLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           LL + +++VE AQQG+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct: 170 LLQKCDYDVEKAQQGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIEGT 223

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024) (taxid: 203122)

>sp|Q47FB7|CLPX_DECAR ATP-dependent Clp protease ATP-binding subunit ClpX OS=Dechloromonas aromatica (strain RCB) GN=clpX PE=3 SV=1

 Score =  223 bits (569), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 110/172 (63%), Positives = 140/172 (81%), Gaps = 15/172 (8%)

Query: 260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDD 319
           DLPTP+EI   LD++VIGQE AK++LSVAVYNHYKR+ H                  N  
Sbjct: 60  DLPTPREISSILDQYVIGQEVAKRILSVAVYNHYKRLRHT---------------AKNAG 104

Query: 320 NVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLL 379
           +VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPFV+ADATTLT+AGYVGEDVE+I+ KLL
Sbjct: 105 DVELSKSNILLIGPTGSGKTLLAQTLARLLNVPFVMADATTLTEAGYVGEDVENIIQKLL 164

Query: 380 AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
            + +++VE AQQG+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct: 165 QKCDYDVEKAQQGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIEGT 216

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Dechloromonas aromatica (strain RCB) (taxid: 159087)

>sp|Q63V40|CLPX_BURPS ATP-dependent Clp protease ATP-binding subunit ClpX OS=Burkholderia pseudomallei (strain K96243) GN=clpX PE=3 SV=2

 Score =  223 bits (569), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 110/172 (63%), Positives = 140/172 (81%), Gaps = 16/172 (9%)

Query: 260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDD 319
           DLP+P+EI   LD++VIGQE+AKK+L+VAVYNHYKR+ H                +D  D
Sbjct: 65  DLPSPQEIRDILDQYVIGQERAKKILAVAVYNHYKRLKH----------------LDKKD 108

Query: 320 NVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLL 379
           +VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPFVIADATTLT+AGYVGEDVE+I+ KLL
Sbjct: 109 DVELSKSNILLIGPTGSGKTLLAQTLARLLNVPFVIADATTLTEAGYVGEDVENIIQKLL 168

Query: 380 AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
               + VE AQ+G+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct: 169 QNCNYEVEKAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLVEGT 220

ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.

Burkholderia pseudomallei (strain K96243) (taxid: 272560)

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	461
449447519	699	PREDICTED: ATP-dependent Clp protease AT	0.878	0.579	0.595	1e-138
359493519	685	PREDICTED: ATP-dependent Clp protease AT	0.887	0.597	0.650	1e-134
147770637	730	hypothetical protein VITISV_013764 [Viti	0.893	0.564	0.610	1e-130
255557853	698	ATP-dependent clp protease ATP-binding s	0.882	0.583	0.610	1e-130
356529352	713	PREDICTED: ATP-dependent Clp protease AT	0.889	0.575	0.557	1e-122
357149618	640	PREDICTED: ATP-dependent Clp protease AT	0.704	0.507	0.658	1e-120
215769357	645	unnamed protein product [Oryza sativa Ja	0.832	0.595	0.595	1e-120
413937331	642	hypothetical protein ZEAMMB73_870207 [Ze	0.830	0.596	0.559	1e-118
356561766	711	PREDICTED: ATP-dependent Clp protease AT	0.889	0.576	0.553	1e-118
413937330	643	hypothetical protein ZEAMMB73_870207 [Ze	0.830	0.595	0.558	1e-117

>gi|449447519|ref|XP_004141515.1| PREDICTED: ATP-dependent Clp protease ATP-binding subunit ClpX-like [Cucumis sativus] gi|449510687|ref|XP_004163734.1| PREDICTED: ATP-dependent Clp protease ATP-binding subunit ClpX-like [Cucumis sativus]

 Score =  498 bits (1281), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 280/470 (59%), Positives = 322/470 (68%), Gaps = 65/470 (13%)

Query: 2   SGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPV----NYLSNNSIGRAAGGHRRQPFFI 57
           S I++WK+    + +  +L  S   F      P+    NYL          GHRR+  FI
Sbjct: 7   SAIFKWKK----LKAMKLLCFSNHNFRLTQISPISTHLNYLH-------VSGHRRRESFI 55

Query: 58  GIQERYKWDHGG---DTF-----------RKIRAEANCPRCSKHMDLLFSN--------P 95
           G+QERYKWD+GG   D F           RKIRAEANCPRCSKHMD+LFSN        P
Sbjct: 56  GVQERYKWDNGGSGSDDFHSQSNITGTPIRKIRAEANCPRCSKHMDILFSNRHFPTLNLP 115

Query: 96  SNLSPPVPAPAVDGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNNNT 155
           S+ S   P  A  G   Y+AVN+CPNCK+AYYFRP++IAPLQGSF+EI  + N+   N++
Sbjct: 116 SSSSGDAPPKAGGGREAYEAVNLCPNCKTAYYFRPYKIAPLQGSFIEIG-NLNSKPKNSS 174

Query: 156 NKRLKKLSSGGSG--------------KLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNG 201
            +R+      G+               ++SF++T RS+GGE          +   G    
Sbjct: 175 ERRITTKDGKGNAIAGFSDENYVNNRLRVSFFETARSFGGE-------PPENWPPGPPPV 227

Query: 202 NGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDL 261
           NGLAVH PPGPPFAPGV  VR  GP+      G  G G          + WGGSNLG+DL
Sbjct: 228 NGLAVHSPPGPPFAPGVNFVRATGPNGSTSGSGGNGAGDGKK------NEWGGSNLGKDL 281

Query: 262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNV 321
           PTPKEICKGLDKFVIGQEKAKKVLSVAV+NHYKRIYHA+L+KGSG E  T   VD+DD+V
Sbjct: 282 PTPKEICKGLDKFVIGQEKAKKVLSVAVHNHYKRIYHASLQKGSGNESGTQDTVDDDDSV 341

Query: 322 ELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQ 381
           ELEKSNVLLMGPTGSGKTLLAKTLAR VNVPFV+ADATTLTQAGYVGEDVESILYKLLA 
Sbjct: 342 ELEKSNVLLMGPTGSGKTLLAKTLARFVNVPFVLADATTLTQAGYVGEDVESILYKLLAA 401

Query: 382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           AEFNV+AAQQGM+YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT
Sbjct: 402 AEFNVQAAQQGMIYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 451

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493519|ref|XP_002264217.2| PREDICTED: ATP-dependent Clp protease ATP-binding subunit ClpX-like [Vitis vinifera]

 Score =  486 bits (1250), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 294/452 (65%), Positives = 327/452 (72%), Gaps = 43/452 (9%)

Query: 3   GIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQER 62
           G+ R KR++ +     +L   R     +   P++    N +    G HRR+   IG+QER
Sbjct: 4   GVLRGKREVVE----RLLMVGRCNHRFMQKSPISTRFANCL--HMGSHRRRESLIGVQER 57

Query: 63  YKWDHGG-DTF--RKIRAEANCPRCSKHMDLLFSN---PSNLSPPVPAPAVDGSGG---Y 113
           YKWDHGG D F  RKIRAEANCPRCSK MDLLFSN   PSN SP VP  + +  G    Y
Sbjct: 58  YKWDHGGSDGFQTRKIRAEANCPRCSKVMDLLFSNRHFPSNFSPAVPTDSSNSKGSGGSY 117

Query: 114 QAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNNNTNK-----RLKKLSSGGSG 168
           QAVN+CPNCK+AYYFRP++IAPLQGSFVEI  S  ++NN NTN        KK S  G G
Sbjct: 118 QAVNLCPNCKTAYYFRPYKIAPLQGSFVEIGRS--DYNNTNTNHPKGKDNEKKSSKNGGG 175

Query: 169 ---------KLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVE 219
                    ++SFW+TLRSYGG+ P          S     GNGLAVH PPGPPFAPGV 
Sbjct: 176 HEEDYGSRLRMSFWETLRSYGGDPPENWPPPPPPPS-----GNGLAVHAPPGPPFAPGVN 230

Query: 220 AVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQE 279
            +R      G G  G GGGG  S G   G   WGGSNLG+DLPTPKEICKGLDKFVIGQE
Sbjct: 231 VIR--AAGPGVGGNGGGGGGNGSFGERNG---WGGSNLGKDLPTPKEICKGLDKFVIGQE 285

Query: 280 KAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKT 339
           +AKKVLSVAVYNHYKRIYH +L+KGSGAE  T+    +DD+VELEKSNVLLMGPTGSGKT
Sbjct: 286 RAKKVLSVAVYNHYKRIYHGSLQKGSGAESGTSEV--DDDSVELEKSNVLLMGPTGSGKT 343

Query: 340 LLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEV 399
           LLAKTLAR VNVPFVIADATTLTQAGYVGEDVESILYKLL  AEFNV+AAQQGMVYIDEV
Sbjct: 344 LLAKTLARFVNVPFVIADATTLTQAGYVGEDVESILYKLLTVAEFNVQAAQQGMVYIDEV 403

Query: 400 DKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           DKITKKAESLN+SRDVSGEGVQQALLKMLEGT
Sbjct: 404 DKITKKAESLNLSRDVSGEGVQQALLKMLEGT 435

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147770637|emb|CAN64542.1| hypothetical protein VITISV_013764 [Vitis vinifera]

 Score =  470 bits (1210), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 295/483 (61%), Positives = 329/483 (68%), Gaps = 71/483 (14%)

Query: 3   GIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQER 62
           G+ R KR++ +     +L   R     +   P++    N +    G HRR+   IG+QER
Sbjct: 4   GVLRGKREVVE----RLLMVGRCNHRFMQKSPISTRFANCL--HMGSHRRRESLIGVQER 57

Query: 63  YKWDHGG-DTF--RKIRAEANCPRCSKHMDLLFSN---PSNLSPPVPAPAVDGSGG---Y 113
           YKWDHGG D F  RKIRAEANCPRCSK MDLLFSN   PSN SP VP  + +  G    Y
Sbjct: 58  YKWDHGGSDGFQTRKIRAEANCPRCSKVMDLLFSNRHFPSNFSPAVPTDSSNSKGSGGSY 117

Query: 114 QAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNNNTNK-----RLKKLSSGGSG 168
           QAVN+CPNCK+AYYFRP++IAPLQGSFVEI  S  ++NN NTN        KK S  G G
Sbjct: 118 QAVNLCPNCKTAYYFRPYKIAPLQGSFVEIGRS--DYNNTNTNHPKGKDNEKKSSKNGGG 175

Query: 169 ---------KLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVE 219
                    ++SFW+TLRSYGG+ P          S     GNGLAVH PPGPPFAPGV 
Sbjct: 176 HEEDYGSRLRMSFWETLRSYGGDPPENWPPPPPPPS-----GNGLAVHAPPGPPFAPGVN 230

Query: 220 AVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQE 279
            +R      G G  G GGGG  S G   G   WGGSNLG+DLPTPKEICKGLDKFVIGQE
Sbjct: 231 VIR--AAGPGVGGNGGGGGGNGSFGERNG---WGGSNLGKDLPTPKEICKGLDKFVIGQE 285

Query: 280 KAKK----------------------------VLSVAVYNHYKRIYHANLKKGSGAEPKT 311
           +AKK                            VLSVAVYNHYKRIYH +L+KGSGAE  T
Sbjct: 286 RAKKFSGIEVYIVEIGKWGHSFKRSNWCQTWEVLSVAVYNHYKRIYHGSLQKGSGAESGT 345

Query: 312 AAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDV 371
           +    +DD+VELEKSNVLLMGPTGSGKTLLAKTLAR VNVPFVIADATTLTQAGYVGEDV
Sbjct: 346 SEV--DDDSVELEKSNVLLMGPTGSGKTLLAKTLARFVNVPFVIADATTLTQAGYVGEDV 403

Query: 372 ESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           ESILYKLL  AEFNV+AAQQGMVYIDEVDKITKKAESLN+SRDVSGEGVQQALLKMLEGT
Sbjct: 404 ESILYKLLTVAEFNVQAAQQGMVYIDEVDKITKKAESLNLSRDVSGEGVQQALLKMLEGT 463

Query: 432 ETK 434
           + K
Sbjct: 464 DLK 466

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255557853|ref|XP_002519956.1| ATP-dependent clp protease ATP-binding subunit clpx, putative [Ricinus communis] gi|223541002|gb|EEF42560.1| ATP-dependent clp protease ATP-binding subunit clpx, putative [Ricinus communis]

 Score =  470 bits (1210), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 284/465 (61%), Positives = 323/465 (69%), Gaps = 58/465 (12%)

Query: 6   RWKR--QLSDIASSSMLPSSRT--RFTPL--VAGPVNYLSNNSIGRAAGGHRRQPFFIGI 59
           RWKR  ++  + S     S+R   R+ P+  ++   NYL+        G +RR+   IG+
Sbjct: 3   RWKRVKEIPKLLSYPDHLSNRDLHRWMPVSTISTYFNYLN-------IGCNRRRESLIGL 55

Query: 60  QERYKWDHGGDT------FRKIRAEANCPRCSKHMDLLFSN----------PSNLSPPVP 103
           QERYKWD  GD        RKIRAE+NCPRCSKHMDLLFSN            NL     
Sbjct: 56  QERYKWDGNGDGNNNNSDVRKIRAESNCPRCSKHMDLLFSNRHFPSPSSNNNPNLDSTSN 115

Query: 104 APAVDGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNNNTNKRLKKL- 162
               + +  YQAVN CP+CK+AYYFRP++I PLQGSF+EI    NN  NN +  R+  L 
Sbjct: 116 NNNCNTNNTYQAVNFCPSCKTAYYFRPYKITPLQGSFIEIGRVGNNSPNNKSRNRIGSLT 175

Query: 163 --------------SSGGSGKL--SFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAV 206
                         S+  SG+L  SFW+TLRSY G+          +      NGNGLAV
Sbjct: 176 KQHPSTEDLEEGFDSNAISGRLRASFWNTLRSYAGD-------PPENWPPPPLNGNGLAV 228

Query: 207 HLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKE 266
           H PPGPPFAPGV  +R       G  GG GG GG    GGGGG  WGGSNLG+DLPTPKE
Sbjct: 229 HTPPGPPFAPGVNVIRA-----NGPGGGGGGEGGGEKSGGGGGGGWGGSNLGKDLPTPKE 283

Query: 267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKS 326
           IC+GLDKFVIGQ++AKKVLSVAVYNHYKRIYHA+LKKG G E  ++ AVD+DDNVELEKS
Sbjct: 284 ICRGLDKFVIGQDRAKKVLSVAVYNHYKRIYHASLKKGPGEESGSSDAVDDDDNVELEKS 343

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNV 386
           NVLLMGPTGSGKTLLAKTLAR VNVPFVIADAT LTQAGYVGEDVESILYKLL+ AEFNV
Sbjct: 344 NVLLMGPTGSGKTLLAKTLARFVNVPFVIADATALTQAGYVGEDVESILYKLLSVAEFNV 403

Query: 387 EAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           +AAQQG+VYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT
Sbjct: 404 QAAQQGIVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 448

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356529352|ref|XP_003533258.1| PREDICTED: ATP-dependent Clp protease ATP-binding subunit ClpX-like [Glycine max]

 Score =  446 bits (1147), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 271/486 (55%), Positives = 320/486 (65%), Gaps = 76/486 (15%)

Query: 1   MSGIW-RWKRQLSDIASSSMLPSSRTR----FTPLVAGPVNYLSNNSIGRAAGGHRRQPF 55
           MS ++ RWK        S  LP    R    F P ++  +N ++         GHR +  
Sbjct: 1   MSRVFGRWKNAKEMALLSGSLPRGHHRTGFNFCP-ISTHLNMIA---------GHRWREA 50

Query: 56  FIGIQERYKWDHGGD---TFRKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGS-- 110
            +G+QERYKWD GG    + RKIRAEANCPRC+K M+L+FSN    +P + +    G   
Sbjct: 51  PVGVQERYKWDRGGSDDTSSRKIRAEANCPRCTKDMNLVFSNRHFPTPQIESELGGGERE 110

Query: 111 GGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEI--------------------------- 143
            GYQ+VN+CP+CK+AYYFRP+   PLQG+FVEI                           
Sbjct: 111 KGYQSVNLCPSCKTAYYFRPYDTTPLQGTFVEIGRVTSTNNNGVNNVSGKGPSPRRITHG 170

Query: 144 SISANNHNNNNTNKRLK---KLSSGGSG--KLSFWDTLRSYGG-------------ELPP 185
                  ++++TNK  +   K +S  S   ++S W+TL +Y G             E  P
Sbjct: 171 KGGGKEGSSSSTNKGEEFGGKSNSNASKWLEVSLWETLMAYNGGAGGGDGSNGEPPESWP 230

Query: 186 LPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGG 245
           LP  D    S GNGNGNGLAVH PPGPPFAPG+  +R  GP NGG  G  GG G  +   
Sbjct: 231 LPPDD---GSNGNGNGNGLAVHTPPGPPFAPGINVIRATGPRNGGSGGAGGGKGEKTA-- 285

Query: 246 GGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGS 305
                 WGGSNLG+D P+PKEICKGLDKFVIGQ++AKKVLSVAVYNHYKRIYHA L+KGS
Sbjct: 286 ------WGGSNLGKDFPSPKEICKGLDKFVIGQQRAKKVLSVAVYNHYKRIYHATLQKGS 339

Query: 306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAG 365
            A+   +  +D+DDNVELEKSNVLLMGPTGSGKTLLAKTLAR VNVPFVIADATTLTQAG
Sbjct: 340 AADSGASEVLDDDDNVELEKSNVLLMGPTGSGKTLLAKTLARFVNVPFVIADATTLTQAG 399

Query: 366 YVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALL 425
           YVGEDVESILYKLL  ++FNV AAQQG++YIDEVDKITKKAESLNISRDVSGEGVQQALL
Sbjct: 400 YVGEDVESILYKLLVVSDFNVAAAQQGIIYIDEVDKITKKAESLNISRDVSGEGVQQALL 459

Query: 426 KMLEGT 431
           KMLEGT
Sbjct: 460 KMLEGT 465

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357149618|ref|XP_003575174.1| PREDICTED: ATP-dependent Clp protease ATP-binding subunit ClpX-like isoform 1 [Brachypodium distachyon]

 Score =  437 bits (1123), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 237/360 (65%), Positives = 278/360 (77%), Gaps = 35/360 (9%)

Query: 73  RKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGSGGYQAVNICPNCKSAYYFRPHR 132
           R+IRAEA+CPRCSKHMD+LFS+ +   PP  APA  G+GGYQA+N+CPNC++AY+FRP+ 
Sbjct: 70  RRIRAEAHCPRCSKHMDILFSHRA---PPSSAPA--GAGGYQALNLCPNCRTAYFFRPNI 124

Query: 133 IAPLQGSFVEISISANNHNNNNTNKRLKKLSSGGSGKLSFWDTLRSYGGELPPLPSGDVT 192
           +APLQG+FVEI     +   +    R            SFW+ +R+             +
Sbjct: 125 LAPLQGTFVEIGRVRADFPPDGVRVR----------DPSFWEAIRA-------------S 161

Query: 193 SNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSRW 252
           S+S+ +G+G+G+AVH+PPGPPF P +  VR  G   GGG+GG GG  G +  G      W
Sbjct: 162 SSSRDDGDGSGVAVHVPPGPPFHPNLNVVRVAGGGGGGGAGGGGGEEGGAKDG------W 215

Query: 253 GGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTA 312
           GGSNLG+D PTPKEI KGLDK+VIGQE+AKKVLSVAVYNHYKRIYH +++KGSGA+  ++
Sbjct: 216 GGSNLGKDFPTPKEISKGLDKYVIGQERAKKVLSVAVYNHYKRIYHQSVQKGSGADLGSS 275

Query: 313 -AAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDV 371
               D DDNVELEKSNVLLMGPTGSGKTLLAKTLAR VNVPFVIADATTLTQAGYVGEDV
Sbjct: 276 DGEADGDDNVELEKSNVLLMGPTGSGKTLLAKTLARFVNVPFVIADATTLTQAGYVGEDV 335

Query: 372 ESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           ESILYKLL  A+FNV+AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT
Sbjct: 336 ESILYKLLTVADFNVQAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 395

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|215769357|dbj|BAH01586.1| unnamed protein product [Oryza sativa Japonica Group] gi|218190998|gb|EEC73425.1| hypothetical protein OsI_07697 [Oryza sativa Indica Group]

 Score =  436 bits (1122), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 266/447 (59%), Positives = 312/447 (69%), Gaps = 63/447 (14%)

Query: 1   MSGIWRWKRQLSDIAS--SSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIG 58
           MSG+ RW+R L+ +A+  +S L +       +VA P               HRR      
Sbjct: 1   MSGLLRWRR-LAAVATRAASTLTAPECCSPAVVAPP---------------HRR------ 38

Query: 59  IQERYKWDHGGDTF-----------RKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAV 107
           +QER KW+  G T            R+IRAEA+CPRCSKHMD+LFS+ +  S    A A 
Sbjct: 39  VQERRKWE--GPTSSSSSSSDEHEPRRIRAEAHCPRCSKHMDILFSHRAPPSSSAAAGAG 96

Query: 108 DGSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEI-SISANNHNNNNTNKRLKKLSSGG 166
            G GGYQA+N+CPNC+SAY+FRPH +APLQG+FVEI  + A+   ++    R        
Sbjct: 97  AGGGGYQALNLCPNCRSAYFFRPHLLAPLQGTFVEIGRVRADLLPHDAVRAR-------- 148

Query: 167 SGKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGP 226
               SFW+ +R              +S+S+ +G+G G+AVH+PPGPPF P +  VR  G 
Sbjct: 149 --GASFWEAIRG-------------SSSSRDDGDGGGVAVHVPPGPPFHPNLNVVRVAGG 193

Query: 227 SNGGGSGGNGGGGGSSGGGGGGGSR-WGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVL 285
             GGG GG GG GG  GG  G G   WGGSNLG+DLPTPKEIC+GLDK+VIGQ++AKKVL
Sbjct: 194 GGGGGGGGGGGAGGGGGGEEGAGKDGWGGSNLGKDLPTPKEICQGLDKYVIGQDRAKKVL 253

Query: 286 SVAVYNHYKRIYHANLKKGSGAEPK-TAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKT 344
           SVAVYNHYKRIYH +L+KGSGA+        D+DD VELEKSNVLLMGPTGSGKTLLAKT
Sbjct: 254 SVAVYNHYKRIYHKSLQKGSGADLGGFDGEADDDDGVELEKSNVLLMGPTGSGKTLLAKT 313

Query: 345 LARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK 404
           LAR VNVPFVIADATTLTQAGYVGEDVESILYKLLA A+FNV+AAQQGMVYIDEVDKITK
Sbjct: 314 LARFVNVPFVIADATTLTQAGYVGEDVESILYKLLAVADFNVQAAQQGMVYIDEVDKITK 373

Query: 405 KAESLNISRDVSGEGVQQALLKMLEGT 431
           KAESLNISRDVSGEGVQQALLKMLEGT
Sbjct: 374 KAESLNISRDVSGEGVQQALLKMLEGT 400

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413937331|gb|AFW71882.1| hypothetical protein ZEAMMB73_870207 [Zea mays]

 Score =  431 bits (1109), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 249/445 (55%), Positives = 299/445 (67%), Gaps = 62/445 (13%)

Query: 1   MSGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQ 60
           MSG+ RW+R L++ A+ +      +  T     P    +  ++ +    HRR      +Q
Sbjct: 1   MSGLLRWRR-LANAATRAA-----STLTAAECSPAAASAAGAVAQPPPPHRR------LQ 48

Query: 61  ERYKWDHGGDTF------------RKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVD 108
           ER KW+    +             R+IRAEA+CPRCSKHMD+LFS+          P   
Sbjct: 49  ERRKWESSSGSGGSSSSSTDEPEPRRIRAEAHCPRCSKHMDILFSHRG-------PPTAA 101

Query: 109 GSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEI-SISANNHNNNNTNKRLKKLSSGGS 167
            + GYQA+N+CPNC+SAY+F PH +APLQG+FVEI  + A+  ++     R +       
Sbjct: 102 AAAGYQALNLCPNCRSAYFFHPHVLAPLQGTFVEIGRVRADLLDHPAARARERDPV---- 157

Query: 168 GKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPS 227
               FW+ +R+             +S+S+ +G G G+AVH+PPGPPF P +  VR  G  
Sbjct: 158 ----FWEAIRA-------------SSSSRDDGEGGGVAVHVPPGPPFHPNLNVVRVAGSG 200

Query: 228 NGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSV 287
            GGG G    G G  G        WGGSNLG DLPTPKEICKGLDK+VIGQ++AKKVLSV
Sbjct: 201 GGGGGGAGDEGAGKEG--------WGGSNLGRDLPTPKEICKGLDKYVIGQDRAKKVLSV 252

Query: 288 AVYNHYKRIYHANLKKGSGAEPK-TAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA 346
           AVYNHYKRIYH +L+KGSGA+        D+D+NVELEKSNVLLMGPTGSGKTLLAKTLA
Sbjct: 253 AVYNHYKRIYHQSLQKGSGADLGGFDGEADDDNNVELEKSNVLLMGPTGSGKTLLAKTLA 312

Query: 347 RHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKA 406
           R VNVPFVIADATTLTQAGYVGEDVESILYKLL  A+FNV+AAQQGMVYIDEVDKITKKA
Sbjct: 313 RFVNVPFVIADATTLTQAGYVGEDVESILYKLLTVADFNVQAAQQGMVYIDEVDKITKKA 372

Query: 407 ESLNISRDVSGEGVQQALLKMLEGT 431
           ESLNISRDVSGEGVQQALLKMLEGT
Sbjct: 373 ESLNISRDVSGEGVQQALLKMLEGT 397

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356561766|ref|XP_003549149.1| PREDICTED: ATP-dependent Clp protease ATP-binding subunit ClpX-like [Glycine max]

 Score =  431 bits (1108), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 268/484 (55%), Positives = 315/484 (65%), Gaps = 74/484 (15%)

Query: 1   MSGIW-RWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGI 59
           MS I+ RWK        S  LP    R T     P++   N        GHRR+   +G+
Sbjct: 1   MSRIFGRWKNAKEMALLSGFLPRGHHR-TGFNFCPISTHLN-----MVAGHRRREAPVGV 54

Query: 60  QERYKWDHGG---DTFRKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVDGSGG---- 112
           QERYKWD GG   ++ RKIRAEANCPRC+K M+L+FSN    +P   +    G G     
Sbjct: 55  QERYKWDRGGSDDNSTRKIRAEANCPRCTKDMNLVFSNRHFPTPSSESELGGGGGEKEKG 114

Query: 113 YQAVNICPNCKSAYYFRPHRIAPLQGSFVEISISANNHNNN--------NTNKRLKKL-- 162
           YQ+VN+CP+CK+AYYFRP+   PLQG+FVEI    +  NN         ++ +R+     
Sbjct: 115 YQSVNLCPSCKTAYYFRPYDTTPLQGTFVEIGRVTSTKNNGVNDLSGKGHSPRRITHGKG 174

Query: 163 ------SSGGSGK---------------LSFWDTLRSYG----------GELP---PL-P 187
                 SS   G+               +S W+TL +Y           GE P   PL P
Sbjct: 175 GGKEGGSSTSKGEEFWGRSNNNASKWLEVSLWETLMTYNRGAGRGNGSNGEPPESWPLAP 234

Query: 188 SGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGG 247
            G        NGNGNGLAVH PPGPPF PG+  +R  GP NGG  GG GG G  +     
Sbjct: 235 DG-------SNGNGNGLAVHTPPGPPFPPGINVIRATGPRNGGSGGGGGGKGEKTA---- 283

Query: 248 GGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGA 307
               WGGSNLG+D P+PKEICKGLDKFVIGQ++AKKVLSVAVYNHYKRIYHA L+KGS A
Sbjct: 284 ----WGGSNLGKDFPSPKEICKGLDKFVIGQQRAKKVLSVAVYNHYKRIYHATLQKGSAA 339

Query: 308 EPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYV 367
           +   +  +D+DDNVELEKSNVLLMGPTGSGKTLLAKTLAR VNVPFV+ DATTLTQAGYV
Sbjct: 340 DSGVSEVLDDDDNVELEKSNVLLMGPTGSGKTLLAKTLARFVNVPFVVTDATTLTQAGYV 399

Query: 368 GEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM 427
           GEDVESILYKLL  ++FNV AAQQG++YIDEVDKITKK++SLNISRDVSGEGVQQALLKM
Sbjct: 400 GEDVESILYKLLTVSDFNVAAAQQGIIYIDEVDKITKKSKSLNISRDVSGEGVQQALLKM 459

Query: 428 LEGT 431
           LEGT
Sbjct: 460 LEGT 463

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413937330|gb|AFW71881.1| hypothetical protein ZEAMMB73_870207 [Zea mays]

 Score =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 249/446 (55%), Positives = 299/446 (67%), Gaps = 63/446 (14%)

Query: 1   MSGIWRWKRQLSDIASSSMLPSSRTRFTPLVAGPVNYLSNNSIGRAAGGHRRQPFFIGIQ 60
           MSG+ RW+R L++ A+ +      +  T     P    +  ++ +    HRR      +Q
Sbjct: 1   MSGLLRWRR-LANAATRAA-----STLTAAECSPAAASAAGAVAQPPPPHRR------LQ 48

Query: 61  ERYKWDHGGDTF------------RKIRAEANCPRCSKHMDLLFSNPSNLSPPVPAPAVD 108
           ER KW+    +             R+IRAEA+CPRCSKHMD+LFS+          P   
Sbjct: 49  ERRKWESSSGSGGSSSSSTDEPEPRRIRAEAHCPRCSKHMDILFSHRG-------PPTAA 101

Query: 109 GSGGYQAVNICPNCKSAYYFRPHRIAPLQGSFVEI-SISANNHNNNNTNKRLKKLSSGGS 167
            + GYQA+N+CPNC+SAY+F PH +APLQG+FVEI  + A+  ++     R +       
Sbjct: 102 AAAGYQALNLCPNCRSAYFFHPHVLAPLQGTFVEIGRVRADLLDHPAARARERDPV---- 157

Query: 168 GKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPS 227
               FW+ +R+             +S+S+ +G G G+AVH+PPGPPF P +  VR  G  
Sbjct: 158 ----FWEAIRA-------------SSSSRDDGEGGGVAVHVPPGPPFHPNLNVVRVAGSG 200

Query: 228 NGGGSGGNGGGGGSSGGGGGGGSRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSV 287
            GGG G    G G  G        WGGSNLG DLPTPKEICKGLDK+VIGQ++AKKVLSV
Sbjct: 201 GGGGGGAGDEGAGKEG--------WGGSNLGRDLPTPKEICKGLDKYVIGQDRAKKVLSV 252

Query: 288 AVYNHYKRIYHANLKKG-SGAEPK-TAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTL 345
           AVYNHYKRIYH +L+KG SGA+        D+D+NVELEKSNVLLMGPTGSGKTLLAKTL
Sbjct: 253 AVYNHYKRIYHQSLQKGRSGADLGGFDGEADDDNNVELEKSNVLLMGPTGSGKTLLAKTL 312

Query: 346 ARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK 405
           AR VNVPFVIADATTLTQAGYVGEDVESILYKLL  A+FNV+AAQQGMVYIDEVDKITKK
Sbjct: 313 ARFVNVPFVIADATTLTQAGYVGEDVESILYKLLTVADFNVQAAQQGMVYIDEVDKITKK 372

Query: 406 AESLNISRDVSGEGVQQALLKMLEGT 431
           AESLNISRDVSGEGVQQALLKMLEGT
Sbjct: 373 AESLNISRDVSGEGVQQALLKMLEGT 398

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	461
TAIR|locus:2006942	656	AT1G33360 [Arabidopsis thalian	0.362	0.254	0.854	2.6e-94
TAIR|locus:2155446	608	AT5G49840 [Arabidopsis thalian	0.370	0.281	0.773	4e-83
TAIR|locus:2154257	579	CLPX "CLP protease regulatory	0.422	0.336	0.767	2.3e-71
TIGR_CMR|APH_0969	415	APH_0969 "ATP-dependent Clp pr	0.329	0.366	0.654	9.9e-52
TIGR_CMR|SPO_1004	424	SPO_1004 "ATP-dependent Clp pr	0.342	0.372	0.635	2.4e-51
TIGR_CMR|SO_1795	426	SO_1795 "ATP-dependent Clp pro	0.340	0.368	0.641	8.3e-51
UNIPROTKB|P0CAU2	420	clpX "ATP-dependent Clp protea	0.340	0.373	0.624	1.1e-50
TIGR_CMR|CHY_0326	418	CHY_0326 "ATP-dependent Clp pr	0.340	0.375	0.641	1.1e-50
TIGR_CMR|BA_4704	419	BA_4704 "ATP-dependent Clp pro	0.340	0.374	0.612	1.1e-50
TIGR_CMR|GSU_1791	417	GSU_1791 "ATP-dependent Clp pr	0.336	0.371	0.608	3.7e-50

TAIR|locus:2006942 AT1G33360 [Arabidopsis thaliana (taxid:3702)]

 Score = 732 (262.7 bits), Expect = 2.6e-94, Sum P(2) = 2.6e-94
 Identities = 147/172 (85%), Positives = 159/172 (92%)

Query:   260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDD 319
             D PTPKEICK LDKFVIGQ +AKKVLSVAVYNHYKRIYH ++KKGS A+P     +D+DD
Sbjct:   248 DFPTPKEICKWLDKFVIGQSRAKKVLSVAVYNHYKRIYHTSMKKGSAAQP-----IDDDD 302

Query:   320 NVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLL 379
             NVEL+KSNVLLMGPTGSGKTLLAKTLAR VNVPFVIADATTLTQAGYVG+DVESIL+KLL
Sbjct:   303 NVELDKSNVLLMGPTGSGKTLLAKTLARLVNVPFVIADATTLTQAGYVGDDVESILHKLL 362

Query:   380 AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
               AEFNV+AAQQG+VYIDEVDKITKKAESLNISRDVSGEGVQQALLK+LEGT
Sbjct:   363 TVAEFNVQAAQQGIVYIDEVDKITKKAESLNISRDVSGEGVQQALLKLLEGT 414

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0006457 "protein folding" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0051082 "unfolded protein binding" evidence=IEA

TAIR|locus:2155446 AT5G49840 [Arabidopsis thaliana (taxid:3702)]

 Score = 649 (233.5 bits), Expect = 4.0e-83, Sum P(2) = 4.0e-83
 Identities = 133/172 (77%), Positives = 148/172 (86%)

Query:   261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVD-NDD 319
             LPTPKEIC+GLD+FVIGQEKAKKVLSVAVYNHYKRIYHA+ KKGS +E       D N D
Sbjct:   197 LPTPKEICQGLDEFVIGQEKAKKVLSVAVYNHYKRIYHASRKKGSASESYNIDMEDDNID 256

Query:   320 NVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLL 379
             +VEL+KSNVLL+GPTGSGKTLLAKTLAR VNVPF IADAT+LTQA YVGEDVESILYKL 
Sbjct:   257 HVELDKSNVLLLGPTGSGKTLLAKTLARIVNVPFAIADATSLTQASYVGEDVESILYKLY 316

Query:   380 AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
              +A  NVE AQ+G+VYIDEVDK+T K+ S N  RDVSGEGVQQ+LLK+LEGT
Sbjct:   317 VEAGCNVEEAQRGIVYIDEVDKMTMKSHSSNGGRDVSGEGVQQSLLKLLEGT 368

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0051082 "unfolded protein binding" evidence=IEA

TAIR|locus:2154257 CLPX "CLP protease regulatory subunit X" [Arabidopsis thaliana (taxid:3702)]

 Score = 722 (259.2 bits), Expect = 2.3e-71, P = 2.3e-71
 Identities = 152/198 (76%), Positives = 165/198 (83%)

Query:   260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYH-ANLKKGSGAEPKTAAAVDND 318
             D PTPKEICKGL+KFVIGQE+AKKVLSVAVYNHYKRIYH ++ K+ +G    TAA   +D
Sbjct:   157 DFPTPKEICKGLNKFVIGQERAKKVLSVAVYNHYKRIYHESSQKRSAGETDSTAAKPADD 216

Query:   319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
             D VELEKSN+LLMGPTGSGKTLLAKTLAR VNVPFVIADATTLTQAGYVGEDVESILYKL
Sbjct:   217 DMVELEKSNILLMGPTGSGKTLLAKTLARFVNVPFVIADATTLTQAGYVGEDVESILYKL 276

Query:   379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKT-FA 437
             L  A++NV AAQQG+VYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT       
Sbjct:   277 LTVADYNVAAAQQGIVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTIVNVPEK 336

Query:   438 AVSKVSR-DNLYIKTSGL 454
                K  R DN+ I T  +
Sbjct:   337 GARKHPRGDNIQIDTKDI 354

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006457 "protein folding" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0005759 "mitochondrial matrix" evidence=IDA

GO:0015996 "chlorophyll catabolic process" evidence=RCA

TIGR_CMR|APH_0969 APH_0969 "ATP-dependent Clp protease, ATP-binding subunit ClpX" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 516 (186.7 bits), Expect = 9.9e-52, Sum P(2) = 9.9e-52
 Identities = 110/168 (65%), Positives = 136/168 (80%)

Query:   264 PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVEL 323
             P+EI + LD++VIGQE +KKVLSVAVYNHYKR+      + SG   +          VE+
Sbjct:    60 PREIKEVLDEYVIGQEHSKKVLSVAVYNHYKRL------RNSGVISE----------VEI 103

Query:   324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAE 383
              KSNVLL+GPTGSGKTLLA+TLAR + VPF +ADATTLT+AGYVGEDVE+IL KLL  A 
Sbjct:   104 SKSNVLLIGPTGSGKTLLARTLARVLQVPFAMADATTLTEAGYVGEDVENILLKLLQAAN 163

Query:   384 FNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
             FNVEAAQ+G++YIDEVDKI++K+E+ +I+RDVSGEGVQQALLK++EGT
Sbjct:   164 FNVEAAQRGIIYIDEVDKISRKSENASITRDVSGEGVQQALLKVIEGT 211

GO:0005524 "ATP binding" evidence=ISS

GO:0006457 "protein folding" evidence=ISS

GO:0009368 "endopeptidase Clp complex" evidence=ISS

GO:0042623 "ATPase activity, coupled" evidence=ISS

TIGR_CMR|SPO_1004 SPO_1004 "ATP-dependent Clp protease, ATP-binding subunit ClpX" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 533 (192.7 bits), Expect = 2.4e-51, P = 2.4e-51
 Identities = 110/173 (63%), Positives = 140/173 (80%)

Query:   259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
             + +PTP++IC  LD +VIGQ  AK+VLSVAV+NHYKR+ HA  K GS             
Sbjct:    63 DGVPTPRDICDVLDDYVIGQSTAKRVLSVAVHNHYKRLNHAQ-KAGS------------- 108

Query:   319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
              ++EL KSN+LL+GPTG GKTLLA+TLAR ++VPF +ADATTLT+AGYVGEDVE+I+ KL
Sbjct:   109 -DIELAKSNILLIGPTGCGKTLLAQTLARILDVPFTMADATTLTEAGYVGEDVENIILKL 167

Query:   379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
             L  +E+NVE AQ+G+VYIDEVDKIT+K+E+ +I+RDVSGEGVQQALLK++EGT
Sbjct:   168 LQASEYNVERAQRGIVYIDEVDKITRKSENPSITRDVSGEGVQQALLKLMEGT 220

GO:0005524 "ATP binding" evidence=ISS

GO:0009368 "endopeptidase Clp complex" evidence=ISS

GO:0051082 "unfolded protein binding" evidence=ISS

TIGR_CMR|SO_1795 SO_1795 "ATP-dependent Clp protease, ATP-binding subunit ClpX" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 528 (190.9 bits), Expect = 8.3e-51, P = 8.3e-51
 Identities = 111/173 (64%), Positives = 140/173 (80%)

Query:   259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
             + LPTP E+   LD +VIGQ++AKKVLSVAVYNHYKR     LK  S   PK        
Sbjct:    63 DKLPTPHELRAHLDDYVIGQDRAKKVLSVAVYNHYKR-----LKNSS---PK-------- 106

Query:   319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
             D VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPF +ADATTLT+AGYVGEDVE+I+ KL
Sbjct:   107 DGVELGKSNILLIGPTGSGKTLLAETLARSLNVPFTMADATTLTEAGYVGEDVENIIQKL 166

Query:   379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
             L + +++VE AQ+G+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct:   167 LQKCDYDVEKAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIEGT 219

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

GO:0005524 "ATP binding" evidence=ISS

GO:0006508 "proteolysis" evidence=ISS

UNIPROTKB|P0CAU2 clpX "ATP-dependent Clp protease ATP-binding subunit ClpX" [Caulobacter crescentus CB15 (taxid:190650)]

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 108/173 (62%), Positives = 142/173 (82%)

Query:   259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
             + +PTP+EIC+ LD +VIGQ  AKKVL+VAV+NHYKR+ HA+                N+
Sbjct:    61 DGVPTPREICEVLDDYVIGQGHAKKVLAVAVHNHYKRLNHAS---------------KNN 105

Query:   319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
             D VEL KSN+LL+GPTG+GKTLLA+TLAR ++VPF +ADATTLT+AGYVGEDVE+I+ KL
Sbjct:   106 D-VELAKSNILLVGPTGTGKTLLAQTLARIIDVPFTMADATTLTEAGYVGEDVENIVLKL 164

Query:   379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
             L  A++NVE AQ+G+VYIDE+DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct:   165 LQAADYNVERAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKIMEGT 217

GO:0005515 "protein binding" evidence=IPI

TIGR_CMR|CHY_0326 CHY_0326 "ATP-dependent Clp protease, ATP-binding subunit ClpX" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 111/173 (64%), Positives = 141/173 (81%)

Query:   259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
             E+LP P+EI   LD++VIGQE+AKKVL+VAVYNHYKRI   NL    G +          
Sbjct:    55 EELPKPQEIKAYLDQYVIGQEEAKKVLAVAVYNHYKRI---NL----GGKI--------- 98

Query:   319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
             D+VEL KSN+L++GPTGSGKTLLA+TLAR +NVPF IADAT LT+AGYVGEDVE+IL KL
Sbjct:    99 DDVELSKSNILMLGPTGSGKTLLAQTLARFLNVPFAIADATALTEAGYVGEDVENILLKL 158

Query:   379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
             +  A++++E A++G+VYIDE+DKI +K+E+ +I+RDVSGEGVQQALLK+LEGT
Sbjct:   159 IQNADYDIERAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGT 211

GO:0005524 "ATP binding" evidence=ISS

GO:0009368 "endopeptidase Clp complex" evidence=ISS

GO:0051082 "unfolded protein binding" evidence=ISS

TIGR_CMR|BA_4704 BA_4704 "ATP-dependent Clp protease, ATP-binding subunit ClpX" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 507 (183.5 bits), Expect = 1.1e-50, Sum P(2) = 1.1e-50
 Identities = 106/173 (61%), Positives = 139/173 (80%)

Query:   259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
             +D+P P EI + LD++VIGQ+ AKK L+VAVYNHYKRI ++N K                
Sbjct:    59 KDVPKPVEIREILDEYVIGQDNAKKALAVAVYNHYKRI-NSNSKI--------------- 102

Query:   319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
             D+VEL KSN+ L+GPTGSGKTLLA+TLAR +NVPF IADAT+LT+AGYVGEDVE+IL KL
Sbjct:   103 DDVELAKSNIALIGPTGSGKTLLAQTLARILNVPFAIADATSLTEAGYVGEDVENILLKL 162

Query:   379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
             +  A+++VE A++G++YIDE+DK+ +K+E+ +I+RDVSGEGVQQALLK+LEGT
Sbjct:   163 IQAADYDVEKAEKGIIYIDEIDKVARKSENPSITRDVSGEGVQQALLKILEGT 215

GO:0006508 "proteolysis" evidence=ISS

TIGR_CMR|GSU_1791 GSU_1791 "ATP-dependent Clp protease, ATP-binding subunit ClpX" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 498 (180.4 bits), Expect = 3.7e-50, Sum P(2) = 3.7e-50
 Identities = 104/171 (60%), Positives = 136/171 (79%)

Query:   261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDN 320
             LP P+EI   LD++VIGQ++AKKVL+VAVYNHYKRI        S  +P          +
Sbjct:    63 LPKPREIKDVLDEYVIGQDQAKKVLAVAVYNHYKRIE-------SMGKPS---------D 106

Query:   321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLA 380
             VE++KSN+LL+GPTGSGKTLLA+TLAR + VPF +ADAT LT+AGYVGEDVE+I+  LL 
Sbjct:   107 VEMQKSNILLLGPTGSGKTLLAQTLARILKVPFAMADATNLTEAGYVGEDVENIILNLLQ 166

Query:   381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
              A+++VE AQ+G++YIDE+DKI +K++S +I+RDVSGEGVQQALLK++EGT
Sbjct:   167 AADYDVERAQKGIIYIDEIDKIARKSDSPSITRDVSGEGVQQALLKIIEGT 217

GO:0005524 "ATP binding" evidence=ISS

GO:0009368 "endopeptidase Clp complex" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.1	0.691

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	461
PRK05342	412	PRK05342, clpX, ATP-dependent protease ATP-binding	1e-111
COG1219	408	COG1219, ClpX, ATP-dependent protease Clp, ATPase	1e-101
TIGR00382	413	TIGR00382, clpX, endopeptidase Clp ATP-binding reg	1e-87
COG1220	444	COG1220, HslU, ATP-dependent protease HslVU (ClpYQ	9e-25
PRK05201	443	PRK05201, hslU, ATP-dependent protease ATP-binding	6e-24
TIGR00390	441	TIGR00390, hslU, ATP-dependent protease HslVU, ATP	4e-22
pfam07724	168	pfam07724, AAA_2, AAA domain (Cdc48 subfamily)	7e-20
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	5e-15
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	5e-14
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	3e-11
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	3e-10
COG1220	444	COG1220, HslU, ATP-dependent protease HslVU (ClpYQ	2e-09
PRK05201	443	PRK05201, hslU, ATP-dependent protease ATP-binding	2e-08
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-08
COG0714	329	COG0714, COG0714, MoxR-like ATPases [General funct	3e-08
smart00382	148	smart00382, AAA, ATPases associated with a variety	4e-08
TIGR00390	441	TIGR00390, hslU, ATP-dependent protease HslVU, ATP	3e-07
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	7e-07
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	1e-06
COG0542	786	COG0542, clpA, ATP-binding subunits of Clp proteas	5e-06
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	7e-06
pfam13401	124	pfam13401, AAA_22, AAA domain	8e-06
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	1e-05
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	2e-05
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	5e-05
COG0542	786	COG0542, clpA, ATP-binding subunits of Clp proteas	9e-05
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	9e-05
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	1e-04
pfam05496	231	pfam05496, RuvB_N, Holliday junction DNA helicase	1e-04
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	2e-04
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	3e-04
cd02021	150	cd02021, GntK, Gluconate kinase (GntK) catalyzes t	3e-04
pfam13207	114	pfam13207, AAA_17, AAA domain	3e-04
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	4e-04
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	4e-04
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	5e-04
PLN02748	468	PLN02748, PLN02748, tRNA dimethylallyltransferase	6e-04
COG1474	366	COG1474, CDC6, Cdc6-related protein, AAA superfami	7e-04
PRK00091	307	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosp	8e-04
PHA00370	297	PHA00370, III, attachment protein	0.001
COG1512	271	COG1512, COG1512, Beta-propeller domains of methan	0.001
pfam07728	135	pfam07728, AAA_5, AAA domain (dynein-related subfa	0.001
cd00464	154	cd00464, SK, Shikimate kinase (SK) is the fifth en	0.001
PLN03138	796	PLN03138, PLN03138, Protein TOC75; Provisional	0.002
PRK00080	328	PRK00080, ruvB, Holliday junction DNA helicase Ruv	0.002
pfam07726	131	pfam07726, AAA_3, ATPase family associated with va	0.002
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	0.002
COG0324	308	COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosph	0.002
pfam12810	248	pfam12810, Gly_rich, Glycine rich protein	0.002
pfam13481	154	pfam13481, AAA_25, AAA domain	0.002
PHA00370	297	PHA00370, III, attachment protein	0.003
COG2255	332	COG2255, RuvB, Holliday junction resolvasome, heli	0.003
TIGR00635	305	TIGR00635, ruvB, Holliday junction DNA helicase, R	0.003
TIGR02928	365	TIGR02928, TIGR02928, orc1/cdc6 family replication	0.003
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	0.004
cd00267	157	cd00267, ABC_ATPase, ATP-binding cassette transpor	0.004
pfam01078	207	pfam01078, Mg_chelatase, Magnesium chelatase, subu	0.004
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	0.004
PRK00131	175	PRK00131, aroK, shikimate kinase; Reviewed	0.004
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	0.004

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

 Score =  334 bits (860), Expect = e-111
 Identities = 115/174 (66%), Positives = 143/174 (82%), Gaps = 15/174 (8%)

Query: 259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
           ++LPTPKEI   LD++VIGQE+AKKVLSVAVYNHYKR+ H +                 D
Sbjct: 57  KELPTPKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGD---------------KKD 101

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
           D+VEL+KSN+LL+GPTGSGKTLLA+TLAR ++VPF IADATTLT+AGYVGEDVE+IL KL
Sbjct: 102 DDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKL 161

Query: 379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTE 432
           L  A+++VE AQ+G+VYIDE+DKI +K+E+ +I+RDVSGEGVQQALLK+LEGT 
Sbjct: 162 LQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTV 215

Length = 412

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

 Score =  309 bits (793), Expect = e-101
 Identities = 113/173 (65%), Positives = 141/173 (81%), Gaps = 16/173 (9%)

Query: 259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
            +LPTPKEI   LD++VIGQE+AKKVLSVAVYNHYKR+ +                 DND
Sbjct: 47  SELPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKE---------------DND 91

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
           D VEL KSN+LL+GPTGSGKTLLA+TLA+ +NVPF IADATTLT+AGYVGEDVE+IL KL
Sbjct: 92  D-VELSKSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKL 150

Query: 379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           L  A+++VE A++G++YIDE+DKI +K+E+ +I+RDVSGEGVQQALLK++EGT
Sbjct: 151 LQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIEGT 203

Length = 408

>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit (clpX)

 Score =  273 bits (699), Expect = 1e-87
 Identities = 114/173 (65%), Positives = 141/173 (81%), Gaps = 13/173 (7%)

Query: 259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
             LPTPKEI   LD++VIGQE+AKKVLSVAVYNHYKR+     KK             +D
Sbjct: 63  SYLPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKK-------------SD 109

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
           + VEL KSN+LL+GPTGSGKTLLA+TLAR +NVPF IADATTLT+AGYVGEDVE+IL KL
Sbjct: 110 NGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKL 169

Query: 379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           L  A+++VE AQ+G++YIDE+DKI++K+E+ +I+RDVSGEGVQQALLK++EGT
Sbjct: 170 LQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGT 222

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 [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 413

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

 Score =  105 bits (265), Expect = 9e-25
 Identities = 54/152 (35%), Positives = 86/152 (56%), Gaps = 27/152 (17%)

Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRI-YHANLKKGSGAEPKTAAAVDNDDNV 321
           TP+EI   LD+++IGQ++AKK +++A+ N ++R+     L+                   
Sbjct: 5   TPREIVSELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRD------------------ 46

Query: 322 ELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQ 381
           E+   N+L++GPTG GKT +A+ LA+    PF+  +AT  T+ GYVG DVESI+  L   
Sbjct: 47  EVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDL--- 103

Query: 382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISR 413
               VE A + +V  ++++K+  KAE L   R
Sbjct: 104 ----VEIAVK-LVREEKIEKVKDKAEELAEER 130

Length = 444

>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU; Provisional

 Score =  103 bits (259), Expect = 6e-24
 Identities = 56/147 (38%), Positives = 84/147 (57%), Gaps = 29/147 (19%)

Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAE--PKTAAAVDNDDN 320
           TP+EI   LDK++IGQ+ AK+ +++A+ N ++R     L +    E  PK          
Sbjct: 5   TPREIVSELDKYIIGQDDAKRAVAIALRNRWRR---MQLPEELRDEVTPK---------- 51

Query: 321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLA 380
                 N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG DVESI+  L  
Sbjct: 52  ------NILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDL-- 103

Query: 381 QAEFNVEAAQQGMVYIDEVDKITKKAE 407
                VE A + MV  ++ +K+ +KAE
Sbjct: 104 -----VEIAVK-MVREEKREKVREKAE 124

Length = 443

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

 Score = 98.0 bits (244), Expect = 4e-22
 Identities = 52/151 (34%), Positives = 84/151 (55%), Gaps = 25/151 (16%)

Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LDK++IGQ++AKK +++A+ N Y+R                   +  +   E
Sbjct: 2   TPREIVAELDKYIIGQDEAKKSVAIALRNRYRRS-----------------QLPEELKDE 44

Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG DVES++  L    
Sbjct: 45  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDL---- 100

Query: 383 EFNVEAAQQGMVYIDEVDKITKKAESLNISR 413
              V+ A + +V  + ++K+  +AE     R
Sbjct: 101 ---VDIAVK-LVKEEMIEKVRDRAEERAEER 127

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in MEDLINE:98389714, is Ser in other members of the seed alignment [Protein fate, Protein folding and stabilization]. Length = 441

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

 Score = 86.1 bits (214), Expect = 7e-20
 Identities = 31/124 (25%), Positives = 45/124 (36%), Gaps = 37/124 (29%)

Query: 324 EKSNVLLMGPTGSGKTLLAKTLARHVNV---PFVIADATTLTQAGYVGEDVESILYKLLA 380
              + L +GPTG GKT LAK LA  +       +  D +   +        E  + +L+ 
Sbjct: 2   PIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME--------EHSVSRLIG 53

Query: 381 QAEFNVEAAQQGM------------VYIDEVDKITKKAESLNISRDVSGEGVQQALLKML 428
                V   + G             V IDE++K                 GVQ  LL++L
Sbjct: 54  APPGYVGYEEGGQLTEAVRRKPYSIVLIDEIEKAHP--------------GVQNDLLQIL 99

Query: 429 EGTE 432
           EG  
Sbjct: 100 EGGT 103

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

>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

 Score = 71.8 bits (176), Expect = 5e-15
 Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 20/108 (18%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ 381
             N+LL GP G+GKT LA+ +A  +     PF+  +A+ L +   V E     L +LL +
Sbjct: 19  PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFE 78

Query: 382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE 429
                E A+ G+++IDE+D +                G Q ALL++LE
Sbjct: 79  L---AEKAKPGVLFIDEIDSL--------------SRGAQNALLRVLE 109

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

 Score = 68.4 bits (168), Expect = 5e-14
 Identities = 32/107 (29%), Positives = 50/107 (46%), Gaps = 9/107 (8%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKT LAK +A+ +  PF+    + L    YVGE  + +  +L   A    +
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVGESEKRLR-ELFEAA----K 54

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK 434
                +++IDE+D +     S     D     V   LL  L+G  + 
Sbjct: 55  KLAPCVIFIDEIDALAGSRGS---GGDSESRRVVNQLLTELDGFTSS 98

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

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

 Score = 64.4 bits (157), Expect = 3e-11
 Identities = 51/159 (32%), Positives = 71/159 (44%), Gaps = 34/159 (21%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           VIGQE+AK+   + +       Y  N ++     PK                NVL  GP 
Sbjct: 123 VIGQEEAKRKCRLIME------YLENPERFGDWAPK----------------NVLFYGPP 160

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESI--LYKLLAQAEFNVEAAQQG 392
           G+GKT++AK LA    VP ++  AT L    +VG+    I  LY+   +A   +      
Sbjct: 161 GTGKTMMAKALANEAKVPLLLVKATELI-GEHVGDGARRIHELYERARKAAPCI------ 213

Query: 393 MVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
            V+IDE+D I        +  DVS E V  ALL  L+G 
Sbjct: 214 -VFIDELDAIALDRRYQELRGDVS-EIV-NALLTELDGI 249

Length = 368

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

 Score = 61.8 bits (150), Expect = 3e-10
 Identities = 37/107 (34%), Positives = 51/107 (47%), Gaps = 9/107 (8%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VLL GP G+GKTLLAK +A      F+    + L    +VGE  E  + +L  +A     
Sbjct: 279 VLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLS-KWVGE-SEKNIRELFEKA----R 332

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK 434
                +++IDE+D +   A     S D SG  V   LL  L+G E  
Sbjct: 333 KLAPSIIFIDEIDSL---ASGRGPSEDGSGRRVVGQLLTELDGIEKA 376

Length = 494

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

 Score = 59.2 bits (144), Expect = 2e-09
 Identities = 30/69 (43%), Positives = 40/69 (57%), Gaps = 6/69 (8%)

Query: 371 VESILYKLLAQAEFNVEA----AQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLK 426
           +E    KL+ Q E   EA     Q G+V+IDE+DKI K+  S     DVS EGVQ+ LL 
Sbjct: 227 IEEEADKLIDQEEIKQEAIDAAEQNGIVFIDEIDKIAKRGGSGG--PDVSREGVQRDLLP 284

Query: 427 MLEGTETKT 435
           ++EG+   T
Sbjct: 285 LVEGSTVST 293

Length = 444

>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU; Provisional

 Score = 56.2 bits (137), Expect = 2e-08
 Identities = 26/59 (44%), Positives = 36/59 (61%), Gaps = 6/59 (10%)

Query: 377 KLLAQAEFNVEA---AQQ-GMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           KL+   E   EA    +Q G+V+IDE+DKI  +  S     DVS EGVQ+ LL ++EG+
Sbjct: 232 KLIDMEEIKQEAIERVEQNGIVFIDEIDKIAARGGS--SGPDVSREGVQRDLLPLVEGS 288

Length = 443

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

 Score = 56.5 bits (136), Expect = 2e-08
 Identities = 37/106 (34%), Positives = 56/106 (52%), Gaps = 15/106 (14%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VLL GP G+GKTLLAK +A      F+  +   +  + Y GE  E  L ++  +AE N  
Sbjct: 215 VLLYGPPGTGKTLLAKAVANEAGAYFISINGPEI-MSKYYGES-EERLREIFKEAEENAP 272

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGE---GVQQALLKMLEG 430
           +    +++IDE+D I  K E      +V+GE    V   LL +++G
Sbjct: 273 S----IIFIDEIDAIAPKRE------EVTGEVEKRVVAQLLTLMDG 308

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

 Score = 54.7 bits (132), Expect = 3e-08
 Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 4/86 (4%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT-TLTQAGYVGEDVESILYKLLAQAEF- 384
           +VLL GP G GKTLLA+ LAR + +PFV    T  L  +  +G    + L     +  F 
Sbjct: 45  HVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFV 104

Query: 385 --NVEAAQQGMVYIDEVDKITKKAES 408
              + AA + ++ +DE+++   + ++
Sbjct: 105 PGPLFAAVRVILLLDEINRAPPEVQN 130

Length = 329

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

 Score = 52.0 bits (124), Expect = 4e-08
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 19/102 (18%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHVNVP---FVIADATTLTQA------------GYVGE 369
              +L++GP GSGKT LA+ LAR +  P    +  D   + +                  
Sbjct: 2   GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61

Query: 370 DVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI 411
             E  L   LA A       +  ++ +DE+  +    +   +
Sbjct: 62  SGELRLRLALALA----RKLKPDVLILDEITSLLDAEQEALL 99

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

 Score = 52.1 bits (125), Expect = 3e-07
 Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 6/69 (8%)

Query: 371 VESILYKLLAQAEFNVEA----AQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLK 426
           +     KL+   E   EA     Q G+++IDE+DKI KK ES     DVS EGVQ+ LL 
Sbjct: 224 IAEEAAKLVDPEEIKQEAIDRVEQSGIIFIDEIDKIAKKGES--SGADVSREGVQRDLLP 281

Query: 427 MLEGTETKT 435
           ++EG+   T
Sbjct: 282 IVEGSTVNT 290

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in MEDLINE:98389714, is Ser in other members of the seed alignment [Protein fate, Protein folding and stabilization]. Length = 441

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

 Score = 50.9 bits (122), Expect = 7e-07
 Identities = 35/103 (33%), Positives = 52/103 (50%), Gaps = 13/103 (12%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESI--LYKLLAQAEFN 385
           VLL GP G+GKT+LAK +A H    F+    +   Q  Y+GE    +  +++L   A  N
Sbjct: 182 VLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQK-YLGEGPRMVRDVFRL---AREN 237

Query: 386 VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML 428
             +    +++IDEVD I  K        D     VQ+ LL++L
Sbjct: 238 APS----IIFIDEVDSIATKRFDAQTGAD---REVQRILLELL 273

Length = 398

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

 Score = 50.2 bits (120), Expect = 1e-06
 Identities = 35/102 (34%), Positives = 55/102 (53%), Gaps = 11/102 (10%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VLL GP G+GKTLLAK +A   N  F+    + L +  Y+GE    ++ ++   A+   E
Sbjct: 159 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRK-YIGEGA-RLVREIFELAK---E 213

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGE-GVQQALLKML 428
            A   +++IDE+D I  K          SG+  VQ+ L+++L
Sbjct: 214 KAPS-IIFIDEIDAIAAK----RTDSGTSGDREVQRTLMQLL 250

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

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

 Score = 48.8 bits (117), Expect = 5e-06
 Identities = 31/105 (29%), Positives = 45/105 (42%), Gaps = 26/105 (24%)

Query: 250 SRWGGSNLGEDLPTPKEICKGLD----KFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGS 305
           +RW G  + + L   KE    L+    K VIGQ++A + +S A+     R   A L   +
Sbjct: 464 ARWTGIPVAKLLEDEKEKLLNLERRLKKRVIGQDEAVEAVSDAI-----RRARAGLGDPN 518

Query: 306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN 350
               +   +              L +GPTG GKT LAK LA  + 
Sbjct: 519 ----RPIGSF-------------LFLGPTGVGKTELAKALAEALF 546

Length = 786

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

 Score = 47.6 bits (114), Expect = 7e-06
 Identities = 35/103 (33%), Positives = 56/103 (54%), Gaps = 13/103 (12%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VLL GP G+GKTLLAK +A   +  F+    + L Q  Y+GE    ++ +L   A     
Sbjct: 188 VLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQK-YIGEG-ARLVRELFELAREKAP 245

Query: 388 AAQQGMVYIDEVDKI-TKKAESLNISRDVSGEG-VQQALLKML 428
           +    +++IDE+D I  K+ +S       SG+  VQ+ +L++L
Sbjct: 246 S----IIFIDEIDAIGAKRFDS-----GTSGDREVQRTMLELL 279

Length = 406

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

 Score = 45.0 bits (107), Expect = 8e-06
 Identities = 28/109 (25%), Positives = 47/109 (43%), Gaps = 11/109 (10%)

Query: 324 EKSNVLLMGPTGSGKTLLAKTLAR-HVNVPFVIADATTLTQAGYVGEDVESIL------- 375
                +L G +GSGKT L + LAR   N   V  +A +L     +   +   L       
Sbjct: 3   GAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGG 62

Query: 376 --YKLLAQAEFNVEAAQQGMVYIDEVDKITKKA-ESLNISRDVSGEGVQ 421
              +LL      ++   + ++ IDE   ++ +A E L    D+S +G+Q
Sbjct: 63  TTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQ 111

Length = 124

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

 Score = 47.1 bits (113), Expect = 1e-05
 Identities = 35/111 (31%), Positives = 57/111 (51%), Gaps = 25/111 (22%)

Query: 326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGE------DVESILYKLL 379
             VLL GP G+GKTLLAK +A   N  F+    + L Q  ++GE      +    L++L 
Sbjct: 166 KGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQK-FIGEGARLVRE----LFELA 220

Query: 380 AQAEFNVEAAQQGMVYIDEVDKI-TKKAESLNISRDVSGEG-VQQALLKML 428
            +   ++       ++IDE+D I  K+ +S       SG+  VQ+ L+++L
Sbjct: 221 REKAPSI-------IFIDEIDAIAAKRTDSGT-----SGDREVQRTLMQLL 259

Length = 389

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

 Score = 46.3 bits (110), Expect = 2e-05
 Identities = 35/103 (33%), Positives = 58/103 (56%), Gaps = 13/103 (12%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           V+L GP G+GKTLLAK +A   +  F+    + L Q  Y+G+    ++ +L   AE N  
Sbjct: 220 VILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQK-YLGDG-PKLVRELFRVAEENAP 277

Query: 388 AAQQGMVYIDEVDKI-TKKAESLNISRDVSGEG-VQQALLKML 428
           +    +V+IDE+D I TK+ ++        GE  +Q+ +L++L
Sbjct: 278 S----IVFIDEIDAIGTKRYDA-----TSGGEKEIQRTMLELL 311

Length = 438

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

 Score = 45.1 bits (108), Expect = 5e-05
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 9/74 (12%)

Query: 326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFN 385
           S+++L GP G+GKT LA+ +A   + PF    A T   +G     V+ +  +++ +A   
Sbjct: 37  SSMILWGPPGTGKTTLARIIAGATDAPFEALSAVT---SG-----VKDLR-EVIEEARQR 87

Query: 386 VEAAQQGMVYIDEV 399
             A ++ +++IDE+
Sbjct: 88  RSAGRRTILFIDEI 101

Length = 413

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

 Score = 44.6 bits (106), Expect = 9e-05
 Identities = 27/89 (30%), Positives = 45/89 (50%), Gaps = 16/89 (17%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT------QAG--YVGEDVES 373
           K+N +L+G  G GKT + + LA+ +   +VP  + D    +       AG  Y GE  E 
Sbjct: 191 KNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGE-FEE 249

Query: 374 ILYKLLAQAEFNVEAAQQGMVYIDEVDKI 402
            L  +L +    VE ++  +++IDE+  I
Sbjct: 250 RLKAVLKE----VEKSKNVILFIDEIHTI 274

Length = 786

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

 Score = 44.6 bits (105), Expect = 9e-05
 Identities = 34/108 (31%), Positives = 55/108 (50%), Gaps = 9/108 (8%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VL++GP G+GKTLLAK +A    VPF     +   +  +VG    S +  +  QA    +
Sbjct: 188 VLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM-FVGVGA-SRVRDMFEQA----K 241

Query: 388 AAQQGMVYIDEVDKITK-KAESLNISRDVSGEGVQQALLKM--LEGTE 432
            A   +++IDE+D + + +   L    D   + + Q L++M   EG E
Sbjct: 242 KAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNE 289

Length = 644

>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 42.2 bits (99), Expect = 1e-04
 Identities = 16/66 (24%), Positives = 26/66 (39%)

Query: 318 DDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYK 377
                    +VLL GP+G+GKT L + L   + V     D           + +  +L +
Sbjct: 17  RRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQ 76

Query: 378 LLAQAE 383
           LL +  
Sbjct: 77  LLRELA 82

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

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

 Score = 42.8 bits (102), Expect = 1e-04
 Identities = 40/138 (28%), Positives = 59/138 (42%), Gaps = 43/138 (31%)

Query: 271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLL 330
           LD++ IGQEK K+ L + +         A  K+G         A+D+          VLL
Sbjct: 23  LDEY-IGQEKVKENLKIFI--------EAAKKRGE--------ALDH----------VLL 55

Query: 331 MGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQ 390
            GP G GKT LA  +A  + V   I     L + G    D+ +IL  L           +
Sbjct: 56  YGPPGLGKTTLANIIANEMGVNIRITSGPALEKPG----DLAAILTNL-----------E 100

Query: 391 QGMV-YIDEVDKITKKAE 407
            G V +IDE+ ++ +  E
Sbjct: 101 PGDVLFIDEIHRLNRAVE 118

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

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 14/58 (24%), Positives = 20/58 (34%)

Query: 291 NHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH 348
           +   RI                 A++    +E     V+L  PTG GKT  +  LA  
Sbjct: 180 SAIARINKFKSFIEHEGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALA 237

Length = 733

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

 Score = 43.0 bits (102), Expect = 3e-04
 Identities = 17/26 (65%), Positives = 20/26 (76%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPF 353
           VLL+GP G+GKTLLAK +A    VPF
Sbjct: 91  VLLVGPPGTGKTLLAKAVAGEAGVPF 116

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

>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

 Score = 40.7 bits (96), Expect = 3e-04
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADA 358
           +++MG +GSGK+ + K LA  +  PF+  D 
Sbjct: 2   IVVMGVSGSGKSTVGKALAERLGAPFIDGDD 32

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits. Length = 150

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

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 1/90 (1%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGY-VGEDVESILYKLLAQAEFNV 386
           +L+ GP GSGK+ LAK LA  + +P +  D     +    + +     +   L   E  +
Sbjct: 2   ILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEIL 61

Query: 387 EAAQQGMVYIDEVDKITKKAESLNISRDVS 416
           +   +    ID V + T +         V 
Sbjct: 62  DELAKQEWVIDGVRESTLELRLEEADLVVF 91

Length = 114

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

 Score = 42.2 bits (99), Expect = 4e-04
 Identities = 31/100 (31%), Positives = 47/100 (47%), Gaps = 7/100 (7%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VLL GP G+GKTLLAK +A      F+      +  + +VGE  E  + ++  +A     
Sbjct: 490 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEIL-SKWVGES-EKAIREIFRKA----R 543

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM 427
            A   +++ DE+D I   A        V+   V Q L +M
Sbjct: 544 QAAPAIIFFDEIDAIA-PARGARFDTSVTDRIVNQLLTEM 582

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|214386 CHL00176, ftsH, cell division protein; Validated

 Score = 42.7 bits (101), Expect = 4e-04
 Identities = 29/85 (34%), Positives = 44/85 (51%), Gaps = 20/85 (23%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVE-------SILYKLLA 380
           VLL+GP G+GKTLLAK +A    VPF        + +G   E VE       + +  L  
Sbjct: 219 VLLVGPPGTGKTLLAKAIAGEAEVPF-------FSISG--SEFVEMFVGVGAARVRDLFK 269

Query: 381 QAEFNVEAAQQGMVYIDEVDKITKK 405
           +A+ N       +V+IDE+D + ++
Sbjct: 270 KAKENSPC----IVFIDEIDAVGRQ 290

Length = 638

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

 Score = 41.8 bits (99), Expect = 5e-04
 Identities = 26/104 (25%), Positives = 45/104 (43%), Gaps = 23/104 (22%)

Query: 326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFN 385
            +++L GP G+GKT LA+ +A   N  F    A T        +D+  I    + +A  N
Sbjct: 49  HSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGV-----KDLREI----IEEARKN 99

Query: 386 VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE 429
               ++ ++++DE+ +  K                Q ALL  +E
Sbjct: 100 RLLGRRTILFLDEIHRFNKAQ--------------QDALLPHVE 129

Length = 436

>gnl|CDD|215399 PLN02748, PLN02748, tRNA dimethylallyltransferase

 Score = 41.8 bits (98), Expect = 6e-04
 Identities = 21/44 (47%), Positives = 27/44 (61%), Gaps = 4/44 (9%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDV 371
           V++MGPTGSGK+ LA  LA H  V  + AD+  +    Y G DV
Sbjct: 25  VVVMGPTGSGKSKLAVDLASHFPVEIINADSMQV----YSGLDV 64

Length = 468

>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

 Score = 41.6 bits (98), Expect = 7e-04
 Identities = 19/110 (17%), Positives = 38/110 (34%), Gaps = 22/110 (20%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQ-AE 383
            SN+++ GPTG+GKT   K +   +       +   +            +L K+L +  +
Sbjct: 42  PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPY--QVLSKILNKLGK 99

Query: 384 FNVEAAQQGMVY-----------------IDEVDKITKKAESL--NISRD 414
             +       +                  +DEVD +  K   +  ++ R 
Sbjct: 100 VPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRA 149

Length = 366

>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

 Score = 40.9 bits (97), Expect = 8e-04
 Identities = 14/31 (45%), Positives = 22/31 (70%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADA 358
           ++++GPT SGKT LA  LA+ +N   + AD+
Sbjct: 7   IVIVGPTASGKTALAIELAKRLNGEIISADS 37

Length = 307

>gnl|CDD|164795 PHA00370, III, attachment protein

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 19/34 (55%), Positives = 21/34 (61%)

Query: 225 GPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLG 258
           G S+ GG  G G  GG SGGG  GGS  GGS+ G
Sbjct: 92  GGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGG 125

Length = 297

>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 19/37 (51%), Positives = 19/37 (51%), Gaps = 7/37 (18%)

Query: 222 RKMGPSNGGGSGGNG------GGGGSSGGGGGGGSRW 252
           R  G    GGSGG        GGGGSSGGGG  G  W
Sbjct: 236 RSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASG-SW 271

Length = 271

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

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 23/97 (23%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVN--VPFVIA--DATTLTQ-------AGYVGEDVESIL 375
            VLL+GP G+GK+ LA+ LA  ++    F +     TT                 V+  L
Sbjct: 1   GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60

Query: 376 YKLLAQAEFNVEAAQQGMV-YIDEVDKITKKA-ESLN 410
                     V AA++G +  +DE+++       SL 
Sbjct: 61  ----------VRAAREGEIAVLDEINRANPDVLNSLL 87

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

>gnl|CDD|238260 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

 Score = 39.1 bits (92), Expect = 0.001
 Identities = 13/31 (41%), Positives = 22/31 (70%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
           N++L+G  G+GKT + + LA+ + +PFV  D
Sbjct: 1   NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD 31

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. Length = 154

>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 29/122 (23%), Positives = 42/122 (34%), Gaps = 15/122 (12%)

Query: 132 RIAPLQGSFVEISISANNHNNNNTNKRLKKLSSGGSGKLSFWDTLRSYGGELPPLPSGDV 191
           R +    S    +  +++    ++       S+  S         R+   +     S   
Sbjct: 2   RSSSTMVSAAASTSLSSSRPQLSSFSSRSPQSATRSP--------RASSIKCSASASASS 53

Query: 192 TSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRKMGPSNGGGSGGNGGGGGSSGGGGGGGSR 251
           ++ S         AV L      + G       G   GGG GG GGGGG  GGGGGG   
Sbjct: 54  SATSSSASLVANGAVALLSASAISGG-------GGGGGGGFGGFGGGGGGGGGGGGGWRF 106

Query: 252 WG 253
           W 
Sbjct: 107 WL 108

Length = 796

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

 Score = 39.7 bits (94), Expect = 0.002
 Identities = 42/140 (30%), Positives = 61/140 (43%), Gaps = 43/140 (30%)

Query: 269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNV 328
           K LD+F IGQEK K+ L + +         A  K+G         A+D+          V
Sbjct: 22  KSLDEF-IGQEKVKENLKIFI--------EAAKKRGE--------ALDH----------V 54

Query: 329 LLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEA 388
           LL GP G GKT LA  +A  + V   I     L + G    D+ +IL  L          
Sbjct: 55  LLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPG----DLAAILTNL---------- 100

Query: 389 AQQGMV-YIDEVDKITKKAE 407
            ++G V +IDE+ +++   E
Sbjct: 101 -EEGDVLFIDEIHRLSPVVE 119

Length = 328

>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular activities (AAA)

 Score = 37.9 bits (89), Expect = 0.002
 Identities = 15/26 (57%), Positives = 18/26 (69%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPF 353
           VLL G  G  KTLLA+TLAR + + F
Sbjct: 2   VLLEGVPGLAKTLLARTLARSLGLDF 27

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 131

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

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 6/81 (7%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL+G  G+GK+L AK +A    +P +  D   L   G VGE  ES + +++  A    E
Sbjct: 262 LLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLF-GGIVGES-ESRMRQMIRIA----E 315

Query: 388 AAQQGMVYIDEVDKITKKAES 408
           A    +++IDE+DK    +ES
Sbjct: 316 ALSPCILWIDEIDKAFSNSES 336

Length = 489

>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
           +++ GPT SGKT LA  LA+ +    +  D
Sbjct: 6   IVIAGPTASGKTALAIALAKRLGGEIISLD 35

Length = 308

>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein

 Score = 39.1 bits (92), Expect = 0.002
 Identities = 29/92 (31%), Positives = 35/92 (38%), Gaps = 9/92 (9%)

Query: 164 SGGSGKLSFWDTLRSYGGELPPLPSGDVTSNSKGNGNGNGLAVHLPPGPPFAPGVEAVRK 223
           +GG G    ++      G       G V      NGN +        G   + G      
Sbjct: 111 AGGGGGSGNYNGGSGGFG------GGLVGGGGTSNGNNSTGGTQTSGGEGASSGGNGGFG 164

Query: 224 MGPSNGGGSGGNG---GGGGSSGGGGGGGSRW 252
            G S  GG GG G   GGGG   GGGGGGS +
Sbjct: 165 YGGSGNGGGGGGGYFGGGGGHYAGGGGGGSSY 196

This family of proteins is greatly expanded in Trichomonas vaginalis. The proteins are composed of several glycine rich motifs interspersed through the sequence. Although many proteins have been annotated by similarity in the family these annotations given the biased composition of the sequences these are unlikely to be functionally relevant. Length = 248

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

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 31/110 (28%), Positives = 45/110 (40%), Gaps = 12/110 (10%)

Query: 324 EKSNVLLMGPTGSGKTLLAKTLARHV--NVPFVIADATTLTQAGYV-GEDVESILYKLLA 380
                LL G  G+GK+ LA  LA  V    PF+        +  Y+ GED E+ L + L 
Sbjct: 32  RGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLDGEDSEAGLRRRLR 91

Query: 381 QAEFNVEAAQQ-GMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE 429
                +E  +   +V ID +  +    E  N +  V       ALL  L+
Sbjct: 92  ALGEALEEIEGPDLVVIDPLASLLGGDE--NDNAAV------GALLAALD 133

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

>gnl|CDD|164795 PHA00370, III, attachment protein

 Score = 39.1 bits (91), Expect = 0.003
 Identities = 20/34 (58%), Positives = 22/34 (64%)

Query: 225 GPSNGGGSGGNGGGGGSSGGGGGGGSRWGGSNLG 258
           G   GGG+ G G GGG +GG GGGGS  GGS  G
Sbjct: 97  GGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGG 130

Length = 297

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

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 39/142 (27%), Positives = 60/142 (42%), Gaps = 43/142 (30%)

Query: 269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNV 328
           K LD+F IGQEK K+ L + +                       AA    + ++    +V
Sbjct: 23  KTLDEF-IGQEKVKEQLQIFI----------------------KAAKKRGEALD----HV 55

Query: 329 LLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEA 388
           LL GP G GKT LA  +A  + V   I     L + G    D+ +IL  L          
Sbjct: 56  LLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPG----DLAAILTNL---------- 101

Query: 389 AQQGMV-YIDEVDKITKKAESL 409
            ++G V +IDE+ +++   E +
Sbjct: 102 -EEGDVLFIDEIHRLSPAVEEV 122

Length = 332

>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 38/142 (26%), Positives = 59/142 (41%), Gaps = 43/142 (30%)

Query: 269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNV 328
           K L +F IGQEK K+ L + +                       AA    + ++    ++
Sbjct: 1   KLLAEF-IGQEKVKEQLQLFI----------------------EAAKMRQEALD----HL 33

Query: 329 LLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEA 388
           LL GP G GKT LA  +A  + V   I     L + G    D+ +IL  L          
Sbjct: 34  LLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPG----DLAAILTNL---------- 79

Query: 389 AQQGMV-YIDEVDKITKKAESL 409
            ++G V +IDE+ +++   E L
Sbjct: 80  -EEGDVLFIDEIHRLSPAVEEL 100

All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 305

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

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 28/116 (24%), Positives = 44/116 (37%), Gaps = 30/116 (25%)

Query: 326 SNVLLMGPTGSGKTLLAK-------TLARHVNVPFVIA-----DATTLTQAGY------- 366
           SNV + G TG+GKT + K         A   +V  V          TL Q          
Sbjct: 41  SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLR 100

Query: 367 -VGEDV------ESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESL--NISR 413
             GE+V       S +++ L   +   E     ++ +DE+D +    + L   +SR
Sbjct: 101 GSGEEVPTTGLSTSEVFRRL--YKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSR 154

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other [DNA metabolism, DNA replication, recombination, and repair]. Length = 365

>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 16/85 (18%)

Query: 326 SNVLLMGPTGSGKTLLAKTLARH---VNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           ++VL+ G +G+GK L+A+ + +       PF+  +   + +       +ES L+     A
Sbjct: 165 ASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPE-----NLLESELFGHEKGA 219

Query: 383 --------EFNVEAAQQGMVYIDEV 399
                       E A  G +++DE+
Sbjct: 220 FTGAITRRIGRFEQANGGTLFLDEI 244

Length = 464

>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter nucleotide-binding domain

 Score = 37.6 bits (88), Expect = 0.004
 Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 317 NDDNVELEK-SNVLLMGPTGSGKTLLAKTLARHVNVP 352
           ++ ++ L+    V L+GP GSGK+ L + +A  +   
Sbjct: 16  DNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPT 52

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Length = 157

>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI

 Score = 38.3 bits (90), Expect = 0.004
 Identities = 23/73 (31%), Positives = 30/73 (41%), Gaps = 33/73 (45%)

Query: 273 KFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMG 332
             V GQE+AK+ L +A                       AA             N+L++G
Sbjct: 3   ADVKGQEQAKRALEIA-----------------------AAG----------GHNLLMIG 29

Query: 333 PTGSGKTLLAKTL 345
           P GSGKT+LAK L
Sbjct: 30  PPGSGKTMLAKRL 42

Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. Length = 207

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

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 12/81 (14%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFV-IADATTLTQAGYVGEDVE--SILYKLLAQAEF 384
           VLL+GP G+GKTLLAK +A    VPF  I+ +  +    +VG        L++   QA+ 
Sbjct: 186 VLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM--FVGVGASRVRDLFE---QAKK 240

Query: 385 NVEAAQQGMVYIDEVDKITKK 405
           N       +++IDE+D + ++
Sbjct: 241 NAPC----IIFIDEIDAVGRQ 257

Length = 596

>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed

 Score = 37.9 bits (89), Expect = 0.004
 Identities = 11/36 (30%), Positives = 22/36 (61%)

Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA 358
           L+  N++L+G  G+GK+ + + LA+ +   F+  D 
Sbjct: 2   LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTDH 37

Length = 175

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

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 36/125 (28%), Positives = 51/125 (40%), Gaps = 34/125 (27%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVES---------ILYKL 378
           VLL GP G GKTL+AK            A A +L          +S         +L K 
Sbjct: 219 VLLYGPPGCGKTLIAK------------AVANSLAARIGAEGGGKSYFLNIKGPELLNKY 266

Query: 379 LAQAEFNV--------EAAQQGM---VYIDEVDKITKKAESLNISRDVSGEGVQQALLKM 427
           + + E  +        E A +G    V+ DE+D + +   S  +S DV    V Q LL  
Sbjct: 267 VGETERQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGS-GVSSDVETTVVPQ-LLAE 324

Query: 428 LEGTE 432
           ++G E
Sbjct: 325 IDGVE 329

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	461
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	100.0
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	100.0
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.93
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.92
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.9
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.84
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.83
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.82
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.82
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.82
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.8
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.8
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.8
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.79
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.77
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.75
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.75
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	99.73
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.69
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.68
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.68
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.67
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.66
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.65
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.64
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	99.64
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.64
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.62
CHL00095	821	clpC Clp protease ATP binding subunit	99.62
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.62
CHL00195	489	ycf46 Ycf46; Provisional	99.62
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.6
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.6
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.6
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.6
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.59
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.59
CHL00176	638	ftsH cell division protein; Validated	99.58
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.58
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.57
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.57
COG0714	329	MoxR-like ATPases [General function prediction onl	99.56
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.55
CHL00181	287	cbbX CbbX; Provisional	99.55
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.55
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.54
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.54
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.54
PF07726	131	AAA_3: ATPase family associated with various cellu	99.53
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.53
PF00004	132	AAA: ATPase family associated with various cellula	99.52
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.52
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.52
PRK10865	857	protein disaggregation chaperone; Provisional	99.52
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.5
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	99.5
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.49
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.49
COG2204	464	AtoC Response regulator containing CheY-like recei	99.47
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.46
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.45
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.45
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.44
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.44
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.43
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.43
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.42
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.41
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.41
PRK13531	498	regulatory ATPase RavA; Provisional	99.4
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.36
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.36
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.35
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.34
CHL00206	2281	ycf2 Ycf2; Provisional	99.34
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.33
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.31
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.31
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.3
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.3
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.3
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.29
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.29
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.29
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.29
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.28
COG0606	490	Predicted ATPase with chaperone activity [Posttran	99.28
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.28
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.28
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.27
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.27
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.26
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.26
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.24
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.24
PLN03025	319	replication factor C subunit; Provisional	99.24
PRK13342	413	recombination factor protein RarA; Reviewed	99.23
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.22
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.22
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.22
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	99.22
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.22
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.21
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.21
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	99.2
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.2
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.2
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.2
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.2
PHA02244	383	ATPase-like protein	99.2
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.19
KOG2028	554	consensus ATPase related to the helicase subunit o	99.18
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.17
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.17
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.16
smart00350	509	MCM minichromosome maintenance proteins.	99.16
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.15
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.15
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.14
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.14
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.14
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.13
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.12
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.12
PRK04195	482	replication factor C large subunit; Provisional	99.11
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.11
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.1
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.1
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.1
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.09
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.08
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.07
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.07
PRK12402	337	replication factor C small subunit 2; Reviewed	99.07
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.07
CHL00095	821	clpC Clp protease ATP binding subunit	99.05
PHA02544	316	44 clamp loader, small subunit; Provisional	99.04
PRK10865	857	protein disaggregation chaperone; Provisional	99.04
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.03
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.02
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.01
PRK13341	725	recombination factor protein RarA/unknown domain f	99.01
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.01
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.01
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.0
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.0
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.0
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.0
PRK09862	506	putative ATP-dependent protease; Provisional	98.99
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.99
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.99
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.99
PRK15115	444	response regulator GlrR; Provisional	98.99
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.98
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.97
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.97
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.95
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.94
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.94
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.94
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.93
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.9
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	98.9
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.9
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.89
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.89
smart00382	148	AAA ATPases associated with a variety of cellular	98.89
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.88
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.87
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	98.86
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	98.84
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.81
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.81
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	98.81
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.8
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.79
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.78
PRK13765	637	ATP-dependent protease Lon; Provisional	98.78
KOG1969	877	consensus DNA replication checkpoint protein CHL12	98.78
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.73
PRK07399	314	DNA polymerase III subunit delta'; Validated	98.72
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.72
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.69
PRK08058	329	DNA polymerase III subunit delta'; Validated	98.68
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.65
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.62
PRK12377	248	putative replication protein; Provisional	98.61
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.6
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.59
PRK08116	268	hypothetical protein; Validated	98.57
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.53
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.52
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.5
PRK08727	233	hypothetical protein; Validated	98.5
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.49
PRK08084	235	DNA replication initiation factor; Provisional	98.48
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.47
PRK06893	229	DNA replication initiation factor; Validated	98.47
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.47
PRK07952	244	DNA replication protein DnaC; Validated	98.46
PRK08181	269	transposase; Validated	98.45
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.42
PRK06526	254	transposase; Provisional	98.41
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.39
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	98.39
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.37
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.36
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.32
PRK08769	319	DNA polymerase III subunit delta'; Validated	98.31
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.3
PRK06871	325	DNA polymerase III subunit delta'; Validated	98.28
PRK05642	234	DNA replication initiation factor; Validated	98.27
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	98.26
PRK09183	259	transposase/IS protein; Provisional	98.26
PRK06921	266	hypothetical protein; Provisional	98.26
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.25
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.24
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	98.23
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	98.23
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.22
PRK06964	342	DNA polymerase III subunit delta'; Validated	98.22
PRK06835	329	DNA replication protein DnaC; Validated	98.22
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	98.21
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.19
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.19
PRK07993	334	DNA polymerase III subunit delta'; Validated	98.18
KOG0736	953	consensus Peroxisome assembly factor 2 containing	98.15
COG1241	682	MCM2 Predicted ATPase involved in replication cont	98.12
PF13173	128	AAA_14: AAA domain	98.12
PRK04132	846	replication factor C small subunit; Provisional	98.11
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	98.11
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	98.1
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.1
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	98.1
PRK12422	445	chromosomal replication initiation protein; Provis	98.09
PRK08939	306	primosomal protein DnaI; Reviewed	98.07
PRK06090	319	DNA polymerase III subunit delta'; Validated	98.06
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.05
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.01
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.99
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	97.97
PRK05917	290	DNA polymerase III subunit delta'; Validated	97.93
PRK06620	214	hypothetical protein; Validated	97.91
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	97.91
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	97.91
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.87
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.87
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.86
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	97.83
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	97.81
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	97.73
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.72
PRK09087	226	hypothetical protein; Validated	97.7
PRK15455	644	PrkA family serine protein kinase; Provisional	97.68
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.66
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.65
PRK00131	175	aroK shikimate kinase; Reviewed	97.63
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.57
PHA00729	226	NTP-binding motif containing protein	97.57
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.56
PRK07276	290	DNA polymerase III subunit delta'; Validated	97.55
PHA02774	613	E1; Provisional	97.55
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	97.52
KOG0481	729	consensus DNA replication licensing factor, MCM5 c	97.51
PRK13947	171	shikimate kinase; Provisional	97.49
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	97.46
PRK13948	182	shikimate kinase; Provisional	97.46
PRK07261	171	topology modulation protein; Provisional	97.45
PRK05818	261	DNA polymerase III subunit delta'; Validated	97.44
KOG0479	818	consensus DNA replication licensing factor, MCM3 c	97.42
PRK08118	167	topology modulation protein; Reviewed	97.42
PRK03839	180	putative kinase; Provisional	97.42
PRK07132	299	DNA polymerase III subunit delta'; Validated	97.4
PRK00625	173	shikimate kinase; Provisional	97.38
PF05729	166	NACHT: NACHT domain	97.37
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.37
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.34
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.33
COG1485	367	Predicted ATPase [General function prediction only	97.33
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.33
cd01128	249	rho_factor Transcription termination factor rho is	97.3
PRK10536	262	hypothetical protein; Provisional	97.3
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.29
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	97.28
PRK06217	183	hypothetical protein; Validated	97.26
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.26
PRK14532	188	adenylate kinase; Provisional	97.25
PRK04296	190	thymidine kinase; Provisional	97.23
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	97.22
PRK06762	166	hypothetical protein; Provisional	97.21
PRK13949	169	shikimate kinase; Provisional	97.21
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.15
PRK09376	416	rho transcription termination factor Rho; Provisio	97.14
PRK14530	215	adenylate kinase; Provisional	97.14
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.13
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.13
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.13
PRK13946	184	shikimate kinase; Provisional	97.12
PRK05057	172	aroK shikimate kinase I; Reviewed	97.11
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.11
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.1
PRK03731	171	aroL shikimate kinase II; Reviewed	97.1
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.08
PRK14531	183	adenylate kinase; Provisional	97.08
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.06
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.05
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	97.04
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.03
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	97.01
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.01
PHA02624	647	large T antigen; Provisional	96.96
TIGR00767	415	rho transcription termination factor Rho. Members	96.96
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.91
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.89
PRK12608	380	transcription termination factor Rho; Provisional	96.88
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.88
PTZ00088	229	adenylate kinase 1; Provisional	96.88
PRK11823	446	DNA repair protein RadA; Provisional	96.84
TIGR01526	325	nadR_NMN_Atrans nicotinamide-nucleotide adenylyltr	96.82
PRK14528	186	adenylate kinase; Provisional	96.81
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.81
PRK14974	336	cell division protein FtsY; Provisional	96.79
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.78
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.77
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.77
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.76
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	96.76
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.74
PRK02496	184	adk adenylate kinase; Provisional	96.74
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	96.72
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.72
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.72
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	96.72
PRK06547	172	hypothetical protein; Provisional	96.71
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.71
PRK06067	234	flagellar accessory protein FlaH; Validated	96.71
KOG1808	1856	consensus AAA ATPase containing von Willebrand fac	96.68
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.68
PRK00279	215	adk adenylate kinase; Reviewed	96.68
PLN02199	303	shikimate kinase	96.67
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.65
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.62
PLN02200	234	adenylate kinase family protein	96.61
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.58
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.58
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.57
PRK04182	180	cytidylate kinase; Provisional	96.57
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.53
PRK14021	542	bifunctional shikimate kinase/3-dehydroquinate syn	96.53
PRK03846	198	adenylylsulfate kinase; Provisional	96.52
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	96.49
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.46
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.46
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.43
KOG1514	767	consensus Origin recognition complex, subunit 1, a	96.42
PRK14527	191	adenylate kinase; Provisional	96.42
PHA02530	300	pseT polynucleotide kinase; Provisional	96.41
PRK08099	399	bifunctional DNA-binding transcriptional repressor	96.41
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.4
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.39
PLN02674	244	adenylate kinase	96.39
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.37
PRK01184	184	hypothetical protein; Provisional	96.34
PRK08233	182	hypothetical protein; Provisional	96.34
PRK14526	211	adenylate kinase; Provisional	96.32
PRK04040	188	adenylate kinase; Provisional	96.32
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.31
PRK00889	175	adenylylsulfate kinase; Provisional	96.31
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	96.3
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.3
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	96.3
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.29
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.29
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.28
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.25
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.25
PF13245	76	AAA_19: Part of AAA domain	96.24
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.23
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	96.18
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.17
PRK06696	223	uridine kinase; Validated	96.15
PRK10416	318	signal recognition particle-docking protein FtsY;	96.15
PRK05541	176	adenylylsulfate kinase; Provisional	96.15
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	96.13
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	96.12
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.12
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	96.12
PRK14529	223	adenylate kinase; Provisional	96.1
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	96.09
KOG0055	1228	consensus Multidrug/pheromone exporter, ABC superf	96.06
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.05
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.04
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.01
PLN02459	261	probable adenylate kinase	96.01
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.0
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.99
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	95.99
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	95.98
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	95.95
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	95.95
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	95.91
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.9
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.9
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	95.88
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.88
PLN02165	334	adenylate isopentenyltransferase	95.86
PF01202	158	SKI: Shikimate kinase; InterPro: IPR000623 Shikima	95.86
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.86
PRK04220	301	2-phosphoglycerate kinase; Provisional	95.85
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	95.85
PF13479	213	AAA_24: AAA domain	95.84
PF07931	174	CPT: Chloramphenicol phosphotransferase-like prote	95.81
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.8
PRK13951	488	bifunctional shikimate kinase/3-dehydroquinate syn	95.78
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.78
PRK13889	988	conjugal transfer relaxase TraA; Provisional	95.77
PRK09825	176	idnK D-gluconate kinase; Provisional	95.76
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.74
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.74
PRK10875	615	recD exonuclease V subunit alpha; Provisional	95.73
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	95.72
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	95.69
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	95.67
COG0283	222	Cmk Cytidylate kinase [Nucleotide transport and me	95.67
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.66
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.66
KOG0055	1228	consensus Multidrug/pheromone exporter, ABC superf	95.66
PRK13808	333	adenylate kinase; Provisional	95.65
KOG0056	790	consensus Heavy metal exporter HMT1, ABC superfami	95.64
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.64
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	95.63
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.63
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.61
cd03216	163	ABC_Carb_Monos_I This family represents the domain	95.6
PRK12338	319	hypothetical protein; Provisional	95.6
PRK13764	602	ATPase; Provisional	95.6
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	95.58
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	95.58
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.58
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	95.56
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.56
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	95.55
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.54
PRK00300	205	gmk guanylate kinase; Provisional	95.54
smart00487	201	DEXDc DEAD-like helicases superfamily.	95.54
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	95.53
PRK05480	209	uridine/cytidine kinase; Provisional	95.53
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.52
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	95.52
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	95.51
PF06048	286	DUF927: Domain of unknown function (DUF927); Inter	95.5
PRK11545	163	gntK gluconate kinase 1; Provisional	95.46
PRK13826	1102	Dtr system oriT relaxase; Provisional	95.44
PRK13975	196	thymidylate kinase; Provisional	95.43
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	95.42
COG4178	604	ABC-type uncharacterized transport system, permeas	95.42
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.41
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	95.41
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.39
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.37
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.36
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.34
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	95.33
COG3172	187	NadR Predicted ATPase/kinase involved in NAD metab	95.33
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	95.3
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.29
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.28
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.28
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	95.28
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	95.23
PRK12337	475	2-phosphoglycerate kinase; Provisional	95.22
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.21
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.21
PRK08356	195	hypothetical protein; Provisional	95.18
PRK10867	433	signal recognition particle protein; Provisional	95.16
PRK00023	225	cmk cytidylate kinase; Provisional	95.14
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	95.13
PRK04328	249	hypothetical protein; Provisional	95.13
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.13
PRK14730	195	coaE dephospho-CoA kinase; Provisional	95.12
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	95.12
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.08
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	95.07
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	95.07
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.07
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.07
PF14516	331	AAA_35: AAA-like domain	95.06
KOG2383	467	consensus Predicted ATPase [General function predi	95.05
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.05
PRK14737	186	gmk guanylate kinase; Provisional	95.0
PRK06761	282	hypothetical protein; Provisional	94.98
PLN02840	421	tRNA dimethylallyltransferase	94.97
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	94.97
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	94.96
PRK12678	672	transcription termination factor Rho; Provisional	94.95
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.95
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	94.94
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	94.93
PRK07667	193	uridine kinase; Provisional	94.92
COG2074	299	2-phosphoglycerate kinase [Carbohydrate transport	94.88

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.8e-38  Score=324.15  Aligned_cols=195  Identities=68%  Similarity=0.970  Sum_probs=172.7

Q ss_pred             CCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHH--hhhccCCC-CCc-------------------h------h
Q 012525          260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYH--ANLKKGSG-AEP-------------------K------T  311 (461)
Q Consensus       260 ~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~--~~~~~g~~-~s~-------------------~------~  311 (461)
                      ..|+|++|++.||++||||+.||++|..+|++||++|+|  ..+++... .+.                   +      .
T Consensus       132 ~~P~PkeI~~~Ldk~VVGQe~AKKvLsVAVYnHYkRI~hn~~s~~~~~a~~s~~~~~~~~P~~~~~~~~~a~~~~~~r~~  211 (564)
T KOG0745|consen  132 PPPTPKEICEYLDKFVVGQEKAKKVLSVAVYNHYKRIYHNEPSRQKELAEASKSAKDRDNPIELEISESNAQWPNNQRQI  211 (564)
T ss_pred             CCCChHHHHHHhhhheechhhhhheeeehhhHHHHHHhcchHHHHHHHhhhhhcccCCCCcccccccccccccccccchh
Confidence            679999999999999999999999999999999999998  33322211 000                   0      1


Q ss_pred             hhhcccc-ccccccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccC
Q 012525          312 AAAVDND-DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQ  390 (461)
Q Consensus       312 ~~~~~~~-~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~  390 (461)
                      ....+.. +.+++.+.||||+||+|+|||+||+.||+.+++||+..+|+.|++++|+|+++|..+.+++..+.+++++++
T Consensus       212 ~~~ld~~~~dv~LeKSNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQ  291 (564)
T KOG0745|consen  212 AKALDEDDEDVELEKSNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQ  291 (564)
T ss_pred             cccccccccceeeecccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHh
Confidence            2223333 388899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc-eeeecC-CeEEEecCCC
Q 012525          391 QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VSKVSR-DNLYIKTSGL  454 (461)
Q Consensus       391 ~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r~~~r-d~IiI~TsNi  454 (461)
                      .||+||||+|+|..+..+.+..+|++++++|++||++|||..++++.. .++.++ +.+.|+|+||
T Consensus       292 qGIVflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnI  357 (564)
T KOG0745|consen  292 QGIVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNI  357 (564)
T ss_pred             cCeEEEehhhhhcccCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccce
Confidence            999999999999988888888899999999999999999999999888 667777 9999999997

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

Probab=100.00  E-value=1e-33  Score=282.16  Aligned_cols=181  Identities=62%  Similarity=0.940  Sum_probs=169.6

Q ss_pred             CCCCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCc
Q 012525          258 GEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSG  337 (461)
Q Consensus       258 ~~~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTG  337 (461)
                      ...+|+|+|+.+.||++|+||++||++|..+|++||+|+.+..                ..+.++..++||||.||+|+|
T Consensus        46 ~~~lPtP~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~----------------~~~dvEL~KSNILLiGPTGsG  109 (408)
T COG1219          46 LSELPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKE----------------DNDDVELSKSNILLIGPTGSG  109 (408)
T ss_pred             hccCCChHHHHHHhhhheecchhhhceeeeeehhHHHHHhccC----------------CCCceeeeeccEEEECCCCCc
Confidence            3468999999999999999999999999999999999987542                123378889999999999999


Q ss_pred             hHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccch
Q 012525          338 KTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSG  417 (461)
Q Consensus       338 KTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~  417 (461)
                      ||+||+.||+.+++||...+++.++++||+|+++|.++.+++..+.+.++.++.|||||||||+++.+.+..+..+++|+
T Consensus       110 KTlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRDVSG  189 (408)
T COG1219         110 KTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSG  189 (408)
T ss_pred             HHHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccccCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999777888899999


Q ss_pred             HHHHHHHHHHHhCceeeeecc-eeeecC-CeEEEecCCC
Q 012525          418 EGVQQALLKMLEGTETKTFAA-VSKVSR-DNLYIKTSGL  454 (461)
Q Consensus       418 ~~v~~aLL~~LEg~~v~i~~~-~r~~~r-d~IiI~TsNi  454 (461)
                      +++|++||++|||+..+++-. .|++|. ++|.|+|+|+
T Consensus       190 EGVQQALLKiiEGTvasVPPqGGRKHP~Qe~iqvDT~NI  228 (408)
T COG1219         190 EGVQQALLKIIEGTVASVPPQGGRKHPQQEFIQVDTSNI  228 (408)
T ss_pred             hHHHHHHHHHHcCceeccCCCCCCCCCccceEEEcccce
Confidence            999999999999999999877 999999 9999999996

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.93  E-value=3.9e-25  Score=231.54  Aligned_cols=179  Identities=66%  Similarity=0.978  Sum_probs=154.5

Q ss_pred             CCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHH
Q 012525          261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTL  340 (461)
Q Consensus       261 l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTt  340 (461)
                      +++|+++...|+++|+||+.||+.|..++++||+++.+....               .+.++....+|||+||||||||+
T Consensus        59 ~~~p~~i~~~L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~---------------~~~~~~~~~~iLl~Gp~GtGKT~  123 (412)
T PRK05342         59 LPTPKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKK---------------DDDVELQKSNILLIGPTGSGKTL  123 (412)
T ss_pred             CCCHHHHHHHHhhHeeChHHHHHHHHHHHHHHHHhhhccccc---------------ccccccCCceEEEEcCCCCCHHH
Confidence            789999999999999999999999999999999988543110               01344556899999999999999


Q ss_pred             HHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          341 LAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       341 LAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      +|++||+.++.||+.++++.+...+|+|.+.+..+..++..+.+.+..+.++||||||||++..++......++++++++
T Consensus       124 lAr~lA~~l~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~v  203 (412)
T PRK05342        124 LAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGV  203 (412)
T ss_pred             HHHHHHHHhCCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcccHHH
Confidence            99999999999999999999988899999988888888877777777789999999999999988555556788999999


Q ss_pred             HHHHHHHHhCceeeeecc-eeeecC-CeEEEecCCC
Q 012525          421 QQALLKMLEGTETKTFAA-VSKVSR-DNLYIKTSGL  454 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i~~~-~r~~~r-d~IiI~TsNi  454 (461)
                      |++||++||+..+.++.. .++++. ++++|+|+|+
T Consensus       204 Q~~LL~~Leg~~~~v~~~gg~~~~~~~~~~i~t~ni  239 (412)
T PRK05342        204 QQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNI  239 (412)
T ss_pred             HHHHHHHHhcCeEEeCCCCCcCcCCCCeEEeccCCc
Confidence            999999999988887654 555655 8999999998

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.92  E-value=8.6e-25  Score=228.61  Aligned_cols=182  Identities=65%  Similarity=0.936  Sum_probs=155.1

Q ss_pred             CCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchH
Q 012525          260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKT  339 (461)
Q Consensus       260 ~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKT  339 (461)
                      .+++|.++...|+++|+||++||+.|..++++||+++.......             ....++..+.++||+||||||||
T Consensus        64 ~~~~p~~i~~~L~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~-------------~~~~~~~~~~~iLL~GP~GsGKT  130 (413)
T TIGR00382        64 YLPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKK-------------SDNGVELSKSNILLIGPTGSGKT  130 (413)
T ss_pred             CCCCHHHHHHHhcceecCHHHHHHHHHHHHHHHHhhhccccccc-------------cccccccCCceEEEECCCCcCHH
Confidence            37899999999999999999999999999999999875310000             00124455689999999999999


Q ss_pred             HHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          340 LLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       340 tLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      ++|++||+.++.+|+.++++.+...+|+|.+.+..+..++..+.+.+..++++||||||||++..+++..+..+++++++
T Consensus       131 ~lAraLA~~l~~pf~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~  210 (413)
T TIGR00382       131 LLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEG  210 (413)
T ss_pred             HHHHHHHHhcCCCeEEechhhccccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccccccccchh
Confidence            99999999999999999999988788999988888888888777777888999999999999999877777788999999


Q ss_pred             HHHHHHHHHhCceeeeecc-eeeecC-CeEEEecCCC
Q 012525          420 VQQALLKMLEGTETKTFAA-VSKVSR-DNLYIKTSGL  454 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~~~-~r~~~r-d~IiI~TsNi  454 (461)
                      +|++||++|||..++++.. .+.++. ++|+|+|+|+
T Consensus       211 vq~~LL~iLeG~~~~v~~~~gr~~~~~~~i~i~TsNi  247 (413)
T TIGR00382       211 VQQALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSNI  247 (413)
T ss_pred             HHHHHHHHhhccceecccCCCccccCCCeEEEEcCCc
Confidence            9999999999877765543 566665 8999999998

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.

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

Probab=99.90  E-value=8.6e-23  Score=208.38  Aligned_cols=150  Identities=27%  Similarity=0.433  Sum_probs=123.5

Q ss_pred             HHhhcCChHHHHHHHHHHHHHH--HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNH--YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~--~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |++ |.|+++||+.|+++|...  +..+++..                     ..+.+.|||.||||||||+||||+|.+
T Consensus       211 W~D-Iagl~~AK~lL~EAVvlPi~mPe~F~Gi---------------------rrPWkgvLm~GPPGTGKTlLAKAvATE  268 (491)
T KOG0738|consen  211 WDD-IAGLHEAKKLLKEAVVLPIWMPEFFKGI---------------------RRPWKGVLMVGPPGTGKTLLAKAVATE  268 (491)
T ss_pred             hHh-hcchHHHHHHHHHHHhhhhhhHHHHhhc---------------------ccccceeeeeCCCCCcHHHHHHHHHHh
Confidence            344 889999999999999754  33444433                     334588999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++..|+.++.++++ ++|.|++ |++++-+|..+++.    .+++|||||||.|+..|...  +.+.+++++.+.||.+|
T Consensus       269 c~tTFFNVSsstlt-SKwRGeS-EKlvRlLFemARfy----APStIFiDEIDslcs~RG~s--~EHEaSRRvKsELLvQm  340 (491)
T KOG0738|consen  269 CGTTFFNVSSSTLT-SKWRGES-EKLVRLLFEMARFY----APSTIFIDEIDSLCSQRGGS--SEHEASRRVKSELLVQM  340 (491)
T ss_pred             hcCeEEEechhhhh-hhhccch-HHHHHHHHHHHHHh----CCceeehhhHHHHHhcCCCc--cchhHHHHHHHHHHHHh
Confidence            99999999999999 5799999 99999999999877    79999999999999987654  67888899999999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ||.+.....     .+-.+++++||+.
T Consensus       341 DG~~~t~e~-----~k~VmVLAATN~P  362 (491)
T KOG0738|consen  341 DGVQGTLEN-----SKVVMVLAATNFP  362 (491)
T ss_pred             hcccccccc-----ceeEEEEeccCCC
Confidence            976544221     1235667888864

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.84  E-value=1.2e-20  Score=196.90  Aligned_cols=103  Identities=45%  Similarity=0.739  Sum_probs=87.6

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      +|+++...|+++|+||++||+.|..++++||++....   ..              ..-+..+.+|||+||||||||++|
T Consensus         2 tP~~I~~~Ld~~IiGQ~eAkk~lsvAl~n~~~r~~~~---~~--------------~~~e~~p~~ILLiGppG~GKT~lA   64 (441)
T TIGR00390         2 TPREIVAELDKYIIGQDNAKKSVAIALRNRYRRSQLN---EE--------------LKDEVTPKNILMIGPTGVGKTEIA   64 (441)
T ss_pred             CHHHHHHHHhhhccCHHHHHHHHHHHHHhhhhhhccc---cc--------------cccccCCceEEEECCCCCCHHHHH
Confidence            7999999999999999999999999999999875321   00              011344689999999999999999


Q ss_pred             HHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhh
Q 012525          343 KTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA  382 (461)
Q Consensus       343 raLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a  382 (461)
                      ++||+.++.+|+.++++.+...+|+|.+.+..++.+|..+
T Consensus        65 raLA~~l~~~fi~vdat~~~e~g~vG~dvE~i~r~l~e~A  104 (441)
T TIGR00390        65 RRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAA  104 (441)
T ss_pred             HHHHHHhCCeEEEeecceeecCCcccCCHHHHHHHHHHHH
Confidence            9999999999999999988877899988888888877654

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.

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

Probab=99.83  E-value=2e-20  Score=189.86  Aligned_cols=153  Identities=28%  Similarity=0.410  Sum_probs=116.2

Q ss_pred             hcCChHHHHHHHHHHHHHHHHH--HHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKR--IYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kr--i~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .|-|+++.++.|+++|..+.+.  +|..   -|                 -.++++||||||||||||+||||+|++.+.
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~---~G-----------------I~PPKGVLLYGPPGTGKTLLAkAVA~~T~A  211 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEE---LG-----------------IDPPKGVLLYGPPGTGKTLLAKAVANQTDA  211 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHH---cC-----------------CCCCCceEeeCCCCCcHHHHHHHHHhccCc
Confidence            3899999999999999644321  2211   11                 134689999999999999999999999999


Q ss_pred             ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          352 PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       352 pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      .|+.+..+++.+ +|+|+. .++++.+|..|...    .++||||||||++..+|-..+.+.+..-.++.-.||..|||.
T Consensus       212 tFIrvvgSElVq-KYiGEG-aRlVRelF~lArek----aPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGF  285 (406)
T COG1222         212 TFIRVVGSELVQ-KYIGEG-ARLVRELFELAREK----APSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGF  285 (406)
T ss_pred             eEEEeccHHHHH-HHhccc-hHHHHHHHHHHhhc----CCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCC
Confidence            999999999995 699999 79999999988766    899999999999999987666665544333444555556665


Q ss_pred             eeeeecceeeecCCeEEEecCC----CCcCcCCC
Q 012525          432 ETKTFAAVSKVSRDNLYIKTSG----LDSKTLWP  461 (461)
Q Consensus       432 ~v~i~~~~r~~~rd~IiI~TsN----id~e~l~P  461 (461)
                      .-.         .+.-+|++||    +|+..++|
T Consensus       286 D~~---------~nvKVI~ATNR~D~LDPALLRP  310 (406)
T COG1222         286 DPR---------GNVKVIMATNRPDILDPALLRP  310 (406)
T ss_pred             CCC---------CCeEEEEecCCccccChhhcCC
Confidence            421         1566777777    34555554

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.82  E-value=4.1e-20  Score=192.87  Aligned_cols=104  Identities=43%  Similarity=0.742  Sum_probs=88.3

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .+|+++...|+++|+||++||+.|..++++||++....   .+              ...+..+.++||+||||||||++
T Consensus         4 ~~p~~I~~~Ld~~IiGQe~AkkalavAl~~~~~r~~l~---~~--------------~~~e~~~~~ILliGp~G~GKT~L   66 (443)
T PRK05201          4 LTPREIVSELDKYIIGQDDAKRAVAIALRNRWRRMQLP---EE--------------LRDEVTPKNILMIGPTGVGKTEI   66 (443)
T ss_pred             CCHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHhcCC---cc--------------cccccCCceEEEECCCCCCHHHH
Confidence            48999999999999999999999999999988764211   00              11223358999999999999999


Q ss_pred             HHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhh
Q 012525          342 AKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA  382 (461)
Q Consensus       342 AraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a  382 (461)
                      |++||+.++.+|+.++++.+.+.+|+|.+.+..++.++..+
T Consensus        67 Ar~LAk~l~~~fi~vD~t~f~e~GyvG~d~e~~ir~L~~~A  107 (443)
T PRK05201         67 ARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDLVEIA  107 (443)
T ss_pred             HHHHHHHhCChheeecchhhccCCcccCCHHHHHHHHHHHH
Confidence            99999999999999999999988999988888888887766

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

Probab=99.82  E-value=6.6e-20  Score=195.29  Aligned_cols=152  Identities=30%  Similarity=0.474  Sum_probs=120.4

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHH--HHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKR--IYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kr--i~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |++ |-++++++.+|..++....++  ++.+   .|                 -..+.+|||+||||||||+||||+|++
T Consensus       510 W~d-IGaL~~vR~eL~~aI~~PiK~pd~~k~---lG-----------------i~~PsGvLL~GPPGCGKTLlAKAVANE  568 (802)
T KOG0733|consen  510 WDD-IGALEEVRLELNMAILAPIKRPDLFKA---LG-----------------IDAPSGVLLCGPPGCGKTLLAKAVANE  568 (802)
T ss_pred             hhh-cccHHHHHHHHHHHHhhhccCHHHHHH---hC-----------------CCCCCceEEeCCCCccHHHHHHHHhhh
Confidence            344 889999999999999765332  2221   11                 122688999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      .+..|+.+...+|. ++|+|+. |..++.+|.+++.+    .+|||||||||.|.+.|+..+   ..++.+++|+||..|
T Consensus       569 ag~NFisVKGPELl-NkYVGES-ErAVR~vFqRAR~s----aPCVIFFDEiDaL~p~R~~~~---s~~s~RvvNqLLtEl  639 (802)
T KOG0733|consen  569 AGANFISVKGPELL-NKYVGES-ERAVRQVFQRARAS----APCVIFFDEIDALVPRRSDEG---SSVSSRVVNQLLTEL  639 (802)
T ss_pred             ccCceEeecCHHHH-HHHhhhH-HHHHHHHHHHhhcC----CCeEEEecchhhcCcccCCCC---chhHHHHHHHHHHHh
Confidence            99999999999999 4699999 99999999998865    899999999999999987644   334566999999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCC----CCcCcCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSG----LDSKTLWP  461 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsN----id~e~l~P  461 (461)
                      ||.+-+         +...+|++||    +|+..++|
T Consensus       640 DGl~~R---------~gV~viaATNRPDiIDpAiLRP  667 (802)
T KOG0733|consen  640 DGLEER---------RGVYVIAATNRPDIIDPAILRP  667 (802)
T ss_pred             cccccc---------cceEEEeecCCCcccchhhcCC
Confidence            987532         1456777777    34555554

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

Probab=99.82  E-value=4.8e-20  Score=200.19  Aligned_cols=155  Identities=28%  Similarity=0.434  Sum_probs=124.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHH--HHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHY--KRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~--kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |++ |-|.+++|..|.+.+..+.  +.++....                     ....+||||||||||||+||||+|.+
T Consensus       671 WdD-VGGLeevK~eIldTIqlPL~hpeLfssgl---------------------rkRSGILLYGPPGTGKTLlAKAVATE  728 (953)
T KOG0736|consen  671 WDD-VGGLEEVKTEILDTIQLPLKHPELFSSGL---------------------RKRSGILLYGPPGTGKTLLAKAVATE  728 (953)
T ss_pred             hhc-ccCHHHHHHHHHHHhcCcccChhhhhccc---------------------cccceeEEECCCCCchHHHHHHHHhh
Confidence            444 8999999999999996432  22332222                     22478999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      +...|+.+...++.. .|+|+. |..++++|++|+..    .||||||||+|.+.+.|+..+.+..+.++ ++++||..|
T Consensus       729 csL~FlSVKGPELLN-MYVGqS-E~NVR~VFerAR~A----~PCVIFFDELDSlAP~RG~sGDSGGVMDR-VVSQLLAEL  801 (953)
T KOG0736|consen  729 CSLNFLSVKGPELLN-MYVGQS-EENVREVFERARSA----APCVIFFDELDSLAPNRGRSGDSGGVMDR-VVSQLLAEL  801 (953)
T ss_pred             ceeeEEeecCHHHHH-HHhcch-HHHHHHHHHHhhcc----CCeEEEeccccccCccCCCCCCccccHHH-HHHHHHHHh
Confidence            999999999999995 599999 99999999998754    89999999999999999887777777654 999999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCC----CCcCcCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSG----LDSKTLWP  461 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsN----id~e~l~P  461 (461)
                      ||....       ...+..+|.+||    +|+..++|
T Consensus       802 Dgls~~-------~s~~VFViGATNRPDLLDpALLRP  831 (953)
T KOG0736|consen  802 DGLSDS-------SSQDVFVIGATNRPDLLDPALLRP  831 (953)
T ss_pred             hcccCC-------CCCceEEEecCCCccccChhhcCC
Confidence            977632       123678888888    34555544

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

Probab=99.80  E-value=1.6e-19  Score=194.02  Aligned_cols=143  Identities=29%  Similarity=0.385  Sum_probs=116.7

Q ss_pred             cCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          275 VIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      |.|+|++|+.|+++|....+  ..|...                    ....+++||||||||||||++||+||++++.+
T Consensus       436 IGGlE~lK~elq~~V~~p~~~pe~F~r~--------------------Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~n  495 (693)
T KOG0730|consen  436 IGGLEELKRELQQAVEWPLKHPEKFARF--------------------GISPPKGVLLYGPPGCGKTLLAKALANEAGMN  495 (693)
T ss_pred             ccCHHHHHHHHHHHHhhhhhchHHHHHh--------------------cCCCCceEEEECCCCcchHHHHHHHhhhhcCC
Confidence            78899999999999964322  111111                    12346889999999999999999999999999


Q ss_pred             eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCce
Q 012525          353 FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       353 fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      |+.+.+.++.. +|+|+. |+.++.+|+.++..    .++||||||||.+..+|++ +.+  ...++++++||+.|||..
T Consensus       496 FlsvkgpEL~s-k~vGeS-Er~ir~iF~kAR~~----aP~IiFfDEiDsi~~~R~g-~~~--~v~~RVlsqLLtEmDG~e  566 (693)
T KOG0730|consen  496 FLSVKGPELFS-KYVGES-ERAIREVFRKARQV----APCIIFFDEIDALAGSRGG-SSS--GVTDRVLSQLLTEMDGLE  566 (693)
T ss_pred             eeeccCHHHHH-HhcCch-HHHHHHHHHHHhhc----CCeEEehhhHHhHhhccCC-Ccc--chHHHHHHHHHHHccccc
Confidence            99999999994 699999 99999999998865    7899999999999999873 222  345679999999999876


Q ss_pred             eeeecceeeecCCeEEEecCCCC
Q 012525          433 TKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       433 v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ..         ++.++|++||..
T Consensus       567 ~~---------k~V~ViAATNRp  580 (693)
T KOG0730|consen  567 AL---------KNVLVIAATNRP  580 (693)
T ss_pred             cc---------CcEEEEeccCCh
Confidence            43         367888999854

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

Probab=99.80  E-value=1.8e-19  Score=176.76  Aligned_cols=145  Identities=32%  Similarity=0.451  Sum_probs=114.2

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+||++||+.-+..+.  |..--.....+                    .++|||||||||||||++|++||++.
T Consensus       119 t~dd-ViGqEeAK~kcrli~~--yLenPe~Fg~W--------------------APknVLFyGppGTGKTm~Akalane~  175 (368)
T COG1223         119 TLDD-VIGQEEAKRKCRLIME--YLENPERFGDW--------------------APKNVLFYGPPGTGKTMMAKALANEA  175 (368)
T ss_pred             cHhh-hhchHHHHHHHHHHHH--HhhChHHhccc--------------------CcceeEEECCCCccHHHHHHHHhccc
Confidence            3455 9999999997665552  22211112222                    26899999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.||+.+.++.+.. .++|+. ...++.++..+...    .+||+||||+|++.-+|+..+...++|  +++|+||..||
T Consensus       176 kvp~l~vkat~liG-ehVGdg-ar~Ihely~rA~~~----aPcivFiDE~DAiaLdRryQelRGDVs--EiVNALLTelD  247 (368)
T COG1223         176 KVPLLLVKATELIG-EHVGDG-ARRIHELYERARKA----APCIVFIDELDAIALDRRYQELRGDVS--EIVNALLTELD  247 (368)
T ss_pred             CCceEEechHHHHH-HHhhhH-HHHHHHHHHHHHhc----CCeEEEehhhhhhhhhhhHHHhcccHH--HHHHHHHHhcc
Confidence            99999999999985 488877 78889999888755    899999999999999998877777765  38999999999


Q ss_pred             CceeeeecceeeecCCeEEEecCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      |..-+         ...+.|++||.
T Consensus       248 gi~en---------eGVvtIaaTN~  263 (368)
T COG1223         248 GIKEN---------EGVVTIAATNR  263 (368)
T ss_pred             CcccC---------CceEEEeecCC
Confidence            76532         24677777774

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

Probab=99.80  E-value=4e-19  Score=176.87  Aligned_cols=146  Identities=24%  Similarity=0.445  Sum_probs=118.0

Q ss_pred             HHhhcCChHHHHHHHHHHHHHH--HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNH--YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~--~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |++ |.|++.||+.|+++|...  +..++...+                     .+.+.|||+|||||||+.||+++|.+
T Consensus       132 WsD-VAGLE~AKeALKEAVILPIKFPqlFtGkR---------------------~PwrgiLLyGPPGTGKSYLAKAVATE  189 (439)
T KOG0739|consen  132 WSD-VAGLEGAKEALKEAVILPIKFPQLFTGKR---------------------KPWRGILLYGPPGTGKSYLAKAVATE  189 (439)
T ss_pred             hhh-hccchhHHHHHHhheeecccchhhhcCCC---------------------CcceeEEEeCCCCCcHHHHHHHHHhh
Confidence            344 899999999999999754  333443332                     23488999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      .+..|+.++.++|. ++|.|+. |+.+.++|..++..    +++||||||||.++..|+.   ....+.+++...||..|
T Consensus       190 AnSTFFSvSSSDLv-SKWmGES-EkLVknLFemARe~----kPSIIFiDEiDslcg~r~e---nEseasRRIKTEfLVQM  260 (439)
T KOG0739|consen  190 ANSTFFSVSSSDLV-SKWMGES-EKLVKNLFEMAREN----KPSIIFIDEIDSLCGSRSE---NESEASRRIKTEFLVQM  260 (439)
T ss_pred             cCCceEEeehHHHH-HHHhccH-HHHHHHHHHHHHhc----CCcEEEeehhhhhccCCCC---CchHHHHHHHHHHHHhh
Confidence            99999999999999 5799999 99999999988866    8999999999999988654   33455677999999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +|.-.+        ....+++.++|+.
T Consensus       261 qGVG~d--------~~gvLVLgATNiP  279 (439)
T KOG0739|consen  261 QGVGND--------NDGVLVLGATNIP  279 (439)
T ss_pred             hccccC--------CCceEEEecCCCc
Confidence            965432        1246777788864

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

Probab=99.79  E-value=3e-19  Score=188.03  Aligned_cols=155  Identities=25%  Similarity=0.381  Sum_probs=120.8

Q ss_pred             CHHHH-HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          263 TPKEI-CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       263 t~~el-~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .|... ...+++ |.|.|+||+.|++.|.  |.+--..                 +-......+++|||.||||||||+|
T Consensus       294 ~p~~~~nv~F~d-VkG~DEAK~ELeEiVe--fLkdP~k-----------------ftrLGGKLPKGVLLvGPPGTGKTlL  353 (752)
T KOG0734|consen  294 DPEQMKNVTFED-VKGVDEAKQELEEIVE--FLKDPTK-----------------FTRLGGKLPKGVLLVGPPGTGKTLL  353 (752)
T ss_pred             Chhhhccccccc-ccChHHHHHHHHHHHH--HhcCcHH-----------------hhhccCcCCCceEEeCCCCCchhHH
Confidence            34333 444555 9999999999999884  2211111                 1111224468899999999999999


Q ss_pred             HHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHH
Q 012525          342 AKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQ  421 (461)
Q Consensus       342 AraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~  421 (461)
                      |||+|.+.++||+....+++.+. |+|.. .+.++.+|..+...    .||||||||||.+..+|......   ..++.+
T Consensus       354 ARAvAGEA~VPFF~~sGSEFdEm-~VGvG-ArRVRdLF~aAk~~----APcIIFIDEiDavG~kR~~~~~~---y~kqTl  424 (752)
T KOG0734|consen  354 ARAVAGEAGVPFFYASGSEFDEM-FVGVG-ARRVRDLFAAAKAR----APCIIFIDEIDAVGGKRNPSDQH---YAKQTL  424 (752)
T ss_pred             HHHhhcccCCCeEeccccchhhh-hhccc-HHHHHHHHHHHHhc----CCeEEEEechhhhcccCCccHHH---HHHHHH
Confidence            99999999999999999999865 89988 79999999988765    89999999999999987644332   456689


Q ss_pred             HHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          422 QALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       422 ~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      |+||..|||...+         ...|+|++||+.
T Consensus       425 NQLLvEmDGF~qN---------eGiIvigATNfp  449 (752)
T KOG0734|consen  425 NQLLVEMDGFKQN---------EGIIVIGATNFP  449 (752)
T ss_pred             HHHHHHhcCcCcC---------CceEEEeccCCh
Confidence            9999999988755         257999999964

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

Probab=99.77  E-value=9.3e-19  Score=192.46  Aligned_cols=150  Identities=27%  Similarity=0.394  Sum_probs=120.1

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ |.|.|+||+.|.+.|.  |.+                 ...++.+.-+..++++||+||||||||+||||+|.+.
T Consensus       309 ~FkD-VAG~deAK~El~E~V~--fLK-----------------NP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA  368 (774)
T KOG0731|consen  309 KFKD-VAGVDEAKEELMEFVK--FLK-----------------NPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA  368 (774)
T ss_pred             cccc-ccCcHHHHHHHHHHHH--Hhc-----------------CHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc
Confidence            4555 9999999999999993  221                 1122333345667999999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhc-cccccccchHHHHHHHHHHH
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAES-LNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~-~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++||+.++++++.+. ++|.. ...++.+|..+..+    .|+||||||||.+...|.. .........+..+|+||..|
T Consensus       369 gVPF~svSGSEFvE~-~~g~~-asrvr~lf~~ar~~----aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~em  442 (774)
T KOG0731|consen  369 GVPFFSVSGSEFVEM-FVGVG-ASRVRDLFPLARKN----APSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEM  442 (774)
T ss_pred             CCceeeechHHHHHH-hcccc-hHHHHHHHHHhhcc----CCeEEEecccccccccccccccCCCChHHHHHHHHHHHHh
Confidence            999999999999975 77776 78999999988766    7999999999999999842 33355566778999999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ||....         ...|++++||.
T Consensus       443 Dgf~~~---------~~vi~~a~tnr  459 (774)
T KOG0731|consen  443 DGFETS---------KGVIVLAATNR  459 (774)
T ss_pred             cCCcCC---------CcEEEEeccCC
Confidence            987543         24688888883

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

Probab=99.75  E-value=4.2e-18  Score=181.68  Aligned_cols=150  Identities=29%  Similarity=0.398  Sum_probs=119.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHh--hhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHA--NLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~--~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|.+ |-|.+.....|.+.+..    +.+.  ....|                 -.++++|||+||||||||+||++||.
T Consensus       188 ~f~d-iGG~d~~~~el~~li~~----i~~Pe~~~~lG-----------------v~PprGvLlHGPPGCGKT~lA~AiAg  245 (802)
T KOG0733|consen  188 SFSD-IGGLDKTLAELCELIIH----IKHPEVFSSLG-----------------VRPPRGVLLHGPPGCGKTSLANAIAG  245 (802)
T ss_pred             chhh-ccChHHHHHHHHHHHHH----hcCchhHhhcC-----------------CCCCCceeeeCCCCccHHHHHHHHhh
Confidence            4444 89999999999888742    1111  11111                 23468999999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      ++++||+.+.+.++. .++.|+. |+.++++|+.+...    .++|+||||||++.++|+.   ......++++.+||..
T Consensus       246 el~vPf~~isApeiv-SGvSGES-EkkiRelF~~A~~~----aPcivFiDeIDAI~pkRe~---aqreMErRiVaQLlt~  316 (802)
T KOG0733|consen  246 ELGVPFLSISAPEIV-SGVSGES-EKKIRELFDQAKSN----APCIVFIDEIDAITPKREE---AQREMERRIVAQLLTS  316 (802)
T ss_pred             hcCCceEeecchhhh-cccCccc-HHHHHHHHHHHhcc----CCeEEEeecccccccchhh---HHHHHHHHHHHHHHHh
Confidence            999999999999999 6899999 89999999998766    8999999999999999875   4455667899999999


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ||+-.....     .....++|.+||..
T Consensus       317 mD~l~~~~~-----~g~~VlVIgATnRP  339 (802)
T KOG0733|consen  317 MDELSNEKT-----KGDPVLVIGATNRP  339 (802)
T ss_pred             hhccccccc-----CCCCeEEEecCCCC
Confidence            997654321     12358899888853

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

Probab=99.75  E-value=1.6e-18  Score=191.51  Aligned_cols=168  Identities=28%  Similarity=0.372  Sum_probs=135.1

Q ss_pred             CCCCCCCCCCCCCCCCHHH----HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccc
Q 012525          248 GGSRWGGSNLGEDLPTPKE----ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVEL  323 (461)
Q Consensus       248 ~~~~w~g~~l~~~l~t~~e----l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~  323 (461)
                      ..++|+++++.+....+.+    +...|.+.|+||+.|++.+..++......+....                      .
T Consensus       462 vv~~~TgIPv~~l~~~e~~kll~le~~L~~rViGQd~AV~avs~aIrraRaGL~dp~----------------------r  519 (786)
T COG0542         462 VVARWTGIPVAKLLEDEKEKLLNLERRLKKRVIGQDEAVEAVSDAIRRARAGLGDPN----------------------R  519 (786)
T ss_pred             HHHHHHCCChhhhchhhHHHHHHHHHHHhcceeChHHHHHHHHHHHHHHhcCCCCCC----------------------C
Confidence            3688999999987766664    7888889999999999999999953322211111                      1


Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhcc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAA  389 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a  389 (461)
                      +....||.||+|+|||.||++||..+.   ..+++++++++.+.           ||+|......|.+.....       
T Consensus       520 PigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLIGaPPGYVGyeeGG~LTEaVRr~-------  592 (786)
T COG0542         520 PIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRK-------  592 (786)
T ss_pred             CceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHhCCCCCCceeccccchhHhhhcC-------
Confidence            124689999999999999999999996   68999999987754           899988777777776544       


Q ss_pred             CceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          390 QQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       390 ~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      ..+||+||||++..++              +++.||++||.+..+......-..+++|+|.|||++.+.
T Consensus       593 PySViLlDEIEKAHpd--------------V~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~  647 (786)
T COG0542         593 PYSVILLDEIEKAHPD--------------VFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEE  647 (786)
T ss_pred             CCeEEEechhhhcCHH--------------HHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHH
Confidence            4569999999999999              999999999999888766655555699999999999764

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

Probab=99.73  E-value=1.7e-17  Score=167.57  Aligned_cols=102  Identities=42%  Similarity=0.756  Sum_probs=89.8

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .||+++...||++|+||++||+.+..++.|+|.+..-..                 .-.-+..+.|||+.||+|+|||.+
T Consensus         4 ~tPreIV~eLd~yIIGQ~~AKkaVAIALRNR~RR~qL~~-----------------~lr~EV~PKNILMIGpTGVGKTEI   66 (444)
T COG1220           4 MTPREIVSELDRYIIGQDEAKKAVAIALRNRWRRMQLEE-----------------ELRDEVTPKNILMIGPTGVGKTEI   66 (444)
T ss_pred             CCHHHHHHHHHhHhcCcHHHHHHHHHHHHHHHHHHhcCH-----------------HHhhccCccceEEECCCCCcHHHH
Confidence            589999999999999999999999999999998754221                 112345689999999999999999


Q ss_pred             HHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHH
Q 012525          342 AKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLA  380 (461)
Q Consensus       342 AraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~  380 (461)
                      ||.||+..+.||+.+.++-+++.||+|.+++++++.+..
T Consensus        67 ARRLAkl~~aPFiKVEATKfTEVGYVGrDVesivRDLve  105 (444)
T COG1220          67 ARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVE  105 (444)
T ss_pred             HHHHHHHhCCCeEEEEeeeeeecccccccHHHHHHHHHH
Confidence            999999999999999999999999999999999887665

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

Probab=99.69  E-value=7.7e-17  Score=180.07  Aligned_cols=166  Identities=20%  Similarity=0.295  Sum_probs=120.6

Q ss_pred             CCCCCCCCCCCCCCCHH----HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhcccccccccc
Q 012525          249 GSRWGGSNLGEDLPTPK----EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELE  324 (461)
Q Consensus       249 ~~~w~g~~l~~~l~t~~----el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~  324 (461)
                      .++|+++++........    .+.+.|.+.|+||++|++.|..++......+...                      ..+
T Consensus       430 ~~~~tgip~~~~~~~~~~~l~~l~~~L~~~ViGQ~~ai~~l~~~i~~~~~gl~~~----------------------~kp  487 (758)
T PRK11034        430 VARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMSRAGLGHE----------------------HKP  487 (758)
T ss_pred             HHHHhCCChhhhhhhHHHHHHHHHHHhcceEeCcHHHHHHHHHHHHHHhccccCC----------------------CCC
Confidence            57899988876554443    5778888889999999999999985332211100                      011


Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhccCceE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAAQQGM  393 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a~~gV  393 (461)
                      ..++||+||||||||++|++||+.++.+|+.++++++.+.           +|+|......+...+.       ....+|
T Consensus       488 ~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~LiG~~~gyvg~~~~g~L~~~v~-------~~p~sV  560 (758)
T PRK11034        488 VGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVI-------KHPHAV  560 (758)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHcCCCCCcccccccchHHHHHH-------hCCCcE
Confidence            2569999999999999999999999999999999876531           3444432333433332       235689


Q ss_pred             EEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          394 VYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       394 LfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      |||||||++.+.              +++.||++||++.+..........++.|+|.|||.+.+
T Consensus       561 lllDEieka~~~--------------v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~  610 (758)
T PRK11034        561 LLLDEIEKAHPD--------------VFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVR  610 (758)
T ss_pred             EEeccHhhhhHH--------------HHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHH
Confidence            999999999988              99999999998877643322222348999999998754

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

Probab=99.68  E-value=9.5e-17  Score=173.68  Aligned_cols=150  Identities=27%  Similarity=0.369  Sum_probs=119.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.+ |.|.|++|+.|.+.|.  +.+                 ...++..--+.-+++|||.||||||||+|||++|.+.
T Consensus       148 ~F~D-VAG~dEakeel~EiVd--fLk-----------------~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA  207 (596)
T COG0465         148 TFAD-VAGVDEAKEELSELVD--FLK-----------------NPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA  207 (596)
T ss_pred             Chhh-hcCcHHHHHHHHHHHH--HHh-----------------CchhhHhcccccccceeEecCCCCCcHHHHHHHhccc
Confidence            4455 8999999999999884  111                 0111111122446889999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ++||+.++.++..+. |+|.. .+.++.+|.++...    .+|||||||||++...|.....+.++..++.+++||..||
T Consensus       208 ~VPFf~iSGS~FVem-fVGvG-AsRVRdLF~qAkk~----aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmD  281 (596)
T COG0465         208 GVPFFSISGSDFVEM-FVGVG-ASRVRDLFEQAKKN----APCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMD  281 (596)
T ss_pred             CCCceeccchhhhhh-hcCCC-cHHHHHHHHHhhcc----CCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhc
Confidence            999999999999975 88888 78999999988765    7899999999999999876656677778889999999999


Q ss_pred             CceeeeecceeeecCCeEEEecCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      |...+         ...|+|++||.
T Consensus       282 GF~~~---------~gviviaaTNR  297 (596)
T COG0465         282 GFGGN---------EGVIVIAATNR  297 (596)
T ss_pred             cCCCC---------CceEEEecCCC
Confidence            77522         24577777774

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

Probab=99.68  E-value=3.7e-16  Score=160.84  Aligned_cols=127  Identities=13%  Similarity=0.161  Sum_probs=95.1

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhh-hccCceEEEEcCcccc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNV-EAAQQGMVYIDEVDKI  402 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v-~~a~~gVLfIDEID~L  402 (461)
                      .+..++|+||||||||++|+++|++++.+|+.+++.++. .+|+|+. |+.++.+|..+.... ...+++||||||||++
T Consensus       147 ~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~-sk~vGEs-Ek~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~  224 (413)
T PLN00020        147 VPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELE-SENAGEP-GKLIRQRYREAADIIKKKGKMSCLFINDLDAG  224 (413)
T ss_pred             CCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhh-cCcCCcH-HHHHHHHHHHHHHHhhccCCCeEEEEehhhhc
Confidence            357899999999999999999999999999999999999 5699999 999999999886543 3457999999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhCce-eeeecc--eeeecCCeEEEecCCC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEGTE-TKTFAA--VSKVSRDNLYIKTSGL  454 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~-v~i~~~--~r~~~rd~IiI~TsNi  454 (461)
                      ...|...  ...+....+..+|+.+||+-. +.....  ......+..+|+|+|.
T Consensus       225 ~g~r~~~--~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNr  277 (413)
T PLN00020        225 AGRFGTT--QYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGND  277 (413)
T ss_pred             CCCCCCC--CcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCC
Confidence            9987532  222222334579999998632 111111  1112235777888873

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

Probab=99.67  E-value=2.1e-16  Score=171.01  Aligned_cols=144  Identities=31%  Similarity=0.423  Sum_probs=114.2

Q ss_pred             cCChHHHHHHHHHHHHHH--HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          275 VIGQEKAKKVLSVAVYNH--YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~--~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      |.|..++|+.|.+.+..+  |..++....-                    ....+||||||||||||+||-++|..++..
T Consensus       669 igg~~~~k~~l~~~i~~P~kyp~if~~~pl--------------------r~~~giLLyGppGcGKT~la~a~a~~~~~~  728 (952)
T KOG0735|consen  669 IGGLFEAKKVLEEVIEWPSKYPQIFANCPL--------------------RLRTGILLYGPPGCGKTLLASAIASNSNLR  728 (952)
T ss_pred             cccHHHHHHHHHHHHhccccchHHHhhCCc--------------------ccccceEEECCCCCcHHHHHHHHHhhCCee
Confidence            789999999999999743  5555543211                    124779999999999999999999999999


Q ss_pred             eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCce
Q 012525          353 FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       353 fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      |+.+...++. .+|+|.. |..++.+|.++..    ++||||||||+|.+.++|+-++.+  +. ++++|+||..|||.+
T Consensus       729 fisvKGPElL-~KyIGaS-Eq~vR~lF~rA~~----a~PCiLFFDEfdSiAPkRGhDsTG--VT-DRVVNQlLTelDG~E  799 (952)
T KOG0735|consen  729 FISVKGPELL-SKYIGAS-EQNVRDLFERAQS----AKPCILFFDEFDSIAPKRGHDSTG--VT-DRVVNQLLTELDGAE  799 (952)
T ss_pred             EEEecCHHHH-HHHhccc-HHHHHHHHHHhhc----cCCeEEEeccccccCcccCCCCCC--ch-HHHHHHHHHhhcccc
Confidence            9999999999 4699999 8999999998864    599999999999999998654333  22 459999999999876


Q ss_pred             eeeecceeeecCCeEEEecCCCC
Q 012525          433 TKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       433 v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      -...        =.|+-+|+.+|
T Consensus       800 gl~G--------V~i~aaTsRpd  814 (952)
T KOG0735|consen  800 GLDG--------VYILAATSRPD  814 (952)
T ss_pred             ccce--------EEEEEecCCcc
Confidence            4311        13555666654

>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=99.66  E-value=6.8e-16  Score=149.67  Aligned_cols=129  Identities=27%  Similarity=0.438  Sum_probs=81.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ ++||+.+++.+...+....        ..+                  ....|+|||||||+||||||+.||+++
T Consensus        22 ~L~e-fiGQ~~l~~~l~i~i~aa~--------~r~------------------~~l~h~lf~GPPG~GKTTLA~IIA~e~   74 (233)
T PF05496_consen   22 SLDE-FIGQEHLKGNLKILIRAAK--------KRG------------------EALDHMLFYGPPGLGKTTLARIIANEL   74 (233)
T ss_dssp             SCCC-S-S-HHHHHHHHHHHHHHH--------CTT------------------S---EEEEESSTTSSHHHHHHHHHHHC
T ss_pred             CHHH-ccCcHHHHhhhHHHHHHHH--------hcC------------------CCcceEEEECCCccchhHHHHHHHhcc
Confidence            4566 7999999999887773211        110                  113689999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+|..+++..+...        ..+..++...      ..+.||||||||++.+.              +++.|+..||
T Consensus        75 ~~~~~~~sg~~i~k~--------~dl~~il~~l------~~~~ILFIDEIHRlnk~--------------~qe~LlpamE  126 (233)
T PF05496_consen   75 GVNFKITSGPAIEKA--------GDLAAILTNL------KEGDILFIDEIHRLNKA--------------QQEILLPAME  126 (233)
T ss_dssp             T--EEEEECCC--SC--------HHHHHHHHT--------TT-EEEECTCCC--HH--------------HHHHHHHHHH
T ss_pred             CCCeEeccchhhhhH--------HHHHHHHHhc------CCCcEEEEechhhccHH--------------HHHHHHHHhc
Confidence            999998887655431        2222333221      24669999999999999              9999999999


Q ss_pred             Cceeeeecce------eeecC-CeEEEecCC
Q 012525          430 GTETKTFAAV------SKVSR-DNLYIKTSG  453 (461)
Q Consensus       430 g~~v~i~~~~------r~~~r-d~IiI~TsN  453 (461)
                      .+.+.+....      ....- .|.+|.+|+
T Consensus       127 d~~idiiiG~g~~ar~~~~~l~~FTligATT  157 (233)
T PF05496_consen  127 DGKIDIIIGKGPNARSIRINLPPFTLIGATT  157 (233)
T ss_dssp             CSEEEEEBSSSSS-BEEEEE----EEEEEES
T ss_pred             cCeEEEEeccccccceeeccCCCceEeeeec
Confidence            9988765441      22222 577775543

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.

>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=99.65  E-value=1.1e-16  Score=149.42  Aligned_cols=126  Identities=40%  Similarity=0.557  Sum_probs=99.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      ..++||+||+|||||.||++||+.+..    +++.++++.+..    +++.+..+..++......+...+.+||||||||
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~----~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEid   78 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSE----GDDVESSVSKLLGSPPGYVGAEEGGVVLLDEID   78 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCS----HHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGG
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccc----cchHHhhhhhhhhcccceeeccchhhhhhHHHh
Confidence            367999999999999999999999996    999999999886    222234455666666666666677799999999


Q ss_pred             ccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          401 KITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       401 ~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ++.+.   .+...+++.+.+++.||++||++.+...........+.|+|+|+|+...
T Consensus        79 Ka~~~---~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~~  132 (171)
T PF07724_consen   79 KAHPS---NSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGAE  132 (171)
T ss_dssp             GCSHT---TTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSSTH
T ss_pred             hcccc---ccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccccc
Confidence            99996   4456788888899999999998888754432333348999999998754

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 ....

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

Probab=99.64  E-value=7e-16  Score=172.40  Aligned_cols=166  Identities=22%  Similarity=0.293  Sum_probs=120.5

Q ss_pred             CCCCCCCCCCCCC----CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhcccccccccc
Q 012525          249 GSRWGGSNLGEDL----PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELE  324 (461)
Q Consensus       249 ~~~w~g~~l~~~l----~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~  324 (461)
                      ...|+++++....    ....++.+.|.+.|+||+.+++.|..++......+.     .                 -...
T Consensus       426 i~~~tgiP~~~~~~~~~~~l~~l~~~l~~~v~GQ~~ai~~l~~~i~~~~~g~~-----~-----------------~~~p  483 (731)
T TIGR02639       426 VAKMAHIPVKTVSVDDREKLKNLEKNLKAKIFGQDEAIDSLVSSIKRSRAGLG-----N-----------------PNKP  483 (731)
T ss_pred             HHHHhCCChhhhhhHHHHHHHHHHHHHhcceeCcHHHHHHHHHHHHHHhcCCC-----C-----------------CCCC
Confidence            4568888765533    233468899999999999999999888842111000     0                 0011


Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhh-----------cCcccccHHHHHHHHHHhhchhhhccCceE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQ-----------AGYVGEDVESILYKLLAQAEFNVEAAQQGM  393 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~-----------~g~vGe~~e~~L~~lf~~a~~~v~~a~~gV  393 (461)
                      ..++||+||+|||||+||++||+.++.+++.++++++.+           .+|+|......+...+..       ...+|
T Consensus       484 ~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~~~~lig~~~gyvg~~~~~~l~~~~~~-------~p~~V  556 (731)
T TIGR02639       484 VGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQGGLLTEAVRK-------HPHCV  556 (731)
T ss_pred             ceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhcccHHHHhcCCCCCcccchhhHHHHHHHh-------CCCeE
Confidence            245899999999999999999999999999999887643           255665544445444432       35679


Q ss_pred             EEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeec-CCeEEEecCCCCcCc
Q 012525          394 VYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVS-RDNLYIKTSGLDSKT  458 (461)
Q Consensus       394 LfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~-rd~IiI~TsNid~e~  458 (461)
                      |||||||++.+.              +++.|+++||++.+.... .+... ++.++|+|||++.+.
T Consensus       557 vllDEieka~~~--------------~~~~Ll~~ld~g~~~d~~-g~~vd~~~~iii~Tsn~g~~~  607 (731)
T TIGR02639       557 LLLDEIEKAHPD--------------IYNILLQVMDYATLTDNN-GRKADFRNVILIMTSNAGASE  607 (731)
T ss_pred             EEEechhhcCHH--------------HHHHHHHhhccCeeecCC-CcccCCCCCEEEECCCcchhh
Confidence            999999999988              999999999988776432 33333 389999999998653

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

Probab=99.64  E-value=8.9e-16  Score=150.44  Aligned_cols=135  Identities=27%  Similarity=0.398  Sum_probs=105.7

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |.|.+-.|+.+++++...... ....++.|                 -.++++||||||||||||+||+++|+.....|+
T Consensus       157 iggld~qkqeireavelplt~-~~ly~qig-----------------idpprgvllygppg~gktml~kava~~t~a~fi  218 (408)
T KOG0727|consen  157 IGGLDVQKQEIREAVELPLTH-ADLYKQIG-----------------IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFI  218 (408)
T ss_pred             cccchhhHHHHHHHHhccchH-HHHHHHhC-----------------CCCCcceEEeCCCCCcHHHHHHHHhhccchhee
Confidence            889999999999998632211 00111112                 134689999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCcee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTET  433 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v  433 (461)
                      ++..+++.+ +|.|+. ...++.+|..+..+    .++||||||||.+..+|=....+.+..-.+++-.||..|||...
T Consensus       219 rvvgsefvq-kylgeg-prmvrdvfrlaken----apsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq  291 (408)
T KOG0727|consen  219 RVVGSEFVQ-KYLGEG-PRMVRDVFRLAKEN----APSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQ  291 (408)
T ss_pred             eeccHHHHH-HHhccC-cHHHHHHHHHHhcc----CCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCc
Confidence            999999995 599999 78999999887765    78999999999999998766666665555566677777887643

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

Probab=99.64  E-value=1.3e-15  Score=162.49  Aligned_cols=145  Identities=32%  Similarity=0.419  Sum_probs=111.5

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +.|.+.+|+.+.+++....+.... ....+                 ...+.++||+||||||||+||+++|.+++.+|+
T Consensus       244 iggl~~~k~~l~e~v~~~~~~~e~-~~~~~-----------------~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi  305 (494)
T COG0464         244 IGGLEEAKEELKEAIETPLKRPEL-FRKLG-----------------LRPPKGVLLYGPPGTGKTLLAKAVALESRSRFI  305 (494)
T ss_pred             hhcHHHHHHHHHHHHHhHhhChHH-HHhcC-----------------CCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEE
Confidence            678999999999998654332211 00000                 122368999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK  434 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~  434 (461)
                      .++..++. .+|+|+. ++.++.+|..+...    .++||||||||++...|...+   +.+.++++++||..|++....
T Consensus       306 ~v~~~~l~-sk~vGes-ek~ir~~F~~A~~~----~p~iiFiDEiDs~~~~r~~~~---~~~~~r~~~~lL~~~d~~e~~  376 (494)
T COG0464         306 SVKGSELL-SKWVGES-EKNIRELFEKARKL----APSIIFIDEIDSLASGRGPSE---DGSGRRVVGQLLTELDGIEKA  376 (494)
T ss_pred             EeeCHHHh-ccccchH-HHHHHHHHHHHHcC----CCcEEEEEchhhhhccCCCCC---chHHHHHHHHHHHHhcCCCcc
Confidence            99999888 5799998 99999999988744    899999999999999975432   222356999999999865422


Q ss_pred             eecceeeecCCeEEEecCCCC
Q 012525          435 TFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       435 i~~~~r~~~rd~IiI~TsNid  455 (461)
                               .+.++|+|||..
T Consensus       377 ---------~~v~vi~aTN~p  388 (494)
T COG0464         377 ---------EGVLVIAATNRP  388 (494)
T ss_pred             ---------CceEEEecCCCc
Confidence                     146778888853

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.62  E-value=2.7e-15  Score=167.67  Aligned_cols=146  Identities=25%  Similarity=0.393  Sum_probs=111.5

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |++ |.|++.+|+.|.+.+....+  .++...   +                 ...+.++||+||||||||++|++||++
T Consensus       452 ~~d-i~g~~~~k~~l~~~v~~~~~~~~~~~~~---g-----------------~~~~~giLL~GppGtGKT~lakalA~e  510 (733)
T TIGR01243       452 WSD-IGGLEEVKQELREAVEWPLKHPEIFEKM---G-----------------IRPPKGVLLFGPPGTGKTLLAKAVATE  510 (733)
T ss_pred             hhh-cccHHHHHHHHHHHHHhhhhCHHHHHhc---C-----------------CCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            444 89999999999998864322  221110   1                 122467999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++.+|+.+.++++.. +|+|+. +..++.+|..+...    .++||||||||.|...|+....  ....++++++||..|
T Consensus       511 ~~~~fi~v~~~~l~~-~~vGes-e~~i~~~f~~A~~~----~p~iifiDEid~l~~~r~~~~~--~~~~~~~~~~lL~~l  582 (733)
T TIGR01243       511 SGANFIAVRGPEILS-KWVGES-EKAIREIFRKARQA----APAIIFFDEIDAIAPARGARFD--TSVTDRIVNQLLTEM  582 (733)
T ss_pred             cCCCEEEEehHHHhh-cccCcH-HHHHHHHHHHHHhc----CCEEEEEEChhhhhccCCCCCC--ccHHHHHHHHHHHHh
Confidence            999999999999884 699988 88899999887644    7899999999999988653221  223456899999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ++...         ..+.++|+|||.
T Consensus       583 dg~~~---------~~~v~vI~aTn~  599 (733)
T TIGR01243       583 DGIQE---------LSNVVVIAATNR  599 (733)
T ss_pred             hcccC---------CCCEEEEEeCCC
Confidence            97431         135788888885

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.62  E-value=1.3e-15  Score=172.11  Aligned_cols=166  Identities=27%  Similarity=0.339  Sum_probs=121.1

Q ss_pred             CCCCCCCCCCCCCCCHH----HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhcccccccccc
Q 012525          249 GSRWGGSNLGEDLPTPK----EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELE  324 (461)
Q Consensus       249 ~~~w~g~~l~~~l~t~~----el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~  324 (461)
                      .+.|+++++.+......    .+.+.|.+.|+||+.|++.|..++......+....                      .+
T Consensus       481 ~~~~tgip~~~~~~~~~~~l~~l~~~L~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~----------------------~p  538 (821)
T CHL00095        481 VSAWTGIPVNKLTKSESEKLLHMEETLHKRIIGQDEAVVAVSKAIRRARVGLKNPN----------------------RP  538 (821)
T ss_pred             HHHHHCCCchhhchhHHHHHHHHHHHhcCcCcChHHHHHHHHHHHHHHhhcccCCC----------------------CC
Confidence            68899999887665543    48889999999999999999998854332221110                      11


Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhh-----------cCcccccHHHHHHHHHHhhchhhhccC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQ-----------AGYVGEDVESILYKLLAQAEFNVEAAQ  390 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~-----------~g~vGe~~e~~L~~lf~~a~~~v~~a~  390 (461)
                      ...+||+||+|||||+||++||+.+.   .+++.++++++.+           .+|+|......+...+..       ..
T Consensus       539 ~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l~g~~~gyvg~~~~~~l~~~~~~-------~p  611 (821)
T CHL00095        539 IASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAVRK-------KP  611 (821)
T ss_pred             ceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccHHHhcCCCCcccCcCccchHHHHHHh-------CC
Confidence            13589999999999999999999873   5788888876532           245555433444443322       24


Q ss_pred             ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          391 QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       391 ~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      .+||||||||++.+.              +++.|+++||.+.+..........++.|+|.|||++..
T Consensus       612 ~~VvllDeieka~~~--------------v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~  664 (821)
T CHL00095        612 YTVVLFDEIEKAHPD--------------IFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSK  664 (821)
T ss_pred             CeEEEECChhhCCHH--------------HHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchH
Confidence            579999999999988              99999999998877654432222348999999998754

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.62  E-value=2e-15  Score=161.69  Aligned_cols=150  Identities=29%  Similarity=0.369  Sum_probs=108.0

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++.+|+.|.+.+.. .+. .......+                 ...+.++||+||||||||++|++||+++
T Consensus        53 ~~~d-i~g~~~~k~~l~~~~~~-l~~-~~~~~~~g-----------------~~~~~giLL~GppGtGKT~la~alA~~~  112 (495)
T TIGR01241        53 TFKD-VAGIDEAKEELMEIVDF-LKN-PSKFTKLG-----------------AKIPKGVLLVGPPGTGKTLLAKAVAGEA  112 (495)
T ss_pred             CHHH-hCCHHHHHHHHHHHHHH-HHC-HHHHHhcC-----------------CCCCCcEEEECCCCCCHHHHHHHHHHHc
Confidence            4666 89999999999987742 110 00000011                 1234789999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+|+.++++++.. .+.|.. +..++.+|..+...    .++||||||||.+..++.......+.....+++.||..|+
T Consensus       113 ~~~~~~i~~~~~~~-~~~g~~-~~~l~~~f~~a~~~----~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d  186 (495)
T TIGR01241       113 GVPFFSISGSDFVE-MFVGVG-ASRVRDLFEQAKKN----APCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMD  186 (495)
T ss_pred             CCCeeeccHHHHHH-HHhccc-HHHHHHHHHHHHhc----CCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhc
Confidence            99999999998874 366766 67888888776543    6889999999999988654322333344568889999998


Q ss_pred             CceeeeecceeeecCCeEEEecCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +..-.         ...++|+|||.
T Consensus       187 ~~~~~---------~~v~vI~aTn~  202 (495)
T TIGR01241       187 GFGTN---------TGVIVIAATNR  202 (495)
T ss_pred             cccCC---------CCeEEEEecCC
Confidence            54311         14678888875

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

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.62  E-value=4.1e-15  Score=159.19  Aligned_cols=140  Identities=25%  Similarity=0.356  Sum_probs=101.8

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |.|++.+|+.|...... +..   .....+                 ...+++|||+||||||||++|+++|++++.+|+
T Consensus       230 vgGl~~lK~~l~~~~~~-~~~---~~~~~g-----------------l~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~  288 (489)
T CHL00195        230 IGGLDNLKDWLKKRSTS-FSK---QASNYG-----------------LPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLL  288 (489)
T ss_pred             hcCHHHHHHHHHHHHHH-hhH---HHHhcC-----------------CCCCceEEEECCCCCcHHHHHHHHHHHhCCCEE
Confidence            89999999988764421 110   001111                 123578999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK  434 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~  434 (461)
                      .+++..+. .+|+|+. +..++.+|..+..    ..++||||||||++...+....  ......++++.|+..|++..  
T Consensus       289 ~l~~~~l~-~~~vGes-e~~l~~~f~~A~~----~~P~IL~IDEID~~~~~~~~~~--d~~~~~rvl~~lL~~l~~~~--  358 (489)
T CHL00195        289 RLDVGKLF-GGIVGES-ESRMRQMIRIAEA----LSPCILWIDEIDKAFSNSESKG--DSGTTNRVLATFITWLSEKK--  358 (489)
T ss_pred             EEEhHHhc-ccccChH-HHHHHHHHHHHHh----cCCcEEEehhhhhhhccccCCC--CchHHHHHHHHHHHHHhcCC--
Confidence            99999888 4689987 7888999976654    3799999999999887533211  12233457888888887421  


Q ss_pred             eecceeeecCCeEEEecCCC
Q 012525          435 TFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       435 i~~~~r~~~rd~IiI~TsNi  454 (461)
                               ...++|+|+|.
T Consensus       359 ---------~~V~vIaTTN~  369 (489)
T CHL00195        359 ---------SPVFVVATANN  369 (489)
T ss_pred             ---------CceEEEEecCC
Confidence                     24677888873

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.60  E-value=2.2e-15  Score=170.66  Aligned_cols=166  Identities=21%  Similarity=0.297  Sum_probs=121.5

Q ss_pred             CCCCCCCCCCCCCCCHH----HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhcccccccccc
Q 012525          249 GSRWGGSNLGEDLPTPK----EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELE  324 (461)
Q Consensus       249 ~~~w~g~~l~~~l~t~~----el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~  324 (461)
                      .++|+++++.+......    ++.+.|.+.|+||+.|++.|..++......+..     .                 ..+
T Consensus       538 v~~~tgip~~~~~~~e~~~l~~l~~~L~~~v~GQ~~Av~~v~~~i~~~~~gl~~-----~-----------------~~p  595 (852)
T TIGR03345       538 VADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGLED-----P-----------------RKP  595 (852)
T ss_pred             HHHHHCCCchhhchhHHHHHHHHHHHhcCeEcChHHHHHHHHHHHHHHhcCCCC-----C-----------------CCC
Confidence            56899999987665444    488999999999999999999988532111100     0                 011


Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhccC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAAQ  390 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a~  390 (461)
                      ...+||+||+|||||.+|++||+.+   ...|+.++++++.+.           +|+|......+...+.       ...
T Consensus       596 ~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~g~~~gyvg~~~~g~L~~~v~-------~~p  668 (852)
T TIGR03345       596 LGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVR-------RKP  668 (852)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhccccCCCCCcccccccchHHHHHH-------hCC
Confidence            2358999999999999999999988   347889998876532           5666553444444433       236


Q ss_pred             ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          391 QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       391 ~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      .+||+||||+++.+.              +++.|+++|+.+.+....+.....++.++|.|||++.+
T Consensus       669 ~svvllDEieka~~~--------------v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~  721 (852)
T TIGR03345       669 YSVVLLDEVEKAHPD--------------VLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSD  721 (852)
T ss_pred             CcEEEEechhhcCHH--------------HHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchH
Confidence            679999999999988              99999999998877654443222348999999999765

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.

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

Probab=99.60  E-value=3.5e-15  Score=146.14  Aligned_cols=137  Identities=27%  Similarity=0.443  Sum_probs=102.8

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHH--HHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHY--KRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~--kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      --+.|-|+++.++.|++.+..+.  ..++.+.   |                 -..+.+||||||||||||+||+++|..
T Consensus       145 tYeMiGgLd~QIkeIkEVIeLPvKHPELF~aL---G-----------------IaQPKGvlLygppgtGktLlaraVahh  204 (404)
T KOG0728|consen  145 TYEMIGGLDKQIKEIKEVIELPVKHPELFEAL---G-----------------IAQPKGVLLYGPPGTGKTLLARAVAHH  204 (404)
T ss_pred             HHHHhccHHHHHHHHHHHHhccccCHHHHHhc---C-----------------CCCCcceEEecCCCCchhHHHHHHHhh
Confidence            34457788888888888775332  1222221   1                 122578999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ..+.|++++.+++.+ +|+|+. ...++++|..++..    .++|||+||||.+...|...+.+.+..-.+..-.||..|
T Consensus       205 t~c~firvsgselvq-k~igeg-srmvrelfvmareh----apsiifmdeidsigs~r~e~~~ggdsevqrtmlellnql  278 (404)
T KOG0728|consen  205 TDCTFIRVSGSELVQ-KYIGEG-SRMVRELFVMAREH----APSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQL  278 (404)
T ss_pred             cceEEEEechHHHHH-HHhhhh-HHHHHHHHHHHHhc----CCceEeeecccccccccccCCCCccHHHHHHHHHHHHhc
Confidence            999999999999995 599998 79999999988766    789999999999999887665555544333444555566


Q ss_pred             hCcee
Q 012525          429 EGTET  433 (461)
Q Consensus       429 Eg~~v  433 (461)
                      ||.+.
T Consensus       279 dgfea  283 (404)
T KOG0728|consen  279 DGFEA  283 (404)
T ss_pred             ccccc
Confidence            66543

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

Probab=99.60  E-value=9e-15  Score=153.11  Aligned_cols=148  Identities=26%  Similarity=0.396  Sum_probs=105.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+++ |.|++.+|+.|.+++...+.  .++..   .+                 ...+.++||+||||||||++|+++|+
T Consensus       143 ~~~d-igGl~~~k~~l~~~v~~pl~~~~~~~~---~G-----------------l~~pkgvLL~GppGTGKT~LAkalA~  201 (398)
T PTZ00454        143 TYSD-IGGLDIQKQEIREAVELPLTCPELYEQ---IG-----------------IDPPRGVLLYGPPGTGKTMLAKAVAH  201 (398)
T ss_pred             CHHH-cCCHHHHHHHHHHHHHHHhcCHHHHHh---cC-----------------CCCCceEEEECCCCCCHHHHHHHHHH
Confidence            3455 89999999999999864432  12211   11                 12357899999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      .++.+|+.+.++.+.. .|+|+. +..++.+|..+..    ..++||||||||.+..+|.....+.+.....++..|+..
T Consensus       202 ~l~~~fi~i~~s~l~~-k~~ge~-~~~lr~lf~~A~~----~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~  275 (398)
T PTZ00454        202 HTTATFIRVVGSEFVQ-KYLGEG-PRMVRDVFRLARE----NAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQ  275 (398)
T ss_pred             hcCCCEEEEehHHHHH-Hhcchh-HHHHHHHHHHHHh----cCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHH
Confidence            9999999999988874 578876 6778888876653    378999999999998876443333333333456667777


Q ss_pred             HhCceeeeecceeeecCCeEEEecCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSG  453 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsN  453 (461)
                      |++...         ..+.++|+|||
T Consensus       276 ld~~~~---------~~~v~VI~aTN  292 (398)
T PTZ00454        276 MDGFDQ---------TTNVKVIMATN  292 (398)
T ss_pred             hhccCC---------CCCEEEEEecC
Confidence            764321         11456677776

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

Probab=99.60  E-value=1.7e-15  Score=154.62  Aligned_cols=161  Identities=24%  Similarity=0.404  Sum_probs=125.5

Q ss_pred             CCCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHH--HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCC
Q 012525          259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNH--YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGS  336 (461)
Q Consensus       259 ~~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~--~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGT  336 (461)
                      ..+..+.++...+++ |-|++.+|+.|++.|..+  ++.++.                   .........+|||+|||||
T Consensus        79 s~~v~p~~I~v~f~D-IggLe~v~~~L~e~VilPlr~pelF~-------------------~g~Ll~p~kGiLL~GPpG~  138 (386)
T KOG0737|consen   79 SDVVPPSEIGVSFDD-IGGLEEVKDALQELVILPLRRPELFA-------------------KGKLLRPPKGILLYGPPGT  138 (386)
T ss_pred             hcccchhhceeehhh-ccchHHHHHHHHHHHhhcccchhhhc-------------------ccccccCCccceecCCCCc
Confidence            345677788888888 899999999999998643  222321                   1112235689999999999


Q ss_pred             chHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccc
Q 012525          337 GKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVS  416 (461)
Q Consensus       337 GKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s  416 (461)
                      |||++|+++|++.+..|+.+..+.++. +|+|+. ++.++.+|..+...    +|+||||||||.+...|.   .+.+..
T Consensus       139 GKTmlAKA~Akeaga~fInv~~s~lt~-KWfgE~-eKlv~AvFslAsKl----~P~iIFIDEvds~L~~R~---s~dHEa  209 (386)
T KOG0737|consen  139 GKTMLAKAIAKEAGANFINVSVSNLTS-KWFGEA-QKLVKAVFSLASKL----QPSIIFIDEVDSFLGQRR---STDHEA  209 (386)
T ss_pred             hHHHHHHHHHHHcCCCcceeeccccch-hhHHHH-HHHHHHHHhhhhhc----CcceeehhhHHHHHhhcc---cchHHH
Confidence            999999999999999999999999996 799988 89999999887744    899999999999998873   344545


Q ss_pred             hHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          417 GEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       417 ~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ...+.++|....||.....       ....+++++||..
T Consensus       210 ~a~mK~eFM~~WDGl~s~~-------~~rVlVlgATNRP  241 (386)
T KOG0737|consen  210 TAMMKNEFMALWDGLSSKD-------SERVLVLGATNRP  241 (386)
T ss_pred             HHHHHHHHHHHhccccCCC-------CceEEEEeCCCCC
Confidence            5557888888888765431       1147888888854

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=99.59  E-value=1.9e-15  Score=140.73  Aligned_cols=128  Identities=24%  Similarity=0.401  Sum_probs=93.0

Q ss_pred             chhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh----
Q 012525          309 PKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ----  381 (461)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~----  381 (461)
                      +.|+.+.+.+..++..+.+|||+|++||||+++|++|++..   +.||+.++|+.+..        +..-..+|..    
T Consensus         6 ~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~--------~~~e~~LFG~~~~~   77 (168)
T PF00158_consen    6 PAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPE--------ELLESELFGHEKGA   77 (168)
T ss_dssp             HHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-H--------HHHHHHHHEBCSSS
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhc--------chhhhhhhcccccc
Confidence            33344444444455566889999999999999999999966   46999999998764        2333445532    


Q ss_pred             -------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          382 -------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       382 -------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                             ..+.++.+++|+||||||+.|...              +|..|+++|+...+.........+.++.+|+||+.
T Consensus        78 ~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~~--------------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~  143 (168)
T PF00158_consen   78 FTGARSDKKGLLEQANGGTLFLDEIEDLPPE--------------LQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSK  143 (168)
T ss_dssp             STTTSSEBEHHHHHTTTSEEEEETGGGS-HH--------------HHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS
T ss_pred             ccccccccCCceeeccceEEeecchhhhHHH--------------HHHHHHHHHhhchhccccccccccccceEEeecCc
Confidence                   235677889999999999999999              99999999998887766665555669999999998


Q ss_pred             CcCc
Q 012525          455 DSKT  458 (461)
Q Consensus       455 d~e~  458 (461)
                      ++++
T Consensus       144 ~l~~  147 (168)
T PF00158_consen  144 DLEE  147 (168)
T ss_dssp             -HHH
T ss_pred             CHHH
Confidence            8654

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 ....

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.59  E-value=1e-14  Score=152.17  Aligned_cols=143  Identities=29%  Similarity=0.461  Sum_probs=100.8

Q ss_pred             hcCChHHHHHHHHHHHHHHHHH--HHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKR--IYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kr--i~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .|.|.+++++.|.+.+......  ++.   ..+                 ...+.+|||+||||||||++|+++|+.++.
T Consensus       132 di~Gl~~~~~~l~~~i~~pl~~~~~~~---~~g-----------------~~~p~gvLL~GppGtGKT~lAkaia~~~~~  191 (389)
T PRK03992        132 DIGGLEEQIREVREAVELPLKKPELFE---EVG-----------------IEPPKGVLLYGPPGTGKTLLAKAVAHETNA  191 (389)
T ss_pred             HhCCcHHHHHHHHHHHHHHhhCHHHHH---hcC-----------------CCCCCceEEECCCCCChHHHHHHHHHHhCC
Confidence            3899999999999988543221  111   111                 123578999999999999999999999999


Q ss_pred             ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH---
Q 012525          352 PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML---  428 (461)
Q Consensus       352 pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L---  428 (461)
                      +|+.++++++.. .|.|+. +..++.+|..+...    .++||||||||.+...|.....+.+   ..++..|++++   
T Consensus       192 ~~i~v~~~~l~~-~~~g~~-~~~i~~~f~~a~~~----~p~IlfiDEiD~l~~~r~~~~~~~~---~~~~~~l~~lL~~l  262 (389)
T PRK03992        192 TFIRVVGSELVQ-KFIGEG-ARLVRELFELAREK----APSIIFIDEIDAIAAKRTDSGTSGD---REVQRTLMQLLAEM  262 (389)
T ss_pred             CEEEeehHHHhH-hhccch-HHHHHHHHHHHHhc----CCeEEEEechhhhhcccccCCCCcc---HHHHHHHHHHHHhc
Confidence            999999999874 577776 67788888766543    6889999999999887654332222   22444444444   


Q ss_pred             hCceeeeecceeeecCCeEEEecCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ++...         ..+.++|+|+|.
T Consensus       263 d~~~~---------~~~v~VI~aTn~  279 (389)
T PRK03992        263 DGFDP---------RGNVKIIAATNR  279 (389)
T ss_pred             cccCC---------CCCEEEEEecCC
Confidence            43210         125678888875

>CHL00176 ftsH cell division protein; Validated

Probab=99.58  E-value=8.8e-15  Score=161.07  Aligned_cols=150  Identities=25%  Similarity=0.373  Sum_probs=106.2

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ |+|.+++|+.|.+.+.. .+. .......+                 ...+.+|||+||||||||++|+++|.++
T Consensus       181 ~f~d-v~G~~~~k~~l~eiv~~-lk~-~~~~~~~g-----------------~~~p~gVLL~GPpGTGKT~LAralA~e~  240 (638)
T CHL00176        181 TFRD-IAGIEEAKEEFEEVVSF-LKK-PERFTAVG-----------------AKIPKGVLLVGPPGTGKTLLAKAIAGEA  240 (638)
T ss_pred             CHHh-ccChHHHHHHHHHHHHH-HhC-HHHHhhcc-----------------CCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            4555 89999999999887742 110 00000011                 1235789999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.||+.++++++... +.|.. ...++.+|..+..    ..++||||||||.+...|.......+...+.+++.||..||
T Consensus       241 ~~p~i~is~s~f~~~-~~g~~-~~~vr~lF~~A~~----~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~d  314 (638)
T CHL00176        241 EVPFFSISGSEFVEM-FVGVG-AARVRDLFKKAKE----NSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMD  314 (638)
T ss_pred             CCCeeeccHHHHHHH-hhhhh-HHHHHHHHHHHhc----CCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhc
Confidence            999999999987743 55554 5667888877654    37889999999999887654333334444567788888887


Q ss_pred             CceeeeecceeeecCCeEEEecCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +...         ..+.++|+|||.
T Consensus       315 g~~~---------~~~ViVIaaTN~  330 (638)
T CHL00176        315 GFKG---------NKGVIVIAATNR  330 (638)
T ss_pred             cccC---------CCCeeEEEecCc
Confidence            5431         124677888776

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.58  E-value=1.2e-14  Score=145.71  Aligned_cols=142  Identities=20%  Similarity=0.278  Sum_probs=98.2

Q ss_pred             CCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchH
Q 012525          260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKT  339 (461)
Q Consensus       260 ~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKT  339 (461)
                      +.+..+++.+.|++.++|++.+|+.|.+.+...  .+.....+.+.              .......++||+||||||||
T Consensus         9 ~~~~~~~~~~~l~~~l~Gl~~vk~~i~e~~~~~--~~~~~r~~~g~--------------~~~~~~~~vll~G~pGTGKT   72 (284)
T TIGR02880         9 EASGITEVLDQLDRELIGLKPVKTRIREIAALL--LVERLRQRLGL--------------ASAAPTLHMSFTGNPGTGKT   72 (284)
T ss_pred             hhccHHHHHHHHHHhccCHHHHHHHHHHHHHHH--HHHHHHHHhCC--------------CcCCCCceEEEEcCCCCCHH
Confidence            345678899999987999999999998877531  11111111120              01112468999999999999


Q ss_pred             HHHHHHHHhcC-------CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          340 LLAKTLARHVN-------VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       340 tLAraLA~~l~-------~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                      ++|+++|+.+.       .+|+.+++.++.. .|+|+. +..+..++..+       .++|||||||+.|...+..    
T Consensus        73 ~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~~-~~~g~~-~~~~~~~~~~a-------~~gvL~iDEi~~L~~~~~~----  139 (284)
T TIGR02880        73 TVALRMAQILHRLGYVRKGHLVSVTRDDLVG-QYIGHT-APKTKEILKRA-------MGGVLFIDEAYYLYRPDNE----  139 (284)
T ss_pred             HHHHHHHHHHHHcCCcccceEEEecHHHHhH-hhcccc-hHHHHHHHHHc-------cCcEEEEechhhhccCCCc----
Confidence            99999998773       2799999988875 577766 34455555443       5689999999998643211    


Q ss_pred             cccchHHHHHHHHHHHhCc
Q 012525          413 RDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg~  431 (461)
                       ......+++.|++.|+..
T Consensus       140 -~~~~~~~~~~Ll~~le~~  157 (284)
T TIGR02880       140 -RDYGQEAIEILLQVMENQ  157 (284)
T ss_pred             -cchHHHHHHHHHHHHhcC
Confidence             112345889999999843

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.57  E-value=1.7e-14  Score=154.93  Aligned_cols=152  Identities=28%  Similarity=0.373  Sum_probs=107.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+++ |.|++..++.|...+...+.  .++...   +                 ...++++||+||||||||++|+++|+
T Consensus       180 ~~~d-IgGl~~~i~~i~~~v~lp~~~~~l~~~~---g-----------------l~~p~GILLyGPPGTGKT~LAKAlA~  238 (512)
T TIGR03689       180 TYAD-IGGLDSQIEQIRDAVELPFLHPELYREY---D-----------------LKPPKGVLLYGPPGCGKTLIAKAVAN  238 (512)
T ss_pred             CHHH-cCChHHHHHHHHHHHHHHhhCHHHHHhc---c-----------------CCCCcceEEECCCCCcHHHHHHHHHH
Confidence            4555 89999999999999864322  122111   1                 12257899999999999999999999


Q ss_pred             hcCCc----------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccch
Q 012525          348 HVNVP----------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSG  417 (461)
Q Consensus       348 ~l~~p----------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~  417 (461)
                      ++..+          |+.+...++. .+|+|+. +..++.+|..+........++||||||||.+...|+... +.+. .
T Consensus       239 eL~~~i~~~~~~~~~fl~v~~~eLl-~kyvGet-e~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~-s~d~-e  314 (512)
T TIGR03689       239 SLAQRIGAETGDKSYFLNIKGPELL-NKYVGET-ERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGV-SSDV-E  314 (512)
T ss_pred             hhccccccccCCceeEEeccchhhc-ccccchH-HHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCc-cchH-H
Confidence            98654          5566666666 3588876 778888888776554455789999999999998765321 1221 2


Q ss_pred             HHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          418 EGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       418 ~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ..++++||..|++....         .+.++|+|||..
T Consensus       315 ~~il~~LL~~LDgl~~~---------~~ViVI~ATN~~  343 (512)
T TIGR03689       315 TTVVPQLLSELDGVESL---------DNVIVIGASNRE  343 (512)
T ss_pred             HHHHHHHHHHhcccccC---------CceEEEeccCCh
Confidence            45788999999864311         257888888853

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.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=99.57  E-value=5.5e-15  Score=141.73  Aligned_cols=139  Identities=23%  Similarity=0.321  Sum_probs=84.9

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC--
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV--  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~--  351 (461)
                      .|+||+.+|+.|..++.                                 ...||||+||||||||++|+.|+..+--  
T Consensus         4 dI~GQe~aKrAL~iAAa---------------------------------G~h~lLl~GppGtGKTmlA~~l~~lLP~l~   50 (206)
T PF01078_consen    4 DIVGQEEAKRALEIAAA---------------------------------GGHHLLLIGPPGTGKTMLARRLPSLLPPLT   50 (206)
T ss_dssp             CSSSTHHHHHHHHHHHH---------------------------------CC--EEEES-CCCTHHHHHHHHHHCS--CC
T ss_pred             hhcCcHHHHHHHHHHHc---------------------------------CCCCeEEECCCCCCHHHHHHHHHHhCCCCc
Confidence            39999999999998882                                 2478999999999999999999987621  


Q ss_pred             --ceEE------ecc-----hhhhhcCcccccHHHHHHHHH----HhhchhhhccCceEEEEcCccccchhhhccccccc
Q 012525          352 --PFVI------ADA-----TTLTQAGYVGEDVESILYKLL----AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRD  414 (461)
Q Consensus       352 --pfv~------i~~-----s~l~~~g~vGe~~e~~L~~lf----~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~  414 (461)
                        ..++      +..     ..+....+.-.........++    ....+.+..+++|||||||+..+...         
T Consensus        51 ~~e~le~~~i~s~~~~~~~~~~~~~~Pfr~phhs~s~~~liGgg~~~~PGeislAh~GVLflDE~~ef~~~---------  121 (206)
T PF01078_consen   51 EEEALEVSKIYSVAGLGPDEGLIRQRPFRAPHHSASEAALIGGGRPPRPGEISLAHRGVLFLDELNEFDRS---------  121 (206)
T ss_dssp             EECCESS--S-TT---S---EEEE---EEEE-TT--HHHHHEEGGGEEE-CGGGGTTSEEEECETTTS-HH---------
T ss_pred             hHHHhhhccccccccCCCCCceecCCCcccCCCCcCHHHHhCCCcCCCcCHHHHhcCCEEEechhhhcCHH---------
Confidence              0000      000     000000000000001111122    22445678899999999999998888         


Q ss_pred             cchHHHHHHHHHHHhCceeeeecc--eeeecCCeEEEecCCCCcCcC
Q 012525          415 VSGEGVQQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGLDSKTL  459 (461)
Q Consensus       415 ~s~~~v~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~e~l  459 (461)
                           ++++|++.||.+.+.+...  ...+|.+|++|+|+|..+--.
T Consensus       122 -----vld~Lr~ple~g~v~i~R~~~~~~~Pa~f~lv~a~NPcpCG~  163 (206)
T PF01078_consen  122 -----VLDALRQPLEDGEVTISRAGGSVTYPARFLLVAAMNPCPCGY  163 (206)
T ss_dssp             -----HHHHHHHHHHHSBEEEEETTEEEEEB--EEEEEEE-S-----
T ss_pred             -----HHHHHHHHHHCCeEEEEECCceEEEecccEEEEEeccccccc
Confidence                 9999999999887776655  667788999999999876543

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.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.56  E-value=8.7e-15  Score=148.85  Aligned_cols=145  Identities=29%  Similarity=0.380  Sum_probs=112.0

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      ....+...+.+.++|+++++..+..++.                                 ...|+||.||||||||++|
T Consensus        14 ~~~~~~~~~~~~~~g~~~~~~~~l~a~~---------------------------------~~~~vll~G~PG~gKT~la   60 (329)
T COG0714          14 ILGKIRSELEKVVVGDEEVIELALLALL---------------------------------AGGHVLLEGPPGVGKTLLA   60 (329)
T ss_pred             HHHHHHhhcCCeeeccHHHHHHHHHHHH---------------------------------cCCCEEEECCCCccHHHHH
Confidence            3445666777778998888887777762                                 2488999999999999999


Q ss_pred             HHHHHhcCCceEEecch-hhhhcCcccccHHHHH---HHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          343 KTLARHVNVPFVIADAT-TLTQAGYVGEDVESIL---YKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       343 raLA~~l~~pfv~i~~s-~l~~~g~vGe~~e~~L---~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                      +.+|+.++.+|+++.++ ++...+.+|.......   ...+....+.+..+..+|+|+|||++..++             
T Consensus        61 ~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEInra~p~-------------  127 (329)
T COG0714          61 RALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEINRAPPE-------------  127 (329)
T ss_pred             HHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEeccccCCHH-------------
Confidence            99999999999999998 6666556665533322   222222222232222369999999999998             


Q ss_pred             HHHHHHHHHHhCceeeeecce-eeecCCeEEEecCCC
Q 012525          419 GVQQALLKMLEGTETKTFAAV-SKVSRDNLYIKTSGL  454 (461)
Q Consensus       419 ~v~~aLL~~LEg~~v~i~~~~-r~~~rd~IiI~TsNi  454 (461)
                       ++++||.+|++.++.+.... ...+..+++|+|+|.
T Consensus       128 -~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np  163 (329)
T COG0714         128 -VQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNP  163 (329)
T ss_pred             -HHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCc
Confidence             99999999999999998887 777779999999994

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

Probab=99.55  E-value=1.4e-14  Score=142.75  Aligned_cols=131  Identities=26%  Similarity=0.384  Sum_probs=98.8

Q ss_pred             cCChHHHHHHHHHHHHHH---HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          275 VIGQEKAKKVLSVAVYNH---YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~---~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      |-|.++.++.|.+++...   ..+....    +                 -.++.++|+|||||||||++||+.|...+.
T Consensus       173 iGGldkQIqELvEAiVLpmth~ekF~~l----g-----------------i~pPKGvLmYGPPGTGKTlmARAcAaqT~a  231 (424)
T KOG0652|consen  173 IGGLDKQIQELVEAIVLPMTHKEKFENL----G-----------------IRPPKGVLMYGPPGTGKTLMARACAAQTNA  231 (424)
T ss_pred             cccHHHHHHHHHHHhccccccHHHHHhc----C-----------------CCCCCceEeeCCCCCcHHHHHHHHHHhccc
Confidence            899999999999988532   2221111    1                 123588999999999999999999999999


Q ss_pred             ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          352 PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       352 pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      .|+.+....+.+. |+|.. .+.++..|..+...    .++||||||+|++..+|-..+...+..-.+..-.||..|||.
T Consensus       232 TFLKLAgPQLVQM-fIGdG-AkLVRDAFaLAKEk----aP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGF  305 (424)
T KOG0652|consen  232 TFLKLAGPQLVQM-FIGDG-AKLVRDAFALAKEK----APTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGF  305 (424)
T ss_pred             hHHHhcchHHHhh-hhcch-HHHHHHHHHHhhcc----CCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCC
Confidence            9999999999965 88887 78999999877654    789999999999999987655555543223333444555555


Q ss_pred             e
Q 012525          432 E  432 (461)
Q Consensus       432 ~  432 (461)
                      .
T Consensus       306 s  306 (424)
T KOG0652|consen  306 S  306 (424)
T ss_pred             C
Confidence            4

>CHL00181 cbbX CbbX; Provisional

Probab=99.55  E-value=2.9e-14  Score=143.25  Aligned_cols=139  Identities=20%  Similarity=0.264  Sum_probs=96.0

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHH-HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNH-YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTL  340 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~-~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTt  340 (461)
                      ...+++.+.|++.++|++.+|+.|.+.+... +.++.   ...+.              .....+.|+||+||||||||+
T Consensus        12 ~~~~~~~~~l~~~l~Gl~~vK~~i~e~~~~~~~~~~~---~~~g~--------------~~~~~~~~ill~G~pGtGKT~   74 (287)
T CHL00181         12 TQIQEVLDILDEELVGLAPVKTRIREIAALLLIDRLR---KNLGL--------------TSSNPGLHMSFTGSPGTGKTT   74 (287)
T ss_pred             cCHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHH---HHcCC--------------CCCCCCceEEEECCCCCCHHH
Confidence            3567899999988999999999998877421 11111   11110              001124679999999999999


Q ss_pred             HHHHHHHhcC-------CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccccc
Q 012525          341 LAKTLARHVN-------VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISR  413 (461)
Q Consensus       341 LAraLA~~l~-------~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~  413 (461)
                      +|+++|+.+.       .+|+.++..++.. .|+|+. +.....++..+       .++||||||++.+...+..     
T Consensus        75 lAr~la~~~~~~g~~~~~~~~~v~~~~l~~-~~~g~~-~~~~~~~l~~a-------~ggVLfIDE~~~l~~~~~~-----  140 (287)
T CHL00181         75 VALKMADILYKLGYIKKGHLLTVTRDDLVG-QYIGHT-APKTKEVLKKA-------MGGVLFIDEAYYLYKPDNE-----  140 (287)
T ss_pred             HHHHHHHHHHHcCCCCCCceEEecHHHHHH-HHhccc-hHHHHHHHHHc-------cCCEEEEEccchhccCCCc-----
Confidence            9999998762       3688999888874 477766 33345555443       5689999999998654211     


Q ss_pred             ccchHHHHHHHHHHHhCc
Q 012525          414 DVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       414 ~~s~~~v~~aLL~~LEg~  431 (461)
                      ...+..+++.|++.||..
T Consensus       141 ~~~~~e~~~~L~~~me~~  158 (287)
T CHL00181        141 RDYGSEAIEILLQVMENQ  158 (287)
T ss_pred             cchHHHHHHHHHHHHhcC
Confidence            112345899999999853

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.55  E-value=2e-14  Score=163.12  Aligned_cols=165  Identities=29%  Similarity=0.401  Sum_probs=117.1

Q ss_pred             CCCCCCCCCCCCCCCHH----HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhcccccccccc
Q 012525          249 GSRWGGSNLGEDLPTPK----EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELE  324 (461)
Q Consensus       249 ~~~w~g~~l~~~l~t~~----el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~  324 (461)
                      .+.|+++++........    ++.+.|.+.|+||+.+++.|..++......+...                      ..+
T Consensus       537 ~~~~tgip~~~~~~~e~~~l~~l~~~l~~~v~GQ~~av~~v~~~i~~~~~gl~~~----------------------~~p  594 (852)
T TIGR03346       537 VSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDP----------------------NRP  594 (852)
T ss_pred             HHHhcCCCcccccHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHhccCCCC----------------------CCC
Confidence            57899998887654443    4778888889999999999999885321110000                      011


Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhccC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAAQ  390 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a~  390 (461)
                      ...+||+||+|||||++|++||+.+   ..+|+.++++.+...           +|+|......+...+.       ...
T Consensus       595 ~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l~g~~~g~~g~~~~g~l~~~v~-------~~p  667 (852)
T TIGR03346       595 IGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVR-------RKP  667 (852)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchHHHhcCCCCCccCcccccHHHHHHH-------cCC
Confidence            2468999999999999999999987   458999998765432           3444432233333332       224


Q ss_pred             ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeec-CCeEEEecCCCCcC
Q 012525          391 QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVS-RDNLYIKTSGLDSK  457 (461)
Q Consensus       391 ~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~-rd~IiI~TsNid~e  457 (461)
                      .+|||||||+++.+.              +++.||++|+.+.+..... +... ++.|+|+|||.+.+
T Consensus       668 ~~vlllDeieka~~~--------------v~~~Ll~~l~~g~l~d~~g-~~vd~rn~iiI~TSn~g~~  720 (852)
T TIGR03346       668 YSVVLFDEVEKAHPD--------------VFNVLLQVLDDGRLTDGQG-RTVDFRNTVIIMTSNLGSQ  720 (852)
T ss_pred             CcEEEEeccccCCHH--------------HHHHHHHHHhcCceecCCC-eEEecCCcEEEEeCCcchH
Confidence            569999999999998              9999999999887764332 3333 48999999999765

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.

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

Probab=99.54  E-value=3e-14  Score=140.70  Aligned_cols=129  Identities=26%  Similarity=0.348  Sum_probs=98.5

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      .|-|..+.++.|++.+......- ......+                 -.++.+||||||||||||++||++|+..+.-|
T Consensus       178 dvggckeqieklrevve~pll~p-erfv~lg-----------------idppkgvllygppgtgktl~aravanrtdacf  239 (435)
T KOG0729|consen  178 DVGGCKEQIEKLREVVELPLLHP-ERFVNLG-----------------IDPPKGVLLYGPPGTGKTLCARAVANRTDACF  239 (435)
T ss_pred             cccchHHHHHHHHHHHhccccCH-HHHhhcC-----------------CCCCCceEEeCCCCCchhHHHHHHhcccCceE
Confidence            38899999999988885322100 0011111                 13468899999999999999999999999999


Q ss_pred             EEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          354 VIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       354 v~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +++-.+++.+ +|+|+. ...++++|..+...    +-|||||||||++...|=.++.+.+.   ++|-++|+++.
T Consensus       240 irvigselvq-kyvgeg-armvrelf~martk----kaciiffdeidaiggarfddg~ggdn---evqrtmleli~  306 (435)
T KOG0729|consen  240 IRVIGSELVQ-KYVGEG-ARMVRELFEMARTK----KACIIFFDEIDAIGGARFDDGAGGDN---EVQRTMLELIN  306 (435)
T ss_pred             EeehhHHHHH-HHhhhh-HHHHHHHHHHhccc----ceEEEEeeccccccCccccCCCCCcH---HHHHHHHHHHH
Confidence            9999999995 699999 79999999988765    77899999999999887555544443   36666666554

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.54  E-value=8.8e-14  Score=137.07  Aligned_cols=132  Identities=18%  Similarity=0.336  Sum_probs=90.7

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ ++|++.+|+.|.+.+...  .+.....+.+.              .......|+||+||||||||++|+++|+
T Consensus         2 ~~~l~~-~~Gl~~vk~~i~~~~~~~--~~~~~~~~~g~--------------~~~~~~~~vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881         2 ERELSR-MVGLDEVKALIKEIYAWI--QINEKRKEEGL--------------KTSKQVLHMIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             hHHHHH-hcChHHHHHHHHHHHHHH--HHHHHHHHcCC--------------CCCCCcceEEEEcCCCCCHHHHHHHHHH
Confidence            356777 799999999999887432  11111111111              1112347899999999999999999998


Q ss_pred             hc-------CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          348 HV-------NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       348 ~l-------~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      .+       ...++.+++.++.. .|+|+. +..+..+|..+       .++||||||||.|...      .........
T Consensus        65 ~l~~~~~~~~~~~v~~~~~~l~~-~~~g~~-~~~~~~~~~~a-------~~~VL~IDE~~~L~~~------~~~~~~~~~  129 (261)
T TIGR02881        65 LFKEMNVLSKGHLIEVERADLVG-EYIGHT-AQKTREVIKKA-------LGGVLFIDEAYSLARG------GEKDFGKEA  129 (261)
T ss_pred             HHHhcCcccCCceEEecHHHhhh-hhccch-HHHHHHHHHhc-------cCCEEEEechhhhccC------CccchHHHH
Confidence            75       23688888888874 477776 55666666544       4679999999998742      111123447


Q ss_pred             HHHHHHHHhCc
Q 012525          421 QQALLKMLEGT  431 (461)
Q Consensus       421 ~~aLL~~LEg~  431 (461)
                      ++.|++.|+..
T Consensus       130 i~~Ll~~~e~~  140 (261)
T TIGR02881       130 IDTLVKGMEDN  140 (261)
T ss_pred             HHHHHHHHhcc
Confidence            89999999854

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.

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

Probab=99.54  E-value=1.3e-14  Score=144.61  Aligned_cols=126  Identities=28%  Similarity=0.407  Sum_probs=98.5

Q ss_pred             cCChHHHHHHHHHHHHHH--HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          275 VIGQEKAKKVLSVAVYNH--YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~--~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      |-|++..++.|.+.+...  ...++...-                    -.++.+|+|||+||||||+||+|+|+.....
T Consensus       187 iGGle~QiQEiKEsvELPLthPE~YeemG--------------------ikpPKGVIlyG~PGTGKTLLAKAVANqTSAT  246 (440)
T KOG0726|consen  187 IGGLESQIQEIKESVELPLTHPEYYEEMG--------------------IKPPKGVILYGEPGTGKTLLAKAVANQTSAT  246 (440)
T ss_pred             cccHHHHHHHHHHhhcCCCCCHHHHHHcC--------------------CCCCCeeEEeCCCCCchhHHHHHHhcccchh
Confidence            899999999999988532  122222211                    1346889999999999999999999999999


Q ss_pred             eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          353 FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       353 fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      |+++-.+++.+ +|.|+. .+.++.+|..+...    .++|+||||||++..+|=..+++..   +++|.++|++|.
T Consensus       247 FlRvvGseLiQ-kylGdG-pklvRqlF~vA~e~----apSIvFiDEIdAiGtKRyds~Sgge---rEiQrtmLELLN  314 (440)
T KOG0726|consen  247 FLRVVGSELIQ-KYLGDG-PKLVRELFRVAEEH----APSIVFIDEIDAIGTKRYDSNSGGE---REIQRTMLELLN  314 (440)
T ss_pred             hhhhhhHHHHH-HHhccc-hHHHHHHHHHHHhc----CCceEEeehhhhhccccccCCCccH---HHHHHHHHHHHH
Confidence            99999999995 599988 79999999887655    7899999999999998755444433   346666655554

>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=99.53  E-value=9.4e-16  Score=137.01  Aligned_cols=112  Identities=26%  Similarity=0.261  Sum_probs=72.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecch-hhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT-TLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s-~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ||||.|+||+|||++|++||+.++..|.++.++ ++...+..|..+...-...|....+.+   -..|+|+|||++..++
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPi---f~~ill~DEiNrappk   77 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPI---FTNILLADEINRAPPK   77 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT----SSEEEEETGGGS-HH
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChh---hhceeeecccccCCHH
Confidence            699999999999999999999999999999886 566554444321110001111111111   1249999999999999


Q ss_pred             hhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                                    +|++||++|+++++.+.......+..+++|+|.|..
T Consensus        78 --------------tQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~  113 (131)
T PF07726_consen   78 --------------TQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPV  113 (131)
T ss_dssp             --------------HHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT
T ss_pred             --------------HHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCcc
Confidence                          999999999999999988889999999999999963

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.

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

Probab=99.53  E-value=8.9e-14  Score=138.30  Aligned_cols=116  Identities=32%  Similarity=0.503  Sum_probs=89.4

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|+++ +||+++|+.|...+.....+        +                  ....|+||+||||.||||||..+|+
T Consensus        22 P~~l~ef-iGQ~~vk~~L~ifI~AAk~r--------~------------------e~lDHvLl~GPPGlGKTTLA~IIA~   74 (332)
T COG2255          22 PKTLDEF-IGQEKVKEQLQIFIKAAKKR--------G------------------EALDHVLLFGPPGLGKTTLAHIIAN   74 (332)
T ss_pred             cccHHHh-cChHHHHHHHHHHHHHHHhc--------C------------------CCcCeEEeeCCCCCcHHHHHHHHHH
Confidence            4567775 99999999999988532221        1                  1237999999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +++..+...+...+...        .-+..++...      ..+-||||||||+|.+.              +...|+..
T Consensus        75 Emgvn~k~tsGp~leK~--------gDlaaiLt~L------e~~DVLFIDEIHrl~~~--------------vEE~LYpa  126 (332)
T COG2255          75 ELGVNLKITSGPALEKP--------GDLAAILTNL------EEGDVLFIDEIHRLSPA--------------VEEVLYPA  126 (332)
T ss_pred             HhcCCeEecccccccCh--------hhHHHHHhcC------CcCCeEEEehhhhcChh--------------HHHHhhhh
Confidence            99999888877777643        2222333221      15569999999999998              88899999


Q ss_pred             HhCceeeeecc
Q 012525          428 LEGTETKTFAA  438 (461)
Q Consensus       428 LEg~~v~i~~~  438 (461)
                      ||...+.+...
T Consensus       127 MEDf~lDI~IG  137 (332)
T COG2255         127 MEDFRLDIIIG  137 (332)
T ss_pred             hhheeEEEEEc
Confidence            99988887755

>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=99.52  E-value=6.4e-14  Score=121.04  Aligned_cols=111  Identities=30%  Similarity=0.525  Sum_probs=85.0

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAE  407 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~  407 (461)
                      |||+||||||||++|+.+|+.++.+++.+++..+.. .+.+.. +..+...|..+....   .++||||||+|.+.... 
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~-~~~~~~-~~~i~~~~~~~~~~~---~~~vl~iDe~d~l~~~~-   74 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELIS-SYAGDS-EQKIRDFFKKAKKSA---KPCVLFIDEIDKLFPKS-   74 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHT-SSTTHH-HHHHHHHHHHHHHTS---TSEEEEEETGGGTSHHC-
T ss_pred             CEEECcCCCCeeHHHHHHHhhccccccccccccccc-cccccc-ccccccccccccccc---cceeeeeccchhccccc-
Confidence            699999999999999999999999999999999883 344444 777888887754331   47999999999999985 


Q ss_pred             ccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          408 SLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       408 ~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                        ..........+++.|+..|+.....        ....++|+|+|.
T Consensus        75 --~~~~~~~~~~~~~~L~~~l~~~~~~--------~~~~~vI~ttn~  111 (132)
T PF00004_consen   75 --QPSSSSFEQRLLNQLLSLLDNPSSK--------NSRVIVIATTNS  111 (132)
T ss_dssp             --STSSSHHHHHHHHHHHHHHHTTTTT--------SSSEEEEEEESS
T ss_pred             --ccccccccccccceeeecccccccc--------cccceeEEeeCC
Confidence              1123333445888999999854321        225788999887

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 ....

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

Probab=99.52  E-value=6.1e-14  Score=148.40  Aligned_cols=147  Identities=28%  Similarity=0.400  Sum_probs=101.6

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +++ |.|++.+++.|.+++.....  .++...   +                 -..+.+|||+||||||||++|+++|++
T Consensus       182 ~~D-IgGl~~qi~~l~e~v~lpl~~p~~~~~~---g-----------------i~~p~gVLL~GPPGTGKT~LAraIA~e  240 (438)
T PTZ00361        182 YAD-IGGLEQQIQEIKEAVELPLTHPELYDDI---G-----------------IKPPKGVILYGPPGTGKTLLAKAVANE  240 (438)
T ss_pred             HHH-hcCHHHHHHHHHHHHHhhhhCHHHHHhc---C-----------------CCCCcEEEEECCCCCCHHHHHHHHHHh
Confidence            444 89999999999998853221  111110   0                 123478999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++.+|+.+..+++.. .|+|+. +..++.+|..+...    .++||||||||.+..+|.....+.+......+..||..|
T Consensus       241 l~~~fi~V~~seL~~-k~~Ge~-~~~vr~lF~~A~~~----~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~L  314 (438)
T PTZ00361        241 TSATFLRVVGSELIQ-KYLGDG-PKLVRELFRVAEEN----APSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQL  314 (438)
T ss_pred             hCCCEEEEecchhhh-hhcchH-HHHHHHHHHHHHhC----CCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHH
Confidence            999999999998875 477776 67788888766543    688999999999988765333222222223444556666


Q ss_pred             hCceeeeecceeeecCCeEEEecCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSG  453 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsN  453 (461)
                      ++...         ..+.++|+|||
T Consensus       315 dg~~~---------~~~V~VI~ATN  330 (438)
T PTZ00361        315 DGFDS---------RGDVKVIMATN  330 (438)
T ss_pred             hhhcc---------cCCeEEEEecC
Confidence            64321         11456777777

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

Probab=99.52  E-value=3.4e-14  Score=146.61  Aligned_cols=86  Identities=29%  Similarity=0.431  Sum_probs=73.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      .+++|||||||||||||++||+..+..|..+++..-.         .+.++.+++.+.......+..|||||||+++...
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~~g---------vkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~  119 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTSG---------VKDLREIIEEARKNRLLGRRTILFLDEIHRFNKA  119 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHHhhCCceEEecccccc---------HHHHHHHHHHHHHHHhcCCceEEEEehhhhcChh
Confidence            6799999999999999999999999999999887543         4667888887766655567889999999999998


Q ss_pred             hhccccccccchHHHHHHHHHHHhCceee
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTETK  434 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v~  434 (461)
                                    .|+.||..||.+.+.
T Consensus       120 --------------QQD~lLp~vE~G~ii  134 (436)
T COG2256         120 --------------QQDALLPHVENGTII  134 (436)
T ss_pred             --------------hhhhhhhhhcCCeEE
Confidence                          899999999966543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.52  E-value=4.9e-14  Score=160.02  Aligned_cols=166  Identities=27%  Similarity=0.381  Sum_probs=116.1

Q ss_pred             CCCCCCCCCCCCCCCHH----HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhcccccccccc
Q 012525          249 GSRWGGSNLGEDLPTPK----EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELE  324 (461)
Q Consensus       249 ~~~w~g~~l~~~l~t~~----el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~  324 (461)
                      .++|+++++.+......    .+.+.|.+.|+||+.+++.|...+......+...                      ..+
T Consensus       540 v~~~tgip~~~~~~~~~~~l~~l~~~l~~~viGQ~~ai~~l~~~i~~~~~gl~~~----------------------~~p  597 (857)
T PRK10865        540 LARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDP----------------------NRP  597 (857)
T ss_pred             HHHHHCCCchhhhhhHHHHHHHHHHHhCCeEeCCHHHHHHHHHHHHHHHhcccCC----------------------CCC
Confidence            57899999988765543    4788888889999999999999884221111000                      001


Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhccC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAAQ  390 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a~  390 (461)
                      ...+||+||+|||||++|++||+.+   +.+|+.++++++...           +|+|......+...+.       ...
T Consensus       598 ~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~~g~l~~~v~-------~~p  670 (857)
T PRK10865        598 IGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVR-------RRP  670 (857)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHHHhCCCCcccccchhHHHHHHHH-------hCC
Confidence            1368999999999999999999987   357899998876432           2334332223332222       224


Q ss_pred             ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          391 QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       391 ~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      .+|||||||+++.+.              +++.|+++|+.+.+..........++.++|.|||.+.+
T Consensus       671 ~~vLllDEieka~~~--------------v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~  723 (857)
T PRK10865        671 YSVILLDEVEKAHPD--------------VFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSD  723 (857)
T ss_pred             CCeEEEeehhhCCHH--------------HHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchH
Confidence            579999999999988              99999999997766542222222337899999999754

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

Probab=99.50  E-value=5.9e-14  Score=146.95  Aligned_cols=148  Identities=29%  Similarity=0.392  Sum_probs=114.4

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      .+.|++.+|+.|.+++.....+-                   +.........+.+||.||||||||+|+++||.+++..|
T Consensus       154 di~gl~~~k~~l~e~vi~p~lr~-------------------d~F~glr~p~rglLLfGPpgtGKtmL~~aiAsE~~atf  214 (428)
T KOG0740|consen  154 DIAGLEDAKQSLKEAVILPLLRP-------------------DLFLGLREPVRGLLLFGPPGTGKTMLAKAIATESGATF  214 (428)
T ss_pred             CCcchhhHHHHhhhhhhhcccch-------------------HhhhccccccchhheecCCCCchHHHHHHHHhhhcceE
Confidence            37899999999999886432210                   11122223347899999999999999999999999999


Q ss_pred             EEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCcee
Q 012525          354 VIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTET  433 (461)
Q Consensus       354 v~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v  433 (461)
                      +.+.++.++ .+|+|+. +..++.+|.-+...    +++|+||||||.+..+|..   ..+.+.++++.++|-.+++...
T Consensus       215 f~iSassLt-sK~~Ge~-eK~vralf~vAr~~----qPsvifidEidslls~Rs~---~e~e~srr~ktefLiq~~~~~s  285 (428)
T KOG0740|consen  215 FNISASSLT-SKYVGES-EKLVRALFKVARSL----QPSVIFIDEIDSLLSKRSD---NEHESSRRLKTEFLLQFDGKNS  285 (428)
T ss_pred             eeccHHHhh-hhccChH-HHHHHHHHHHHHhc----CCeEEEechhHHHHhhcCC---cccccchhhhhHHHhhhccccC
Confidence            999999999 5799999 99999999877654    8999999999999999832   3445555677777777774432


Q ss_pred             eeecceeeecCCeEEEecCCCCc
Q 012525          434 KTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       434 ~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      .       ...+.++|.|||..-
T Consensus       286 ~-------~~drvlvigaTN~P~  301 (428)
T KOG0740|consen  286 A-------PDDRVLVIGATNRPW  301 (428)
T ss_pred             C-------CCCeEEEEecCCCch
Confidence            2       112688999999764

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

Probab=99.50  E-value=1.2e-13  Score=155.15  Aligned_cols=166  Identities=26%  Similarity=0.357  Sum_probs=128.7

Q ss_pred             CCCCCCCCCCCCCCCC----HHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccc
Q 012525          248 GGSRWGGSNLGEDLPT----PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVEL  323 (461)
Q Consensus       248 ~~~~w~g~~l~~~l~t----~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~  323 (461)
                      ...+|+++++......    ...+++.|.+.|+||++|...|..+|..........                       .
T Consensus       533 ~~s~~tgip~~~~~~~e~~~l~~L~~~L~~~V~gQ~eAv~aIa~AI~~sr~gl~~~-----------------------~  589 (898)
T KOG1051|consen  533 VVSRWTGIPVDRLAEAEAERLKKLEERLHERVIGQDEAVAAIAAAIRRSRAGLKDP-----------------------N  589 (898)
T ss_pred             hhhhhcCCchhhhhhhHHHHHHHHHHHHHhhccchHHHHHHHHHHHHhhhcccCCC-----------------------C
Confidence            4689999888776543    345899999999999999999999995322111100                       1


Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchh--------hhhcCcccccHHHHHHHHHHhhchhhhccCce
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATT--------LTQAGYVGEDVESILYKLLAQAEFNVEAAQQG  392 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~--------l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~g  392 (461)
                      ...-+||.||.|+|||-||++||..+-   -.|+.+++++        -...+|+|......|.+.+...       ..+
T Consensus       590 ~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskligsp~gyvG~e~gg~Lteavrrr-------P~s  662 (898)
T KOG1051|consen  590 PDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEEGGQLTEAVKRR-------PYS  662 (898)
T ss_pred             CCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhccCCCcccccchhHHHHHHHHhcC-------Cce
Confidence            235689999999999999999999883   3789999986        2334788888777777776554       456


Q ss_pred             EEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          393 MVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       393 VLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ||||||||+..+.              +++.|+++||.+.+....+.....++.|||.|+|.+..
T Consensus       663 VVLfdeIEkAh~~--------------v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~~~~  713 (898)
T KOG1051|consen  663 VVLFEEIEKAHPD--------------VLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSNVGSS  713 (898)
T ss_pred             EEEEechhhcCHH--------------HHHHHHHHHhcCccccCCCcEeeccceEEEEecccchH
Confidence            9999999999998              99999999998887765554444459999999998765

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

Probab=99.49  E-value=1.6e-14  Score=152.30  Aligned_cols=139  Identities=22%  Similarity=0.374  Sum_probs=120.9

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhh----cCcccccHHHHHHH
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQ----AGYVGEDVESILYK  377 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~----~g~vGe~~e~~L~~  377 (461)
                      ++.|+.|....+.++.++.+..+|||.|++||||..+||+|++..   ..|||.++|+.+-+    +..+|.. ...+..
T Consensus       226 IG~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPesLlESELFGHe-KGAFTG  304 (550)
T COG3604         226 IGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPESLLESELFGHE-KGAFTG  304 (550)
T ss_pred             eecCHHHHHHHHHHHHHhcCCCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccchHHHHHHHhccc-cccccc
Confidence            578899999999999999999999999999999999999999977   46999999987654    3344444 445556


Q ss_pred             HHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          378 LLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       378 lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      .+....+.++.+++|.||||||..|...              +|..||..|+++++......+.+..|..+|++||.|.+
T Consensus       305 A~~~r~GrFElAdGGTLFLDEIGelPL~--------------lQaKLLRvLQegEieRvG~~r~ikVDVRiIAATNRDL~  370 (550)
T COG3604         305 AINTRRGRFELADGGTLFLDEIGELPLA--------------LQAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRDLE  370 (550)
T ss_pred             chhccCcceeecCCCeEechhhccCCHH--------------HHHHHHHHHhhcceeecCCCceeEEEEEEEeccchhHH
Confidence            6667778899999999999999999999              99999999999999988888887789999999999976


Q ss_pred             c
Q 012525          458 T  458 (461)
Q Consensus       458 ~  458 (461)
                      +
T Consensus       371 ~  371 (550)
T COG3604         371 E  371 (550)
T ss_pred             H
Confidence            4

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.49  E-value=2.2e-13  Score=140.40  Aligned_cols=146  Identities=27%  Similarity=0.401  Sum_probs=96.6

Q ss_pred             hcCChHHHHHHHHHHHHHHHHH--HHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKR--IYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kr--i~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .|.|++++++.|.+++......  ++.   ..+                 ...+.++||+||||||||++|+++|+.++.
T Consensus       123 di~Gl~~~~~~l~~~i~~~~~~~~~~~---~~g-----------------~~~p~gvLL~GppGtGKT~lakaia~~l~~  182 (364)
T TIGR01242       123 DIGGLEEQIREIREAVELPLKHPELFE---EVG-----------------IEPPKGVLLYGPPGTGKTLLAKAVAHETNA  182 (364)
T ss_pred             HhCChHHHHHHHHHHHHHHhcCHHHHH---hcC-----------------CCCCceEEEECCCCCCHHHHHHHHHHhCCC
Confidence            3899999999999988532211  111   011                 122467999999999999999999999999


Q ss_pred             ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          352 PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       352 pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      +|+.+....+.. .|.|+. ...++.+|..+..    ..++||||||||.+...+.....+.+......+..|+..|++.
T Consensus       183 ~~~~v~~~~l~~-~~~g~~-~~~i~~~f~~a~~----~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~  256 (364)
T TIGR01242       183 TFIRVVGSELVR-KYIGEG-ARLVREIFELAKE----KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGF  256 (364)
T ss_pred             CEEecchHHHHH-HhhhHH-HHHHHHHHHHHHh----cCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCC
Confidence            999998887764 366665 5667777765543    2678999999999987754333222222122333444444432


Q ss_pred             eeeeecceeeecCCeEEEecCCC
Q 012525          432 ETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       432 ~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ..         ..+.++|+|+|.
T Consensus       257 ~~---------~~~v~vI~ttn~  270 (364)
T TIGR01242       257 DP---------RGNVKVIAATNR  270 (364)
T ss_pred             CC---------CCCEEEEEecCC
Confidence            11         114677777774

Many proteins may score above the trusted cutoff because an internal

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

Probab=99.47  E-value=8.1e-14  Score=147.58  Aligned_cols=140  Identities=19%  Similarity=0.334  Sum_probs=114.9

Q ss_pred             CCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhhc----CcccccHHHHHH
Q 012525          304 GSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQA----GYVGEDVESILY  376 (461)
Q Consensus       304 g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~~----g~vGe~~e~~L~  376 (461)
                      -.+.|+.|..+.+.+.+++.+..+|||+|++||||.++||+|++...   .||+.++|..+.+.    .++|.. ...+.
T Consensus       143 liG~S~am~~l~~~i~kvA~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~l~ESELFGhe-kGAFT  221 (464)
T COG2204         143 LVGESPAMQQLRRLIAKVAPSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENLLESELFGHE-KGAFT  221 (464)
T ss_pred             ceecCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHHHHHHHhhccc-ccCcC
Confidence            35788999999999999999999999999999999999999998774   59999999987742    122222 11222


Q ss_pred             HHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          377 KLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       377 ~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      .......+.++.+++|+||||||..|...              +|..||++|+.+++......+....|..+|++||.++
T Consensus       222 GA~~~r~G~fE~A~GGTLfLDEI~~mpl~--------------~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~dL  287 (464)
T COG2204         222 GAITRRIGRFEQANGGTLFLDEIGEMPLE--------------LQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDL  287 (464)
T ss_pred             CcccccCcceeEcCCceEEeeccccCCHH--------------HHHHHHHHHHcCeeEecCCCcccceeeEEEeecCcCH
Confidence            22233456788899999999999999998              9999999999999988777777777999999999987


Q ss_pred             Cc
Q 012525          457 KT  458 (461)
Q Consensus       457 e~  458 (461)
                      +.
T Consensus       288 ~~  289 (464)
T COG2204         288 EE  289 (464)
T ss_pred             HH
Confidence            64

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

Probab=99.46  E-value=1.7e-13  Score=154.97  Aligned_cols=148  Identities=26%  Similarity=0.408  Sum_probs=116.5

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHH--HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNH--YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~--~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraL  345 (461)
                      ...|++ |.|++.++..|++.|...  |..++.....                    .+++.|||+||||||||++|++|
T Consensus       261 ~v~fd~-vggl~~~i~~LKEmVl~PLlyPE~f~~~~i--------------------tpPrgvL~~GppGTGkTl~araL  319 (1080)
T KOG0732|consen  261 SVGFDS-VGGLENYINQLKEMVLLPLLYPEFFDNFNI--------------------TPPRGVLFHGPPGTGKTLMARAL  319 (1080)
T ss_pred             ccCccc-cccHHHHHHHHHHHHHhHhhhhhHhhhccc--------------------CCCcceeecCCCCCchhHHHHhh
Confidence            345566 899999999999998754  4444432221                    23578999999999999999999


Q ss_pred             HHhcC-----CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          346 ARHVN-----VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       346 A~~l~-----~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      |..+.     ..|+.-..++.. .+|+|+. +..++-+|.++...    +++|||+||||-|++.|++...+.+.+   +
T Consensus       320 a~~~s~~~~kisffmrkgaD~l-skwvgEa-ERqlrllFeeA~k~----qPSIIffdeIdGlapvrSskqEqih~S---I  390 (1080)
T KOG0732|consen  320 AAACSRGNRKISFFMRKGADCL-SKWVGEA-ERQLRLLFEEAQKT----QPSIIFFDEIDGLAPVRSSKQEQIHAS---I  390 (1080)
T ss_pred             hhhhcccccccchhhhcCchhh-ccccCcH-HHHHHHHHHHHhcc----CceEEeccccccccccccchHHHhhhh---H
Confidence            99883     466666777777 4799998 99999999988765    899999999999999998776666666   9


Q ss_pred             HHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          421 QQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +.+||.+|+|...+-         ..++|.++|.
T Consensus       391 vSTLLaLmdGldsRg---------qVvvigATnR  415 (1080)
T KOG0732|consen  391 VSTLLALMDGLDSRG---------QVVVIGATNR  415 (1080)
T ss_pred             HHHHHHhccCCCCCC---------ceEEEcccCC
Confidence            999999999765321         4678888764

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.45  E-value=4.2e-13  Score=148.28  Aligned_cols=157  Identities=25%  Similarity=0.348  Sum_probs=113.0

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      ++..+...+++ |.|.+.+++.|...+......  ......+                 ...+.+|||+||||||||++|
T Consensus       143 ~~~~~~~~~~d-i~g~~~~~~~l~~i~~~~~~~--~~~~~~~-----------------~~~~~gill~G~~G~GKt~~~  202 (644)
T PRK10733        143 TEDQIKTTFAD-VAGCDEAKEEVAELVEYLREP--SRFQKLG-----------------GKIPKGVLMVGPPGTGKTLLA  202 (644)
T ss_pred             CchhhhCcHHH-HcCHHHHHHHHHHHHHHhhCH--HHHHhcC-----------------CCCCCcEEEECCCCCCHHHHH
Confidence            34556667777 799999999998877421100  0000000                 122467999999999999999


Q ss_pred             HHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          343 KTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       343 raLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                      +++|++++.+|+.++++++.. .+++.. ...++.+|..+..    ..++||||||||.+...|.....+.+...+.+++
T Consensus       203 ~~~a~~~~~~f~~is~~~~~~-~~~g~~-~~~~~~~f~~a~~----~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln  276 (644)
T PRK10733        203 KAIAGEAKVPFFTISGSDFVE-MFVGVG-ASRVRDMFEQAKK----AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLN  276 (644)
T ss_pred             HHHHHHcCCCEEEEehHHhHH-hhhccc-HHHHHHHHHHHHh----cCCcEEEehhHhhhhhccCCCCCCCchHHHHHHH
Confidence            999999999999999998874 366766 5677888876643    3789999999999998776433334444566889


Q ss_pred             HHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          423 ALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       423 aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      .||..||+...         ....++|+|||.
T Consensus       277 ~lL~~mdg~~~---------~~~vivIaaTN~  299 (644)
T PRK10733        277 QMLVEMDGFEG---------NEGIIVIAATNR  299 (644)
T ss_pred             HHHHhhhcccC---------CCCeeEEEecCC
Confidence            99999986432         125788888885

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.45  E-value=1.7e-13  Score=135.53  Aligned_cols=118  Identities=22%  Similarity=0.253  Sum_probs=80.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchh-hhhcCccccc----HHHHHHHHHH------------hhchhh-
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATT-LTQAGYVGED----VESILYKLLA------------QAEFNV-  386 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~-l~~~g~vGe~----~e~~L~~lf~------------~a~~~v-  386 (461)
                      ..+|||.||||||||++|++||+.++.+|+.+++.. +....++|..    ....+.....            +..+.+ 
T Consensus        21 g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~  100 (262)
T TIGR02640        21 GYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLT  100 (262)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCchHH
Confidence            478999999999999999999999999999998763 2222222221    1111111100            001111 


Q ss_pred             -hccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeeccee-----eecCCeEEEecCCCCc
Q 012525          387 -EAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVS-----KVSRDNLYIKTSGLDS  456 (461)
Q Consensus       387 -~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r-----~~~rd~IiI~TsNid~  456 (461)
                       ....+++||||||+++.++              +++.|+.+||++.+.++....     ....++.+|+|+|...
T Consensus       101 ~A~~~g~~lllDEi~r~~~~--------------~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~  162 (262)
T TIGR02640       101 LAVREGFTLVYDEFTRSKPE--------------TNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVE  162 (262)
T ss_pred             HHHHcCCEEEEcchhhCCHH--------------HHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCcc
Confidence             1246679999999999888              999999999998887765421     1223789999999763

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).

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

Probab=99.44  E-value=3.3e-13  Score=135.57  Aligned_cols=128  Identities=26%  Similarity=0.373  Sum_probs=95.6

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |.|.-.....+.+.+..|...-+ .+.+.+                 -..+..++||||||||||++|+++|..+++.|+
T Consensus       134 ~ggl~~qirelre~ielpl~np~-lf~rvg-----------------Ik~Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl  195 (388)
T KOG0651|consen  134 VGGLFYQIRELREVIELPLTNPE-LFLRVG-----------------IKPPKGLLLYGPPGTGKTLLARAVAATMGVNFL  195 (388)
T ss_pred             hCChHHHHHHHHhheEeeccCch-hccccC-----------------CCCCceeEEeCCCCCchhHHHHHHHHhcCCceE
Confidence            67777777777777754432210 000001                 123578999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      .+..+.+.+ +|.|+. .+.+++.|..+...    .+||||+||||++...+.+...+.   .+.+|.+|.++++
T Consensus       196 ~v~ss~lv~-kyiGEs-aRlIRemf~yA~~~----~pciifmdeiDAigGRr~se~Ts~---dreiqrTLMeLln  261 (388)
T KOG0651|consen  196 KVVSSALVD-KYIGES-ARLIRDMFRYAREV----IPCIIFMDEIDAIGGRRFSEGTSS---DREIQRTLMELLN  261 (388)
T ss_pred             EeeHhhhhh-hhcccH-HHHHHHHHHHHhhh----CceEEeehhhhhhccEEeccccch---hHHHHHHHHHHHH
Confidence            999999994 699998 79999999988766    679999999999998874433333   3446777766665

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

Probab=99.44  E-value=8.1e-14  Score=148.37  Aligned_cols=139  Identities=19%  Similarity=0.357  Sum_probs=111.9

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc----CcccccHHHHHHH
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA----GYVGEDVESILYK  377 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~----g~vGe~~e~~L~~  377 (461)
                      .+.++.|.......+.++.....|||.|++||||.++|++|++..   +.||+.++|+.+-+.    .++|.. ...+..
T Consensus       248 ig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFGye-~GAFTG  326 (560)
T COG3829         248 IGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFGYE-KGAFTG  326 (560)
T ss_pred             ccCCHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCCHHHHHHHHhCcC-Cccccc
Confidence            466778888888888889999999999999999999999999876   569999999876643    222222 111111


Q ss_pred             HHHh-hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          378 LLAQ-AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       378 lf~~-a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      .... ..+.++.|++|.||||||..|...              +|..||++|++.++.........+.|..+|++||.++
T Consensus       327 A~~~GK~GlfE~A~gGTLFLDEIgempl~--------------LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL  392 (560)
T COG3829         327 ASKGGKPGLFELANGGTLFLDEIGEMPLP--------------LQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNL  392 (560)
T ss_pred             cccCCCCcceeeccCCeEEehhhccCCHH--------------HHHHHHHHHhhceEEecCCCCceeeEEEEEeccCcCH
Confidence            1111 445678899999999999999998              9999999999999998888888888999999999987


Q ss_pred             Cc
Q 012525          457 KT  458 (461)
Q Consensus       457 e~  458 (461)
                      +.
T Consensus       393 ~~  394 (560)
T COG3829         393 EK  394 (560)
T ss_pred             HH
Confidence            54

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.43  E-value=5.2e-13  Score=136.93  Aligned_cols=141  Identities=21%  Similarity=0.316  Sum_probs=93.0

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |.. |+||+++|+.|..++..                               ....|+||+|+||||||++|++||+.+.
T Consensus         7 f~~-i~Gq~~~~~~l~~~~~~-------------------------------~~~~~vLl~G~pG~gKT~lar~la~llP   54 (334)
T PRK13407          7 FSA-IVGQEEMKQAMVLTAID-------------------------------PGIGGVLVFGDRGTGKSTAVRALAALLP   54 (334)
T ss_pred             HHH-hCCHHHHHHHHHHHHhc-------------------------------cCCCcEEEEcCCCCCHHHHHHHHHHHCC
Confidence            344 89999999988765520                               1126899999999999999999999883


Q ss_pred             -------Cc--eEEecch-hh----------------------hhcCcccc-cHHHHH-HHHHHhhchhhhccCceEEEE
Q 012525          351 -------VP--FVIADAT-TL----------------------TQAGYVGE-DVESIL-YKLLAQAEFNVEAAQQGMVYI  396 (461)
Q Consensus       351 -------~p--fv~i~~s-~l----------------------~~~g~vGe-~~e~~L-~~lf~~a~~~v~~a~~gVLfI  396 (461)
                             .+  +..+.+. ++                      .....+|. +++..+ ...+....+.+..+++++|||
T Consensus        55 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~l  134 (334)
T PRK13407         55 LIKAVEGCPVNSARPEDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYI  134 (334)
T ss_pred             CcchhcccccccCcccCCcccccccCCcccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEe
Confidence                   21  1111110 00                      00012221 111111 112223345556678899999


Q ss_pred             cCccccchhhhccccccccchHHHHHHHHHHHhCceeeee--cceeeecCCeEEEecCCCCcC
Q 012525          397 DEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTF--AAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       397 DEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~--~~~r~~~rd~IiI~TsNid~e  457 (461)
                      |||+.+.++              +|+.|++.|+.+++.+.  ......+.++++|+|.|....
T Consensus       135 DEInrl~~~--------------~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~  183 (334)
T PRK13407        135 DEVNLLEDH--------------IVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEG  183 (334)
T ss_pred             cChHhCCHH--------------HHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccC
Confidence            999999988              99999999998775443  335566679999999998644

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

Probab=99.43  E-value=6.5e-13  Score=144.86  Aligned_cols=156  Identities=26%  Similarity=0.309  Sum_probs=115.4

Q ss_pred             CCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchH
Q 012525          260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKT  339 (461)
Q Consensus       260 ~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKT  339 (461)
                      +....++..+.||+.-+|++++|+++.+.+.-...  .  ..                     ..+.-++|.||||+|||
T Consensus       310 ~~~Dl~~a~~iLd~dHYGLekVKeRIlEyLAV~~l--~--~~---------------------~kGpILcLVGPPGVGKT  364 (782)
T COG0466         310 DKLDLKKAEKILDKDHYGLEKVKERILEYLAVQKL--T--KK---------------------LKGPILCLVGPPGVGKT  364 (782)
T ss_pred             hhhhHHHHHHHhcccccCchhHHHHHHHHHHHHHH--h--cc---------------------CCCcEEEEECCCCCCch
Confidence            44566788999999999999999999998741111  0  01                     11245789999999999


Q ss_pred             HHHHHHHHhcCCceEEecchhhhhc--------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccc
Q 012525          340 LLAKTLARHVNVPFVIADATTLTQA--------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI  411 (461)
Q Consensus       340 tLAraLA~~l~~pfv~i~~s~l~~~--------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~  411 (461)
                      +|++.||+.++..|++++..-+.+.        .|+|....++++.+-....      .+.|++|||||+|..+-.    
T Consensus       365 SLgkSIA~al~RkfvR~sLGGvrDEAEIRGHRRTYIGamPGrIiQ~mkka~~------~NPv~LLDEIDKm~ss~r----  434 (782)
T COG0466         365 SLGKSIAKALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKAGV------KNPVFLLDEIDKMGSSFR----  434 (782)
T ss_pred             hHHHHHHHHhCCCEEEEecCccccHHHhccccccccccCChHHHHHHHHhCC------cCCeEEeechhhccCCCC----
Confidence            9999999999999999988655532        5788887777777664333      456999999999998732    


Q ss_pred             ccccchHHHHHHHHHHHhCceeeeecc-eeeecC---CeEEEecCCCCc
Q 012525          412 SRDVSGEGVQQALLKMLEGTETKTFAA-VSKVSR---DNLYIKTSGLDS  456 (461)
Q Consensus       412 ~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r~~~r---d~IiI~TsNid~  456 (461)
                       .+     -.++||+.||-.+.+.+.+ ....+.   +.+||+|+|.-.
T Consensus       435 -GD-----PaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~  477 (782)
T COG0466         435 -GD-----PASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLD  477 (782)
T ss_pred             -CC-----hHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccc
Confidence             22     5689999999666655554 222232   799999999644

>TIGR00763 lon ATP-dependent protease La

Probab=99.42  E-value=1e-12  Score=148.09  Aligned_cols=154  Identities=25%  Similarity=0.316  Sum_probs=102.6

Q ss_pred             CCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHH
Q 012525          261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTL  340 (461)
Q Consensus       261 l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTt  340 (461)
                      ......+.+.|++.++|++++|+.|.+.+.....+        +                 ...+.++||+||||||||+
T Consensus       308 ~~~~~~~~~~l~~~~~G~~~~k~~i~~~~~~~~~~--------~-----------------~~~~~~lll~GppG~GKT~  362 (775)
T TIGR00763       308 NLDLKRAKEILDEDHYGLKKVKERILEYLAVQKLR--------G-----------------KMKGPILCLVGPPGVGKTS  362 (775)
T ss_pred             hhhHHHHHHHhhhhcCChHHHHHHHHHHHHHHHhh--------c-----------------CCCCceEEEECCCCCCHHH
Confidence            33567788999999999999999998876422110        0                 0112479999999999999


Q ss_pred             HHHHHHHhcCCceEEecchhhhh--------cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          341 LAKTLARHVNVPFVIADATTLTQ--------AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       341 LAraLA~~l~~pfv~i~~s~l~~--------~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                      +|++||+.++.+|+.+++..+..        ..|+|... ..+...+..+..     ...||||||||++.....     
T Consensus       363 lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~-g~i~~~l~~~~~-----~~~villDEidk~~~~~~-----  431 (775)
T TIGR00763       363 LGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMP-GRIIQGLKKAKT-----KNPLFLLDEIDKIGSSFR-----  431 (775)
T ss_pred             HHHHHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCCCC-chHHHHHHHhCc-----CCCEEEEechhhcCCccC-----
Confidence            99999999999999987654321        24555553 333344443321     345999999999986421     


Q ss_pred             cccchHHHHHHHHHHHhCceeeeecc---eeeec-CCeEEEecCCCC
Q 012525          413 RDVSGEGVQQALLKMLEGTETKTFAA---VSKVS-RDNLYIKTSGLD  455 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg~~v~i~~~---~r~~~-rd~IiI~TsNid  455 (461)
                      .+     ..++||++||..+...+..   ..... .+.++|+|+|.-
T Consensus       432 ~~-----~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~  473 (775)
T TIGR00763       432 GD-----PASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSI  473 (775)
T ss_pred             CC-----HHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCc
Confidence            11     4689999998532221111   11222 268899999963

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.41  E-value=1.1e-12  Score=135.32  Aligned_cols=138  Identities=21%  Similarity=0.320  Sum_probs=92.1

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN----  350 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~----  350 (461)
                      |+||+++|..|...+.+                               ....+|||.|++|||||++||++++.+.    
T Consensus        19 ivGq~~~k~al~~~~~~-------------------------------p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~   67 (350)
T CHL00081         19 IVGQEEMKLALILNVID-------------------------------PKIGGVMIMGDRGTGKSTTIRALVDLLPEIEV   67 (350)
T ss_pred             HhChHHHHHHHHHhccC-------------------------------CCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCc
Confidence            89999999999887731                               1126799999999999999999988763    


Q ss_pred             ---CceEEecch-------hh--------------------------hhcCccc-ccHHHHHHHHH-HhhchhhhccCce
Q 012525          351 ---VPFVIADAT-------TL--------------------------TQAGYVG-EDVESILYKLL-AQAEFNVEAAQQG  392 (461)
Q Consensus       351 ---~pfv~i~~s-------~l--------------------------~~~g~vG-e~~e~~L~~lf-~~a~~~v~~a~~g  392 (461)
                         .||. .+..       .+                          ....++| -+.+..+..-. ....+.+..++++
T Consensus        68 ~~~~pf~-~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~G  146 (350)
T CHL00081         68 VKDDPFN-SHPSDPELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRG  146 (350)
T ss_pred             cCCCCCC-CCCCChhhhchhhhhhhcccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCC
Confidence               2332 0000       00                          0000111 12222221111 1124456678899


Q ss_pred             EEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeee--cceeeecCCeEEEecCCCCcCc
Q 012525          393 MVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTF--AAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       393 VLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~--~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      |||||||+.+.++              +|+.|++.|+.+++.+.  ......+.++++|+|.|+....
T Consensus       147 iL~lDEInrL~~~--------------~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~  200 (350)
T CHL00081        147 ILYVDEVNLLDDH--------------LVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGE  200 (350)
T ss_pred             EEEecChHhCCHH--------------HHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCC
Confidence            9999999999999              99999999997655543  3355666799999999987543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.41  E-value=1.3e-12  Score=146.23  Aligned_cols=146  Identities=28%  Similarity=0.448  Sum_probs=105.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+++ |+|++++++.|.+.+.....  .++.   ..+                 ...+.+|||+||||||||+||++||+
T Consensus       176 ~~~d-i~G~~~~~~~l~~~i~~~~~~~~~~~---~~g-----------------i~~~~giLL~GppGtGKT~laraia~  234 (733)
T TIGR01243       176 TYED-IGGLKEAKEKIREMVELPMKHPELFE---HLG-----------------IEPPKGVLLYGPPGTGKTLLAKAVAN  234 (733)
T ss_pred             CHHH-hcCHHHHHHHHHHHHHHHhhCHHHHH---hcC-----------------CCCCceEEEECCCCCChHHHHHHHHH
Confidence            4555 89999999999998853221  1111   111                 12347899999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +++.+|+.+++.++.. .+.|+. +..++.+|..+...    .++||||||||.+..+++...   ......+++.|+.+
T Consensus       235 ~~~~~~i~i~~~~i~~-~~~g~~-~~~l~~lf~~a~~~----~p~il~iDEid~l~~~r~~~~---~~~~~~~~~~Ll~~  305 (733)
T TIGR01243       235 EAGAYFISINGPEIMS-KYYGES-EERLREIFKEAEEN----APSIIFIDEIDAIAPKREEVT---GEVEKRVVAQLLTL  305 (733)
T ss_pred             HhCCeEEEEecHHHhc-ccccHH-HHHHHHHHHHHHhc----CCcEEEeehhhhhcccccCCc---chHHHHHHHHHHHH
Confidence            9999999999998874 577766 67788888776533    678999999999998764321   12234588999999


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      |++....         ...++|+++|.
T Consensus       306 ld~l~~~---------~~vivI~atn~  323 (733)
T TIGR01243       306 MDGLKGR---------GRVIVIGATNR  323 (733)
T ss_pred             hhccccC---------CCEEEEeecCC
Confidence            9854211         14577777774

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.40  E-value=1.2e-12  Score=139.32  Aligned_cols=139  Identities=20%  Similarity=0.225  Sum_probs=96.5

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHH
Q 012525          265 KEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       265 ~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAra  344 (461)
                      ..+...|.+.|+|++++++.+..++                                 ....||||+||||||||++|++
T Consensus        12 ~~l~~~l~~~i~gre~vI~lll~aa---------------------------------lag~hVLL~GpPGTGKT~LAra   58 (498)
T PRK13531         12 SRLSSALEKGLYERSHAIRLCLLAA---------------------------------LSGESVFLLGPPGIAKSLIARR   58 (498)
T ss_pred             HHHHHHHhhhccCcHHHHHHHHHHH---------------------------------ccCCCEEEECCCChhHHHHHHH
Confidence            4578889999999999999888877                                 2358899999999999999999


Q ss_pred             HHHhcCC--ceEEecchhhhhcCcccccHHHHH--HHHHH-hhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          345 LARHVNV--PFVIADATTLTQAGYVGEDVESIL--YKLLA-QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       345 LA~~l~~--pfv~i~~s~l~~~g~vGe~~e~~L--~~lf~-~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      ||+.+..  +|....+...+....+|...-...  ...|. ...+.+..++  |||+|||+++.++              
T Consensus        59 La~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~--lLfLDEI~rasp~--------------  122 (498)
T PRK13531         59 LKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYQRLTSGYLPEAE--IVFLDEIWKAGPA--------------  122 (498)
T ss_pred             HHHHhcccCcceeeeeeecCcHHhcCcHHHhhhhhcCchhhhcCCcccccc--EEeecccccCCHH--------------
Confidence            9997743  455444432122223332100110  11121 1112221222  9999999999998              


Q ss_pred             HHHHHHHHHhCceeeeecceeeecCCeEEEecCC
Q 012525          420 VQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSG  453 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsN  453 (461)
                      +|++||..|+++.+++.......+.++++++| |
T Consensus       123 ~QsaLLeam~Er~~t~g~~~~~lp~rfiv~AT-N  155 (498)
T PRK13531        123 ILNTLLTAINERRFRNGAHEEKIPMRLLVTAS-N  155 (498)
T ss_pred             HHHHHHHHHHhCeEecCCeEEeCCCcEEEEEC-C
Confidence            99999999999998876557777777777777 5

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

Probab=99.36  E-value=8.2e-13  Score=139.85  Aligned_cols=116  Identities=32%  Similarity=0.484  Sum_probs=89.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC-ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhc----cCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV-PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEA----AQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~-pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~----a~~gVLfIDEID  400 (461)
                      ++||||||||||||++||.|.+.++. +=-.++..++. .+|+|++ |..++++|..++.....    ..=.||+|||||
T Consensus       257 KGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPeIL-~KYVGeS-E~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiD  334 (744)
T KOG0741|consen  257 KGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPEIL-NKYVGES-EENVRKLFADAEEEQRRLGANSGLHIIIFDEID  334 (744)
T ss_pred             eeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHHHH-HHhhccc-HHHHHHHHHhHHHHHHhhCccCCceEEEehhhH
Confidence            57999999999999999999999976 23457778887 4699999 89999999987755433    222599999999


Q ss_pred             ccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCC
Q 012525          401 KITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSG  453 (461)
Q Consensus       401 ~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsN  453 (461)
                      +++..|.+...+..+. +.++|+||.-|||.+..         .+.++|.-||
T Consensus       335 AICKqRGS~~g~TGVh-D~VVNQLLsKmDGVeqL---------NNILVIGMTN  377 (744)
T KOG0741|consen  335 AICKQRGSMAGSTGVH-DTVVNQLLSKMDGVEQL---------NNILVIGMTN  377 (744)
T ss_pred             HHHHhcCCCCCCCCcc-HHHHHHHHHhcccHHhh---------hcEEEEeccC
Confidence            9999998766555543 55999999999976432         1356666665

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.36  E-value=1.5e-12  Score=133.10  Aligned_cols=130  Identities=21%  Similarity=0.305  Sum_probs=93.3

Q ss_pred             chhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhhcCcccccHHHHHHH----HHH-
Q 012525          309 PKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQAGYVGEDVESILYK----LLA-  380 (461)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~~g~vGe~~e~~L~~----lf~-  380 (461)
                      +.|..+.+.+..++....+|||+|++||||+++|++|+....   .||+.++|..+.+.     ..+..+..    .|. 
T Consensus         6 ~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~~-----~l~~~lfG~~~g~~~g   80 (329)
T TIGR02974         6 NAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSEN-----LLDSELFGHEAGAFTG   80 (329)
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCChH-----HHHHHHhccccccccC
Confidence            334444444444555678899999999999999999998664   69999999876531     11111110    111 


Q ss_pred             ---hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          381 ---QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       381 ---~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                         ...+.++.+++++||||||+.|...              +|..|+.+|+...+...........++.+|+++|.+.+
T Consensus        81 a~~~~~G~~~~a~gGtL~Ldei~~L~~~--------------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~  146 (329)
T TIGR02974        81 AQKRHQGRFERADGGTLFLDELATASLL--------------VQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLP  146 (329)
T ss_pred             cccccCCchhhCCCCEEEeCChHhCCHH--------------HHHHHHHHHHcCcEEecCCCceeccceEEEEechhhHH
Confidence               1233466778999999999999998              99999999998776655555555568999999998753

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

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.35  E-value=3.6e-12  Score=140.74  Aligned_cols=138  Identities=25%  Similarity=0.289  Sum_probs=97.5

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc----
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV----  349 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l----  349 (461)
                      .|+||+.+|..|..++.+                               ....+|||.|++|||||++|++|++.+    
T Consensus         5 ~ivGq~~~~~al~~~av~-------------------------------~~~g~vli~G~~GtgKs~lar~l~~~lp~~~   53 (633)
T TIGR02442         5 AIVGQEDLKLALLLNAVD-------------------------------PRIGGVLIRGEKGTAKSTAARGLAALLPPID   53 (633)
T ss_pred             hhcChHHHHHHHHHHhhC-------------------------------CCCCeEEEEcCCCCcHHHHHHHHHHhCCCce
Confidence            389999999888766621                               112569999999999999999999988    


Q ss_pred             -------------------------------CCceEEecchhhhhcCcccc-cHHHHHHH-HHHhhchhhhccCceEEEE
Q 012525          350 -------------------------------NVPFVIADATTLTQAGYVGE-DVESILYK-LLAQAEFNVEAAQQGMVYI  396 (461)
Q Consensus       350 -------------------------------~~pfv~i~~s~l~~~g~vGe-~~e~~L~~-lf~~a~~~v~~a~~gVLfI  396 (461)
                                                     ..||+.+.+..... .++|. +++..+.. .+....+.+..++++||||
T Consensus        54 ~~~~~~~~c~p~~~~~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~-~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~l  132 (633)
T TIGR02442        54 VVAGCPFSCDPDDPEEWCEECRRKYRPSEQRPVPFVNLPLGATED-RVVGSLDIERALREGEKAFQPGLLAEAHRGILYI  132 (633)
T ss_pred             eccCCcCCCCCCCccccChhhhhcccccccCCCCeeeCCCCCcHH-HcCCcccHHHHhhcCCeeecCcceeecCCCeEEe
Confidence                                           24677666554332 23332 33322221 1112345566778999999


Q ss_pred             cCccccchhhhccccccccchHHHHHHHHHHHhCceeeee--cceeeecCCeEEEecCCCCcC
Q 012525          397 DEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTF--AAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       397 DEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~--~~~r~~~rd~IiI~TsNid~e  457 (461)
                      |||++|...              +|+.|++.|+.+.+.+.  ......+.++++|+|+|.+..
T Consensus       133 DEi~~l~~~--------------~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg  181 (633)
T TIGR02442       133 DEVNLLDDH--------------LVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEG  181 (633)
T ss_pred             ChhhhCCHH--------------HHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCC
Confidence            999999998              99999999997754433  335566678999999997643

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.

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

Probab=99.34  E-value=2e-12  Score=130.56  Aligned_cols=119  Identities=27%  Similarity=0.383  Sum_probs=90.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC---------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCc-eEEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV---------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQ-GMVY  395 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~---------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~-gVLf  395 (461)
                      +-|||+||||||||+|+|+||+.+..         .++++++..+. ++|+++. .+.+.++|......++..+. -.++
T Consensus       178 RliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLF-SKWFsES-gKlV~kmF~kI~ELv~d~~~lVfvL  255 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLF-SKWFSES-GKLVAKMFQKIQELVEDRGNLVFVL  255 (423)
T ss_pred             eEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHH-HHHHhhh-hhHHHHHHHHHHHHHhCCCcEEEEE
Confidence            56899999999999999999998843         57899999988 4699998 78889999877665544222 2457


Q ss_pred             EcCccccchhhhccccc-cccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          396 IDEVDKITKKAESLNIS-RDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       396 IDEID~L~~~R~~~~~~-~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      |||++.|...|...... .....-+++|+||..||.-+..         .++++++|+|+.
T Consensus       256 IDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~---------~NvliL~TSNl~  307 (423)
T KOG0744|consen  256 IDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRY---------PNVLILATSNLT  307 (423)
T ss_pred             eHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccC---------CCEEEEeccchH
Confidence            99999999998544433 3334457999999999933211         168888999975

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.34  E-value=2.7e-12  Score=151.17  Aligned_cols=113  Identities=16%  Similarity=0.250  Sum_probs=82.4

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCc----------cc-----------------------
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGY----------VG-----------------------  368 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~----------vG-----------------------  368 (461)
                      ...+++|||+||||||||+|||+||.++++||+.++++++... +          +|                       
T Consensus      1627 l~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~-~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~~ 1705 (2281)
T CHL00206       1627 LSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDN-KPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMM 1705 (2281)
T ss_pred             CCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhc-ccccccccccccccccccccccccccccchhhhhhc
Confidence            3557899999999999999999999999999999999988743 2          11                       


Q ss_pred             --------ccH-HHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecce
Q 012525          369 --------EDV-ESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV  439 (461)
Q Consensus       369 --------e~~-e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~  439 (461)
                              ..+ ...++.+|+.|...    .||||||||||.+..+.+         ....++.|+..|++....     
T Consensus      1706 n~~~~~m~~~e~~~rIr~lFelARk~----SPCIIFIDEIDaL~~~ds---------~~ltL~qLLneLDg~~~~----- 1767 (2281)
T CHL00206       1706 NALTMDMMPKIDRFYITLQFELAKAM----SPCIIWIPNIHDLNVNES---------NYLSLGLLVNSLSRDCER----- 1767 (2281)
T ss_pred             chhhhhhhhhhhHHHHHHHHHHHHHC----CCeEEEEEchhhcCCCcc---------ceehHHHHHHHhcccccc-----
Confidence                    110 11256677766543    899999999999987621         112478999999864211     


Q ss_pred             eeecCCeEEEecCCC
Q 012525          440 SKVSRDNLYIKTSGL  454 (461)
Q Consensus       440 r~~~rd~IiI~TsNi  454 (461)
                       ...+..|+|+|||.
T Consensus      1768 -~s~~~VIVIAATNR 1781 (2281)
T CHL00206       1768 -CSTRNILVIASTHI 1781 (2281)
T ss_pred             -CCCCCEEEEEeCCC
Confidence             11236789999983

>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=99.33  E-value=3.2e-13  Score=119.70  Aligned_cols=114  Identities=24%  Similarity=0.339  Sum_probs=75.2

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhc-CcccccHHHHHHHHHHhhchhhh--ccCceEEEEcCccccc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA-GYVGEDVESILYKLLAQAEFNVE--AAQQGMVYIDEVDKIT  403 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~-g~vGe~~e~~L~~lf~~a~~~v~--~a~~gVLfIDEID~L~  403 (461)
                      +|||+||||||||+||+.+|+.++.+++.+.++...+. .+.|.-...  ...+......+.  ..++.|+|||||+++.
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~--~~~~~~~~~~l~~a~~~~~il~lDEin~a~   78 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPS--NGQFEFKDGPLVRAMRKGGILVLDEINRAP   78 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET---TTTTCEEE-CCCTTHHEEEEEEESSCGG--
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeec--ccccccccccccccccceeEEEECCcccCC
Confidence            58999999999999999999999999999888764432 111111000  011111111111  1367899999999988


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecC--------CeEEEecCCCCc
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSR--------DNLYIKTSGLDS  456 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~r--------d~IiI~TsNid~  456 (461)
                      +.              +++.|+.+||+..+.+.........        ++++|+|+|...
T Consensus        79 ~~--------------v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~  125 (139)
T PF07728_consen   79 PE--------------VLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRD  125 (139)
T ss_dssp             HH--------------HHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST
T ss_pred             HH--------------HHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCC
Confidence            87              9999999999888776655322222        299999999775

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.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.31  E-value=1.5e-12  Score=135.93  Aligned_cols=137  Identities=20%  Similarity=0.311  Sum_probs=101.5

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc----CCceEEecchhhhhcC----cccccHHHHHHH
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADATTLTQAG----YVGEDVESILYK  377 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~s~l~~~g----~vGe~~e~~L~~  377 (461)
                      +.+..+.+..+.+..++....+||++|++||||+++|++|+...    ..||+.++|..+.++.    ++|.. +..+..
T Consensus        82 G~~~~~~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~eLFG~~-kGaftG  160 (403)
T COG1221          82 GESPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFGHE-KGAFTG  160 (403)
T ss_pred             ccCHHHHHHHHHHHhhCCCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHHHHhccc-cceeec
Confidence            33444444444444556667899999999999999999998533    5699999999988641    11111 111222


Q ss_pred             HHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          378 LLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       378 lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ......+.++.+.+|+||||||..|...              .|..|+.+||.+.++........+.++.+|++||.+..
T Consensus       161 a~~~k~Glfe~A~GGtLfLDEI~~LP~~--------------~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~  226 (403)
T COG1221         161 AQGGKAGLFEQANGGTLFLDEIHRLPPE--------------GQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLE  226 (403)
T ss_pred             ccCCcCchheecCCCEEehhhhhhCCHh--------------HHHHHHHHHHcCceEecCCCCCcCCCceeeeccccCHH
Confidence            2233445678899999999999999999              99999999999988877666666669999999998754

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.31  E-value=9.4e-12  Score=136.31  Aligned_cols=109  Identities=28%  Similarity=0.418  Sum_probs=76.6

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ ||||+.+++.|..++...                              ...+.+||+||+|||||++|+.||+.
T Consensus        13 qtFdd-VIGQe~vv~~L~~al~~g------------------------------RLpHA~LFtGP~GvGKTTLAriLAka   61 (700)
T PRK12323         13 RDFTT-LVGQEHVVRALTHALEQQ------------------------------RLHHAYLFTGTRGVGKTTLSRILAKS   61 (700)
T ss_pred             CcHHH-HcCcHHHHHHHHHHHHhC------------------------------CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            45666 899999999998888411                              01244799999999999999999998


Q ss_pred             cCC-----------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCc
Q 012525          349 VNV-----------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       349 l~~-----------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                      +++                             .+++++...-       .. .+.++++...........+..|+||||+
T Consensus        62 LnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas~-------~g-VDdIReLie~~~~~P~~gr~KViIIDEa  133 (700)
T PRK12323         62 LNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAASN-------RG-VDEMAQLLDKAVYAPTAGRFKVYMIDEV  133 (700)
T ss_pred             hcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEeccccc-------CC-HHHHHHHHHHHHhchhcCCceEEEEECh
Confidence            876                             1222222110       11 2345555554444333456779999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      |+|+..              .+|+||+.||+
T Consensus       134 h~Ls~~--------------AaNALLKTLEE  150 (700)
T PRK12323        134 HMLTNH--------------AFNAMLKTLEE  150 (700)
T ss_pred             HhcCHH--------------HHHHHHHhhcc
Confidence            999987              89999999995

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.30  E-value=6.5e-12  Score=129.04  Aligned_cols=139  Identities=22%  Similarity=0.326  Sum_probs=91.3

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-----  349 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-----  349 (461)
                      |+||+.+|..|..++..                               ....+|||.|++|+|||||+++|+..+     
T Consensus         6 ivgq~~~~~al~~~~~~-------------------------------~~~g~vli~G~~G~gKttl~r~~~~~~~~~~~   54 (337)
T TIGR02030         6 IVGQDEMKLALLLNVID-------------------------------PKIGGVMVMGDRGTGKSTAVRALAALLPEIKA   54 (337)
T ss_pred             cccHHHHHHHHHHHhcC-------------------------------CCCCeEEEEcCCCCCHHHHHHHHHHhhccccc
Confidence            89999999988776631                               123689999999999999999999877     


Q ss_pred             --CCceE---------Eecchhh-----------------------hhcCcccc-cHHHHHH-HHHHhhchhhhccCceE
Q 012525          350 --NVPFV---------IADATTL-----------------------TQAGYVGE-DVESILY-KLLAQAEFNVEAAQQGM  393 (461)
Q Consensus       350 --~~pfv---------~i~~s~l-----------------------~~~g~vGe-~~e~~L~-~lf~~a~~~v~~a~~gV  393 (461)
                        +.+|-         ..+|...                       ....++|. +.+..+. ..+....+.+..+++++
T Consensus        55 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~Gv  134 (337)
T TIGR02030        55 VAGCPFNSSPSDPEMMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGI  134 (337)
T ss_pred             ccCCCCCCCCCCccccChHHhhhhhcccccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCE
Confidence              22221         0011100                       00012222 1111111 11222344566678899


Q ss_pred             EEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeee--ecceeeecCCeEEEecCCCCcCc
Q 012525          394 VYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKT--FAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       394 LfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i--~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      ||||||+.|.++              +|+.|++.|+.+++.+  .......+.++++|+|.|.....
T Consensus       135 L~lDEi~~L~~~--------------~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~  187 (337)
T TIGR02030       135 LYIDEVNLLEDH--------------LVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGE  187 (337)
T ss_pred             EEecChHhCCHH--------------HHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCC
Confidence            999999999988              9999999999765433  23355556689999999987543

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.

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

Probab=99.30  E-value=7.7e-12  Score=125.65  Aligned_cols=119  Identities=28%  Similarity=0.286  Sum_probs=82.2

Q ss_pred             CCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHH
Q 012525          261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTL  340 (461)
Q Consensus       261 l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTt  340 (461)
                      .++++...+.+++ ++||+.++.+|..++..                               ....|+|||||||||||+
T Consensus        25 swteKYrPkt~de-~~gQe~vV~~L~~a~~~-------------------------------~~lp~~LFyGPpGTGKTS   72 (346)
T KOG0989|consen   25 SWTEKYRPKTFDE-LAGQEHVVQVLKNALLR-------------------------------RILPHYLFYGPPGTGKTS   72 (346)
T ss_pred             chHHHhCCCcHHh-hcchHHHHHHHHHHHhh-------------------------------cCCceEEeeCCCCCcHhH
Confidence            3466667778888 79999999999998841                               113789999999999999


Q ss_pred             HHHHHHHhcCCc------eEEecchhhhhcCcccccHHHHHHHHHHhhchh------hhccCceEEEEcCccccchhhhc
Q 012525          341 LAKTLARHVNVP------FVIADATTLTQAGYVGEDVESILYKLLAQAEFN------VEAAQQGMVYIDEVDKITKKAES  408 (461)
Q Consensus       341 LAraLA~~l~~p------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~------v~~a~~gVLfIDEID~L~~~R~~  408 (461)
                      .|+++|++++.+      +.+.++++...     -.+...-.+-|+.....      ......-||+|||.|.|+.+   
T Consensus        73 talafar~L~~~~~~~~rvl~lnaSderG-----isvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsd---  144 (346)
T KOG0989|consen   73 TALAFARALNCEQLFPCRVLELNASDERG-----ISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSD---  144 (346)
T ss_pred             HHHHHHHHhcCccccccchhhhccccccc-----ccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhHH---
Confidence            999999999762      23334444332     22211111222221111      11223369999999999998   


Q ss_pred             cccccccchHHHHHHHHHHHhC
Q 012525          409 LNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       409 ~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                 .+++|++.||.
T Consensus       145 -----------aq~aLrr~mE~  155 (346)
T KOG0989|consen  145 -----------AQAALRRTMED  155 (346)
T ss_pred             -----------HHHHHHHHHhc
Confidence                       99999999995

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.30  E-value=4.9e-12  Score=137.04  Aligned_cols=134  Identities=24%  Similarity=0.347  Sum_probs=104.4

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh-----------cCCceEEecchhhhhcCcccccHHH
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH-----------VNVPFVIADATTLTQAGYVGEDVES  373 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~-----------l~~pfv~i~~s~l~~~g~vGe~~e~  373 (461)
                      .+.+..|..+.+.+..++....+|||+|++||||+++|++|++.           .+.||+.++|..+.+.     ..+.
T Consensus       222 iG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e~-----lles  296 (538)
T PRK15424        222 LGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAES-----LLEA  296 (538)
T ss_pred             eeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCChh-----hHHH
Confidence            45677888888888888889999999999999999999999987           3569999999987642     1122


Q ss_pred             HHHH----HHH-----hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecC
Q 012525          374 ILYK----LLA-----QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSR  444 (461)
Q Consensus       374 ~L~~----lf~-----~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~r  444 (461)
                      .+..    .|.     ...+.++.+++|+||||||+.|...              +|..|+.+|+...+......+..+.
T Consensus       297 eLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~--------------~Q~kLl~~L~e~~~~r~G~~~~~~~  362 (538)
T PRK15424        297 ELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLP--------------LQTRLLRVLEEKEVTRVGGHQPVPV  362 (538)
T ss_pred             HhcCCccccccCccccccCCchhccCCCEEEEcChHhCCHH--------------HHHHHHhhhhcCeEEecCCCceecc
Confidence            2111    111     1124566788999999999999999              9999999999888776555555566


Q ss_pred             CeEEEecCCCCcC
Q 012525          445 DNLYIKTSGLDSK  457 (461)
Q Consensus       445 d~IiI~TsNid~e  457 (461)
                      ++.+|+++|.+++
T Consensus       363 dvRiIaat~~~L~  375 (538)
T PRK15424        363 DVRVISATHCDLE  375 (538)
T ss_pred             ceEEEEecCCCHH
Confidence            8899999998864

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.29  E-value=1.4e-11  Score=131.39  Aligned_cols=110  Identities=29%  Similarity=0.335  Sum_probs=75.3

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ |+||+.+++.|..++...                              ..++.+||+||+|||||++|+.||+
T Consensus        14 P~~f~d-vVGQe~iv~~L~~~i~~~------------------------------ri~ha~Lf~GP~GtGKTTlAriLAk   62 (484)
T PRK14956         14 PQFFRD-VIHQDLAIGALQNALKSG------------------------------KIGHAYIFFGPRGVGKTTIARILAK   62 (484)
T ss_pred             CCCHHH-HhChHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            345666 899999999988887310                              0123489999999999999999999


Q ss_pred             hcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          348 HVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       348 ~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      .+++.                        |+++++..-     .|   ...++.+...........+..|+||||+|+|.
T Consensus        63 ~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas~-----~g---Vd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls  134 (484)
T PRK14956         63 RLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAASN-----RG---IENIRELRDNVKFAPMGGKYKVYIIDEVHMLT  134 (484)
T ss_pred             hcCcccccCccccCCCcHHHHHHccCCccceeechhhc-----cc---HHHHHHHHHHHHhhhhcCCCEEEEEechhhcC
Confidence            98752                        222222110     01   22344444433332223456799999999999


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhC
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ..              .+++||+.||+
T Consensus       135 ~~--------------A~NALLKtLEE  147 (484)
T PRK14956        135 DQ--------------SFNALLKTLEE  147 (484)
T ss_pred             HH--------------HHHHHHHHhhc
Confidence            87              89999999995

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

Probab=99.29  E-value=3.7e-11  Score=135.50  Aligned_cols=163  Identities=20%  Similarity=0.316  Sum_probs=108.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEE
Q 012525          250 SRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVL  329 (461)
Q Consensus       250 ~~w~g~~l~~~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VL  329 (461)
                      =.|...  ..+.....+..+.|++..+|++++|++|.+.+......    ..                     .....++
T Consensus       301 ~pw~~~--~~~~~~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~~----~~---------------------~~g~~i~  353 (784)
T PRK10787        301 VPWNAR--SKVKKDLRQAQEILDTDHYGLERVKDRILEYLAVQSRV----NK---------------------IKGPILC  353 (784)
T ss_pred             CCCCCC--CcccccHHHHHHHhhhhccCHHHHHHHHHHHHHHHHhc----cc---------------------CCCceEE
Confidence            345443  23344677899999999999999999998877422110    00                     1135699


Q ss_pred             EEccCCCchHHHHHHHHHhcCCceEEecchhhhhc--------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          330 LMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA--------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       330 L~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~--------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      |+||||||||++++.+|+.++.+|++++...+.+.        .|.|......++ .+..+.     ....||||||||+
T Consensus       354 l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~G~~~~-~l~~~~-----~~~~villDEidk  427 (784)
T PRK10787        354 LVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQ-KMAKVG-----VKNPLFLLDEIDK  427 (784)
T ss_pred             EECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccchhccCCCCCcHHHH-HHHhcC-----CCCCEEEEEChhh
Confidence            99999999999999999999999998887654321        244444222222 222211     1345999999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHhCceeeeecc-ee--eecC-CeEEEecCCCC
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VS--KVSR-DNLYIKTSGLD  455 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r--~~~r-d~IiI~TsNid  455 (461)
                      +.....     .+     .+++|+++||..+...+.+ ..  ..+. +.++|+|+|.-
T Consensus       428 ~~~~~~-----g~-----~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~  475 (784)
T PRK10787        428 MSSDMR-----GD-----PASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM  475 (784)
T ss_pred             cccccC-----CC-----HHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC
Confidence            987621     11     5789999999654433333 11  1222 78999999964

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.29  E-value=3.8e-12  Score=129.94  Aligned_cols=115  Identities=18%  Similarity=0.243  Sum_probs=83.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchh-hhhcCcccccHHHHHH---HHHHhhchhh--hccCceEEEEcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATT-LTQAGYVGEDVESILY---KLLAQAEFNV--EAAQQGMVYIDE  398 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~-l~~~g~vGe~~e~~L~---~lf~~a~~~v--~~a~~gVLfIDE  398 (461)
                      .++|||.|+||||||++|+.||+.++.+++.+++.. +...+++|...-. ++   ..+....+.+  ....+.+||+||
T Consensus        64 ~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~-l~~g~~~~~f~~GpL~~A~~~g~illlDE  142 (327)
T TIGR01650        64 DRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIV-LKDGKQITEFRDGILPWALQHNVALCFDE  142 (327)
T ss_pred             CCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceee-ccCCcceeEEecCcchhHHhCCeEEEech
Confidence            368999999999999999999999999999999874 3333466653210 00   0111111111  123677899999


Q ss_pred             ccccchhhhccccccccchHHHHHHHHHHHh-Cceeeeecceeee-cC-CeEEEecCCC
Q 012525          399 VDKITKKAESLNISRDVSGEGVQQALLKMLE-GTETKTFAAVSKV-SR-DNLYIKTSGL  454 (461)
Q Consensus       399 ID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE-g~~v~i~~~~r~~-~r-d~IiI~TsNi  454 (461)
                      ||++.++              +++.|..+|| ++++.+....+.. +. ++.+|+|.|.
T Consensus       143 in~a~p~--------------~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np  187 (327)
T TIGR01650       143 YDAGRPD--------------VMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANT  187 (327)
T ss_pred             hhccCHH--------------HHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCC
Confidence            9999888              8999999999 6677776654444 44 7999999996

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.29  E-value=1.7e-11  Score=122.41  Aligned_cols=131  Identities=24%  Similarity=0.356  Sum_probs=85.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ ++||+++++.|...+......                          .....+++|+||||||||+||+++|+++
T Consensus         2 ~~~~-~iG~~~~~~~l~~~l~~~~~~--------------------------~~~~~~~ll~Gp~G~GKT~la~~ia~~~   54 (305)
T TIGR00635         2 LLAE-FIGQEKVKEQLQLFIEAAKMR--------------------------QEALDHLLLYGPPGLGKTTLAHIIANEM   54 (305)
T ss_pred             CHHH-HcCHHHHHHHHHHHHHHHHhc--------------------------CCCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            3556 799999999988877311100                          0113679999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.++..+....+...        ..+...+...      ..+.|||||||+.+...              .++.|+.+|+
T Consensus        55 ~~~~~~~~~~~~~~~--------~~l~~~l~~~------~~~~vl~iDEi~~l~~~--------------~~e~l~~~~~  106 (305)
T TIGR00635        55 GVNLKITSGPALEKP--------GDLAAILTNL------EEGDVLFIDEIHRLSPA--------------VEELLYPAME  106 (305)
T ss_pred             CCCEEEeccchhcCc--------hhHHHHHHhc------ccCCEEEEehHhhhCHH--------------HHHHhhHHHh
Confidence            988776665443321        1122222111      24579999999999877              6788899998


Q ss_pred             Cceeeeeccee------eecC-CeEEEecCCCC
Q 012525          430 GTETKTFAAVS------KVSR-DNLYIKTSGLD  455 (461)
Q Consensus       430 g~~v~i~~~~r------~~~r-d~IiI~TsNid  455 (461)
                      .....+.....      .... .+++|.++|..
T Consensus       107 ~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~  139 (305)
T TIGR00635       107 DFRLDIVIGKGPSARSVRLDLPPFTLVGATTRA  139 (305)
T ss_pred             hhheeeeeccCccccceeecCCCeEEEEecCCc
Confidence            76654432211      1111 36677666543

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.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.28  E-value=7.3e-12  Score=127.82  Aligned_cols=115  Identities=22%  Similarity=0.327  Sum_probs=85.4

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhhcCcccccHHHHHHHHHH-----------hhchhh
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQAGYVGEDVESILYKLLA-----------QAEFNV  386 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~-----------~a~~~v  386 (461)
                      ++....+|||+|++||||+++|++|+....   .||+.++|..+.+.        ..-..+|.           ...+.+
T Consensus        25 ~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~~--------~~~~~lfg~~~~~~~g~~~~~~g~l   96 (326)
T PRK11608         25 LAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNEN--------LLDSELFGHEAGAFTGAQKRHPGRF   96 (326)
T ss_pred             HhCCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCHH--------HHHHHHccccccccCCcccccCCch
Confidence            344567899999999999999999997663   59999999986531        11111221           112345


Q ss_pred             hccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          387 EAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       387 ~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ..+.+|+||||||+.|...              +|..|+.+|+...+...........++.+|+|++.+.+
T Consensus        97 ~~a~gGtL~l~~i~~L~~~--------------~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~l~  153 (326)
T PRK11608         97 ERADGGTLFLDELATAPML--------------VQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLP  153 (326)
T ss_pred             hccCCCeEEeCChhhCCHH--------------HHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCchhHH
Confidence            6678999999999999998              99999999998776544444444457899999988753

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=99.28  E-value=3.4e-12  Score=134.52  Aligned_cols=139  Identities=22%  Similarity=0.298  Sum_probs=93.0

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |.+ |+||+.||+.|..+.                                 ...+|+||+||||||||+||+.+...+-
T Consensus       178 ~~D-V~GQ~~AKrAleiAA---------------------------------AGgHnLl~~GpPGtGKTmla~Rl~~lLP  223 (490)
T COG0606         178 FKD-VKGQEQAKRALEIAA---------------------------------AGGHNLLLVGPPGTGKTMLASRLPGLLP  223 (490)
T ss_pred             hhh-hcCcHHHHHHHHHHH---------------------------------hcCCcEEEecCCCCchHHhhhhhcccCC
Confidence            444 999999999998877                                 2358999999999999999999976551


Q ss_pred             C----ceEEec------chhhh------hcCcccccHHHHHHHHHH----hhchhhhccCceEEEEcCccccchhhhccc
Q 012525          351 V----PFVIAD------ATTLT------QAGYVGEDVESILYKLLA----QAEFNVEAAQQGMVYIDEVDKITKKAESLN  410 (461)
Q Consensus       351 ~----pfv~i~------~s~l~------~~g~vGe~~e~~L~~lf~----~a~~~v~~a~~gVLfIDEID~L~~~R~~~~  410 (461)
                      -    .++++.      .....      ..-+.....+..+..++.    ...+.+..+++|||||||+-.+..+     
T Consensus       224 pls~~E~lE~s~I~s~~g~~~~~~~~~~~rPFr~PHHsaS~~aLvGGG~~p~PGeIsLAH~GVLFLDElpef~~~-----  298 (490)
T COG0606         224 PLSIPEALEVSAIHSLAGDLHEGCPLKIHRPFRAPHHSASLAALVGGGGVPRPGEISLAHNGVLFLDELPEFKRS-----  298 (490)
T ss_pred             CCChHHHHHHHHHhhhcccccccCccceeCCccCCCccchHHHHhCCCCCCCCCceeeecCCEEEeeccchhhHH-----
Confidence            1    000000      00000      000111111111222221    2345567789999999999887776     


Q ss_pred             cccccchHHHHHHHHHHHhCceeeeecc--eeeecCCeEEEecCCCCcC
Q 012525          411 ISRDVSGEGVQQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       411 ~~~~~s~~~v~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~e  457 (461)
                               +++.|.+.||.+++.+-..  .-.++.+|++|+++|+.+-
T Consensus       299 ---------iLe~LR~PLE~g~i~IsRa~~~v~ypa~Fqlv~AmNpcpc  338 (490)
T COG0606         299 ---------ILEALREPLENGKIIISRAGSKVTYPARFQLVAAMNPCPC  338 (490)
T ss_pred             ---------HHHHHhCccccCcEEEEEcCCeeEEeeeeEEhhhcCCCCc
Confidence                     9999999999888777665  3344559999999998864

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.28  E-value=1.8e-11  Score=135.74  Aligned_cols=111  Identities=29%  Similarity=0.366  Sum_probs=76.6

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      -.+.|++ |+||+.+++.|...+...                              ...+.+||+||+|||||++|++||
T Consensus        11 RPqtFdE-VIGQe~Vv~~L~~aL~~g------------------------------RL~HAyLFtGPpGvGKTTlAriLA   59 (830)
T PRK07003         11 RPKDFAS-LVGQEHVVRALTHALDGG------------------------------RLHHAYLFTGTRGVGKTTLSRIFA   59 (830)
T ss_pred             CCCcHHH-HcCcHHHHHHHHHHHhcC------------------------------CCCeEEEEECCCCCCHHHHHHHHH
Confidence            3345666 899999999998877310                              012446999999999999999999


Q ss_pred             HhcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          347 RHVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       347 ~~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      +.+++.                        +++++..+-       .. ...++.++..........+..||||||+|.|
T Consensus        60 KaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas~-------rg-VDdIReLIe~a~~~P~~gr~KVIIIDEah~L  131 (830)
T PRK07003         60 KALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAASN-------RG-VDEMAALLERAVYAPVDARFKVYMIDEVHML  131 (830)
T ss_pred             HHhcCccCCCCCCCcccHHHHHHhcCCCceEEEeccccc-------cc-HHHHHHHHHHHHhccccCCceEEEEeChhhC
Confidence            988652                        222222210       11 2334555554433333456679999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ...              .+|+||+.||+
T Consensus       132 T~~--------------A~NALLKtLEE  145 (830)
T PRK07003        132 TNH--------------AFNAMLKTLEE  145 (830)
T ss_pred             CHH--------------HHHHHHHHHHh
Confidence            887              79999999995

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.28  E-value=1.2e-11  Score=134.15  Aligned_cols=144  Identities=28%  Similarity=0.394  Sum_probs=92.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ ++||+.+++.|..++.                               ...+.+|||+||||||||++|+++++.+
T Consensus        63 ~f~~-iiGqs~~i~~l~~al~-------------------------------~~~~~~vLi~Ge~GtGKt~lAr~i~~~~  110 (531)
T TIGR02902        63 SFDE-IIGQEEGIKALKAALC-------------------------------GPNPQHVIIYGPPGVGKTAAARLVLEEA  110 (531)
T ss_pred             CHHH-eeCcHHHHHHHHHHHh-------------------------------CCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3444 7999988887765441                               1124789999999999999999998753


Q ss_pred             ----------CCceEEecchhhh--hcCc----ccccHHHHHH--HHH------HhhchhhhccCceEEEEcCccccchh
Q 012525          350 ----------NVPFVIADATTLT--QAGY----VGEDVESILY--KLL------AQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       350 ----------~~pfv~i~~s~l~--~~g~----vGe~~e~~L~--~lf------~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                                +.+|+.++|+...  +.++    ++........  ..+      ....+.+..+++++||||||+.|...
T Consensus       111 ~~~~~s~~~~~~~fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~  190 (531)
T TIGR02902       111 KKNPASPFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPV  190 (531)
T ss_pred             hhccCCCcCCCCCEEEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCHH
Confidence                      3589999987421  1111    1110000000  001      11233455678899999999999998


Q ss_pred             hhccccccccchHHHHHHHHHHHhCceeeeecc-----------------eeeecCCeEEEecCCCCcCcC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTETKTFAA-----------------VSKVSRDNLYIKTSGLDSKTL  459 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-----------------~r~~~rd~IiI~TsNid~e~l  459 (461)
                                    .|+.||+.||...+.+...                 ....+.++++|++|+.+++.+
T Consensus       191 --------------~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L  247 (531)
T TIGR02902       191 --------------QMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEI  247 (531)
T ss_pred             --------------HHHHHHHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccC
Confidence                          8999999999766543211                 122345778887777666544

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.27  E-value=3.7e-11  Score=122.23  Aligned_cols=111  Identities=31%  Similarity=0.479  Sum_probs=78.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ ++||+++++.|...+.....        .+                  ....++||+||||||||++|+++|+++
T Consensus        23 ~~~~-~vG~~~~~~~l~~~l~~~~~--------~~------------------~~~~~~ll~GppG~GKT~la~~ia~~l   75 (328)
T PRK00080         23 SLDE-FIGQEKVKENLKIFIEAAKK--------RG------------------EALDHVLLYGPPGLGKTTLANIIANEM   75 (328)
T ss_pred             CHHH-hcCcHHHHHHHHHHHHHHHh--------cC------------------CCCCcEEEECCCCccHHHHHHHHHHHh
Confidence            4566 79999999999887742110        00                  123689999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +..+..++...+..        ...+..++...      ..+.||||||||.+...              .++.|+..|+
T Consensus        76 ~~~~~~~~~~~~~~--------~~~l~~~l~~l------~~~~vl~IDEi~~l~~~--------------~~e~l~~~~e  127 (328)
T PRK00080         76 GVNIRITSGPALEK--------PGDLAAILTNL------EEGDVLFIDEIHRLSPV--------------VEEILYPAME  127 (328)
T ss_pred             CCCeEEEecccccC--------hHHHHHHHHhc------ccCCEEEEecHhhcchH--------------HHHHHHHHHH
Confidence            99887666554332        12233333221      25679999999999876              6777888998


Q ss_pred             Cceeee
Q 012525          430 GTETKT  435 (461)
Q Consensus       430 g~~v~i  435 (461)
                      .....+
T Consensus       128 ~~~~~~  133 (328)
T PRK00080        128 DFRLDI  133 (328)
T ss_pred             hcceee
Confidence            765543

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

Probab=99.27  E-value=1.5e-11  Score=133.25  Aligned_cols=144  Identities=26%  Similarity=0.335  Sum_probs=108.4

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      .+.|.......+.+.+....   .+....+               ..-...++++|+|||||||||.+++++|++.+..+
T Consensus       185 ~~gg~~~~~~~i~e~v~~pl---~~~~~~~---------------s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~  246 (693)
T KOG0730|consen  185 DIGGLKRQLSVIRELVELPL---RHPALFK---------------SIGIKPPRGLLLYGPPGTGKTFLVRAVANEYGAFL  246 (693)
T ss_pred             ccchhHHHHHHHHHHHHhhh---cchhhhh---------------hcCCCCCCCccccCCCCCChHHHHHHHHHHhCcee
Confidence            36788888888888775321   1111111               01123468899999999999999999999999999


Q ss_pred             EEecchhhhhcCcccccHHHHHHHHHHhhchhhhccC-ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCce
Q 012525          354 VIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQ-QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       354 v~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~-~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      +.+++.++.. ++.|+. ++.+++.|.++...    + +.+|||||+|.+.++|.....    -..++..+|+++|++..
T Consensus       247 ~~i~~peli~-k~~gEt-e~~LR~~f~~a~k~----~~psii~IdEld~l~p~r~~~~~----~e~Rv~sqlltL~dg~~  316 (693)
T KOG0730|consen  247 FLINGPELIS-KFPGET-ESNLRKAFAEALKF----QVPSIIFIDELDALCPKREGADD----VESRVVSQLLTLLDGLK  316 (693)
T ss_pred             EecccHHHHH-hcccch-HHHHHHHHHHHhcc----CCCeeEeHHhHhhhCCcccccch----HHHHHHHHHHHHHhhCc
Confidence            9999999984 588888 99999999988765    4 899999999999998765433    23458999999999664


Q ss_pred             eeeecceeeecCCeEEEecCCC
Q 012525          433 TKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       433 v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      -         ....|+|+++|.
T Consensus       317 ~---------~~~vivl~atnr  329 (693)
T KOG0730|consen  317 P---------DAKVIVLAATNR  329 (693)
T ss_pred             C---------cCcEEEEEecCC
Confidence            1         124677777764

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

Probab=99.26  E-value=2.1e-11  Score=132.83  Aligned_cols=163  Identities=26%  Similarity=0.341  Sum_probs=111.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEE
Q 012525          250 SRWGGSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVL  329 (461)
Q Consensus       250 ~~w~g~~l~~~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VL  329 (461)
                      -.|+.....  ........+.||+.-+|.+++|+++.+.+.-.  ++.      +                 ...+.-++
T Consensus       390 LPWgk~S~E--n~dl~~Ak~iLdeDHYgm~dVKeRILEfiAV~--kLr------g-----------------s~qGkIlC  442 (906)
T KOG2004|consen  390 LPWGKSSTE--NLDLARAKEILDEDHYGMEDVKERILEFIAVG--KLR------G-----------------SVQGKILC  442 (906)
T ss_pred             CCCCCCChh--hhhHHHHHHhhcccccchHHHHHHHHHHHHHH--hhc------c-----------------cCCCcEEE
Confidence            445544322  22445577889988999999999999988411  110      0                 01135578


Q ss_pred             EEccCCCchHHHHHHHHHhcCCceEEecchhhhhc--------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          330 LMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA--------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       330 L~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~--------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      |+||||+|||.+|+.||+.++..|++++..-+.+.        .|+|....++++.+-.-..      .+.+++|||||+
T Consensus       443 f~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHRRTYVGAMPGkiIq~LK~v~t------~NPliLiDEvDK  516 (906)
T KOG2004|consen  443 FVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKVKT------ENPLILIDEVDK  516 (906)
T ss_pred             EeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhcccceeeeccCChHHHHHHHhhCC------CCceEEeehhhh
Confidence            99999999999999999999999999987654432        5788776777666553222      456889999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHhCceeeeecc-eeeecC---CeEEEecCCCC
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VSKVSR---DNLYIKTSGLD  455 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r~~~r---d~IiI~TsNid  455 (461)
                      +...     .+.+     --++||++||-.+...+-+ ....+.   ..+||+|.|.-
T Consensus       517 lG~g-----~qGD-----PasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~i  564 (906)
T KOG2004|consen  517 LGSG-----HQGD-----PASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVI  564 (906)
T ss_pred             hCCC-----CCCC-----hHHHHHHhcChhhccchhhhccccccchhheEEEEecccc
Confidence            9843     1222     5689999999555443333 222222   68999999954

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.26  E-value=2e-11  Score=131.67  Aligned_cols=110  Identities=27%  Similarity=0.344  Sum_probs=78.6

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ |+||+.+++.|..++...                              ..++.+||+||+|||||++|++||+
T Consensus        12 P~~f~d-ivGq~~v~~~L~~~~~~~------------------------------~l~ha~Lf~Gp~G~GKTt~A~~lAk   60 (509)
T PRK14958         12 PRCFQE-VIGQAPVVRALSNALDQQ------------------------------YLHHAYLFTGTRGVGKTTISRILAK   60 (509)
T ss_pred             CCCHHH-hcCCHHHHHHHHHHHHhC------------------------------CCCeeEEEECCCCCCHHHHHHHHHH
Confidence            345666 899999999998888310                              0124479999999999999999999


Q ss_pred             hcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          348 HVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       348 ~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      .+++.                        ++++++..-       .. ...++.+...........+..|+||||+|+|+
T Consensus        61 ~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~-------~~-v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls  132 (509)
T PRK14958         61 CLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASR-------TK-VEDTRELLDNIPYAPTKGRFKVYLIDEVHMLS  132 (509)
T ss_pred             HhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEccccc-------CC-HHHHHHHHHHHhhccccCCcEEEEEEChHhcC
Confidence            88652                        344443321       11 23345555544444344566799999999999


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhC
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ..              .+++||+.||+
T Consensus       133 ~~--------------a~naLLk~LEe  145 (509)
T PRK14958        133 GH--------------SFNALLKTLEE  145 (509)
T ss_pred             HH--------------HHHHHHHHHhc
Confidence            88              89999999995

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.24  E-value=1.6e-11  Score=132.96  Aligned_cols=135  Identities=22%  Similarity=0.347  Sum_probs=103.9

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHH----
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYK----  377 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~----  377 (461)
                      .+.++.|..+.+.+..++....+|||+|++||||+++|++|++..   +.||+.++|..+.+.     ..+..+..    
T Consensus       215 iG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~e~-----lleseLFG~~~g  289 (526)
T TIGR02329       215 LGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAES-----LLEAELFGYEEG  289 (526)
T ss_pred             eeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCChh-----HHHHHhcCCccc
Confidence            466788888888888899999999999999999999999999765   569999999987632     11211111    


Q ss_pred             HHH-----hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecC
Q 012525          378 LLA-----QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTS  452 (461)
Q Consensus       378 lf~-----~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~Ts  452 (461)
                      .|.     ...+.++.+++|+||||||+.|...              +|..|+.+|+...+......+..+.+..+|+++
T Consensus       290 aftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~--------------~Q~~Ll~~L~~~~~~r~g~~~~~~~dvRiIaat  355 (526)
T TIGR02329       290 AFTGARRGGRTGLIEAAHRGTLFLDEIGEMPLP--------------LQTRLLRVLEEREVVRVGGTEPVPVDVRVVAAT  355 (526)
T ss_pred             ccccccccccccchhhcCCceEEecChHhCCHH--------------HHHHHHHHHhcCcEEecCCCceeeecceEEecc
Confidence            111     1223456678999999999999999              999999999988776655555555588999999


Q ss_pred             CCCcCc
Q 012525          453 GLDSKT  458 (461)
Q Consensus       453 Nid~e~  458 (461)
                      |.+++.
T Consensus       356 ~~~l~~  361 (526)
T TIGR02329       356 HCALTT  361 (526)
T ss_pred             CCCHHH
Confidence            988643

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.24  E-value=1.5e-11  Score=132.87  Aligned_cols=131  Identities=27%  Similarity=0.412  Sum_probs=101.9

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ  381 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~  381 (461)
                      .+.+..|..+.+.+..++....+|||+|++||||+++|++|+...   +.||+.++|..+.+.     ..+   ..+|..
T Consensus       199 iG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~~~-----~~~---~~lfg~  270 (534)
T TIGR01817       199 IGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSET-----LLE---SELFGH  270 (534)
T ss_pred             EECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCCHH-----HHH---HHHcCC
Confidence            467888999999999999999999999999999999999999875   469999999887531     111   122211


Q ss_pred             -----------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEe
Q 012525          382 -----------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIK  450 (461)
Q Consensus       382 -----------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~  450 (461)
                                 ..+.++.+++++||||||+.|...              +|..|+.+|+...+......+....++.+|+
T Consensus       271 ~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~~--------------~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~  336 (534)
T TIGR01817       271 EKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPA--------------FQAKLLRVLQEGEFERVGGNRTLKVDVRLVA  336 (534)
T ss_pred             CCCccCCCCcCCCCcccccCCCeEEEechhhCCHH--------------HHHHHHHHHhcCcEEECCCCceEeecEEEEE
Confidence                       123355678999999999999998              9999999999877665444444444789999


Q ss_pred             cCCCCcC
Q 012525          451 TSGLDSK  457 (461)
Q Consensus       451 TsNid~e  457 (461)
                      |++.+++
T Consensus       337 ~s~~~l~  343 (534)
T TIGR01817       337 ATNRDLE  343 (534)
T ss_pred             eCCCCHH
Confidence            9988753

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.

>PLN03025 replication factor C subunit; Provisional

Probab=99.24  E-value=3.3e-11  Score=122.19  Aligned_cols=109  Identities=28%  Similarity=0.385  Sum_probs=73.8

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ |+|++++++.|...+..                               ....|+||+||||||||++|+++|+
T Consensus         9 P~~l~~-~~g~~~~~~~L~~~~~~-------------------------------~~~~~lll~Gp~G~GKTtla~~la~   56 (319)
T PLN03025          9 PTKLDD-IVGNEDAVSRLQVIARD-------------------------------GNMPNLILSGPPGTGKTTSILALAH   56 (319)
T ss_pred             CCCHHH-hcCcHHHHHHHHHHHhc-------------------------------CCCceEEEECCCCCCHHHHHHHHHH
Confidence            345666 79999999988776620                               0125799999999999999999999


Q ss_pred             hcCC-----ceEEecchhhhhcCcccccHHHHHHHHH---HhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          348 HVNV-----PFVIADATTLTQAGYVGEDVESILYKLL---AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       348 ~l~~-----pfv~i~~s~l~~~g~vGe~~e~~L~~lf---~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      ++..     .+++++.++..     +.   ..++...   .............||||||+|.|...              
T Consensus        57 ~l~~~~~~~~~~eln~sd~~-----~~---~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~--------------  114 (319)
T PLN03025         57 ELLGPNYKEAVLELNASDDR-----GI---DVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSG--------------  114 (319)
T ss_pred             HHhcccCccceeeecccccc-----cH---HHHHHHHHHHHhccccCCCCCeEEEEEechhhcCHH--------------
Confidence            8732     35556655432     11   1223222   22111111234679999999999987              


Q ss_pred             HHHHHHHHHhC
Q 012525          420 VQQALLKMLEG  430 (461)
Q Consensus       420 v~~aLL~~LEg  430 (461)
                      .+++|++.||.
T Consensus       115 aq~aL~~~lE~  125 (319)
T PLN03025        115 AQQALRRTMEI  125 (319)
T ss_pred             HHHHHHHHHhc
Confidence            79999999983

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.23  E-value=3.7e-11  Score=126.18  Aligned_cols=85  Identities=32%  Similarity=0.491  Sum_probs=64.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      .+++|+||||||||++|++||+.++.+|+.+++....         ...++.++..+.......+..||||||||++...
T Consensus        37 ~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~~~---------~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~~  107 (413)
T PRK13342         37 SSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTSG---------VKDLREVIEEARQRRSAGRRTILFIDEIHRFNKA  107 (413)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccc---------HHHHHHHHHHHHHhhhcCCceEEEEechhhhCHH
Confidence            5799999999999999999999999999998876432         2233444443332222336779999999999877


Q ss_pred             hhccccccccchHHHHHHHHHHHhCcee
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTET  433 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v  433 (461)
                                    .++.|+..|+...+
T Consensus       108 --------------~q~~LL~~le~~~i  121 (413)
T PRK13342        108 --------------QQDALLPHVEDGTI  121 (413)
T ss_pred             --------------HHHHHHHHhhcCcE
Confidence                          78999999996543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.22  E-value=5.1e-11  Score=130.85  Aligned_cols=109  Identities=28%  Similarity=0.385  Sum_probs=77.7

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ...+.+||+||+|||||++|+++|+.
T Consensus        12 ktFdd-VIGQe~vv~~L~~aI~~g------------------------------rl~HAyLF~GPpGvGKTTlAriLAK~   60 (702)
T PRK14960         12 RNFNE-LVGQNHVSRALSSALERG------------------------------RLHHAYLFTGTRGVGKTTIARILAKC   60 (702)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45666 899999999998887310                              11255799999999999999999999


Q ss_pred             cCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++                        .++.+++++-.       . ...++.+...........+..|+||||+|.|..
T Consensus        61 LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~~-------~-VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~  132 (702)
T PRK14960         61 LNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRT-------K-VEDTRELLDNVPYAPTQGRFKVYLIDEVHMLST  132 (702)
T ss_pred             hCCCcCCCCCCCccCHHHHHHhcCCCCceEEecccccC-------C-HHHHHHHHHHHhhhhhcCCcEEEEEechHhcCH
Confidence            875                        23333333211       1 234555555444433345667999999999988


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||+
T Consensus       133 ~--------------A~NALLKtLEE  144 (702)
T PRK14960        133 H--------------SFNALLKTLEE  144 (702)
T ss_pred             H--------------HHHHHHHHHhc
Confidence            7              79999999995

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.22  E-value=1.7e-11  Score=135.11  Aligned_cols=130  Identities=20%  Similarity=0.316  Sum_probs=98.3

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh-
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ-  381 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~-  381 (461)
                      +.++.+..+.+....++....+|||+|++||||+++|++|++..   +.||+.++|..+...        .....+|.. 
T Consensus       329 g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~~--------~~~~elfg~~  400 (638)
T PRK11388        329 QDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDE--------ALAEEFLGSD  400 (638)
T ss_pred             ECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCChH--------HHHHHhcCCC
Confidence            45566677777777777778899999999999999999999876   469999999887531        111222221 


Q ss_pred             -------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          382 -------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       382 -------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                             ..+.++.+++++||||||+.|...              +|..|+.+|+...+......+..+.++.+|+|++.
T Consensus       401 ~~~~~~~~~g~~~~a~~GtL~ldei~~l~~~--------------~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~  466 (638)
T PRK11388        401 RTDSENGRLSKFELAHGGTLFLEKVEYLSPE--------------LQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTA  466 (638)
T ss_pred             CcCccCCCCCceeECCCCEEEEcChhhCCHH--------------HHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccC
Confidence                   123455678999999999999999              99999999998776654444444557899999998


Q ss_pred             CcC
Q 012525          455 DSK  457 (461)
Q Consensus       455 d~e  457 (461)
                      ++.
T Consensus       467 ~l~  469 (638)
T PRK11388        467 DLA  469 (638)
T ss_pred             CHH
Confidence            753

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

Probab=99.22  E-value=4.5e-11  Score=134.05  Aligned_cols=121  Identities=25%  Similarity=0.356  Sum_probs=89.0

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++...+.+...+..                               ..+.|+||+||||||||++|++||+.+
T Consensus       180 ~l~~-~igr~~ei~~~~~~L~~-------------------------------~~~~n~lL~G~pG~GKT~l~~~la~~~  227 (731)
T TIGR02639       180 KIDP-LIGREDELERTIQVLCR-------------------------------RKKNNPLLVGEPGVGKTAIAEGLALRI  227 (731)
T ss_pred             CCCc-ccCcHHHHHHHHHHHhc-------------------------------CCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            4454 89999999877766621                               124789999999999999999999987


Q ss_pred             ----------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          350 ----------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       350 ----------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                                +..++.+++..+.. ..|.|+. +..++.+++++...    .+.||||||||.+....+..+     +..
T Consensus       228 ~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~-e~~l~~i~~~~~~~----~~~ILfiDEih~l~~~g~~~~-----~~~  297 (731)
T TIGR02639       228 AEGKVPENLKNAKIYSLDMGSLLAGTKYRGDF-EERLKAVVSEIEKE----PNAILFIDEIHTIVGAGATSG-----GSM  297 (731)
T ss_pred             HhCCCchhhcCCeEEEecHHHHhhhccccchH-HHHHHHHHHHHhcc----CCeEEEEecHHHHhccCCCCC-----ccH
Confidence                      66788999887764 3466654 88889988876432    578999999999987632211     112


Q ss_pred             HHHHHHHHHHhCce
Q 012525          419 GVQQALLKMLEGTE  432 (461)
Q Consensus       419 ~v~~aLL~~LEg~~  432 (461)
                      .+.+.|+..|+.+.
T Consensus       298 ~~~~~L~~~l~~g~  311 (731)
T TIGR02639       298 DASNLLKPALSSGK  311 (731)
T ss_pred             HHHHHHHHHHhCCC
Confidence            26778888887544

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=99.22  E-value=4.1e-11  Score=124.89  Aligned_cols=146  Identities=24%  Similarity=0.308  Sum_probs=99.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+...|+|||..|..|.....+                               ..-.++|+.|+.||||||++|+||..|
T Consensus        14 ~pf~aivGqd~lk~aL~l~av~-------------------------------P~iggvLI~G~kGtaKSt~~Rala~LL   62 (423)
T COG1239          14 LPFTAIVGQDPLKLALGLNAVD-------------------------------PQIGGALIAGEKGTAKSTLARALADLL   62 (423)
T ss_pred             cchhhhcCchHHHHHHhhhhcc-------------------------------cccceeEEecCCCccHHHHHHHHHHhC
Confidence            3445689999999977554321                               112679999999999999999999877


Q ss_pred             CC-------ce---------------------------------EEecchhhhhcCcccc-cHHHHHHH-HHHhhchhhh
Q 012525          350 NV-------PF---------------------------------VIADATTLTQAGYVGE-DVESILYK-LLAQAEFNVE  387 (461)
Q Consensus       350 ~~-------pf---------------------------------v~i~~s~l~~~g~vGe-~~e~~L~~-lf~~a~~~v~  387 (461)
                      .-       +|                                 +.+......+ -.+|. ++++.+.. .-....+.+.
T Consensus        63 p~~~~V~gc~f~cdP~~P~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateD-rvvGslDi~ka~~~g~~af~PGlLa  141 (423)
T COG1239          63 PEIEVVIGCPFNCDPDDPEEMCDECRAKGDELEWLPREKRKVPFVALPLGATED-RLVGSLDIEKALEEGPKAFQPGLLA  141 (423)
T ss_pred             CccceecCCCCCCCCCChhhhhHHHHhhccccccccccceecceecCCCccchh-hhccccCHHHHHhcCccccCCcchh
Confidence            32       11                                 1111000000 02222 33333332 1112445677


Q ss_pred             ccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc--eeeeecceeeecCCeEEEecCCCCcCcCCC
Q 012525          388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT--ETKTFAAVSKVSRDNLYIKTSGLDSKTLWP  461 (461)
Q Consensus       388 ~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~--~v~i~~~~r~~~rd~IiI~TsNid~e~l~P  461 (461)
                      .++.|||||||++.|...              +++.||..++.+  .+.+......++.++++|+|+|....++.|
T Consensus       142 ~AnRGIlYvDEvnlL~d~--------------lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrp  203 (423)
T COG1239         142 RANRGILYVDEVNLLDDH--------------LVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRP  203 (423)
T ss_pred             hccCCEEEEeccccccHH--------------HHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccch
Confidence            899999999999999888              999999999976  344334478888899999999999887765

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.22  E-value=5.8e-11  Score=127.05  Aligned_cols=109  Identities=30%  Similarity=0.431  Sum_probs=74.8

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ..++.+||+|||||||||+|+++|+.
T Consensus        11 ~~~~d-ivGq~~i~~~L~~~i~~~------------------------------~l~~~~Lf~GPpGtGKTTlA~~lA~~   59 (472)
T PRK14962         11 KTFSE-VVGQDHVKKLIINALKKN------------------------------SISHAYIFAGPRGTGKTTVARILAKS   59 (472)
T ss_pred             CCHHH-ccCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35666 899999999888777310                              01245899999999999999999998


Q ss_pred             cCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      ++.                        .++.++++.-.     |   ...++.+...+..........||||||+|.|..
T Consensus        60 l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~~~-----g---id~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~  131 (472)
T PRK14962         60 LNCENRKGVEPCNECRACRSIDEGTFMDVIELDAASNR-----G---IDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTK  131 (472)
T ss_pred             hccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcccC-----C---HHHHHHHHHHHhhChhcCCeEEEEEEChHHhHH
Confidence            865                        24444433211     1   223444444333222234667999999999987


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||..|+.
T Consensus       132 ~--------------a~~~LLk~LE~  143 (472)
T PRK14962        132 E--------------AFNALLKTLEE  143 (472)
T ss_pred             H--------------HHHHHHHHHHh
Confidence            6              78999999994

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

Probab=99.21  E-value=1.1e-11  Score=128.22  Aligned_cols=112  Identities=27%  Similarity=0.409  Sum_probs=87.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      -+|||||||||||||++|+-||+..+.+|..+...++..   .|.+....+.++|+++..+   .++-+|||||+|.+..
T Consensus       384 fRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAP---lG~qaVTkiH~lFDWakkS---~rGLllFIDEADAFLc  457 (630)
T KOG0742|consen  384 FRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAP---LGAQAVTKIHKLFDWAKKS---RRGLLLFIDEADAFLC  457 (630)
T ss_pred             hhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCccc---cchHHHHHHHHHHHHHhhc---ccceEEEehhhHHHHH
Confidence            489999999999999999999999999999999998885   4566678899999998764   3566899999999999


Q ss_pred             hhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +|....++.+     ...+|-.+|-.+        -...++++++.++|..
T Consensus       458 eRnktymSEa-----qRsaLNAlLfRT--------GdqSrdivLvlAtNrp  495 (630)
T KOG0742|consen  458 ERNKTYMSEA-----QRSALNALLFRT--------GDQSRDIVLVLATNRP  495 (630)
T ss_pred             HhchhhhcHH-----HHHHHHHHHHHh--------cccccceEEEeccCCc
Confidence            9988777665     445555544411        0123467777777754

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.21  E-value=6.5e-11  Score=124.03  Aligned_cols=117  Identities=22%  Similarity=0.263  Sum_probs=77.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |++ |+||+.+++.|..++...... ...                    .....++.+||+||+|+|||++|+++|+.+.
T Consensus         4 f~~-IiGq~~~~~~L~~~i~~~~~~-~~~--------------------~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~   61 (394)
T PRK07940          4 WDD-LVGQEAVVAELRAAARAARAD-VAA--------------------AGSGMTHAWLFTGPPGSGRSVAARAFAAALQ   61 (394)
T ss_pred             hhh-ccChHHHHHHHHHHHHhcccc-ccc--------------------cCCCCCeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            455 899999999999998522110 000                    0001246699999999999999999999875


Q ss_pred             Cce-----------------------EEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhh
Q 012525          351 VPF-----------------------VIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAE  407 (461)
Q Consensus       351 ~pf-----------------------v~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~  407 (461)
                      +..                       ..+....    ..  .. ...++.++..+.......+..|+||||+|+|...  
T Consensus        62 c~~~~~~~Cg~C~~C~~~~~~~hpD~~~i~~~~----~~--i~-i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~--  132 (394)
T PRK07940         62 CTDPDEPGCGECRACRTVLAGTHPDVRVVAPEG----LS--IG-VDEVRELVTIAARRPSTGRWRIVVIEDADRLTER--  132 (394)
T ss_pred             CCCCCCCCCCCCHHHHHHhcCCCCCEEEecccc----cc--CC-HHHHHHHHHHHHhCcccCCcEEEEEechhhcCHH--
Confidence            531                       1111110    00  11 2345666665554444456779999999999988  


Q ss_pred             ccccccccchHHHHHHHHHHHhC
Q 012525          408 SLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       408 ~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                  .+++||+.||+
T Consensus       133 ------------aanaLLk~LEe  143 (394)
T PRK07940        133 ------------AANALLKAVEE  143 (394)
T ss_pred             ------------HHHHHHHHhhc
Confidence                        78999999995

>TIGR00368 Mg chelatase-related protein

Probab=99.20  E-value=4.2e-11  Score=128.87  Aligned_cols=140  Identities=21%  Similarity=0.246  Sum_probs=89.6

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+||+.+++.|..++                                 ....+++|+||||||||++|+.|+..+
T Consensus       190 d~~d-v~Gq~~~~~al~~aa---------------------------------~~g~~vlliG~pGsGKTtlar~l~~ll  235 (499)
T TIGR00368       190 DLKD-IKGQQHAKRALEIAA---------------------------------AGGHNLLLFGPPGSGKTMLASRLQGIL  235 (499)
T ss_pred             CHHH-hcCcHHHHhhhhhhc---------------------------------cCCCEEEEEecCCCCHHHHHHHHhccc
Confidence            3444 899999988777665                                 123789999999999999999999755


Q ss_pred             CC--ceEEecchhhhh-------------cCccc----ccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccc
Q 012525          350 NV--PFVIADATTLTQ-------------AGYVG----EDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLN  410 (461)
Q Consensus       350 ~~--pfv~i~~s~l~~-------------~g~vG----e~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~  410 (461)
                      .-  .-..+..+.+..             .-|.-    ......+-.......+.+..++++|||||||+.+...     
T Consensus       236 p~~~~~~~le~~~i~s~~g~~~~~~~~~~~Pf~~p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~~~~-----  310 (499)
T TIGR00368       236 PPLTNEEAIETARIWSLVGKLIDRKQIKQRPFRSPHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFKRS-----  310 (499)
T ss_pred             CCCCCcEEEeccccccchhhhccccccccCCccccccccchhhhhCCccccchhhhhccCCCeEecCChhhCCHH-----
Confidence            21  001111111110             00000    0000010000112234566788999999999999888     


Q ss_pred             cccccchHHHHHHHHHHHhCceeeeecc--eeeecCCeEEEecCCCCcC
Q 012525          411 ISRDVSGEGVQQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       411 ~~~~~s~~~v~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~e  457 (461)
                               +++.|++.||...+.+...  ....+.++.+|+++|..+.
T Consensus       311 ---------~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~Npcpc  350 (499)
T TIGR00368       311 ---------VLDALREPIEDGSISISRASAKIFYPARFQLVAAMNPCPC  350 (499)
T ss_pred             ---------HHHHHHHHHHcCcEEEEecCcceeccCCeEEEEecCCccc
Confidence                     9999999999887665443  4445568999999998653

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.20  E-value=6.9e-11  Score=133.65  Aligned_cols=110  Identities=31%  Similarity=0.330  Sum_probs=75.5

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ ||||+.+++.|..++...                              ...+.+||+||+|||||++|+.||+
T Consensus        11 P~~f~e-iiGqe~v~~~L~~~i~~~------------------------------ri~Ha~Lf~Gp~G~GKTt~A~~lAr   59 (824)
T PRK07764         11 PATFAE-VIGQEHVTEPLSTALDSG------------------------------RINHAYLFSGPRGCGKTSSARILAR   59 (824)
T ss_pred             CCCHHH-hcCcHHHHHHHHHHHHhC------------------------------CCCceEEEECCCCCCHHHHHHHHHH
Confidence            345666 899999999998887310                              0123479999999999999999999


Q ss_pred             hcCCc--------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          348 HVNVP--------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       348 ~l~~p--------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      .+++.                          |++++....     .  . ...++.+.....+.....+..|+||||+|+
T Consensus        60 ~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~eidaas~-----~--~-Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~  131 (824)
T PRK07764         60 SLNCVEGPTSTPCGECDSCVALAPGGPGSLDVTEIDAASH-----G--G-VDDARELRERAFFAPAESRYKIFIIDEAHM  131 (824)
T ss_pred             HhCcccCCCCCCCcccHHHHHHHcCCCCCCcEEEeccccc-----C--C-HHHHHHHHHHHHhchhcCCceEEEEechhh
Confidence            98642                          122221110     0  1 233444444333333345677999999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHhC
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      |+..              .+|+||++||+
T Consensus       132 lt~~--------------a~NaLLK~LEE  146 (824)
T PRK07764        132 VTPQ--------------GFNALLKIVEE  146 (824)
T ss_pred             cCHH--------------HHHHHHHHHhC
Confidence            9988              89999999995

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.20  E-value=3.3e-11  Score=129.83  Aligned_cols=131  Identities=24%  Similarity=0.378  Sum_probs=103.1

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHH-
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLA-  380 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~-  380 (461)
                      .+.+..|..+.+.+..++....+|||+|++||||+++|++|+...   +.||+.++|..+.+.     ..+.   .+|. 
T Consensus       190 ig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~~-----~~e~---~lfG~  261 (509)
T PRK05022        190 IGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPES-----LAES---ELFGH  261 (509)
T ss_pred             eecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCChH-----HHHH---HhcCc
Confidence            477889999999999999999999999999999999999999875   469999999987532     1111   1222 


Q ss_pred             ----------hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEe
Q 012525          381 ----------QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIK  450 (461)
Q Consensus       381 ----------~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~  450 (461)
                                ...+.++.+++++||||||+.|...              +|..|+.+|+...+...........++.+|+
T Consensus       262 ~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~~~--------------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~  327 (509)
T PRK05022        262 VKGAFTGAISNRSGKFELADGGTLFLDEIGELPLA--------------LQAKLLRVLQYGEIQRVGSDRSLRVDVRVIA  327 (509)
T ss_pred             cccccCCCcccCCcchhhcCCCEEEecChhhCCHH--------------HHHHHHHHHhcCCEeeCCCCcceecceEEEE
Confidence                      1223456678999999999999998              9999999999877655444444444889999


Q ss_pred             cCCCCcC
Q 012525          451 TSGLDSK  457 (461)
Q Consensus       451 TsNid~e  457 (461)
                      ++|.+.+
T Consensus       328 ~t~~~l~  334 (509)
T PRK05022        328 ATNRDLR  334 (509)
T ss_pred             ecCCCHH
Confidence            9998764

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.20  E-value=7.4e-11  Score=130.05  Aligned_cols=109  Identities=28%  Similarity=0.354  Sum_probs=75.6

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ...+.+||+||+||||||+|++||+.
T Consensus        13 ~~f~d-ivGQe~vv~~L~~~l~~~------------------------------rl~hAyLf~Gp~GvGKTTlAr~lAk~   61 (647)
T PRK07994         13 QTFAE-VVGQEHVLTALANALDLG------------------------------RLHHAYLFSGTRGVGKTTIARLLAKG   61 (647)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            45666 899999999998887310                              01233699999999999999999998


Q ss_pred             cCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++.                        |++++...     ..  . ...++.+..............|+||||+|+|..
T Consensus        62 L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas-----~~--~-VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~  133 (647)
T PRK07994         62 LNCETGITATPCGECDNCREIEQGRFVDLIEIDAAS-----RT--K-VEDTRELLDNVQYAPARGRFKVYLIDEVHMLSR  133 (647)
T ss_pred             hhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccc-----cC--C-HHHHHHHHHHHHhhhhcCCCEEEEEechHhCCH
Confidence            8762                        22222221     01  1 233455544433333334667999999999998


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+|+||+.||+
T Consensus       134 ~--------------a~NALLKtLEE  145 (647)
T PRK07994        134 H--------------SFNALLKTLEE  145 (647)
T ss_pred             H--------------HHHHHHHHHHc
Confidence            8              89999999995

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.20  E-value=7.1e-11  Score=133.03  Aligned_cols=116  Identities=24%  Similarity=0.340  Sum_probs=74.9

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|..++...  +                            ..+.+||+||+|||||++|++||+.
T Consensus        13 ~tFdd-IIGQe~Iv~~LknaI~~~--r----------------------------l~HAyLFtGPpGtGKTTLARiLAk~   61 (944)
T PRK14949         13 ATFEQ-MVGQSHVLHALTNALTQQ--R----------------------------LHHAYLFTGTRGVGKTSLARLFAKG   61 (944)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHhC--C----------------------------CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            45666 899999999988877310  0                            0233699999999999999999999


Q ss_pred             cCCce-------EEe-cchhhhhcC------ccc---ccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccc
Q 012525          349 VNVPF-------VIA-DATTLTQAG------YVG---EDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI  411 (461)
Q Consensus       349 l~~pf-------v~i-~~s~l~~~g------~vG---e~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~  411 (461)
                      +++..       ..+ .|-.+....      +-+   .. ...++.+...........+..|+||||+|+|...      
T Consensus        62 Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas~~k-VDdIReLie~v~~~P~~gk~KViIIDEAh~LT~e------  134 (944)
T PRK14949         62 LNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAASRTK-VDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRS------  134 (944)
T ss_pred             ccCccCCCCCCCCCchHHHHHhcCCCceEEEeccccccC-HHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHH------
Confidence            87631       110 011111000      000   11 2334554444333333356679999999999988      


Q ss_pred             ccccchHHHHHHHHHHHhC
Q 012525          412 SRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       412 ~~~~s~~~v~~aLL~~LEg  430 (461)
                              .+++||+.||+
T Consensus       135 --------AqNALLKtLEE  145 (944)
T PRK14949        135 --------SFNALLKTLEE  145 (944)
T ss_pred             --------HHHHHHHHHhc
Confidence                    89999999995

>PHA02244 ATPase-like protein

Probab=99.20  E-value=3.7e-11  Score=124.43  Aligned_cols=128  Identities=16%  Similarity=0.234  Sum_probs=88.3

Q ss_pred             CCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhh--hcCcccccHHHHHHHHHHhhch
Q 012525          307 AEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLT--QAGYVGEDVESILYKLLAQAEF  384 (461)
Q Consensus       307 ~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~--~~g~vGe~~e~~L~~lf~~a~~  384 (461)
                      .++.+.........+.....+|||+||||||||++|++||..++.+|+.++...-.  -.+++... .     .+.....
T Consensus       101 ~sp~~~~~~~ri~r~l~~~~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~-g-----~~~dgpL  174 (383)
T PHA02244        101 SNPTFHYETADIAKIVNANIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDAN-G-----KFHETPF  174 (383)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecChHHHhhccccccc-c-----cccchHH
Confidence            33445555556666677788999999999999999999999999999988743110  00111111 0     1110011


Q ss_pred             hhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          385 NVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       385 ~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      .-....+++||||||+.+.+.              ++..|..+|+...+...........++.+|+|+|.
T Consensus       175 l~A~~~GgvLiLDEId~a~p~--------------vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~  230 (383)
T PHA02244        175 YEAFKKGGLFFIDEIDASIPE--------------ALIIINSAIANKFFDFADERVTAHEDFRVISAGNT  230 (383)
T ss_pred             HHHhhcCCEEEEeCcCcCCHH--------------HHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCC
Confidence            111246789999999999988              89999999998766655444333348999999997

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.19  E-value=1e-10  Score=125.49  Aligned_cols=109  Identities=25%  Similarity=0.327  Sum_probs=77.8

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++..            +                  ..++++||+||+||||||+|+.+|+.
T Consensus        10 ~~f~d-liGQe~vv~~L~~a~~~------------~------------------ri~ha~Lf~Gp~G~GKTT~ArilAk~   58 (491)
T PRK14964         10 SSFKD-LVGQDVLVRILRNAFTL------------N------------------KIPQSILLVGASGVGKTTCARIISLC   58 (491)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHc------------C------------------CCCceEEEECCCCccHHHHHHHHHHH
Confidence            45666 89999999988877631            0                  11357999999999999999999997


Q ss_pred             cCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++                        .++++++++-.     +   ...++.+...+......++..|+||||+|.|..
T Consensus        59 LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~-----~---vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~  130 (491)
T PRK14964         59 LNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNT-----S---VDDIKVILENSCYLPISSKFKVYIIDEVHMLSN  130 (491)
T ss_pred             HcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCC-----C---HHHHHHHHHHHHhccccCCceEEEEeChHhCCH
Confidence            643                        34455443221     1   234555555444333345778999999999988


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||+
T Consensus       131 ~--------------A~NaLLK~LEe  142 (491)
T PRK14964        131 S--------------AFNALLKTLEE  142 (491)
T ss_pred             H--------------HHHHHHHHHhC
Confidence            7              89999999995

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

Probab=99.18  E-value=4.1e-11  Score=122.79  Aligned_cols=87  Identities=26%  Similarity=0.432  Sum_probs=67.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc---eEEecchhhhhcCcccccHHHHHHHHHHhhchhh-hccCceEEEEcCccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP---FVIADATTLTQAGYVGEDVESILYKLLAQAEFNV-EAAQQGMVYIDEVDK  401 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p---fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v-~~a~~gVLfIDEID~  401 (461)
                      ..++|+||||||||+||+.|+.....+   |++++++.-.         ...++.+|+.+.... ...+..|||||||++
T Consensus       163 pSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~---------t~dvR~ife~aq~~~~l~krkTilFiDEiHR  233 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAK---------TNDVRDIFEQAQNEKSLTKRKTILFIDEIHR  233 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccccc---------hHHHHHHHHHHHHHHhhhcceeEEEeHHhhh
Confidence            568999999999999999999988765   7777766543         345666676554332 235678999999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHhCceeee
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLEGTETKT  435 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i  435 (461)
                      +...              .|+.||..+|.+.+..
T Consensus       234 FNks--------------QQD~fLP~VE~G~I~l  253 (554)
T KOG2028|consen  234 FNKS--------------QQDTFLPHVENGDITL  253 (554)
T ss_pred             hhhh--------------hhhcccceeccCceEE
Confidence            9988              7899999999665443

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.17  E-value=1.7e-10  Score=126.15  Aligned_cols=109  Identities=30%  Similarity=0.354  Sum_probs=75.0

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ..++.+||+||+|||||++|++||+.
T Consensus        10 ~~f~e-ivGq~~i~~~L~~~i~~~------------------------------r~~ha~Lf~Gp~G~GKTt~A~~lAk~   58 (584)
T PRK14952         10 ATFAE-VVGQEHVTEPLSSALDAG------------------------------RINHAYLFSGPRGCGKTSSARILARS   58 (584)
T ss_pred             CcHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45666 899999999998888310                              01133799999999999999999998


Q ss_pred             cCCc--------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          349 VNVP--------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       349 l~~p--------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      +++.                          +++++++..     .|   ...++.+..............|+||||+|.|
T Consensus        59 l~c~~~~~~~pCg~C~~C~~i~~~~~~~~dvieidaas~-----~g---vd~iRel~~~~~~~P~~~~~KVvIIDEah~L  130 (584)
T PRK14952         59 LNCAQGPTATPCGVCESCVALAPNGPGSIDVVELDAASH-----GG---VDDTRELRDRAFYAPAQSRYRIFIVDEAHMV  130 (584)
T ss_pred             hccccCCCCCcccccHHHHHhhcccCCCceEEEeccccc-----cC---HHHHHHHHHHHHhhhhcCCceEEEEECCCcC
Confidence            8642                          222222111     11   2334444444333333356779999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ...              .+++||+.||+
T Consensus       131 t~~--------------A~NALLK~LEE  144 (584)
T PRK14952        131 TTA--------------GFNALLKIVEE  144 (584)
T ss_pred             CHH--------------HHHHHHHHHhc
Confidence            987              89999999995

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.17  E-value=2e-10  Score=118.77  Aligned_cols=116  Identities=23%  Similarity=0.283  Sum_probs=72.9

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.+++ |+||+.+++.|..++...                              ..++.+||+||+|||||++|+++|+.
T Consensus        13 ~~~~~-iiGq~~~~~~l~~~~~~~------------------------------~~~h~~L~~Gp~G~GKTtla~~la~~   61 (363)
T PRK14961         13 QYFRD-IIGQKHIVTAISNGLSLG------------------------------RIHHAWLLSGTRGVGKTTIARLLAKS   61 (363)
T ss_pred             Cchhh-ccChHHHHHHHHHHHHcC------------------------------CCCeEEEEecCCCCCHHHHHHHHHHH
Confidence            45666 899999999988877310                              01244799999999999999999998


Q ss_pred             cCCceEE--------ecchhhhhcC---cc------cccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccc
Q 012525          349 VNVPFVI--------ADATTLTQAG---YV------GEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI  411 (461)
Q Consensus       349 l~~pfv~--------i~~s~l~~~g---~v------Ge~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~  411 (461)
                      +.+....        ..|..+....   +.      ... ...++.+..............|+||||+|+|...      
T Consensus        62 l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~~~~-v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~------  134 (363)
T PRK14961         62 LNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASRTK-VEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRH------  134 (363)
T ss_pred             hcCCCCCCCCCCCCCHHHHHHhcCCCCceEEecccccCC-HHHHHHHHHHHhcCcccCCceEEEEEChhhcCHH------
Confidence            8642100        0011111000   00      011 2334444443332222335679999999999876      


Q ss_pred             ccccchHHHHHHHHHHHhC
Q 012525          412 SRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       412 ~~~~s~~~v~~aLL~~LEg  430 (461)
                              .+++||+.||.
T Consensus       135 --------a~naLLk~lEe  145 (363)
T PRK14961        135 --------SFNALLKTLEE  145 (363)
T ss_pred             --------HHHHHHHHHhc
Confidence                    78999999995

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.16  E-value=1.9e-10  Score=124.62  Aligned_cols=109  Identities=29%  Similarity=0.440  Sum_probs=76.1

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ...+.+||+||+|||||++|+++|+.
T Consensus        13 ~~f~d-ivGq~~v~~~L~~~i~~~------------------------------~~~ha~Lf~Gp~G~GKTt~A~~lAk~   61 (527)
T PRK14969         13 KSFSE-LVGQEHVVRALTNALEQQ------------------------------RLHHAYLFTGTRGVGKTTLARILAKS   61 (527)
T ss_pred             CcHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            35566 899999999988887310                              01234799999999999999999999


Q ss_pred             cCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++.                        ++.++...       ... ...++.+...+.......+..|+||||+|+|..
T Consensus        62 l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~-------~~~-vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~  133 (527)
T PRK14969         62 LNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAAS-------NTQ-VDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSK  133 (527)
T ss_pred             hcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeeccc-------cCC-HHHHHHHHHHHhhCcccCCceEEEEcCcccCCH
Confidence            8652                        11221110       011 334555555544433345677999999999998


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||+
T Consensus       134 ~--------------a~naLLK~LEe  145 (527)
T PRK14969        134 S--------------AFNAMLKTLEE  145 (527)
T ss_pred             H--------------HHHHHHHHHhC
Confidence            7              89999999995

>smart00350 MCM minichromosome maintenance proteins

Probab=99.16  E-value=7.6e-11  Score=127.16  Aligned_cols=153  Identities=17%  Similarity=0.240  Sum_probs=96.8

Q ss_pred             HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHH
Q 012525          266 EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       266 el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraL  345 (461)
                      .+...+...|+|++.+|+.|..++...              .....    .....+ ....||||+|+||||||++|+++
T Consensus       196 ~l~~si~p~i~G~~~~k~~l~l~l~gg--------------~~~~~----~~~~~~-r~~~~vLL~G~pGtGKs~lar~l  256 (509)
T smart00350      196 RLSRSLAPSIYGHEDIKKAILLLLFGG--------------VHKNL----PDGMKI-RGDINILLLGDPGTAKSQLLKYV  256 (509)
T ss_pred             HHHHhhCccccCcHHHHHHHHHHHhCC--------------Ccccc----CCCccc-cccceEEEeCCCChhHHHHHHHH
Confidence            355666777899999988887766310              00000    000001 22468999999999999999999


Q ss_pred             HHhcCCc-eEEe---cchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHH
Q 012525          346 ARHVNVP-FVIA---DATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQ  421 (461)
Q Consensus       346 A~~l~~p-fv~i---~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~  421 (461)
                      ++..... |+..   ++..+... ..    .......+....+.+..+++++++|||+|+|...              .+
T Consensus       257 ~~~~~r~~~~~~~~~~~~~l~~~-~~----~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~~~--------------~q  317 (509)
T smart00350      257 EKTAPRAVYTTGKGSSAVGLTAA-VT----RDPETREFTLEGGALVLADNGVCCIDEFDKMDDS--------------DR  317 (509)
T ss_pred             HHHcCcceEcCCCCCCcCCcccc-ce----EccCcceEEecCccEEecCCCEEEEechhhCCHH--------------HH
Confidence            9987542 3221   22222210 00    0000011111234455678999999999999988              89


Q ss_pred             HHHHHHHhCceeeeec--ceeeecCCeEEEecCCCCc
Q 012525          422 QALLKMLEGTETKTFA--AVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       422 ~aLL~~LEg~~v~i~~--~~r~~~rd~IiI~TsNid~  456 (461)
                      ..|++.||...+.+.-  .....+.++.+|+|+|...
T Consensus       318 ~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~  354 (509)
T smart00350      318 TAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIG  354 (509)
T ss_pred             HHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCC
Confidence            9999999988776542  2555666899999999753

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.15  E-value=1.4e-10  Score=129.02  Aligned_cols=138  Identities=22%  Similarity=0.328  Sum_probs=100.9

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc----CcccccHHHHHHH
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA----GYVGEDVESILYK  377 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~----g~vGe~~e~~L~~  377 (461)
                      .+.+..+..+.+.+..++....+|||+|++|||||++|++|+...   +.+|+.++|..+...    .++|... ..+..
T Consensus       379 iG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~~~~~~~lfg~~~-~~~~g  457 (686)
T PRK15429        379 IGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHER-GAFTG  457 (686)
T ss_pred             eecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCChhHhhhhhcCccc-ccccc
Confidence            467788888888889899999999999999999999999999865   469999999876431    1112110 00000


Q ss_pred             HHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          378 LLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       378 lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ......+.++.+.+++||||||+.|...              +|..|+.+|+...+...........+..+|+|++.+..
T Consensus       458 ~~~~~~g~le~a~~GtL~Ldei~~L~~~--------------~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~  523 (686)
T PRK15429        458 ASAQRIGRFELADKSSLFLDEVGDMPLE--------------LQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLK  523 (686)
T ss_pred             cccchhhHHHhcCCCeEEEechhhCCHH--------------HHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCCHH
Confidence            0001122345567899999999999998              99999999998776655544444457899999998764

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.15  E-value=6.8e-11  Score=127.84  Aligned_cols=129  Identities=23%  Similarity=0.354  Sum_probs=91.5

Q ss_pred             CCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh--
Q 012525          307 AEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ--  381 (461)
Q Consensus       307 ~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~--  381 (461)
                      .++.+..+.+....++....+|||+|++||||+++|++++...   ..||+.++|..+.+.     ..+   ..+|..  
T Consensus       209 ~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~~~-----~~e---~elFG~~~  280 (520)
T PRK10820        209 VSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDD-----VVE---SELFGHAP  280 (520)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCCHH-----HHH---HHhcCCCC
Confidence            3444444444555555667889999999999999999998765   369999999987631     111   122221  


Q ss_pred             ---------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecC
Q 012525          382 ---------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTS  452 (461)
Q Consensus       382 ---------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~Ts  452 (461)
                               ..+.++.+.+++||||||+.|...              +|..|+.+|+.+.+...........+..+|+|+
T Consensus       281 ~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~~--------------~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st  346 (520)
T PRK10820        281 GAYPNALEGKKGFFEQANGGSVLLDEIGEMSPR--------------MQAKLLRFLNDGTFRRVGEDHEVHVDVRVICAT  346 (520)
T ss_pred             CCcCCcccCCCChhhhcCCCEEEEeChhhCCHH--------------HHHHHHHHHhcCCcccCCCCcceeeeeEEEEec
Confidence                     123355678899999999999998              999999999977665444333334478899988


Q ss_pred             CCCcC
Q 012525          453 GLDSK  457 (461)
Q Consensus       453 Nid~e  457 (461)
                      +.+++
T Consensus       347 ~~~l~  351 (520)
T PRK10820        347 QKNLV  351 (520)
T ss_pred             CCCHH
Confidence            87753

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.14  E-value=2.6e-10  Score=123.01  Aligned_cols=116  Identities=28%  Similarity=0.380  Sum_probs=77.2

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ ++||+.+++.|..++...                              ....++||+||+|||||++|+++|+.
T Consensus        18 ~~f~d-liGq~~vv~~L~~ai~~~------------------------------ri~~a~Lf~Gp~G~GKTT~ArilAk~   66 (507)
T PRK06645         18 SNFAE-LQGQEVLVKVLSYTILND------------------------------RLAGGYLLTGIRGVGKTTSARIIAKA   66 (507)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCceEEEECCCCCCHHHHHHHHHHH
Confidence            45666 899999999888877310                              11367999999999999999999998


Q ss_pred             cCCceE------------Eecchhhhhc---Ccc------cccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhh
Q 012525          349 VNVPFV------------IADATTLTQA---GYV------GEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAE  407 (461)
Q Consensus       349 l~~pfv------------~i~~s~l~~~---g~v------Ge~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~  407 (461)
                      +++...            ..+|..+...   ++.      ... ...++.++..+.......+..|+||||+|.|...  
T Consensus        67 Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~-vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~--  143 (507)
T PRK06645         67 VNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTS-VDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKG--  143 (507)
T ss_pred             hcCccccccCcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCC-HHHHHHHHHHHHhccccCCcEEEEEEChhhcCHH--
Confidence            865210            0011111100   000      011 3455666655544444457789999999999876  


Q ss_pred             ccccccccchHHHHHHHHHHHhC
Q 012525          408 SLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       408 ~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                  .+++|++.||.
T Consensus       144 ------------a~naLLk~LEe  154 (507)
T PRK06645        144 ------------AFNALLKTLEE  154 (507)
T ss_pred             ------------HHHHHHHHHhh
Confidence                        79999999994

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.14  E-value=1.9e-10  Score=126.51  Aligned_cols=110  Identities=27%  Similarity=0.387  Sum_probs=76.3

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ |+||+.+++.|..++...                              ...+.+||+||+|||||++|++||+
T Consensus        12 P~~f~d-viGQe~vv~~L~~~l~~~------------------------------rl~ha~Lf~Gp~GvGKTtlAr~lAk   60 (618)
T PRK14951         12 PRSFSE-MVGQEHVVQALTNALTQQ------------------------------RLHHAYLFTGTRGVGKTTVSRILAK   60 (618)
T ss_pred             CCCHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            345676 789999999998887310                              0124469999999999999999999


Q ss_pred             hcCCc-----------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcC
Q 012525          348 HVNVP-----------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDE  398 (461)
Q Consensus       348 ~l~~p-----------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDE  398 (461)
                      .+++.                             |++++..+-       .. ...++.+...........+..|+||||
T Consensus        61 ~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas~-------~~-Vd~iReli~~~~~~p~~g~~KV~IIDE  132 (618)
T PRK14951         61 SLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAASN-------RG-VDEVQQLLEQAVYKPVQGRFKVFMIDE  132 (618)
T ss_pred             HhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCcccc-------cC-HHHHHHHHHHHHhCcccCCceEEEEEC
Confidence            88651                             222222110       11 234555555444433344567999999


Q ss_pred             ccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          399 VDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       399 ID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      +|.|+..              .+|+||+.||+
T Consensus       133 vh~Ls~~--------------a~NaLLKtLEE  150 (618)
T PRK14951        133 VHMLTNT--------------AFNAMLKTLEE  150 (618)
T ss_pred             hhhCCHH--------------HHHHHHHhccc
Confidence            9999988              79999999995

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.14  E-value=2.4e-10  Score=126.29  Aligned_cols=117  Identities=28%  Similarity=0.385  Sum_probs=76.5

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ |+||+.+++.|..++...                              ..++.+||+||+|||||++|++||+
T Consensus        12 P~tFdd-IIGQe~vv~~L~~ai~~~------------------------------rl~Ha~Lf~GP~GvGKTTlAriLAk   60 (709)
T PRK08691         12 PKTFAD-LVGQEHVVKALQNALDEG------------------------------RLHHAYLLTGTRGVGKTTIARILAK   60 (709)
T ss_pred             CCCHHH-HcCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCcHHHHHHHHHH
Confidence            345666 899999999998887310                              1125689999999999999999999


Q ss_pred             hcCCceE-------Ee-cchhhhhcCc---------ccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccc
Q 012525          348 HVNVPFV-------IA-DATTLTQAGY---------VGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLN  410 (461)
Q Consensus       348 ~l~~pfv-------~i-~~s~l~~~g~---------vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~  410 (461)
                      .+++.-.       .+ .|..+....+         .... ...++.++..........+..||||||+|.|...     
T Consensus        61 ~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaAs~~g-Vd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~-----  134 (709)
T PRK08691         61 SLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTG-IDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKS-----  134 (709)
T ss_pred             HhcccCCCCCCCCcccHHHHHHhccCccceEEEeccccCC-HHHHHHHHHHHHhhhhhCCcEEEEEECccccCHH-----
Confidence            8865310       00 0111110000         0111 2345555554433333346679999999998876     


Q ss_pred             cccccchHHHHHHHHHHHhC
Q 012525          411 ISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       411 ~~~~~s~~~v~~aLL~~LEg  430 (461)
                               .+++||+.||+
T Consensus       135 ---------A~NALLKtLEE  145 (709)
T PRK08691        135 ---------AFNAMLKTLEE  145 (709)
T ss_pred             ---------HHHHHHHHHHh
Confidence                     78999999994

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.13  E-value=2.7e-10  Score=123.73  Aligned_cols=109  Identities=28%  Similarity=0.380  Sum_probs=74.3

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|..++...                              ...+.+||+||+|||||++|++||+.
T Consensus        13 ~~f~d-iiGq~~~v~~L~~~i~~~------------------------------rl~ha~Lf~Gp~GvGKTTlAr~lAk~   61 (546)
T PRK14957         13 QSFAE-VAGQQHALNSLVHALETQ------------------------------KVHHAYLFTGTRGVGKTTLGRLLAKC   61 (546)
T ss_pred             CcHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45666 899999999988877310                              01244899999999999999999998


Q ss_pred             cCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++                        .+++++...     ..|   ...++.++.............|+||||+|+|..
T Consensus        62 L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas-----~~g---vd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~  133 (546)
T PRK14957         62 LNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAAS-----RTG---VEETKEILDNIQYMPSQGRYKVYLIDEVHMLSK  133 (546)
T ss_pred             hCCCCCCCCCCCcccHHHHHHhcCCCCceEEeeccc-----ccC---HHHHHHHHHHHHhhhhcCCcEEEEEechhhccH
Confidence            864                        222222211     111   123344444333333334677999999999998


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||+
T Consensus       134 ~--------------a~naLLK~LEe  145 (546)
T PRK14957        134 Q--------------SFNALLKTLEE  145 (546)
T ss_pred             H--------------HHHHHHHHHhc
Confidence            7              89999999995

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.12  E-value=2.9e-10  Score=124.76  Aligned_cols=111  Identities=28%  Similarity=0.335  Sum_probs=74.6

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      -.+.|++ |+||+.+++.|..++...                              .....+||+||+|||||++|++||
T Consensus        11 RP~sf~d-IiGQe~v~~~L~~ai~~~------------------------------ri~ha~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         11 RPQTFAE-VAGQETVKAILSRAAQEN------------------------------RVAPAYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             CCCCHHH-hcCCHHHHHHHHHHHHcC------------------------------CCCceEEEECCCCCCHHHHHHHHH
Confidence            3445666 799999999998888310                              012568999999999999999999


Q ss_pred             HhcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          347 RHVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       347 ~~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      +.+.+.                        +++++...     ..+   ...++.+..............||||||+|.|
T Consensus        60 k~L~C~~~~~~~pCg~C~sC~~i~~g~hpDv~eId~a~-----~~~---Id~iR~L~~~~~~~p~~g~~kVIIIDEad~L  131 (624)
T PRK14959         60 KALNCETAPTGEPCNTCEQCRKVTQGMHVDVVEIDGAS-----NRG---IDDAKRLKEAIGYAPMEGRYKVFIIDEAHML  131 (624)
T ss_pred             HhccccCCCCCCCCcccHHHHHHhcCCCCceEEEeccc-----ccC---HHHHHHHHHHHHhhhhcCCceEEEEEChHhC
Confidence            988652                        22332211     011   1223333222222222345679999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ...              .+++||+.||+
T Consensus       132 t~~--------------a~naLLk~LEE  145 (624)
T PRK14959        132 TRE--------------AFNALLKTLEE  145 (624)
T ss_pred             CHH--------------HHHHHHHHhhc
Confidence            877              79999999995

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

Probab=99.12  E-value=1.6e-10  Score=121.12  Aligned_cols=116  Identities=23%  Similarity=0.302  Sum_probs=83.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++.|||||||||||++.-|||++++..++.++.+++...        ..|+.++....      ..+||+|++||.-..
T Consensus       235 KRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n--------~dLr~LL~~t~------~kSIivIEDIDcs~~  300 (457)
T KOG0743|consen  235 KRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLD--------SDLRHLLLATP------NKSILLIEDIDCSFD  300 (457)
T ss_pred             hccceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCc--------HHHHHHHHhCC------CCcEEEEeecccccc
Confidence            3779999999999999999999999999999999887742        33888875544      678999999998765


Q ss_pred             hhhccccc----cccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCC----CCcCcCCC
Q 012525          405 KAESLNIS----RDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSG----LDSKTLWP  461 (461)
Q Consensus       405 ~R~~~~~~----~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsN----id~e~l~P  461 (461)
                      -+......    ......-.++-||..+||-...-.       ..-|+|+|||    +|+..++|
T Consensus       301 l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg-------~ERIivFTTNh~EkLDPALlRp  358 (457)
T KOG0743|consen  301 LRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCG-------DERIIVFTTNHKEKLDPALLRP  358 (457)
T ss_pred             cccccccccccccCCcceeehHHhhhhhccccccCC-------CceEEEEecCChhhcCHhhcCC
Confidence            33221111    101122368889999997653311       1469999999    45666555

>PRK04195 replication factor C large subunit; Provisional

Probab=99.11  E-value=3.5e-10  Score=121.11  Aligned_cols=121  Identities=30%  Similarity=0.421  Sum_probs=82.9

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHH
Q 012525          264 PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       264 ~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAr  343 (461)
                      .+.-.+.|++ |+|++.+++.|...+....         .+                  ....++||+||||||||++|+
T Consensus         6 eKyrP~~l~d-lvg~~~~~~~l~~~l~~~~---------~g------------------~~~~~lLL~GppG~GKTtla~   57 (482)
T PRK04195          6 EKYRPKTLSD-VVGNEKAKEQLREWIESWL---------KG------------------KPKKALLLYGPPGVGKTSLAH   57 (482)
T ss_pred             hhcCCCCHHH-hcCCHHHHHHHHHHHHHHh---------cC------------------CCCCeEEEECCCCCCHHHHHH
Confidence            3344456677 8999999999988884211         11                  113679999999999999999


Q ss_pred             HHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchh--hhccCceEEEEcCccccchhhhccccccccchHHHH
Q 012525          344 TLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFN--VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQ  421 (461)
Q Consensus       344 aLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~--v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~  421 (461)
                      +||++++..++.+++++...        ...+..+...+...  +......||||||+|.|....          ..+.+
T Consensus        58 ala~el~~~~ielnasd~r~--------~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~~----------d~~~~  119 (482)
T PRK04195         58 ALANDYGWEVIELNASDQRT--------ADVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNE----------DRGGA  119 (482)
T ss_pred             HHHHHcCCCEEEEccccccc--------HHHHHHHHHHhhccCcccCCCCeEEEEecCccccccc----------chhHH
Confidence            99999999999999887542        12233333222111  111256799999999987631          11257


Q ss_pred             HHHHHHHhC
Q 012525          422 QALLKMLEG  430 (461)
Q Consensus       422 ~aLL~~LEg  430 (461)
                      ++|+.+|+.
T Consensus       120 ~aL~~~l~~  128 (482)
T PRK04195        120 RAILELIKK  128 (482)
T ss_pred             HHHHHHHHc
Confidence            889998884

>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=99.11  E-value=8.6e-10  Score=94.56  Aligned_cols=109  Identities=29%  Similarity=0.433  Sum_probs=68.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHH-HHHhhchhhhccCceEEEEcCcc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYK-LLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~-lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      ..+++|+||||||||++++.+++.+   +.+++.+++....... ..   ...... .............+.+|+|||++
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~-~~---~~~~~~~~~~~~~~~~~~~~~~~lilDe~~   94 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGL-VV---AELFGHFLVRLLFELAEKAKPGVLFIDEID   94 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhh-HH---HHHhhhhhHhHHHHhhccCCCeEEEEeChh
Confidence            3679999999999999999999998   7888888887665321 10   000000 00111111223467899999999


Q ss_pred             ccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          401 KITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       401 ~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      .+...              ....++..|+......     ....+..+|+++|...
T Consensus        95 ~~~~~--------------~~~~~~~~i~~~~~~~-----~~~~~~~ii~~~~~~~  131 (151)
T cd00009          95 SLSRG--------------AQNALLRVLETLNDLR-----IDRENVRVIGATNRPL  131 (151)
T ss_pred             hhhHH--------------HHHHHHHHHHhcCcee-----ccCCCeEEEEecCccc
Confidence            88555              5667777777443221     1123567777777544

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.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.10  E-value=2.1e-10  Score=111.90  Aligned_cols=111  Identities=29%  Similarity=0.397  Sum_probs=85.0

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|.+ |+|.++..+.|......                 .+              -.|++|.|||||||||-+.+||+
T Consensus        23 P~~l~d-IVGNe~tv~rl~via~~-----------------gn--------------mP~liisGpPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   23 PSVLQD-IVGNEDTVERLSVIAKE-----------------GN--------------MPNLIISGPPGTGKTTSILCLAR   70 (333)
T ss_pred             chHHHH-hhCCHHHHHHHHHHHHc-----------------CC--------------CCceEeeCCCCCchhhHHHHHHH
Confidence            344555 99999999999887730                 11              27899999999999999999999


Q ss_pred             hcCC-----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          348 HVNV-----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       348 ~l~~-----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                      ++-.     -++++++++-.     |-++...--+.|.+....+......||+|||+|.|+..              .|+
T Consensus        71 ~LLG~~~ke~vLELNASdeR-----GIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~g--------------AQQ  131 (333)
T KOG0991|consen   71 ELLGDSYKEAVLELNASDER-----GIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTAG--------------AQQ  131 (333)
T ss_pred             HHhChhhhhHhhhccCcccc-----ccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhhH--------------HHH
Confidence            8733     34555555543     45555555667777766666677789999999999988              899


Q ss_pred             HHHHHHh
Q 012525          423 ALLKMLE  429 (461)
Q Consensus       423 aLL~~LE  429 (461)
                      +|.+.||
T Consensus       132 AlRRtME  138 (333)
T KOG0991|consen  132 ALRRTME  138 (333)
T ss_pred             HHHHHHH
Confidence            9999999

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.10  E-value=4e-10  Score=117.98  Aligned_cols=117  Identities=19%  Similarity=0.249  Sum_probs=73.6

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..+++ |+||+.+++.|..++...                              ..++.+||+||+|||||++|+++|+.
T Consensus        13 ~~~~e-iiGq~~~~~~L~~~~~~~------------------------------~~~ha~lf~Gp~G~GKtt~A~~~a~~   61 (397)
T PRK14955         13 KKFAD-ITAQEHITRTIQNSLRMG------------------------------RVGHGYIFSGLRGVGKTTAARVFAKA   61 (397)
T ss_pred             CcHhh-ccChHHHHHHHHHHHHhC------------------------------CcceeEEEECCCCCCHHHHHHHHHHH
Confidence            35566 899999999888877310                              01245999999999999999999998


Q ss_pred             cCCce-E---------Eecc------hhhhh---cC---cccc--cHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNVPF-V---------IADA------TTLTQ---AG---YVGE--DVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~pf-v---------~i~~------s~l~~---~g---~vGe--~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +.+.- .         .-.|      ..+..   ..   +.+.  .....++.+..........+...|+||||+|.|..
T Consensus        62 l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~  141 (397)
T PRK14955         62 VNCQRMIDDADYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSI  141 (397)
T ss_pred             hcCCCCcCcccccccCCCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCH
Confidence            86521 0         0000      00000   00   0010  00233444444333333335667999999999987


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .++.|++.||.
T Consensus       142 ~--------------~~~~LLk~LEe  153 (397)
T PRK14955        142 A--------------AFNAFLKTLEE  153 (397)
T ss_pred             H--------------HHHHHHHHHhc
Confidence            6              78999999994

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.10  E-value=4.4e-10  Score=123.05  Aligned_cols=109  Identities=25%  Similarity=0.325  Sum_probs=75.6

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ..++.+||+||+|||||++|++||+.
T Consensus        13 ~~f~~-iiGq~~v~~~L~~~i~~~------------------------------~~~hayLf~Gp~G~GKtt~A~~lak~   61 (576)
T PRK14965         13 QTFSD-LTGQEHVSRTLQNAIDTG------------------------------RVAHAFLFTGARGVGKTSTARILAKA   61 (576)
T ss_pred             CCHHH-ccCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            35666 899999999998887310                              01245799999999999999999998


Q ss_pred             cCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++.                        +++++...-     .  . ...++.+..........+...|+||||+|.|+.
T Consensus        62 l~c~~~~~~~~c~~c~~c~~i~~g~~~d~~eid~~s~-----~--~-v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~  133 (576)
T PRK14965         62 LNCEQGLTAEPCNVCPPCVEITEGRSVDVFEIDGASN-----T--G-VDDIRELRENVKYLPSRSRYKIFIIDEVHMLST  133 (576)
T ss_pred             hcCCCCCCCCCCCccHHHHHHhcCCCCCeeeeeccCc-----c--C-HHHHHHHHHHHHhccccCCceEEEEEChhhCCH
Confidence            8642                        222222110     1  1 233455544443333345677999999999998


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||+
T Consensus       134 ~--------------a~naLLk~LEe  145 (576)
T PRK14965        134 N--------------AFNALLKTLEE  145 (576)
T ss_pred             H--------------HHHHHHHHHHc
Confidence            7              89999999995

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.09  E-value=4.8e-10  Score=123.63  Aligned_cols=116  Identities=26%  Similarity=0.341  Sum_probs=77.2

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ....++||+||+|||||++|+++|+.
T Consensus        13 ~~f~~-liGq~~i~~~L~~~l~~~------------------------------rl~~a~Lf~Gp~G~GKttlA~~lAk~   61 (620)
T PRK14948         13 QRFDE-LVGQEAIATTLKNALISN------------------------------RIAPAYLFTGPRGTGKTSSARILAKS   61 (620)
T ss_pred             CcHhh-ccChHHHHHHHHHHHHcC------------------------------CCCceEEEECCCCCChHHHHHHHHHH
Confidence            45566 899999999998888310                              01267999999999999999999998


Q ss_pred             cCCceEEe----c---c---hhhh--------hc-CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcc
Q 012525          349 VNVPFVIA----D---A---TTLT--------QA-GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESL  409 (461)
Q Consensus       349 l~~pfv~i----~---~---s~l~--------~~-g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~  409 (461)
                      +.+.....    .   |   ..+.        .. ...... ...++.++..+..........||||||+|.|...    
T Consensus        62 L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~~~~~~-vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~----  136 (620)
T PRK14948         62 LNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDAASNTG-VDNIRELIERAQFAPVQARWKVYVIDECHMLSTA----  136 (620)
T ss_pred             hcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEeccccCC-HHHHHHHHHHHhhChhcCCceEEEEECccccCHH----
Confidence            86521100    0   0   0000        00 000112 3455666655544333456679999999999887    


Q ss_pred             ccccccchHHHHHHHHHHHhC
Q 012525          410 NISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       410 ~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                .+++||+.||+
T Consensus       137 ----------a~naLLK~LEe  147 (620)
T PRK14948        137 ----------AFNALLKTLEE  147 (620)
T ss_pred             ----------HHHHHHHHHhc
Confidence                      89999999994

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.08  E-value=9.2e-10  Score=118.79  Aligned_cols=109  Identities=29%  Similarity=0.333  Sum_probs=72.8

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|..++...                              ..++.+||+|||||||||+|+++|+.
T Consensus        11 ~~~~d-vvGq~~v~~~L~~~i~~~------------------------------~l~ha~Lf~GppGtGKTTlA~~lA~~   59 (504)
T PRK14963         11 ITFDE-VVGQEHVKEVLLAALRQG------------------------------RLGHAYLFSGPRGVGKTTTARLIAMA   59 (504)
T ss_pred             CCHHH-hcChHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35666 899999999998887310                              01234699999999999999999998


Q ss_pred             cCCc-----------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          349 VNVP-----------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       349 l~~p-----------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      +.+.                       ++.++...     ..  . ...++.+..............||||||+|.+...
T Consensus        60 l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~-----~~--~-vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~  131 (504)
T PRK14963         60 VNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAAS-----NN--S-VEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKS  131 (504)
T ss_pred             HhccCCCCCCCCcChhhHHHhcCCCCceEEecccc-----cC--C-HHHHHHHHHHHhhccccCCCeEEEEECccccCHH
Confidence            8531                       33333321     01  1 2233444333222222346679999999988766


Q ss_pred             hhccccccccchHHHHHHHHHHHhC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                    .+++|++.|+.
T Consensus       132 --------------a~naLLk~LEe  142 (504)
T PRK14963        132 --------------AFNALLKTLEE  142 (504)
T ss_pred             --------------HHHHHHHHHHh
Confidence                          79999999985

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.07  E-value=7.1e-10  Score=121.02  Aligned_cols=109  Identities=29%  Similarity=0.401  Sum_probs=77.3

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++...                              ...+.+||+||+|||||++|+.+|+.
T Consensus        13 ~~f~~-viGq~~v~~~L~~~i~~~------------------------------~~~hayLf~Gp~GtGKTt~Ak~lAka   61 (559)
T PRK05563         13 QTFED-VVGQEHITKTLKNAIKQG------------------------------KISHAYLFSGPRGTGKTSAAKIFAKA   61 (559)
T ss_pred             CcHHh-ccCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35666 899999999998887310                              01245899999999999999999998


Q ss_pred             cCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +++                        ++++++++.       ... ...++.+..........++..|+||||+|.|+.
T Consensus        62 l~c~~~~~~~pC~~C~~C~~i~~g~~~dv~eidaas-------~~~-vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~  133 (559)
T PRK05563         62 VNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAAS-------NNG-VDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLST  133 (559)
T ss_pred             hcCCCCCCCCCCCccHHHHHHhcCCCCCeEEeeccc-------cCC-HHHHHHHHHHHhhCcccCCeEEEEEECcccCCH
Confidence            864                        223333221       011 344555555554444456778999999999987


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||+
T Consensus       134 ~--------------a~naLLKtLEe  145 (559)
T PRK05563        134 G--------------AFNALLKTLEE  145 (559)
T ss_pred             H--------------HHHHHHHHhcC
Confidence            7              89999999994

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.07  E-value=3.9e-10  Score=123.79  Aligned_cols=116  Identities=22%  Similarity=0.247  Sum_probs=85.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC--ceEEecchhhhhcCcccc-cHHHHHH-HHHHhhchhhhccCceEEEEcCccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV--PFVIADATTLTQAGYVGE-DVESILY-KLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~--pfv~i~~s~l~~~g~vGe-~~e~~L~-~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      .+|||.|+||||||++|++|++.+..  ||+.+...... ..++|. +++..+. ..+....+.+..++++|||||||+.
T Consensus        17 g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~~t~-d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~lDEi~r   95 (589)
T TIGR02031        17 GGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTE-DRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYVDMANL   95 (589)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcccch-hhcccchhhhhhhhcCcccCCCCCeeeCCCCcEeccchhh
Confidence            68999999999999999999998854  69988863222 223333 1111111 1122334456678899999999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHhCceeeeec--ceeeecCCeEEEecCCCCc
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFA--AVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~--~~r~~~rd~IiI~TsNid~  456 (461)
                      +.+.              +|+.|++.|+.+++++..  ....++.++.+|+|+|...
T Consensus        96 l~~~--------------~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e  138 (589)
T TIGR02031        96 LDDG--------------LSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAE  138 (589)
T ss_pred             CCHH--------------HHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCcc
Confidence            9999              999999999988766553  3556677899999999874

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.07  E-value=9.8e-10  Score=110.57  Aligned_cols=122  Identities=26%  Similarity=0.362  Sum_probs=77.6

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      ..+.....+++ ++|++.+++.|..++..                               ....++||+||||||||++|
T Consensus         6 ~~ky~P~~~~~-~~g~~~~~~~L~~~~~~-------------------------------~~~~~lll~Gp~GtGKT~la   53 (337)
T PRK12402          6 TEKYRPALLED-ILGQDEVVERLSRAVDS-------------------------------PNLPHLLVQGPPGSGKTAAV   53 (337)
T ss_pred             HHhhCCCcHHH-hcCCHHHHHHHHHHHhC-------------------------------CCCceEEEECCCCCCHHHHH
Confidence            33444556777 68999999988887720                               01147999999999999999


Q ss_pred             HHHHHhcC-----CceEEecchhhhhcC--c----------ccc------cHHHHHHHHHHhhchhh-hccCceEEEEcC
Q 012525          343 KTLARHVN-----VPFVIADATTLTQAG--Y----------VGE------DVESILYKLLAQAEFNV-EAAQQGMVYIDE  398 (461)
Q Consensus       343 raLA~~l~-----~pfv~i~~s~l~~~g--~----------vGe------~~e~~L~~lf~~a~~~v-~~a~~gVLfIDE  398 (461)
                      +++++++.     .+++.+++.++....  .          .+.      .....++.+........ ......+|||||
T Consensus        54 ~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe  133 (337)
T PRK12402         54 RALARELYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDN  133 (337)
T ss_pred             HHHHHHhcCcccccceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeC
Confidence            99999874     356777776643210  0          000      01122333222221111 123456999999


Q ss_pred             ccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          399 VDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       399 ID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      +|.+...              .++.|+.+|+.
T Consensus       134 ~~~l~~~--------------~~~~L~~~le~  151 (337)
T PRK12402        134 AEALRED--------------AQQALRRIMEQ  151 (337)
T ss_pred             cccCCHH--------------HHHHHHHHHHh
Confidence            9998766              67889888883

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.07  E-value=1e-09  Score=120.98  Aligned_cols=97  Identities=32%  Similarity=0.468  Sum_probs=65.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc----------CCceEEecchhhhh------cCcccccHHHH---HHHHHH-----
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV----------NVPFVIADATTLTQ------AGYVGEDVESI---LYKLLA-----  380 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l----------~~pfv~i~~s~l~~------~g~vGe~~e~~---L~~lf~-----  380 (461)
                      +.+++|+||+||||||+|+++++..          +.+|+.+++..+..      ..+++...+..   ....+.     
T Consensus       175 ~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~  254 (615)
T TIGR02903       175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVP  254 (615)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCC
Confidence            4679999999999999999998765          35789999876521      01222111111   011111     


Q ss_pred             -hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeee
Q 012525          381 -QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKT  435 (461)
Q Consensus       381 -~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i  435 (461)
                       .....+..+.++||||||++.|...              .|+.|+++|+...+.+
T Consensus       255 ~~~~g~v~~asgGvL~LDEi~~Ld~~--------------~Q~~Ll~~Le~~~v~~  296 (615)
T TIGR02903       255 EPKTGLVTDAHGGVLFIDEIGELDPL--------------LQNKLLKVLEDKRVEF  296 (615)
T ss_pred             chhcCchhhcCCCeEEEeccccCCHH--------------HHHHHHHHHhhCeEEe
Confidence             1223344567899999999999988              8999999999766543

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.05  E-value=3.8e-10  Score=128.16  Aligned_cols=121  Identities=26%  Similarity=0.321  Sum_probs=88.8

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      ++. |+|+++.++.+...+..                               ..+.|+||+||||||||++|+.||+.+ 
T Consensus       178 ~~~-~igr~~ei~~~~~~L~r-------------------------------~~~~n~lL~G~pGvGKTal~~~la~~i~  225 (821)
T CHL00095        178 LDP-VIGREKEIERVIQILGR-------------------------------RTKNNPILIGEPGVGKTAIAEGLAQRIV  225 (821)
T ss_pred             CCC-CCCcHHHHHHHHHHHcc-------------------------------cccCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            444 89999999998888731                               124789999999999999999999876 


Q ss_pred             ---------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          350 ---------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       350 ---------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                               +..++.++...+.. ..|.|+. +..++.++..+..    ..+.||||||||.+....... ...     .
T Consensus       226 ~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~-e~rl~~i~~~~~~----~~~~ILfiDEih~l~~~g~~~-g~~-----~  294 (821)
T CHL00095        226 NRDVPDILEDKLVITLDIGLLLAGTKYRGEF-EERLKRIFDEIQE----NNNIILVIDEVHTLIGAGAAE-GAI-----D  294 (821)
T ss_pred             hCCCChhhcCCeEEEeeHHHHhccCCCccHH-HHHHHHHHHHHHh----cCCeEEEEecHHHHhcCCCCC-Ccc-----c
Confidence                     36789999887653 4566654 7888888876643    267899999999998763211 111     2


Q ss_pred             HHHHHHHHHhCceee
Q 012525          420 VQQALLKMLEGTETK  434 (461)
Q Consensus       420 v~~aLL~~LEg~~v~  434 (461)
                      +.+.|...|..+.+.
T Consensus       295 ~a~lLkp~l~rg~l~  309 (821)
T CHL00095        295 AANILKPALARGELQ  309 (821)
T ss_pred             HHHHhHHHHhCCCcE
Confidence            667777788755443

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.04  E-value=1.1e-09  Score=109.86  Aligned_cols=115  Identities=21%  Similarity=0.268  Sum_probs=74.5

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHH
Q 012525          264 PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       264 ~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAr  343 (461)
                      .+...+.|++ |+|++.+++.|...+..            +                  ..+..+||+||+|+|||++|+
T Consensus        13 ~kyrP~~~~~-~~~~~~~~~~l~~~~~~------------~------------------~~~~~lll~G~~G~GKT~la~   61 (316)
T PHA02544         13 QKYRPSTIDE-CILPAADKETFKSIVKK------------G------------------RIPNMLLHSPSPGTGKTTVAK   61 (316)
T ss_pred             eccCCCcHHH-hcCcHHHHHHHHHHHhc------------C------------------CCCeEEEeeCcCCCCHHHHHH
Confidence            3344456676 79999999988887730            0                  012345569999999999999


Q ss_pred             HHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHH
Q 012525          344 TLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQA  423 (461)
Q Consensus       344 aLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~a  423 (461)
                      ++++.++.+++.+++.+ ...    ......+........   ......||||||+|.+...             ..++.
T Consensus        62 ~l~~~~~~~~~~i~~~~-~~~----~~i~~~l~~~~~~~~---~~~~~~vliiDe~d~l~~~-------------~~~~~  120 (316)
T PHA02544         62 ALCNEVGAEVLFVNGSD-CRI----DFVRNRLTRFASTVS---LTGGGKVIIIDEFDRLGLA-------------DAQRH  120 (316)
T ss_pred             HHHHHhCccceEeccCc-ccH----HHHHHHHHHHHHhhc---ccCCCeEEEEECcccccCH-------------HHHHH
Confidence            99999998888888876 210    011111222111111   1135679999999988332             15677


Q ss_pred             HHHHHhC
Q 012525          424 LLKMLEG  430 (461)
Q Consensus       424 LL~~LEg  430 (461)
                      |..+|+.
T Consensus       121 L~~~le~  127 (316)
T PHA02544        121 LRSFMEA  127 (316)
T ss_pred             HHHHHHh
Confidence            8888884

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.04  E-value=4.2e-10  Score=128.27  Aligned_cols=122  Identities=25%  Similarity=0.316  Sum_probs=86.5

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+. |+|++...+.+...+..                               ....++||+||||||||++|++||+.
T Consensus       175 ~~l~~-vigr~~ei~~~i~iL~r-------------------------------~~~~n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        175 GKLDP-VIGRDEEIRRTIQVLQR-------------------------------RTKNNPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             CCCCc-CCCCHHHHHHHHHHHhc-------------------------------CCcCceEEECCCCCCHHHHHHHHHHH
Confidence            34555 89999987777776631                               12368999999999999999999998


Q ss_pred             c----------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccch
Q 012525          349 V----------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSG  417 (461)
Q Consensus       349 l----------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~  417 (461)
                      +          +.+++.++...+.. ..|.|+. +..++.++.....   ...+.||||||||.+....+..      +.
T Consensus       223 i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~-e~~lk~~~~~~~~---~~~~~ILfIDEih~l~~~~~~~------~~  292 (857)
T PRK10865        223 IINGEVPEGLKGRRVLALDMGALVAGAKYRGEF-EERLKGVLNDLAK---QEGNVILFIDELHTMVGAGKAD------GA  292 (857)
T ss_pred             hhcCCCchhhCCCEEEEEehhhhhhccchhhhh-HHHHHHHHHHHHH---cCCCeEEEEecHHHhccCCCCc------cc
Confidence            7          66888888876653 3456654 7788888865432   1257799999999998763211      11


Q ss_pred             HHHHHHHHHHHhCce
Q 012525          418 EGVQQALLKMLEGTE  432 (461)
Q Consensus       418 ~~v~~aLL~~LEg~~  432 (461)
                      ..+.+.|...|+.+.
T Consensus       293 ~d~~~~lkp~l~~g~  307 (857)
T PRK10865        293 MDAGNMLKPALARGE  307 (857)
T ss_pred             hhHHHHhcchhhcCC
Confidence            226777877777443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.03  E-value=1.3e-09  Score=119.76  Aligned_cols=115  Identities=29%  Similarity=0.358  Sum_probs=77.5

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+.|++ |+||+.+++.|..++..            +                  ..+..+||+||+|+|||++|++||+
T Consensus        20 P~~f~d-liGq~~~v~~L~~~~~~------------g------------------ri~ha~L~~Gp~GvGKTt~Ar~lAk   68 (598)
T PRK09111         20 PQTFDD-LIGQEAMVRTLTNAFET------------G------------------RIAQAFMLTGVRGVGKTTTARILAR   68 (598)
T ss_pred             CCCHHH-hcCcHHHHHHHHHHHHc------------C------------------CCCceEEEECCCCCCHHHHHHHHHH
Confidence            345666 89999999998887731            0                  1135699999999999999999999


Q ss_pred             hcCCceEEec-------------chhhhh-----------cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          348 HVNVPFVIAD-------------ATTLTQ-----------AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       348 ~l~~pfv~i~-------------~s~l~~-----------~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      .+++.....+             |..+..           ....+   ...++.++.........+...|+||||+|.|.
T Consensus        69 ~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~g---vd~IReIie~~~~~P~~a~~KVvIIDEad~Ls  145 (598)
T PRK09111         69 ALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTG---VDDIREIIESVRYRPVSARYKVYIIDEVHMLS  145 (598)
T ss_pred             hhCcCCccccCCCccccCcccHHHHHHhcCCCCceEEecccccCC---HHHHHHHHHHHHhchhcCCcEEEEEEChHhCC
Confidence            8865321111             111110           00111   23455555544444344577899999999998


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhC
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ..              .+++||+.||+
T Consensus       146 ~~--------------a~naLLKtLEe  158 (598)
T PRK09111        146 TA--------------AFNALLKTLEE  158 (598)
T ss_pred             HH--------------HHHHHHHHHHh
Confidence            77              79999999994

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.02  E-value=6.6e-10  Score=116.70  Aligned_cols=131  Identities=21%  Similarity=0.363  Sum_probs=98.6

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHH-
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLA-  380 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~-  380 (461)
                      .+.+..+..+.+....+.....+|+|+|++||||+++|++++...   ..+|+.++|..+.+.     ..+   ..+|. 
T Consensus       142 ig~s~~~~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~~-----~~~---~~lfg~  213 (445)
T TIGR02915       142 ITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPEN-----LLE---SELFGY  213 (445)
T ss_pred             eecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCChH-----HHH---HHhcCC
Confidence            345566777777777777778899999999999999999999876   458999999987531     111   11222 


Q ss_pred             ----------hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEe
Q 012525          381 ----------QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIK  450 (461)
Q Consensus       381 ----------~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~  450 (461)
                                ...+.+..+++++||||||+.|...              +|..|+++|+...+.........+.++.+|+
T Consensus       214 ~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~--------------~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~  279 (445)
T TIGR02915       214 EKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLN--------------LQAKLLRFLQERVIERLGGREEIPVDVRIVC  279 (445)
T ss_pred             CCCCcCCCccCCCCceeECCCCEEEEechhhCCHH--------------HHHHHHHHHhhCeEEeCCCCceeeeceEEEE
Confidence                      1223455678999999999999998              9999999999877665444444455889999


Q ss_pred             cCCCCcC
Q 012525          451 TSGLDSK  457 (461)
Q Consensus       451 TsNid~e  457 (461)
                      |++.+.+
T Consensus       280 ~~~~~l~  286 (445)
T TIGR02915       280 ATNQDLK  286 (445)
T ss_pred             ecCCCHH
Confidence            9998854

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).

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.01  E-value=2.6e-09  Score=108.59  Aligned_cols=109  Identities=30%  Similarity=0.458  Sum_probs=74.0

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..+++ |+||+.+++.|...+..            +                  ..+..+||+||+|+|||++|+++|+.
T Consensus        11 ~~~~~-iig~~~~~~~l~~~~~~------------~------------------~~~~~~Ll~G~~G~GKt~~a~~la~~   59 (355)
T TIGR02397        11 QTFED-VIGQEHIVQTLKNAIKN------------G------------------RIAHAYLFSGPRGTGKTSIARIFAKA   59 (355)
T ss_pred             CcHhh-ccCcHHHHHHHHHHHHc------------C------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34555 89999999999887731            0                  11245899999999999999999998


Q ss_pred             cCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +...                        ++.++...       ... ...++.++..+.......+..||+|||+|.+..
T Consensus        60 l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~~~~~~~-------~~~-~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~  131 (355)
T TIGR02397        60 LNCQNGPDGEPCNECESCKEINSGSSLDVIEIDAAS-------NNG-VDDIREILDNVKYAPSSGKYKVYIIDEVHMLSK  131 (355)
T ss_pred             hcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeeccc-------cCC-HHHHHHHHHHHhcCcccCCceEEEEeChhhcCH
Confidence            7532                        12222110       011 223455555443333335667999999999987


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++|++.||+
T Consensus       132 ~--------------~~~~Ll~~le~  143 (355)
T TIGR02397       132 S--------------AFNALLKTLEE  143 (355)
T ss_pred             H--------------HHHHHHHHHhC
Confidence            6              78999999985

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.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.01  E-value=1.5e-09  Score=121.56  Aligned_cols=85  Identities=31%  Similarity=0.451  Sum_probs=61.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhh-ccCceEEEEcCccccch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE-AAQQGMVYIDEVDKITK  404 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~-~a~~gVLfIDEID~L~~  404 (461)
                      .+++|+||||||||++|+++|+.++..|+.+++....         ...++..+..+...+. ..+..||||||||.+..
T Consensus        53 ~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~~~~---------i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~  123 (725)
T PRK13341         53 GSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAG---------VKDLRAEVDRAKERLERHGKRTILFIDEVHRFNK  123 (725)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhcCcceeehhhhhh---------hHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCH
Confidence            5799999999999999999999999999888876321         1112222222211111 12467999999999988


Q ss_pred             hhhccccccccchHHHHHHHHHHHhCcee
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEGTET  433 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg~~v  433 (461)
                      .              .+++|+..|+...+
T Consensus       124 ~--------------qQdaLL~~lE~g~I  138 (725)
T PRK13341        124 A--------------QQDALLPWVENGTI  138 (725)
T ss_pred             H--------------HHHHHHHHhcCceE
Confidence            7              78999999986543

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=99.01  E-value=7.4e-10  Score=117.21  Aligned_cols=131  Identities=23%  Similarity=0.366  Sum_probs=97.6

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ  381 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~  381 (461)
                      .+.+..+..+.+....+.....+|||.|++|||||++|++|++..   +.+|+.++|..+.+.        ..-..+|..
T Consensus       141 ig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~~--------~~~~~lfg~  212 (469)
T PRK10923        141 IGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKD--------LIESELFGH  212 (469)
T ss_pred             eecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCHH--------HHHHHhcCC
Confidence            344566666666777777788999999999999999999999976   469999999887531        111222221


Q ss_pred             -----------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEe
Q 012525          382 -----------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIK  450 (461)
Q Consensus       382 -----------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~  450 (461)
                                 ..+.++.+.+|+||||||+.|...              +|..|+++|+...+...........++.+|+
T Consensus       213 ~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~~--------------~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~  278 (469)
T PRK10923        213 EKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPLD--------------VQTRLLRVLADGQFYRVGGYAPVKVDVRIIA  278 (469)
T ss_pred             CCCCCCCCCcCCCCCeeECCCCEEEEeccccCCHH--------------HHHHHHHHHhcCcEEeCCCCCeEEeeEEEEE
Confidence                       123355678899999999999998              9999999999877665444333344789999


Q ss_pred             cCCCCcC
Q 012525          451 TSGLDSK  457 (461)
Q Consensus       451 TsNid~e  457 (461)
                      |++.+.+
T Consensus       279 ~~~~~l~  285 (469)
T PRK10923        279 ATHQNLE  285 (469)
T ss_pred             eCCCCHH
Confidence            9988753

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.01  E-value=2.6e-09  Score=116.93  Aligned_cols=109  Identities=28%  Similarity=0.396  Sum_probs=74.4

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|..++..            +                  ..++.+||+||+|||||++|+++|+.
T Consensus        13 ~~F~d-IIGQe~iv~~L~~aI~~------------~------------------rl~hA~Lf~GP~GvGKTTlA~~lAk~   61 (605)
T PRK05896         13 HNFKQ-IIGQELIKKILVNAILN------------N------------------KLTHAYIFSGPRGIGKTSIAKIFAKA   61 (605)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHc------------C------------------CCCceEEEECCCCCCHHHHHHHHHHH
Confidence            35666 89999999988887731            0                  11255899999999999999999998


Q ss_pred             cCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +.+                        .++.+++..     ..  . ...++.+...........+..|++|||+|.|..
T Consensus        62 L~C~~~~~~~~Cg~C~sCr~i~~~~h~DiieIdaas-----~i--g-Vd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~  133 (605)
T PRK05896         62 INCLNPKDGDCCNSCSVCESINTNQSVDIVELDAAS-----NN--G-VDEIRNIIDNINYLPTTFKYKVYIIDEAHMLST  133 (605)
T ss_pred             hcCCCCCCCCCCcccHHHHHHHcCCCCceEEecccc-----cc--C-HHHHHHHHHHHHhchhhCCcEEEEEechHhCCH
Confidence            853                        122222211     01  1 233455544433333334677999999999987


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||+
T Consensus       134 ~--------------A~NaLLKtLEE  145 (605)
T PRK05896        134 S--------------AWNALLKTLEE  145 (605)
T ss_pred             H--------------HHHHHHHHHHh
Confidence            6              78999999994

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.00  E-value=1.6e-09  Score=108.01  Aligned_cols=99  Identities=27%  Similarity=0.363  Sum_probs=69.4

Q ss_pred             Cc-EEEEccCCCchHHHHHHHHHhcC------------------------CceEEecchhhhhcCcccccHHHHHHHHHH
Q 012525          326 SN-VLLMGPTGSGKTLLAKTLARHVN------------------------VPFVIADATTLTQAGYVGEDVESILYKLLA  380 (461)
Q Consensus       326 ~~-VLL~GPPGTGKTtLAraLA~~l~------------------------~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~  380 (461)
                      .| +||+||||||||++|.+||+.+.                        -.|+++++++.....    .....++.+..
T Consensus        24 ~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~----i~~~~vr~~~~   99 (325)
T COG0470          24 PHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKID----IIVEQVRELAE   99 (325)
T ss_pred             CceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCc----chHHHHHHHHH
Confidence            44 99999999999999999999886                        367777777655321    11333444443


Q ss_pred             hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCC
Q 012525          381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSG  453 (461)
Q Consensus       381 ~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsN  453 (461)
                      .........+.-|++|||+|.|+..              .+++|++.||...           .+..+|.++|
T Consensus       100 ~~~~~~~~~~~kviiidead~mt~~--------------A~nallk~lEep~-----------~~~~~il~~n  147 (325)
T COG0470         100 FLSESPLEGGYKVVIIDEADKLTED--------------AANALLKTLEEPP-----------KNTRFILITN  147 (325)
T ss_pred             HhccCCCCCCceEEEeCcHHHHhHH--------------HHHHHHHHhccCC-----------CCeEEEEEcC
Confidence            3322222245669999999999998              8999999999443           2456666666

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.00  E-value=2.5e-09  Score=117.34  Aligned_cols=116  Identities=25%  Similarity=0.319  Sum_probs=73.1

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|..++...                              ...+.+||+||+|+|||++|++||+.
T Consensus        13 ~~~~e-iiGq~~~~~~L~~~i~~~------------------------------~i~~a~Lf~Gp~G~GKTtlA~~lA~~   61 (585)
T PRK14950         13 QTFAE-LVGQEHVVQTLRNAIAEG------------------------------RVAHAYLFTGPRGVGKTSTARILAKA   61 (585)
T ss_pred             CCHHH-hcCCHHHHHHHHHHHHhC------------------------------CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            35566 899999999998877310                              01245799999999999999999998


Q ss_pred             cCCceEE--------e-cchhhhhc---Cc------ccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccc
Q 012525          349 VNVPFVI--------A-DATTLTQA---GY------VGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLN  410 (461)
Q Consensus       349 l~~pfv~--------i-~~s~l~~~---g~------vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~  410 (461)
                      +++....        + .|..+...   ++      .... ...++.+..............||||||+|.|...     
T Consensus        62 l~c~~~~~~~~~c~~c~~c~~i~~~~~~d~~~i~~~~~~~-vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~-----  135 (585)
T PRK14950         62 VNCTTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTS-VDDAREIIERVQFRPALARYKVYIIDEVHMLSTA-----  135 (585)
T ss_pred             hcCCCCCCCCCCCccCHHHHHHhcCCCCeEEEEeccccCC-HHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHH-----
Confidence            8642110        0 00111100   00      0011 2233444433332222356779999999999877     


Q ss_pred             cccccchHHHHHHHHHHHhC
Q 012525          411 ISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       411 ~~~~~s~~~v~~aLL~~LEg  430 (461)
                               .++.||+.||+
T Consensus       136 ---------a~naLLk~LEe  146 (585)
T PRK14950        136 ---------AFNALLKTLEE  146 (585)
T ss_pred             ---------HHHHHHHHHhc
Confidence                     78999999995

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.00  E-value=6.4e-10  Score=119.62  Aligned_cols=117  Identities=30%  Similarity=0.425  Sum_probs=83.0

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+.+++.|..++.+  .++                            .+..||.||-|||||++||.+|+.
T Consensus        13 ~~F~e-vvGQe~v~~~L~nal~~--~ri----------------------------~hAYlfsG~RGvGKTt~Ari~Aka   61 (515)
T COG2812          13 KTFDD-VVGQEHVVKTLSNALEN--GRI----------------------------AHAYLFSGPRGVGKTTIARILAKA   61 (515)
T ss_pred             ccHHH-hcccHHHHHHHHHHHHh--Ccc----------------------------hhhhhhcCCCCcCchhHHHHHHHH
Confidence            45666 79999999999999952  122                            145899999999999999999999


Q ss_pred             cCCc-------eEEec-chhhhhcCc---c-----cccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          349 VNVP-------FVIAD-ATTLTQAGY---V-----GEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       349 l~~p-------fv~i~-~s~l~~~g~---v-----Ge~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                      +++.       +-.+. |..+....+   +     .....+.++.+.+...+.....+.-|++|||+|.|+..       
T Consensus        62 lNC~~~~~~ePC~~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~-------  134 (515)
T COG2812          62 LNCENGPTAEPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQ-------  134 (515)
T ss_pred             hcCCCCCCCCcchhhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHH-------
Confidence            8763       11111 111111000   0     00113556777777777777778889999999999988       


Q ss_pred             cccchHHHHHHHHHHHhC
Q 012525          413 RDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg  430 (461)
                             ..|+||+.||+
T Consensus       135 -------afNALLKTLEE  145 (515)
T COG2812         135 -------AFNALLKTLEE  145 (515)
T ss_pred             -------HHHHHhccccc
Confidence                   89999999994

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.00  E-value=2.8e-09  Score=117.46  Aligned_cols=116  Identities=19%  Similarity=0.267  Sum_probs=74.1

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+||+.+++.|..++...                              ...+.+||+||+||||||+|++||+.+
T Consensus        14 ~f~e-ivGQe~i~~~L~~~i~~~------------------------------ri~ha~Lf~Gp~GvGKttlA~~lAk~L   62 (620)
T PRK14954         14 KFAD-ITAQEHITHTIQNSLRMD------------------------------RVGHGYIFSGLRGVGKTTAARVFAKAV   62 (620)
T ss_pred             CHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeeEEEECCCCCCHHHHHHHHHHHh
Confidence            4555 899999999988877310                              112459999999999999999999998


Q ss_pred             CCceEE----------ec------chhhhh---cC---cccc--cHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          350 NVPFVI----------AD------ATTLTQ---AG---YVGE--DVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       350 ~~pfv~----------i~------~s~l~~---~g---~vGe--~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      .+.-..          -.      |..+..   ..   +.+.  .....++.+..........+...|+||||+|.|...
T Consensus        63 ~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~  142 (620)
T PRK14954         63 NCQRMIDDPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTA  142 (620)
T ss_pred             CCCCcCCccccccccCCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHH
Confidence            762100          00      000100   00   0110  002344444444333233456779999999999877


Q ss_pred             hhccccccccchHHHHHHHHHHHhC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                    .+++||+.||+
T Consensus       143 --------------a~naLLK~LEe  153 (620)
T PRK14954        143 --------------AFNAFLKTLEE  153 (620)
T ss_pred             --------------HHHHHHHHHhC
Confidence                          78999999995

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.99  E-value=8.1e-10  Score=119.01  Aligned_cols=121  Identities=16%  Similarity=0.247  Sum_probs=79.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc--eEEecchhhhh-------------cCcccccHHHHHHHHHH----hhchh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP--FVIADATTLTQ-------------AGYVGEDVESILYKLLA----QAEFN  385 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p--fv~i~~s~l~~-------------~g~vGe~~e~~L~~lf~----~a~~~  385 (461)
                      ..+++|+||+|+|||+|++.|+..+.-.  -..+..+.+..             .-|.-.........++.    ...+.
T Consensus       210 G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG~  289 (506)
T PRK09862        210 GHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGE  289 (506)
T ss_pred             CcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhhccccccCCcCCCCccCCCccchHHHHhCCCceehhhH
Confidence            4789999999999999999999866321  01112111110             00100000011111221    23355


Q ss_pred             hhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc--eeeecCCeEEEecCCCCcCcC
Q 012525          386 VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGLDSKTL  459 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~e~l  459 (461)
                      +..++++|||||||+.+..+              +++.|++.||.+.+.+...  ....+.++.+|+|+|..+...
T Consensus       290 l~~A~gGvLfLDEi~e~~~~--------------~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~  351 (506)
T PRK09862        290 ISLAHNGVLFLDELPEFERR--------------TLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGH  351 (506)
T ss_pred             hhhccCCEEecCCchhCCHH--------------HHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCcccee
Confidence            67789999999999998887              9999999999888876554  444567999999999986443

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.99  E-value=4.2e-10  Score=100.54  Aligned_cols=108  Identities=30%  Similarity=0.507  Sum_probs=74.4

Q ss_pred             CCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC---ceEEecchhhhhcCcccccHHHHHHHHHHhhc
Q 012525          307 AEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV---PFVIADATTLTQAGYVGEDVESILYKLLAQAE  383 (461)
Q Consensus       307 ~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~---pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~  383 (461)
                      .|..|+++.+....++....+|||+|++||||+++|++|+.....   +|+.+++..+.             .+++..  
T Consensus         3 ~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-------------~~~l~~--   67 (138)
T PF14532_consen    3 KSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-------------AELLEQ--   67 (138)
T ss_dssp             SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-------------HHHHHH--
T ss_pred             CCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-------------HHHHHH--
Confidence            344455555555555666789999999999999999999987653   77777777543             122222  


Q ss_pred             hhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          384 FNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       384 ~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                           +.+++|||+|||.|...              .|..|+..|+...          ..+..+|+|+..+.+.
T Consensus        68 -----a~~gtL~l~~i~~L~~~--------------~Q~~L~~~l~~~~----------~~~~RlI~ss~~~l~~  113 (138)
T PF14532_consen   68 -----AKGGTLYLKNIDRLSPE--------------AQRRLLDLLKRQE----------RSNVRLIASSSQDLEE  113 (138)
T ss_dssp             -----CTTSEEEEECGCCS-HH--------------HHHHHHHHHHHCT----------TTTSEEEEEECC-CCC
T ss_pred             -----cCCCEEEECChHHCCHH--------------HHHHHHHHHHhcC----------CCCeEEEEEeCCCHHH
Confidence                 37889999999999998              8999999998421          1245777777766554

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.99  E-value=2.9e-09  Score=113.51  Aligned_cols=109  Identities=27%  Similarity=0.358  Sum_probs=72.5

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|...+..            +                  ..+..+||+||+|+|||++|+++|+.
T Consensus        14 ~~~~d-iiGq~~~v~~L~~~i~~------------~------------------~i~ha~Lf~Gp~G~GKtt~A~~lAk~   62 (451)
T PRK06305         14 QTFSE-ILGQDAVVAVLKNALRF------------N------------------RAAHAYLFSGIRGTGKTTLARIFAKA   62 (451)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHc------------C------------------CCceEEEEEcCCCCCHHHHHHHHHHH
Confidence            45666 89999999988887731            0                  11255899999999999999999998


Q ss_pred             cCCc-------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          349 VNVP-------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       349 l~~p-------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      +...                         ++.++...     ..+   ...++.+..............||||||+|.|.
T Consensus        63 l~c~~~~~~~~~c~~c~~C~~i~~~~~~d~~~i~g~~-----~~g---id~ir~i~~~l~~~~~~~~~kvvIIdead~lt  134 (451)
T PRK06305         63 LNCQNPTEDQEPCNQCASCKEISSGTSLDVLEIDGAS-----HRG---IEDIRQINETVLFTPSKSRYKIYIIDEVHMLT  134 (451)
T ss_pred             hcCCCcccCCCCCcccHHHHHHhcCCCCceEEeeccc-----cCC---HHHHHHHHHHHHhhhhcCCCEEEEEecHHhhC
Confidence            7542                         11221110     111   12233333222222223567899999999998


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhC
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ..              .+++|++.||.
T Consensus       135 ~~--------------~~n~LLk~lEe  147 (451)
T PRK06305        135 KE--------------AFNSLLKTLEE  147 (451)
T ss_pred             HH--------------HHHHHHHHhhc
Confidence            77              78999999995

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.99  E-value=9.9e-10  Score=115.48  Aligned_cols=130  Identities=21%  Similarity=0.384  Sum_probs=97.4

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh-
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ-  381 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~-  381 (461)
                      +.+..+..+.+....+.....++|+.|++||||+++|++++...   +.+|+.++|..+.+.        ..-..+|.. 
T Consensus       147 ~~S~~~~~~~~~~~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~~--------~~~~~lfg~~  218 (457)
T PRK11361        147 TNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPES--------LLESELFGHE  218 (457)
T ss_pred             cccHHHhHHHHHHHHHcCCCcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCHH--------HHHHHhcCCC
Confidence            44566777777777777888999999999999999999998765   469999999877531        111122221 


Q ss_pred             ----------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEec
Q 012525          382 ----------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKT  451 (461)
Q Consensus       382 ----------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~T  451 (461)
                                ..+.+..+.+++||||||+.|...              +|..|+.+|+...+...........++.+|+|
T Consensus       219 ~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~~--------------~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~  284 (457)
T PRK11361        219 KGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLV--------------LQAKLLRILQEREFERIGGHQTIKVDIRIIAA  284 (457)
T ss_pred             CCCCCCCCCCCCCceEECCCCEEEEechhhCCHH--------------HHHHHHHHHhcCcEEeCCCCceeeeceEEEEe
Confidence                      123455678899999999999998              89999999998776544444444457899999


Q ss_pred             CCCCcC
Q 012525          452 SGLDSK  457 (461)
Q Consensus       452 sNid~e  457 (461)
                      +|.+.+
T Consensus       285 t~~~l~  290 (457)
T PRK11361        285 TNRDLQ  290 (457)
T ss_pred             CCCCHH
Confidence            998754

>PRK15115 response regulator GlrR; Provisional

Probab=98.99  E-value=1.9e-09  Score=113.12  Aligned_cols=130  Identities=21%  Similarity=0.362  Sum_probs=94.5

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh-
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ-  381 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~-  381 (461)
                      +.+..+....+....+.....+|+|.|++|||||++|+++++..   +.+|+.++|..+.+.        ..-..+|.. 
T Consensus       138 g~s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~~--------~~~~~lfg~~  209 (444)
T PRK15115        138 TRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQ--------LLESELFGHA  209 (444)
T ss_pred             ccCHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCHH--------HHHHHhcCCC
Confidence            34455555666666666677889999999999999999999875   469999999987531        111122221 


Q ss_pred             ----------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEec
Q 012525          382 ----------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKT  451 (461)
Q Consensus       382 ----------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~T  451 (461)
                                ..+.+..+.+++||||||+.|...              .|..|+..|+...+...........++.+|+|
T Consensus       210 ~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~--------------~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~  275 (444)
T PRK15115        210 RGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAP--------------LQVKLLRVLQERKVRPLGSNRDIDIDVRIISA  275 (444)
T ss_pred             cCCCCCCccCCCCcEEECCCCEEEEEccccCCHH--------------HHHHHHHHHhhCCEEeCCCCceeeeeEEEEEe
Confidence                      123456678899999999999998              89999999997776544333333347899999


Q ss_pred             CCCCcC
Q 012525          452 SGLDSK  457 (461)
Q Consensus       452 sNid~e  457 (461)
                      ++.++.
T Consensus       276 ~~~~l~  281 (444)
T PRK15115        276 THRDLP  281 (444)
T ss_pred             CCCCHH
Confidence            987753

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.98  E-value=2e-09  Score=111.27  Aligned_cols=56  Identities=21%  Similarity=0.223  Sum_probs=47.2

Q ss_pred             hhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          386 VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +..++.||+-|+|+.+...+              +++.||.+++++.+.+.......+.+.++|+|+|..
T Consensus       232 l~~aNrGi~~f~Ei~K~~~~--------------~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~  287 (361)
T smart00763      232 LNRANRGILEFVEMFKADIK--------------FLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNES  287 (361)
T ss_pred             cccccCceEEEeehhcCCHH--------------HHHHHhhhhhcceEecCCcccccccceEEEEeCCHH
Confidence            45577899999999999888              999999999999988776555666688999999965

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.97  E-value=4e-09  Score=117.45  Aligned_cols=117  Identities=24%  Similarity=0.327  Sum_probs=76.8

Q ss_pred             HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          268 CKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       268 ~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|++ |+||+.+++.|..++...                              ...+.+||+||+|||||++|+++|+
T Consensus        14 P~~f~d-IiGQe~~v~~L~~aI~~~------------------------------rl~HAYLF~GP~GtGKTt~AriLAk   62 (725)
T PRK07133         14 PKTFDD-IVGQDHIVQTLKNIIKSN------------------------------KISHAYLFSGPRGTGKTSVAKIFAN   62 (725)
T ss_pred             CCCHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCcHHHHHHHHHH
Confidence            345666 899999999998888310                              0124579999999999999999999


Q ss_pred             hcCCceEE---ecchhh---hh--cCcc-----c-ccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccccc
Q 012525          348 HVNVPFVI---ADATTL---TQ--AGYV-----G-EDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISR  413 (461)
Q Consensus       348 ~l~~pfv~---i~~s~l---~~--~g~v-----G-e~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~  413 (461)
                      .+.+.-..   -.|...   ..  ..++     + .. ...++.+..............|+||||+|.|...        
T Consensus        63 ~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaasn~~-vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~--------  133 (725)
T PRK07133         63 ALNCSHKTDLLEPCQECIENVNNSLDIIEMDAASNNG-VDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKS--------  133 (725)
T ss_pred             HhcccccCCCCCchhHHHHhhcCCCcEEEEeccccCC-HHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHH--------
Confidence            88653110   001000   00  0000     0 11 2335555555444434457789999999999877        


Q ss_pred             ccchHHHHHHHHHHHhC
Q 012525          414 DVSGEGVQQALLKMLEG  430 (461)
Q Consensus       414 ~~s~~~v~~aLL~~LEg  430 (461)
                            .+++||+.||+
T Consensus       134 ------A~NALLKtLEE  144 (725)
T PRK07133        134 ------AFNALLKTLEE  144 (725)
T ss_pred             ------HHHHHHHHhhc
Confidence                  89999999995

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.97  E-value=4.4e-09  Score=114.90  Aligned_cols=117  Identities=21%  Similarity=0.292  Sum_probs=74.4

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|...+...                              ..++.+||+||+|+|||++|++||+.
T Consensus        13 ~~f~d-iiGqe~iv~~L~~~i~~~------------------------------~i~hayLf~Gp~G~GKTt~Ar~lAk~   61 (563)
T PRK06647         13 RDFNS-LEGQDFVVETLKHSIESN------------------------------KIANAYIFSGPRGVGKTSSARAFARC   61 (563)
T ss_pred             CCHHH-ccCcHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            34565 899999999988888310                              01245899999999999999999998


Q ss_pred             cCCc-------eEEe-cchhhhhc---C---cccc--cHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          349 VNVP-------FVIA-DATTLTQA---G---YVGE--DVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       349 l~~p-------fv~i-~~s~l~~~---g---~vGe--~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                      +.+.       +-.+ +|-.+...   +   +-|.  .....++.+...........+..|+||||+|.|...       
T Consensus        62 L~c~~~~~~~pC~~C~~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~-------  134 (563)
T PRK06647         62 LNCVNGPTPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNS-------  134 (563)
T ss_pred             hccccCCCCCCCccchHHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHH-------
Confidence            8642       1100 01111100   0   0010  002333444433333333456779999999999877       


Q ss_pred             cccchHHHHHHHHHHHhC
Q 012525          413 RDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg  430 (461)
                             .+++||+.||.
T Consensus       135 -------a~naLLK~LEe  145 (563)
T PRK06647        135 -------AFNALLKTIEE  145 (563)
T ss_pred             -------HHHHHHHhhcc
Confidence                   89999999994

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.95  E-value=2e-09  Score=122.67  Aligned_cols=124  Identities=23%  Similarity=0.304  Sum_probs=85.6

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+. |+|++...+.+...+..                               ....|+||+||||||||++|+.||+.
T Consensus       184 ~~ld~-~iGr~~ei~~~i~~l~r-------------------------------~~~~n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       184 GKIDP-VLGRDDEIRQMIDILLR-------------------------------RRQNNPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             CCCCc-ccCCHHHHHHHHHHHhc-------------------------------CCcCceeEECCCCCCHHHHHHHHHHH
Confidence            34555 89999987777665521                               12368999999999999999999987


Q ss_pred             cC----------CceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccch
Q 012525          349 VN----------VPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSG  417 (461)
Q Consensus       349 l~----------~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~  417 (461)
                      +.          ..++.++...+.. ..+.|+. +..++.++......   ..+.||||||||.+...++.. .+.+   
T Consensus       232 i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~-e~~lk~ii~e~~~~---~~~~ILfIDEih~l~~~g~~~-~~~d---  303 (852)
T TIGR03345       232 IAAGDVPPALRNVRLLSLDLGLLQAGASVKGEF-ENRLKSVIDEVKAS---PQPIILFIDEAHTLIGAGGQA-GQGD---  303 (852)
T ss_pred             HhhCCCCccccCCeEEEeehhhhhcccccchHH-HHHHHHHHHHHHhc---CCCeEEEEeChHHhccCCCcc-cccc---
Confidence            62          3567777776653 3455554 78888888766421   257899999999998764321 1122   


Q ss_pred             HHHHHHHHHHHhCceee
Q 012525          418 EGVQQALLKMLEGTETK  434 (461)
Q Consensus       418 ~~v~~aLL~~LEg~~v~  434 (461)
                        +-+.|+..|+.+.+.
T Consensus       304 --~~n~Lkp~l~~G~l~  318 (852)
T TIGR03345       304 --AANLLKPALARGELR  318 (852)
T ss_pred             --HHHHhhHHhhCCCeE
Confidence              446788888855443

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.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.94  E-value=5.9e-09  Score=112.10  Aligned_cols=115  Identities=27%  Similarity=0.361  Sum_probs=72.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+||+.+++.|..++...                              ...+.+||+||+|+|||++|+.+|+.+
T Consensus        14 ~f~d-iiGq~~i~~~L~~~i~~~------------------------------~i~hayLf~Gp~G~GKTtlAr~lAk~L   62 (486)
T PRK14953         14 FFKE-VIGQEIVVRILKNAVKLQ------------------------------RVSHAYIFAGPRGTGKTTIARILAKVL   62 (486)
T ss_pred             cHHH-ccChHHHHHHHHHHHHcC------------------------------CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4555 899999999998888310                              002347899999999999999999988


Q ss_pred             CC-------ceEE-ecchhhhhc---Ccc------cccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          350 NV-------PFVI-ADATTLTQA---GYV------GEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       350 ~~-------pfv~-i~~s~l~~~---g~v------Ge~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                      ++       |+-. .+|..+...   +++      ... ...++.+..........+...|+||||+|.|...       
T Consensus        63 ~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eidaas~~g-vd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~-------  134 (486)
T PRK14953         63 NCLNPQEGEPCGKCENCVEIDKGSFPDLIEIDAASNRG-IDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKE-------  134 (486)
T ss_pred             cCcCCCCCCCCCccHHHHHHhcCCCCcEEEEeCccCCC-HHHHHHHHHHHHhCcccCCeeEEEEEChhhcCHH-------
Confidence            64       1100 111111100   000      001 1223344333333333456779999999999877       


Q ss_pred             cccchHHHHHHHHHHHhC
Q 012525          413 RDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg  430 (461)
                             .+++||+.|+.
T Consensus       135 -------a~naLLk~LEe  145 (486)
T PRK14953        135 -------AFNALLKTLEE  145 (486)
T ss_pred             -------HHHHHHHHHhc
Confidence                   78999999995

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.94  E-value=2.4e-09  Score=121.12  Aligned_cols=158  Identities=16%  Similarity=0.117  Sum_probs=96.5

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      +...+...|+|++.+|+.|...+.       ....+... ....++..  +...--....||||.|+||||||++|+.++
T Consensus       444 L~~SiaP~I~G~e~vK~ailL~L~-------gG~~k~~~-~~~~~dg~--~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih  513 (915)
T PTZ00111        444 LLDSFAPSIKARNNVKIGLLCQLF-------SGNKNSSD-FNKSPDAC--YKVDNFRGIINVLLCGDPGTAKSQLLHYTH  513 (915)
T ss_pred             HHHHhCCeEECCHHHHHHHHHHHh-------cCCccccc-cccccccc--cccccccCCceEEEeCCCCccHHHHHHHHH
Confidence            455556668999999988866652       11100000 00000000  000011334699999999999999999999


Q ss_pred             HhcC-------CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          347 RHVN-------VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       347 ~~l~-------~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      +...       .++..+.++....  +...     ....+....+.+..+.+|+++|||+++|...              
T Consensus       514 ~lspR~~ytsG~~~s~vgLTa~~~--~~d~-----~tG~~~le~GaLvlAdgGtL~IDEidkms~~--------------  572 (915)
T PTZ00111        514 LLSPRSIYTSGKSSSSVGLTASIK--FNES-----DNGRAMIQPGAVVLANGGVCCIDELDKCHNE--------------  572 (915)
T ss_pred             HhCCccccCCCCCCccccccchhh--hccc-----ccCcccccCCcEEEcCCCeEEecchhhCCHH--------------
Confidence            8653       2444444332211  0000     0011122234566788999999999999988              


Q ss_pred             HHHHHHHHHhCceeeeecc--eeeecCCeEEEecCCCC
Q 012525          420 VQQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid  455 (461)
                      .|.+|+++||...+.+.-.  ....+.++.+|+|+|.-
T Consensus       573 ~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~  610 (915)
T PTZ00111        573 SRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPI  610 (915)
T ss_pred             HHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCc
Confidence            8999999999887765432  45556689999999974

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.94  E-value=6.5e-09  Score=112.73  Aligned_cols=109  Identities=35%  Similarity=0.421  Sum_probs=74.0

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|..++...                              ..++.+||+||+|+|||++|+++|+.
T Consensus        11 ~~fde-iiGqe~v~~~L~~~I~~g------------------------------rl~hayLf~Gp~G~GKTt~Ar~LAk~   59 (535)
T PRK08451         11 KHFDE-LIGQESVSKTLSLALDNN------------------------------RLAHAYLFSGLRGSGKTSSARIFARA   59 (535)
T ss_pred             CCHHH-ccCcHHHHHHHHHHHHcC------------------------------CCCeeEEEECCCCCcHHHHHHHHHHH
Confidence            45666 899999999998888310                              01244699999999999999999998


Q ss_pred             cCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          349 VNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       349 l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +..                        .++.++...-     .  . -..++.+..........+...|+||||+|.|..
T Consensus        60 L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas~-----~--g-Id~IRelie~~~~~P~~~~~KVvIIDEad~Lt~  131 (535)
T PRK08451         60 LVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAASN-----R--G-IDDIRELIEQTKYKPSMARFKIFIIDEVHMLTK  131 (535)
T ss_pred             hcCCCCCCCCCCcccHHHHHHhhcCCCeEEEeccccc-----c--C-HHHHHHHHHHHhhCcccCCeEEEEEECcccCCH
Confidence            743                        1222222110     0  1 233444443322222234667999999999998


Q ss_pred             hhhccccccccchHHHHHHHHHHHhC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .              .+++||+.||.
T Consensus       132 ~--------------A~NALLK~LEE  143 (535)
T PRK08451        132 E--------------AFNALLKTLEE  143 (535)
T ss_pred             H--------------HHHHHHHHHhh
Confidence            8              89999999995

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.93  E-value=7.4e-09  Score=106.70  Aligned_cols=114  Identities=29%  Similarity=0.373  Sum_probs=74.2

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|...+..            +                  ..+.++||+||+|+|||++|+++|+.
T Consensus        14 ~~~~~-iig~~~~~~~l~~~i~~------------~------------------~~~~~~L~~G~~G~GKt~~a~~la~~   62 (367)
T PRK14970         14 QTFDD-VVGQSHITNTLLNAIEN------------N------------------HLAQALLFCGPRGVGKTTCARILARK   62 (367)
T ss_pred             CcHHh-cCCcHHHHHHHHHHHHc------------C------------------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45666 79999999988887731            0                  11367999999999999999999998


Q ss_pred             cCCceEEecc-------hhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHH
Q 012525          349 VNVPFVIADA-------TTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQ  421 (461)
Q Consensus       349 l~~pfv~i~~-------s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~  421 (461)
                      +..+......       .++....  ... ...++.++..+.......+..||||||+|.+...              .+
T Consensus        63 l~~~~~~~~~~~~~~~~~~l~~~~--~~~-~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~~--------------~~  125 (367)
T PRK14970         63 INQPGYDDPNEDFSFNIFELDAAS--NNS-VDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSA--------------AF  125 (367)
T ss_pred             hcCCCCCCCCCCCCcceEEecccc--CCC-HHHHHHHHHHHhhccccCCcEEEEEeChhhcCHH--------------HH
Confidence            8652211100       0111000  011 2445555554332222346679999999988876              68


Q ss_pred             HHHHHHHhC
Q 012525          422 QALLKMLEG  430 (461)
Q Consensus       422 ~aLL~~LEg  430 (461)
                      +.|++.|++
T Consensus       126 ~~ll~~le~  134 (367)
T PRK14970        126 NAFLKTLEE  134 (367)
T ss_pred             HHHHHHHhC
Confidence            899999985

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.90  E-value=4.9e-09  Score=119.62  Aligned_cols=121  Identities=26%  Similarity=0.352  Sum_probs=83.2

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .++. |+|++...+.+...+..                               ....+++|+||||||||++|++||+.+
T Consensus       171 ~~~~-~igr~~ei~~~~~~l~r-------------------------------~~~~n~lL~G~pGvGKT~l~~~la~~i  218 (852)
T TIGR03346       171 KLDP-VIGRDEEIRRTIQVLSR-------------------------------RTKNNPVLIGEPGVGKTAIVEGLAQRI  218 (852)
T ss_pred             CCCc-CCCcHHHHHHHHHHHhc-------------------------------CCCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            4454 89999987777776631                               123789999999999999999999875


Q ss_pred             ----------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          350 ----------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       350 ----------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                                +.+++.++...+.. ..|.|+. +..+..++......   ..+.||||||||.|.......      +..
T Consensus       219 ~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~-e~~l~~~l~~~~~~---~~~~ILfIDEih~l~~~g~~~------~~~  288 (852)
T TIGR03346       219 VNGDVPESLKNKRLLALDMGALIAGAKYRGEF-EERLKAVLNEVTKS---EGQIILFIDELHTLVGAGKAE------GAM  288 (852)
T ss_pred             hccCCchhhcCCeEEEeeHHHHhhcchhhhhH-HHHHHHHHHHHHhc---CCCeEEEeccHHHhhcCCCCc------chh
Confidence                      56788888776642 2455544 77778887755321   257899999999998642211      111


Q ss_pred             HHHHHHHHHHhCce
Q 012525          419 GVQQALLKMLEGTE  432 (461)
Q Consensus       419 ~v~~aLL~~LEg~~  432 (461)
                      .+.+.|..+|+.+.
T Consensus       289 d~~~~Lk~~l~~g~  302 (852)
T TIGR03346       289 DAGNMLKPALARGE  302 (852)
T ss_pred             HHHHHhchhhhcCc
Confidence            25666766666443

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.

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=98.90  E-value=2.8e-09  Score=109.35  Aligned_cols=130  Identities=25%  Similarity=0.387  Sum_probs=99.5

Q ss_pred             CCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhh-
Q 012525          307 AEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQA-  382 (461)
Q Consensus       307 ~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a-  382 (461)
                      .|..|+.++....+++....++||.|++||||.++||+.+...   ..||+.++|+.+-+.     ..|   .++|..+ 
T Consensus       209 ~S~~mk~~v~qA~k~AmlDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNCA~lPe~-----~aE---sElFG~ap  280 (511)
T COG3283         209 VSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLPED-----AAE---SELFGHAP  280 (511)
T ss_pred             ccHHHHHHHHHHHHhhccCCCeEEecCCCchHHHHHHHHhhcCcccCCCeeEeecCCCchh-----HhH---HHHhcCCC
Confidence            3455556666666677778899999999999999999998755   569999999987652     122   2334332 


Q ss_pred             -----chhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          383 -----EFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       383 -----~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                           .+.++.+++|.+|+|||..|++.              +|..||++|..+.++.....+.+-.|..+|+||.....
T Consensus       281 g~~gk~GffE~AngGTVlLDeIgEmSp~--------------lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~  346 (511)
T COG3283         281 GDEGKKGFFEQANGGTVLLDEIGEMSPR--------------LQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLV  346 (511)
T ss_pred             CCCCccchhhhccCCeEEeehhhhcCHH--------------HHHHHHHHhcCCceeecCCcceEEEEEEEEecccccHH
Confidence                 24466788999999999999999              99999999998888776665555558999999877654


Q ss_pred             c
Q 012525          458 T  458 (461)
Q Consensus       458 ~  458 (461)
                      +
T Consensus       347 ~  347 (511)
T COG3283         347 E  347 (511)
T ss_pred             H
Confidence            3

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.90  E-value=6.4e-09  Score=114.03  Aligned_cols=115  Identities=11%  Similarity=0.063  Sum_probs=91.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC--ceEEecchhhhhcCcccccHHHHHHHHHH-hhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV--PFVIADATTLTQAGYVGEDVESILYKLLA-QAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~--pfv~i~~s~l~~~g~vGe~~e~~L~~lf~-~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      .+|||.|+.||+||+++++|+..+..  ||+.+..+.-...-+.|-+++..|..--. ...+.+..++++||||||++.+
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            67999999999999999999999854  88877776544432233455555544332 4566778899999999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhCceeeeecc--eeeecCCeEEEecCCC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGL  454 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNi  454 (461)
                      .++              ++++|++.||.++++|...  ...++.+|++|+|.|.
T Consensus       106 ~~~--------------~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~  145 (584)
T PRK13406        106 EPG--------------TAARLAAALDTGEVRLERDGLALRLPARFGLVALDEG  145 (584)
T ss_pred             CHH--------------HHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCC
Confidence            998              9999999999998888444  7788889999999654

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.89  E-value=5.8e-09  Score=114.98  Aligned_cols=56  Identities=29%  Similarity=0.469  Sum_probs=44.1

Q ss_pred             hhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc----------eeeecCCeEEEecCCCC
Q 012525          386 VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA----------VSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~----------~r~~~rd~IiI~TsNid  455 (461)
                      ++.+++|+|||||++.|...              .|..|++.|+..++.+...          ....+.++.+|+++|.+
T Consensus       213 L~~AngGtL~Ldei~~L~~~--------------~q~~Ll~~L~~~~i~~~g~~e~~~~~~~~~~~ip~dvrvIa~~~~~  278 (608)
T TIGR00764       213 IHRAHKGVLYIDEIKTMPLE--------------VQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLD  278 (608)
T ss_pred             eEECCCCEEEEEChHhCCHH--------------HHHHHHHHHHhCcEEecCccccccccccCCCCCccceEEEEECCHH
Confidence            44677899999999999987              8999999999887766432          12334589999999976

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

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

Probab=98.89  E-value=4.3e-09  Score=118.45  Aligned_cols=120  Identities=26%  Similarity=0.379  Sum_probs=80.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      ++. ++|.+...+.+...+..                               ..+.++||+||||||||++|+.+|..+ 
T Consensus       185 ~~~-liGR~~ei~~~i~iL~r-------------------------------~~~~n~LLvGppGvGKT~lae~la~~i~  232 (758)
T PRK11034        185 IDP-LIGREKELERAIQVLCR-------------------------------RRKNNPLLVGESGVGKTAIAEGLAWRIV  232 (758)
T ss_pred             CCc-CcCCCHHHHHHHHHHhc-------------------------------cCCCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            444 88999888888877731                               123789999999999999999999764 


Q ss_pred             ---------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          350 ---------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       350 ---------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                               +..++.++...+.. ..|.|+. +..++.++....    ...++||||||||.|...+...+     ....
T Consensus       233 ~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~-e~rl~~l~~~l~----~~~~~ILfIDEIh~L~g~g~~~~-----g~~d  302 (758)
T PRK11034        233 QGDVPEVMADCTIYSLDIGSLLAGTKYRGDF-EKRFKALLKQLE----QDTNSILFIDEIHTIIGAGAASG-----GQVD  302 (758)
T ss_pred             hcCCCchhcCCeEEeccHHHHhcccchhhhH-HHHHHHHHHHHH----hcCCCEEEeccHHHHhccCCCCC-----cHHH
Confidence                     34555666555442 2345544 677777776543    23678999999999987632111     1222


Q ss_pred             HHHHHHHHHhCce
Q 012525          420 VQQALLKMLEGTE  432 (461)
Q Consensus       420 v~~aLL~~LEg~~  432 (461)
                      +.+.|..+|+.+.
T Consensus       303 ~~nlLkp~L~~g~  315 (758)
T PRK11034        303 AANLIKPLLSSGK  315 (758)
T ss_pred             HHHHHHHHHhCCC
Confidence            5666777776443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.89  E-value=9.1e-09  Score=86.93  Aligned_cols=77  Identities=29%  Similarity=0.411  Sum_probs=53.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc---eEEecchhhhhc------------CcccccHHHHHHHHHHhhchhhhcc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP---FVIADATTLTQA------------GYVGEDVESILYKLLAQAEFNVEAA  389 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p---fv~i~~s~l~~~------------g~vGe~~e~~L~~lf~~a~~~v~~a  389 (461)
                      ..+++|+||||||||++++.||..+...   ++.+++......            ..........+..++..+...    
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----   77 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKL----   77 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhc----
Confidence            3679999999999999999999999775   777777654321            011112234444555444432    


Q ss_pred             CceEEEEcCccccchh
Q 012525          390 QQGMVYIDEVDKITKK  405 (461)
Q Consensus       390 ~~gVLfIDEID~L~~~  405 (461)
                      ...||||||++.+...
T Consensus        78 ~~~viiiDei~~~~~~   93 (148)
T smart00382       78 KPDVLILDEITSLLDA   93 (148)
T ss_pred             CCCEEEEECCcccCCH
Confidence            3589999999998887

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.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.88  E-value=2e-08  Score=100.18  Aligned_cols=113  Identities=28%  Similarity=0.390  Sum_probs=71.3

Q ss_pred             HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHH
Q 012525          266 EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       266 el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraL  345 (461)
                      .-.+.|++ ++|++++++.|...+..                               ....+++|+||+|||||++|+++
T Consensus        11 yrP~~~~~-~~g~~~~~~~l~~~i~~-------------------------------~~~~~~ll~G~~G~GKt~~~~~l   58 (319)
T PRK00440         11 YRPRTLDE-IVGQEEIVERLKSYVKE-------------------------------KNMPHLLFAGPPGTGKTTAALAL   58 (319)
T ss_pred             hCCCcHHH-hcCcHHHHHHHHHHHhC-------------------------------CCCCeEEEECCCCCCHHHHHHHH
Confidence            33356676 68999999988877720                               01246999999999999999999


Q ss_pred             HHhcCC-----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          346 ARHVNV-----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       346 A~~l~~-----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      ++.+..     .++.+++++....    ......+.......  .+......+|+|||+|.+...              .
T Consensus        59 ~~~l~~~~~~~~~i~~~~~~~~~~----~~~~~~i~~~~~~~--~~~~~~~~vviiDe~~~l~~~--------------~  118 (319)
T PRK00440         59 ARELYGEDWRENFLELNASDERGI----DVIRNKIKEFARTA--PVGGAPFKIIFLDEADNLTSD--------------A  118 (319)
T ss_pred             HHHHcCCccccceEEeccccccch----HHHHHHHHHHHhcC--CCCCCCceEEEEeCcccCCHH--------------H
Confidence            998733     3444444332210    00111122211111  111134669999999999776              6


Q ss_pred             HHHHHHHHhC
Q 012525          421 QQALLKMLEG  430 (461)
Q Consensus       421 ~~aLL~~LEg  430 (461)
                      ++.|+.+|+.
T Consensus       119 ~~~L~~~le~  128 (319)
T PRK00440        119 QQALRRTMEM  128 (319)
T ss_pred             HHHHHHHHhc
Confidence            7889988874

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.87  E-value=1.6e-08  Score=111.56  Aligned_cols=109  Identities=27%  Similarity=0.364  Sum_probs=75.2

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++ |+||+.+++.|...+...                              ..++.+||+||+|+|||++|+++|+.
T Consensus        14 ~~f~~-viGq~~~~~~L~~~i~~~------------------------------~l~hayLf~Gp~G~GKtt~A~~lAk~   62 (614)
T PRK14971         14 STFES-VVGQEALTTTLKNAIATN------------------------------KLAHAYLFCGPRGVGKTTCARIFAKT   62 (614)
T ss_pred             CCHHH-hcCcHHHHHHHHHHHHcC------------------------------CCCeeEEEECCCCCCHHHHHHHHHHH
Confidence            34566 899999999998887310                              01244899999999999999999998


Q ss_pred             cCCc-------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          349 VNVP-------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       349 l~~p-------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      +.+.                         ++.+++...       .. ...++.+...+......+...|+||||+|.|.
T Consensus        63 l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~~ld~~~~-------~~-vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls  134 (614)
T PRK14971         63 INCQNLTADGEACNECESCVAFNEQRSYNIHELDAASN-------NS-VDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLS  134 (614)
T ss_pred             hCCCCCCCCCCCCCcchHHHHHhcCCCCceEEeccccc-------CC-HHHHHHHHHHHhhCcccCCcEEEEEECcccCC
Confidence            8632                         222222110       01 23445555444333334567799999999998


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhC
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ..              .+++||+.||.
T Consensus       135 ~~--------------a~naLLK~LEe  147 (614)
T PRK14971        135 QA--------------AFNAFLKTLEE  147 (614)
T ss_pred             HH--------------HHHHHHHHHhC
Confidence            87              89999999994

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=98.86  E-value=1.7e-08  Score=101.60  Aligned_cols=152  Identities=23%  Similarity=0.288  Sum_probs=101.8

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .....+++.|+..++||.-+++.+..++..++..-             .+           ..+-.+-|+|++||||..+
T Consensus        71 ~~~~~Le~dL~~~lfGQHla~~~Vv~alk~~~~n~-------------~p-----------~KPLvLSfHG~tGTGKN~V  126 (344)
T KOG2170|consen   71 NDLDGLEKDLARALFGQHLAKQLVVNALKSHWANP-------------NP-----------RKPLVLSFHGWTGTGKNYV  126 (344)
T ss_pred             ccchHHHHHHHHHhhchHHHHHHHHHHHHHHhcCC-------------CC-----------CCCeEEEecCCCCCchhHH
Confidence            34567999999999999999999999997654321             01           1123355999999999999


Q ss_pred             HHHHHHhcC-----CceEEecchhhhhcCcccc-cHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccccccc
Q 012525          342 AKTLARHVN-----VPFVIADATTLTQAGYVGE-DVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDV  415 (461)
Q Consensus       342 AraLA~~l~-----~pfv~i~~s~l~~~g~vGe-~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~  415 (461)
                      ++.||+.+-     .+||..-.+...   +.-. .++..-.++-.+....+..++.+++++||+|+|.+.          
T Consensus       127 a~iiA~n~~~~Gl~S~~V~~fvat~h---FP~~~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKmp~g----------  193 (344)
T KOG2170|consen  127 AEIIAENLYRGGLRSPFVHHFVATLH---FPHASKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKLPPG----------  193 (344)
T ss_pred             HHHHHHHHHhccccchhHHHhhhhcc---CCChHHHHHHHHHHHHHHHHHHHhcCCceEEechhhhcCHh----------
Confidence            999999773     244322222111   1111 123333344455566677889999999999999998          


Q ss_pred             chHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          416 SGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       416 s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                          ++++|-..||-.....    ....+..|+|..+|.+-.+
T Consensus       194 ----Lld~lkpfLdyyp~v~----gv~frkaIFIfLSN~gg~e  228 (344)
T KOG2170|consen  194 ----LLDVLKPFLDYYPQVS----GVDFRKAIFIFLSNAGGSE  228 (344)
T ss_pred             ----HHHHHhhhhccccccc----cccccceEEEEEcCCcchH
Confidence                8899988888322111    1122368999999987544

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=98.84  E-value=1.2e-09  Score=118.34  Aligned_cols=137  Identities=22%  Similarity=0.335  Sum_probs=104.0

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc--CCceEEecchhhhhc----CcccccHHHHHHHHH
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV--NVPFVIADATTLTQA----GYVGEDVESILYKLL  379 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l--~~pfv~i~~s~l~~~----g~vGe~~e~~L~~lf  379 (461)
                      ..+.......+....+.....+|||.|+|||||..+||+|++..  ..||+.++|..+.+.    .++|.. ...+...+
T Consensus       317 ~~d~s~a~l~rk~~rv~~~~~pvll~GEtGtGKe~laraiH~~s~~~gpfvAvNCaAip~~liesELFGy~-~GafTga~  395 (606)
T COG3284         317 LLDPSRATLLRKAERVAATDLPVLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPEALIESELFGYV-AGAFTGAR  395 (606)
T ss_pred             ccCHHHHHHHHHHHHHhhcCCCeEecCCcchhHHHHHHHHHhcccccCCeEEEEeccchHHhhhHHHhccC-ccccccch
Confidence            34455666666777788888999999999999999999999765  459999999876643    122222 11111111


Q ss_pred             -HhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          380 -AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       380 -~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                       ....+.++.++++.+|+|||..|...              +|..||++|+++++.-....+ .+.|+.+|++|+-|.+.
T Consensus       396 ~kG~~g~~~~A~gGtlFldeIgd~p~~--------------~Qs~LLrVl~e~~v~p~g~~~-~~vdirvi~ath~dl~~  460 (606)
T COG3284         396 RKGYKGKLEQADGGTLFLDEIGDMPLA--------------LQSRLLRVLQEGVVTPLGGTR-IKVDIRVIAATHRDLAQ  460 (606)
T ss_pred             hccccccceecCCCccHHHHhhhchHH--------------HHHHHHHHHhhCceeccCCcc-eeEEEEEEeccCcCHHH
Confidence             22345577789999999999999988              999999999999888766666 67799999999988754

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.81  E-value=1e-08  Score=108.17  Aligned_cols=133  Identities=23%  Similarity=0.373  Sum_probs=94.8

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHH------
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILY------  376 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~------  376 (461)
                      +.++.+..+.+....+.....++++.|++||||+++|+++++..   ..+|+.++|..+.+.     ..+..+.      
T Consensus       138 g~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~~-----~~~~~lfg~~~~~  212 (463)
T TIGR01818       138 GEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKD-----LIESELFGHEKGA  212 (463)
T ss_pred             ecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCHH-----HHHHHhcCCCCCC
Confidence            34456666666666667777889999999999999999999875   469999999877531     1111110      


Q ss_pred             --HHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          377 --KLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       377 --~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                        .......+.+..+.+++||||||+.|...              +|..|+++|+.+.+...........+..+|+|++.
T Consensus       213 ~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~~--------------~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~  278 (463)
T TIGR01818       213 FTGANTRRQGRFEQADGGTLFLDEIGDMPLD--------------AQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQ  278 (463)
T ss_pred             CCCcccCCCCcEEECCCCeEEEEchhhCCHH--------------HHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCC
Confidence              00111223355678899999999999998              89999999997776554443333347789999988


Q ss_pred             CcC
Q 012525          455 DSK  457 (461)
Q Consensus       455 d~e  457 (461)
                      +.+
T Consensus       279 ~l~  281 (463)
T TIGR01818       279 NLE  281 (463)
T ss_pred             CHH
Confidence            754

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.

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.81  E-value=1.7e-08  Score=105.51  Aligned_cols=130  Identities=22%  Similarity=0.364  Sum_probs=96.3

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh-
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ-  381 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~-  381 (461)
                      +.+..+....+.+..++.....++++|++||||+++|++++...   ..+|+.++|..+...        ..-..+|.. 
T Consensus       143 g~s~~~~~~~~~i~~~~~~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~~--------~~~~~lfg~~  214 (441)
T PRK10365        143 GKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNES--------LLESELFGHE  214 (441)
T ss_pred             ecCHHHHHHHHHHhhccCCCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCHH--------HHHHHhcCCC
Confidence            34556666666677777788999999999999999999999765   469999999976531        111112221 


Q ss_pred             ----------hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEec
Q 012525          382 ----------AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKT  451 (461)
Q Consensus       382 ----------a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~T  451 (461)
                                ..+.+..+.+|+||||||+.|...              +|..|+..|+...+...........++.+|+|
T Consensus       215 ~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~~--------------~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~  280 (441)
T PRK10365        215 KGAFTGADKRREGRFVEADGGTLFLDEIGDISPM--------------MQVRLLRAIQEREVQRVGSNQTISVDVRLIAA  280 (441)
T ss_pred             CCCcCCCCcCCCCceeECCCCEEEEeccccCCHH--------------HHHHHHHHHccCcEEeCCCCceeeeceEEEEe
Confidence                      123355678999999999999998              89999999998776655554444557889988


Q ss_pred             CCCCcC
Q 012525          452 SGLDSK  457 (461)
Q Consensus       452 sNid~e  457 (461)
                      ++.++.
T Consensus       281 t~~~~~  286 (441)
T PRK10365        281 THRDLA  286 (441)
T ss_pred             CCCCHH
Confidence            887753

>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=98.81  E-value=6e-08  Score=89.64  Aligned_cols=106  Identities=28%  Similarity=0.407  Sum_probs=69.8

Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCc----
Q 012525          277 GQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVP----  352 (461)
Q Consensus       277 Gqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~p----  352 (461)
                      ||+++++.|...+...                              ..+..+||+||.|+||+++|+++|+.+...    
T Consensus         1 gq~~~~~~L~~~~~~~------------------------------~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~   50 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSG------------------------------RLPHALLFHGPSGSGKKTLALAFARALLCSNPNE   50 (162)
T ss_dssp             S-HHHHHHHHHHHHCT------------------------------C--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CT
T ss_pred             CcHHHHHHHHHHHHcC------------------------------CcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCC
Confidence            7888888888877310                              113558999999999999999999977431    


Q ss_pred             -------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccccc
Q 012525          353 -------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISR  413 (461)
Q Consensus       353 -------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~  413 (461)
                                         ++.+.......    .-. .+.++.+.............-|++|||+|+|...        
T Consensus        51 ~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~----~i~-i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~~--------  117 (162)
T PF13177_consen   51 DPCGECRSCRRIEEGNHPDFIIIKPDKKKK----SIK-IDQIREIIEFLSLSPSEGKYKVIIIDEADKLTEE--------  117 (162)
T ss_dssp             T--SSSHHHHHHHTT-CTTEEEEETTTSSS----SBS-HHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-HH--------
T ss_pred             CCCCCCHHHHHHHhccCcceEEEecccccc----hhh-HHHHHHHHHHHHHHHhcCCceEEEeehHhhhhHH--------
Confidence                               22221111100    012 3455566665554444457789999999999999        


Q ss_pred             ccchHHHHHHHHHHHhCc
Q 012525          414 DVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       414 ~~s~~~v~~aLL~~LEg~  431 (461)
                            .+++||+.||+-
T Consensus       118 ------a~NaLLK~LEep  129 (162)
T PF13177_consen  118 ------AQNALLKTLEEP  129 (162)
T ss_dssp             ------HHHHHHHHHHST
T ss_pred             ------HHHHHHHHhcCC
Confidence                  999999999954

...

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.80  E-value=4.7e-08  Score=101.70  Aligned_cols=112  Identities=24%  Similarity=0.291  Sum_probs=73.2

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |+||+.+++.|..++...                              ..++.+||+||+|+||+++|.++|+.+.+.--
T Consensus        21 iiGq~~~~~~L~~~~~~~------------------------------rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~   70 (365)
T PRK07471         21 LFGHAAAEAALLDAYRSG------------------------------RLHHAWLIGGPQGIGKATLAYRMARFLLATPP   70 (365)
T ss_pred             ccChHHHHHHHHHHHHcC------------------------------CCCceEEEECCCCCCHHHHHHHHHHHHhCCCC
Confidence            899999999999888310                              11245999999999999999999997743100


Q ss_pred             ---------------Eecc---hhhhh---cCc--c-------c-----ccHHHHHHHHHHhhchhhhccCceEEEEcCc
Q 012525          355 ---------------IADA---TTLTQ---AGY--V-------G-----EDVESILYKLLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       355 ---------------~i~~---s~l~~---~g~--v-------G-----e~~e~~L~~lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                                     .-.|   ..+..   .++  +       +     .-..+.++.+............+.||+|||+
T Consensus        71 ~~~~~~~~~~~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDea  150 (365)
T PRK07471         71 PGGDGAVPPPTSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTA  150 (365)
T ss_pred             CCCCccccccccccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEech
Confidence                           0000   00000   000  0       0     0012345555555444444556779999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      |.|...              .+++||+.||+
T Consensus       151 d~m~~~--------------aanaLLK~LEe  167 (365)
T PRK07471        151 DEMNAN--------------AANALLKVLEE  167 (365)
T ss_pred             HhcCHH--------------HHHHHHHHHhc
Confidence            999988              89999999995

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.79  E-value=5.1e-08  Score=98.70  Aligned_cols=109  Identities=19%  Similarity=0.309  Sum_probs=73.6

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |++ |+||+.+++.|...+..            +                  .-++.+||+||.|+|||++|+++|+.+.
T Consensus         3 ~~~-i~g~~~~~~~l~~~~~~------------~------------------~~~ha~Lf~G~~G~Gk~~la~~~a~~l~   51 (313)
T PRK05564          3 FHT-IIGHENIKNRIKNSIIK------------N------------------RFSHAHIIVGEDGIGKSLLAKEIALKIL   51 (313)
T ss_pred             hhh-ccCcHHHHHHHHHHHHc------------C------------------CCCceEEeECCCCCCHHHHHHHHHHHHc
Confidence            455 89999999998887731            0                  1124579999999999999999999774


Q ss_pred             C--------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          351 V--------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       351 ~--------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                      +        .+..+...+   ....  . ...++.+...........+..|++|||+|+|...              .+|
T Consensus        52 c~~~~~~h~D~~~~~~~~---~~~i--~-v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~--------------a~n  111 (313)
T PRK05564         52 GKSQQREYVDIIEFKPIN---KKSI--G-VDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQ--------------AQN  111 (313)
T ss_pred             CCCCCCCCCCeEEecccc---CCCC--C-HHHHHHHHHHHhcCcccCCceEEEEechhhcCHH--------------HHH
Confidence            3        222222210   0001  1 2335555543333333456779999999999988              899


Q ss_pred             HHHHHHhC
Q 012525          423 ALLKMLEG  430 (461)
Q Consensus       423 aLL~~LEg  430 (461)
                      +||+.||+
T Consensus       112 aLLK~LEe  119 (313)
T PRK05564        112 AFLKTIEE  119 (313)
T ss_pred             HHHHHhcC
Confidence            99999995

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=98.78  E-value=3.2e-08  Score=105.13  Aligned_cols=118  Identities=25%  Similarity=0.362  Sum_probs=70.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC--c-----eEEecch----hhhhcCc----ccccH-HHHHHHHHHhhchhhhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV--P-----FVIADAT----TLTQAGY----VGEDV-ESILYKLLAQAEFNVEA  388 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~--p-----fv~i~~s----~l~~~g~----vGe~~-e~~L~~lf~~a~~~v~~  388 (461)
                      ..+++|+||||||||++|+.||+.+..  .     ++.+...    ++.. ++    +|... ...+.++...+...  .
T Consensus       194 ~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~-G~rP~~vgy~~~~G~f~~~~~~A~~~--p  270 (459)
T PRK11331        194 KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQ-GYRPNGVGFRRKDGIFYNFCQQAKEQ--P  270 (459)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhc-ccCCCCCCeEecCchHHHHHHHHHhc--c
Confidence            478999999999999999999998743  1     2222211    1110 11    11110 11233333333321  1


Q ss_pred             cCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCce----eeee----c---ceeeecCCeEEEecCCCCcC
Q 012525          389 AQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTE----TKTF----A---AVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       389 a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~----v~i~----~---~~r~~~rd~IiI~TsNid~e  457 (461)
                      .++.|||||||++....+             +...|+.+||...    ..++    .   .....+.++.+|+|+|....
T Consensus       271 ~~~~vliIDEINRani~k-------------iFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMNt~Dr  337 (459)
T PRK11331        271 EKKYVFIIDEINRANLSK-------------VFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYIIGLMNTADR  337 (459)
T ss_pred             cCCcEEEEehhhccCHHH-------------hhhhhhhhccccccccccceeeeccccccccccCCCCeEEEEecCcccc
Confidence            256899999999877552             6778888888321    1111    1   12355669999999998764


Q ss_pred             c
Q 012525          458 T  458 (461)
Q Consensus       458 ~  458 (461)
                      .
T Consensus       338 s  338 (459)
T PRK11331        338 S  338 (459)
T ss_pred             c
Confidence            4

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=98.78  E-value=1.2e-08  Score=112.71  Aligned_cols=57  Identities=23%  Similarity=0.438  Sum_probs=44.7

Q ss_pred             hhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc----------eeeecCCeEEEecCCCC
Q 012525          386 VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA----------VSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~----------~r~~~rd~IiI~TsNid  455 (461)
                      ++.+++|+|||||++.|.+.              +|..|++.|+.+++.+...          ....+.++.+|+++|.+
T Consensus       222 L~kAnGGtL~LDei~~L~~~--------------~q~~Llr~L~~~~i~i~g~~e~~~~~~~~~~~ip~dvrvI~a~~~~  287 (637)
T PRK13765        222 IHKAHKGVLFIDEINTLDLE--------------SQQSLLTAMQEKKFPITGQSERSSGAMVRTEPVPCDFIMVAAGNLD  287 (637)
T ss_pred             eeECCCcEEEEeChHhCCHH--------------HHHHHHHHHHhCCEEecccccccccccCCCcceeeeeEEEEecCcC
Confidence            45678899999999999777              8999999999887766432          23344588999999987


Q ss_pred             c
Q 012525          456 S  456 (461)
Q Consensus       456 ~  456 (461)
                      .
T Consensus       288 l  288 (637)
T PRK13765        288 A  288 (637)
T ss_pred             H
Confidence            4

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.78  E-value=6.4e-08  Score=106.44  Aligned_cols=88  Identities=24%  Similarity=0.329  Sum_probs=64.8

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      ..+-+||+||||.||||||+.+|+++|..++++++++-...    ..+...+..+...-...-...+|..|+|||||-..
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqaGYsVvEINASDeRt~----~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~  400 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQAGYSVVEINASDERTA----PMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAP  400 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhcCceEEEecccccccH----HHHHHHHHHHHhhccccccCCCcceEEEecccCCc
Confidence            34667899999999999999999999999999999987753    23333333333322211122577889999999766


Q ss_pred             hhhhccccccccchHHHHHHHHHHHh
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ..              +++.||.++.
T Consensus       401 ~~--------------~Vdvilslv~  412 (877)
T KOG1969|consen  401 RA--------------AVDVILSLVK  412 (877)
T ss_pred             HH--------------HHHHHHHHHH
Confidence            54              7888888887

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.73  E-value=4.7e-08  Score=93.07  Aligned_cols=65  Identities=25%  Similarity=0.335  Sum_probs=47.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      ..+++|+||+|||||++|+++++.+   +.+++.+++..+... .         ...+...      ....+|||||++.
T Consensus        38 ~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~~~-~---------~~~~~~~------~~~~lLvIDdi~~  101 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQA-D---------PEVLEGL------EQADLVCLDDVEA  101 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHHHh-H---------HHHHhhc------ccCCEEEEeChhh
Confidence            3679999999999999999999876   457888888877631 0         1112111      1345999999998


Q ss_pred             cchh
Q 012525          402 ITKK  405 (461)
Q Consensus       402 L~~~  405 (461)
                      +...
T Consensus       102 l~~~  105 (226)
T TIGR03420       102 IAGQ  105 (226)
T ss_pred             hcCC
Confidence            8764

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=98.72  E-value=1e-07  Score=97.31  Aligned_cols=115  Identities=22%  Similarity=0.268  Sum_probs=74.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |++ |+||+.+++.|..++...                              ..++.+||+||.|+||+++|+++|+.+.
T Consensus         3 f~~-iiGq~~~~~~L~~~i~~~------------------------------rl~ha~Lf~G~~G~Gk~~~A~~~a~~ll   51 (314)
T PRK07399          3 FAN-LIGQPLAIELLTAAIKQN------------------------------RIAPAYLFAGPEGVGRKLAALCFIEGLL   51 (314)
T ss_pred             HHH-hCCHHHHHHHHHHHHHhC------------------------------CCCceEEEECCCCCCHHHHHHHHHHHHc
Confidence            344 899999999999988310                              1136799999999999999999999774


Q ss_pred             Cc------------------eEEecchhhhhcC--------ccc-------ccHHHHHHHHHHhhchhhhccCceEEEEc
Q 012525          351 VP------------------FVIADATTLTQAG--------YVG-------EDVESILYKLLAQAEFNVEAAQQGMVYID  397 (461)
Q Consensus       351 ~p------------------fv~i~~s~l~~~g--------~vG-------e~~e~~L~~lf~~a~~~v~~a~~gVLfID  397 (461)
                      +.                  ++.+.........        ..|       .--...++.+..........+...|++||
T Consensus        52 c~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~  131 (314)
T PRK07399         52 SQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIE  131 (314)
T ss_pred             CCCCCCCcHhcccccCCCCCEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEE
Confidence            31                  1222211000000        000       00012344554444433334567899999


Q ss_pred             CccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          398 EVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       398 EID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ++|+|...              ..|+||+.||+
T Consensus       132 ~ae~m~~~--------------aaNaLLK~LEE  150 (314)
T PRK07399        132 DAETMNEA--------------AANALLKTLEE  150 (314)
T ss_pred             chhhcCHH--------------HHHHHHHHHhC
Confidence            99999988              89999999995

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.72  E-value=6.7e-08  Score=90.34  Aligned_cols=84  Identities=24%  Similarity=0.354  Sum_probs=56.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQ  381 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~  381 (461)
                      ..+||+||+|+|||++|+.+++.+...                        |..+....    ...  . .+.++.+...
T Consensus        15 ~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~----~~~--~-~~~i~~i~~~   87 (188)
T TIGR00678        15 HAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEG----QSI--K-VDQVRELVEF   87 (188)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEecccc----CcC--C-HHHHHHHHHH
Confidence            569999999999999999999987432                        11111110    001  1 2344444444


Q ss_pred             hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       382 a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ...........||||||+|.|...              .++.||+.||.
T Consensus        88 ~~~~~~~~~~kviiide~~~l~~~--------------~~~~Ll~~le~  122 (188)
T TIGR00678        88 LSRTPQESGRRVVIIEDAERMNEA--------------AANALLKTLEE  122 (188)
T ss_pred             HccCcccCCeEEEEEechhhhCHH--------------HHHHHHHHhcC
Confidence            433333356779999999999987              78999999984

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.69  E-value=1.6e-07  Score=97.31  Aligned_cols=111  Identities=26%  Similarity=0.364  Sum_probs=70.7

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC---
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV---  351 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~---  351 (461)
                      |+||+.+++.|..++..            +                  ..+..+||+||+|+|||++|+.+|+.+.+   
T Consensus        25 l~Gh~~a~~~L~~a~~~------------g------------------rl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~   74 (351)
T PRK09112         25 LFGHEEAEAFLAQAYRE------------G------------------KLHHALLFEGPEGIGKATLAFHLANHILSHPD   74 (351)
T ss_pred             ccCcHHHHHHHHHHHHc------------C------------------CCCeeEeeECCCCCCHHHHHHHHHHHHcCCCc
Confidence            89999999999988831            0                  11245999999999999999999998854   


Q ss_pred             ----ceEEe----cch---hhhhc---Cc--c-------------cccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          352 ----PFVIA----DAT---TLTQA---GY--V-------------GEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       352 ----pfv~i----~~s---~l~~~---g~--v-------------Ge~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                          +....    .|.   .+...   ++  +             .-. .+.++.+..............||||||+|.|
T Consensus        75 ~~~~~~~~~~~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~-vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l  153 (351)
T PRK09112         75 PAEAPETLADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAIT-VDEIRRVGHFLSQTSGDGNWRIVIIDPADDM  153 (351)
T ss_pred             cccCccccCCCCCCCHHHHHHHcCCCCCEEEeecccccccccccccCC-HHHHHHHHHHhhhccccCCceEEEEEchhhc
Confidence                11100    110   11000   00  0             001 1233333332222222345669999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ...              .+++||+.||+
T Consensus       154 ~~~--------------aanaLLk~LEE  167 (351)
T PRK09112        154 NRN--------------AANAILKTLEE  167 (351)
T ss_pred             CHH--------------HHHHHHHHHhc
Confidence            988              89999999995

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=98.68  E-value=1.2e-07  Score=97.13  Aligned_cols=115  Identities=19%  Similarity=0.213  Sum_probs=70.0

Q ss_pred             HHhhcCC-hHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          271 LDKFVIG-QEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       271 Ld~~VvG-qd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ++. |+| |+.+++.|...+..            +                  ..++.+||+||+|+||+++|+++|+.+
T Consensus         4 ~~~-i~~~q~~~~~~L~~~~~~------------~------------------~l~ha~Lf~G~~G~gk~~~a~~la~~l   52 (329)
T PRK08058          4 WEQ-LTALQPVVVKMLQNSIAK------------N------------------RLSHAYLFEGAKGTGKKATALWLAKSL   52 (329)
T ss_pred             HHH-HHhhHHHHHHHHHHHHHc------------C------------------CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            344 666 99999988887731            0                  112457999999999999999999987


Q ss_pred             CCce--EE------ecch--------hhhhcCccccc-HHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          350 NVPF--VI------ADAT--------TLTQAGYVGED-VESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       350 ~~pf--v~------i~~s--------~l~~~g~vGe~-~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                      .+.-  -.      -+|.        ++.-....+.. ....++.+..........+...|+||||+|+|...       
T Consensus        53 ~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~-------  125 (329)
T PRK08058         53 FCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTAS-------  125 (329)
T ss_pred             CCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHH-------
Confidence            4321  00      0000        00000000110 01334444433322222345679999999999988       


Q ss_pred             cccchHHHHHHHHHHHhC
Q 012525          413 RDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg  430 (461)
                             .+|+||+.||+
T Consensus       126 -------a~NaLLK~LEE  136 (329)
T PRK08058        126 -------AANSLLKFLEE  136 (329)
T ss_pred             -------HHHHHHHHhcC
Confidence                   89999999995

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

Probab=98.65  E-value=2.8e-07  Score=90.99  Aligned_cols=123  Identities=26%  Similarity=0.360  Sum_probs=83.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ ++|.|+.|+.|.........         +                  .+..|+||+|+.|||||+++|++..++
T Consensus        25 ~l~~-L~Gie~Qk~~l~~Nt~~Fl~---------G------------------~pannvLL~G~rGtGKSSlVkall~~y   76 (249)
T PF05673_consen   25 RLDD-LIGIERQKEALIENTEQFLQ---------G------------------LPANNVLLWGARGTGKSSLVKALLNEY   76 (249)
T ss_pred             CHHH-hcCHHHHHHHHHHHHHHHHc---------C------------------CCCcceEEecCCCCCHHHHHHHHHHHH
Confidence            3455 79999999988776632211         1                  234789999999999999999999876


Q ss_pred             ---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHH
Q 012525          350 ---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLK  426 (461)
Q Consensus       350 ---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~  426 (461)
                         +..+|++...++..       ...++..+- ...      ..=|||+|++- +...            +.-...|-.
T Consensus        77 ~~~GLRlIev~k~~L~~-------l~~l~~~l~-~~~------~kFIlf~DDLs-Fe~~------------d~~yk~LKs  129 (249)
T PF05673_consen   77 ADQGLRLIEVSKEDLGD-------LPELLDLLR-DRP------YKFILFCDDLS-FEEG------------DTEYKALKS  129 (249)
T ss_pred             hhcCceEEEECHHHhcc-------HHHHHHHHh-cCC------CCEEEEecCCC-CCCC------------cHHHHHHHH
Confidence               56788888887763       233333322 222      34499999854 2222            224678888


Q ss_pred             HHhCceeeeecceeeecCCeEEEecCCC
Q 012525          427 MLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       427 ~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +|||..-       ..|.+.++.+|||.
T Consensus       130 ~LeGgle-------~~P~NvliyATSNR  150 (249)
T PF05673_consen  130 VLEGGLE-------ARPDNVLIYATSNR  150 (249)
T ss_pred             HhcCccc-------cCCCcEEEEEecch
Confidence            9997653       23567899999995

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.62  E-value=7.6e-08  Score=96.97  Aligned_cols=116  Identities=28%  Similarity=0.397  Sum_probs=82.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH------hcCCceEEecchhhhhcC----cccccHHHHHHHHHHhhchhhhccCceEE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR------HVNVPFVIADATTLTQAG----YVGEDVESILYKLLAQAEFNVEAAQQGMV  394 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~------~l~~pfv~i~~s~l~~~g----~vGe~~e~~L~~lf~~a~~~v~~a~~gVL  394 (461)
                      ..+|||.||+|.||+.||+.|.+      .+..+|++++|..+...+    ++|.. ...+...-....+.+..+.+++|
T Consensus       208 r~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghv-kgaftga~~~r~gllrsadggml  286 (531)
T COG4650         208 RAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHV-KGAFTGARESREGLLRSADGGML  286 (531)
T ss_pred             cCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhh-ccccccchhhhhhhhccCCCceE
Confidence            46799999999999999999975      456799999999887421    01110 11111111233445667899999


Q ss_pred             EEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       395 fIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      |+|||..|..+              -|.-||+.+|+..+......+....++.+|+-+-.|
T Consensus       287 fldeigelgad--------------eqamllkaieekrf~pfgsdr~v~sdfqliagtvrd  333 (531)
T COG4650         287 FLDEIGELGAD--------------EQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAGTVRD  333 (531)
T ss_pred             ehHhhhhcCcc--------------HHHHHHHHHHhhccCCCCCccccccchHHhhhhHHH
Confidence            99999998887              688899999998887777666666677777655433

>PRK12377 putative replication protein; Provisional

Probab=98.61  E-value=6.4e-08  Score=95.76  Aligned_cols=103  Identities=15%  Similarity=0.247  Sum_probs=62.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---CcccccHHHHHHHHHHhhchhhhccCceEEEEcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDE  398 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDE  398 (461)
                      ..+++|+|+||||||+||.+||+.+   +..++.++..++...   .+....   ....++..      ...-.+|+|||
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~~~l~~~~~~~~---~~~~~l~~------l~~~dLLiIDD  171 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVMSRLHESYDNGQ---SGEKFLQE------LCKVDLLVLDE  171 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHHHHHHHHHhccc---hHHHHHHH------hcCCCEEEEcC
Confidence            3679999999999999999999987   456667776665531   000000   00111111      12455999999


Q ss_pred             ccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          399 VDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       399 ID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      +......            +..+..|..+|+.....          ..=.|.|||+..++
T Consensus       172 lg~~~~s------------~~~~~~l~~ii~~R~~~----------~~ptiitSNl~~~~  209 (248)
T PRK12377        172 IGIQRET------------KNEQVVLNQIIDRRTAS----------MRSVGMLTNLNHEA  209 (248)
T ss_pred             CCCCCCC------------HHHHHHHHHHHHHHHhc----------CCCEEEEcCCCHHH
Confidence            9754322            11567888888844311          12346678876543

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

Probab=98.60  E-value=2.3e-07  Score=103.93  Aligned_cols=131  Identities=26%  Similarity=0.313  Sum_probs=94.8

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      |.......||. |+|.++.++++...|..                               ..+.|.+|.|+||+|||.++
T Consensus       161 t~~Ar~gklDP-vIGRd~EI~r~iqIL~R-------------------------------R~KNNPvLiGEpGVGKTAIv  208 (786)
T COG0542         161 TELAREGKLDP-VIGRDEEIRRTIQILSR-------------------------------RTKNNPVLVGEPGVGKTAIV  208 (786)
T ss_pred             HHHHhcCCCCC-CcChHHHHHHHHHHHhc-------------------------------cCCCCCeEecCCCCCHHHHH
Confidence            44445556666 89999999988888831                               22467899999999999999


Q ss_pred             HHHHHhc----------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccc
Q 012525          343 KTLARHV----------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI  411 (461)
Q Consensus       343 raLA~~l----------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~  411 (461)
                      +.||..+          +..++.++...+.. .+|.|+- |..++.+..+....    .+.||||||||.+...-...+.
T Consensus       209 EGLA~rIv~g~VP~~L~~~~i~sLD~g~LvAGakyRGeF-EeRlk~vl~ev~~~----~~vILFIDEiHtiVGAG~~~G~  283 (786)
T COG0542         209 EGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEF-EERLKAVLKEVEKS----KNVILFIDEIHTIVGAGATEGG  283 (786)
T ss_pred             HHHHHHHhcCCCCHHHcCCEEEEecHHHHhccccccCcH-HHHHHHHHHHHhcC----CCeEEEEechhhhcCCCccccc
Confidence            9999865          34678888887664 3566655 88888888765533    5789999999999877221110


Q ss_pred             ccccchHHHHHHHHHHHhCceeee
Q 012525          412 SRDVSGEGVQQALLKMLEGTETKT  435 (461)
Q Consensus       412 ~~~~s~~~v~~aLL~~LEg~~v~i  435 (461)
                      +-+     +-|.|..+|..+++..
T Consensus       284 a~D-----AaNiLKPaLARGeL~~  302 (786)
T COG0542         284 AMD-----AANLLKPALARGELRC  302 (786)
T ss_pred             ccc-----hhhhhHHHHhcCCeEE
Confidence            122     6678888888665543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.59  E-value=1.5e-07  Score=96.29  Aligned_cols=60  Identities=27%  Similarity=0.432  Sum_probs=44.9

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN----  350 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~----  350 (461)
                      ++|++...+.|...+.....         +                  ..+.+++|+||||||||++++.+++.+.    
T Consensus        17 l~gRe~e~~~l~~~l~~~~~---------~------------------~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~   69 (365)
T TIGR02928        17 IVHRDEQIEELAKALRPILR---------G------------------SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAE   69 (365)
T ss_pred             CCCcHHHHHHHHHHHHHHHc---------C------------------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhh
Confidence            78999999999888742110         0                  1236799999999999999999998653    


Q ss_pred             -----CceEEecchhh
Q 012525          351 -----VPFVIADATTL  361 (461)
Q Consensus       351 -----~pfv~i~~s~l  361 (461)
                           ..++.++|...
T Consensus        70 ~~~~~~~~v~in~~~~   85 (365)
T TIGR02928        70 DRDVRVVTVYVNCQIL   85 (365)
T ss_pred             ccCCceEEEEEECCCC
Confidence                 46778887643

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.

>PRK08116 hypothetical protein; Validated

Probab=98.57  E-value=5.5e-07  Score=89.93  Aligned_cols=104  Identities=18%  Similarity=0.328  Sum_probs=62.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---CcccccHHHHHHHHHHhhchhhhccCceEEEEcCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                      .+++|+|++|||||+||.+||+.+   +.+++.++..++...   .|.... ......++...      ....+|+|||+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~i~~~~~~~~-~~~~~~~~~~l------~~~dlLviDDl  187 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSG-KEDENEIIRSL------VNADLLILDDL  187 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhccc-cccHHHHHHHh------cCCCEEEEecc
Confidence            459999999999999999999976   667888887765531   010000 00011111111      13349999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      ......            +..+..|+.+|+...          .....+|.|||..+.+
T Consensus       188 g~e~~t------------~~~~~~l~~iin~r~----------~~~~~~IiTsN~~~~e  224 (268)
T PRK08116        188 GAERDT------------EWAREKVYNIIDSRY----------RKGLPTIVTTNLSLEE  224 (268)
T ss_pred             cCCCCC------------HHHHHHHHHHHHHHH----------HCCCCEEEECCCCHHH
Confidence            642111            126778888888432          1123578888887654

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.53  E-value=3.5e-07  Score=93.94  Aligned_cols=87  Identities=23%  Similarity=0.319  Sum_probs=59.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLA  380 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~  380 (461)
                      ++.+||+||+|+|||++|+.+|+.+.+.                        ++.+....-.  ..+  . .+.++.+..
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~--~~i--~-id~iR~l~~   96 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEAD--KTI--K-VDQVRELVS   96 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCC--CCC--C-HHHHHHHHH
Confidence            3669999999999999999999988541                        2222111000  001  1 244555555


Q ss_pred             hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       381 ~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ............|++|||+|+|...              .+|+||+.||+
T Consensus        97 ~~~~~~~~~~~kv~iI~~a~~m~~~--------------aaNaLLK~LEE  132 (328)
T PRK05707         97 FVVQTAQLGGRKVVLIEPAEAMNRN--------------AANALLKSLEE  132 (328)
T ss_pred             HHhhccccCCCeEEEECChhhCCHH--------------HHHHHHHHHhC
Confidence            4444334456779999999999998              89999999995

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.52  E-value=7.7e-07  Score=92.01  Aligned_cols=61  Identities=26%  Similarity=0.371  Sum_probs=45.4

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc----
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV----  349 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l----  349 (461)
                      .++|+++..+.|...+.....         +                  ..+.+++|+||||||||++++.+++.+    
T Consensus        31 ~l~~Re~e~~~l~~~l~~~~~---------~------------------~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~   83 (394)
T PRK00411         31 NLPHREEQIEELAFALRPALR---------G------------------SRPLNVLIYGPPGTGKTTTVKKVFEELEEIA   83 (394)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC---------C------------------CCCCeEEEECCCCCCHHHHHHHHHHHHHHhc
Confidence            378899888888887742110         0                  123679999999999999999999877    


Q ss_pred             -CCceEEecchhh
Q 012525          350 -NVPFVIADATTL  361 (461)
Q Consensus       350 -~~pfv~i~~s~l  361 (461)
                       +..++.+++...
T Consensus        84 ~~~~~v~in~~~~   96 (394)
T PRK00411         84 VKVVYVYINCQID   96 (394)
T ss_pred             CCcEEEEEECCcC
Confidence             467888887643

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.50  E-value=5e-07  Score=78.36  Aligned_cols=102  Identities=23%  Similarity=0.411  Sum_probs=59.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc--------CCceEEecchhhhhc-----------Cc--cc-ccHHHHHHHHHHhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV--------NVPFVIADATTLTQA-----------GY--VG-EDVESILYKLLAQA  382 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l--------~~pfv~i~~s~l~~~-----------g~--vG-e~~e~~L~~lf~~a  382 (461)
                      ...++++|++|+|||++++.+++.+        ..+++.+++......           +.  .. ....... ..+.. 
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~-~~~~~-   81 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELR-SLLID-   81 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHH-HHHHH-
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHH-HHHHH-
Confidence            3678999999999999999999977        667777777644411           00  01 1111122 22211 


Q ss_pred             chhhhccCceEEEEcCcccc-chhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          383 EFNVEAAQQGMVYIDEVDKI-TKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       383 ~~~v~~a~~gVLfIDEID~L-~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                        .+......+|+|||+|.+ ...              +.+.|..+++...+           .++++.+.+++
T Consensus        82 --~l~~~~~~~lviDe~~~l~~~~--------------~l~~l~~l~~~~~~-----------~vvl~G~~~l~  128 (131)
T PF13401_consen   82 --ALDRRRVVLLVIDEADHLFSDE--------------FLEFLRSLLNESNI-----------KVVLVGTPELE  128 (131)
T ss_dssp             --HHHHCTEEEEEEETTHHHHTHH--------------HHHHHHHHTCSCBE-----------EEEEEESSTTT
T ss_pred             --HHHhcCCeEEEEeChHhcCCHH--------------HHHHHHHHHhCCCC-----------eEEEEEChhhH
Confidence              112223359999999998 433              78888887773332           25666666544

>PRK08727 hypothetical protein; Validated

Probab=98.50  E-value=9.9e-07  Score=86.01  Aligned_cols=64  Identities=25%  Similarity=0.317  Sum_probs=41.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      ..++|+|++|||||+|+++++..+   +...+.++..++..          .+...+....      +.-+|+||||+.+
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~~~----------~~~~~~~~l~------~~dlLiIDDi~~l  105 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAG----------RLRDALEALE------GRSLVALDGLESI  105 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHhhh----------hHHHHHHHHh------cCCEEEEeCcccc
Confidence            348999999999999999998765   34445555444331          1112222111      2348999999988


Q ss_pred             chh
Q 012525          403 TKK  405 (461)
Q Consensus       403 ~~~  405 (461)
                      ...
T Consensus       106 ~~~  108 (233)
T PRK08727        106 AGQ  108 (233)
T ss_pred             cCC
Confidence            755

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.49  E-value=3.7e-06  Score=92.62  Aligned_cols=73  Identities=12%  Similarity=0.276  Sum_probs=46.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      ..++|+|++|||||+|+++|++++     +..++++++.++... +........ ...|...   +  ....+|+||||+
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~e-l~~al~~~~-~~~f~~~---y--~~~DLLlIDDIq  387 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNE-FINSIRDGK-GDSFRRR---Y--REMDILLVDDIQ  387 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHH-HHHHHHhcc-HHHHHHH---h--hcCCEEEEehhc
Confidence            348999999999999999999876     456778888776531 211100000 1112111   1  134599999999


Q ss_pred             ccchh
Q 012525          401 KITKK  405 (461)
Q Consensus       401 ~L~~~  405 (461)
                      .+..+
T Consensus       388 ~l~gk  392 (617)
T PRK14086        388 FLEDK  392 (617)
T ss_pred             cccCC
Confidence            88765

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.48  E-value=1.1e-06  Score=85.91  Aligned_cols=64  Identities=17%  Similarity=0.244  Sum_probs=40.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      .+++|+||+|||||+|++++++.+.   ..++.+........      ....+ +.+.         .-.+||||||+.+
T Consensus        46 ~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~~~------~~~~~-~~~~---------~~dlliiDdi~~~  109 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRAWF------VPEVL-EGME---------QLSLVCIDNIECI  109 (235)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHhhh------hHHHH-HHhh---------hCCEEEEeChhhh
Confidence            5799999999999999999998764   23444444332210      01111 1111         1138999999988


Q ss_pred             chh
Q 012525          403 TKK  405 (461)
Q Consensus       403 ~~~  405 (461)
                      ..+
T Consensus       110 ~~~  112 (235)
T PRK08084        110 AGD  112 (235)
T ss_pred             cCC
Confidence            754

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.47  E-value=5.9e-07  Score=86.33  Aligned_cols=70  Identities=21%  Similarity=0.318  Sum_probs=51.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      .+++|+||+|||||+||+++++.+   +..++.+++..+...              +..      .....+|||||+|.+
T Consensus        43 ~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~~~~--------------~~~------~~~~~~liiDdi~~l  102 (227)
T PRK08903         43 RFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPLLA--------------FDF------DPEAELYAVDDVERL  102 (227)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHhHHH--------------Hhh------cccCCEEEEeChhhc
Confidence            679999999999999999999875   557777777665421              000      113568999999988


Q ss_pred             chhhhccccccccchHHHHHHHHHHHh
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ...              .+..|+.+|+
T Consensus       103 ~~~--------------~~~~L~~~~~  115 (227)
T PRK08903        103 DDA--------------QQIALFNLFN  115 (227)
T ss_pred             Cch--------------HHHHHHHHHH
Confidence            765              5667777775

>PRK06893 DNA replication initiation factor; Validated

Probab=98.47  E-value=3.1e-07  Score=89.26  Aligned_cols=64  Identities=19%  Similarity=0.270  Sum_probs=40.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      ..++|+||||||||+|++++|+++   +...+.++......          .....+...      .+..+|+||||+.+
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~~~----------~~~~~~~~~------~~~dlLilDDi~~~  103 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQY----------FSPAVLENL------EQQDLVCLDDLQAV  103 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHhhh----------hhHHHHhhc------ccCCEEEEeChhhh
Confidence            347999999999999999999876   23334444432211          001111111      13459999999988


Q ss_pred             chh
Q 012525          403 TKK  405 (461)
Q Consensus       403 ~~~  405 (461)
                      ...
T Consensus       104 ~~~  106 (229)
T PRK06893        104 IGN  106 (229)
T ss_pred             cCC
Confidence            654

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.47  E-value=1.5e-07  Score=88.46  Aligned_cols=101  Identities=24%  Similarity=0.352  Sum_probs=58.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---CcccccHHHHHHHHHHhhchhhhccCceEEEEcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDE  398 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDE  398 (461)
                      ..+++|+|++|||||+||.++++++   +.+++.++..++...   .+.....+..+..+.          .-.+|+|||
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~----------~~dlLilDD  116 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLK----------RVDLLILDD  116 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHH----------TSSCEEEET
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCccc----------cccEecccc
Confidence            4789999999999999999999865   667777777766532   111112222222222          334899999


Q ss_pred             ccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          399 VDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       399 ID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      +......            +...+.|+++|+...          .+. -.|.|||++.++
T Consensus       117 lG~~~~~------------~~~~~~l~~ii~~R~----------~~~-~tIiTSN~~~~~  153 (178)
T PF01695_consen  117 LGYEPLS------------EWEAELLFEIIDERY----------ERK-PTIITSNLSPSE  153 (178)
T ss_dssp             CTSS---------------HHHHHCTHHHHHHHH----------HT--EEEEEESS-HHH
T ss_pred             cceeeec------------ccccccchhhhhHhh----------ccc-CeEeeCCCchhh
Confidence            9854332            114566777777332          112 345588887543

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.46  E-value=5.8e-07  Score=88.83  Aligned_cols=104  Identities=15%  Similarity=0.226  Sum_probs=62.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccc--cHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGE--DVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe--~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      .+++|+|++|||||+||.+||+++   +..++.++..++... +...  ........++...      ....+|+|||++
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~~l~~~-l~~~~~~~~~~~~~~l~~l------~~~dlLvIDDig  172 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVADIMSA-MKDTFSNSETSEEQLLNDL------SNVDLLVIDEIG  172 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHHHHHHH-HHHHHhhccccHHHHHHHh------ccCCEEEEeCCC
Confidence            579999999999999999999987   567777777766531 1000  0000111122111      134599999998


Q ss_pred             ccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          401 KITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       401 ~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      .....            +-....|..+++...          ....-.|.|||+..++
T Consensus       173 ~~~~s------------~~~~~~l~~Ii~~Ry----------~~~~~tiitSNl~~~~  208 (244)
T PRK07952        173 VQTES------------RYEKVIINQIVDRRS----------SSKRPTGMLTNSNMEE  208 (244)
T ss_pred             CCCCC------------HHHHHHHHHHHHHHH----------hCCCCEEEeCCCCHHH
Confidence            75432            113456667777332          1123566777776543

>PRK08181 transposase; Validated

Probab=98.45  E-value=2e-07  Score=93.28  Aligned_cols=87  Identities=23%  Similarity=0.372  Sum_probs=54.8

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      ...+++|+||+|||||+||.+|+.++   +..++.++..++... +.....+..+...+...      .+..+|+|||++
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~-l~~a~~~~~~~~~l~~l------~~~dLLIIDDlg  177 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQK-LQVARRELQLESAIAKL------DKFDLLILDDLA  177 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHH-HHHHHhCCcHHHHHHHH------hcCCEEEEeccc
Confidence            46789999999999999999999755   556777777766642 10000000111111111      134599999999


Q ss_pred             ccchhhhccccccccchHHHHHHHHHHHh
Q 012525          401 KITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       401 ~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      .+....            ..+..|+++++
T Consensus       178 ~~~~~~------------~~~~~Lf~lin  194 (269)
T PRK08181        178 YVTKDQ------------AETSVLFELIS  194 (269)
T ss_pred             cccCCH------------HHHHHHHHHHH
Confidence            765541            14667788877

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.42  E-value=2.9e-08  Score=101.82  Aligned_cols=156  Identities=19%  Similarity=0.234  Sum_probs=84.7

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      +...+...|+|.+.+|..|.-.+..       ......            ....-....-||||+|.||||||.|.+.++
T Consensus        18 l~~s~aP~i~g~~~iK~aill~L~~-------~~~~~~------------~~~~~~r~~ihiLlvGdpg~gKS~ll~~~~   78 (331)
T PF00493_consen   18 LANSIAPSIYGHEDIKKAILLQLFG-------GVEKND------------PDGTRIRGNIHILLVGDPGTGKSQLLKYVA   78 (331)
T ss_dssp             CHHHCSSTTTT-HHHHHHHCCCCTT---------SCCC------------CT-TEE--S--EEEECSCHHCHHHHHHCCC
T ss_pred             HHHHhCCcCcCcHHHHHHHHHHHHh-------cccccc------------ccccccccccceeeccchhhhHHHHHHHHH
Confidence            5566667799999999877655521       000000            000012235799999999999999999887


Q ss_pred             HhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHH
Q 012525          347 RHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLK  426 (461)
Q Consensus       347 ~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~  426 (461)
                      +.....+ .++.......++...........-+.-..+.+..+++||++|||+|+|...              ..++|++
T Consensus        79 ~~~pr~v-~~~g~~~s~~gLta~~~~d~~~~~~~leaGalvlad~GiccIDe~dk~~~~--------------~~~~l~e  143 (331)
T PF00493_consen   79 KLAPRSV-YTSGKGSSAAGLTASVSRDPVTGEWVLEAGALVLADGGICCIDEFDKMKED--------------DRDALHE  143 (331)
T ss_dssp             CT-SSEE-EEECCGSTCCCCCEEECCCGGTSSECEEE-HHHHCTTSEEEECTTTT--CH--------------HHHHHHH
T ss_pred             hhCCceE-EECCCCcccCCccceeccccccceeEEeCCchhcccCceeeecccccccch--------------HHHHHHH
Confidence            6654432 333222221221110000000000111223445678999999999999987              7899999


Q ss_pred             HHhCceeeeecc--eeeecCCeEEEecCCCCc
Q 012525          427 MLEGTETKTFAA--VSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       427 ~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~  456 (461)
                      .||...+.+--.  ....+.+.-+++++|+..
T Consensus       144 aMEqq~isi~kagi~~~l~ar~svlaa~NP~~  175 (331)
T PF00493_consen  144 AMEQQTISIAKAGIVTTLNARCSVLAAANPKF  175 (331)
T ss_dssp             HHHCSCEEECTSSSEEEEE---EEEEEE--TT
T ss_pred             HHHcCeeccchhhhcccccchhhhHHHHhhhh
Confidence            999888877654  444555889999988754

; 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.

>PRK06526 transposase; Provisional

Probab=98.41  E-value=2.5e-07  Score=91.78  Aligned_cols=87  Identities=24%  Similarity=0.350  Sum_probs=51.9

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      ...+++|+||||||||+||.+|+.++   +..++.+.+.++... +........+...+..      ..+..+|+|||++
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~-l~~~~~~~~~~~~l~~------l~~~dlLIIDD~g  169 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVAR-LAAAHHAGRLQAELVK------LGRYPLLIVDEVG  169 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHH-HHHHHhcCcHHHHHHH------hccCCEEEEcccc
Confidence            46799999999999999999998765   455555555544421 0000000011111111      1244699999999


Q ss_pred             ccchhhhccccccccchHHHHHHHHHHHh
Q 012525          401 KITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       401 ~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      .+.....            .++.|+++++
T Consensus       170 ~~~~~~~------------~~~~L~~li~  186 (254)
T PRK06526        170 YIPFEPE------------AANLFFQLVS  186 (254)
T ss_pred             cCCCCHH------------HHHHHHHHHH
Confidence            7654311            4567777776

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.39  E-value=6.9e-07  Score=88.63  Aligned_cols=73  Identities=23%  Similarity=0.404  Sum_probs=49.0

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---CcccccHHHHHHHHHHhhchhhhccCceEEEEc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGEDVESILYKLLAQAEFNVEAAQQGMVYID  397 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfID  397 (461)
                      ...+++|+|+||||||+||-||++++   +..++.+...++...   .+-....+..+...+.         .--|||||
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~~Lk~~~~~~~~~~~l~~~l~---------~~dlLIiD  174 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLEEKLLRELK---------KVDLLIID  174 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhcCchHHHHHHHhh---------cCCEEEEe
Confidence            56799999999999999999999877   567777777776642   0110111222222221         33499999


Q ss_pred             Cccccchh
Q 012525          398 EVDKITKK  405 (461)
Q Consensus       398 EID~L~~~  405 (461)
                      |+-.....
T Consensus       175 DlG~~~~~  182 (254)
T COG1484         175 DIGYEPFS  182 (254)
T ss_pred             cccCccCC
Confidence            99976554

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=98.39  E-value=2.3e-06  Score=76.70  Aligned_cols=109  Identities=21%  Similarity=0.245  Sum_probs=69.7

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .....+.+.|.+.|+||+-|++.+..++..+...-      .       +           ..+-.+.|+|++|||||.+
T Consensus        14 ~~~~~L~~~L~~~l~GQhla~~~v~~ai~~~l~~~------~-------p-----------~KpLVlSfHG~tGtGKn~v   69 (127)
T PF06309_consen   14 YNITGLEKDLQRNLFGQHLAVEVVVNAIKGHLANP------N-------P-----------RKPLVLSFHGWTGTGKNFV   69 (127)
T ss_pred             CCHHHHHHHHHHHccCcHHHHHHHHHHHHHHHcCC------C-------C-----------CCCEEEEeecCCCCcHHHH
Confidence            45678999999999999999999999997554310      0       0           1123455999999999999


Q ss_pred             HHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEE
Q 012525          342 AKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYI  396 (461)
Q Consensus       342 AraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfI  396 (461)
                      ++.||+.+     +.+||..-.+...-.  -...+...-..+-.+....+.....+++++
T Consensus        70 ~~liA~~ly~~G~~S~~V~~f~~~~hFP--~~~~v~~Yk~~L~~~I~~~v~~C~rslFIF  127 (127)
T PF06309_consen   70 SRLIAEHLYKSGMKSPFVHQFIATHHFP--HNSNVDEYKEQLKSWIRGNVSRCPRSLFIF  127 (127)
T ss_pred             HHHHHHHHHhcccCCCceeeecccccCC--CchHHHHHHHHHHHHHHHHHHhCCcCeeeC
Confidence            99999986     335553332221110  011223333444455556666666666653

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

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.37  E-value=3e-06  Score=95.87  Aligned_cols=86  Identities=19%  Similarity=0.324  Sum_probs=53.7

Q ss_pred             EEEEccCCCchHHHHHHHHHhc----------CCceEEecchhhhhcC---------c------ccccHHHHHHHHHHhh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV----------NVPFVIADATTLTQAG---------Y------VGEDVESILYKLLAQA  382 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l----------~~pfv~i~~s~l~~~g---------~------vGe~~e~~L~~lf~~a  382 (461)
                      ++|+|+||||||++++.+.+++          ...++.++|..+....         +      .|......+..+|...
T Consensus       784 LYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L  863 (1164)
T PTZ00112        784 LYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQN  863 (1164)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhh
Confidence            4699999999999999998766          1457889885533210         0      1112223444444432


Q ss_pred             chhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          383 EFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       383 ~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ...  .....||+|||||.|...              .+..|+.+++
T Consensus       864 ~k~--~r~v~IIILDEID~L~kK--------------~QDVLYnLFR  894 (1164)
T PTZ00112        864 KKD--NRNVSILIIDEIDYLITK--------------TQKVLFTLFD  894 (1164)
T ss_pred             hcc--cccceEEEeehHhhhCcc--------------HHHHHHHHHH
Confidence            110  112358999999999876              3566777766

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.36  E-value=8.3e-07  Score=92.97  Aligned_cols=73  Identities=18%  Similarity=0.359  Sum_probs=45.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      .+++|+|++|||||+|++++++++     +..++.+++.++... +........+.. |..   .+.  ...+|+||||+
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~-~~~~~~~~~~~~-~~~---~~~--~~dlLiiDDi~  209 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTND-FVNALRNNKMEE-FKE---KYR--SVDLLLIDDIQ  209 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHHHH-HHHHHHcCCHHH-HHH---HHH--hCCEEEEehhh
Confidence            458999999999999999999877     466788887765421 110000000001 111   111  23499999999


Q ss_pred             ccchh
Q 012525          401 KITKK  405 (461)
Q Consensus       401 ~L~~~  405 (461)
                      .+..+
T Consensus       210 ~l~~~  214 (405)
T TIGR00362       210 FLAGK  214 (405)
T ss_pred             hhcCC
Confidence            88654

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).

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.32  E-value=2e-06  Score=73.93  Aligned_cols=95  Identities=24%  Similarity=0.326  Sum_probs=57.4

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCce--------EEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPF--------VIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pf--------v~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                      |.|+|+||+|||++|+.||+.+...+        +.....+---.+|.                      ...++++||+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~----------------------~q~vvi~DD~   58 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQ----------------------GQPVVIIDDF   58 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccC----------------------CCcEEEEeec
Confidence            57999999999999999998774322        11111111101111                      3458999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhCceeeeecc-ee-e-ecC-CeEEEecCCC
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VS-K-VSR-DNLYIKTSGL  454 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r-~-~~r-d~IiI~TsNi  454 (461)
                      ......-          .......|+++++...+..... .. + ... -.++|.|||.
T Consensus        59 ~~~~~~~----------~~~~~~~l~~l~s~~~~~~~~a~~~~K~~~~~s~~vi~tsN~  107 (107)
T PF00910_consen   59 GQDNDGY----------NYSDESELIRLISSNPFQPNMADLEDKGTPFNSKLVIITSNF  107 (107)
T ss_pred             Ccccccc----------chHHHHHHHHHHhcCCcccccccHhhCCCccCCCEEEEcCCC
Confidence            9766430          1125778889998666655433 11 1 111 4688889884

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

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=98.31  E-value=5.3e-06  Score=85.09  Aligned_cols=92  Identities=28%  Similarity=0.355  Sum_probs=57.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCce--E--Eecchhhhhc----Cc--c-------cc-----cHHHHHHHHHHhhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPF--V--IADATTLTQA----GY--V-------GE-----DVESILYKLLAQAE  383 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pf--v--~i~~s~l~~~----g~--v-------Ge-----~~e~~L~~lf~~a~  383 (461)
                      +.+||+||+|+||+++|+++|+.+.+.-  -  ...+..+...    ++  +       +.     -..+.++.+.....
T Consensus        27 HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~~~~  106 (319)
T PRK08769         27 HGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQKLA  106 (319)
T ss_pred             eeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHHHHHh
Confidence            4599999999999999999998774310  0  0000000000    00  0       10     01334455554444


Q ss_pred             hhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          384 FNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       384 ~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      .........|++||++|+|...              ..|+||+.||+-
T Consensus       107 ~~p~~g~~kV~iI~~ae~m~~~--------------AaNaLLKtLEEP  140 (319)
T PRK08769        107 LTPQYGIAQVVIVDPADAINRA--------------ACNALLKTLEEP  140 (319)
T ss_pred             hCcccCCcEEEEeccHhhhCHH--------------HHHHHHHHhhCC
Confidence            3333345679999999999988              899999999953

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.30  E-value=8.6e-07  Score=94.31  Aligned_cols=73  Identities=18%  Similarity=0.328  Sum_probs=46.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      .+++|+||+|||||+|++++++++     +..++.+++.++... +...-...... .|..   .+.  ...+|+||||+
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~-~~~~~~~~~~~-~~~~---~~~--~~dlLiiDDi~  221 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKFTND-FVNALRNNTME-EFKE---KYR--SVDVLLIDDIQ  221 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHH-HHHHHHcCcHH-HHHH---HHh--cCCEEEEehhh
Confidence            458999999999999999999987     455778888766531 11100000001 1111   111  34499999999


Q ss_pred             ccchh
Q 012525          401 KITKK  405 (461)
Q Consensus       401 ~L~~~  405 (461)
                      .+..+
T Consensus       222 ~l~~~  226 (450)
T PRK00149        222 FLAGK  226 (450)
T ss_pred             hhcCC
Confidence            88665

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=98.28  E-value=7e-06  Score=84.38  Aligned_cols=86  Identities=21%  Similarity=0.339  Sum_probs=58.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLA  380 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~  380 (461)
                      ++.+||+||.|+||+++|+++|+.+.+.                        |+.+...+   ...+  . .+.++.+..
T Consensus        24 ~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~---~~~I--~-id~iR~l~~   97 (325)
T PRK06871         24 HHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPID---NKDI--G-VDQVREINE   97 (325)
T ss_pred             ceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEcccc---CCCC--C-HHHHHHHHH
Confidence            3568899999999999999999977431                        11221110   0011  1 344555554


Q ss_pred             hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       381 ~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ............|++||++|+|...              ..|+||+.||+
T Consensus        98 ~~~~~~~~g~~KV~iI~~a~~m~~~--------------AaNaLLKtLEE  133 (325)
T PRK06871         98 KVSQHAQQGGNKVVYIQGAERLTEA--------------AANALLKTLEE  133 (325)
T ss_pred             HHhhccccCCceEEEEechhhhCHH--------------HHHHHHHHhcC
Confidence            4444434456679999999999998              89999999994

>PRK05642 DNA replication initiation factor; Validated

Probab=98.27  E-value=3e-06  Score=82.73  Aligned_cols=64  Identities=27%  Similarity=0.354  Sum_probs=43.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      .+++|+|++|||||+|++++++++   +..++.++..++...      ....+ +.+.         .--+|+|||++.+
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~~~------~~~~~-~~~~---------~~d~LiiDDi~~~  109 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDR------GPELL-DNLE---------QYELVCLDDLDVI  109 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHHhh------hHHHH-Hhhh---------hCCEEEEechhhh
Confidence            568999999999999999999754   456777777766531      01111 1111         1238999999977


Q ss_pred             chh
Q 012525          403 TKK  405 (461)
Q Consensus       403 ~~~  405 (461)
                      ..+
T Consensus       110 ~~~  112 (234)
T PRK05642        110 AGK  112 (234)
T ss_pred             cCC
Confidence            654

>TIGR00602 rad24 checkpoint protein rad24

Probab=98.26  E-value=3.4e-06  Score=93.51  Aligned_cols=66  Identities=17%  Similarity=0.207  Sum_probs=45.9

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      ..+-..+.+++ |+|+++.++.|..++......                          .....-++|+||+|||||+++
T Consensus        75 ~eKyrP~~lde-l~~~~~ki~~l~~~l~~~~~~--------------------------~~~~~illL~GP~GsGKTTl~  127 (637)
T TIGR00602        75 VEKYKPETQHE-LAVHKKKIEEVETWLKAQVLE--------------------------NAPKRILLITGPSGCGKSTTI  127 (637)
T ss_pred             HHHhCCCCHHH-hcCcHHHHHHHHHHHHhcccc--------------------------cCCCcEEEEECCCCCCHHHHH
Confidence            33444556666 899999999888777321000                          011234899999999999999


Q ss_pred             HHHHHhcCCceEE
Q 012525          343 KTLARHVNVPFVI  355 (461)
Q Consensus       343 raLA~~l~~pfv~  355 (461)
                      +.+|+.++..+++
T Consensus       128 ~~la~~l~~~~~E  140 (637)
T TIGR00602       128 KILSKELGIQVQE  140 (637)
T ss_pred             HHHHHHhhhHHHH
Confidence            9999998776544

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09183 transposase/IS protein; Provisional

Probab=98.26  E-value=1.3e-06  Score=86.76  Aligned_cols=106  Identities=21%  Similarity=0.278  Sum_probs=61.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                      ....+++|+||+|||||+||.+|+..+   +..+..++..++... +........+...+...     .....+|+|||+
T Consensus       100 ~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~-l~~a~~~~~~~~~~~~~-----~~~~dlLiiDdl  173 (259)
T PRK09183        100 ERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQ-LSTAQRQGRYKTTLQRG-----VMAPRLLIIDEI  173 (259)
T ss_pred             hcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHH-HHHHHHCCcHHHHHHHH-----hcCCCEEEEccc
Confidence            345789999999999999999997654   556666666555421 10000000111222111     124459999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      +.+...+.            ..+.|+++++...-          +. -+|.|||....
T Consensus       174 g~~~~~~~------------~~~~lf~li~~r~~----------~~-s~iiTsn~~~~  208 (259)
T PRK09183        174 GYLPFSQE------------EANLFFQVIAKRYE----------KG-SMILTSNLPFG  208 (259)
T ss_pred             ccCCCChH------------HHHHHHHHHHHHHh----------cC-cEEEecCCCHH
Confidence            87544421            45677777763211          11 25668887654

>PRK06921 hypothetical protein; Provisional

Probab=98.26  E-value=3e-06  Score=84.58  Aligned_cols=37  Identities=30%  Similarity=0.398  Sum_probs=29.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc----CCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~s~l~  362 (461)
                      .+++|+|++|||||+||.+||+++    +..++.+...++.
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~  158 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGF  158 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHH
Confidence            679999999999999999999876    4456666665544

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

Probab=98.25  E-value=1.1e-05  Score=86.77  Aligned_cols=94  Identities=29%  Similarity=0.405  Sum_probs=66.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch-hhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT-TLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s-~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      ..+||.||||+|||+||-.+|...+.||+.+-.. ++.  |+....--..+.+.|..+..+    .-+||++|+|++|..
T Consensus       539 vSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~mi--G~sEsaKc~~i~k~F~DAYkS----~lsiivvDdiErLiD  612 (744)
T KOG0741|consen  539 VSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMI--GLSESAKCAHIKKIFEDAYKS----PLSIIVVDDIERLLD  612 (744)
T ss_pred             eEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHcc--CccHHHHHHHHHHHHHHhhcC----cceEEEEcchhhhhc
Confidence            5699999999999999999999999999966544 433  222222234567788877765    567999999999876


Q ss_pred             hhhccccccccchHHHHHHHHHHHh
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      -   ..++. ..+.-++++|+.+|.
T Consensus       613 ~---vpIGP-RfSN~vlQaL~VllK  633 (744)
T KOG0741|consen  613 Y---VPIGP-RFSNLVLQALLVLLK  633 (744)
T ss_pred             c---cccCc-hhhHHHHHHHHHHhc
Confidence            4   11122 223447778887776

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=98.24  E-value=4.2e-06  Score=87.30  Aligned_cols=78  Identities=28%  Similarity=0.438  Sum_probs=51.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc-----eEEecchhhhhc--------------CcccccHHHHHHHHHHhhchh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP-----FVIADATTLTQA--------------GYVGEDVESILYKLLAQAEFN  385 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p-----fv~i~~s~l~~~--------------g~vGe~~e~~L~~lf~~a~~~  385 (461)
                      +.|++++|+||||||.+++.+++++...     ++.++|..+...              -..|......+..+...... 
T Consensus        42 p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~-  120 (366)
T COG1474          42 PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSK-  120 (366)
T ss_pred             CccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHh-
Confidence            4679999999999999999999988543     889999765532              01122222222222221111 


Q ss_pred             hhccCceEEEEcCccccchh
Q 012525          386 VEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~  405 (461)
                        ....-||+|||+|.|...
T Consensus       121 --~~~~~IvvLDEid~L~~~  138 (366)
T COG1474         121 --KGKTVIVILDEVDALVDK  138 (366)
T ss_pred             --cCCeEEEEEcchhhhccc
Confidence              234568999999999987

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

Probab=98.23  E-value=3.2e-06  Score=93.20  Aligned_cols=77  Identities=27%  Similarity=0.448  Sum_probs=60.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcCC----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcC
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVNV----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDE  398 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~~----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDE  398 (461)
                      ....+|||+||+|+|||.|++++++++..    .+..++|+.+....  -+.+.+.+...|..+...    .|+||+||+
T Consensus       429 ~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~--~e~iQk~l~~vfse~~~~----~PSiIvLDd  502 (952)
T KOG0735|consen  429 FRHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSS--LEKIQKFLNNVFSEALWY----APSIIVLDD  502 (952)
T ss_pred             cccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchh--HHHHHHHHHHHHHHHHhh----CCcEEEEcc
Confidence            45689999999999999999999998864    35578888887542  234456677777766554    899999999


Q ss_pred             ccccchh
Q 012525          399 VDKITKK  405 (461)
Q Consensus       399 ID~L~~~  405 (461)
                      +|.|...
T Consensus       503 ld~l~~~  509 (952)
T KOG0735|consen  503 LDCLASA  509 (952)
T ss_pred             hhhhhcc
Confidence            9999884

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=98.23  E-value=1.1e-06  Score=96.14  Aligned_cols=149  Identities=19%  Similarity=0.277  Sum_probs=89.6

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      +...+...|.|.|.+|+.|.-.|.       ....+... ....           -....||||+|.||||||.|.+.++
T Consensus       423 La~SiAPsIye~edvKkglLLqLf-------GGt~k~~~-~~~~-----------~R~~INILL~GDPGtsKSqlLqyv~  483 (804)
T KOG0478|consen  423 LARSIAPSIYELEDVKKGLLLQLF-------GGTRKEDE-KSGR-----------FRGDINILLVGDPGTSKSQLLQYCH  483 (804)
T ss_pred             HHHhhchhhhcccchhhhHHHHHh-------cCCccccc-cccc-----------ccccceEEEecCCCcCHHHHHHHHH
Confidence            444455567888888887766552       11111110 0000           0123789999999999999999999


Q ss_pred             HhcCCceEEe-cch---hhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          347 RHVNVPFVIA-DAT---TLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       347 ~~l~~pfv~i-~~s---~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                      +.+..-.+.- ..+   .++.  |+-.+.+   .+.+-...+.+..+.+||-.|||+|+|...              .++
T Consensus       484 ~l~pRg~yTSGkGsSavGLTa--yVtrd~d---tkqlVLesGALVLSD~GiCCIDEFDKM~dS--------------trS  544 (804)
T KOG0478|consen  484 RLLPRGVYTSGKGSSAVGLTA--YVTKDPD---TRQLVLESGALVLSDNGICCIDEFDKMSDS--------------TRS  544 (804)
T ss_pred             HhCCcceeecCCccchhccee--eEEecCc---cceeeeecCcEEEcCCceEEchhhhhhhHH--------------HHH
Confidence            9885432210 001   1110  1111100   011112234455678999999999999888              789


Q ss_pred             HHHHHHhCceeeeecc--eeeecCCeEEEecCC
Q 012525          423 ALLKMLEGTETKTFAA--VSKVSRDNLYIKTSG  453 (461)
Q Consensus       423 aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsN  453 (461)
                      .|++.||...+++.-.  ....+.+.-++++.|
T Consensus       545 vLhEvMEQQTvSIAKAGII~sLNAR~SVLAaAN  577 (804)
T KOG0478|consen  545 VLHEVMEQQTLSIAKAGIIASLNARCSVLAAAN  577 (804)
T ss_pred             HHHHHHHHhhhhHhhcceeeeccccceeeeeec
Confidence            9999999888776544  333444677788888

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.22  E-value=9e-06  Score=83.52  Aligned_cols=92  Identities=17%  Similarity=0.242  Sum_probs=61.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC-------------------------ceEEecchhh-hhcCc--ccccHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV-------------------------PFVIADATTL-TQAGY--VGEDVESILY  376 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~-------------------------pfv~i~~s~l-~~~g~--vGe~~e~~L~  376 (461)
                      ++.+||+||+|+|||++|+.+|+.+.+                         +|+.+....- .+.+.  ..-. .+.++
T Consensus        21 ~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~-id~iR   99 (325)
T PRK08699         21 PNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIK-IDAVR   99 (325)
T ss_pred             ceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcC-HHHHH
Confidence            356999999999999999999997743                         2333332210 00000  0001 34456


Q ss_pred             HHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          377 KLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       377 ~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      .+..............|++||+++.|...              .+++|++.||+.
T Consensus       100 ~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~--------------a~naLLk~LEep  140 (325)
T PRK08699        100 EIIDNVYLTSVRGGLRVILIHPAESMNLQ--------------AANSLLKVLEEP  140 (325)
T ss_pred             HHHHHHhhCcccCCceEEEEechhhCCHH--------------HHHHHHHHHHhC
Confidence            66655554444456779999999999998              899999999954

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=98.22  E-value=8.8e-06  Score=84.19  Aligned_cols=92  Identities=24%  Similarity=0.270  Sum_probs=59.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc-------------------------eEEecchhhh----------------h
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP-------------------------FVIADATTLT----------------Q  363 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p-------------------------fv~i~~s~l~----------------~  363 (461)
                      ++.+||+||+|+||+++|+.+|+.+.+.                         |+.+......                .
T Consensus        21 ~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~~~~~  100 (342)
T PRK06964         21 PHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEADADE  100 (342)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccchhhc
Confidence            4679999999999999999999987542                         1112111000                0


Q ss_pred             cC-----cccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          364 AG-----YVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       364 ~g-----~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .+     ....-..+.++.+..............|+|||++|+|...              ..|+||+.||+
T Consensus       101 ~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~--------------AaNaLLKtLEE  158 (342)
T PRK06964        101 GGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALNVA--------------AANALLKTLEE  158 (342)
T ss_pred             ccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhcCHH--------------HHHHHHHHhcC
Confidence            00     0000012345555554444444456679999999999998              89999999994

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.22  E-value=2.6e-06  Score=87.65  Aligned_cols=103  Identities=19%  Similarity=0.325  Sum_probs=61.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCccc---ccHHHHHHHHHHhhchhhhccCceEEEEcCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVG---EDVESILYKLLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vG---e~~e~~L~~lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                      .+++|+|++|||||+||.+||+++   +..++.++..++... +..   .. .......+..    +  ..--+|+|||+
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~-l~~~~~~~-~~~~~~~~~~----l--~~~DLLIIDDl  255 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEI-LREIRFNN-DKELEEVYDL----L--INCDLLIIDDL  255 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHH-HHHHHhcc-chhHHHHHHH----h--ccCCEEEEecc
Confidence            679999999999999999999977   557777777766531 100   00 0000000111    1  12248999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      ......            ...++.|+.+++....          ...-+|.|||..+++
T Consensus       256 G~e~~t------------~~~~~~Lf~iin~R~~----------~~k~tIiTSNl~~~e  292 (329)
T PRK06835        256 GTEKIT------------EFSKSELFNLINKRLL----------RQKKMIISTNLSLEE  292 (329)
T ss_pred             CCCCCC------------HHHHHHHHHHHHHHHH----------CCCCEEEECCCCHHH
Confidence            765432            1156777777773321          122467777776544

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=98.21  E-value=1.6e-06  Score=94.43  Aligned_cols=155  Identities=19%  Similarity=0.226  Sum_probs=95.4

Q ss_pred             HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHH
Q 012525          266 EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       266 el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraL  345 (461)
                      .+...|-.-|.|.+.+|.-|...+.       ..- ++.+.          .... -...-||++.|.||||||.+.++.
T Consensus       338 ~lv~Sl~PsIyGhe~VK~GilL~Lf-------GGv-~K~a~----------eg~~-lRGDinv~iVGDPgt~KSQfLk~v  398 (764)
T KOG0480|consen  338 NLVNSLFPSIYGHELVKAGILLSLF-------GGV-HKSAG----------EGTS-LRGDINVCIVGDPGTGKSQFLKAV  398 (764)
T ss_pred             HHHHhhCccccchHHHHhhHHHHHh-------CCc-cccCC----------CCcc-ccCCceEEEeCCCCccHHHHHHHH
Confidence            3566666668899999988776662       110 01000          0000 123478999999999999999999


Q ss_pred             HHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHH
Q 012525          346 ARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALL  425 (461)
Q Consensus       346 A~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL  425 (461)
                      +..+-..++.--- .-..+|+...-+......-|.-..+.+..+.+||-.|||+|+|..+              -+.+|+
T Consensus       399 ~~fsPR~vYtsGk-aSSaAGLTaaVvkD~esgdf~iEAGALmLADnGICCIDEFDKMd~~--------------dqvAih  463 (764)
T KOG0480|consen  399 CAFSPRSVYTSGK-ASSAAGLTAAVVKDEESGDFTIEAGALMLADNGICCIDEFDKMDVK--------------DQVAIH  463 (764)
T ss_pred             hccCCcceEecCc-ccccccceEEEEecCCCCceeeecCcEEEccCceEEechhcccChH--------------hHHHHH
Confidence            9988665442221 1111222111101111112322334555689999999999999986              588999


Q ss_pred             HHHhCceeeeecc--eeeecCCeEEEecCCC
Q 012525          426 KMLEGTETKTFAA--VSKVSRDNLYIKTSGL  454 (461)
Q Consensus       426 ~~LEg~~v~i~~~--~r~~~rd~IiI~TsNi  454 (461)
                      +.||...+++--.  ....+.+.-+|+++|+
T Consensus       464 EAMEQQtISIaKAGv~aTLnARtSIlAAANP  494 (764)
T KOG0480|consen  464 EAMEQQTISIAKAGVVATLNARTSILAAANP  494 (764)
T ss_pred             HHHHhheehheecceEEeecchhhhhhhcCC
Confidence            9999887776533  4444456777777774

>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=98.19  E-value=9.1e-06  Score=84.68  Aligned_cols=106  Identities=17%  Similarity=0.263  Sum_probs=62.1

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcCCc-eEEecchhhhh----c--Cccc--ccHHHHHHHHHHhhchhhhccCceE
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVP-FVIADATTLTQ----A--GYVG--EDVESILYKLLAQAEFNVEAAQQGM  393 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~~p-fv~i~~s~l~~----~--g~vG--e~~e~~L~~lf~~a~~~v~~a~~gV  393 (461)
                      ..++++.|+|++|+|||+|.-++...+... -.++.......    .  .+.+  ..+......+.         ..-.|
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~---------~~~~l  130 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELA---------KESRL  130 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHH---------hcCCE
Confidence            457899999999999999999999887541 11111111110    0  0000  01111111111         12339


Q ss_pred             EEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCcCCC
Q 012525          394 VYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKTLWP  461 (461)
Q Consensus       394 LfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~l~P  461 (461)
                      |+|||++--.           .+...++..|+..|-             .+..++|+|||..++.+++
T Consensus       131 LcfDEF~V~D-----------iaDAmil~rLf~~l~-------------~~gvvlVaTSN~~P~~Ly~  174 (362)
T PF03969_consen  131 LCFDEFQVTD-----------IADAMILKRLFEALF-------------KRGVVLVATSNRPPEDLYK  174 (362)
T ss_pred             EEEeeeeccc-----------hhHHHHHHHHHHHHH-------------HCCCEEEecCCCChHHHcC
Confidence            9999988322           222336667776654             2357999999999998875

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

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.19  E-value=3.1e-06  Score=90.18  Aligned_cols=74  Identities=19%  Similarity=0.307  Sum_probs=45.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      .+++||||+|||||+|++++++++     +..++.+++.++... +...-....+.. |...   + .....+|+|||++
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f~~~-~~~~~~~~~~~~-f~~~---~-~~~~dvLlIDDi~  204 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLND-LVDSMKEGKLNE-FREK---Y-RKKVDVLLIDDVQ  204 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHH-HHHHHhcccHHH-HHHH---H-HhcCCEEEEechh
Confidence            459999999999999999999876     345677777665421 100000000111 1110   0 0135599999999


Q ss_pred             ccchh
Q 012525          401 KITKK  405 (461)
Q Consensus       401 ~L~~~  405 (461)
                      .+..+
T Consensus       205 ~l~~~  209 (440)
T PRK14088        205 FLIGK  209 (440)
T ss_pred             hhcCc
Confidence            87654

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=98.18  E-value=1.2e-05  Score=82.80  Aligned_cols=87  Identities=16%  Similarity=0.211  Sum_probs=58.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC------------------------ceEEecchhhhhcCcccccHHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV------------------------PFVIADATTLTQAGYVGEDVESILYKLLA  380 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~------------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~  380 (461)
                      ++.+||+||.|+||+++|+++|+.+.+                        +|+.+....-.  ..+  . .+.++.+..
T Consensus        24 ~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~--~~I--~-idqiR~l~~   98 (334)
T PRK07993         24 HHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGK--SSL--G-VDAVREVTE   98 (334)
T ss_pred             ceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEeccccc--ccC--C-HHHHHHHHH
Confidence            366899999999999999999997743                        11112111000  001  1 234455554


Q ss_pred             hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       381 ~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ............|+|||++|+|...              ..|+||+.||+
T Consensus        99 ~~~~~~~~g~~kV~iI~~ae~m~~~--------------AaNaLLKtLEE  134 (334)
T PRK07993         99 KLYEHARLGGAKVVWLPDAALLTDA--------------AANALLKTLEE  134 (334)
T ss_pred             HHhhccccCCceEEEEcchHhhCHH--------------HHHHHHHHhcC
Confidence            4443334456779999999999998              89999999994

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

Probab=98.15  E-value=1.1e-05  Score=89.67  Aligned_cols=111  Identities=20%  Similarity=0.327  Sum_probs=79.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ..+||+|+||||||++.+++|++++.++++++|.++...  .....+..+...|..+...    .+.||||-.+|-+.-+
T Consensus       432 ~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~--s~~~~etkl~~~f~~a~~~----~pavifl~~~dvl~id  505 (953)
T KOG0736|consen  432 PSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAE--SASHTETKLQAIFSRARRC----SPAVLFLRNLDVLGID  505 (953)
T ss_pred             eEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhc--ccchhHHHHHHHHHHHhhc----CceEEEEeccceeeec
Confidence            568999999999999999999999999999999999864  2334478888888877654    8999999999988754


Q ss_pred             hhccccccccchHHHHHHHHHHHhCceeeeecceeeecC-CeEEEecCCCC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSR-DNLYIKTSGLD  455 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~r-d~IiI~TsNid  455 (461)
                      +..   +.+   .+++..+...|+       ......+. ..|+|+|++-.
T Consensus       506 ~dg---ged---~rl~~~i~~~ls-------~e~~~~~~~~~ivv~t~~s~  543 (953)
T KOG0736|consen  506 QDG---GED---ARLLKVIRHLLS-------NEDFKFSCPPVIVVATTSSI  543 (953)
T ss_pred             CCC---chh---HHHHHHHHHHHh-------cccccCCCCceEEEEecccc
Confidence            322   112   235555555555       11112223 57888777644

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=98.12  E-value=1.2e-06  Score=97.14  Aligned_cols=152  Identities=19%  Similarity=0.234  Sum_probs=92.8

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      +...+...|.|.+.+|+.|.-.+..-..+                  ...... --...-||||.|.|||+||.|.+.++
T Consensus       280 l~~SiaPsIyG~e~VKkAilLqLfgGv~k------------------~~~~g~-~iRGDInILLvGDPgtaKSqlLk~v~  340 (682)
T COG1241         280 LIKSIAPSIYGHEDVKKAILLQLFGGVKK------------------NLPDGT-RIRGDIHILLVGDPGTAKSQLLKYVA  340 (682)
T ss_pred             HHHHhcccccCcHHHHHHHHHHhcCCCcc------------------cCCCCc-ccccceeEEEcCCCchhHHHHHHHHH
Confidence            44555666889999999887766311000                  000000 01224789999999999999999999


Q ss_pred             HhcCCceE-Eecch---hhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          347 RHVNVPFV-IADAT---TLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       347 ~~l~~pfv-~i~~s---~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                      +.+-..++ ....+   .|+.. .+- +   ....-+.-..+.+..+.+||..|||+|+|...              -..
T Consensus       341 ~~aPr~vytsgkgss~~GLTAa-v~r-d---~~tge~~LeaGALVlAD~Gv~cIDEfdKm~~~--------------dr~  401 (682)
T COG1241         341 KLAPRGVYTSGKGSSAAGLTAA-VVR-D---KVTGEWVLEAGALVLADGGVCCIDEFDKMNEE--------------DRV  401 (682)
T ss_pred             hhCCceEEEccccccccCceeE-EEE-c---cCCCeEEEeCCEEEEecCCEEEEEeccCCChH--------------HHH
Confidence            98855432 11111   12211 000 0   00000112234556689999999999999988              789


Q ss_pred             HHHHHHhCceeeeecc--eeeecCCeEEEecCCCCc
Q 012525          423 ALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       423 aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~  456 (461)
                      +|.+.||...+++--.  ....+.++-++++.|.-.
T Consensus       402 aihEaMEQQtIsIaKAGI~atLnARcsvLAAaNP~~  437 (682)
T COG1241         402 AIHEAMEQQTISIAKAGITATLNARCSVLAAANPKF  437 (682)
T ss_pred             HHHHHHHhcEeeecccceeeecchhhhhhhhhCCCC
Confidence            9999999888776533  223334666777777543

>PF13173 AAA_14: AAA domain

Probab=98.12  E-value=1e-05  Score=71.32  Aligned_cols=70  Identities=23%  Similarity=0.381  Sum_probs=46.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC--CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN--VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~--~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      ..++|+||.||||||+++.+++.+.  ..++.+++.+.......  . .. +...+....    ..+..+||||||+.+.
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~--~-~~-~~~~~~~~~----~~~~~~i~iDEiq~~~   74 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLA--D-PD-LLEYFLELI----KPGKKYIFIDEIQYLP   74 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHh--h-hh-hHHHHHHhh----ccCCcEEEEehhhhhc
Confidence            4589999999999999999998876  67777877766532110  0 01 222222211    1156799999999875

>PRK04132 replication factor C small subunit; Provisional

Probab=98.11  E-value=6.6e-06  Score=93.67  Aligned_cols=84  Identities=24%  Similarity=0.298  Sum_probs=61.0

Q ss_pred             CCcEEEEc--cCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhch--hhhccCceEEE
Q 012525          325 KSNVLLMG--PTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEF--NVEAAQQGMVY  395 (461)
Q Consensus       325 ~~~VLL~G--PPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~--~v~~a~~gVLf  395 (461)
                      +-+-+..|  |.+.||||+|++||+.+     +..|+++++++...        ...++........  .+...+..|+|
T Consensus       564 ~~~~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rg--------id~IR~iIk~~a~~~~~~~~~~KVvI  635 (846)
T PRK04132        564 GYHNFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERG--------INVIREKVKEFARTKPIGGASFKIIF  635 (846)
T ss_pred             chhhhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCccc--------HHHHHHHHHHHHhcCCcCCCCCEEEE
Confidence            44456678  99999999999999998     45799999998542        2234444332211  11112346999


Q ss_pred             EcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          396 IDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       396 IDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      |||+|.|+..              .|++|++.||.
T Consensus       636 IDEaD~Lt~~--------------AQnALLk~lEe  656 (846)
T PRK04132        636 LDEADALTQD--------------AQQALRRTMEM  656 (846)
T ss_pred             EECcccCCHH--------------HHHHHHHHhhC
Confidence            9999999987              89999999994

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=98.11  E-value=1.8e-06  Score=93.79  Aligned_cols=155  Identities=18%  Similarity=0.267  Sum_probs=83.5

Q ss_pred             HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHH
Q 012525          266 EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       266 el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraL  345 (461)
                      .+...+..-|+|.+.+|..+..++.       .. .++-.+.          .+++ ....||||+|.||||||.+.|-+
T Consensus       442 rIiaSiaPsIyGh~~VK~AvAlaLf-------GG-v~kn~~~----------khkv-RGDinvLL~GDPGTaKSQFLKY~  502 (854)
T KOG0477|consen  442 RIIASIAPSIYGHEDVKRAVALALF-------GG-VPKNPGG----------KHKV-RGDINVLLLGDPGTAKSQFLKYA  502 (854)
T ss_pred             HHHHhhCchhhchHHHHHHHHHHHh-------cC-CccCCCC----------Ccee-ccceeEEEecCCCccHHHHHHHH
Confidence            3556666668999999998888773       11 0110000          1111 22478999999999999999999


Q ss_pred             HHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHH
Q 012525          346 ARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALL  425 (461)
Q Consensus       346 A~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL  425 (461)
                      ++.....++..-...-. .|+........+...-.-..+.+..+.+||-+|||+|+|....              ...+-
T Consensus       503 eK~s~RAV~tTGqGASa-vGLTa~v~KdPvtrEWTLEaGALVLADkGvClIDEFDKMndqD--------------RtSIH  567 (854)
T KOG0477|consen  503 EKTSPRAVFTTGQGASA-VGLTAYVRKDPVTREWTLEAGALVLADKGVCLIDEFDKMNDQD--------------RTSIH  567 (854)
T ss_pred             HhcCcceeEeccCCccc-cceeEEEeeCCccceeeeccCeEEEccCceEEeehhhhhcccc--------------cchHH
Confidence            98776644422211100 0110000000000000011234556789999999999999862              23455


Q ss_pred             HHHhCceeeeecc--eeeecCCeEEEecCCC
Q 012525          426 KMLEGTETKTFAA--VSKVSRDNLYIKTSGL  454 (461)
Q Consensus       426 ~~LEg~~v~i~~~--~r~~~rd~IiI~TsNi  454 (461)
                      +.||...+.|--.  ....-.++.+|+++|.
T Consensus       568 EAMEQQSISISKAGIVtsLqArctvIAAanP  598 (854)
T KOG0477|consen  568 EAMEQQSISISKAGIVTSLQARCTVIAAANP  598 (854)
T ss_pred             HHHHhcchhhhhhhHHHHHHhhhhhheecCC
Confidence            5566554443221  1111124566666664

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=98.10  E-value=3.2e-05  Score=76.42  Aligned_cols=123  Identities=25%  Similarity=0.376  Sum_probs=82.6

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      |.. ++|.|+.|+.|......-.         .|                  .+..||||+|--|||||.|.||+..++ 
T Consensus        59 L~~-l~Gvd~qk~~L~~NT~~F~---------~G------------------~pANnVLLwGaRGtGKSSLVKA~~~e~~  110 (287)
T COG2607          59 LAD-LVGVDRQKEALVRNTEQFA---------EG------------------LPANNVLLWGARGTGKSSLVKALLNEYA  110 (287)
T ss_pred             HHH-HhCchHHHHHHHHHHHHHH---------cC------------------CcccceEEecCCCCChHHHHHHHHHHHH
Confidence            444 7999999998876552111         11                  223789999999999999999999877 


Q ss_pred             --CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          350 --NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       350 --~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                        +..+|+++-.++..-       ..++..+- ...      +.-|||.|+.-   -+          .++...-+|-.+
T Consensus       111 ~~glrLVEV~k~dl~~L-------p~l~~~Lr-~~~------~kFIlFcDDLS---Fe----------~gd~~yK~LKs~  163 (287)
T COG2607         111 DEGLRLVEVDKEDLATL-------PDLVELLR-ARP------EKFILFCDDLS---FE----------EGDDAYKALKSA  163 (287)
T ss_pred             hcCCeEEEEcHHHHhhH-------HHHHHHHh-cCC------ceEEEEecCCC---CC----------CCchHHHHHHHH
Confidence              457888888888741       23333332 222      34489999854   11          122256788889


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      |||...-       .|.+.++.+|+|..
T Consensus       164 LeG~ve~-------rP~NVl~YATSNRR  184 (287)
T COG2607         164 LEGGVEG-------RPANVLFYATSNRR  184 (287)
T ss_pred             hcCCccc-------CCCeEEEEEecCCc
Confidence            9977543       34568888999964

>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=98.10  E-value=1.2e-05  Score=77.92  Aligned_cols=81  Identities=21%  Similarity=0.421  Sum_probs=52.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcc----cccHHHHHHHHHHhhchhhhccCceEEEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYV----GEDVESILYKLLAQAEFNVEAAQQGMVYI  396 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~v----Ge~~e~~L~~lf~~a~~~v~~a~~gVLfI  396 (461)
                      ..++|+|++|+|||+|.+++++++     +..++.+++.++... +.    .... ..+...+         ..--+|+|
T Consensus        35 ~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~-~~~~~~~~~~-~~~~~~~---------~~~DlL~i  103 (219)
T PF00308_consen   35 NPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIRE-FADALRDGEI-EEFKDRL---------RSADLLII  103 (219)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHH-HHHHHHTTSH-HHHHHHH---------CTSSEEEE
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHH-HHHHHHcccc-hhhhhhh---------hcCCEEEE
Confidence            458999999999999999999865     456777877765531 10    0010 1111111         13349999


Q ss_pred             cCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          397 DEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       397 DEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      |+|+.+..+..            .+..|+.+++
T Consensus       104 DDi~~l~~~~~------------~q~~lf~l~n  124 (219)
T PF00308_consen  104 DDIQFLAGKQR------------TQEELFHLFN  124 (219)
T ss_dssp             ETGGGGTTHHH------------HHHHHHHHHH
T ss_pred             ecchhhcCchH------------HHHHHHHHHH
Confidence            99999887622            5677777766

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.

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=98.10  E-value=1.1e-05  Score=84.03  Aligned_cols=81  Identities=27%  Similarity=0.423  Sum_probs=55.5

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC--C
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN--V  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~--~  351 (461)
                      -++||.+|+++.-..+..-     ...+                     ..++.+||.||||||||.||-+||++++  .
T Consensus        25 GlVGQ~~AReAagiiv~mI-----k~~K---------------------~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~   78 (398)
T PF06068_consen   25 GLVGQEKAREAAGIIVDMI-----KEGK---------------------IAGRAILIAGPPGTGKTALAMAIAKELGEDV   78 (398)
T ss_dssp             TEES-HHHHHHHHHHHHHH-----HTT-----------------------TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS
T ss_pred             cccChHHHHHHHHHHHHHH-----hccc---------------------ccCcEEEEeCCCCCCchHHHHHHHHHhCCCC
Confidence            4899999999887777321     1111                     2348899999999999999999999997  6


Q ss_pred             ceEEecchhhhhcCcccccHHHHHHHHHHhhc
Q 012525          352 PFVIADATTLTQAGYVGEDVESILYKLLAQAE  383 (461)
Q Consensus       352 pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~  383 (461)
                      ||+.++++++-...   -.-...|.+.|.++.
T Consensus        79 PF~~isgSEiyS~e---~kKTE~L~qa~RraI  107 (398)
T PF06068_consen   79 PFVSISGSEIYSSE---VKKTEALTQAFRRAI  107 (398)
T ss_dssp             -EEEEEGGGG-BTT---C-HHHHHHHHHHCSE
T ss_pred             CeeEcccceeeecc---cCchHHHHHHHHHhh
Confidence            99999999887431   122456777777554

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.09  E-value=7.2e-06  Score=87.57  Aligned_cols=73  Identities=19%  Similarity=0.328  Sum_probs=45.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      .+++|+||+|+|||+|++++++.+   +..++.++...+... +...-....+ ..|....     ....+|+||||+.+
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~-~~~~l~~~~~-~~f~~~~-----~~~dvLiIDDiq~l  214 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEH-LVSAIRSGEM-QRFRQFY-----RNVDALFIEDIEVF  214 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHH-HHHHHhcchH-HHHHHHc-----ccCCEEEEcchhhh
Confidence            468999999999999999999876   567777777655421 1000000000 1121111     13459999999988


Q ss_pred             chh
Q 012525          403 TKK  405 (461)
Q Consensus       403 ~~~  405 (461)
                      ..+
T Consensus       215 ~~k  217 (445)
T PRK12422        215 SGK  217 (445)
T ss_pred             cCC
Confidence            754

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.07  E-value=1e-05  Score=82.51  Aligned_cols=38  Identities=21%  Similarity=0.336  Sum_probs=31.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT  362 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~  362 (461)
                      ..+++|+|++|||||+||.+||+++   +..++.+...++.
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~  196 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFI  196 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHH
Confidence            3679999999999999999999987   5666666666544

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=98.06  E-value=3.7e-05  Score=78.93  Aligned_cols=87  Identities=17%  Similarity=0.199  Sum_probs=57.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC-----------------------ceEEecchhhhhcCcccccHHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV-----------------------PFVIADATTLTQAGYVGEDVESILYKLLAQ  381 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~-----------------------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~  381 (461)
                      ++.+||.||.|+||+++|+.+|+.+.+                       +|+.+....-  .+.+  . .+.++.+...
T Consensus        25 ~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~--~~~I--~-vdqiR~l~~~   99 (319)
T PRK06090         25 PGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKE--GKSI--T-VEQIRQCNRL   99 (319)
T ss_pred             ceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcC--CCcC--C-HHHHHHHHHH
Confidence            356999999999999999999997743                       1222221100  0001  1 2334544444


Q ss_pred             hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       382 a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ...........|++||++|+|...              ..|+||+.||+
T Consensus       100 ~~~~~~~~~~kV~iI~~ae~m~~~--------------AaNaLLKtLEE  134 (319)
T PRK06090        100 AQESSQLNGYRLFVIEPADAMNES--------------ASNALLKTLEE  134 (319)
T ss_pred             HhhCcccCCceEEEecchhhhCHH--------------HHHHHHHHhcC
Confidence            333333445679999999999988              89999999994

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.05  E-value=5.4e-06  Score=84.44  Aligned_cols=93  Identities=27%  Similarity=0.352  Sum_probs=59.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec-chhhhhcCcccccHHHHHHHHHHhhc--hhhhc-cCceEEEEcCccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD-ATTLTQAGYVGEDVESILYKLLAQAE--FNVEA-AQQGMVYIDEVDK  401 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~-~s~l~~~g~vGe~~e~~L~~lf~~a~--~~v~~-a~~gVLfIDEID~  401 (461)
                      .|+|||||||||||+...+.|+.+..+.=.-+ ..++..+.-.|-++...-...|....  ..+.. +....++|||+|+
T Consensus        63 Ph~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaSd~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADa  142 (360)
T KOG0990|consen   63 PHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADA  142 (360)
T ss_pred             CcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhccCccCCcchHHHHHHHHhhccceeccccCceeEEEecchhH
Confidence            58999999999999999999998866411111 11222222233333333333343222  11111 3556899999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHhCce
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      |+..              +|++|.+.+|...
T Consensus       143 MT~~--------------AQnALRRviek~t  159 (360)
T KOG0990|consen  143 MTRD--------------AQNALRRVIEKYT  159 (360)
T ss_pred             hhHH--------------HHHHHHHHHHHhc
Confidence            9998              9999999888544

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.01  E-value=1.1e-05  Score=86.17  Aligned_cols=75  Identities=20%  Similarity=0.317  Sum_probs=45.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      .+++|+|++|||||+|++++++++     +..++.+++.++... +... .... ...+......+  ....+|+||||+
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~-~~~~-l~~~-~~~~~~~~~~~--~~~dvLiIDDiq  216 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARK-AVDI-LQKT-HKEIEQFKNEI--CQNDVLIIDDVQ  216 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHH-HHHH-HHHh-hhHHHHHHHHh--ccCCEEEEeccc
Confidence            458999999999999999999865     356677777765531 1100 0000 01111111111  134499999999


Q ss_pred             ccchh
Q 012525          401 KITKK  405 (461)
Q Consensus       401 ~L~~~  405 (461)
                      .+..+
T Consensus       217 ~l~~k  221 (450)
T PRK14087        217 FLSYK  221 (450)
T ss_pred             cccCC
Confidence            88754

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=97.99  E-value=3.5e-05  Score=75.25  Aligned_cols=25  Identities=32%  Similarity=0.639  Sum_probs=22.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..++|+||+|+||||+++.+++.+.
T Consensus        44 ~~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        44 GFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHhcC
Confidence            4588999999999999999999876

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.

>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=97.97  E-value=5.2e-05  Score=74.42  Aligned_cols=67  Identities=24%  Similarity=0.334  Sum_probs=50.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ....+.||+|||||.+.+.||+.++..++.++|++..+        ...+.+++.....     .+.-+.|||+++|..+
T Consensus        33 ~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~--------~~~l~ril~G~~~-----~GaW~cfdefnrl~~~   99 (231)
T PF12774_consen   33 LGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMD--------YQSLSRILKGLAQ-----SGAWLCFDEFNRLSEE   99 (231)
T ss_dssp             TEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS---------HHHHHHHHHHHHH-----HT-EEEEETCCCSSHH
T ss_pred             CCCCCcCCCCCCchhHHHHHHHHhCCeEEEeccccccc--------HHHHHHHHHHHhh-----cCchhhhhhhhhhhHH
Confidence            34678999999999999999999999999999998664        3445555543222     3568999999999987

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=97.93  E-value=5.8e-05  Score=76.52  Aligned_cols=91  Identities=21%  Similarity=0.136  Sum_probs=58.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecch--------h---hhhcCccc-ccHHHHHHHHHHhhchhhhccCce
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT--------T---LTQAGYVG-EDVESILYKLLAQAEFNVEAAQQG  392 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s--------~---l~~~g~vG-e~~e~~L~~lf~~a~~~v~~a~~g  392 (461)
                      ++.+||+||.|+||+++|.++|+.+-+.-..-.|.        +   +...+... -. .+.++.+..............
T Consensus        19 ~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~-idqiR~l~~~~~~~p~e~~~k   97 (290)
T PRK05917         19 PSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHS-IETPRAIKKQIWIHPYESPYK   97 (290)
T ss_pred             CeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCc-HHHHHHHHHHHhhCccCCCce
Confidence            36689999999999999999999775421000110        1   10000000 01 233455554444433345667


Q ss_pred             EEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          393 MVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       393 VLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      |++||++|+|+..              .+|+||+.||+
T Consensus        98 v~ii~~ad~mt~~--------------AaNaLLK~LEE  121 (290)
T PRK05917         98 IYIIHEADRMTLD--------------AISAFLKVLED  121 (290)
T ss_pred             EEEEechhhcCHH--------------HHHHHHHHhhc
Confidence            9999999999998              89999999994

>PRK06620 hypothetical protein; Validated

Probab=97.91  E-value=3.7e-05  Score=74.35  Aligned_cols=27  Identities=37%  Similarity=0.495  Sum_probs=24.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..++|+||+|||||+|++++++..+..
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~~   71 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNAY   71 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCCE
Confidence            568999999999999999999987653

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=97.91  E-value=4.9e-05  Score=82.72  Aligned_cols=32  Identities=34%  Similarity=0.432  Sum_probs=27.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +-+||+||+||||||++++||++++..+++-.
T Consensus        46 ~iLlLtGP~G~GKtttv~~La~elg~~v~Ew~   77 (519)
T PF03215_consen   46 RILLLTGPSGCGKTTTVKVLAKELGFEVQEWI   77 (519)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCeeEEec
Confidence            35789999999999999999999998777643

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.91  E-value=1.8e-05  Score=81.82  Aligned_cols=63  Identities=35%  Similarity=0.601  Sum_probs=49.2

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC--C
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN--V  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~--~  351 (461)
                      -++||.+|+++--..+..    + ...                     ...++.|||.||||||||.||-+||++|+  .
T Consensus        40 G~VGQ~~AReAaGvIv~m----i-k~g---------------------k~aGrgiLi~GppgTGKTAlA~gIa~eLG~dv   93 (450)
T COG1224          40 GLVGQEEAREAAGVIVKM----I-KQG---------------------KMAGRGILIVGPPGTGKTALAMGIARELGEDV   93 (450)
T ss_pred             cccchHHHHHhhhHHHHH----H-HhC---------------------cccccEEEEECCCCCcHHHHHHHHHHHhCCCC
Confidence            379999999977665531    1 111                     13358899999999999999999999996  6


Q ss_pred             ceEEecchhhh
Q 012525          352 PFVIADATTLT  362 (461)
Q Consensus       352 pfv~i~~s~l~  362 (461)
                      ||+.++.+++-
T Consensus        94 PF~~isgsEiY  104 (450)
T COG1224          94 PFVAISGSEIY  104 (450)
T ss_pred             Cceeeccceee
Confidence            99999988765

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.87  E-value=4.8e-05  Score=67.11  Aligned_cols=32  Identities=47%  Similarity=0.657  Sum_probs=25.2

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ++|+|+||+|||++++.++..+   +.+++.++..
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e   36 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIE   36 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECC
Confidence            7899999999999999998876   3455554443

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.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.87  E-value=2.8e-05  Score=70.99  Aligned_cols=59  Identities=24%  Similarity=0.305  Sum_probs=34.8

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCc--
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVP--  352 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~p--  352 (461)
                      .+|.++..+.|...+.                            ......+.+++|+|++|+|||+|.+.+.+.+...  
T Consensus         2 fvgR~~e~~~l~~~l~----------------------------~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~   53 (185)
T PF13191_consen    2 FVGREEEIERLRDLLD----------------------------AAQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGG   53 (185)
T ss_dssp             -TT-HHHHHHHHHTTG----------------------------GTSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT-
T ss_pred             CCCHHHHHHHHHHHHH----------------------------HHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCC
Confidence            4788888888777661                            0011224779999999999999999888766433  


Q ss_pred             -eEEecchhh
Q 012525          353 -FVIADATTL  361 (461)
Q Consensus       353 -fv~i~~s~l  361 (461)
                       ++.+++...
T Consensus        54 ~~~~~~~~~~   63 (185)
T PF13191_consen   54 YVISINCDDS   63 (185)
T ss_dssp             -EEEEEEETT
T ss_pred             EEEEEEEecc
Confidence             555555433

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.86  E-value=8.3e-05  Score=75.62  Aligned_cols=118  Identities=20%  Similarity=0.206  Sum_probs=67.0

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      +..+.+.....+..||..+|++.|...-.     +.+.  ++                  .....++||+|+++.|||++
T Consensus        23 ~~~eRI~~i~~~rWIgY~~A~~~L~~L~~-----Ll~~--P~------------------~~Rmp~lLivG~snnGKT~I   77 (302)
T PF05621_consen   23 SDEERIAYIRADRWIGYPRAKEALDRLEE-----LLEY--PK------------------RHRMPNLLIVGDSNNGKTMI   77 (302)
T ss_pred             CHHHHHHHHhcCCeecCHHHHHHHHHHHH-----HHhC--Cc------------------ccCCCceEEecCCCCcHHHH
Confidence            34444556666778999999998876542     1110  00                  01237899999999999999


Q ss_pred             HHHHHHhcC---------CceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          342 AKTLARHVN---------VPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       342 AraLA~~l~---------~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      ++.+.+...         .|++.+.+..--..           +..... ...+..+.......+...+-.+|+|||++.
T Consensus        78 i~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~-~~~~~~~~~~~~~llr~~~vrmLIIDE~H~  156 (302)
T PF05621_consen   78 IERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRP-RDRVAKLEQQVLRLLRRLGVRMLIIDEFHN  156 (302)
T ss_pred             HHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCC-CCCHHHHHHHHHHHHHHcCCcEEEeechHH
Confidence            999997552         36666665321110           000000 000111111111223334566999999999


Q ss_pred             cchh
Q 012525          402 ITKK  405 (461)
Q Consensus       402 L~~~  405 (461)
                      +...
T Consensus       157 lLaG  160 (302)
T PF05621_consen  157 LLAG  160 (302)
T ss_pred             Hhcc
Confidence            7654

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>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=97.83  E-value=6.1e-05  Score=75.54  Aligned_cols=115  Identities=16%  Similarity=0.224  Sum_probs=64.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC-ce--EEecchhhhhcCcccccHHHHHHHHHHh----hch---hhhccCceEE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV-PF--VIADATTLTQAGYVGEDVESILYKLLAQ----AEF---NVEAAQQGMV  394 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~-pf--v~i~~s~l~~~g~vGe~~e~~L~~lf~~----a~~---~v~~a~~gVL  394 (461)
                      ..++||.||+|||||++++.+-+.+.. .+  ..+.++..+.        ...++..++.    ..+   .....+..|+
T Consensus        33 ~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tt--------s~~~q~~ie~~l~k~~~~~~gP~~~k~lv~  104 (272)
T PF12775_consen   33 GRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTT--------SNQLQKIIESKLEKRRGRVYGPPGGKKLVL  104 (272)
T ss_dssp             TEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHH--------HHHHHHCCCTTECECTTEEEEEESSSEEEE
T ss_pred             CCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCC--------HHHHHHHHhhcEEcCCCCCCCCCCCcEEEE
Confidence            478999999999999999887665543 22  2344433332        2223322211    111   1122455699


Q ss_pred             EEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc-eeeecCCeEEEecCCCC
Q 012525          395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       395 fIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r~~~rd~IiI~TsNid  455 (461)
                      ||||++.-..+.-        +.......|.++||.+-...... ..+...+..+|++.|..
T Consensus       105 fiDDlN~p~~d~y--------gtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~  158 (272)
T PF12775_consen  105 FIDDLNMPQPDKY--------GTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPT  158 (272)
T ss_dssp             EEETTT-S---TT--------S--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESST
T ss_pred             EecccCCCCCCCC--------CCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCC
Confidence            9999996554421        11225677778898555544333 33444578888888753

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=97.81  E-value=1.2e-05  Score=86.08  Aligned_cols=152  Identities=17%  Similarity=0.230  Sum_probs=88.5

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHH
Q 012525          265 KEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       265 ~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAra  344 (461)
                      +.+.+.+...|+|.+++|+.|..++.-                  .......+..++ ...-||+|+|.||+.||.|.+.
T Consensus       334 ekLa~SiAPEIyGheDVKKaLLLlLVG------------------gvd~~~~dGMKI-RGdINicLmGDPGVAKSQLLky  394 (721)
T KOG0482|consen  334 EKLAASIAPEIYGHEDVKKALLLLLVG------------------GVDKSPGDGMKI-RGDINICLMGDPGVAKSQLLKY  394 (721)
T ss_pred             HHHHHhhchhhccchHHHHHHHHHhhC------------------CCCCCCCCCcee-ecceeEEecCCCchhHHHHHHH
Confidence            347777788899999999999887731                  011111111111 1246899999999999999999


Q ss_pred             HHHhcCCceEEecchhhhhcCcccccHHHHHHH----HHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          345 LARHVNVPFVIADATTLTQAGYVGEDVESILYK----LLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       345 LA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~----lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      +.+..-...+..--..   + =+|-. ...++.    ...-.-+.+..+.+||-.|||+|+|.+.              -
T Consensus       395 i~rlapRgvYTTGrGS---S-GVGLT-AAVmkDpvTgEM~LEGGALVLAD~GICCIDEfDKM~e~--------------D  455 (721)
T KOG0482|consen  395 ISRLAPRGVYTTGRGS---S-GVGLT-AAVMKDPVTGEMVLEGGALVLADGGICCIDEFDKMDES--------------D  455 (721)
T ss_pred             HHhcCcccceecCCCC---C-ccccc-hhhhcCCCCCeeEeccceEEEccCceEeehhhhhhhhh--------------h
Confidence            9987754333211110   0 01111 011111    0111123455678999999999999987              3


Q ss_pred             HHHHHHHHhCceeeeecc--eeeecCCeEEEecCCC
Q 012525          421 QQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGL  454 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNi  454 (461)
                      ..++-+.||...++|--.  .-....++-++++.|.
T Consensus       456 RtAIHEVMEQQTISIaKAGI~TtLNAR~sILaAANP  491 (721)
T KOG0482|consen  456 RTAIHEVMEQQTISIAKAGINTTLNARTSILAAANP  491 (721)
T ss_pred             hHHHHHHHHhhhhhhhhhccccchhhhHHhhhhcCc
Confidence            467788888766654322  1111224555666654

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

Probab=97.73  E-value=6.4e-05  Score=80.77  Aligned_cols=99  Identities=34%  Similarity=0.563  Sum_probs=78.1

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      .+.+++++||||||||++++++|.. +..+..++...+. .+++++. +..++.+|..+...    .++++++||+|.+.
T Consensus        17 ~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~a~~~----~~~ii~~d~~~~~~   89 (494)
T COG0464          17 PPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEIL-SKYVGES-ELRLRELFEEAEKL----APSIIFIDEIDALA   89 (494)
T ss_pred             CCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhh-hhhhhHH-HHHHHHHHHHHHHh----CCCeEeechhhhcc
Confidence            3578999999999999999999999 6655666666666 4577776 77888888777654    55899999999999


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhCce
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      +.+..   ........+...|+..|++..
T Consensus        90 ~~~~~---~~~~~~~~v~~~l~~~~d~~~  115 (494)
T COG0464          90 PKRSS---DQGEVERRVVAQLLALMDGLK  115 (494)
T ss_pred             cCccc---cccchhhHHHHHHHHhccccc
Confidence            99765   333344568999999999766

>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=97.72  E-value=3.1e-05  Score=66.51  Aligned_cols=31  Identities=42%  Similarity=0.777  Sum_probs=28.4

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      |+|.|+||+||||+|+.||+.++.+++.++.
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEecc
Confidence            7899999999999999999999988877766

...

>PRK09087 hypothetical protein; Validated

Probab=97.70  E-value=9.5e-05  Score=72.10  Aligned_cols=29  Identities=38%  Similarity=0.573  Sum_probs=24.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ..++|+||+|+|||+|++++++..+..++
T Consensus        45 ~~l~l~G~~GsGKThLl~~~~~~~~~~~i   73 (226)
T PRK09087         45 PVVVLAGPVGSGKTHLASIWREKSDALLI   73 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhcCCEEe
Confidence            34899999999999999999988765433

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.68  E-value=0.0002  Score=78.60  Aligned_cols=62  Identities=26%  Similarity=0.436  Sum_probs=44.2

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ ++|++++++.|...+......+                         ......++|.||||+|||+||+.||+.+
T Consensus        74 fF~d-~yGlee~ieriv~~l~~Aa~gl-------------------------~~~~~IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         74 AFEE-FYGMEEAIEQIVSYFRHAAQGL-------------------------EEKKQILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             chhc-ccCcHHHHHHHHHHHHHHHHhc-------------------------CCCCceEEEecCCCCCchHHHHHHHHHH
Confidence            4454 7999999999988874332221                         0123568899999999999999999876


Q ss_pred             C-CceEEec
Q 012525          350 N-VPFVIAD  357 (461)
Q Consensus       350 ~-~pfv~i~  357 (461)
                      . .+++.+.
T Consensus       128 e~~~~Y~~k  136 (644)
T PRK15455        128 ERVPIYVLK  136 (644)
T ss_pred             HhCcceeec
Confidence            3 3555443

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.66  E-value=0.00019  Score=76.26  Aligned_cols=103  Identities=16%  Similarity=0.203  Sum_probs=61.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh--cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH--VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~--l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      ..|+++.||+|||||+||.+|+..  +-.- ..++.+.+             +..+.....+.+  ...-+|+|||+..+
T Consensus       209 ~~Nli~lGp~GTGKThla~~l~~~~a~~sG-~f~T~a~L-------------f~~L~~~~lg~v--~~~DlLI~DEvgyl  272 (449)
T TIGR02688       209 NYNLIELGPKGTGKSYIYNNLSPYVILISG-GTITVAKL-------------FYNISTRQIGLV--GRWDVVAFDEVATL  272 (449)
T ss_pred             CCcEEEECCCCCCHHHHHHHHhHHHHHHcC-CcCcHHHH-------------HHHHHHHHHhhh--ccCCEEEEEcCCCC
Confidence            478999999999999999998765  2110 11222222             222222222221  24458999999986


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSG  453 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsN  453 (461)
                      .-.+.          +.+++.|...|+.+.+............++++.-.|
T Consensus       273 p~~~~----------~~~v~imK~yMesg~fsRG~~~~~a~as~vfvGNi~  313 (449)
T TIGR02688       273 KFAKP----------KELIGILKNYMESGSFTRGDETKSSDASFVFLGNVP  313 (449)
T ss_pred             cCCch----------HHHHHHHHHHHHhCceeccceeeeeeeEEEEEcccC
Confidence            65421          237889999999888887544322222455544333

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.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.65  E-value=0.00011  Score=67.89  Aligned_cols=36  Identities=31%  Similarity=0.619  Sum_probs=30.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLT  362 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~  362 (461)
                      ..|||++|-|||||||+|..||+.++.+++.+  +++.
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~~i~i--sd~v   42 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLEYIEI--SDLV   42 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCceEeh--hhHH
Confidence            47899999999999999999999999887654  4444

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.63  E-value=5.8e-05  Score=68.37  Aligned_cols=34  Identities=29%  Similarity=0.589  Sum_probs=30.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +..|+|+|+|||||||+|+.||+.++.+|+..+.
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d~   37 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTDH   37 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEChH
Confidence            4679999999999999999999999999886553

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.57  E-value=5.5e-05  Score=89.29  Aligned_cols=122  Identities=20%  Similarity=0.189  Sum_probs=83.7

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhc-CcccccHHHHHHH--HHHhhchhhhccCceEEEEc
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA-GYVGEDVESILYK--LLAQAEFNVEAAQQGMVYID  397 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~-g~vGe~~e~~L~~--lf~~a~~~v~~a~~gVLfID  397 (461)
                      ++...+++||.|.||+|||.|..+||+..|..+++++.++.++- +.+|.+..-.-..  .+..+...-...+++-|+||
T Consensus      1539 Amqv~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVlLD 1618 (4600)
T COG5271        1539 AMQVGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVLLD 1618 (4600)
T ss_pred             HHhcCCceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhhcCCEEEee
Confidence            34457899999999999999999999999999999998754431 1233221111001  11123333334577889999


Q ss_pred             CccccchhhhccccccccchHHHHHHHHHHHh-CceeeeecceeeecC--CeEEEecCCCCc
Q 012525          398 EVDKITKKAESLNISRDVSGEGVQQALLKMLE-GTETKTFAAVSKVSR--DNLYIKTSGLDS  456 (461)
Q Consensus       398 EID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE-g~~v~i~~~~r~~~r--d~IiI~TsNid~  456 (461)
                      |++-.+..              ++.-|-..|| .++..|++.......  ++.+.+|.|...
T Consensus      1619 EiNLaSQS--------------VlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~ 1666 (4600)
T COG5271        1619 EINLASQS--------------VLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQD 1666 (4600)
T ss_pred             hhhhhHHH--------------HHHHHHHHHhhccccccccccceeeccCCeeeeeecCchh
Confidence            99966555              8888888899 566777777433333  799999998653

>PHA00729 NTP-binding motif containing protein

Probab=97.57  E-value=0.00014  Score=71.33  Aligned_cols=25  Identities=40%  Similarity=0.561  Sum_probs=23.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .+|+|+|+||||||+||.+|++.++
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4799999999999999999999875

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.56  E-value=0.00012  Score=68.93  Aligned_cols=35  Identities=34%  Similarity=0.708  Sum_probs=32.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATT  360 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~  360 (461)
                      .+|+|.|++|+||||+.++||+.++.+|+..|...
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D~~I   37 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTDQEI   37 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccchHHH
Confidence            57999999999999999999999999999887653

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=97.55  E-value=0.00065  Score=68.98  Aligned_cols=89  Identities=18%  Similarity=0.197  Sum_probs=55.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceE-------E-ecchhhhhc---C--cc---ccc-HHHHHHHHHHhhchhhhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFV-------I-ADATTLTQA---G--YV---GED-VESILYKLLAQAEFNVEA  388 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv-------~-i~~s~l~~~---g--~v---Ge~-~e~~L~~lf~~a~~~v~~  388 (461)
                      +.+||+||  +||+++|+.+|+.+.+.-.       . -+|..+...   +  ++   |.. -.+.++.+..........
T Consensus        25 hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~~p~~  102 (290)
T PRK07276         25 HAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSGYE  102 (290)
T ss_pred             eeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhhCccc
Confidence            56899996  6899999999987743110       0 011111100   0  11   110 023445555444433334


Q ss_pred             cCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          389 AQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       389 a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      +...|++||++|+|...              ..|+||+.||+
T Consensus       103 ~~~kV~II~~ad~m~~~--------------AaNaLLKtLEE  130 (290)
T PRK07276        103 GKQQVFIIKDADKMHVN--------------AANSLLKVIEE  130 (290)
T ss_pred             CCcEEEEeehhhhcCHH--------------HHHHHHHHhcC
Confidence            56679999999999998              89999999994

>PHA02774 E1; Provisional

Probab=97.55  E-value=0.00042  Score=76.04  Aligned_cols=100  Identities=16%  Similarity=0.253  Sum_probs=62.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEE-ecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVI-ADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~-i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      ...++|+||||||||++|-+|++.++..++. ++...   .-|        |+.+.          .--|++|||+-.-.
T Consensus       434 knciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s---~Fw--------Lqpl~----------d~ki~vlDD~t~~~  492 (613)
T PHA02774        434 KNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKS---HFW--------LQPLA----------DAKIALLDDATHPC  492 (613)
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECcc---ccc--------cchhc----------cCCEEEEecCcchH
Confidence            3679999999999999999999998654432 44311   101        11111          22389999993221


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhCceeeeecce--eeecCCeEEEecCCCCcCc
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV--SKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~--r~~~rd~IiI~TsNid~e~  458 (461)
                      -.             -+...|..+|+|..+.+..+-  ...-+-.=+|.|||++...
T Consensus       493 w~-------------y~d~~Lrn~LdG~~v~lD~Khk~~~q~k~pPlIITSN~d~~~  536 (613)
T PHA02774        493 WD-------------YIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKA  536 (613)
T ss_pred             HH-------------HHHHHHHHHcCCCcceeeecccCcccccCCCEEEecCCCccc
Confidence            11             145578889999977765541  1111234567899988653

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=97.52  E-value=0.00014  Score=68.06  Aligned_cols=23  Identities=35%  Similarity=0.712  Sum_probs=20.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      |++|+|+||+||||+++.+.+.+
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHH
T ss_pred             CEEEECcCCCCHHHHHHHHHHHh
Confidence            58999999999999999999887

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.

>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]

Probab=97.51  E-value=2.7e-05  Score=83.41  Aligned_cols=115  Identities=23%  Similarity=0.308  Sum_probs=66.3

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      +.+.+..-|+|.+++|+.+.-+|.       ...++.-      ++.      -.....-||||.|.|||.|+.|.+-+-
T Consensus       325 is~sIAPSIfG~~DiKkAiaClLF-------gGsrK~L------pDg------~~lRGDINVLLLGDPgtAKSQlLKFvE  385 (729)
T KOG0481|consen  325 ISKSIAPSIFGHEDIKKAIACLLF-------GGSRKRL------PDG------VTLRGDINVLLLGDPGTAKSQLLKFVE  385 (729)
T ss_pred             HhhccCchhcCchhHHHHHHHHhh-------cCccccC------CCc------ceeccceeEEEecCCchhHHHHHHHHH
Confidence            455556668999999999987773       1111110      000      011234789999999999999999887


Q ss_pred             HhcCCceEEec----chhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          347 RHVNVPFVIAD----ATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       347 ~~l~~pfv~i~----~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      +..-.-++.--    ++.|+.+ ....    ....-|-..-+.+..+.+||+.|||+|+|-+.
T Consensus       386 kvsPIaVYTSGKGSSAAGLTAS-V~RD----~~tReFylEGGAMVLADgGVvCIDEFDKMre~  443 (729)
T KOG0481|consen  386 KVSPIAVYTSGKGSSAAGLTAS-VIRD----PSTREFYLEGGAMVLADGGVVCIDEFDKMRED  443 (729)
T ss_pred             hcCceEEEecCCCcccccceee-EEec----CCcceEEEecceEEEecCCEEEeehhhccCch
Confidence            76544333111    1111111 0000    00111212223345579999999999999877

>PRK13947 shikimate kinase; Provisional

Probab=97.49  E-value=0.0001  Score=67.38  Aligned_cols=33  Identities=33%  Similarity=0.584  Sum_probs=30.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      +|+|.|+||||||++|+.||+.++.+|+..+..
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d~~   35 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTDKE   35 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECchh
Confidence            699999999999999999999999999876653

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.46  E-value=0.00066  Score=68.51  Aligned_cols=86  Identities=23%  Similarity=0.364  Sum_probs=55.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC---c--------------------------eEEecchhhhhcCcccccHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV---P--------------------------FVIADATTLTQAGYVGEDVESILY  376 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~---p--------------------------fv~i~~s~l~~~g~vGe~~e~~L~  376 (461)
                      .|+|+|||+|+||-|.+.+|-+++..   .                          .++++.++      .|....-.++
T Consensus        35 PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEitPSD------aG~~DRvViQ  108 (351)
T KOG2035|consen   35 PHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEITPSD------AGNYDRVVIQ  108 (351)
T ss_pred             CeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEeChhh------cCcccHHHHH
Confidence            78999999999999999999887722   1                          11222222      2222244445


Q ss_pred             HHHHhhchh----hh-ccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          377 KLLAQAEFN----VE-AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       377 ~lf~~a~~~----v~-~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      +++.+....    .. ...-.|++|.|+|.|+.+              +|.+|.+-||..
T Consensus       109 ellKevAQt~qie~~~qr~fKvvvi~ead~LT~d--------------AQ~aLRRTMEkY  154 (351)
T KOG2035|consen  109 ELLKEVAQTQQIETQGQRPFKVVVINEADELTRD--------------AQHALRRTMEKY  154 (351)
T ss_pred             HHHHHHHhhcchhhccccceEEEEEechHhhhHH--------------HHHHHHHHHHHH
Confidence            554432111    11 112349999999999998              999999999944

>PRK13948 shikimate kinase; Provisional

Probab=97.46  E-value=0.00025  Score=67.18  Aligned_cols=38  Identities=29%  Similarity=0.353  Sum_probs=33.6

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      +..+.+|+|.|.+|+||||+++.||+.++.+|+..|..
T Consensus         7 ~~~~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D~~   44 (182)
T PRK13948          7 ERPVTWVALAGFMGTGKSRIGWELSRALMLHFIDTDRY   44 (182)
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEECCHH
Confidence            34568899999999999999999999999999977743

>PRK07261 topology modulation protein; Provisional

Probab=97.45  E-value=0.00033  Score=65.24  Aligned_cols=34  Identities=35%  Similarity=0.648  Sum_probs=29.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecchh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATT  360 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~  360 (461)
                      .|+++|++|+||||||+.|++.++.+++.++.-.
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~   35 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLH   35 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEE
Confidence            3899999999999999999999999888776543

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=97.44  E-value=0.00075  Score=67.54  Aligned_cols=91  Identities=14%  Similarity=0.163  Sum_probs=55.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCce-----EE-ecchhhhhc---C--ccc-----ccHHHHHHHHHHhhchh-hh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPF-----VI-ADATTLTQA---G--YVG-----EDVESILYKLLAQAEFN-VE  387 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pf-----v~-i~~s~l~~~---g--~vG-----e~~e~~L~~lf~~a~~~-v~  387 (461)
                      ++.+||+|+.|+||..+|.++|+.+-+.-     -. .+|..+...   +  ++.     -. .+.++.+....... ++
T Consensus         7 ~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          7 THPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIK-KEDALSIINKLNRPSVE   85 (261)
T ss_pred             CcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCC-HHHHHHHHHHHccCchh
Confidence            46799999999999999999998763310     00 001111100   0  000     01 23333333322211 12


Q ss_pred             ccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       388 ~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .....|++||++|+|...              ..|+||+.||+
T Consensus        86 ~~~~KV~II~~ae~m~~~--------------AaNaLLK~LEE  114 (261)
T PRK05818         86 SNGKKIYIIYGIEKLNKQ--------------SANSLLKLIEE  114 (261)
T ss_pred             cCCCEEEEeccHhhhCHH--------------HHHHHHHhhcC
Confidence            235679999999999998              89999999994

>KOG0479 consensus DNA replication licensing factor, MCM3 component [Replication, recombination and repair]

Probab=97.42  E-value=0.00022  Score=77.56  Aligned_cols=144  Identities=19%  Similarity=0.236  Sum_probs=87.8

Q ss_pred             HHHHHHhhcCChHHHHHHHHHHHHHHH-HHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHH
Q 012525          267 ICKGLDKFVIGQEKAKKVLSVAVYNHY-KRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       267 l~~~Ld~~VvGqd~aK~~L~~al~~~~-kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraL  345 (461)
                      +.+.|..-|.|.+.+|+.|.-++.--. +.+.+..+                    -...-||||.|.|-|.||.|.|.+
T Consensus       295 La~SLAPSI~GH~~vKkAillLLlGGvEk~L~NGsh--------------------lRGDINiLlvGDPSvAKSQLLRyV  354 (818)
T KOG0479|consen  295 LARSLAPSIYGHDYVKKAILLLLLGGVEKNLENGSH--------------------LRGDINILLVGDPSVAKSQLLRYV  354 (818)
T ss_pred             HhhccCcccccHHHHHHHHHHHHhccceeccCCCce--------------------eccceeEEEecCchHHHHHHHHHH
Confidence            445566779999999999987774111 11111111                    122478999999999999999988


Q ss_pred             HHhcCCce---------EEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccc
Q 012525          346 ARHVNVPF---------VIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVS  416 (461)
Q Consensus       346 A~~l~~pf---------v~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s  416 (461)
                      -+....-.         |-+.++-.++ .-.|   |.   .+-   .+....+..||+.|||+|+|+.-           
T Consensus       355 LntAplAI~TTGRGSSGVGLTAAVTtD-~eTG---ER---RLE---AGAMVLADRGVVCIDEFDKMsDi-----------  413 (818)
T KOG0479|consen  355 LNTAPLAIATTGRGSSGVGLTAAVTTD-QETG---ER---RLE---AGAMVLADRGVVCIDEFDKMSDI-----------  413 (818)
T ss_pred             HhcccccccccCCCCCCccceeEEeec-cccc---hh---hhh---cCceEEccCceEEehhcccccch-----------
Confidence            76552211         0111111110 0111   21   222   12334578999999999999986           


Q ss_pred             hHHHHHHHHHHHhCceeeeecceee--ecCCeEEEecCCC
Q 012525          417 GEGVQQALLKMLEGTETKTFAAVSK--VSRDNLYIKTSGL  454 (461)
Q Consensus       417 ~~~v~~aLL~~LEg~~v~i~~~~r~--~~rd~IiI~TsNi  454 (461)
                         -.-++-+.||...++|--...+  ...++-+|++.|.
T Consensus       414 ---DRvAIHEVMEQqtVTIaKAGIHasLNARCSVlAAANP  450 (818)
T KOG0479|consen  414 ---DRVAIHEVMEQQTVTIAKAGIHASLNARCSVLAAANP  450 (818)
T ss_pred             ---hHHHHHHHHhcceEEeEeccchhhhccceeeeeecCc
Confidence               3468889999888776544222  2237888888875

>PRK08118 topology modulation protein; Reviewed

Probab=97.42  E-value=0.00013  Score=67.81  Aligned_cols=33  Identities=39%  Similarity=0.700  Sum_probs=30.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      .|+++|+||+||||||+.|++.++.+++.++.-
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l   35 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDAL   35 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchh
Confidence            489999999999999999999999998877754

>PRK03839 putative kinase; Provisional

Probab=97.42  E-value=0.00014  Score=67.51  Aligned_cols=32  Identities=28%  Similarity=0.428  Sum_probs=29.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|+|.|+||+||||+++.||+.++.+|+.++-
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~~~~id~d~   33 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLGYEYVDLTE   33 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEehhh
Confidence            38999999999999999999999999987663

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=97.40  E-value=0.00082  Score=68.49  Aligned_cols=84  Identities=18%  Similarity=0.223  Sum_probs=55.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC-----------c--eEEecchhhhhcCcccccHHHHHHHHHHhhchhh-hccCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV-----------P--FVIADATTLTQAGYVGEDVESILYKLLAQAEFNV-EAAQQ  391 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~-----------p--fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v-~~a~~  391 (461)
                      +.+||+|+.|.||+++|+.+++.+.+           |  ++.++...   . .  -. ...++.+........ +....
T Consensus        19 haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g---~-~--i~-vd~Ir~l~~~~~~~~~~~~~~   91 (299)
T PRK07132         19 HSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFD---K-D--LS-KSEFLSAINKLYFSSFVQSQK   91 (299)
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCC---C-c--CC-HHHHHHHHHHhccCCcccCCc
Confidence            55789999999999999999998732           1  11221000   0 0  11 234444444443322 22467


Q ss_pred             eEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          392 GMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       392 gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .|++||++|+|...              .+++||+.||+
T Consensus        92 KvvII~~~e~m~~~--------------a~NaLLK~LEE  116 (299)
T PRK07132         92 KILIIKNIEKTSNS--------------LLNALLKTIEE  116 (299)
T ss_pred             eEEEEecccccCHH--------------HHHHHHHHhhC
Confidence            79999999999887              89999999994

>PRK00625 shikimate kinase; Provisional

Probab=97.38  E-value=0.00016  Score=67.81  Aligned_cols=33  Identities=33%  Similarity=0.564  Sum_probs=30.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      +|+|.|.||+||||+++.||+.++.+|+.++..
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D~~   34 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTDDL   34 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhhHH
Confidence            589999999999999999999999999888754

>PF05729 NACHT: NACHT domain

Probab=97.37  E-value=0.00073  Score=60.13  Aligned_cols=78  Identities=18%  Similarity=0.384  Sum_probs=43.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCC--------c-eEEecchhhhhcCcccccHHHHHHHHHHhh--------chhhhcc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNV--------P-FVIADATTLTQAGYVGEDVESILYKLLAQA--------EFNVEAA  389 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~--------p-fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a--------~~~v~~a  389 (461)
                      -++|+|++|+|||++++.++..+..        + ++.+...+....... ......+...+...        .......
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNS-RSLADLLFDQLPESIAPIEELLQELLEKN   80 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhcccc-chHHHHHHHhhccchhhhHHHHHHHHHcC
Confidence            4789999999999999999976621        1 223333333322111 11122222211111        1112235


Q ss_pred             CceEEEEcCccccchh
Q 012525          390 QQGMVYIDEVDKITKK  405 (461)
Q Consensus       390 ~~gVLfIDEID~L~~~  405 (461)
                      ...+|+||.+|.+...
T Consensus        81 ~~~llilDglDE~~~~   96 (166)
T PF05729_consen   81 KRVLLILDGLDELEEQ   96 (166)
T ss_pred             CceEEEEechHhcccc
Confidence            6679999999998875

>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=97.37  E-value=0.00018  Score=64.13  Aligned_cols=32  Identities=41%  Similarity=0.742  Sum_probs=28.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +|+|+|++|+||||+|+.||+.++.+++..+.
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d~   32 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLDE   32 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEchH
Confidence            48999999999999999999999999886663

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.

>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=97.34  E-value=0.00044  Score=64.82  Aligned_cols=25  Identities=44%  Similarity=0.743  Sum_probs=23.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .+++|+||.|+|||+|++.+.+.+.
T Consensus        21 ~~~~l~G~rg~GKTsLl~~~~~~~~   45 (234)
T PF01637_consen   21 QHILLYGPRGSGKTSLLKEFINELK   45 (234)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHCT
T ss_pred             cEEEEEcCCcCCHHHHHHHHHHHhh
Confidence            6799999999999999999999883

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.33  E-value=0.0011  Score=62.10  Aligned_cols=24  Identities=29%  Similarity=0.545  Sum_probs=22.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|+++|+||+||||++..+|+.+
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHH
Confidence            568999999999999999999776

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.33  E-value=0.0022  Score=66.45  Aligned_cols=107  Identities=21%  Similarity=0.248  Sum_probs=62.6

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhcCCce-EEecchhhh----hc--Cccccc--HHHHHHHHHHhhchhhhccCce
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHVNVPF-VIADATTLT----QA--GYVGED--VESILYKLLAQAEFNVEAAQQG  392 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pf-v~i~~s~l~----~~--g~vGe~--~e~~L~~lf~~a~~~v~~a~~g  392 (461)
                      ...++++.|+|+.|.|||+|.-.+...+...- .++......    +.  .+.|+.  +..+-.++..         +-.
T Consensus        62 ~~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~FM~~vH~~l~~l~g~~dpl~~iA~~~~~---------~~~  132 (367)
T COG1485          62 HGPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQGQTDPLPPIADELAA---------ETR  132 (367)
T ss_pred             CCCCceEEEECCCCccHHHHHHHHHhhCCccccccccHHHHHHHHHHHHHHHcCCCCccHHHHHHHHh---------cCC
Confidence            34568999999999999999988888774421 112111111    00  011221  0111111221         234


Q ss_pred             EEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCcCCC
Q 012525          393 MVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKTLWP  461 (461)
Q Consensus       393 VLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~l~P  461 (461)
                      ||.|||+.--           |...--++..|+..|-             .+..++|+|||..++.+++
T Consensus       133 vLCfDEF~Vt-----------DI~DAMiL~rL~~~Lf-------------~~GV~lvaTSN~~P~~LY~  177 (367)
T COG1485         133 VLCFDEFEVT-----------DIADAMILGRLLEALF-------------ARGVVLVATSNTAPDNLYK  177 (367)
T ss_pred             EEEeeeeeec-----------ChHHHHHHHHHHHHHH-------------HCCcEEEEeCCCChHHhcc
Confidence            9999998721           1122237777777664             2356899999999988874

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.33  E-value=0.0012  Score=63.34  Aligned_cols=94  Identities=21%  Similarity=0.318  Sum_probs=58.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ..++|.|+-|+|||++.+.|+...    +.-......     .   .+.+..+.          ..-|+.|||++.+..+
T Consensus        53 ~~lvl~G~QG~GKStf~~~L~~~~----~~d~~~~~~-----~---kd~~~~l~----------~~~iveldEl~~~~k~  110 (198)
T PF05272_consen   53 TVLVLVGKQGIGKSTFFRKLGPEY----FSDSINDFD-----D---KDFLEQLQ----------GKWIVELDELDGLSKK  110 (198)
T ss_pred             eeeeEecCCcccHHHHHHHHhHHh----ccCccccCC-----C---cHHHHHHH----------HhHheeHHHHhhcchh
Confidence            347899999999999999997662    111111111     0   11111111          1227899999988855


Q ss_pred             hhccccccccchHHHHHHHHHHHhCceeeeec--c--eeeecCCeEEEecCCCC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTETKTFA--A--VSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~--~--~r~~~rd~IiI~TsNid  455 (461)
                                    -+++|-.+|.........  .  ....++..++|+|+|.+
T Consensus       111 --------------~~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~  150 (198)
T PF05272_consen  111 --------------DVEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDD  150 (198)
T ss_pred             --------------hHHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCc
Confidence                          456777777754443332  2  45566789999999975

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=97.30  E-value=0.00051  Score=68.23  Aligned_cols=83  Identities=18%  Similarity=0.309  Sum_probs=48.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc------eEEecch------hhhhc-------CcccccHHH---HHHHHHHhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP------FVIADAT------TLTQA-------GYVGEDVES---ILYKLLAQA  382 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p------fv~i~~s------~l~~~-------g~vGe~~e~---~L~~lf~~a  382 (461)
                      +..++|.||+|+|||||++.|++.+...      ++.+...      ++...       .-.++....   ........+
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a   95 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKA   95 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHH
Confidence            4668999999999999999999877542      2221111      11110       001122222   222333344


Q ss_pred             chhhhccCceEEEEcCccccchhhh
Q 012525          383 EFNVEAAQQGMVYIDEVDKITKKAE  407 (461)
Q Consensus       383 ~~~v~~a~~gVLfIDEID~L~~~R~  407 (461)
                      .......+..+|||||+.++....+
T Consensus        96 ~~~~~~G~~vll~iDei~r~a~a~~  120 (249)
T cd01128          96 KRLVEHGKDVVILLDSITRLARAYN  120 (249)
T ss_pred             HHHHHCCCCEEEEEECHHHhhhhhh
Confidence            4333345677999999999987643

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.

>PRK10536 hypothetical protein; Provisional

Probab=97.30  E-value=0.0021  Score=64.42  Aligned_cols=23  Identities=26%  Similarity=0.431  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..+++.||+|||||+||.+++..
T Consensus        75 ~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         75 QLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999999874

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.29  E-value=0.0015  Score=62.23  Aligned_cols=90  Identities=21%  Similarity=0.312  Sum_probs=47.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCc---ccccHHHHHHHHHHhhchhh-----hccCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGY---VGEDVESILYKLLAQAEFNV-----EAAQQGMV  394 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~---vGe~~e~~L~~lf~~a~~~v-----~~a~~gVL  394 (461)
                      +.++|.|++|||||++.+.+++.+   +..++.+..+.-....+   .+.. ...+..++.......     ......+|
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~~~~-a~Ti~~~l~~~~~~~~~~~~~~~~~~vl   97 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKTGIE-AQTIHSFLYRIPNGDDEGRPELPKKDVL   97 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHTS--EEEHHHHTTEECCEECCSSCC-TSTSEE
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhhCcc-hhhHHHHHhcCCcccccccccCCcccEE
Confidence            457889999999999999988765   44555544432221000   0000 011111111111100     02344699


Q ss_pred             EEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       395 fIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ||||+-.+...              ....|+..++.
T Consensus        98 iVDEasmv~~~--------------~~~~ll~~~~~  119 (196)
T PF13604_consen   98 IVDEASMVDSR--------------QLARLLRLAKK  119 (196)
T ss_dssp             EESSGGG-BHH--------------HHHHHHHHS-T
T ss_pred             EEecccccCHH--------------HHHHHHHHHHh
Confidence            99999988877              67777777764

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=97.28  E-value=0.0004  Score=70.60  Aligned_cols=64  Identities=30%  Similarity=0.455  Sum_probs=47.1

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC--C
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN--V  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~--~  351 (461)
                      -++||+.|++.--..+.....     .                     ...++.|||.||||||||.||-+|+++++  .
T Consensus        39 g~vGQ~~AReAagiivdlik~-----K---------------------kmaGravLlaGppgtGKTAlAlaisqELG~kv   92 (456)
T KOG1942|consen   39 GFVGQENAREAAGIIVDLIKS-----K---------------------KMAGRAVLLAGPPGTGKTALALAISQELGPKV   92 (456)
T ss_pred             ccccchhhhhhhhHHHHHHHh-----h---------------------hccCcEEEEecCCCCchhHHHHHHHHHhCCCC
Confidence            379999999876554421110     0                     12357899999999999999999999996  5


Q ss_pred             ceEEecchhhhh
Q 012525          352 PFVIADATTLTQ  363 (461)
Q Consensus       352 pfv~i~~s~l~~  363 (461)
                      ||.-+..+++-.
T Consensus        93 PFcpmvgSEvyS  104 (456)
T KOG1942|consen   93 PFCPMVGSEVYS  104 (456)
T ss_pred             Ccccccchhhhh
Confidence            888777776553

>PRK06217 hypothetical protein; Validated

Probab=97.26  E-value=0.00027  Score=66.06  Aligned_cols=32  Identities=31%  Similarity=0.610  Sum_probs=29.2

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|+|.|.+|+||||+|++|++.++.+++.++.
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D~   34 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTDD   34 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcCc
Confidence            48999999999999999999999999887664

>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=97.26  E-value=0.00021  Score=62.99  Aligned_cols=29  Identities=41%  Similarity=0.723  Sum_probs=24.7

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      |+|+|+||+||||+|+.+++.++..++..
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~~~i~~   30 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGAVVISQ   30 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTEEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCEEEeH
Confidence            78999999999999999999998544433

...

>PRK14532 adenylate kinase; Provisional

Probab=97.25  E-value=0.00026  Score=65.94  Aligned_cols=30  Identities=30%  Similarity=0.470  Sum_probs=27.2

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      +|+|.|+||+||||+|+.||+.++.+++..
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            589999999999999999999999877655

>PRK04296 thymidine kinase; Provisional

Probab=97.23  E-value=0.0011  Score=62.66  Aligned_cols=30  Identities=17%  Similarity=0.170  Sum_probs=22.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc---CCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV---NVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i  356 (461)
                      -+|++||+|+||||++..++..+   +..++.+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            37899999999999998887655   4444444

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.22  E-value=0.0022  Score=69.78  Aligned_cols=32  Identities=28%  Similarity=0.511  Sum_probs=28.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +-+||+||+||||||..+.|+++++..+++-.
T Consensus       111 ~iLLltGPsGcGKSTtvkvLskelg~~~~Ew~  142 (634)
T KOG1970|consen  111 RILLLTGPSGCGKSTTVKVLSKELGYQLIEWS  142 (634)
T ss_pred             eEEEEeCCCCCCchhHHHHHHHhhCceeeeec
Confidence            45789999999999999999999998777555

>PRK06762 hypothetical protein; Provisional

Probab=97.21  E-value=0.00039  Score=63.42  Aligned_cols=37  Identities=24%  Similarity=0.440  Sum_probs=29.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~  362 (461)
                      .-|+|+|+||+||||+|+.|++.++..++.++...+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~~D~~r   39 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERLGRGTLLVSQDVVR   39 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEEecHHHHH
Confidence            3478999999999999999999986556666655444

>PRK13949 shikimate kinase; Provisional

Probab=97.21  E-value=0.00031  Score=65.41  Aligned_cols=34  Identities=38%  Similarity=0.620  Sum_probs=30.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      .+|+|+|+||+||||+++.||+.++.+|+..+..
T Consensus         2 ~~I~liG~~GsGKstl~~~La~~l~~~~id~D~~   35 (169)
T PRK13949          2 ARIFLVGYMGAGKTTLGKALARELGLSFIDLDFF   35 (169)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCCeecccHH
Confidence            3589999999999999999999999999887743

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.15  E-value=0.0005  Score=67.15  Aligned_cols=24  Identities=33%  Similarity=0.387  Sum_probs=20.9

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHH
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+..+||||+||+|||++|+.++.
T Consensus        11 ~~~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        11 IPNMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             CCcEEEEECCCCCCHHHHHHhcCC
Confidence            346699999999999999999973

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.14  E-value=0.00077  Score=71.18  Aligned_cols=82  Identities=17%  Similarity=0.342  Sum_probs=48.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc------eEEecch---h---hh--------hcCcccccHHHHHH---HHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP------FVIADAT---T---LT--------QAGYVGEDVESILY---KLLAQ  381 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p------fv~i~~s---~---l~--------~~g~vGe~~e~~L~---~lf~~  381 (461)
                      +...+|.||+|+|||+|++.|++.+...      ++.+...   +   +.        .+.+ -+..+..++   ..+..
T Consensus       169 GQR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~-d~~~~~~~~~a~~~ie~  247 (416)
T PRK09376        169 GQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTF-DEPAERHVQVAEMVIEK  247 (416)
T ss_pred             CceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECC-CCCHHHHHHHHHHHHHH
Confidence            3558889999999999999999866431      1111111   1   11        0111 112122222   34444


Q ss_pred             hchhhhccCceEEEEcCccccchhhh
Q 012525          382 AEFNVEAAQQGMVYIDEVDKITKKAE  407 (461)
Q Consensus       382 a~~~v~~a~~gVLfIDEID~L~~~R~  407 (461)
                      +.......+..+||||||+++....+
T Consensus       248 Ae~~~e~G~dVlL~iDsItR~arAqr  273 (416)
T PRK09376        248 AKRLVEHGKDVVILLDSITRLARAYN  273 (416)
T ss_pred             HHHHHHcCCCEEEEEEChHHHHHHHH
Confidence            55444556778999999999988644

>PRK14530 adenylate kinase; Provisional

Probab=97.14  E-value=0.00045  Score=66.17  Aligned_cols=31  Identities=32%  Similarity=0.546  Sum_probs=27.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.|+||+||||+|+.||+.++.+++..
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            4699999999999999999999999887744

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.13  E-value=0.00044  Score=63.89  Aligned_cols=29  Identities=24%  Similarity=0.431  Sum_probs=25.8

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      |+|+|+||+||||+|+.||+.++..++.+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is~   30 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLSA   30 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            78999999999999999999998766554

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.

>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=97.13  E-value=0.00043  Score=60.98  Aligned_cols=30  Identities=37%  Similarity=0.739  Sum_probs=28.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      |+|.|++|+||||+|+.||+.++.+++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            689999999999999999999999998776

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.13  E-value=0.0011  Score=60.20  Aligned_cols=31  Identities=39%  Similarity=0.666  Sum_probs=26.4

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      |+|.||+|+||||+|+.|++.++..++..+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v~~D~   31 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFIEGDD   31 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEEeCcc
Confidence            4789999999999999999999877765444

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.

>PRK13946 shikimate kinase; Provisional

Probab=97.12  E-value=0.00045  Score=64.76  Aligned_cols=34  Identities=38%  Similarity=0.683  Sum_probs=31.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +.+|+|+|.+|+|||++++.||+.++.+|+..+.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D~   43 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDADT   43 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcCH
Confidence            4679999999999999999999999999987775

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.11  E-value=0.00054  Score=63.84  Aligned_cols=35  Identities=37%  Similarity=0.745  Sum_probs=31.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..+|+|.|++|+||||+++.||+.++.+|+..+..
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~~~~vd~D~~   38 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQE   38 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcCCcEEECCch
Confidence            35799999999999999999999999999877753

>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=97.11  E-value=0.00048  Score=63.91  Aligned_cols=30  Identities=40%  Similarity=0.739  Sum_probs=26.8

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      |+|+|+||+||||+|+.||+.++.+++.++
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~~   31 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHISTG   31 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEECc
Confidence            899999999999999999999988776543

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=97.10  E-value=0.0014  Score=68.04  Aligned_cols=54  Identities=31%  Similarity=0.423  Sum_probs=40.0

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +++.++|.+++++.|...+..       +.+                  ..+..++-++|.||+|+|||+|++.|.+-+
T Consensus        59 f~~~~~G~~~~i~~lV~~fk~-------AA~------------------g~~~~krIl~L~GPvg~GKSsl~~~Lk~~l  112 (358)
T PF08298_consen   59 FEDEFYGMEETIERLVNYFKS-------AAQ------------------GLEERKRILLLLGPVGGGKSSLAELLKRGL  112 (358)
T ss_pred             ccccccCcHHHHHHHHHHHHH-------HHh------------------ccCccceEEEEECCCCCCHHHHHHHHHHHh
Confidence            444589999999988886631       111                  112345678999999999999999999866

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.10  E-value=0.00054  Score=62.76  Aligned_cols=34  Identities=32%  Similarity=0.492  Sum_probs=30.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      .+++|+|.+|+|||++|+.||+.++.+|+..+..
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~~~~d~D~~   36 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGYRFVDTDQW   36 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEEccHH
Confidence            4589999999999999999999999999876643

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.08  E-value=0.00051  Score=61.50  Aligned_cols=30  Identities=40%  Similarity=0.789  Sum_probs=26.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ++|+|+||+||||+|+.|++.++..++..+
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~~D   31 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFIDGD   31 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEeCc
Confidence            689999999999999999999988776443

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK14531 adenylate kinase; Provisional

Probab=97.08  E-value=0.00056  Score=64.01  Aligned_cols=31  Identities=26%  Similarity=0.470  Sum_probs=27.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|+|+||+||||+++.||+.++.+++.+
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            4599999999999999999999999877654

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.06  E-value=0.0028  Score=64.60  Aligned_cols=35  Identities=34%  Similarity=0.640  Sum_probs=31.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..+|+|+|.+|+|||++++.||+.++.+|+.++..
T Consensus       133 ~~~I~l~G~~GsGKStvg~~La~~Lg~~~id~D~~  167 (309)
T PRK08154        133 RRRIALIGLRGAGKSTLGRMLAARLGVPFVELNRE  167 (309)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHcCCCEEeHHHH
Confidence            46799999999999999999999999999976643

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.05  E-value=0.0024  Score=63.18  Aligned_cols=80  Identities=21%  Similarity=0.289  Sum_probs=46.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC--------CceEEecchhhhhcCcccccHHHHHHH--HHH---hh---chhhhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN--------VPFVIADATTLTQAGYVGEDVESILYK--LLA---QA---EFNVEA  388 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~--------~pfv~i~~s~l~~~g~vGe~~e~~L~~--lf~---~a---~~~v~~  388 (461)
                      ..|.||.|||+|||||+.|-||+.+.        ..+..++...-......|......-+.  +++   .+   ...+..
T Consensus       137 ~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cpk~~gmmmaIrs  216 (308)
T COG3854         137 WLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCPKAEGMMMAIRS  216 (308)
T ss_pred             ceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccchHHHHHHHHHHh
Confidence            46799999999999999999998663        345566655333223333321111000  000   00   011233


Q ss_pred             cCceEEEEcCccccch
Q 012525          389 AQQGMVYIDEVDKITK  404 (461)
Q Consensus       389 a~~gVLfIDEID~L~~  404 (461)
                      ..|-|+++|||.....
T Consensus       217 m~PEViIvDEIGt~~d  232 (308)
T COG3854         217 MSPEVIIVDEIGTEED  232 (308)
T ss_pred             cCCcEEEEeccccHHH
Confidence            4677999999986544

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=97.04  E-value=0.0011  Score=60.50  Aligned_cols=34  Identities=29%  Similarity=0.450  Sum_probs=24.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecchhhh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLT  362 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~  362 (461)
                      |+|+|.+|||||||++.|++. +.+++.-.+..+.
T Consensus         2 I~i~G~~stGKTTL~~~L~~~-g~~~v~E~ar~~~   35 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR-GYPVVPEYAREII   35 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH-T-EEE--TTHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc-CCeEEeecHHHHH
Confidence            789999999999999999999 8887744444444

>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=97.03  E-value=0.0015  Score=60.03  Aligned_cols=31  Identities=29%  Similarity=0.312  Sum_probs=23.2

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      +|++||||||||+++..++...   +.+++.++.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~   35 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTL   35 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEEC
Confidence            7899999999999998876543   445554443

A related protein is found in archaea.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=97.01  E-value=0.0026  Score=57.78  Aligned_cols=35  Identities=29%  Similarity=0.571  Sum_probs=28.2

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT  362 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~  362 (461)
                      ++|.|.||+||||+|+.|++.+   +...+.++...+.
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~~d~~r   39 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLDGDNVR   39 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCHHHH
Confidence            7899999999999999999988   5556666654443

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.01  E-value=0.00064  Score=62.99  Aligned_cols=34  Identities=21%  Similarity=0.396  Sum_probs=28.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..|+|.|+||+||||+|+.|++.+..+++.++..
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~~~~~~~~~D   36 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLAEPWLHFGVD   36 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhCCCccccCcc
Confidence            4589999999999999999999988777655443

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PHA02624 large T antigen; Provisional

Probab=96.96  E-value=0.0017  Score=71.70  Aligned_cols=92  Identities=20%  Similarity=0.170  Sum_probs=55.0

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      .++.+||+||||||||+++.+|++.++...+.++...-...=|.        .-+.          ..-+++||++-.-.
T Consensus       430 Kk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt~ks~FwL--------~pl~----------D~~~~l~dD~t~~~  491 (647)
T PHA02624        430 KRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPPDKLNFEL--------GCAI----------DQFMVVFEDVKGQP  491 (647)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCcchhHHHh--------hhhh----------hceEEEeeeccccc
Confidence            35679999999999999999999999665666664432211011        1111          33478899986444


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhCc-eeeee
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEGT-ETKTF  436 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg~-~v~i~  436 (461)
                      -.......+....   -..-|+..|||. .+++.
T Consensus       492 ~~~~~Lp~G~~~d---Nl~~lRn~LDG~V~v~ld  522 (647)
T PHA02624        492 ADNKDLPSGQGMN---NLDNLRDYLDGSVPVNLE  522 (647)
T ss_pred             cccccCCcccccc---hhhHHHhhcCCCCccccc
Confidence            3211000011100   246889999998 55543

>TIGR00767 rho transcription termination factor Rho

Probab=96.96  E-value=0.0016  Score=68.86  Aligned_cols=83  Identities=16%  Similarity=0.305  Sum_probs=48.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc------eEEecch------hhhhc-------CcccccHHH---HHHHHHHhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP------FVIADAT------TLTQA-------GYVGEDVES---ILYKLLAQA  382 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p------fv~i~~s------~l~~~-------g~vGe~~e~---~L~~lf~~a  382 (461)
                      +..++|.||+|+|||+|++.|++.+...      ++.+...      ++...       .-.++....   ....+...+
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~A  247 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKA  247 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHH
Confidence            4669999999999999999999976432      2211101      11100       001111111   122333344


Q ss_pred             chhhhccCceEEEEcCccccchhhh
Q 012525          383 EFNVEAAQQGMVYIDEVDKITKKAE  407 (461)
Q Consensus       383 ~~~v~~a~~gVLfIDEID~L~~~R~  407 (461)
                      .......+..|||||||+++....+
T Consensus       248 e~~~~~GkdVVLlIDEitR~arAqr  272 (415)
T TIGR00767       248 KRLVEHKKDVVILLDSITRLARAYN  272 (415)
T ss_pred             HHHHHcCCCeEEEEEChhHHHHHHH
Confidence            4444455677999999999987643

Members of this family differ in the specificity of RNA binding.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.91  E-value=0.0024  Score=60.40  Aligned_cols=30  Identities=23%  Similarity=0.385  Sum_probs=26.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|+++|.|||||||+++.|+ .++..++.++
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~lg~~~i~l~   31 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-ELGYKVIELN   31 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-HhCCceeeHH
Confidence            48899999999999999999 8988877666

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.89  E-value=0.0018  Score=54.60  Aligned_cols=23  Identities=52%  Similarity=0.628  Sum_probs=20.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ++++.||+|+|||+++..++..+
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~   24 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILEL   24 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHH
Confidence            68999999999999988877655

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.88  E-value=0.0045  Score=65.05  Aligned_cols=82  Identities=21%  Similarity=0.359  Sum_probs=46.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC-----ceEE--ecc-----hhhhhc--Cccc-----ccHHH---HHHHHHHhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV-----PFVI--ADA-----TTLTQA--GYVG-----EDVES---ILYKLLAQA  382 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~-----pfv~--i~~-----s~l~~~--g~vG-----e~~e~---~L~~lf~~a  382 (461)
                      +..++|.||+|||||+|++.|++.+..     .++.  +..     .++...  +.+.     +....   ....+...+
T Consensus       133 GQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~A  212 (380)
T PRK12608        133 GQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERA  212 (380)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHH
Confidence            356899999999999999999987632     1121  111     111100  0000     11111   112233344


Q ss_pred             chhhhccCceEEEEcCccccchhh
Q 012525          383 EFNVEAAQQGMVYIDEVDKITKKA  406 (461)
Q Consensus       383 ~~~v~~a~~gVLfIDEID~L~~~R  406 (461)
                      .......+..||++||+.++....
T Consensus       213 e~f~~~GkdVVLvlDsltr~A~A~  236 (380)
T PRK12608        213 KRLVEQGKDVVILLDSLTRLARAY  236 (380)
T ss_pred             HHHHHcCCCEEEEEeCcHHHHHHH
Confidence            444445677799999999987753

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.88  E-value=0.0023  Score=62.71  Aligned_cols=34  Identities=29%  Similarity=0.602  Sum_probs=27.5

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEEecchhh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTL  361 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l  361 (461)
                      |+|+|.||+||||+|+.|++.+   +.+++.++...+
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~~D~l   38 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLI   38 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEccHHH
Confidence            7899999999999999999987   455666655444

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.

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.88  E-value=0.0011  Score=65.13  Aligned_cols=33  Identities=24%  Similarity=0.456  Sum_probs=29.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ..|+|.||||+||||+|+.||+.++.+++.++.
T Consensus         7 mrIvl~G~PGsGK~T~a~~La~~~g~~~is~gd   39 (229)
T PTZ00088          7 LKIVLFGAPGVGKGTFAEILSKKENLKHINMGN   39 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEEECCh
Confidence            459999999999999999999999988776554

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.84  E-value=0.0041  Score=66.67  Aligned_cols=35  Identities=26%  Similarity=0.304  Sum_probs=27.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ..-+||+|+||+|||+|+..+|..+   +.++++++..
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~E  117 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGE  117 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            3568999999999999999998755   4566666654

>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type

Probab=96.82  E-value=0.003  Score=64.94  Aligned_cols=38  Identities=24%  Similarity=0.304  Sum_probs=31.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQ  363 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~  363 (461)
                      ..|+|.|++|+|||||++.|++.++.+++.-...++..
T Consensus       163 ~~~~~~G~~~~gkstl~~~l~~~~~~~~v~E~~R~~~~  200 (325)
T TIGR01526       163 KTVAILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVE  200 (325)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCCCEEeehhHHHHH
Confidence            46899999999999999999999999887666554443

E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.

>PRK14528 adenylate kinase; Provisional

Probab=96.81  E-value=0.0012  Score=62.16  Aligned_cols=32  Identities=34%  Similarity=0.700  Sum_probs=27.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .+|++.||||+||||+|+.||+.++.+++.+.
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~~~~~is~~   33 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERLSIPQISTG   33 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeeeCC
Confidence            35899999999999999999999998876543

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.81  E-value=0.0012  Score=62.36  Aligned_cols=28  Identities=43%  Similarity=0.924  Sum_probs=24.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      .|+|.|+||+||||+|+.||+.++.+.+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~hl   29 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLPHL   29 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4899999999999999999999766544

>PRK14974 cell division protein FtsY; Provisional

Probab=96.79  E-value=0.019  Score=59.63  Aligned_cols=25  Identities=28%  Similarity=0.413  Sum_probs=21.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.|++|+||||++..||..+
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~~l  164 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAYYL  164 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4678999999999999988888765

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.78  E-value=0.0081  Score=55.86  Aligned_cols=38  Identities=34%  Similarity=0.539  Sum_probs=32.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQ  363 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~  363 (461)
                      ..|+|+|.+|+||||||++|.+.+   +.+.+.++...+..
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~lR~   43 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGDNLRH   43 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHHCT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcchhh
Confidence            458899999999999999999877   67888888887774

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 ....

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.77  E-value=0.0014  Score=60.42  Aligned_cols=31  Identities=16%  Similarity=0.348  Sum_probs=26.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .-|+|.|+||+||||+|+.|++.++..++..
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~g~~~~~~   34 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKYGFTHLST   34 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            3478999999999999999999998765544

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.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.77  E-value=0.0025  Score=65.87  Aligned_cols=24  Identities=42%  Similarity=0.711  Sum_probs=21.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+++.|.||||||.||-.+++.+
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            348899999999999999999987

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.76  E-value=0.0017  Score=68.79  Aligned_cols=69  Identities=17%  Similarity=0.329  Sum_probs=43.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC-----CceEEecchhhhhcCcccccHHHHHH---HHHHhhchhhhccCceEEEEc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN-----VPFVIADATTLTQAGYVGEDVESILY---KLLAQAEFNVEAAQQGMVYID  397 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~-----~pfv~i~~s~l~~~g~vGe~~e~~L~---~lf~~a~~~v~~a~~gVLfID  397 (461)
                      ..++|+|++|.|||+|++|++.++.     ..++.+........ ++    .....   ..|....      .--+|+||
T Consensus       114 nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~-~v----~a~~~~~~~~Fk~~y------~~dlllID  182 (408)
T COG0593         114 NPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTND-FV----KALRDNEMEKFKEKY------SLDLLLID  182 (408)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHH-HH----HHHHhhhHHHHHHhh------ccCeeeec
Confidence            5699999999999999999998662     24666666554421 11    11111   1111111      12289999


Q ss_pred             Cccccchh
Q 012525          398 EVDKITKK  405 (461)
Q Consensus       398 EID~L~~~  405 (461)
                      +|+.+..+
T Consensus       183 Diq~l~gk  190 (408)
T COG0593         183 DIQFLAGK  190 (408)
T ss_pred             hHhHhcCC
Confidence            99998877

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.76  E-value=0.01  Score=59.02  Aligned_cols=27  Identities=30%  Similarity=0.485  Sum_probs=22.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-|.|.||+|||||||.+.||...
T Consensus        27 ~~GEfvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          27 EKGEFVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            345668899999999999999999654

>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=96.74  E-value=0.0011  Score=56.66  Aligned_cols=22  Identities=45%  Similarity=0.629  Sum_probs=20.9

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      |+|.|+|||||||+|+.|++.+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999986

...

>PRK02496 adk adenylate kinase; Provisional

Probab=96.74  E-value=0.0014  Score=60.86  Aligned_cols=30  Identities=33%  Similarity=0.739  Sum_probs=26.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .++|.|+||+||||+|+.||+.++.+++.+
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            389999999999999999999998877654

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.72  E-value=0.012  Score=70.79  Aligned_cols=110  Identities=27%  Similarity=0.327  Sum_probs=79.7

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhc-CcccccH----------HHHHHHHHHhhchhhhccCc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA-GYVGEDV----------ESILYKLLAQAEFNVEAAQQ  391 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~-g~vGe~~----------e~~L~~lf~~a~~~v~~a~~  391 (461)
                      ...-++||.||+-+|||.+.+-+|++.+..||+++-.+-++. .|+|.-+          |..+-..+         .++
T Consensus       886 ~~~fP~LiQGpTSSGKTSMI~yla~~tghkfVRINNHEHTdlqeYiGTyvTdd~G~lsFkEGvLVeAl---------R~G  956 (4600)
T COG5271         886 LSNFPLLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEGVLVEAL---------RRG  956 (4600)
T ss_pred             hcCCcEEEecCCCCCcchHHHHHHHHhCccEEEecCcccchHHHHhhceeecCCCceeeehhHHHHHH---------hcC
Confidence            345789999999999999999999999999999998643321 2333211          11222211         133


Q ss_pred             eEEEEcCccccchhhhccccccccchHHHHHHHHHHHh-Cceeeeecc-eeeecC-CeEEEecCCCC
Q 012525          392 GMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE-GTETKTFAA-VSKVSR-DNLYIKTSGLD  455 (461)
Q Consensus       392 gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE-g~~v~i~~~-~r~~~r-d~IiI~TsNid  455 (461)
                      --|+|||.+-....              ++.+|-++|| .+++.|++. .--+|. ++.+.+|.|..
T Consensus       957 yWIVLDELNLApTD--------------VLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNpp 1009 (4600)
T COG5271         957 YWIVLDELNLAPTD--------------VLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPP 1009 (4600)
T ss_pred             cEEEeeccccCcHH--------------HHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCC
Confidence            36889999976666              9999999999 678888877 344455 79999999954

>TIGR01351 adk adenylate kinases

Probab=96.72  E-value=0.0015  Score=62.39  Aligned_cols=29  Identities=38%  Similarity=0.706  Sum_probs=26.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      |+|+|+||+||||+|+.||+.++.+++.+
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            79999999999999999999998877654

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.

>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=96.72  E-value=0.0041  Score=62.49  Aligned_cols=76  Identities=25%  Similarity=0.278  Sum_probs=40.2

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh--hcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT--QAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~--~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      |+|+|-||+|||++|+.|++.+   +..++.++...+.  ...|.-...|+..+..+..+..... .+..||++|....+
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~l-s~~~iVI~Dd~nYi   82 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERAL-SKDTIVILDDNNYI   82 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHH-TT-SEEEE-S---S
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhh-ccCeEEEEeCCchH
Confidence            7899999999999999999875   4566666655444  2223223336666655543322221 24468888986655


Q ss_pred             ch
Q 012525          403 TK  404 (461)
Q Consensus       403 ~~  404 (461)
                      -.
T Consensus        83 Kg   84 (270)
T PF08433_consen   83 KG   84 (270)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.72  E-value=0.0063  Score=68.03  Aligned_cols=41  Identities=22%  Similarity=0.263  Sum_probs=30.7

Q ss_pred             cCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc
Q 012525          389 AQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA  438 (461)
Q Consensus       389 a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~  438 (461)
                      .+|.||+|||+-......         |..-++.+|-+.|++..+.++.-
T Consensus       621 r~P~VLILDEATSALDae---------SE~lVq~aL~~~~~~rTVlvIAH  661 (716)
T KOG0058|consen  621 RNPRVLILDEATSALDAE---------SEYLVQEALDRLMQGRTVLVIAH  661 (716)
T ss_pred             cCCCEEEEechhhhcchh---------hHHHHHHHHHHhhcCCeEEEEeh
Confidence            478999999998776652         22347888889999977766655

>PRK06547 hypothetical protein; Provisional

Probab=96.71  E-value=0.0015  Score=61.31  Aligned_cols=33  Identities=42%  Similarity=0.525  Sum_probs=28.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ..|++.|++|+||||+|+.|++.++.+++.++.
T Consensus        16 ~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d~   48 (172)
T PRK06547         16 ITVLIDGRSGSGKTTLAGALAARTGFQLVHLDD   48 (172)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCeecccc
Confidence            457888999999999999999999887775543

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.71  E-value=0.0019  Score=67.77  Aligned_cols=35  Identities=23%  Similarity=0.302  Sum_probs=26.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ..-++|+|+||+|||+|+..+|..+   +.+++.++..
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~E  119 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE  119 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            3568999999999999999998655   2355555543

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.71  E-value=0.0079  Score=58.21  Aligned_cols=36  Identities=19%  Similarity=0.304  Sum_probs=26.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      ..+..++++|+||+|||+++..++...   +.+.+.++.
T Consensus        23 ~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         23 PFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            335778999999999999999996532   445544443

>KOG1808 consensus AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.68  E-value=0.0044  Score=75.43  Aligned_cols=116  Identities=23%  Similarity=0.261  Sum_probs=77.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhc-CcccccHHHHHHH-HHHhhchhhhccCceEEEEcCccccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA-GYVGEDVESILYK-LLAQAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~-g~vGe~~e~~L~~-lf~~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      ..+||.||+++|||.+++-+|+..+..+++++-.+.++. .|+|..+.....+ .|......-..-++..+|+||++...
T Consensus       441 ~pillqG~tssGKtsii~~la~~~g~~~vrinnhehtd~qeyig~y~~~~~g~l~freg~LV~Alr~G~~~vlD~lnla~  520 (1856)
T KOG1808|consen  441 FPILLQGPTSSGKTSIIKELARATGKNIVRINNHEHTDLQEYIGTYVADDNGDLVFREGVLVQALRNGDWIVLDELNLAP  520 (1856)
T ss_pred             CCeEEecCcCcCchhHHHHHHHHhccCceehhccccchHHHHHHhhhcCCCCCeeeehhHHHHHHHhCCEEEeccccccc
Confidence            469999999999999999999999999998887644321 1332110000000 00000000011256789999999877


Q ss_pred             hhhhccccccccchHHHHHHHHHHHhC-ceeeeecceeeecC--CeEEEecCCCC
Q 012525          404 KKAESLNISRDVSGEGVQQALLKMLEG-TETKTFAAVSKVSR--DNLYIKTSGLD  455 (461)
Q Consensus       404 ~~R~~~~~~~~~s~~~v~~aLL~~LEg-~~v~i~~~~r~~~r--d~IiI~TsNid  455 (461)
                      ..              ++.+|.++++. +++.+++..+-...  ++++.+|-|..
T Consensus       521 ~d--------------vL~aLnrllddnRel~ipe~~rlv~~h~~f~lfatqn~~  561 (1856)
T KOG1808|consen  521 HD--------------VLEALNRLLDDNRELFIPETQRLVKAHPEFMLFATQNPP  561 (1856)
T ss_pred             hH--------------HHHHHHhhhhhhccccccccceeeccCcchhhhhhccCc
Confidence            77              89999999995 88888887444333  68888888865

>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=96.68  E-value=0.011  Score=59.35  Aligned_cols=69  Identities=25%  Similarity=0.339  Sum_probs=46.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      ..|+||.|..|+||++++|..|-.++..++.+..+.    +|.-.+....++.++..+..   ..++.+++|+|-+
T Consensus        31 ~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~----~y~~~~f~~dLk~~~~~ag~---~~~~~vfll~d~q   99 (268)
T PF12780_consen   31 RGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITK----GYSIKDFKEDLKKALQKAGI---KGKPTVFLLTDSQ   99 (268)
T ss_dssp             TEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTST----TTHHHHHHHHHHHHHHHHHC---S-S-EEEEEECCC
T ss_pred             CCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeC----CcCHHHHHHHHHHHHHHHhc---cCCCeEEEecCcc
Confidence            378999999999999999999988888888777542    23223334555555544332   2356788887744

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.

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.68  E-value=0.0018  Score=62.03  Aligned_cols=30  Identities=33%  Similarity=0.677  Sum_probs=26.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+++|+||+||||+|+.||+.++.+++.+
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            389999999999999999999999877654

>PLN02199 shikimate kinase

Probab=96.67  E-value=0.0031  Score=64.33  Aligned_cols=35  Identities=29%  Similarity=0.458  Sum_probs=31.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..+|+|.|.+|+|||++++.||+.++.+|+..+..
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD~l  136 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCDTL  136 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEehHHH
Confidence            47899999999999999999999999999877753

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.65  E-value=0.0016  Score=61.06  Aligned_cols=28  Identities=39%  Similarity=0.643  Sum_probs=26.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      |.+.|+|||||||+|+.||+.++.+++.
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vs   30 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVS   30 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceee
Confidence            6789999999999999999999999875

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.62  E-value=0.0027  Score=60.09  Aligned_cols=36  Identities=31%  Similarity=0.392  Sum_probs=27.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATT  360 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~  360 (461)
                      ..-++|+||||+|||+++..++...   +...+.++...
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~   50 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG   50 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            4668899999999999999888644   44566666653

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

>PLN02200 adenylate kinase family protein

Probab=96.61  E-value=0.002  Score=63.18  Aligned_cols=30  Identities=17%  Similarity=0.297  Sum_probs=26.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +..|+|.|+||+||||+|+.||+.++.+++
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~~g~~hi   72 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVETFGFKHL   72 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCeEE
Confidence            456889999999999999999999987654

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.58  E-value=0.029  Score=60.19  Aligned_cols=36  Identities=33%  Similarity=0.465  Sum_probs=27.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      .+..|+|+|++|+||||++..||..+   +..+..+++.
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D  132 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAAD  132 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            35779999999999999999999866   3444444443

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.58  E-value=0.0071  Score=57.53  Aligned_cols=24  Identities=42%  Similarity=0.628  Sum_probs=21.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      -++|.||+|+||||++++|+..+.
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            489999999999999999988774

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.

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

Probab=96.57  E-value=0.012  Score=67.74  Aligned_cols=96  Identities=21%  Similarity=0.311  Sum_probs=62.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC----------CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN----------VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV  394 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~----------~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVL  394 (461)
                      +.|-+|.|+||+|||.+++-+|+...          ..++.++...+..-...-.+++..++.+..+...   ...+-||
T Consensus       208 k~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~---~~~gvIL  284 (898)
T KOG1051|consen  208 KNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVES---GGGGVIL  284 (898)
T ss_pred             CCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhc---CCCcEEE
Confidence            36789999999999999999998662          2456666665443222223457777777765442   2356689


Q ss_pred             EEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       395 fIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ||||++-+......      .+...+.+.|-.++.
T Consensus       285 figelh~lvg~g~~------~~~~d~~nlLkp~L~  313 (898)
T KOG1051|consen  285 FLGELHWLVGSGSN------YGAIDAANLLKPLLA  313 (898)
T ss_pred             EecceeeeecCCCc------chHHHHHHhhHHHHh
Confidence            99999998877322      112234555555555

>PRK04182 cytidylate kinase; Provisional

Probab=96.57  E-value=0.0022  Score=58.49  Aligned_cols=30  Identities=40%  Similarity=0.609  Sum_probs=27.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+|.|++|+||||+|+.||+.++.+++..
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg~~~id~   31 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLGLKHVSA   31 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEecH
Confidence            388999999999999999999999988764

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.53  E-value=0.032  Score=58.96  Aligned_cols=25  Identities=44%  Similarity=0.570  Sum_probs=22.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..|+|+||+|+||||++..||..+
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~  198 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIY  198 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4679999999999999999998755

>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=96.53  E-value=0.0044  Score=67.99  Aligned_cols=34  Identities=32%  Similarity=0.600  Sum_probs=31.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..|+|.|.+|+||||+++.||+.++.+|+.+|..
T Consensus         7 ~~i~LiG~~GaGKttvg~~LA~~L~~~fiD~D~~   40 (542)
T PRK14021          7 PQAVIIGMMGAGKTRVGKEVAQMMRLPFADADVE   40 (542)
T ss_pred             ccEEEECCCCCCHHHHHHHHHHHhCCCEEEchHH
Confidence            5699999999999999999999999999988864

>PRK03846 adenylylsulfate kinase; Provisional

Probab=96.52  E-value=0.014  Score=55.19  Aligned_cols=37  Identities=24%  Similarity=0.379  Sum_probs=28.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTL  361 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l  361 (461)
                      +..|.|+|++|+||||||++|++.+   +...+.++...+
T Consensus        24 ~~~i~i~G~~GsGKSTla~~l~~~l~~~~~~~~~ld~d~~   63 (198)
T PRK03846         24 GVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLLDGDNV   63 (198)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhCCCCEEEEcCEeH
Confidence            3568899999999999999999977   334555655433

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=96.49  E-value=0.0023  Score=60.98  Aligned_cols=22  Identities=36%  Similarity=0.599  Sum_probs=19.9

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +++.|+||+|||++.+.+.+..
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc
Confidence            4789999999999999999885

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.46  E-value=0.013  Score=66.54  Aligned_cols=90  Identities=22%  Similarity=0.326  Sum_probs=50.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---C--CceEEecchhhhhc---CcccccHHHHHHHHHHhhchh-----hh-ccC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---N--VPFVIADATTLTQA---GYVGEDVESILYKLLAQAEFN-----VE-AAQ  390 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~--~pfv~i~~s~l~~~---g~vGe~~e~~L~~lf~~a~~~-----v~-~a~  390 (461)
                      ...++|.|+|||||||+++++.+.+   +  .+++.+..+--...   ...|.. ...+..++......     .. ...
T Consensus       338 ~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~g~~-a~Tih~lL~~~~~~~~~~~~~~~~~  416 (720)
T TIGR01448       338 HKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEVTGLT-ASTIHRLLGYGPDTFRHNHLEDPID  416 (720)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHhcCCc-cccHHHHhhccCCccchhhhhcccc
Confidence            3568999999999999999997755   3  33333332211100   011211 12233333321110     00 124


Q ss_pred             ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          391 QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       391 ~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ..+|+|||+-.+...              ....|+..+.
T Consensus       417 ~~llIvDEaSMvd~~--------------~~~~Ll~~~~  441 (720)
T TIGR01448       417 CDLLIVDESSMMDTW--------------LALSLLAALP  441 (720)
T ss_pred             CCEEEEeccccCCHH--------------HHHHHHHhCC
Confidence            569999999988776              6677777665

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.

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.46  E-value=0.0029  Score=57.36  Aligned_cols=30  Identities=40%  Similarity=0.680  Sum_probs=27.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      |+|.|++|+|||++|+.||+.++.+++..+
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~~~~   32 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLISAG   32 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCceecHH
Confidence            789999999999999999999999887653

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.43  E-value=0.0086  Score=62.34  Aligned_cols=39  Identities=23%  Similarity=0.491  Sum_probs=28.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC---ceEEecchhhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV---PFVIADATTLTQ  363 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~---pfv~i~~s~l~~  363 (461)
                      +.++++.|+.|||||+|.++|...+..   .++.+..+-+.+
T Consensus        22 ~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~AA   63 (364)
T PF05970_consen   22 GLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIAA   63 (364)
T ss_pred             CcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHHH
Confidence            467899999999999999999887743   344444444443

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=96.42  E-value=0.0052  Score=68.47  Aligned_cols=87  Identities=22%  Similarity=0.337  Sum_probs=58.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC----------CceEEecchhhhhc---------CcccccH-----HHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN----------VPFVIADATTLTQA---------GYVGEDV-----ESILYKLLAQ  381 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~----------~pfv~i~~s~l~~~---------g~vGe~~-----e~~L~~lf~~  381 (461)
                      .-+.+.|-||||||.+++.+-+.|.          .+|+++++..+...         .+.|+..     -..|...|. 
T Consensus       423 ~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~-  501 (767)
T KOG1514|consen  423 SCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFT-  501 (767)
T ss_pred             eeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhc-
Confidence            4678999999999999988877553          47889998777643         1122211     112222222 


Q ss_pred             hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       382 a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                        ..-.....+||+|||.|.|...              -|..|..+++
T Consensus       502 --~~k~~~~~~VvLiDElD~Lvtr--------------~QdVlYn~fd  533 (767)
T KOG1514|consen  502 --VPKPKRSTTVVLIDELDILVTR--------------SQDVLYNIFD  533 (767)
T ss_pred             --cCCCCCCCEEEEeccHHHHhcc--------------cHHHHHHHhc
Confidence              1112356789999999998876              5778888877

>PRK14527 adenylate kinase; Provisional

Probab=96.42  E-value=0.0026  Score=59.73  Aligned_cols=31  Identities=29%  Similarity=0.529  Sum_probs=26.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .-|+|+||||+||||+|+.||+.++...+..
T Consensus         7 ~~i~i~G~pGsGKsT~a~~La~~~~~~~is~   37 (191)
T PRK14527          7 KVVIFLGPPGAGKGTQAERLAQELGLKKLST   37 (191)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCCCCc
Confidence            4589999999999999999999988765433

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.41  E-value=0.0028  Score=63.23  Aligned_cols=30  Identities=30%  Similarity=0.351  Sum_probs=25.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-CCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-NVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-~~pfv~  355 (461)
                      ..|+|.|+||+||||+|+.|++.+ +..++.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l~   33 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVN   33 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEEe
Confidence            347899999999999999999998 554443

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=96.41  E-value=0.012  Score=62.45  Aligned_cols=30  Identities=30%  Similarity=0.386  Sum_probs=27.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..|+|.|++|||||||+++||+.++..++.
T Consensus       220 ~~IvI~G~~gsGKTTL~~~La~~~g~~~v~  249 (399)
T PRK08099        220 RTVAILGGESSGKSTLVNKLANIFNTTSAW  249 (399)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHhCCCeee
Confidence            679999999999999999999999887654

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

Probab=96.40  E-value=0.018  Score=55.20  Aligned_cols=36  Identities=33%  Similarity=0.365  Sum_probs=24.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc----CCceEEecc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADA  358 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~  358 (461)
                      ..+..+|+.|+||||||+++..++...    +.+.+.+..
T Consensus        17 p~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~   56 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSF   56 (226)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEES
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEe
Confidence            445779999999999999998766322    555554443

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 ....

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.39  E-value=0.0032  Score=58.96  Aligned_cols=30  Identities=33%  Similarity=0.600  Sum_probs=25.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..++|.||+|+|||||++.|+..++.+|+.
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~~~~~~   32 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQTQLLV   32 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCCCeEEE
Confidence            458999999999999999999988765543

>PLN02674 adenylate kinase

Probab=96.39  E-value=0.0034  Score=62.35  Aligned_cols=31  Identities=23%  Similarity=0.432  Sum_probs=27.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .+|+|.||||+||+|+|+.||+.++.+++.+
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~~~~~his~   62 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDEYCLCHLAT   62 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHcCCcEEch
Confidence            5699999999999999999999998766533

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.37  E-value=0.035  Score=58.40  Aligned_cols=26  Identities=42%  Similarity=0.557  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..++|+||+|+||||++..||..+
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            35789999999999999999999753

>PRK01184 hypothetical protein; Provisional

Probab=96.34  E-value=0.0036  Score=58.11  Aligned_cols=29  Identities=34%  Similarity=0.615  Sum_probs=25.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+|+|+||+||||+|+ +++.++.+++..
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            47899999999999998 788888887665

>PRK08233 hypothetical protein; Provisional

Probab=96.34  E-value=0.0042  Score=56.86  Aligned_cols=32  Identities=22%  Similarity=0.345  Sum_probs=25.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC-CceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN-VPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~-~pfv~i~  357 (461)
                      .-|.+.|+||+||||+|+.|++.+. ..++..+
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~~l~~~~~~~~d   36 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKLKNSKALYFD   36 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCCCCceEEEC
Confidence            3478899999999999999999885 3444443

>PRK14526 adenylate kinase; Provisional

Probab=96.32  E-value=0.0039  Score=60.37  Aligned_cols=29  Identities=34%  Similarity=0.643  Sum_probs=25.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      +++|+|+||+||||+|+.||+.++.+++.
T Consensus         2 ~i~l~G~pGsGKsT~a~~La~~~~~~~is   30 (211)
T PRK14526          2 KLVFLGPPGSGKGTIAKILSNELNYYHIS   30 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            48899999999999999999998876553

>PRK04040 adenylate kinase; Provisional

Probab=96.32  E-value=0.0037  Score=59.34  Aligned_cols=31  Identities=23%  Similarity=0.297  Sum_probs=26.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc--CCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV--NVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l--~~pfv~i  356 (461)
                      ..|+|+|.||+||||+++.|++.+  +..++..
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~~~~   35 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLKEDYKIVNF   35 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhccCCeEEec
Confidence            458999999999999999999999  5665543

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.31  E-value=0.035  Score=55.94  Aligned_cols=25  Identities=40%  Similarity=0.555  Sum_probs=21.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.||+|+||||++..||..+
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~  218 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARF  218 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4678999999999999999998755

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.31  E-value=0.014  Score=53.83  Aligned_cols=35  Identities=31%  Similarity=0.559  Sum_probs=27.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATT  360 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~  360 (461)
                      ..|+|.|+||+||||+|+.|+..+   +..++.++...
T Consensus         5 ~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id~D~   42 (175)
T PRK00889          5 VTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDGDA   42 (175)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEcCcc
Confidence            468899999999999999999987   33345455443

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=96.30  E-value=0.012  Score=56.00  Aligned_cols=38  Identities=21%  Similarity=0.422  Sum_probs=32.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQ  363 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~  363 (461)
                      ..|.|+|.+|+||||+|.+|.+.|   +...+.++...+..
T Consensus        24 ~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDGDnvR~   64 (197)
T COG0529          24 AVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGDNVRH   64 (197)
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecChhHhh
Confidence            568899999999999999999877   66788888876663

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.30  E-value=0.017  Score=55.78  Aligned_cols=22  Identities=36%  Similarity=0.597  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      +.++|+||.|+|||++.+.++.
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            5689999999999999999984

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

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=96.30  E-value=0.016  Score=54.16  Aligned_cols=33  Identities=24%  Similarity=0.364  Sum_probs=27.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      .+|+.|+||+|||++|..++..++.+++.+...
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~   35 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATA   35 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCC
Confidence            489999999999999999999988776655543

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.29  E-value=0.0091  Score=57.27  Aligned_cols=35  Identities=29%  Similarity=0.402  Sum_probs=27.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ..-++|+|+||+|||++|..+|..+   +...+.++..
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            4668999999999999999998644   5566666665

>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=96.29  E-value=0.003  Score=56.91  Aligned_cols=26  Identities=38%  Similarity=0.643  Sum_probs=22.7

Q ss_pred             EEccCCCchHHHHHHHHHhcCCceEE
Q 012525          330 LMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       330 L~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      |.||||+||||+|+.||+.++..++.
T Consensus         1 i~G~PgsGK~t~~~~la~~~~~~~is   26 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYGLVHIS   26 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHTSEEEE
T ss_pred             CcCCCCCChHHHHHHHHHhcCcceec
Confidence            57999999999999999999875543

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 ....

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.28  E-value=0.0048  Score=48.98  Aligned_cols=22  Identities=41%  Similarity=0.708  Sum_probs=20.7

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.+.|++|+|||+++++|++.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6889999999999999999986

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.25  E-value=0.031  Score=54.59  Aligned_cols=33  Identities=24%  Similarity=0.405  Sum_probs=23.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHH-Hhc--CCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLA-RHV--NVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA-~~l--~~pfv~i~  357 (461)
                      ...++|.|++|||||++|..++ ..+  +...+.+.
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            4678999999999999975554 333  34444444

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.25  E-value=0.0038  Score=56.53  Aligned_cols=27  Identities=37%  Similarity=0.557  Sum_probs=24.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..|+|.|+.|+||||++|.+++.++..
T Consensus        23 ~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        23 TVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            568899999999999999999998763

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.

>PF13245 AAA_19: Part of AAA domain

Probab=96.24  E-value=0.0067  Score=49.51  Aligned_cols=23  Identities=39%  Similarity=0.644  Sum_probs=17.6

Q ss_pred             cEEEEccCCCchH-HHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKT-LLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKT-tLAraLA~~l  349 (461)
                      .+++.|||||||| ++++.++..+
T Consensus        12 ~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   12 LFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHH
Confidence            3556999999999 6666666665

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.23  E-value=0.024  Score=54.26  Aligned_cols=24  Identities=42%  Similarity=0.618  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..++|.||+|+||||.+-.||..+
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~   25 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARL   25 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCchHhHHHHHHHHH
Confidence            458999999999999988887655

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=96.18  E-value=0.037  Score=52.92  Aligned_cols=22  Identities=27%  Similarity=0.517  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .-++|+||.|+||||+.|.|+.
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~   47 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGV   47 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHH
Confidence            5678999999999999999985

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

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.17  E-value=0.011  Score=67.32  Aligned_cols=80  Identities=18%  Similarity=0.179  Sum_probs=43.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---CcccccHHHHHHHHH-HhhchhhhccCceEEEEc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGEDVESILYKLL-AQAEFNVEAAQQGMVYID  397 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~~e~~L~~lf-~~a~~~v~~a~~gVLfID  397 (461)
                      ..-++|.|++||||||+++++...+   +..++.+..+.....   ...|.. ...+..+. .............+|+||
T Consensus       368 ~~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg~Aa~~L~~~~g~~-a~Ti~~~~~~~~~~~~~~~~~~llIvD  446 (744)
T TIGR02768       368 GDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKAAEGLQAESGIE-SRTLASLEYAWANGRDLLSDKDVLVID  446 (744)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHhccCCc-eeeHHHHHhhhccCcccCCCCcEEEEE
Confidence            4567899999999999999997654   445554433322211   011111 11112221 111111111355699999


Q ss_pred             Cccccchh
Q 012525          398 EVDKITKK  405 (461)
Q Consensus       398 EID~L~~~  405 (461)
                      |+-.+...
T Consensus       447 EasMv~~~  454 (744)
T TIGR02768       447 EAGMVGSR  454 (744)
T ss_pred             CcccCCHH
Confidence            99987766

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK06696 uridine kinase; Validated

Probab=96.15  E-value=0.0054  Score=59.19  Aligned_cols=33  Identities=36%  Similarity=0.450  Sum_probs=27.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      .-|.+.|++|+||||+|+.|++.+   +.+++.+..
T Consensus        23 ~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~   58 (223)
T PRK06696         23 LRVAIDGITASGKTTFADELAEEIKKRGRPVIRASI   58 (223)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecc
Confidence            457899999999999999999998   556666443

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.15  E-value=0.089  Score=54.15  Aligned_cols=25  Identities=32%  Similarity=0.404  Sum_probs=22.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.||+|+||||++..||..+
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l  138 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKY  138 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            4678899999999999999999866

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.15  E-value=0.0065  Score=56.06  Aligned_cols=37  Identities=30%  Similarity=0.450  Sum_probs=28.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC---ceEEecchhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV---PFVIADATTL  361 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~---pfv~i~~s~l  361 (461)
                      +..|+|.|++|+||||+|+.|++.+..   ..+.++...+
T Consensus         7 ~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~~d~~   46 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDGDEL   46 (176)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEecHHH
Confidence            467899999999999999999998852   2444554444

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=96.13  E-value=0.021  Score=54.21  Aligned_cols=21  Identities=38%  Similarity=0.648  Sum_probs=19.5

Q ss_pred             CcEEEEccCCCchHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA  346 (461)
                      +.++|+||.|+||||+.+.|+
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            359999999999999999998

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

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=96.12  E-value=0.0049  Score=57.62  Aligned_cols=34  Identities=32%  Similarity=0.581  Sum_probs=29.8

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .+..++++|++|+||||++++|+++++.+|+.-+
T Consensus        11 ~k~~i~vmGvsGsGKSTigk~L~~~l~~~F~dgD   44 (191)
T KOG3354|consen   11 FKYVIVVMGVSGSGKSTIGKALSEELGLKFIDGD   44 (191)
T ss_pred             CceeEEEEecCCCChhhHHHHHHHHhCCcccccc
Confidence            3457899999999999999999999999987554

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.12  E-value=0.079  Score=56.76  Aligned_cols=34  Identities=26%  Similarity=0.322  Sum_probs=26.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      +..|+|.|++|+||||++..||..+   +..+..+++
T Consensus       100 ~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~  136 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCA  136 (429)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcC
Confidence            4568899999999999999999766   445555554

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>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=96.12  E-value=0.0078  Score=59.16  Aligned_cols=23  Identities=43%  Similarity=0.602  Sum_probs=21.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|.|+|++|+|||+||+.+++.
T Consensus        20 ~~v~I~G~~G~GKT~LA~~~~~~   42 (287)
T PF00931_consen   20 RVVAIVGMGGIGKTTLARQVARD   42 (287)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHCH
T ss_pred             EEEEEEcCCcCCcceeeeecccc
Confidence            56889999999999999999977

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.

>PRK14529 adenylate kinase; Provisional

Probab=96.10  E-value=0.0049  Score=60.40  Aligned_cols=28  Identities=29%  Similarity=0.647  Sum_probs=25.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +|+|.||||+||||+|+.||+.++.+++
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~~~~~i   29 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKYDLAHI   29 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCCCc
Confidence            4899999999999999999999988765

>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=96.09  E-value=0.021  Score=54.17  Aligned_cols=22  Identities=23%  Similarity=0.463  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..++|+||.|+||||+.+.|+.
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            5689999999999999999994

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

>KOG0055 consensus Multidrug/pheromone exporter, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]

Probab=96.06  E-value=0.04  Score=65.16  Aligned_cols=53  Identities=23%  Similarity=0.236  Sum_probs=37.1

Q ss_pred             cCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecC--CeEEEe
Q 012525          389 AQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSR--DNLYIK  450 (461)
Q Consensus       389 a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~r--d~IiI~  450 (461)
                      .+|.||+|||+-.....         .|.+-+|++|=+.+++....+..-.....+  |.|.|.
T Consensus      1143 RnPkILLLDEATSALDs---------eSErvVQeALd~a~~gRT~IvIAHRLSTIqnaD~I~Vi 1197 (1228)
T KOG0055|consen 1143 RNPKILLLDEATSALDS---------ESERVVQEALDRAMEGRTTIVIAHRLSTIQNADVIAVL 1197 (1228)
T ss_pred             cCCCeeeeeccchhhhh---------hhHHHHHHHHHHhhcCCcEEEEecchhhhhcCCEEEEE
Confidence            47889999999877765         234558999999999977666555322222  666654

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=96.05  E-value=0.014  Score=62.66  Aligned_cols=101  Identities=18%  Similarity=0.244  Sum_probs=61.0

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN----  350 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~----  350 (461)
                      +.|.+.....+.+.+..|.-.                           .....+.+.|-||||||.+...+-..+.    
T Consensus       152 l~gRe~e~~~v~~F~~~hle~---------------------------~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~  204 (529)
T KOG2227|consen  152 LKGRELEMDIVREFFSLHLEL---------------------------NTSGSLYVSGQPGTGKTALLSRVLDSLSKSSK  204 (529)
T ss_pred             ccchHHHHHHHHHHHHhhhhc---------------------------ccCcceEeeCCCCcchHHHHHHHHHhhhhhcc
Confidence            678888888888888654321                           1236689999999999998876654332    


Q ss_pred             C-ceEEecchhhhhcCc-------------ccccHHHHHHHHHHhhchhhhc-cCceEEEEcCccccchh
Q 012525          351 V-PFVIADATTLTQAGY-------------VGEDVESILYKLLAQAEFNVEA-AQQGMVYIDEVDKITKK  405 (461)
Q Consensus       351 ~-pfv~i~~s~l~~~g~-------------vGe~~e~~L~~lf~~a~~~v~~-a~~gVLfIDEID~L~~~  405 (461)
                      . ..+.++|..+....-             .+...+..+...|..   .+.. ...-||++||+|.|...
T Consensus       205 ~~~~v~inc~sl~~~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~---h~~q~k~~~llVlDEmD~L~tr  271 (529)
T KOG2227|consen  205 SPVTVYINCTSLTEASAIFKKIFSSLLQDLVSPGTGMQHLEKFEK---HTKQSKFMLLLVLDEMDHLITR  271 (529)
T ss_pred             cceeEEEeeccccchHHHHHHHHHHHHHHhcCCchhHHHHHHHHH---HHhcccceEEEEechhhHHhhc
Confidence            2 347888887664311             111111111112211   1111 23558999999999865

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.04  E-value=0.024  Score=52.01  Aligned_cols=32  Identities=34%  Similarity=0.451  Sum_probs=25.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ++|.|+||+|||++++.+|..+   +..++.+++.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D   37 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAAD   37 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcC
Confidence            6899999999999999998765   4455555544

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>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=96.01  E-value=0.03  Score=50.51  Aligned_cols=27  Identities=30%  Similarity=0.439  Sum_probs=23.6

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.|+.|+|||||+++|+..+
T Consensus        24 ~~Ge~~~i~G~nGsGKStLl~~l~G~~   50 (144)
T cd03221          24 NPGDRIGLVGRNGAGKSTLLKLIAGEL   50 (144)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHcCCC
Confidence            345678899999999999999999876

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.

>PLN02459 probable adenylate kinase

Probab=96.01  E-value=0.007  Score=60.70  Aligned_cols=31  Identities=29%  Similarity=0.513  Sum_probs=27.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .+++|.||||+||||+|+.||+.++..++.+
T Consensus        30 ~~ii~~G~PGsGK~T~a~~la~~~~~~~is~   60 (261)
T PLN02459         30 VNWVFLGCPGVGKGTYASRLSKLLGVPHIAT   60 (261)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCcEEeC
Confidence            5689999999999999999999998776543

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.00  E-value=0.014  Score=61.69  Aligned_cols=70  Identities=20%  Similarity=0.387  Sum_probs=44.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      .++|+||-.|||||+++.+.+.+...++.++..++....   ......++.+.....    . ....||||||+.+..
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~---~~l~d~~~~~~~~~~----~-~~~yifLDEIq~v~~  108 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDR---IELLDLLRAYIELKE----R-EKSYIFLDEIQNVPD  108 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcch---hhHHHHHHHHHHhhc----c-CCceEEEecccCchh
Confidence            689999999999999999998886656666666555321   111112222221111    1 456899999996554

>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=95.99  E-value=0.0012  Score=65.28  Aligned_cols=27  Identities=44%  Similarity=0.742  Sum_probs=24.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      ..+|++.|++|+||||+++++.+.+..
T Consensus       127 ~~~ili~G~tGSGKTT~l~all~~i~~  153 (270)
T PF00437_consen  127 RGNILISGPTGSGKTTLLNALLEEIPP  153 (270)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHCHT
T ss_pred             ceEEEEECCCccccchHHHHHhhhccc
Confidence            378999999999999999999987744

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 ....

>TIGR00017 cmk cytidylate kinase

Probab=95.99  E-value=0.018  Score=56.04  Aligned_cols=29  Identities=28%  Similarity=0.575  Sum_probs=26.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      .|.|.||+|+||||+|+.||+.++.+++.
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~~~~~~~~   32 (217)
T TIGR00017         4 IIAIDGPSGAGKSTVAKAVAEKLGYAYLD   32 (217)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            47899999999999999999999987664

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.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=95.98  E-value=0.053  Score=52.03  Aligned_cols=24  Identities=42%  Similarity=0.452  Sum_probs=20.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..-+.|+|+||+|||++|..++..
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~   42 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVT   42 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            466889999999999999999754

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 .

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=95.95  E-value=0.045  Score=50.93  Aligned_cols=37  Identities=24%  Similarity=0.447  Sum_probs=28.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~  362 (461)
                      .-++|.|++|+||||+|+.|+..+   +...+.++...+.
T Consensus        19 ~~i~i~G~~GsGKstla~~l~~~l~~~~~~~~~l~~d~~r   58 (184)
T TIGR00455        19 VVIWLTGLSGSGKSTIANALEKKLESKGYRVYVLDGDNVR   58 (184)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECChHHH
Confidence            568899999999999999999887   3345566655544

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=95.95  E-value=0.039  Score=58.05  Aligned_cols=61  Identities=26%  Similarity=0.274  Sum_probs=46.2

Q ss_pred             HhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          272 DKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       272 d~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      ...|.+.+..++.|...+.+                +            -...+.+|+|+|..|||||.+.+.+-+.++.
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~----------------~------------~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~   56 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGN----------------N------------SCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL   56 (438)
T ss_pred             ccCccchHHHHHHHHHHhCC----------------C------------CcccceeEEEeccCCCchhHHHHHHHhhcCC
Confidence            34467778788877776620                0            0123578899999999999999999999999


Q ss_pred             ceEEecchh
Q 012525          352 PFVIADATT  360 (461)
Q Consensus       352 pfv~i~~s~  360 (461)
                      +.+.+++-+
T Consensus        57 ~~vw~n~~e   65 (438)
T KOG2543|consen   57 ENVWLNCVE   65 (438)
T ss_pred             cceeeehHH
Confidence            988887754

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.91  E-value=0.056  Score=53.16  Aligned_cols=25  Identities=36%  Similarity=0.640  Sum_probs=21.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHH
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..+..+.++||+|+|||||.|+|..
T Consensus        26 ~~Gevv~iiGpSGSGKSTlLRclN~   50 (240)
T COG1126          26 EKGEVVVIIGPSGSGKSTLLRCLNG   50 (240)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHC
Confidence            3456789999999999999999985

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.90  E-value=0.022  Score=58.88  Aligned_cols=25  Identities=36%  Similarity=0.616  Sum_probs=22.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..+||.||+|+||||+.+++.+.+.
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~i~  147 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDYIN  147 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhC
Confidence            5689999999999999999998765

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.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.90  E-value=0.0077  Score=60.18  Aligned_cols=25  Identities=40%  Similarity=0.570  Sum_probs=21.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..++|.|++|+||||+++++...+.
T Consensus        81 GlilisG~tGSGKTT~l~all~~i~  105 (264)
T cd01129          81 GIILVTGPTGSGKTTTLYSALSELN  105 (264)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhhhC
Confidence            4589999999999999999977664

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.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.88  E-value=0.032  Score=56.17  Aligned_cols=35  Identities=23%  Similarity=0.267  Sum_probs=27.0

Q ss_pred             cccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          316 DNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       316 ~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +.....-..+..+-|.|++||||||++|.|.+...
T Consensus        30 d~Vsf~i~~ge~~glVGESG~GKSTlgr~i~~L~~   64 (268)
T COG4608          30 DGVSFSIKEGETLGLVGESGCGKSTLGRLILGLEE   64 (268)
T ss_pred             cceeEEEcCCCEEEEEecCCCCHHHHHHHHHcCcC
Confidence            33333344457788999999999999999998774

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.88  E-value=0.0091  Score=57.26  Aligned_cols=29  Identities=31%  Similarity=0.452  Sum_probs=25.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ..+++.|.||+||||+|+.||+.++..++
T Consensus         4 ~~i~i~G~~G~GKst~a~~l~~~~~~~~~   32 (197)
T PRK12339          4 TIHFIGGIPGVGKTSISGYIARHRAIDIV   32 (197)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCeEE
Confidence            45899999999999999999999887543

>PLN02165 adenylate isopentenyltransferase

Probab=95.86  E-value=0.0081  Score=62.20  Aligned_cols=33  Identities=36%  Similarity=0.536  Sum_probs=28.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +..++|.||+|+|||+||..||+.++..++..+
T Consensus        43 g~iivIiGPTGSGKStLA~~LA~~l~~eIIsaD   75 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSVDLATRFPSEIINSD   75 (334)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHcCCceecCC
Confidence            356899999999999999999999987666554

>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2

Probab=95.86  E-value=0.012  Score=53.89  Aligned_cols=27  Identities=37%  Similarity=0.602  Sum_probs=24.8

Q ss_pred             CCCchHHHHHHHHHhcCCceEEecchh
Q 012525          334 TGSGKTLLAKTLARHVNVPFVIADATT  360 (461)
Q Consensus       334 PGTGKTtLAraLA~~l~~pfv~i~~s~  360 (461)
                      ||+||||+++.||+.++.+|+.+|...
T Consensus         1 ~GsGKStvg~~lA~~L~~~fiD~D~~i   27 (158)
T PF01202_consen    1 MGSGKSTVGKLLAKRLGRPFIDLDDEI   27 (158)
T ss_dssp             TTSSHHHHHHHHHHHHTSEEEEHHHHH
T ss_pred             CCCcHHHHHHHHHHHhCCCccccCHHH
Confidence            799999999999999999999888754

7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.86  E-value=0.0075  Score=55.63  Aligned_cols=24  Identities=25%  Similarity=0.508  Sum_probs=21.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      -++|.||+|+|||||+++|+..++
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARLA   26 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            478999999999999999999775

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.

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=95.85  E-value=0.029  Score=57.44  Aligned_cols=29  Identities=24%  Similarity=0.373  Sum_probs=26.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      +..|++.|++|||||++|+.||+.++.+.
T Consensus        92 p~iIlI~G~sgsGKStlA~~La~~l~~~~  120 (301)
T PRK04220         92 PIIILIGGASGVGTSTIAFELASRLGIRS  120 (301)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            35689999999999999999999998874

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=95.85  E-value=0.027  Score=63.87  Aligned_cols=28  Identities=32%  Similarity=0.364  Sum_probs=23.5

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -..+..|.+.|++|+|||||+|.|....
T Consensus       496 I~~Ge~vaIvG~SGsGKSTL~KLL~gly  523 (709)
T COG2274         496 IPPGEKVAIVGRSGSGKSTLLKLLLGLY  523 (709)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3445669999999999999999999755

>PF13479 AAA_24: AAA domain

Probab=95.84  E-value=0.015  Score=56.00  Aligned_cols=20  Identities=55%  Similarity=0.904  Sum_probs=18.2

Q ss_pred             CcEEEEccCCCchHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraL  345 (461)
                      -.+||||+||+|||++|..+
T Consensus         4 ~~~lIyG~~G~GKTt~a~~~   23 (213)
T PF13479_consen    4 IKILIYGPPGSGKTTLAASL   23 (213)
T ss_pred             eEEEEECCCCCCHHHHHHhC
Confidence            46999999999999998888

>PF07931 CPT: Chloramphenicol phosphotransferase-like protein; InterPro: IPR012853 The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Q56148 from SWISSPROT) expressed by Streptomyces venezuelae

Probab=95.81  E-value=0.041  Score=51.98  Aligned_cols=37  Identities=27%  Similarity=0.544  Sum_probs=31.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQ  363 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~  363 (461)
                      -|+|.|++=+|||+||++|.+.+..||+.+....+..
T Consensus         3 iI~LNG~sSSGKSsia~~Lq~~~~~p~~~l~~D~f~~   39 (174)
T PF07931_consen    3 IIILNGPSSSGKSSIARALQERLPEPWLHLSVDTFVD   39 (174)
T ss_dssp             EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHHHHhCcCCeEEEecChHHh
Confidence            4899999999999999999999999999888776654

Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite [, ]. ; GO: 0005524 ATP binding, 0016740 transferase activity; PDB: 1QHX_A 1QHN_A 1GRR_A 1QHY_A 1QHS_A 1GRQ_A.

>TIGR02012 tigrfam_recA protein RecA

Probab=95.80  E-value=0.041  Score=56.78  Aligned_cols=78  Identities=24%  Similarity=0.235  Sum_probs=45.1

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcC---cccc-----------cHHHHHHHHHHhhchhh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAG---YVGE-----------DVESILYKLLAQAEFNV  386 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g---~vGe-----------~~e~~L~~lf~~a~~~v  386 (461)
                      ...-++|+||||||||+||..++...   +.+.+.++........   ..|.           ..+..+..    ....+
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~----~~~li  129 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEI----AETLV  129 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHH----HHHHh
Confidence            34678899999999999988776543   4566666654322110   0111           11222211    11122


Q ss_pred             hccCceEEEEcCccccchh
Q 012525          387 EAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       387 ~~a~~gVLfIDEID~L~~~  405 (461)
                      ......+|+||-|..+.+.
T Consensus       130 ~~~~~~lIVIDSv~al~~~  148 (321)
T TIGR02012       130 RSGAVDIIVVDSVAALVPK  148 (321)
T ss_pred             hccCCcEEEEcchhhhccc
Confidence            2345679999999988764

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.

>PRK13951 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=95.78  E-value=0.018  Score=62.45  Aligned_cols=33  Identities=27%  Similarity=0.574  Sum_probs=30.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      +|+|+|++|+||||+++.||+.++.+|+..+..
T Consensus         2 ~I~l~G~~GsGKSTv~~~La~~lg~~~id~D~~   34 (488)
T PRK13951          2 RIFLVGMMGSGKSTIGKRVSEVLDLQFIDMDEE   34 (488)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcCCeEEECcHH
Confidence            589999999999999999999999999977754

>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=95.78  E-value=0.059  Score=50.80  Aligned_cols=25  Identities=36%  Similarity=0.583  Sum_probs=22.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...+.|.||.|+|||||.+.|+..+
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl~   49 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQL   49 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC
Confidence            4567899999999999999999866

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.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=95.77  E-value=0.025  Score=66.22  Aligned_cols=90  Identities=12%  Similarity=0.120  Sum_probs=50.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCc---ccccHHHHHHHHHHh-hchhhhccCceEEEEc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGY---VGEDVESILYKLLAQ-AEFNVEAAQQGMVYID  397 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~---vGe~~e~~L~~lf~~-a~~~v~~a~~gVLfID  397 (461)
                      ...++|.|.+||||||+.+++.+.+   +..++-+..+......+   .|.. ...+..++.. ...........|||||
T Consensus       362 ~~v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTGkAA~~L~e~tGi~-a~TI~sll~~~~~~~~~l~~~~vlIVD  440 (988)
T PRK13889        362 RDLGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIAAENLEGGSGIA-SRTIASLEHGWGQGRDLLTSRDVLVID  440 (988)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcHHHHHHHhhccCcc-hhhHHHHHhhhcccccccccCcEEEEE
Confidence            3457899999999999988776544   55555444433221111   1211 2223333211 1111112245699999


Q ss_pred             CccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          398 EVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       398 EID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      |+-.+...              ....|+...+
T Consensus       441 EASMv~~~--------------~m~~LL~~a~  458 (988)
T PRK13889        441 EAGMVGTR--------------QLERVLSHAA  458 (988)
T ss_pred             CcccCCHH--------------HHHHHHHhhh
Confidence            99977766              5666666554

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=95.76  E-value=0.011  Score=55.52  Aligned_cols=29  Identities=34%  Similarity=0.670  Sum_probs=25.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ..++|+|++|+||||+++.|+..++..++
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~~~~i   32 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFSAKFI   32 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCEEE
Confidence            45899999999999999999998876544

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.74  E-value=0.049  Score=54.11  Aligned_cols=35  Identities=20%  Similarity=0.354  Sum_probs=25.3

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      ...-++++|+||||||++|..+|...   +.+.+.++.
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~   72 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTV   72 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            35678999999999999998876532   345444443

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

>TIGR00416 sms DNA repair protein RadA

Probab=95.74  E-value=0.013  Score=63.14  Aligned_cols=35  Identities=23%  Similarity=0.334  Sum_probs=26.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ..-+||.|+||+|||+|+..++..+   +.++++++..
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~E  131 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGE  131 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECc
Confidence            3568999999999999999987654   2455555553

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)).

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=95.73  E-value=0.056  Score=60.39  Aligned_cols=25  Identities=24%  Similarity=0.372  Sum_probs=20.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..-++|.|+|||||||+++.+...+
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~~l  191 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLAAL  191 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHH
Confidence            4568899999999999987776544

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=95.72  E-value=0.034  Score=52.20  Aligned_cols=20  Identities=25%  Similarity=0.527  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      ++|+||.|.|||++.|.++-
T Consensus         2 ~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            68999999999999999983

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=95.69  E-value=0.01  Score=68.42  Aligned_cols=90  Identities=20%  Similarity=0.220  Sum_probs=57.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccH------HHHHHHHHH--hhchhhhccCceEEEEcC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDV------ESILYKLLA--QAEFNVEAAQQGMVYIDE  398 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~------e~~L~~lf~--~a~~~v~~a~~gVLfIDE  398 (461)
                      .+|++||||+|||+.|.+.|+.++..+++.++.+... ++.....      ...+...+.  ..... ......||++||
T Consensus       359 ~~l~~G~pGigKT~~~h~~~k~~g~~v~E~Nas~~RS-k~~l~~~~~~~~~s~si~~~~~~~~~~~~-~~~~~~vil~de  436 (871)
T KOG1968|consen  359 ALLLSGPPGIGKTTAAHKAAKELGFKVVEKNASDVRS-KKELLNKLGNATSSHSIKGSKKKKGNRQS-LNSDHFLILMDE  436 (871)
T ss_pred             HHHhcCCCCCCchhhHhhhhhhcccceeecCcccccc-ccHHHhhhhccccccchhhhhcccccccc-cccceeEEEEec
Confidence            3699999999999999999999999999999998773 2211110      011111110  00000 112344999999


Q ss_pred             ccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          399 VDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       399 ID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +|-+...           .++....|-.+..
T Consensus       437 vD~~~~~-----------dRg~v~~l~~l~~  456 (871)
T KOG1968|consen  437 VDGMFGE-----------DRGGVSKLSSLCK  456 (871)
T ss_pred             cccccch-----------hhhhHHHHHHHHH
Confidence            9988773           1225666666666

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=95.67  E-value=0.035  Score=55.92  Aligned_cols=25  Identities=40%  Similarity=0.618  Sum_probs=23.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .+++|.||+|+|||||.++|+..+.
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccC
Confidence            5799999999999999999998774

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.

>COG0283 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.67  E-value=0.022  Score=55.69  Aligned_cols=30  Identities=33%  Similarity=0.547  Sum_probs=26.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..|-+-||.|+||+|+|+.||+.++..|+.
T Consensus         5 ~~IAIDGPagsGKsTvak~lA~~Lg~~yld   34 (222)
T COG0283           5 IIIAIDGPAGSGKSTVAKILAEKLGFHYLD   34 (222)
T ss_pred             eEEEEeCCCccChHHHHHHHHHHhCCCeec
Confidence            347799999999999999999999998764

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.66  E-value=0.012  Score=59.83  Aligned_cols=26  Identities=38%  Similarity=0.681  Sum_probs=23.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..++++.|++|+||||++++|...+.
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~~~  169 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDEIP  169 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHccCC
Confidence            47899999999999999999998774

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.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.66  E-value=0.0088  Score=55.93  Aligned_cols=22  Identities=32%  Similarity=0.640  Sum_probs=16.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .++.||||||||+++..+...+
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            7899999999997665555444

>KOG0055 consensus Multidrug/pheromone exporter, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]

Probab=95.66  E-value=0.051  Score=64.30  Aligned_cols=28  Identities=43%  Similarity=0.659  Sum_probs=24.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..+.-|.|.|++||||||+.+.|++..+
T Consensus       377 ~~G~~valVG~SGsGKST~i~LL~Rfyd  404 (1228)
T KOG0055|consen  377 PSGQTVALVGPSGSGKSTLIQLLARFYD  404 (1228)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4457799999999999999999998763

>PRK13808 adenylate kinase; Provisional

Probab=95.65  E-value=0.011  Score=61.35  Aligned_cols=30  Identities=27%  Similarity=0.541  Sum_probs=26.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+|+||||+||||+++.||+.++.+++.+
T Consensus         2 rIiv~GpPGSGK~T~a~~LA~~ygl~~is~   31 (333)
T PRK13808          2 RLILLGPPGAGKGTQAQRLVQQYGIVQLST   31 (333)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceecc
Confidence            489999999999999999999998876654

>KOG0056 consensus Heavy metal exporter HMT1, ABC superfamily [Inorganic ion transport and metabolism]

Probab=95.64  E-value=0.065  Score=58.19  Aligned_cols=38  Identities=26%  Similarity=0.443  Sum_probs=31.0

Q ss_pred             hccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          314 AVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       314 ~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      ..+++......+..|-|.||+|.||||+.|.|-+..+.
T Consensus       553 vl~disF~v~pGktvAlVG~SGaGKSTimRlLfRffdv  590 (790)
T KOG0056|consen  553 VLSDISFTVQPGKTVALVGPSGAGKSTIMRLLFRFFDV  590 (790)
T ss_pred             eeecceEEecCCcEEEEECCCCCchhHHHHHHHHHhhc
Confidence            44555666677888999999999999999999987743

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.64  E-value=0.031  Score=52.34  Aligned_cols=32  Identities=28%  Similarity=0.436  Sum_probs=26.2

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      +|++|++|+|||++|..++...+.+.+.+...
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~   33 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATA   33 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEcc
Confidence            68999999999999999998876666655443

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.

>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=95.63  E-value=0.011  Score=57.76  Aligned_cols=33  Identities=42%  Similarity=0.691  Sum_probs=26.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecchh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATT  360 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~  360 (461)
                      ++|+||+|||||.+|-++|+.++.|++..|.-.
T Consensus         4 ~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Driq   36 (233)
T PF01745_consen    4 YLIVGPTGTGKTALAIALAQKTGAPVISLDRIQ   36 (233)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH--EEEEE-SGG
T ss_pred             EEEECCCCCChhHHHHHHHHHhCCCEEEeccee
Confidence            789999999999999999999999999877643

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

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

Probab=95.63  E-value=0.048  Score=52.00  Aligned_cols=25  Identities=36%  Similarity=0.377  Sum_probs=21.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..-+.|+|+||+|||++|..+|...
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~   43 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEA   43 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHh
Confidence            4568899999999999999998653

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.61  E-value=0.082  Score=56.50  Aligned_cols=25  Identities=44%  Similarity=0.543  Sum_probs=21.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...++|.||+|+||||++..||..+
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~  245 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARY  245 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4578999999999999998887644

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.60  E-value=0.062  Score=49.35  Aligned_cols=28  Identities=29%  Similarity=0.336  Sum_probs=24.1

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -..+..+.|.|+.|+|||||.+.|+...
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~i~G~~   50 (163)
T cd03216          23 VRRGEVHALLGENGAGKSTLMKILSGLY   50 (163)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3445778899999999999999999865

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.

>PRK12338 hypothetical protein; Provisional

Probab=95.60  E-value=0.012  Score=60.74  Aligned_cols=30  Identities=30%  Similarity=0.495  Sum_probs=26.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +..|++.|+||+||||+|++||+.++..++
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l~~~~~   33 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTLNIKHL   33 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHCCCeEE
Confidence            356899999999999999999999987654

>PRK13764 ATPase; Provisional

Probab=95.60  E-value=0.011  Score=65.78  Aligned_cols=25  Identities=32%  Similarity=0.618  Sum_probs=23.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .+||+.|+||+||||++++|+..+.
T Consensus       258 ~~ILIsG~TGSGKTTll~AL~~~i~  282 (602)
T PRK13764        258 EGILIAGAPGAGKSTFAQALAEFYA  282 (602)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHh
Confidence            6799999999999999999998875

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=95.58  E-value=0.031  Score=62.04  Aligned_cols=25  Identities=28%  Similarity=0.363  Sum_probs=20.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ....+|.|+|||||||++..|...+
T Consensus       160 ~~~~vitGgpGTGKTt~v~~ll~~l  184 (586)
T TIGR01447       160 SNFSLITGGPGTGKTTTVARLLLAL  184 (586)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHH
Confidence            3568899999999999887766543

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=95.58  E-value=0.045  Score=52.96  Aligned_cols=22  Identities=27%  Similarity=0.474  Sum_probs=19.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .-++|+||.|+|||++.+.++.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            4588999999999999999974

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.58  E-value=0.01  Score=54.66  Aligned_cols=24  Identities=33%  Similarity=0.588  Sum_probs=21.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      -++|.||+|+|||||++.|++...
T Consensus         3 ii~l~G~~GsGKsTl~~~L~~~~~   26 (180)
T TIGR03263         3 LIVISGPSGVGKSTLVKALLEEDP   26 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHccCc
Confidence            488999999999999999998664

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.

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=95.56  E-value=0.012  Score=60.15  Aligned_cols=33  Identities=42%  Similarity=0.646  Sum_probs=28.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .-|++.||+|+|||+||..||+.++..++..|.
T Consensus         5 ~~i~i~GptgsGKt~la~~la~~~~~~iis~Ds   37 (307)
T PRK00091          5 KVIVIVGPTASGKTALAIELAKRLNGEIISADS   37 (307)
T ss_pred             eEEEEECCCCcCHHHHHHHHHHhCCCcEEeccc
Confidence            458899999999999999999999887665554

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=95.56  E-value=0.016  Score=56.08  Aligned_cols=24  Identities=42%  Similarity=0.648  Sum_probs=18.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+++.||.|||||+||-+.|-.+
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~   43 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALEL   43 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHH
Confidence            458899999999999998888544

; GO: 0005524 ATP binding; PDB: 3B85_A.

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=95.55  E-value=0.014  Score=54.45  Aligned_cols=29  Identities=41%  Similarity=0.630  Sum_probs=25.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      |.|+|.+|+||||+++.|++ ++.+++..+
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            68999999999999999999 777766554

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.54  E-value=0.013  Score=52.63  Aligned_cols=26  Identities=38%  Similarity=0.703  Sum_probs=22.6

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCce
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      ++|.||+|+|||+|++.|++.+...|
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~~~~   27 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFDPNF   27 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCCccc
Confidence            68999999999999999999875443

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.54  E-value=0.014  Score=54.95  Aligned_cols=26  Identities=35%  Similarity=0.547  Sum_probs=23.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +..++|.||+|+|||+|++.|++.+.
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            46689999999999999999999875

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=95.54  E-value=0.028  Score=50.27  Aligned_cols=24  Identities=42%  Similarity=0.581  Sum_probs=18.7

Q ss_pred             CcEEEEccCCCchHH-HHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTL-LAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTt-LAraLA~~l  349 (461)
                      .++++.|++|+|||+ ++..+.+.+
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~   49 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEAL   49 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHh
Confidence            568999999999999 555555544

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=95.53  E-value=0.087  Score=53.35  Aligned_cols=28  Identities=21%  Similarity=0.285  Sum_probs=24.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      .-++|+|+.|+|||++.+.|...++...
T Consensus        77 ~~~~l~G~g~nGKStl~~~l~~l~G~~~  104 (304)
T TIGR01613        77 KLFFLYGNGGNGKSTFQNLLSNLLGDYA  104 (304)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHhChhh
Confidence            3478999999999999999999887654

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.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.53  E-value=0.016  Score=54.95  Aligned_cols=26  Identities=31%  Similarity=0.415  Sum_probs=23.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +..|.|.|++|+|||||+++|++.+.
T Consensus         6 ~~iI~I~G~sGsGKTTl~~~l~~~l~   31 (209)
T PRK05480          6 PIIIGIAGGSGSGKTTVASTIYEELG   31 (209)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35688999999999999999999883

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.52  E-value=0.057  Score=52.65  Aligned_cols=34  Identities=26%  Similarity=0.513  Sum_probs=24.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHh-c--CCceEEec
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARH-V--NVPFVIAD  357 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~-l--~~pfv~i~  357 (461)
                      .+..+|++|+||+|||++|..++.. +  +.+.+.+.
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            3577999999999999999876543 2  44444443

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.

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=95.52  E-value=0.028  Score=62.18  Aligned_cols=37  Identities=27%  Similarity=0.476  Sum_probs=29.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC----ceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV----PFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~----pfv~i~~s~l~  362 (461)
                      ..|+|+|.+|+||||+|++||+.++.    +++.++...+.
T Consensus       393 ~~Ivl~Gl~GSGKSTia~~La~~L~~~~g~~~~~lD~D~vr  433 (568)
T PRK05537        393 FTVFFTGLSGAGKSTIAKALMVKLMEMRGRPVTLLDGDVVR  433 (568)
T ss_pred             eEEEEECCCCChHHHHHHHHHHHhhhccCceEEEeCCcHHH
Confidence            56899999999999999999998874    34555555443

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=95.51  E-value=0.045  Score=55.07  Aligned_cols=27  Identities=41%  Similarity=0.629  Sum_probs=22.6

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-++|.||+||||||+.|.|-+.+
T Consensus        25 ~~gef~vliGpSGsGKTTtLkMINrLi   51 (309)
T COG1125          25 EEGEFLVLIGPSGSGKTTTLKMINRLI   51 (309)
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHhccc
Confidence            334567899999999999999998765

>PF06048 DUF927: Domain of unknown function (DUF927); InterPro: IPR009270 This entry is represented by Bacteriophage PT1028, Orf1

Probab=95.50  E-value=0.14  Score=51.65  Aligned_cols=103  Identities=20%  Similarity=0.167  Sum_probs=62.5

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      +.++..+.+.+.+.|.....-.|..++......+.                        ......+-|+|.+++|||+++
T Consensus       155 tle~W~~~v~~~~~~n~~~~~~l~~afa~pLL~~l------------------------~~~~~~~hl~G~Ss~GKTt~~  210 (286)
T PF06048_consen  155 TLEEWQEMVAALAKGNPRLMLALCAAFAAPLLSLL------------------------GVEGFGFHLYGQSSSGKTTAL  210 (286)
T ss_pred             CHHHHHHHHHHHHccChHHHHHHHHHHHHHHHHHh------------------------CCCceEEEEEeCCCCCHHHHH
Confidence            56666666667677777666666555543333221                        122345779999999999999


Q ss_pred             HHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          343 KTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       343 raLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ++.+...+.|-      .+.. .|-...  ..+....       ...+...|+|||+....++
T Consensus       211 ~~a~Sv~G~p~------~l~~-sw~~T~--n~le~~a-------~~~nd~~l~lDE~~~~~~~  257 (286)
T PF06048_consen  211 QLAASVWGNPD------GLIR-SWNSTD--NGLERTA-------AAHNDLPLVLDELSQADPK  257 (286)
T ss_pred             HHhhhhCcCch------hhhh-cchhhH--HHHHHHH-------HHcCCcceEehhccccchh
Confidence            99999998875      2221 122211  1111111       1225668999999866554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=95.46  E-value=0.01  Score=54.76  Aligned_cols=27  Identities=37%  Similarity=0.658  Sum_probs=23.2

Q ss_pred             EccCCCchHHHHHHHHHhcCCceEEec
Q 012525          331 MGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       331 ~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +|++|+||||++++|+..++..++.-+
T Consensus         1 ~G~sGsGKSTla~~la~~l~~~~~~~d   27 (163)
T PRK11545          1 MGVSGSGKSAVASEVAHQLHAAFLDGD   27 (163)
T ss_pred             CCCCCCcHHHHHHHHHHHhCCeEEeCc
Confidence            599999999999999999987666544

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=95.44  E-value=0.029  Score=66.17  Aligned_cols=92  Identities=13%  Similarity=0.115  Sum_probs=52.5

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---CcccccHHHHHHHH-HHhhchhhhccCceEEE
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGEDVESILYKL-LAQAEFNVEAAQQGMVY  395 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~~e~~L~~l-f~~a~~~v~~a~~gVLf  395 (461)
                      ....-++|.|++||||||+.+++.+.+   +..++-+-.+.-...   .-.|.. ...+..+ +.............|||
T Consensus       395 ~~~r~~~v~G~AGTGKTt~l~~~~~~~e~~G~~V~g~ApTgkAA~~L~e~~Gi~-a~TIas~ll~~~~~~~~l~~~~vlV  473 (1102)
T PRK13826        395 GPARIAAVVGRAGAGKTTMMKAAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQ-SRTLSSWELRWNQGRDQLDNKTVFV  473 (1102)
T ss_pred             ccCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEcCcHHHHHHHHHhhCCC-eeeHHHHHhhhccCccCCCCCcEEE
Confidence            345678899999999999999997754   555554433321110   001111 1112221 12111111223456999


Q ss_pred             EcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          396 IDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       396 IDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      |||+-.+...              ....|++.++
T Consensus       474 IDEAsMv~~~--------------~m~~Ll~~~~  493 (1102)
T PRK13826        474 LDEAGMVASR--------------QMALFVEAVT  493 (1102)
T ss_pred             EECcccCCHH--------------HHHHHHHHHH
Confidence            9999987766              6677777775

>PRK13975 thymidylate kinase; Provisional

Probab=95.43  E-value=0.013  Score=54.71  Aligned_cols=27  Identities=41%  Similarity=0.466  Sum_probs=24.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      .-|+|.|++|+||||+|+.||+.++..
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~~~   29 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLNAF   29 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            348999999999999999999999853

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=95.42  E-value=0.012  Score=55.46  Aligned_cols=23  Identities=57%  Similarity=0.826  Sum_probs=21.6

Q ss_pred             EEEEccCCCchHHHHHHHHHhcC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |.+.|++|+||||+|+.|+..++
T Consensus         2 IgI~G~sgSGKTTla~~L~~~L~   24 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLAKRLAQILN   24 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            67899999999999999999996

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=95.42  E-value=0.049  Score=60.45  Aligned_cols=28  Identities=32%  Similarity=0.421  Sum_probs=24.0

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -..+..+|+.||+|||||+|.|+||...
T Consensus       416 v~~G~~llI~G~SG~GKTsLlRaiaGLW  443 (604)
T COG4178         416 VRPGERLLITGESGAGKTSLLRALAGLW  443 (604)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            3446789999999999999999999744

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.41  E-value=0.068  Score=51.43  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=19.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..++|+||.|+|||++.+.++.
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5589999999999999999974

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

>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=95.41  E-value=0.082  Score=47.81  Aligned_cols=26  Identities=38%  Similarity=0.624  Sum_probs=23.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ...+.|.|+.|+|||||.++|+..+.
T Consensus        25 g~~~~i~G~nGsGKStll~~l~g~~~   50 (157)
T cd00267          25 GEIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            46788999999999999999998764

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.

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.39  E-value=0.17  Score=52.39  Aligned_cols=78  Identities=24%  Similarity=0.387  Sum_probs=52.1

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc------------------CcccccHHHHHHHHHHhh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA------------------GYVGEDVESILYKLLAQA  382 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~------------------g~vGe~~e~~L~~lf~~a  382 (461)
                      .+..+||.|-.|+||||..--||..+   +..++...+.++...                  +-.|.+........+..+
T Consensus       138 ~p~Vil~vGVNG~GKTTTIaKLA~~l~~~g~~VllaA~DTFRAaAiEQL~~w~er~gv~vI~~~~G~DpAaVafDAi~~A  217 (340)
T COG0552         138 KPFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISGKEGADPAAVAFDAIQAA  217 (340)
T ss_pred             CcEEEEEEecCCCchHhHHHHHHHHHHHCCCeEEEEecchHHHHHHHHHHHHHHHhCCeEEccCCCCCcHHHHHHHHHHH
Confidence            36778999999999999888888766   445554444333321                  114556566666655544


Q ss_pred             chhhhccCceEEEEcCccccchh
Q 012525          383 EFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       383 ~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ..    ..-.||++|=+.+|..+
T Consensus       218 ka----r~~DvvliDTAGRLhnk  236 (340)
T COG0552         218 KA----RGIDVVLIDTAGRLHNK  236 (340)
T ss_pred             HH----cCCCEEEEeCcccccCc
Confidence            32    25569999999998877

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.37  E-value=0.04  Score=55.34  Aligned_cols=25  Identities=32%  Similarity=0.499  Sum_probs=21.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|+|++|+||||++..||..+
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~~l   96 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLANKL   96 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            4568899999999999999998766

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.36  E-value=0.14  Score=56.25  Aligned_cols=25  Identities=40%  Similarity=0.616  Sum_probs=21.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...|+|+||+|+||||++..||..+
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            5678899999999999999888643

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.34  E-value=0.016  Score=55.27  Aligned_cols=30  Identities=47%  Similarity=0.489  Sum_probs=24.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhc-CCceEEec
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV-NVPFVIAD  357 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l-~~pfv~i~  357 (461)
                      |.+.|++|+||||+|+.|++.+ +..++.++
T Consensus         2 i~i~G~sgsGKTtla~~l~~~~~~~~~i~~D   32 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRILPNCCVIHQD   32 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeEEccc
Confidence            6789999999999999999998 44444333

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>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=95.33  E-value=0.037  Score=58.49  Aligned_cols=102  Identities=15%  Similarity=0.201  Sum_probs=60.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      +.+.-++|+|||.||||+++-.|-+.++..++..--+.-. - |...                  ...-.|.+||++-.-
T Consensus       260 PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViSf~Ns~Sh-F-WLqP------------------L~d~Ki~llDDAT~~  319 (432)
T PF00519_consen  260 PKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKSH-F-WLQP------------------LADAKIALLDDATYP  319 (432)
T ss_dssp             TTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-GGGTTSC-G-GGGG------------------GCT-SSEEEEEE-HH
T ss_pred             CcccEEEEECCCCCchhHHHHHHHHHhCCEEEEecCCCCc-c-cccc------------------hhcCcEEEEcCCccc
Confidence            3356688999999999999999999998876653222100 0 1100                  012237888998754


Q ss_pred             chhhhccccccccchHHHHHH-HHHHHhCceeeeeccee--eecCCeEEEecCCCCcCc
Q 012525          403 TKKAESLNISRDVSGEGVQQA-LLKMLEGTETKTFAAVS--KVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~a-LL~~LEg~~v~i~~~~r--~~~rd~IiI~TsNid~e~  458 (461)
                      .=.              -.+. |..+|||..+.+...-+  ...+-.=++.|||+|...
T Consensus       320 cW~--------------Y~D~ylRNaLDGN~vsiD~KHkap~Qik~PPLlITsN~dv~~  364 (432)
T PF00519_consen  320 CWD--------------YIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKK  364 (432)
T ss_dssp             HHH--------------HHHHHTHHHHCTSEEEEEESSSEEEEEE---EEEEESS-TTT
T ss_pred             HHH--------------HHHHHHHhccCCCeeeeeccCCCceEeecCceEEecCCCCCc
Confidence            444              3444 56899999888766511  111222345788888643

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.

>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]

Probab=95.33  E-value=0.03  Score=52.73  Aligned_cols=72  Identities=22%  Similarity=0.236  Sum_probs=43.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCccc------ccHHHHHHHHHHhhchhhhccCceEEEEcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVG------EDVESILYKLLAQAEFNVEAAQQGMVYIDE  398 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vG------e~~e~~L~~lf~~a~~~v~~a~~gVLfIDE  398 (461)
                      +.|.|+|+--||||+|++.||+.++.++...-..+.......|      .+..++...........+ ...+.|+|||-
T Consensus         9 K~VailG~ESsGKStLv~kLA~~fnt~~~wEY~Re~v~~~l~gdeal~y~Dy~~ia~Gq~~~~d~av-~~a~~v~fiDT   86 (187)
T COG3172           9 KTVAILGGESSGKSTLVNKLANIFNTTSAWEYGREYVFEHLGGDEALQYSDYAKIALGQAAYEDAAV-RYANKVAFIDT   86 (187)
T ss_pred             eeeeeecCcccChHHHHHHHHHHhCCCchhHHHHHHHHHHhCCchhhhhccHHHHHhhhHHHHHHHH-hCCCceEEEec
Confidence            4578999999999999999999999876644443333221222      222333333332222222 23457888884

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=95.30  E-value=0.084  Score=58.72  Aligned_cols=15  Identities=40%  Similarity=0.762  Sum_probs=13.3

Q ss_pred             CcEEEEccCCCchHH
Q 012525          326 SNVLLMGPTGSGKTL  340 (461)
Q Consensus       326 ~~VLL~GPPGTGKTt  340 (461)
                      ..+++.|++||||||
T Consensus        67 qvlIviGeTGsGKST   81 (674)
T KOG0922|consen   67 QVLIVIGETGSGKST   81 (674)
T ss_pred             CEEEEEcCCCCCccc
Confidence            458899999999998

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.29  E-value=0.02  Score=52.65  Aligned_cols=22  Identities=36%  Similarity=0.605  Sum_probs=21.0

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      |.|.|+.|+||||+++.|++.+
T Consensus         3 I~ieG~~GsGKtT~~~~L~~~l   24 (200)
T cd01672           3 IVFEGIDGAGKTTLIELLAERL   24 (200)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999988

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>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=95.28  E-value=0.021  Score=53.53  Aligned_cols=33  Identities=36%  Similarity=0.563  Sum_probs=25.7

Q ss_pred             EEEEccCCCchHHHHHHHHHhcC---CceEEecchh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVN---VPFVIADATT  360 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~  360 (461)
                      |.+.|++|+||||+|+.|++.+.   .+...++..+
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~~~~~~~i~~Dd   37 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDD   37 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEehhh
Confidence            68999999999999999999873   3444444443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.28  E-value=0.07  Score=57.77  Aligned_cols=35  Identities=29%  Similarity=0.418  Sum_probs=25.9

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      .+..+|+.||||+|||+|+..++...   +.+.+.+..
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s~  299 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENACANKERAILFAY  299 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEe
Confidence            34779999999999999998887644   334444444

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.

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=95.28  E-value=0.011  Score=52.91  Aligned_cols=27  Identities=37%  Similarity=0.617  Sum_probs=23.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..|+|.|+-|+||||++|.+++.++..
T Consensus        16 ~vi~L~GdLGaGKTtf~r~l~~~lg~~   42 (123)
T PF02367_consen   16 DVILLSGDLGAGKTTFVRGLARALGID   42 (123)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTT--
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            568999999999999999999999763

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.

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=95.23  E-value=0.077  Score=58.24  Aligned_cols=27  Identities=33%  Similarity=0.567  Sum_probs=23.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.|++|+|||||++.|++..
T Consensus       374 ~~G~~vaIvG~SGsGKSTL~~lL~g~~  400 (588)
T PRK11174        374 PAGQRIALVGPSGAGKTSLLNALLGFL  400 (588)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            356778999999999999999999876

>PRK12337 2-phosphoglycerate kinase; Provisional

Probab=95.22  E-value=0.069  Score=57.72  Aligned_cols=34  Identities=38%  Similarity=0.571  Sum_probs=28.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc-eEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP-FVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p-fv~i~~  358 (461)
                      +..|+++|++|+||||+|..||..++.. ++..|.
T Consensus       255 p~vil~~G~~G~GKSt~a~~LA~~lg~~~ii~tD~  289 (475)
T PRK12337        255 PLHVLIGGVSGVGKSVLASALAYRLGITRIVSTDA  289 (475)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCcEEeehhH
Confidence            5678999999999999999999999875 334443

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

Probab=95.21  E-value=0.099  Score=54.12  Aligned_cols=81  Identities=23%  Similarity=0.302  Sum_probs=45.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcC---cccccHHHHH-------HHHHHhhchhhhccCc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAG---YVGEDVESIL-------YKLLAQAEFNVEAAQQ  391 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g---~vGe~~e~~L-------~~lf~~a~~~v~~a~~  391 (461)
                      .+-++++||||+|||+||-.++...   +...+.++...-....   ..|.+....+       ..++......+.....
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~s~~~  134 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSLVRSGAV  134 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHHHhccCC
Confidence            4568899999999999998877533   5566666654311110   0111111100       0111111112233456


Q ss_pred             eEEEEcCccccchh
Q 012525          392 GMVYIDEVDKITKK  405 (461)
Q Consensus       392 gVLfIDEID~L~~~  405 (461)
                      .+|+||-|..+.+.
T Consensus       135 ~lIVIDSvaal~~~  148 (325)
T cd00983         135 DLIVVDSVAALVPK  148 (325)
T ss_pred             CEEEEcchHhhccc
Confidence            79999999988763

RecA couples ATP hydrolysis to DNA strand exchange.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.21  E-value=0.04  Score=57.94  Aligned_cols=24  Identities=42%  Similarity=0.598  Sum_probs=21.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+|+.||+|+||||++++|.+.+
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i  173 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHC  173 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            458999999999999999998877

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).

>PRK08356 hypothetical protein; Provisional

Probab=95.18  E-value=0.021  Score=53.90  Aligned_cols=28  Identities=29%  Similarity=0.236  Sum_probs=22.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ..|+|+||||+||||+|+.|++ .+.+.+
T Consensus         6 ~~i~~~G~~gsGK~t~a~~l~~-~g~~~i   33 (195)
T PRK08356          6 MIVGVVGKIAAGKTTVAKFFEE-KGFCRV   33 (195)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-CCCcEE
Confidence            3478999999999999999964 666543

>PRK10867 signal recognition particle protein; Provisional

Probab=95.16  E-value=0.29  Score=52.62  Aligned_cols=35  Identities=26%  Similarity=0.441  Sum_probs=25.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc----CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~s  359 (461)
                      +..|+|.|++|+||||++-.||..+    +..+..+++.
T Consensus       100 p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D  138 (433)
T PRK10867        100 PTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAAD  138 (433)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEcc
Confidence            4678899999999999888887644    4445555543

>PRK00023 cmk cytidylate kinase; Provisional

Probab=95.14  E-value=0.019  Score=56.03  Aligned_cols=30  Identities=33%  Similarity=0.551  Sum_probs=26.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..|.|.|++|+|||++|+.||+.++.+++.
T Consensus         5 ~~i~i~g~~gsGksti~~~la~~~~~~~~~   34 (225)
T PRK00023          5 IVIAIDGPAGSGKGTVAKILAKKLGFHYLD   34 (225)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            468899999999999999999999887764

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=95.13  E-value=0.053  Score=54.31  Aligned_cols=26  Identities=35%  Similarity=0.524  Sum_probs=22.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .-+.++|+.|+|||+++|++...++.
T Consensus        52 g~~~vtGevGsGKTv~~Ral~~s~~~   77 (269)
T COG3267          52 GILAVTGEVGSGKTVLRRALLASLNE   77 (269)
T ss_pred             ceEEEEecCCCchhHHHHHHHHhcCC
Confidence            45789999999999999988877653

>PRK04328 hypothetical protein; Provisional

Probab=95.13  E-value=0.1  Score=51.41  Aligned_cols=24  Identities=33%  Similarity=0.641  Sum_probs=20.3

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHH
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+..+|+.|+||||||+||..++.
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~   45 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLW   45 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357789999999999999987654

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.13  E-value=0.11  Score=49.93  Aligned_cols=81  Identities=17%  Similarity=0.149  Sum_probs=45.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc-------hh---hhh----------cC--cccccH---HHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA-------TT---LTQ----------AG--YVGEDV---ESILY  376 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~-------s~---l~~----------~g--~vGe~~---e~~L~  376 (461)
                      ...|++++.+|.|||++|-.+|-..   +.++..+..       .+   +..          .+  |..+..   ....+
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~~  101 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAAR  101 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHHH
Confidence            3679999999999999998887433   222211110       00   000          00  111111   12334


Q ss_pred             HHHHhhchhhhccCceEEEEcCccccchh
Q 012525          377 KLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       377 ~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ..+..+...+......+|+||||..+...
T Consensus       102 ~~~~~a~~~l~~~~ydlvVLDEi~~Al~~  130 (191)
T PRK05986        102 EGWEEAKRMLADESYDLVVLDELTYALKY  130 (191)
T ss_pred             HHHHHHHHHHhCCCCCEEEEehhhHHHHC
Confidence            45555665565667789999999876653

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=95.12  E-value=0.022  Score=54.33  Aligned_cols=31  Identities=32%  Similarity=0.488  Sum_probs=26.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|.|+|++|+||||+++.|++.++.+++..+
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~~g~~~i~~D   33 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQKGIPILDAD   33 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCeEeeCc
Confidence            3789999999999999999998888776444

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=95.12  E-value=0.017  Score=54.21  Aligned_cols=22  Identities=32%  Similarity=0.573  Sum_probs=20.7

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      |.|.|++|+|||||++.|++.+
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6799999999999999999987

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.08  E-value=0.049  Score=58.98  Aligned_cols=29  Identities=31%  Similarity=0.424  Sum_probs=24.6

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .-..+..+.|.||+|+|||||+++|++..
T Consensus       357 ~i~~G~~vaIvG~SGsGKSTLl~lL~g~~  385 (529)
T TIGR02868       357 DLPPGERVAILGPSGSGKSTLLMLLTGLL  385 (529)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            33456778999999999999999999766

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=95.07  E-value=0.024  Score=57.65  Aligned_cols=31  Identities=39%  Similarity=0.704  Sum_probs=26.8

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      |++.||+|+|||+||..||+.++..++.++.
T Consensus         2 i~i~G~t~~GKs~la~~l~~~~~~~iis~Ds   32 (287)
T TIGR00174         2 IFIMGPTAVGKSQLAIQLAKKLNAEIISVDS   32 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCcEEEech
Confidence            7899999999999999999999876665544

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.07  E-value=0.016  Score=56.70  Aligned_cols=23  Identities=48%  Similarity=0.751  Sum_probs=21.6

Q ss_pred             EEEEccCCCchHHHHHHHHHhcC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |+|+|+||+||||+|+-||+++.
T Consensus         4 iIlTGyPgsGKTtfakeLak~L~   26 (261)
T COG4088           4 IILTGYPGSGKTTFAKELAKELR   26 (261)
T ss_pred             EEEecCCCCCchHHHHHHHHHHH
Confidence            78999999999999999999884

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.07  E-value=0.14  Score=47.72  Aligned_cols=20  Identities=35%  Similarity=0.348  Sum_probs=17.6

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |.+|..+|+|||++|-.+|-
T Consensus         5 i~vy~g~G~Gkt~~a~g~~~   24 (159)
T cd00561           5 IQVYTGNGKGKTTAALGLAL   24 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67888889999999988874

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.

>TIGR00235 udk uridine kinase

Probab=95.07  E-value=0.018  Score=54.82  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=22.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..|.|.|++|+|||||+++|+..+.
T Consensus         7 ~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         7 IIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4577999999999999999998775

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PF14516 AAA_35: AAA-like domain

Probab=95.06  E-value=0.1  Score=53.70  Aligned_cols=38  Identities=26%  Similarity=0.262  Sum_probs=29.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT  362 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~  362 (461)
                      +..+.+.||..+|||+|...+.+.+   +...+.+++..+.
T Consensus        31 G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~   71 (331)
T PF14516_consen   31 GSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLG   71 (331)
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCC
Confidence            3678999999999999998887655   5566777766543

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=95.05  E-value=0.039  Score=58.36  Aligned_cols=25  Identities=28%  Similarity=0.498  Sum_probs=21.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ++++.|||..|||||+|--.+...+
T Consensus       114 PkGlYlYG~VGcGKTmLMDlFy~~~  138 (467)
T KOG2383|consen  114 PKGLYLYGSVGCGKTMLMDLFYDAL  138 (467)
T ss_pred             CceEEEecccCcchhHHHHHHhhcC
Confidence            6899999999999999998887544

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.05  E-value=0.014  Score=54.72  Aligned_cols=26  Identities=42%  Similarity=0.653  Sum_probs=23.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ...++|.||+|+||||++++|+..+.
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            47799999999999999999998774

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.

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.00  E-value=0.021  Score=54.10  Aligned_cols=25  Identities=16%  Similarity=0.304  Sum_probs=21.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.-|+|.||+|+|||+|++.|.+..
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcC
Confidence            3558999999999999999998765

>PRK06761 hypothetical protein; Provisional

Probab=94.98  E-value=0.025  Score=57.41  Aligned_cols=28  Identities=25%  Similarity=0.299  Sum_probs=24.2

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      -|+|.|++|+||||+++.|++.+....+
T Consensus         5 lIvI~G~~GsGKTTla~~L~~~L~~~g~   32 (282)
T PRK06761          5 LIIIEGLPGFGKSTTAKMLNDILSQNGI   32 (282)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCcCce
Confidence            4889999999999999999999875433

>PLN02840 tRNA dimethylallyltransferase

Probab=94.97  E-value=0.025  Score=60.33  Aligned_cols=33  Identities=39%  Similarity=0.646  Sum_probs=28.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ..|+|.||+|+|||+||..||+.++..++.++.
T Consensus        22 ~vi~I~GptgsGKTtla~~La~~~~~~iis~Ds   54 (421)
T PLN02840         22 KVIVISGPTGAGKSRLALELAKRLNGEIISADS   54 (421)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHCCCCeEeccc
Confidence            458899999999999999999999876665553

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=94.97  E-value=0.13  Score=56.32  Aligned_cols=33  Identities=33%  Similarity=0.399  Sum_probs=26.4

Q ss_pred             cccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          318 DDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       318 ~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ....-..+..+.|.||+|+||||++++|.+...
T Consensus       348 is~~i~~Ge~vaiVG~sGsGKSTl~~LL~r~~~  380 (567)
T COG1132         348 ISFSIEPGEKVAIVGPSGSGKSTLIKLLLRLYD  380 (567)
T ss_pred             ceEEEcCCCEEEEECCCCCCHHHHHHHHhccCC
Confidence            333344567788999999999999999998764

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=94.96  E-value=0.47  Score=48.78  Aligned_cols=25  Identities=32%  Similarity=0.274  Sum_probs=20.7

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHH
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ....-+.|+||||+|||+|+..+|-
T Consensus        94 ~~G~iteI~G~~GsGKTql~lqla~  118 (313)
T TIGR02238        94 ESMSITEVFGEFRCGKTQLSHTLCV  118 (313)
T ss_pred             cCCeEEEEECCCCCCcCHHHHHHHH
Confidence            3456677999999999999988774

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK12678 transcription termination factor Rho; Provisional

Probab=94.95  E-value=0.079  Score=58.74  Aligned_cols=25  Identities=24%  Similarity=0.468  Sum_probs=22.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +...||.||||||||+|++.||+.+
T Consensus       416 GQR~LIvgpp~aGKTtLL~~IAn~i  440 (672)
T PRK12678        416 GQRGLIVSPPKAGKTTILQNIANAI  440 (672)
T ss_pred             CCEeEEeCCCCCCHHHHHHHHHHHH
Confidence            4568999999999999999999855

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

Probab=94.95  E-value=0.12  Score=50.88  Aligned_cols=39  Identities=28%  Similarity=0.417  Sum_probs=29.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhh
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTL  361 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l  361 (461)
                      .....+|++|+||||||+++..++...   +.+.+.+...+.
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e~   62 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEES   62 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecCC
Confidence            345789999999999999998876533   567776665543

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=94.94  E-value=0.022  Score=64.41  Aligned_cols=30  Identities=27%  Similarity=0.510  Sum_probs=26.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|.|.|||||||||+|+.||+.++..|+..
T Consensus         3 ~i~I~G~~GsGKST~ak~la~~l~~~~~~~   32 (712)
T PRK09518          3 IVAIDGPAGVGKSSVSRALAQYLGYAYLDT   32 (712)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEeec
Confidence            478999999999999999999998776643

>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=94.93  E-value=0.032  Score=52.81  Aligned_cols=39  Identities=31%  Similarity=0.494  Sum_probs=30.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc-CCceEEecchhhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV-NVPFVIADATTLTQ  363 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l-~~pfv~i~~s~l~~  363 (461)
                      +.-++|.|+||+|||++++.+...+ ...++.++..++..
T Consensus        15 P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~r~   54 (199)
T PF06414_consen   15 PTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEFRQ   54 (199)
T ss_dssp             -EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGGGG
T ss_pred             CEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHHHH
Confidence            4557888999999999999999988 77788888887764

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.

>PRK07667 uridine kinase; Provisional

Probab=94.92  E-value=0.028  Score=53.21  Aligned_cols=34  Identities=26%  Similarity=0.358  Sum_probs=25.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC---CceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s  359 (461)
                      .-|.|.|++|+||||+|+.|++.+.   .++..++..
T Consensus        18 ~iIgI~G~~gsGKStla~~L~~~l~~~~~~~~~i~~D   54 (193)
T PRK07667         18 FILGIDGLSRSGKTTFVANLKENMKQEGIPFHIFHID   54 (193)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEEcC
Confidence            3477999999999999999999874   344444443

>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]

Probab=94.88  E-value=0.093  Score=52.68  Aligned_cols=30  Identities=33%  Similarity=0.507  Sum_probs=26.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +.-|||=|+||+||||+|.-||+.++.+.+
T Consensus        89 p~IILIGGasGVGkStIA~ElA~rLgI~~v  118 (299)
T COG2074          89 PLIILIGGASGVGKSTIAGELARRLGIRSV  118 (299)
T ss_pred             CeEEEecCCCCCChhHHHHHHHHHcCCcee
Confidence            355888899999999999999999998643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	461
3hws_A	363	Crystal Structure Of Nucleotide-Bound Hexameric Clp		2e-54
3hte_A	363	Crystal Structure Of Nucleotide-Free Hexameric Clpx		2e-54
1um8_A	376	Crystal Structure Of Helicobacter Pylori Clpx Lengt		1e-50
1ofh_A	310	Asymmetric Complex Between Hslv And I-domain Delete		2e-26
1g4a_E	443	Crystal Structures Of The Hslvu Peptidase-Atpase Co		3e-17
1g4a_E	443	Crystal Structures Of The Hslvu Peptidase-Atpase Co		1e-04
1do2_A	442	Trigonal Crystal Form Of Heat Shock Locus U (Hslu)		4e-17
1do2_A	442	Trigonal Crystal Form Of Heat Shock Locus U (Hslu)		1e-04
1e94_E	449	Hslv-Hslu From E.Coli Length = 449		4e-17
1e94_E	449	Hslv-Hslu From E.Coli Length = 449		1e-04
1g3i_A	444	Crystal Structure Of The Hsluv Protease-Chaperone C		4e-16
1g3i_A	444	Crystal Structure Of The Hsluv Protease-Chaperone C		1e-04
1im2_A	444	Hslu, Haemophilus Influenzae, Selenomethionine Vari		2e-15
1im2_A	444	Hslu, Haemophilus Influenzae, Selenomethionine Vari		1e-04
3vfd_A	389	Human Spastin Aaa Domain Length = 389		2e-05
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-05
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		5e-05
3b9p_A	297	Spastin Length = 297		5e-05
2ce7_A	476	Edta Treated Length = 476		5e-05
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		6e-05
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		7e-05
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		7e-05
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		7e-05
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		8e-05
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		2e-04
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		2e-04
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		2e-04
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		2e-04
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		2e-04
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-04
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		3e-04
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		3e-04
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		3e-04
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		3e-04
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		4e-04
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		5e-04
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		6e-04

>pdb|3HWS|A Chain A, Crystal Structure Of Nucleotide-Bound Hexameric Clpx Length = 363

Iteration: 1
 Score =  210 bits (534), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 104/171 (60%), Positives = 137/171 (80%), Gaps = 16/171 (9%)
Query: 261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDN 320
           LPTP EI   LD +VIGQE+AKKVL+VAVYNHYKR+ +                 D  + 
Sbjct: 3   LPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNG----------------DTSNG 46
Query: 321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLA 380
           VEL KSN+LL+GPTGSGKTLLA+TLAR ++VPF +ADATTLT+AGYVGEDVE+I+ KLL 
Sbjct: 47  VELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQ 106
Query: 381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           + +++V+ AQ+G+VYID++DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct: 107 KCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGT 157

>pdb|3HTE|A Chain A, Crystal Structure Of Nucleotide-Free Hexameric Clpx Length = 363

Iteration: 1
 Score =  210 bits (534), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 104/171 (60%), Positives = 137/171 (80%), Gaps = 16/171 (9%)
Query: 261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDN 320
           LPTP EI   LD +VIGQE+AKKVL+VAVYNHYKR+ +                 D  + 
Sbjct: 3   LPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNG----------------DTSNG 46
Query: 321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLA 380
           VEL KSN+LL+GPTGSGKTLLA+TLAR ++VPF +ADATTLT+AGYVGEDVE+I+ KLL 
Sbjct: 47  VELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQ 106
Query: 381 QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
           + +++V+ AQ+G+VYID++DKI++K+++ +I+RDVSGEGVQQALLK++EGT
Sbjct: 107 KCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGT 157

>pdb|1UM8|A Chain A, Crystal Structure Of Helicobacter Pylori Clpx Length = 376

Iteration: 1
 Score =  197 bits (501), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 100/172 (58%), Positives = 137/172 (79%), Gaps = 3/172 (1%)
Query: 261 LPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRI-YHANLKKGSGAEPKTAAAVDNDD 319
           +P PKE+   LD +VIGQE+AKKV SVAVYNHYKR+ +   LKK    +           
Sbjct: 9   IPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLE-- 66
Query: 320 NVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLL 379
            VEL KSN+LL+GPTGSGKTL+A+TLA+H+++P  I+DAT+LT+AGYVGEDVE+IL +LL
Sbjct: 67  EVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLL 126
Query: 380 AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
             +++NV+ AQ+G+V+IDE+DKI++ +E+ +I+RDVSGEGVQQALLK++EG+
Sbjct: 127 QASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGS 178

>pdb|1OFH|A Chain A, Asymmetric Complex Between Hslv And I-domain Deleted Hslu (h. Influenzae) Length = 310

Iteration: 1
 Score =  117 bits (292), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 73/192 (38%), Positives = 111/192 (57%), Gaps = 22/192 (11%)
Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LD+ +IGQ  AK+ +++A+ N ++R+           EP            E
Sbjct: 5   TPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQ--------EPLRH---------E 47
Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L   A
Sbjct: 48  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA 107
Query: 383 EFNVEAAQQ-GMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSK 441
              ++A +Q G+V+IDE+DKI KK E      DVS EGVQ+ LL ++EG+   T   + K
Sbjct: 108 GGAIDAVEQNGIVFIDEIDKICKKGEYSGA--DVSREGVQRDLLPLVEGSTVSTKHGMVK 165
Query: 442 VSRDNLYIKTSG 453
              D++    SG
Sbjct: 166 T--DHILFIASG 175

>pdb|1G4A|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex Reveal An Atp-Dependent Proteolysis Mechanism Length = 443

Iteration: 1
 Score = 86.3 bits (212), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 51/151 (33%), Positives = 85/151 (56%), Gaps = 25/151 (16%)
Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LDK +IGQ+ AK+ +++A+ N ++R+                  ++ +   E
Sbjct: 5   TPREIVSELDKHIIGQDNAKRSVAIALRNRWRRMQ-----------------LNEELRHE 47
Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L    
Sbjct: 48  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDL---- 103
Query: 383 EFNVEAAQQGMVYIDEVDKITKKAESLNISR 413
               +AA + MV +  ++K   +AE L   R
Sbjct: 104 ---TDAAVK-MVRVQAIEKNRYRAEELAEER 130

>pdb|1G4A|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex Reveal An Atp-Dependent Proteolysis Mechanism Length = 443

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 390 QQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYI 449
           Q G+V+IDE+DKI K+ ES     DVS EGVQ+ LL ++EG    T   + K   D++  
Sbjct: 249 QHGIVFIDEIDKICKRGESS--GPDVSREGVQRDLLPLVEGCTVSTKHGMVKT--DHILF 304
Query: 450 KTSG 453
             SG
Sbjct: 305 IASG 308

>pdb|1DO2|A Chain A, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From Escherichia Coli Length = 442

Iteration: 1
 Score = 86.3 bits (212), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 51/151 (33%), Positives = 85/151 (56%), Gaps = 25/151 (16%)
Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LDK +IGQ+ AK+ +++A+ N ++R+                  ++ +   E
Sbjct: 4   TPREIVSELDKHIIGQDNAKRSVAIALRNRWRRMQ-----------------LNEELRHE 46
Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L    
Sbjct: 47  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDL---- 102
Query: 383 EFNVEAAQQGMVYIDEVDKITKKAESLNISR 413
               +AA + MV +  ++K   +AE L   R
Sbjct: 103 ---TDAAVK-MVRVQAIEKNRYRAEELAEER 129

>pdb|1DO2|A Chain A, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From Escherichia Coli Length = 442

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 390 QQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYI 449
           Q G+V+IDE+DKI K+ ES     DVS EGVQ+ LL ++EG    T   + K   D++  
Sbjct: 248 QHGIVFIDEIDKICKRGESS--GPDVSREGVQRDLLPLVEGCTVSTKHGMVKT--DHILF 303
Query: 450 KTSG 453
             SG
Sbjct: 304 IASG 307

>pdb|1E94|E Chain E, Hslv-Hslu From E.Coli Length = 449

Iteration: 1
 Score = 86.3 bits (212), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 51/151 (33%), Positives = 85/151 (56%), Gaps = 25/151 (16%)
Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LDK +IGQ+ AK+ +++A+ N ++R+                  ++ +   E
Sbjct: 11  TPREIVSELDKHIIGQDNAKRSVAIALRNRWRRMQ-----------------LNEELRHE 53
Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L    
Sbjct: 54  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDL---- 109
Query: 383 EFNVEAAQQGMVYIDEVDKITKKAESLNISR 413
               +AA + MV +  ++K   +AE L   R
Sbjct: 110 ---TDAAVK-MVRVQAIEKNRYRAEELAEER 136

>pdb|1E94|E Chain E, Hslv-Hslu From E.Coli Length = 449

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 390 QQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYI 449
           Q G+V+IDE+DKI K+ ES     DVS EGVQ+ LL ++EG    T   + K   D++  
Sbjct: 255 QHGIVFIDEIDKICKRGESS--GPDVSREGVQRDLLPLVEGCTVSTKHGMVKT--DHILF 310
Query: 450 KTSG 453
             SG
Sbjct: 311 IASG 314

>pdb|1G3I|A Chain A, Crystal Structure Of The Hsluv Protease-Chaperone Complex Length = 444

Iteration: 1
 Score = 82.8 bits (203), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 85/163 (52%), Gaps = 31/163 (19%)
Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LD+ +IGQ  AK+ +++A+ N ++R+           EP            E
Sbjct: 5   TPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQ--------EPLRH---------E 47
Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L   A
Sbjct: 48  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA 107
Query: 383 EFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALL 425
                     +V   E+ K   +AE      DV+ E +  ALL
Sbjct: 108 --------MKLVRQQEIAKNRARAE------DVAEERILDALL 136

>pdb|1G3I|A Chain A, Crystal Structure Of The Hsluv Protease-Chaperone Complex Length = 444

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 390 QQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYI 449
           Q G+V+IDE+DKI KK E      DVS EGVQ+ LL ++EG+   T   + K   D++  
Sbjct: 250 QNGIVFIDEIDKICKKGEYSGA--DVSREGVQRDLLPLVEGSTVSTKHGMVKT--DHILF 305
Query: 450 KTSG 453
             SG
Sbjct: 306 IASG 309

>pdb|1IM2|A Chain A, Hslu, Haemophilus Influenzae, Selenomethionine Variant Length = 444

Iteration: 1
 Score = 80.1 bits (196), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 83/163 (50%), Gaps = 31/163 (19%)
Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LD+ +IGQ  AK+ +++A+ N ++R            EP            E
Sbjct: 5   TPREIVSELDQHIIGQADAKRAVAIALRNRWRRXQLQ--------EPLRH---------E 47
Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L +GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L   A
Sbjct: 48  VTPKNILXIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA 107
Query: 383 EFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALL 425
                     +V   E+ K   +AE      DV+ E +  ALL
Sbjct: 108 --------XKLVRQQEIAKNRARAE------DVAEERILDALL 136

>pdb|1IM2|A Chain A, Hslu, Haemophilus Influenzae, Selenomethionine Variant Length = 444

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 31/46 (67%), Gaps = 2/46 (4%)
Query: 390 QQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKT 435
           Q G+V+IDE+DKI KK E      DVS EGVQ+ LL ++EG+   T
Sbjct: 250 QNGIVFIDEIDKICKKGEYSGA--DVSREGVQRDLLPLVEGSTVST 293

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 43/75 (57%), Gaps = 6/75 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKT+LAK +A   N  F    A +LT + YVGE  E ++  L A A     
Sbjct: 151 LLLFGPPGNGKTMLAKAVAAESNATFFNISAASLT-SKYVGEG-EKLVRALFAVA----R 204
Query: 388 AAQQGMVYIDEVDKI 402
             Q  +++ID+VD +
Sbjct: 205 ELQPSIIFIDQVDSL 219

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 68/139 (48%), Gaps = 11/139 (7%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VLL GP G+GKTLLAK +A  +   F+ + A+ +    Y+GE    I+ ++ A A    +
Sbjct: 218 VLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDK-YIGESA-RIIREMFAYA----K 271
Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG----TETKTFAAVSK-V 442
             +  ++++DEVD I  +  S   S D   +     LL  ++G     +TK   A ++  
Sbjct: 272 EHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPD 331
Query: 443 SRDNLYIKTSGLDSKTLWP 461
           + D   ++   LD K   P
Sbjct: 332 TLDPALLRPGRLDRKVEIP 350

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 43/149 (28%), Positives = 68/149 (45%), Gaps = 31/149 (20%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           V+L GP G+GKTLLA+ +A H +  F+      L Q  Y+GE    +        E  V 
Sbjct: 185 VILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQK-YIGEGSRMV-------RELFVM 236
Query: 388 AAQQG--MVYIDEVDKITKKAESLNISRDVSGEG-----VQQALLKM---LEGTET-KTF 436
           A +    ++++DE+D I         S  V G G     VQ+ +L++   L+G ET K  
Sbjct: 237 AREHAPSIIFMDEIDSIG--------STRVEGSGGGDSEVQRTMLELLNQLDGFETSKNI 288
Query: 437 AAVSKVSR----DNLYIKTSGLDSKTLWP 461
             +   +R    D   ++   +D K  +P
Sbjct: 289 KIIMATNRLDILDPALLRPGRIDRKIEFP 317

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTLLA+ +A   +  F+   A +LT + YVG D E ++  L A A     
Sbjct: 57  LLLFGPPGNGKTLLARAVATECSATFLNISAASLT-SKYVG-DGEKLVRALFAVARH--- 111
Query: 388 AAQQGMVYIDEVD 400
             Q  +++IDEVD
Sbjct: 112 -MQPSIIFIDEVD 123

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 53/101 (52%), Gaps = 7/101 (6%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL+GP G+GKTLLA+ +A   NVPF     +   +  +VG     +   L AQA    +
Sbjct: 52  ILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVEL-FVGVGAARV-RDLFAQA----K 105
Query: 388 AAQQGMVYIDEVDKITK-KAESLNISRDVSGEGVQQALLKM 427
           A    +V+IDE+D + + +   L    D   + + Q L++M
Sbjct: 106 AHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEM 146

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 329 LLMGPTGSGKTLLAKTLARHVNVPFV-IADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           LL+GP G GKTLLAK +A    VPF+ +A A  +   G +G      L+K          
Sbjct: 43  LLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGLGAARVRSLFK-------EAR 95
Query: 388 AAQQGMVYIDEVDKITKK 405
           A    +VYIDE+D + KK
Sbjct: 96  ARAPCIVYIDEIDAVGKK 113

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 62/138 (44%), Gaps = 11/138 (7%)
Query: 329 LLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEA 388
           L+ GP G+GKTLLA+  A   N  F+   A  L Q  Y+GE       KL+  A    + 
Sbjct: 219 LMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQM-YIGEGA-----KLVRDAFALAKE 272
Query: 389 AQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG----TETKTFAAVSKVS- 443
               +++IDE+D I  K      S D   +     LL  L+G       K  AA ++V  
Sbjct: 273 KAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDV 332
Query: 444 RDNLYIKTSGLDSKTLWP 461
            D   +++  LD K  +P
Sbjct: 333 LDPALLRSGRLDRKIEFP 350

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFN 385
           S +LL GP G+GK+ LAK +A   N  F    ++ L  + ++GE  E ++ +L A A  N
Sbjct: 61  SGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV-SKWMGES-EKLVKQLFAMAREN 118
Query: 386 VEAAQQGMVYIDEVDKIT 403
               +  +++IDEVD +T
Sbjct: 119 ----KPSIIFIDEVDALT 132

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 9/109 (8%)
Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNV 386
            VL++GP G+GKTLLAK +A    VPF     +   +  +VG    S +  +  QA    
Sbjct: 47  GVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM-FVGVGA-SRVRDMFEQA---- 100
Query: 387 EAAQQGMVYIDEVDKITK-KAESLNISRDVSGEGVQQALLKM--LEGTE 432
           + A   +++IDE+D + + +   L    D   + + Q L++M   EG E
Sbjct: 101 KKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNE 149

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 8/76 (10%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTL+ K +A      F    A++LT + +VGE       + + +A F V 
Sbjct: 120 ILLFGPPGTGKTLIGKCIASQSGATFFSISASSLT-SKWVGEG------EKMVRALFAVA 172
Query: 388 AAQQ-GMVYIDEVDKI 402
             QQ  +++IDE+D +
Sbjct: 173 RCQQPAVIFIDEIDSL 188

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFN 385
           S +LL GP G+GK+ LAK +A   N  F    ++ L  + ++GE  E ++ +L A A  N
Sbjct: 85  SGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV-SKWMGES-EKLVKQLFAMAREN 142
Query: 386 VEAAQQGMVYIDEVDKIT 403
               +  +++ID+VD +T
Sbjct: 143 ----KPSIIFIDQVDALT 156

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFN 385
           S +LL GP G+GK+ LAK +A   N  F    ++ L  + ++GE  E ++ +L A A  N
Sbjct: 70  SGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV-SKWMGES-EKLVKQLFAMAREN 127
Query: 386 VEAAQQGMVYIDEVDKIT 403
               +  +++ID+VD +T
Sbjct: 128 ----KPSIIFIDQVDALT 141

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 9/112 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTL+A+ +A      F + +   +  +   GE  ES L K   +AE N  
Sbjct: 241 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM-SKLAGES-ESNLRKAFEEAEKNAP 298
Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV 439
           A    +++IDE+D I  K E  +   +V    V Q LL +++G + +    V
Sbjct: 299 A----IIFIDELDAIAPKREKTH--GEVERRIVSQ-LLTLMDGLKQRAHVIV 343

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFN 385
           S +LL GP G+GK+ LAK +A   N  F    ++ L  + ++GE  E ++ +L A A  N
Sbjct: 52  SGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV-SKWMGES-EKLVKQLFAMAREN 109
Query: 386 VEAAQQGMVYIDEVDKIT 403
               +  +++ID+VD +T
Sbjct: 110 ----KPSIIFIDQVDALT 123

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 9/112 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTL+A+ +A      F + +   +  +   GE  ES L K   +AE N  
Sbjct: 241 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM-SKLAGES-ESNLRKAFEEAEKNAP 298
Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV 439
           A    +++IDE+D I  K E  +   +V    V Q LL +++G + +    V
Sbjct: 299 A----IIFIDELDAIAPKREKTH--GEVERRIVSQ-LLTLMDGLKQRAHVIV 343

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 52/101 (51%), Gaps = 7/101 (6%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL+GP G+G TLLA+ +A   NVPF     +   +  +VG     +   L AQA    +
Sbjct: 52  ILLVGPPGTGATLLARAVAGEANVPFFHISGSDFVEL-FVGVGAARV-RDLFAQA----K 105
Query: 388 AAQQGMVYIDEVDKITK-KAESLNISRDVSGEGVQQALLKM 427
           A    +V+IDE+D + + +   L    D   + + Q L++M
Sbjct: 106 AHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEM 146

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 9/112 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTL+A+ +A      F + +   +  +   GE  ES L K   +AE N  
Sbjct: 241 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-MSKLAGES-ESNLRKAFEEAEKNAP 298
Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV 439
           A    +++IDE+D I  K E  +   +V    V Q LL +++G + +    V
Sbjct: 299 A----IIFIDELDAIAPKREKTH--GEVERRIVSQ-LLTLMDGLKQRAHVIV 343

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 9/112 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTL+A+ +A      F + +   +  +   GE  ES L K   +AE N  
Sbjct: 241 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-MSKLAGES-ESNLRKAFEEAEKNAP 298
Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV 439
           A    +++IDE+D I  K E  +   +V    V Q LL +++G + +    V
Sbjct: 299 A----IIFIDELDAIAPKREKTH--GEVERRIVSQ-LLTLMDGLKQRAHVIV 343

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 9/112 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTL+A+ +A      F + +   +  +   GE  ES L K   +AE N  
Sbjct: 241 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-MSKLAGES-ESNLRKAFEEAEKNAP 298
Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV 439
           A    +++IDE+D I  K E  +   +V    V Q LL +++G + +    V
Sbjct: 299 A----IIFIDELDAIAPKREKTH--GEVERRIVSQ-LLTLMDGLKQRAHVIV 343

>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 = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 9/112 (8%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           +LL GP G+GKTL+A+ +A      F + +   +  +   GE  ES L K   +AE N  
Sbjct: 241 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-MSKLAGES-ESNLRKAFEEAEKNAP 298
Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAV 439
           A    +++IDE+D I  K E  +   +V    V Q LL +++G + +    V
Sbjct: 299 A----IIFIDELDAIAPKREKTH--GEVERRIVSQ-LLTLMDGLKQRAHVIV 343

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 55/110 (50%), Gaps = 8/110 (7%)
Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNV 386
            VLL+GP G GKT LA+ +A    VPF+ A  +   +  +VG     +   L   A+ + 
Sbjct: 75  GVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM-FVGVGAARV-RDLFETAKRHA 132
Query: 387 EAAQQGMVYIDEVDKITKKAES-LNISRDVSGEGVQQALLKMLEGTETKT 435
                 +V+IDE+D + +K  S +    D   + + Q L++M +G E  T
Sbjct: 133 PC----IVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEM-DGFEKDT 177

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 51/103 (49%), Gaps = 13/103 (12%)
Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESI--LYKLLAQAEFN 385
           +LL GP G+GKTLLAK +A   N  F+    + L +  ++GE    +  ++KL  +    
Sbjct: 54  ILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKK-FIGEGASLVKDIFKLAKE---- 108
Query: 386 VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML 428
                  +++IDE+D I  K        D     VQ+ L+++L
Sbjct: 109 ---KAPSIIFIDEIDAIAAKRTDALTGGDRE---VQRTLMQLL 145

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 56/114 (49%), Gaps = 8/114 (7%)
Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNV 386
            VLL+GP G GKT LA+ +A    VPF+ A  +   +  +VG     +   L   A+ + 
Sbjct: 51  GVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM-FVGVGAARV-RDLFETAKRHA 108
Query: 387 EAAQQGMVYIDEVDKITKKAES-LNISRDVSGEGVQQALLKMLEGTETKTFAAV 439
                 +V+IDE+D + +K  S +    D   + + Q L++M +G E  T   V
Sbjct: 109 PC----IVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEM-DGFEKDTAIVV 157

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	461
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.86
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.84
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.83
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.82
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.81
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.8
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.8
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.79
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.77
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.74
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.71
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.68
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.67
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.66
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.65
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.64
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.62
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.61
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.6
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.59
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.59
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.59
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.58
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.58
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.58
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.57
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.57
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.56
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.55
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.52
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.5
3co5_A	143	Putative two-component system transcriptional RES	99.49
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.48
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.46
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.46
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.46
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.46
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.45
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.44
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.43
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.41
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.4
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.39
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.39
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.39
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.38
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.37
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.35
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.35
3pvs_A	447	Replication-associated recombination protein A; ma	99.34
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.31
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.29
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.29
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.28
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.25
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.23
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.22
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.2
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.19
3f8t_A	506	Predicted ATPase involved in replication control,	99.18
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.17
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.13
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.12
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.08
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.07
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.03
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.01
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.0
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.0
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.99
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.97
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.96
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.95
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.95
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.92
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.9
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.88
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.88
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.86
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.86
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.86
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.85
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.84
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.81
3bos_A	242	Putative DNA replication factor; P-loop containing	98.77
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.77
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.6
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.6
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.42
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.42
2qgz_A	308	Helicase loader, putative primosome component; str	98.37
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.35
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.26
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.24
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.1
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.05
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.02
2fna_A	357	Conserved hypothetical protein; structural genomic	97.78
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	97.76
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	97.73
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.57
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.57
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.53
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	97.52
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.4
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.38
1via_A	175	Shikimate kinase; structural genomics, transferase	97.36
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.35
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.34
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.31
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.29
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.28
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.25
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	97.22
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.21
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.21
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.15
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.14
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.12
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.11
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.11
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.1
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.1
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.09
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.09
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.06
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.05
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.04
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.03
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.02
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.01
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.01
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.0
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	97.0
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.99
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.98
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.98
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.97
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.96
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.96
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.96
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.95
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.95
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	96.93
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.9
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.88
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.85
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	96.83
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.83
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.78
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.78
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.76
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.74
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.74
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.74
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.74
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.72
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.7
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.69
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.64
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.62
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.6
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.6
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	96.6
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.59
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.57
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.55
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.55
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.54
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.53
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.53
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.52
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.52
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.52
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.5
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.47
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.47
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	96.46
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.39
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.39
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.36
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.35
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.34
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.33
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	96.32
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.31
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.24
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.24
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.24
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.22
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.22
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.21
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.14
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.13
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	96.09
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	96.06
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	96.05
3b6e_A	216	Interferon-induced helicase C domain-containing P;	96.05
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.05
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.05
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.03
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	95.98
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.93
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.86
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	95.84
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	95.8
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.8
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.79
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.79
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.75
1xp8_A	366	RECA protein, recombinase A; recombination, radior	95.73
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	95.72
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.72
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	95.71
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.71
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.71
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.7
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.69
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.66
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.57
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.56
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.55
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.53
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.43
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	95.42
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	95.39
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.39
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.35
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.24
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.23
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	95.16
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.14
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.01
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.98
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	94.95
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.86
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	94.85
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	94.84
3io5_A	333	Recombination and repair protein; storage dimer, i	94.84
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	94.76
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	94.73
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.73
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.71
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.7
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.68
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	94.67
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	94.65
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	94.63
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.61
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	94.6
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	94.53
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.48
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	94.26
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	94.23
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.22
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.2
2og2_A	359	Putative signal recognition particle receptor; nuc	94.2
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.19
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.18
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.15
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	94.14
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	94.11
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	94.09
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	93.92
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.91
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.82
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.82
2eyu_A	261	Twitching motility protein PILT; pilus retraction	93.73
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.7
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	93.69
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	93.64
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.6
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	93.54
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	93.52
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	93.44
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	93.4
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.37
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.35
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	93.3
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	93.27
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.13
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	93.1
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.03
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	93.03
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	92.91
3ice_A	422	Transcription termination factor RHO; transcriptio	92.85
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.79
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	92.71
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	92.71
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	92.66
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	92.63
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	92.63
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	92.59
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.59
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.54
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	92.52
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.42
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	92.42
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	92.4
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	92.39
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	92.38
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	92.37
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	92.34
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	92.29
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	92.21
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	92.18
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.17
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	92.16
1g6h_A	257	High-affinity branched-chain amino acid transport	92.07
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	92.06
1sgw_A	214	Putative ABC transporter; structural genomics, P p	92.04
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	92.04
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.03
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	92.0
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	91.98
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	91.97
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	91.95
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.93
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	91.92
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	91.88
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	91.86
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.85
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	91.85
2ged_A	193	SR-beta, signal recognition particle receptor beta	91.84
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	91.81
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	91.8
1nrj_B	218	SR-beta, signal recognition particle receptor beta	91.79
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	91.76
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	91.76
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	91.75
2ghi_A	260	Transport protein; multidrug resistance protein, M	91.74
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.73
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	91.69
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.69
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.66
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	91.64
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	91.62
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	91.54
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	91.51
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	91.49
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	91.45
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	91.42
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.41
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.4
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	91.4
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	91.31
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.3
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	91.29
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.25
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	91.23
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	91.2
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	91.2
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	91.19
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	91.15
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	91.14
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	91.07
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	91.06
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	91.05
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	90.99
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	90.94
2wji_A	165	Ferrous iron transport protein B homolog; membrane	90.92
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	90.91
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	90.88
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	90.87
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	90.86
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	90.85
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	90.84
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	90.82
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	90.77
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	90.77
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	90.75
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	90.67
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	90.65
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	90.64
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	90.63
4gl2_A	699	Interferon-induced helicase C domain-containing P;	90.62
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	90.62
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	90.55
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	90.52
2xxa_A	433	Signal recognition particle protein; protein trans	90.52
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	90.51
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	90.46
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	90.43
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	90.41
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	90.35
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	90.32
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	90.3
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	90.29
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	90.28
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	90.19
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	90.19
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	90.17
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	90.15
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	90.14
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	90.13
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	90.12
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	90.11
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	89.99
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	89.98
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	89.95
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	89.93
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	89.9
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	89.89
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	89.87
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	89.83
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	89.82
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	89.75
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	89.74
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	89.66
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	89.66
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	89.65
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	89.64
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	89.62
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	89.5
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	89.5
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	89.5
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	89.47
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	89.44
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	89.44
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	89.4
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	89.38
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	89.36
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	89.33
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	89.31
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	89.28
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	89.27
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	89.22
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	89.21
2hf9_A	226	Probable hydrogenase nickel incorporation protein	89.18
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	89.15
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	89.05
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	89.02
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	89.02
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	89.01
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	89.0
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	88.97
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	88.94
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	88.86
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	88.84
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	88.83
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	88.83
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	88.81
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	88.79
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	88.77
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	88.75
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	88.74
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	88.73
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	88.71
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	88.71
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	88.7
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	88.69
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	88.64
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	88.63
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	88.55
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	88.55
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	88.44
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	88.42
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	88.39
2r6a_A	454	DNAB helicase, replicative helicase; replication,	88.35
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	88.34
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	88.32
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	88.27
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	88.25
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	88.16
2fh5_B	214	SR-beta, signal recognition particle receptor beta	88.09
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	88.05
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	88.0
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	87.99
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	87.86
1dek_A	241	Deoxynucleoside monophosphate kinase; transferase,	87.83
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	87.77
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	87.76
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	87.73
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	87.73
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	87.68
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	87.66
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	87.66
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	87.58
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	87.58
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	87.55
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	87.54
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	87.49
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	87.46
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	87.44
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	87.39
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	87.38
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	87.24
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	87.19
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	87.11
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	87.06
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	87.04
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	87.03
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	86.96
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	86.9
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	86.87
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	86.81
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	86.76
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	86.72
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	86.71
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	86.65

>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=99.86  E-value=4.3e-22  Score=201.25  Aligned_cols=179  Identities=60%  Similarity=0.919  Sum_probs=134.3

Q ss_pred             CCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchH
Q 012525          260 DLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKT  339 (461)
Q Consensus       260 ~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKT  339 (461)
                      .++++.++.+.|++.|+||+.+++.|..++..++.+......                .......+.+|||+||||||||
T Consensus         2 ~~~~~~~l~~~l~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~----------------~~~~~~~~~~vll~GppGtGKT   65 (363)
T 3hws_A            2 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDT----------------SNGVELGKSNILLIGPTGSGKT   65 (363)
T ss_dssp             CCCCHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHTTSC----------------SSSCCCCCCCEEEECCTTSSHH
T ss_pred             CCCCHHHHHHHHHhhccCHHHHHHHHHHHHHHHHhhhccccc----------------cccccCCCCeEEEECCCCCCHH
Confidence            367899999999999999999999999999877765432111                1122334688999999999999


Q ss_pred             HHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          340 LLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       340 tLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      ++|++||+.++.+|+.++++.+...+|+|...+..+..++..+...+..+.++||||||||++...++..+.+.+.+.++
T Consensus        66 ~la~~ia~~~~~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~  145 (363)
T 3hws_A           66 LLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEG  145 (363)
T ss_dssp             HHHHHHHHHTTCCEEEEEHHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHH
T ss_pred             HHHHHHHHHcCCCEEEechHHhcccccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHH
Confidence            99999999999999999999998777888877788888888877777777899999999999999877766677777778


Q ss_pred             HHHHHHHHHhCceeeeecc-eeeecC-CeEEEecCCC
Q 012525          420 VQQALLKMLEGTETKTFAA-VSKVSR-DNLYIKTSGL  454 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~~~-~r~~~r-d~IiI~TsNi  454 (461)
                      +++.||++||+..+.+... .+.... +.++|+|+|.
T Consensus       146 ~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~~i~tsn~  182 (363)
T 3hws_A          146 VQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSKI  182 (363)
T ss_dssp             HHHHHHHHHHCC----------------CCCCCTTSS
T ss_pred             HHHHHHHHhcCceeeccCccccccCCCceEEEECCCc
Confidence            9999999999665544332 222222 4556666665

>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=99.84  E-value=2e-20  Score=189.65  Aligned_cols=178  Identities=55%  Similarity=0.858  Sum_probs=117.0

Q ss_pred             CCCCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCc
Q 012525          258 GEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSG  337 (461)
Q Consensus       258 ~~~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTG  337 (461)
                      -+.+++++++.+.|+++|+||+++|+.|..++.+++.+......-.. .....+.........+.....++||+||||||
T Consensus         6 ~~~~~~~~~l~~~L~~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~-~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtG   84 (376)
T 1um8_A            6 LSYIPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKK-QDNQDSNVELEHLEEVELSKSNILLIGPTGSG   84 (376)
T ss_dssp             CSCCCCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHH-HCSHHHHHHHHHHHHTTCCCCCEEEECCTTSS
T ss_pred             hcCCCCHHHHHHHHhhHccCcHHHHHHHHHHHHHHHHHHHhhhhhhh-ccccccccccccccccccCCCCEEEECCCCCC
Confidence            35678999999999999999999999999999877776543110000 00000111000111223346789999999999


Q ss_pred             hHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccch
Q 012525          338 KTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSG  417 (461)
Q Consensus       338 KTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~  417 (461)
                      ||++|++||+.++.+|+.+++..+...+++|...+..+..++......+..+.++||||||||++...+.......+.+.
T Consensus        85 KT~la~~la~~l~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~  164 (376)
T 1um8_A           85 KTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSG  164 (376)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------C
T ss_pred             HHHHHHHHHHHhCCCEEEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCceecccch
Confidence            99999999999999999999999887778887767777888877666666678899999999999988666555667777


Q ss_pred             HHHHHHHHHHHhCceeeee
Q 012525          418 EGVQQALLKMLEGTETKTF  436 (461)
Q Consensus       418 ~~v~~aLL~~LEg~~v~i~  436 (461)
                      +.++++|+++||+..+.+.
T Consensus       165 ~~~~~~Ll~~le~~~~~~~  183 (376)
T 1um8_A          165 EGVQQALLKIVEGSLVNIP  183 (376)
T ss_dssp             HHHHHHHHHHHHCCEEC--
T ss_pred             HHHHHHHHHHhhccceecc
Confidence            7799999999998765443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.83  E-value=2.6e-20  Score=193.30  Aligned_cols=149  Identities=25%  Similarity=0.371  Sum_probs=118.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHH--HHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHY--KRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~--kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|++ |.|++++|+.|.++|..+.  +.++.....                    ..+++||||||||||||+||+++|.
T Consensus       146 ~~~d-IgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi--------------------~~prGvLL~GPPGTGKTllAkAiA~  204 (405)
T 4b4t_J          146 TYDM-VGGLTKQIKEIKEVIELPVKHPELFESLGI--------------------AQPKGVILYGPPGTGKTLLARAVAH  204 (405)
T ss_dssp             CGGG-SCSCHHHHHHHHHHTHHHHHCHHHHHHHTC--------------------CCCCCEEEESCSSSSHHHHHHHHHH
T ss_pred             CHHH-hCCHHHHHHHHHHHHHHHHhCHHHHHhCCC--------------------CCCCceEEeCCCCCCHHHHHHHHHH
Confidence            4555 9999999999999987532  223322111                    2358899999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +++.+|+.++++++. .+|+|+. +..++.+|..+...    .++||||||||.+...|...+.+.+.....+++.||..
T Consensus       205 e~~~~f~~v~~s~l~-sk~vGes-e~~vr~lF~~Ar~~----aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~  278 (405)
T 4b4t_J          205 HTDCKFIRVSGAELV-QKYIGEG-SRMVRELFVMAREH----APSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQ  278 (405)
T ss_dssp             HHTCEEEEEEGGGGS-CSSTTHH-HHHHHHHHHHHHHT----CSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHH
T ss_pred             hhCCCceEEEhHHhh-ccccchH-HHHHHHHHHHHHHh----CCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHh
Confidence            999999999999999 4699988 89999999988754    79999999999999987665555555556688999999


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ||+....         .+.++|+|||.
T Consensus       279 lDg~~~~---------~~V~vIaATNr  296 (405)
T 4b4t_J          279 LDGFETS---------KNIKIIMATNR  296 (405)
T ss_dssp             HHTTTCC---------CCEEEEEEESC
T ss_pred             hhccCCC---------CCeEEEeccCC
Confidence            9975421         25788888884

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.1e-19  Score=189.84  Aligned_cols=149  Identities=25%  Similarity=0.336  Sum_probs=117.6

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|++ |.|++++|+.|.+.+....+  .++....                    ...+++||||||||||||+||++||.
T Consensus       180 ~~~D-IgGld~~k~~L~e~v~~Pl~~pe~f~~~G--------------------i~~prGvLLyGPPGTGKTlLAkAiA~  238 (437)
T 4b4t_I          180 SYSD-IGGLESQIQEIKESVELPLTHPELYEEMG--------------------IKPPKGVILYGAPGTGKTLLAKAVAN  238 (437)
T ss_dssp             CGGG-TCSCHHHHHHHHHHHHHHHHCCHHHHHHT--------------------CCCCSEEEEESSTTTTHHHHHHHHHH
T ss_pred             ccee-cCcHHHHHHHHHHHHHHHHhCHHHHHhCC--------------------CCCCCCCceECCCCchHHHHHHHHHH
Confidence            5666 99999999999999964322  2222211                    12358899999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +++.+|+.++.+++.. +|+|+. +..++.+|..+...    .++||||||||.+...|...+...+.....+++.||..
T Consensus       239 e~~~~fi~v~~s~l~s-k~vGes-ek~ir~lF~~Ar~~----aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~  312 (437)
T 4b4t_I          239 QTSATFLRIVGSELIQ-KYLGDG-PRLCRQIFKVAGEN----APSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQ  312 (437)
T ss_dssp             HHTCEEEEEESGGGCC-SSSSHH-HHHHHHHHHHHHHT----CSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHH
T ss_pred             HhCCCEEEEEHHHhhh-ccCchH-HHHHHHHHHHHHhc----CCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHH
Confidence            9999999999999994 699988 89999999887654    79999999999999998765555554555678888998


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ||+....         .+.++|+|||.
T Consensus       313 lDg~~~~---------~~ViVIaATNr  330 (437)
T 4b4t_I          313 LDGFDDR---------GDVKVIMATNK  330 (437)
T ss_dssp             HHHCCCS---------SSEEEEEEESC
T ss_pred             hhCcCCC---------CCEEEEEeCCC
Confidence            8854321         25788888883

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.81  E-value=9.7e-20  Score=190.85  Aligned_cols=149  Identities=26%  Similarity=0.376  Sum_probs=117.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|++ |.|++++|+.|.++|....+  .++....                    ...+++||||||||||||+||++||.
T Consensus       179 ~~~d-igGl~~~k~~l~e~v~~pl~~p~~f~~~g--------------------~~~prGvLL~GPPGtGKTllAkAiA~  237 (437)
T 4b4t_L          179 TFDG-IGGLTEQIRELREVIELPLKNPEIFQRVG--------------------IKPPKGVLLYGPPGTGKTLLAKAVAA  237 (437)
T ss_dssp             CSGG-GCSCHHHHHHHHHHHHHHHHCHHHHHHHC--------------------CCCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             ChhH-hCChHHHHHHHHHHHHHHHhCHHHHHhCC--------------------CCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            4555 89999999999999975322  2332211                    12358899999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +++.+|+.++++++. .+|+|+. +..++.+|..+...    .++||||||||.+..+|...+...+.....+++.||..
T Consensus       238 e~~~~~~~v~~s~l~-sk~~Ges-e~~ir~~F~~A~~~----~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~  311 (437)
T 4b4t_L          238 TIGANFIFSPASGIV-DKYIGES-ARIIREMFAYAKEH----EPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQ  311 (437)
T ss_dssp             HHTCEEEEEEGGGTC-CSSSSHH-HHHHHHHHHHHHHS----CSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHH
T ss_pred             HhCCCEEEEehhhhc-cccchHH-HHHHHHHHHHHHhc----CCceeeeecccccccccccCCCCcchHHHHHHHHHHHH
Confidence            999999999999998 4699988 88999999887654    89999999999999988665555554555678899999


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ||+....         .+.++|+|||.
T Consensus       312 lDg~~~~---------~~vivI~ATNr  329 (437)
T 4b4t_L          312 MDGFDNL---------GQTKIIMATNR  329 (437)
T ss_dssp             HHSSSCT---------TSSEEEEEESS
T ss_pred             hhcccCC---------CCeEEEEecCC
Confidence            9975421         24688888883

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.9e-19  Score=188.43  Aligned_cols=149  Identities=26%  Similarity=0.341  Sum_probs=116.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|++ |.|++++|+.|.+.+....+  .++...   +                 ...+++||||||||||||+||+++|.
T Consensus       179 t~~d-igGl~~~k~~l~e~v~~pl~~pe~f~~~---g-----------------~~~prGvLLyGPPGTGKTllAkAiA~  237 (434)
T 4b4t_M          179 TYSD-VGGLDKQIEELVEAIVLPMKRADKFKDM---G-----------------IRAPKGALMYGPPGTGKTLLARACAA  237 (434)
T ss_dssp             CGGG-SCSCHHHHHHHHHHTHHHHHCSHHHHHH---C-----------------CCCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             ChHh-cCcHHHHHHHHHHHHHHHHhCHHHHHhC---C-----------------CCCCCeeEEECcCCCCHHHHHHHHHH
Confidence            4555 99999999999998864432  222211   1                 12358899999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +++.+|+.++++++. .+|+|+. +..++.+|..+...    .++||||||||.+..+|.....+.......+++.||..
T Consensus       238 e~~~~f~~v~~s~l~-~~~vGes-e~~ir~lF~~A~~~----aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~  311 (434)
T 4b4t_M          238 QTNATFLKLAAPQLV-QMYIGEG-AKLVRDAFALAKEK----APTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQ  311 (434)
T ss_dssp             HHTCEEEEEEGGGGC-SSCSSHH-HHHHHHHHHHHHHH----CSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHH
T ss_pred             HhCCCEEEEehhhhh-hcccchH-HHHHHHHHHHHHhc----CCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHH
Confidence            999999999999999 4699988 89999999887655    79999999999999987655444443444577889999


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      |++..-.         .+.++|+|||.
T Consensus       312 ldg~~~~---------~~ViVIaaTNr  329 (434)
T 4b4t_M          312 LDGFSSD---------DRVKVLAATNR  329 (434)
T ss_dssp             HTTSCSS---------CSSEEEEECSS
T ss_pred             hhccCCC---------CCEEEEEeCCC
Confidence            9965421         24688888884

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.8e-19  Score=188.31  Aligned_cols=149  Identities=25%  Similarity=0.376  Sum_probs=117.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .+++ |.|++++|+.|.+.+....+  .++...   +                 ...+++||||||||||||+||++||+
T Consensus       170 ~~~d-igGl~~~k~~l~e~v~~pl~~p~~~~~~---g-----------------~~~prGiLL~GPPGtGKT~lakAiA~  228 (428)
T 4b4t_K          170 TYAD-VGGLDMQKQEIREAVELPLVQADLYEQI---G-----------------IDPPRGVLLYGPPGTGKTMLVKAVAN  228 (428)
T ss_dssp             CGGG-SCSCHHHHHHHHHHHHHHHHCHHHHHHH---C-----------------CCCCCEEEEESCTTTTHHHHHHHHHH
T ss_pred             CHHH-hccHHHHHHHHHHHHHHHHhCHHHHHhC---C-----------------CCCCceEEEECCCCCCHHHHHHHHHH
Confidence            3455 99999999999999864322  222221   1                 12358899999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +++.+|+.++++++.. +|+|+. +..++.+|..+...    .++||||||+|.+...|.......+....++++.||..
T Consensus       229 ~~~~~~~~v~~~~l~~-~~~Ge~-e~~ir~lF~~A~~~----aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~  302 (428)
T 4b4t_K          229 STKAAFIRVNGSEFVH-KYLGEG-PRMVRDVFRLAREN----APSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQ  302 (428)
T ss_dssp             HHTCEEEEEEGGGTCC-SSCSHH-HHHHHHHHHHHHHT----CSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHH
T ss_pred             HhCCCeEEEecchhhc-cccchh-HHHHHHHHHHHHHc----CCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHH
Confidence            9999999999999984 699988 89999999887654    78999999999999988665555555556789999999


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      |||....         .+.++|+|||.
T Consensus       303 ldg~~~~---------~~v~vI~aTN~  320 (428)
T 4b4t_K          303 MDGFDQS---------TNVKVIMATNR  320 (428)
T ss_dssp             HHHSCSS---------CSEEEEEEESC
T ss_pred             hhCCCCC---------CCEEEEEecCC
Confidence            9975321         25788888884

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.79  E-value=4e-19  Score=187.00  Aligned_cols=148  Identities=21%  Similarity=0.280  Sum_probs=116.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHH--HHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHY--KRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~--kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |++ |.|++++|+.|.+.|....  ..++....                    ...+++||||||||||||+||++||++
T Consensus       208 ~~D-IgGl~~~k~~L~e~V~~pl~~pe~f~~~G--------------------i~pprGILLyGPPGTGKTlLAkAiA~e  266 (467)
T 4b4t_H          208 YSD-VGGCKDQIEKLREVVELPLLSPERFATLG--------------------IDPPKGILLYGPPGTGKTLCARAVANR  266 (467)
T ss_dssp             CSS-CTTCHHHHHHHHHHTHHHHHCHHHHHHHT--------------------CCCCSEEEECSCTTSSHHHHHHHHHHH
T ss_pred             HHH-hccHHHHHHHHHHHHHHHhcCHHHHHHCC--------------------CCCCCceEeeCCCCCcHHHHHHHHHhc
Confidence            444 9999999999999886432  22222211                    123688999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++.+|+.++++++.. +|+|+. +..++.+|..+...    .++||||||||.+...|.....+.......+++.||..|
T Consensus       267 ~~~~fi~vs~s~L~s-k~vGes-ek~ir~lF~~Ar~~----aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~l  340 (467)
T 4b4t_H          267 TDATFIRVIGSELVQ-KYVGEG-ARMVRELFEMARTK----KACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQL  340 (467)
T ss_dssp             HTCEEEEEEGGGGCC-CSSSHH-HHHHHHHHHHHHHT----CSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHH
T ss_pred             cCCCeEEEEhHHhhc-ccCCHH-HHHHHHHHHHHHhc----CCceEeecccccccccccCcCCCccHHHHHHHHHHHHHh
Confidence            999999999999994 699988 89999999887654    799999999999999887655555555556788889999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ++...         ..+.++|+|||.
T Consensus       341 Dg~~~---------~~~ViVIaATNr  357 (467)
T 4b4t_H          341 DGFDP---------RGNIKVMFATNR  357 (467)
T ss_dssp             HSSCC---------TTTEEEEEECSC
T ss_pred             hccCC---------CCcEEEEeCCCC
Confidence            86432         125788899884

>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=2.6e-18  Score=180.36  Aligned_cols=104  Identities=40%  Similarity=0.699  Sum_probs=82.1

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      ++|+++...|+++|+||+++|+.|..++.++|++....   ..              ......+.+|||+||||||||++
T Consensus         4 ~tP~~i~~~Ld~~IvGqe~ak~~l~~av~~~~~r~~~~---~~--------------~~~~~~~~~iLl~GppGtGKT~l   66 (444)
T 1g41_A            4 MTPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQ---EP--------------LRHEVTPKNILMIGPTGVGKTEI   66 (444)
T ss_dssp             CCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHSC---TT--------------TTTTCCCCCEEEECCTTSSHHHH
T ss_pred             CCHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhccc---cc--------------cccccCCceEEEEcCCCCCHHHH
Confidence            68999999999999999999999999998888764311   00              01123357899999999999999


Q ss_pred             HHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhh
Q 012525          342 AKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA  382 (461)
Q Consensus       342 AraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a  382 (461)
                      |++||+.++.+|+.++++.+...+|+|.+.+..++.+|..+
T Consensus        67 ar~lA~~l~~~~~~v~~~~~~~~g~vG~d~e~~lr~lf~~a  107 (444)
T 1g41_A           67 ARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA  107 (444)
T ss_dssp             HHHHHHHTTCCEEEEEGGGGC----CCCCTHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCceeecchhhcccceeeccHHHHHHHHHHHH
Confidence            99999999999999999998877899976677777666543

>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=99.74  E-value=1.2e-17  Score=162.15  Aligned_cols=173  Identities=40%  Similarity=0.653  Sum_probs=125.0

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .++.++...|++.|+||+.+++.|..++..++.+...         ....        .....+.++||+||||||||++
T Consensus         4 ~~~~~l~~~l~~~i~G~~~~~~~l~~~l~~~~~~~~~---------~~~~--------~~~~~~~~vll~G~~GtGKT~l   66 (310)
T 1ofh_A            4 MTPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQL---------QEPL--------RHEVTPKNILMIGPTGVGKTEI   66 (310)
T ss_dssp             CCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSS---------CHHH--------HHHCCCCCEEEECCTTSSHHHH
T ss_pred             CCHHHHHHHHhhhcCChHHHHHHHHHHHHHHHhhhhh---------cccc--------cccCCCceEEEECCCCCCHHHH
Confidence            5789999999999999999999999888654322100         0000        0012357899999999999999


Q ss_pred             HHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhcc-CceEEEEcCccccchhhhccccccccchHHH
Q 012525          342 AKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAA-QQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       342 AraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a-~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      |+++|+.++.+++.+++..+...+|++...+..+..++..+.+.+..+ .++||||||||++......  ...+.+...+
T Consensus        67 a~~la~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~--~~~~~~~~~~  144 (310)
T 1ofh_A           67 ARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEY--SGADVSREGV  144 (310)
T ss_dssp             HHHHHHHHTCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSC--CSSHHHHHHH
T ss_pred             HHHHHHHhCCCEEEEcchhcccCCccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccc--cccchhHHHH
Confidence            999999999999999999988667888776677788777654433332 4789999999999877431  1233344457


Q ss_pred             HHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          421 QQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ++.|+++||+..+..... .......++|+++|.
T Consensus       145 ~~~Ll~~le~~~~~~~~~-~~~~~~~~~i~~~~~  177 (310)
T 1ofh_A          145 QRDLLPLVEGSTVSTKHG-MVKTDHILFIASGAF  177 (310)
T ss_dssp             HHHHHHHHHCCEEEETTE-EEECTTCEEEEEECC
T ss_pred             HHHHHHHhcCCeEecccc-cccCCcEEEEEcCCc
Confidence            999999999876554332 122236788888654

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.71  E-value=1.7e-17  Score=185.11  Aligned_cols=148  Identities=24%  Similarity=0.323  Sum_probs=106.0

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |.|++++|+.|.+++....+.   ..               .........+++|||+||||||||++|++||.+++.+|+
T Consensus       479 iggl~~~k~~l~e~v~~p~~~---p~---------------~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~  540 (806)
T 3cf2_A          479 IGGLEDVKRELQELVQYPVEH---PD---------------KFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFI  540 (806)
T ss_dssp             CCSCHHHHHHHTTTTTTTTTC---SG---------------GGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEE
T ss_pred             hCCHHHHHHHHHHHHHhhhhC---HH---------------HHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceE
Confidence            789999999999888421110   00               000111234688999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK  434 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~  434 (461)
                      .++.+++. .+|+|+. ++.++.+|..+...    .++||||||||.+...|+......+...++++++||..||+....
T Consensus       541 ~v~~~~l~-s~~vGes-e~~vr~lF~~Ar~~----~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~  614 (806)
T 3cf2_A          541 SIKGPELL-TMWFGES-EANVREIFDKARQA----APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK  614 (806)
T ss_dssp             ECCHHHHH-TTTCSSC-HHHHHHHHHHHHTT----CSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSS
T ss_pred             Eeccchhh-ccccchH-HHHHHHHHHHHHHc----CCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCC
Confidence            99999999 4699999 89999999988654    799999999999999886443333334456999999999976421


Q ss_pred             eecceeeecCCeEEEecCCCC
Q 012525          435 TFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       435 i~~~~r~~~rd~IiI~TsNid  455 (461)
                               .+.++|+|||.-
T Consensus       615 ---------~~V~vi~aTN~p  626 (806)
T 3cf2_A          615 ---------KNVFIIGATNRP  626 (806)
T ss_dssp             ---------SSEEEECC-CCS
T ss_pred             ---------CCEEEEEeCCCc
Confidence                     257888898853

>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=99.68  E-value=2e-16  Score=157.63  Aligned_cols=147  Identities=29%  Similarity=0.434  Sum_probs=107.3

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |++ |+|++.+|+.|..++......   ...                .......+.+|||+||||||||+||++||++++
T Consensus        17 ~~d-i~G~~~~~~~l~~~i~~~~~~---~~~----------------~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~   76 (322)
T 3eie_A           17 WED-VAGLEGAKEALKEAVILPVKF---PHL----------------FKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN   76 (322)
T ss_dssp             GGG-SCSCHHHHHHHHHHTHHHHHC---GGG----------------CCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHT
T ss_pred             HHH-hcChHHHHHHHHHHHHHHHhC---HHH----------------HhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHC
Confidence            555 899999999999988533211   100                011123357899999999999999999999999


Q ss_pred             CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          351 VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       351 ~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .+|+.+++.++.. .|+|+. +..++.+|..+...    +++||||||||.|..++...   .....+.+++.|+..|++
T Consensus        77 ~~~~~v~~~~l~~-~~~g~~-~~~~~~~f~~a~~~----~~~vl~iDEid~l~~~~~~~---~~~~~~~~~~~ll~~l~~  147 (322)
T 3eie_A           77 STFFSVSSSDLVS-KWMGES-EKLVKQLFAMAREN----KPSIIFIDQVDALTGTRGEG---ESEASRRIKTELLVQMNG  147 (322)
T ss_dssp             CEEEEEEHHHHHT-TTGGGH-HHHHHHHHHHHHHT----SSEEEEEECGGGGSCC---------CCTHHHHHHHHHHHGG
T ss_pred             CCEEEEchHHHhh-cccchH-HHHHHHHHHHHHhc----CCeEEEechhhhhhccCCCC---cchHHHHHHHHHHHHhcc
Confidence            9999999999874 577766 78888888776543    78999999999999876432   223445689999999985


Q ss_pred             ceeeeecceeeecCCeEEEecCCC
Q 012525          431 TETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       431 ~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ....        ..+.++|+|+|.
T Consensus       148 ~~~~--------~~~v~vi~atn~  163 (322)
T 3eie_A          148 VGND--------SQGVLVLGATNI  163 (322)
T ss_dssp             GGTS--------CCCEEEEEEESC
T ss_pred             cccc--------CCceEEEEecCC
Confidence            4311        125788888885

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.67  E-value=4.5e-16  Score=155.83  Aligned_cols=148  Identities=24%  Similarity=0.392  Sum_probs=109.8

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      |++ |+|++.+|+.|.+++....+.   ....                ......+++|||+||||||||+||+++|+++ 
T Consensus        11 ~~d-i~G~~~~k~~l~~~v~~p~~~---~~~~----------------~~~~~~~~~iLL~GppGtGKT~la~ala~~~~   70 (322)
T 1xwi_A           11 WSD-VAGLEGAKEALKEAVILPIKF---PHLF----------------TGKRTPWRGILLFGPPGTGKSYLAKAVATEAN   70 (322)
T ss_dssp             GGG-SCSCHHHHHHHHHHHHHHHHC---GGGS----------------CTTCCCCSEEEEESSSSSCHHHHHHHHHHHTT
T ss_pred             HHH-hcCHHHHHHHHHHHHHHHHhC---HHHH----------------hCCCCCCceEEEECCCCccHHHHHHHHHHHcC
Confidence            455 899999999999988543221   1000                0111234789999999999999999999999 


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+|+.+++.++.. .|+|+. +..++.+|..+..    .+++||||||||.+...+...   .......+++.|+..|+
T Consensus        71 ~~~~~~i~~~~l~~-~~~g~~-~~~~~~lf~~a~~----~~~~vl~iDEid~l~~~~~~~---~~~~~~~~~~~ll~~ld  141 (322)
T 1xwi_A           71 NSTFFSISSSDLVS-KWLGES-EKLVKNLFQLARE----NKPSIIFIDEIDSLCGSRSEN---ESEAARRIKTEFLVQMQ  141 (322)
T ss_dssp             SCEEEEEECCSSCC-SSCCSC-HHHHHHHHHHHHH----TSSEEEEEETTTGGGCCSSSC---CTTHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEhHHHHh-hhhhHH-HHHHHHHHHHHHh----cCCcEEEeecHHHhccccccc---cchHHHHHHHHHHHHHh
Confidence            88999999998884 588887 7888888876653    378999999999998876432   22234568899999999


Q ss_pred             CceeeeecceeeecCCeEEEecCCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +....        ..+.++|+|+|..
T Consensus       142 ~~~~~--------~~~v~vI~atn~~  159 (322)
T 1xwi_A          142 GVGVD--------NDGILVLGATNIP  159 (322)
T ss_dssp             CSSSC--------CTTEEEEEEESCT
T ss_pred             ccccc--------CCCEEEEEecCCc
Confidence            65321        1357888888864

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.66  E-value=1.9e-16  Score=176.67  Aligned_cols=147  Identities=26%  Similarity=0.390  Sum_probs=113.2

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +++ |.|++++|+.|++.+..+.+   +......               .....+++|||+||||||||+||++||++++
T Consensus       203 ~~d-IgGl~~~~~~l~e~v~~pl~---~p~~f~~---------------~g~~~p~GILL~GPPGTGKT~LAraiA~elg  263 (806)
T 3cf2_A          203 YDD-IGGCRKQLAQIKEMVELPLR---HPALFKA---------------IGVKPPRGILLYGPPGTGKTLIARAVANETG  263 (806)
T ss_dssp             GGG-CCSCCTTHHHHHHHHHHHHH---CCGGGTS---------------CCCCCCCEEEEECCTTSCHHHHHHHHHTTTT
T ss_pred             hhh-hcCHHHHHHHHHHHHHHHcc---CHHHHhh---------------cCCCCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            444 99999999999998853322   1111111               1123468999999999999999999999999


Q ss_pred             CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          351 VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       351 ~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .+|+.+++.++.. +|+|+. +..++.+|..+...    .++||||||||.|..+|+...   ....+++.++||..|++
T Consensus       264 ~~~~~v~~~~l~s-k~~ges-e~~lr~lF~~A~~~----~PsIIfIDEiDal~~~r~~~~---~~~~~riv~~LL~~mdg  334 (806)
T 3cf2_A          264 AFFFLINGPEIMS-KLAGES-ESNLRKAFEEAEKN----APAIIFIDELDAIAPKREKTH---GEVERRIVSQLLTLMDG  334 (806)
T ss_dssp             CEEEEEEHHHHHS-SCTTHH-HHHHHHHHHHHTTS----CSEEEEEESGGGTCCTTTTCC---CTTHHHHHHHHHTHHHH
T ss_pred             CeEEEEEhHHhhc-ccchHH-HHHHHHHHHHHHHc----CCeEEEEehhcccccccCCCC---ChHHHHHHHHHHHHHhc
Confidence            9999999999984 688887 88999999987654    799999999999999876432   23345689999999996


Q ss_pred             ceeeeecceeeecCCeEEEecCCC
Q 012525          431 TETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       431 ~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ...+         ...++|+|||.
T Consensus       335 ~~~~---------~~V~VIaaTN~  349 (806)
T 3cf2_A          335 LKQR---------AHVIVMAATNR  349 (806)
T ss_dssp             CCGG---------GCEEEEEECSS
T ss_pred             cccc---------CCEEEEEecCC
Confidence            5321         24678888874

>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=99.65  E-value=5e-16  Score=153.51  Aligned_cols=149  Identities=23%  Similarity=0.348  Sum_probs=107.5

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |++ |+|++.+|+.|.+.+.....  .++...   +                 ...+.+|||+||||||||+||++||+.
T Consensus        14 ~~d-i~G~~~~~~~l~~~v~~~~~~~~~~~~~---~-----------------~~~~~~vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           14 WED-IGGLEDVKRELQELVQYPVEHPDKFLKF---G-----------------MTPSKGVLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             GGG-SCSCHHHHHHHHHHHHHHHHCHHHHHHH---C-----------------CCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HHH-hCCHHHHHHHHHHHHHHHhhCHHHHHHc---C-----------------CCCCceEEEECCCCcCHHHHHHHHHHH
Confidence            444 89999999999998863321  111110   0                 122478999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++.+|+.+++.++.. .|+|+. +..++.+|..+...    .++||||||||.+...+.............+++.||..|
T Consensus        73 ~~~~~i~v~~~~l~~-~~~g~~-~~~~~~~f~~a~~~----~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l  146 (301)
T 3cf0_A           73 CQANFISIKGPELLT-MWFGES-EANVREIFDKARQA----APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEM  146 (301)
T ss_dssp             TTCEEEEECHHHHHH-HHHTTC-TTHHHHHHHHHHHT----CSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHH
T ss_pred             hCCCEEEEEhHHHHh-hhcCch-HHHHHHHHHHHHhc----CCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHh
Confidence            999999999998874 366766 56677778766433    688999999999998865432222223345889999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ++...         ..+.++|+|+|..
T Consensus       147 ~~~~~---------~~~v~vi~atn~~  164 (301)
T 3cf0_A          147 DGMST---------KKNVFIIGATNRP  164 (301)
T ss_dssp             HSSCT---------TSSEEEEEEESCG
T ss_pred             hcccC---------CCCEEEEEecCCc
Confidence            95421         1257888888854

>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=99.64  E-value=9.9e-16  Score=155.33  Aligned_cols=149  Identities=28%  Similarity=0.415  Sum_probs=103.6

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++.+|+.|..++..+...   ...                .........+|||+||||||||+||++||+++
T Consensus        49 ~~~d-i~G~~~~~~~l~~~v~~~~~~---~~~----------------~~~~~~~~~~iLL~GppGtGKT~la~ala~~~  108 (355)
T 2qp9_X           49 KWED-VAGLEGAKEALKEAVILPVKF---PHL----------------FKGNRKPTSGILLYGPPGTGKSYLAKAVATEA  108 (355)
T ss_dssp             CGGG-SCCGGGHHHHHHHHTHHHHHC---GGG----------------GCSSCCCCCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CHHH-hCCHHHHHHHHHHHHHHHHhC---HHH----------------HhcCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            4555 899999999999988533211   100                00112335789999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+|+.+++.++.. .|+|+. +..++.+|..+..    ..++||||||||.|...+...   .......+++.||..|+
T Consensus       109 ~~~~~~v~~~~l~~-~~~g~~-~~~~~~~f~~a~~----~~~~vl~iDEid~l~~~r~~~---~~~~~~~~~~~ll~~l~  179 (355)
T 2qp9_X          109 NSTFFSVSSSDLVS-KWMGES-EKLVKQLFAMARE----NKPSIIFIDQVDALTGTRGEG---ESEASRRIKTELLVQMN  179 (355)
T ss_dssp             TCEEEEEEHHHHHS-CC---C-HHHHHHHHHHHHH----TSSEEEEEECGGGGTC---------CTHHHHHHHHHHHHHH
T ss_pred             CCCEEEeeHHHHhh-hhcchH-HHHHHHHHHHHHH----cCCeEEEEechHhhcccCCCC---cchHHHHHHHHHHHHhh
Confidence            99999999999884 577776 7778888876543    378999999999999876432   22234558899999998


Q ss_pred             CceeeeecceeeecCCeEEEecCCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +....        ..+.++|+|+|..
T Consensus       180 ~~~~~--------~~~v~vI~atn~~  197 (355)
T 2qp9_X          180 GVGND--------SQGVLVLGATNIP  197 (355)
T ss_dssp             HCC-----------CCEEEEEEESCG
T ss_pred             ccccc--------CCCeEEEeecCCc
Confidence            54311        1257888888854

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.62  E-value=8.4e-16  Score=151.83  Aligned_cols=128  Identities=15%  Similarity=0.207  Sum_probs=84.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      +.++||+||||||||+||++||+.++.+|+.++++++.. .|+|+. +..++.+|..+........++||||||||++..
T Consensus        36 p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~-~~~g~~-~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~  113 (293)
T 3t15_A           36 PLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELES-GNAGEP-AKLIRQRYREAAEIIRKGNMCCLFINDLDAGAG  113 (293)
T ss_dssp             CSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHC-C---HH-HHHHHHHHHHHHHHHTTSSCCCEEEECCC----
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhh-ccCchh-HHHHHHHHHHHHHHHhcCCCeEEEEechhhhcC
Confidence            578999999999999999999999999999999999884 577766 677888887775444456789999999999988


Q ss_pred             hhhccccccccchHHHHHHHHHHHhCceeeeecc-eee-ecCCeEEEecCCCC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VSK-VSRDNLYIKTSGLD  455 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r~-~~rd~IiI~TsNid  455 (461)
                      .+.... ........+++.|+++||+........ ... ...+.++|+|||..
T Consensus       114 ~~~~~~-~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~  165 (293)
T 3t15_A          114 RMGGTT-QYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDF  165 (293)
T ss_dssp             -----------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSC
T ss_pred             CCCCCc-cccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCc
Confidence            543211 122234458899999999665433222 111 12268899999954

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.61  E-value=2.4e-15  Score=153.56  Aligned_cols=148  Identities=28%  Similarity=0.414  Sum_probs=98.8

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |++ |+|++.+++.|...+......   .                +....+.....+|||+||||||||+||++||+.++
T Consensus       114 ~~~-iiG~~~~~~~l~~~~~~~~~~---~----------------~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~  173 (389)
T 3vfd_A          114 FDD-IAGQDLAKQALQEIVILPSLR---P----------------ELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESN  173 (389)
T ss_dssp             GGG-SCSCHHHHHHHHHHTHHHHHC---T----------------TTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTT
T ss_pred             hHH-hCCHHHHHHHHHHHHHHhccC---H----------------HHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhc
Confidence            444 899999999999988532210   0                01112223458899999999999999999999999


Q ss_pred             CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          351 VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       351 ~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .+|+.+++.++.. .|.|.. +..+..+|..+...    .++||||||||.|...+..   ........+++.|+..|++
T Consensus       174 ~~~~~v~~~~l~~-~~~g~~-~~~~~~~~~~a~~~----~~~il~iDEid~l~~~~~~---~~~~~~~~~~~~ll~~l~~  244 (389)
T 3vfd_A          174 ATFFNISAASLTS-KYVGEG-EKLVRALFAVAREL----QPSIIFIDQVDSLLCERRE---GEHDASRRLKTEFLIEFDG  244 (389)
T ss_dssp             CEEEEECSCCC--------C-HHHHHHHHHHHHHS----SSEEEEEETGGGGC-----------CTHHHHHHHHHHHHHH
T ss_pred             CcEEEeeHHHhhc-cccchH-HHHHHHHHHHHHhc----CCeEEEEECchhhcccCCC---ccchHHHHHHHHHHHHhhc
Confidence            9999999998884 477776 66777787765533    6789999999999876542   1223345688999999985


Q ss_pred             ceeeeecceeeecCCeEEEecCCC
Q 012525          431 TETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       431 ~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ....       ...++++|+|+|.
T Consensus       245 ~~~~-------~~~~v~vI~atn~  261 (389)
T 3vfd_A          245 VQSA-------GDDRVLVMGATNR  261 (389)
T ss_dssp             HC------------CEEEEEEESC
T ss_pred             cccc-------CCCCEEEEEecCC
Confidence            4321       1235788888886

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.60  E-value=5.8e-15  Score=142.77  Aligned_cols=149  Identities=26%  Similarity=0.389  Sum_probs=99.8

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +++ |+|++.+++.|...+.....  .++...   +                 ...+.++||+||||||||++|++||+.
T Consensus        16 ~~~-i~G~~~~~~~l~~~~~~~~~~~~~~~~~---~-----------------~~~~~~~ll~G~~GtGKT~la~~la~~   74 (285)
T 3h4m_A           16 YED-IGGLEKQMQEIREVVELPLKHPELFEKV---G-----------------IEPPKGILLYGPPGTGKTLLAKAVATE   74 (285)
T ss_dssp             GGG-SCSCHHHHHHHHHHTHHHHHCHHHHHHH---C-----------------CCCCSEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HHH-hcCHHHHHHHHHHHHHHHhhCHHHHHhc---C-----------------CCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            444 89999999999988853321  111110   0                 122478999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++.+|+.+++.++.. .+.+.. +..+..+|..+..    ..++||||||||.+..++..............+..|+..|
T Consensus        75 ~~~~~~~v~~~~~~~-~~~~~~-~~~~~~~~~~~~~----~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~  148 (285)
T 3h4m_A           75 TNATFIRVVGSELVK-KFIGEG-ASLVKDIFKLAKE----KAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEM  148 (285)
T ss_dssp             TTCEEEEEEGGGGCC-CSTTHH-HHHHHHHHHHHHH----TCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHH
T ss_pred             hCCCEEEEehHHHHH-hccchH-HHHHHHHHHHHHH----cCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHh
Confidence            999999999998874 466655 5667777765543    3678999999999987754332222222222344444444


Q ss_pred             hCceeeeecceeeecCCeEEEecCCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ++...         ..+.++|+|+|..
T Consensus       149 ~~~~~---------~~~~~vI~ttn~~  166 (285)
T 3h4m_A          149 DGFDA---------RGDVKIIGATNRP  166 (285)
T ss_dssp             HTTCS---------SSSEEEEEECSCG
T ss_pred             hCCCC---------CCCEEEEEeCCCc
Confidence            43211         1257888888854

>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=99.59  E-value=5e-15  Score=150.01  Aligned_cols=146  Identities=27%  Similarity=0.414  Sum_probs=102.6

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |+|++.+++.|.+.+......   .                +..........+|||+||||||||+||++||+.++.+|+
T Consensus        86 i~G~~~~~~~l~~~i~~~~~~---~----------------~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~  146 (357)
T 3d8b_A           86 IAGVEFAKATIKEIVVWPMLR---P----------------DIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGATFF  146 (357)
T ss_dssp             SCSCHHHHHHHHHHTHHHHHC---T----------------TTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTCEEE
T ss_pred             hCChHHHHHHHHHHHHHHhhC---h----------------HhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCCeEE
Confidence            899999999999988532210   0                001112234678999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK  434 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~  434 (461)
                      .+++.++.. .+.|+. +..++.+|..+..    ..++||||||||.|...+..   ........+++.||..|++....
T Consensus       147 ~i~~~~l~~-~~~g~~-~~~~~~~~~~a~~----~~~~vl~iDEid~l~~~~~~---~~~~~~~~~~~~lL~~l~~~~~~  217 (357)
T 3d8b_A          147 SISASSLTS-KWVGEG-EKMVRALFAVARC----QQPAVIFIDEIDSLLSQRGD---GEHESSRRIKTEFLVQLDGATTS  217 (357)
T ss_dssp             EEEGGGGCC-SSTTHH-HHHHHHHHHHHHH----TCSEEEEEETHHHHTBC---------CHHHHHHHHHHHHHHC----
T ss_pred             EEehHHhhc-cccchH-HHHHHHHHHHHHh----cCCeEEEEeCchhhhccCCC---CcchHHHHHHHHHHHHHhccccc
Confidence            999998874 466655 6677777765543    36889999999999876532   12333456889999999965321


Q ss_pred             eecceeeecCCeEEEecCCCC
Q 012525          435 TFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       435 i~~~~r~~~rd~IiI~TsNid  455 (461)
                             ...++++|+|+|..
T Consensus       218 -------~~~~v~vI~atn~~  231 (357)
T 3d8b_A          218 -------SEDRILVVGATNRP  231 (357)
T ss_dssp             -------CCCCEEEEEEESCG
T ss_pred             -------CCCCEEEEEecCCh
Confidence                   12357888888863

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.59  E-value=3.7e-15  Score=164.33  Aligned_cols=164  Identities=22%  Similarity=0.310  Sum_probs=113.5

Q ss_pred             CCCCCCCCCCCCC----HHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCC
Q 012525          251 RWGGSNLGEDLPT----PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKS  326 (461)
Q Consensus       251 ~w~g~~l~~~l~t----~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~  326 (461)
                      .|++.+.......    ..++.+.|.+.|+||+.+++.|..++....         .+..             .......
T Consensus       432 ~~~~ip~~~~~~~~~~~l~~l~~~l~~~v~g~~~~~~~l~~~i~~~~---------~g~~-------------~~~~p~~  489 (758)
T 1r6b_X          432 RIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMAR---------AGLG-------------HEHKPVG  489 (758)
T ss_dssp             HHSCCCCCCSSSSHHHHHHHHHHHHTTTSCSCHHHHHHHHHHHHHHH---------TTCS-------------CTTSCSE
T ss_pred             HhcCCCccccchhHHHHHHHHHHHHHhhccCHHHHHHHHHHHHHHHh---------cccC-------------CCCCCce
Confidence            4445444443333    335677788889999999999988774211         0100             0001224


Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhccCceEEE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAAQQGMVY  395 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLf  395 (461)
                      ++||+||||||||++|++||+.++.+|+.++++++.+.           +|+|......+...+       ..+.++|||
T Consensus       490 ~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~~~l~g~~~g~~g~~~~~~l~~~~-------~~~~~~vl~  562 (758)
T 1r6b_X          490 SFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAV-------IKHPHAVLL  562 (758)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHH-------HHCSSEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhHhhhcCCCCCCcCccccchHHHHH-------HhCCCcEEE
Confidence            79999999999999999999999999999999987642           244432222233333       234678999


Q ss_pred             EcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          396 IDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       396 IDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ||||+++.+.              +++.|+++||.+.+..........+++++|+|+|.+.+
T Consensus       563 lDEi~~~~~~--------------~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~  610 (758)
T 1r6b_X          563 LDEIEKAHPD--------------VFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVR  610 (758)
T ss_dssp             EETGGGSCHH--------------HHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC
T ss_pred             EeCccccCHH--------------HHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchh
Confidence            9999999887              99999999998777654432222348999999998653

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.59  E-value=8.7e-15  Score=142.54  Aligned_cols=149  Identities=26%  Similarity=0.406  Sum_probs=102.4

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +++ |+|++.+++.|...+......   ..                ....+.....++||+||||||||++|+++|+.++
T Consensus        20 ~~~-i~G~~~~~~~l~~~i~~~~~~---~~----------------~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~   79 (297)
T 3b9p_A           20 WTD-IAGQDVAKQALQEMVILPSVR---PE----------------LFTGLRAPAKGLLLFGPPGNGKTLLARAVATECS   79 (297)
T ss_dssp             GGG-SCCCHHHHHHHHHHTHHHHHC---GG----------------GSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTT
T ss_pred             HHH-hCChHHHHHHHHHHHHhhhhC---HH----------------HHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhC
Confidence            444 899999999999888532210   00                0111223457899999999999999999999999


Q ss_pred             CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          351 VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       351 ~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .+|+.+++.++.. .+.+.. +..++.+|..+..    ..++||||||||.+...+....   ......+++.|+..|++
T Consensus        80 ~~~~~i~~~~l~~-~~~~~~-~~~~~~~~~~~~~----~~~~vl~iDEid~l~~~~~~~~---~~~~~~~~~~ll~~l~~  150 (297)
T 3b9p_A           80 ATFLNISAASLTS-KYVGDG-EKLVRALFAVARH----MQPSIIFIDEVDSLLSERSSSE---HEASRRLKTEFLVEFDG  150 (297)
T ss_dssp             CEEEEEESTTTSS-SSCSCH-HHHHHHHHHHHHH----TCSEEEEEETGGGTSBCC--------CCSHHHHHHHHHHHHH
T ss_pred             CCeEEeeHHHHhh-cccchH-HHHHHHHHHHHHH----cCCcEEEeccHHHhccccccCc---chHHHHHHHHHHHHHhc
Confidence            9999999998874 466654 6677777765543    3789999999999988754321   22334578899999985


Q ss_pred             ceeeeecceeeecCCeEEEecCCC
Q 012525          431 TETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       431 ~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      .....      .....++|+|+|.
T Consensus       151 ~~~~~------~~~~v~vi~~tn~  168 (297)
T 3b9p_A          151 LPGNP------DGDRIVVLAATNR  168 (297)
T ss_dssp             CC------------CEEEEEEESC
T ss_pred             ccccC------CCCcEEEEeecCC
Confidence            43221      0124677787775

>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=99.58  E-value=4.3e-15  Score=155.16  Aligned_cols=149  Identities=23%  Similarity=0.369  Sum_probs=100.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++.+|+.|..++..+...   ..                ........+++|||+||||||||+||++||+++
T Consensus       132 ~~~d-i~G~~~~k~~l~~~v~~p~~~---~~----------------~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~  191 (444)
T 2zan_A          132 KWSD-VAGLEGAKEALKEAVILPIKF---PH----------------LFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA  191 (444)
T ss_dssp             CGGG-SCSCHHHHHHHHHHHTHHHHC---TT----------------TTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             CHHH-hcCHHHHHHHHHHHHHHHhhC---HH----------------HhhccCCCCceEEEECCCCCCHHHHHHHHHHHc
Confidence            3455 899999999999988532210   00                000111235789999999999999999999999


Q ss_pred             -CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          350 -NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       350 -~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                       +.+|+.+++.++.. .|+|+. +..++.+|..+..    ..++||||||||.+...+...   .......+++.||..|
T Consensus       192 ~~~~~~~v~~~~l~~-~~~g~~-~~~~~~~f~~a~~----~~~~vl~iDEid~l~~~~~~~---~~~~~~~~~~~lL~~l  262 (444)
T 2zan_A          192 NNSTFFSISSSDLVS-KWLGES-EKLVKNLFQLARE----NKPSIIFIDEIDSLCGSRSEN---ESEAARRIKTEFLVQM  262 (444)
T ss_dssp             CSSEEEEECCC----------C-CCTHHHHHHHHHH----SCSEEEEESCTTTTCCCSSCC---CCGGGHHHHHHHHTTT
T ss_pred             CCCCEEEEeHHHHHh-hhcchH-HHHHHHHHHHHHH----cCCeEEEEechHhhccCCCCc---cccHHHHHHHHHHHHH
Confidence             88999999998874 477765 5667777765543    378999999999998875432   2223456889999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ++....        ..+.++|+|+|..
T Consensus       263 ~~~~~~--------~~~v~vI~atn~~  281 (444)
T 2zan_A          263 QGVGVD--------NDGILVLGATNIP  281 (444)
T ss_dssp             TCSSCC--------CSSCEEEEEESCG
T ss_pred             hCcccC--------CCCEEEEecCCCc
Confidence            864311        1257888888854

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.58  E-value=1.4e-14  Score=138.68  Aligned_cols=151  Identities=24%  Similarity=0.335  Sum_probs=103.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++.+|+.|...+..    +.+.....               ......+.++||+||||||||++|++||+.+
T Consensus        10 ~~~~-i~G~~~~~~~l~~~~~~----~~~~~~~~---------------~~~~~~~~~vll~G~~GtGKT~la~~la~~~   69 (257)
T 1lv7_A           10 TFAD-VAGCDEAKEEVAELVEY----LREPSRFQ---------------KLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA   69 (257)
T ss_dssp             CGGG-SCSCHHHHHHTHHHHHH----HHCGGGC--------------------CCCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CHHH-hcCcHHHHHHHHHHHHH----HhCHHHHH---------------HcCCCCCCeEEEECcCCCCHHHHHHHHHHHc
Confidence            3455 89999999999887631    11110000               0001224679999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+|+.+++.++.. .+.+.. +..+..+|..+..    ..++||||||||.+...+.............+++.|+..|+
T Consensus        70 ~~~~~~i~~~~~~~-~~~~~~-~~~~~~~~~~a~~----~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~  143 (257)
T 1lv7_A           70 KVPFFTISGSDFVE-MFVGVG-ASRVRDMFEQAKK----AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMD  143 (257)
T ss_dssp             TCCEEEECSCSSTT-SCCCCC-HHHHHHHHHHHHT----TCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeHHHHHH-Hhhhhh-HHHHHHHHHHHHH----cCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhh
Confidence            99999999998874 466766 5667777776543    25789999999999876543221222223357888898888


Q ss_pred             CceeeeecceeeecCCeEEEecCCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +...         ..+.++|+|+|..
T Consensus       144 ~~~~---------~~~~~vI~~tn~~  160 (257)
T 1lv7_A          144 GFEG---------NEGIIVIAATNRP  160 (257)
T ss_dssp             TCCS---------SSCEEEEEEESCT
T ss_pred             Cccc---------CCCEEEEEeeCCc
Confidence            5421         1257888888754

>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=99.58  E-value=5.9e-15  Score=156.16  Aligned_cols=151  Identities=26%  Similarity=0.349  Sum_probs=104.3

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++++|+.|.+.+.. ++. .......+                 ...+.+|||+||||||||+||++||.++
T Consensus        14 ~f~d-i~G~~~~~~~l~e~v~~-l~~-~~~~~~~g-----------------~~~p~gvLL~GppGtGKT~Laraia~~~   73 (476)
T 2ce7_A           14 TFKD-VGGAEEAIEELKEVVEF-LKD-PSKFNRIG-----------------ARMPKGILLVGPPGTGKTLLARAVAGEA   73 (476)
T ss_dssp             CGGG-CCSCHHHHHHHHHHHHH-HHC-THHHHTTT-----------------CCCCSEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CHHH-hCCcHHHHHHHHHHHHH-hhC-hHHHhhcC-----------------CCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            3455 89999999999988742 110 00000000                 1224679999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+|+.++++++.. .++|.. +..++.+|..+...    .++||||||||.+..+|.....+.+.....+++.||..|+
T Consensus        74 ~~~f~~is~~~~~~-~~~g~~-~~~~r~lf~~A~~~----~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld  147 (476)
T 2ce7_A           74 NVPFFHISGSDFVE-LFVGVG-AARVRDLFAQAKAH----APCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMD  147 (476)
T ss_dssp             TCCEEEEEGGGTTT-CCTTHH-HHHHHHHHHHHHHT----CSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHH
T ss_pred             CCCeeeCCHHHHHH-HHhccc-HHHHHHHHHHHHhc----CCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHh
Confidence            99999999998885 477765 56777888776543    6899999999999987654333334445568899999998


Q ss_pred             CceeeeecceeeecCCeEEEecCCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +...         ..+.++|+|+|..
T Consensus       148 ~~~~---------~~~viVIaaTn~~  164 (476)
T 2ce7_A          148 GFDS---------KEGIIVMAATNRP  164 (476)
T ss_dssp             HSCG---------GGTEEEEEEESCG
T ss_pred             ccCC---------CCCEEEEEecCCh
Confidence            5321         1257888888864

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.57  E-value=1.8e-14  Score=140.55  Aligned_cols=151  Identities=23%  Similarity=0.281  Sum_probs=103.8

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      ...++...|++.|+|++.+|+.|...+.....  .......+.              .......++||+||||||||++|
T Consensus        21 ~~~~~~~~l~~~i~G~~~~~~~l~~~~~~~~~--~~~~~~~g~--------------~~~~~~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           21 GAKEVLEELDRELIGLKPVKDRIRETAALLLV--ERARQKLGL--------------AHETPTLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             THHHHHHHHHHHSSSCHHHHHHHHHHHHHHHH--HHHHHHHTC--------------CSSCCCCEEEEEECTTSSHHHHH
T ss_pred             cHHHHHHHHHHHccChHHHHHHHHHHHHHHHh--HHHHHHcCC--------------CCCCCCceEEEECCCCCCHHHHH
Confidence            45678889997799999999999988753321  111111110              00122468999999999999999


Q ss_pred             HHHHHhcC-------CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccccccc
Q 012525          343 KTLARHVN-------VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDV  415 (461)
Q Consensus       343 raLA~~l~-------~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~  415 (461)
                      +++|+.+.       .+++.+++.++.. .++|.. ...+..+|..+       .++||||||||.|...+..     ..
T Consensus        85 ~~la~~l~~~~~~~~~~~~~~~~~~l~~-~~~g~~-~~~~~~~~~~~-------~~~vl~iDEid~l~~~~~~-----~~  150 (309)
T 3syl_A           85 LKMAGLLHRLGYVRKGHLVSVTRDDLVG-QYIGHT-APKTKEVLKRA-------MGGVLFIDEAYYLYRPDNE-----RD  150 (309)
T ss_dssp             HHHHHHHHHTTSSSSCCEEEECGGGTCC-SSTTCH-HHHHHHHHHHH-------TTSEEEEETGGGSCCCC--------C
T ss_pred             HHHHHHHHhcCCcCCCcEEEEcHHHhhh-hccccc-HHHHHHHHHhc-------CCCEEEEEChhhhccCCCc-----cc
Confidence            99999883       3899999998874 466665 45556666544       4679999999999755321     12


Q ss_pred             chHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          416 SGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       416 s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ....+++.|++.|+...           .+.++|+|+|.
T Consensus       151 ~~~~~~~~Ll~~l~~~~-----------~~~~~i~~~~~  178 (309)
T 3syl_A          151 YGQEAIEILLQVMENNR-----------DDLVVILAGYA  178 (309)
T ss_dssp             CTHHHHHHHHHHHHHCT-----------TTCEEEEEECH
T ss_pred             ccHHHHHHHHHHHhcCC-----------CCEEEEEeCCh
Confidence            23458999999999432           24566666653

>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=99.57  E-value=1.1e-14  Score=138.32  Aligned_cols=147  Identities=25%  Similarity=0.319  Sum_probs=89.9

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |+|++.+|+.|...+..    +.....               +.......+.++||+||||||||++|+++|+.++.+|+
T Consensus         8 i~G~~~~~~~l~~~~~~----~~~~~~---------------~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~   68 (262)
T 2qz4_A            8 VAGMHEAKLEVREFVDY----LKSPER---------------FLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFL   68 (262)
T ss_dssp             SCSCHHHHHHHHHHHHH----HHCCC---------------------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEE
T ss_pred             hCCHHHHHHHHHHHHHH----HHCHHH---------------HHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            89999999999887742    110000               00001123578999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc-cccchHHHHHHHHHHHhCcee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS-RDVSGEGVQQALLKMLEGTET  433 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~-~~~s~~~v~~aLL~~LEg~~v  433 (461)
                      .+++.++.. .+.+.. +..+..+|..+..    ..++||||||||.+..++...... ........++.|+..|++...
T Consensus        69 ~~~~~~~~~-~~~~~~-~~~~~~~~~~a~~----~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~  142 (262)
T 2qz4_A           69 AMAGAEFVE-VIGGLG-AARVRSLFKEARA----RAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGT  142 (262)
T ss_dssp             EEETTTTSS-SSTTHH-HHHHHHHHHHHHH----TCSEEEEEECC-------------------CHHHHHHHHHHHTCCT
T ss_pred             EechHHHHh-hccChh-HHHHHHHHHHHHh----cCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCC
Confidence            999998874 355544 5667777766543    257899999999998765432111 011122356677777774321


Q ss_pred             eeecceeeecCCeEEEecCCCC
Q 012525          434 KTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       434 ~i~~~~r~~~rd~IiI~TsNid  455 (461)
                               ....++|+|+|..
T Consensus       143 ---------~~~~~vi~~tn~~  155 (262)
T 2qz4_A          143 ---------TDHVIVLASTNRA  155 (262)
T ss_dssp             ---------TCCEEEEEEESCG
T ss_pred             ---------CCCEEEEecCCCh
Confidence                     1257888888754

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.56  E-value=8.6e-15  Score=142.81  Aligned_cols=148  Identities=27%  Similarity=0.346  Sum_probs=101.5

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHH
Q 012525          265 KEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       265 ~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAra  344 (461)
                      .++.+.|.+.++||+.+++.|...+......+.     .                 ......++||+||||||||++|++
T Consensus         9 ~~l~~~l~~~i~G~~~~~~~l~~~i~~~~~~~~-----~-----------------~~~~~~~~ll~G~~GtGKt~la~~   66 (311)
T 4fcw_A            9 LRLEEELHKRVVGQDEAIRAVADAIRRARAGLK-----D-----------------PNRPIGSFLFLGPTGVGKTELAKT   66 (311)
T ss_dssp             HTHHHHHHTTCCSCHHHHHHHHHHHHHHHHTCS-----C-----------------TTSCSEEEEEESCSSSSHHHHHHH
T ss_pred             HHHHHHHhhhcCCHHHHHHHHHHHHHHHhcCCC-----C-----------------CCCCceEEEEECCCCcCHHHHHHH
Confidence            457888888899999999999998853221100     0                 001225799999999999999999


Q ss_pred             HHHhc---CCceEEecchhhhhcC-----------cccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccc
Q 012525          345 LARHV---NVPFVIADATTLTQAG-----------YVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLN  410 (461)
Q Consensus       345 LA~~l---~~pfv~i~~s~l~~~g-----------~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~  410 (461)
                      ||+.+   +.+|+.+++..+....           +.+......+...       +..+.++||||||||++...     
T Consensus        67 la~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~-------~~~~~~~vl~lDEi~~l~~~-----  134 (311)
T 4fcw_A           67 LAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEA-------VRRRPYSVILFDAIEKAHPD-----  134 (311)
T ss_dssp             HHHHHHSCGGGEEEEEGGGCCSTTHHHHHHCCCTTSTTTTTCCHHHHH-------HHHCSSEEEEEETGGGSCHH-----
T ss_pred             HHHHHcCCCcceEEeecccccccccHHHhcCCCCccccccccchHHHH-------HHhCCCeEEEEeChhhcCHH-----
Confidence            99988   4579999988765321           1111100112222       22345689999999999887     


Q ss_pred             cccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          411 ISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       411 ~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                               +++.|+++|+...+..........++.++|+|+|.+
T Consensus       135 ---------~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~  170 (311)
T 4fcw_A          135 ---------VFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLG  170 (311)
T ss_dssp             ---------HHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTT
T ss_pred             ---------HHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccC
Confidence                     899999999977765332222223378899999983

>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=99.55  E-value=8.8e-15  Score=155.17  Aligned_cols=143  Identities=25%  Similarity=0.389  Sum_probs=107.3

Q ss_pred             cCChHHHHHHHHHHHHHH--HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          275 VIGQEKAKKVLSVAVYNH--YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~--~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      |+|++.+++.|.+.+...  +..++...   +                 ...+.+|||+||||||||++|++||+.++.+
T Consensus       206 i~G~~~~~~~l~~~i~~~l~~~~~~~~~---g-----------------~~~~~~vLL~GppGtGKT~lAraia~~~~~~  265 (489)
T 3hu3_A          206 IGGCRKQLAQIKEMVELPLRHPALFKAI---G-----------------VKPPRGILLYGPPGTGKTLIARAVANETGAF  265 (489)
T ss_dssp             CCSCHHHHHHHHHHTHHHHHCHHHHHHH---T-----------------CCCCCEEEEECSTTSSHHHHHHHHHHHCSSE
T ss_pred             cCCHHHHHHHHHHHHHHHhhCHHHHHhc---C-----------------CCCCCcEEEECcCCCCHHHHHHHHHHHhCCC
Confidence            899999999999988532  11222111   0                 1235789999999999999999999999999


Q ss_pred             eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCce
Q 012525          353 FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       353 fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      |+.+++.++.. .+.|+. +..++.+|..+...    .++||||||||.|..+++..   .......+++.||..|++..
T Consensus       266 fv~vn~~~l~~-~~~g~~-~~~~~~~f~~A~~~----~p~iLfLDEId~l~~~~~~~---~~~~~~~~~~~LL~~ld~~~  336 (489)
T 3hu3_A          266 FFLINGPEIMS-KLAGES-ESNLRKAFEEAEKN----APAIIFIDELDAIAPKREKT---HGEVERRIVSQLLTLMDGLK  336 (489)
T ss_dssp             EEEEEHHHHHT-SCTTHH-HHHHHHHHHHHHHT----CSEEEEEESHHHHCBCTTSC---CCHHHHHHHHHHHHHHHHSC
T ss_pred             EEEEEchHhhh-hhcchh-HHHHHHHHHHHHhc----CCcEEEecchhhhccccccc---cchHHHHHHHHHHHHhhccc
Confidence            99999999884 577766 67778888776543    67899999999999875432   12233468999999999432


Q ss_pred             eeeecceeeecCCeEEEecCCCC
Q 012525          433 TKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       433 v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      .         ..+.++|+|+|..
T Consensus       337 ~---------~~~v~vIaaTn~~  350 (489)
T 3hu3_A          337 Q---------RAHVIVMAATNRP  350 (489)
T ss_dssp             T---------TSCEEEEEEESCG
T ss_pred             c---------CCceEEEEecCCc
Confidence            1         2268899999865

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.52  E-value=1.4e-14  Score=159.97  Aligned_cols=162  Identities=23%  Similarity=0.301  Sum_probs=105.3

Q ss_pred             CCCCCCCCCCCCC----CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccC
Q 012525          250 SRWGGSNLGEDLP----TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEK  325 (461)
Q Consensus       250 ~~w~g~~l~~~l~----t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~  325 (461)
                      ..|++.+......    ....+...|.+.|+||+.+++.|..++.....         +.             .......
T Consensus       464 ~~~~~ip~~~~~~~~~~~l~~l~~~l~~~viGq~~a~~~l~~~i~~~~~---------~~-------------~~~~~p~  521 (758)
T 3pxi_A          464 SSWTGVPVSKIAQTETDKLLNMENILHSRVIGQDEAVVAVAKAVRRARA---------GL-------------KDPKRPI  521 (758)
T ss_dssp             HTTC-------CHHHHSCC-CHHHHHHTTSCSCHHHHHHHHHHHHHHTT---------TC-------------SCTTSCS
T ss_pred             HHHhCCChHHhhHHHHHHHHHHHHHHhCcCcChHHHHHHHHHHHHHHHc---------cc-------------CCCCCCc
Confidence            4555554443221    12246778888899999999999888842110         00             0000112


Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      .++||+||||||||++|++||+.+   +.+|+.++++++... +...  ...+...+       ....++|||||||+++
T Consensus       522 ~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~-~~~~--~~~l~~~~-------~~~~~~vl~lDEi~~~  591 (758)
T 3pxi_A          522 GSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEK-HSTS--GGQLTEKV-------RRKPYSVVLLDAIEKA  591 (758)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSS-CCCC-----CHHHH-------HHCSSSEEEEECGGGS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhcccc-cccc--cchhhHHH-------HhCCCeEEEEeCcccc
Confidence            379999999999999999999987   679999999988854 2222  12222222       2235679999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ...              +++.|+++||++.+...........++++|+|||.+..
T Consensus       592 ~~~--------------~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~  632 (758)
T 3pxi_A          592 HPD--------------VFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGAS  632 (758)
T ss_dssp             CHH--------------HHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTT
T ss_pred             CHH--------------HHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChh
Confidence            887              99999999998776654443333448999999997553

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.50  E-value=8.2e-15  Score=129.70  Aligned_cols=113  Identities=20%  Similarity=0.226  Sum_probs=82.3

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---CC
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NV  351 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~  351 (461)
                      ++|++.+.+.+...+..                             ++....+|||+||||||||++|++|++..   +.
T Consensus         3 iiG~s~~~~~~~~~~~~-----------------------------~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~   53 (145)
T 3n70_A            3 LIGRSEWINQYRRRLQQ-----------------------------LSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQG   53 (145)
T ss_dssp             -CCSSHHHHHHHHHHHH-----------------------------HTTCCSCEEEESSTTSSHHHHHHHHHHSSTTTTS
T ss_pred             ceeCCHHHHHHHHHHHH-----------------------------HhCCCCCEEEECCCCCCHHHHHHHHHHhCCccCC
Confidence            67888877777766631                             11234789999999999999999999987   67


Q ss_pred             ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          352 PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       352 pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      +|+ +++..+...        .....++.       .+++++|||||||.+...              .|..|+.+|+..
T Consensus        54 ~~v-~~~~~~~~~--------~~~~~~~~-------~a~~g~l~ldei~~l~~~--------------~q~~Ll~~l~~~  103 (145)
T 3n70_A           54 EFV-YRELTPDNA--------PQLNDFIA-------LAQGGTLVLSHPEHLTRE--------------QQYHLVQLQSQE  103 (145)
T ss_dssp             CCE-EEECCTTTS--------SCHHHHHH-------HHTTSCEEEECGGGSCHH--------------HHHHHHHHHHSS
T ss_pred             CEE-EECCCCCcc--------hhhhcHHH-------HcCCcEEEEcChHHCCHH--------------HHHHHHHHHhhc
Confidence            999 999887643        11222332       235689999999999887              899999999422


Q ss_pred             eeeeecceeeecCCeEEEecCCCCcC
Q 012525          432 ETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       432 ~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                                 ..+..+|+|+|.+.+
T Consensus       104 -----------~~~~~~I~~t~~~~~  118 (145)
T 3n70_A          104 -----------HRPFRLIGIGDTSLV  118 (145)
T ss_dssp             -----------SCSSCEEEEESSCHH
T ss_pred             -----------CCCEEEEEECCcCHH
Confidence                       224678888887653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.49  E-value=1e-14  Score=129.00  Aligned_cols=114  Identities=18%  Similarity=0.285  Sum_probs=85.3

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ++|++.+.+.+...+...                             .....+|||+||||||||++|++|++... +|+
T Consensus         6 ~iG~s~~~~~l~~~~~~~-----------------------------~~~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~   55 (143)
T 3co5_A            6 KLGNSAAIQEMNREVEAA-----------------------------AKRTSPVFLTGEAGSPFETVARYFHKNGT-PWV   55 (143)
T ss_dssp             --CCCHHHHHHHHHHHHH-----------------------------HTCSSCEEEEEETTCCHHHHHGGGCCTTS-CEE
T ss_pred             ceeCCHHHHHHHHHHHHH-----------------------------hCCCCcEEEECCCCccHHHHHHHHHHhCC-CeE
Confidence            789988888877776311                             12246899999999999999999999888 999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK  434 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~  434 (461)
                      .+++..+... +        ...++..       +++++|||||||.+...              .+..|+++|+...  
T Consensus        56 ~~~~~~~~~~-~--------~~~~~~~-------a~~~~l~lDei~~l~~~--------------~q~~Ll~~l~~~~--  103 (143)
T 3co5_A           56 SPARVEYLID-M--------PMELLQK-------AEGGVLYVGDIAQYSRN--------------IQTGITFIIGKAE--  103 (143)
T ss_dssp             CCSSTTHHHH-C--------HHHHHHH-------TTTSEEEEEECTTCCHH--------------HHHHHHHHHHHHT--
T ss_pred             EechhhCChH-h--------hhhHHHh-------CCCCeEEEeChHHCCHH--------------HHHHHHHHHHhCC--
Confidence            9999887642 1        2333332       35689999999999887              8899999998542  


Q ss_pred             eecceeeecCCeEEEecCCCCcCc
Q 012525          435 TFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       435 i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                              ..+..+|+|+|.+...
T Consensus       104 --------~~~~~iI~~tn~~~~~  119 (143)
T 3co5_A          104 --------RCRVRVIASCSYAAGS  119 (143)
T ss_dssp             --------TTTCEEEEEEEECTTT
T ss_pred             --------CCCEEEEEecCCCHHH
Confidence                    2357888888877544

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.48  E-value=2.1e-13  Score=133.74  Aligned_cols=146  Identities=25%  Similarity=0.426  Sum_probs=96.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHH--HHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKR--IYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kr--i~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|++ |.|.+++|+.|.+.+...+..  ++...   +                + ..+.+++|+|||||||||||++||.
T Consensus         8 ~~~d-i~g~~~~~~~l~~~i~~~~~~~~~l~~~---~----------------l-~~~~GvlL~Gp~GtGKTtLakala~   66 (274)
T 2x8a_A            8 TWAD-IGALEDIREELTMAILAPVRNPDQFKAL---G----------------L-VTPAGVLLAGPPGCGKTLLAKAVAN   66 (274)
T ss_dssp             -----CCHHHHHHHHHHHHHTHHHHSHHHHHHT---T----------------C-CCCSEEEEESSTTSCHHHHHHHHHH
T ss_pred             CHHH-hCCHHHHHHHHHHHHHHHhhCHHHHHHc---C----------------C-CCCCeEEEECCCCCcHHHHHHHHHH
Confidence            4555 899999999999887544332  11110   0                0 1135699999999999999999999


Q ss_pred             hcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          348 HVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       348 ~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      .++.+++.++..++.. .+.++. +..+..+|..+...    .++++|+||||.+...+.....   .....+.+.++..
T Consensus        67 ~~~~~~i~i~g~~l~~-~~~~~~-~~~i~~vf~~a~~~----~p~i~~~Deid~~~~~r~~~~~---~~~~~~~~~~l~~  137 (274)
T 2x8a_A           67 ESGLNFISVKGPELLN-MYVGES-ERAVRQVFQRAKNS----APCVIFFDEVDALCPRRSDRET---GASVRVVNQLLTE  137 (274)
T ss_dssp             HTTCEEEEEETTTTCS-STTHHH-HHHHHHHHHHHHHT----CSEEEEEETCTTTCC------------CTTHHHHHHHH
T ss_pred             HcCCCEEEEEcHHHHh-hhhhHH-HHHHHHHHHHHHhc----CCCeEeeehhhhhhcccCCCcc---hHHHHHHHHHHHh
Confidence            9999999999988874 355554 56777788765332    5789999999998766432211   1122478899999


Q ss_pred             HhCceeeeecceeeecCCeEEEecCCC
Q 012525          428 LEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       428 LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      |++.+..         +..++++++|.
T Consensus       138 Lsgg~~~---------~~~i~ia~tn~  155 (274)
T 2x8a_A          138 MDGLEAR---------QQVFIMAATNR  155 (274)
T ss_dssp             HHTCCST---------TCEEEEEEESC
T ss_pred             hhccccc---------CCEEEEeecCC
Confidence            9976422         23456666653

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.46  E-value=2.7e-13  Score=144.21  Aligned_cols=150  Identities=27%  Similarity=0.343  Sum_probs=101.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |++ |+|++++|+.|...+.. +.   .......               .-...+.+|||+||||||||+||++||..++
T Consensus        30 f~d-v~G~~~~k~~l~~lv~~-l~---~~~~~~~---------------lg~~ip~GvLL~GppGtGKTtLaraIa~~~~   89 (499)
T 2dhr_A           30 FKD-VAGAEEAKEELKEIVEF-LK---NPSRFHE---------------MGARIPKGVLLVGPPGVGKTHLARAVAGEAR   89 (499)
T ss_dssp             TTS-SCSCHHHHHHHHHHHHH-HH---CGGGTTT---------------TSCCCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             HHH-cCCcHHHHHHHHHHHHH-hh---chhhhhh---------------ccCCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            444 89999999999987742 11   1100000               0011246699999999999999999999999


Q ss_pred             CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          351 VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       351 ~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .+|+.+++.++.. .+++.. ...++.+|..+..    ..++|+||||||.+...+...........+..++.|+..|++
T Consensus        90 ~~~i~i~g~~~~~-~~~g~~-~~~v~~lfq~a~~----~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg  163 (499)
T 2dhr_A           90 VPFITASGSDFVE-MFVGVG-AARVRDLFETAKR----HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDG  163 (499)
T ss_dssp             CCEEEEEGGGGTS-SCTTHH-HHHHHHHTTTSSS----SSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGG
T ss_pred             CCEEEEehhHHHH-hhhhhH-HHHHHHHHHHHHh----cCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcc
Confidence            9999999998874 356554 4556677765432    257899999999998765421111122234577888988886


Q ss_pred             ceeeeecceeeecCCeEEEecCCCC
Q 012525          431 TETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       431 ~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      .+.         .+..++|+++|..
T Consensus       164 ~~~---------~~~viviAatn~p  179 (499)
T 2dhr_A          164 FEK---------DTAIVVMAATNRP  179 (499)
T ss_dssp             CCS---------SCCCEEEECCSCG
T ss_pred             ccc---------CccEEEEEecCCh
Confidence            542         1246788888743

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.46  E-value=1.6e-14  Score=143.15  Aligned_cols=137  Identities=26%  Similarity=0.331  Sum_probs=96.4

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHH
Q 012525          265 KEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       265 ~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAra  344 (461)
                      ..+...+.+.|+|++++++.+..++..                                 ..++||+||||||||++|++
T Consensus        19 ~~~~~~~~~~i~g~~~~~~~l~~~l~~---------------------------------~~~vll~G~pGtGKT~la~~   65 (331)
T 2r44_A           19 KEVIDEVGKVVVGQKYMINRLLIGICT---------------------------------GGHILLEGVPGLAKTLSVNT   65 (331)
T ss_dssp             HHHHHHHTTTCCSCHHHHHHHHHHHHH---------------------------------TCCEEEESCCCHHHHHHHHH
T ss_pred             HHHHHHhccceeCcHHHHHHHHHHHHc---------------------------------CCeEEEECCCCCcHHHHHHH
Confidence            346666777799999999888776621                                 26799999999999999999


Q ss_pred             HHHhcCCceEEecch-hhhhcCcccccHHHHHHHHHHhhchh--hhc--cCceEEEEcCccccchhhhccccccccchHH
Q 012525          345 LARHVNVPFVIADAT-TLTQAGYVGEDVESILYKLLAQAEFN--VEA--AQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       345 LA~~l~~pfv~i~~s-~l~~~g~vGe~~e~~L~~lf~~a~~~--v~~--a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      +|+.++.+++.+++. ++....+.|...       +......  +..  -..+||||||||.+..+              
T Consensus        66 la~~~~~~~~~i~~~~~~~~~~l~g~~~-------~~~~~~~~~~~~g~l~~~vl~iDEi~~~~~~--------------  124 (331)
T 2r44_A           66 LAKTMDLDFHRIQFTPDLLPSDLIGTMI-------YNQHKGNFEVKKGPVFSNFILADEVNRSPAK--------------  124 (331)
T ss_dssp             HHHHTTCCEEEEECCTTCCHHHHHEEEE-------EETTTTEEEEEECTTCSSEEEEETGGGSCHH--------------
T ss_pred             HHHHhCCCeEEEecCCCCChhhcCCcee-------ecCCCCceEeccCcccccEEEEEccccCCHH--------------
Confidence            999999999988874 221111111100       0000000  000  02379999999998887              


Q ss_pred             HHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          420 VQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      +++.|++.|+...+.+.......+.++++|+|+|..
T Consensus       125 ~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~  160 (331)
T 2r44_A          125 VQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPV  160 (331)
T ss_dssp             HHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTT
T ss_pred             HHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCC
Confidence            899999999988877754455556689999999944

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.46  E-value=4.3e-13  Score=132.90  Aligned_cols=131  Identities=21%  Similarity=0.342  Sum_probs=92.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ ++|++.+++.|...+.....        .                  .....+|||+||||||||++|+++|+.+
T Consensus        27 ~~~~-iiG~~~~~~~l~~~l~~~~~--------~------------------~~~~~~vll~G~~GtGKT~la~~ia~~~   79 (338)
T 3pfi_A           27 NFDG-YIGQESIKKNLNVFIAAAKK--------R------------------NECLDHILFSGPAGLGKTTLANIISYEM   79 (338)
T ss_dssp             SGGG-CCSCHHHHHHHHHHHHHHHH--------T------------------TSCCCCEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CHHH-hCChHHHHHHHHHHHHHHHh--------c------------------CCCCCeEEEECcCCCCHHHHHHHHHHHh
Confidence            3455 89999999999888742210        0                  0123679999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+|+.+++..+..        ...+...+..      .+++++||||||+.+...              .++.|+..|+
T Consensus        80 ~~~~~~~~~~~~~~--------~~~~~~~~~~------~~~~~vl~lDEi~~l~~~--------------~~~~Ll~~l~  131 (338)
T 3pfi_A           80 SANIKTTAAPMIEK--------SGDLAAILTN------LSEGDILFIDEIHRLSPA--------------IEEVLYPAME  131 (338)
T ss_dssp             TCCEEEEEGGGCCS--------HHHHHHHHHT------CCTTCEEEEETGGGCCHH--------------HHHHHHHHHH
T ss_pred             CCCeEEecchhccc--------hhHHHHHHHh------ccCCCEEEEechhhcCHH--------------HHHHHHHHHH
Confidence            99999999987652        2333444432      247889999999999877              8999999999


Q ss_pred             Cceeeeeccee----e--ecC-CeEEEecCCCC
Q 012525          430 GTETKTFAAVS----K--VSR-DNLYIKTSGLD  455 (461)
Q Consensus       430 g~~v~i~~~~r----~--~~r-d~IiI~TsNid  455 (461)
                      ...+.+.....    .  ... ++++|+++|..
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~  164 (338)
T 3pfi_A          132 DYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRA  164 (338)
T ss_dssp             TSCC---------CCCCCCCCCCCEEEEEESCG
T ss_pred             hccchhhcccCccccceecCCCCeEEEEeCCCc
Confidence            87655432211    1  111 47888888863

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.46  E-value=2.1e-13  Score=152.90  Aligned_cols=164  Identities=28%  Similarity=0.396  Sum_probs=106.0

Q ss_pred             CCCCCCCCCCCCCCCHH----HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhcccccccccc
Q 012525          249 GSRWGGSNLGEDLPTPK----EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELE  324 (461)
Q Consensus       249 ~~~w~g~~l~~~l~t~~----el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~  324 (461)
                      ..+|++.+..+......    .+...+.+.|+||+.+++.|..++.....         +.             ......
T Consensus       530 v~~~~~ip~~~~~~~~~~~l~~l~~~l~~~viG~~~a~~~l~~~i~~~~~---------g~-------------~~~~~p  587 (854)
T 1qvr_A          530 VSRWTGIPVSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARA---------GL-------------KDPNRP  587 (854)
T ss_dssp             HHTTSSCHHHHTTCCHHHHHHSHHHHHHHHSCSCHHHHHHHHHHHHHHGG---------GC-------------SCSSSC
T ss_pred             HHHHhCCChHhhcHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHhc---------cc-------------CCCCCC
Confidence            35566654443333332    24556667799999999999888842100         00             000011


Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc-----------CcccccHHHHHHHHHHhhchhhhccC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA-----------GYVGEDVESILYKLLAQAEFNVEAAQ  390 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~-----------g~vGe~~e~~L~~lf~~a~~~v~~a~  390 (461)
                      ..++||+||||||||++|++||+.+   +.+|+.++++.+...           +|+|......+...+       ....
T Consensus       588 ~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~s~l~g~~~~~~G~~~~g~l~~~~-------~~~~  660 (854)
T 1qvr_A          588 IGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAV-------RRRP  660 (854)
T ss_dssp             SEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC--------------CHHHHH-------HHCS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHHHHHcCCCCCCcCccccchHHHHH-------HhCC
Confidence            2479999999999999999999998   779999999876542           122322112222222       2235


Q ss_pred             ceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          391 QGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       391 ~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ++|||||||+++...              +++.|+++||.+.+..........++.++|+|||.+
T Consensus       661 ~~vl~lDEi~~l~~~--------------~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~  711 (854)
T 1qvr_A          661 YSVILFDEIEKAHPD--------------VFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLG  711 (854)
T ss_dssp             SEEEEESSGGGSCHH--------------HHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTT
T ss_pred             CeEEEEecccccCHH--------------HHHHHHHHhccCceECCCCCEeccCCeEEEEecCcC
Confidence            689999999999887              999999999987765322222222478999999984

>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=99.45  E-value=9.4e-14  Score=133.48  Aligned_cols=142  Identities=20%  Similarity=0.281  Sum_probs=89.7

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ ++|++.+.+.+...+...                             .....+|||+||||||||++|++|++.+
T Consensus         4 ~f~~-~ig~~~~~~~~~~~~~~~-----------------------------~~~~~~vll~G~~GtGKt~la~~i~~~~   53 (265)
T 2bjv_A            4 YKDN-LLGEANSFLEVLEQVSHL-----------------------------APLDKPVLIIGERGTGKELIASRLHYLS   53 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHH-----------------------------TTSCSCEEEECCTTSCHHHHHHHHHHTS
T ss_pred             cccc-ceeCCHHHHHHHHHHHHH-----------------------------hCCCCCEEEECCCCCcHHHHHHHHHHhc
Confidence            3555 689988888777666310                             0123689999999999999999999987


Q ss_pred             C---CceEEecchhhhhc----CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          350 N---VPFVIADATTLTQA----GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       350 ~---~pfv~i~~s~l~~~----g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                      .   .+|+.++|+.+...    .+.|.. ...+........+.+..+.+++||||||+.+...              +++
T Consensus        54 ~~~~~~~~~v~~~~~~~~~~~~~l~g~~-~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~~--------------~q~  118 (265)
T 2bjv_A           54 SRWQGPFISLNCAALNENLLDSELFGHE-AGAFTGAQKRHPGRFERADGGTLFLDELATAPMM--------------VQE  118 (265)
T ss_dssp             TTTTSCEEEEEGGGSCHHHHHHHHHCCC----------CCCCHHHHTTTSEEEEESGGGSCHH--------------HHH
T ss_pred             CccCCCeEEEecCCCChhHHHHHhcCCc-ccccccccccccchhhhcCCcEEEEechHhcCHH--------------HHH
Confidence            5   68999999876421    001110 0000001111122344457889999999999887              899


Q ss_pred             HHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          423 ALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       423 aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      .|+.+|+...+...........++.+|+|+|.++
T Consensus       119 ~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~  152 (265)
T 2bjv_A          119 KLLRVIEYGELERVGGSQPLQVNVRLVCATNADL  152 (265)
T ss_dssp             HHHHHHHHCEECCCCC--CEECCCEEEEEESSCH
T ss_pred             HHHHHHHhCCeecCCCcccccCCeEEEEecCcCH
Confidence            9999999766543333333344788999999864

>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=99.44  E-value=8.9e-15  Score=140.43  Aligned_cols=147  Identities=28%  Similarity=0.408  Sum_probs=92.3

Q ss_pred             cCChHHHHHHHHHHHHHH-HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          275 VIGQEKAKKVLSVAVYNH-YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~-~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      |+|++.+++.|...+... +...+...   +                 ...+.++||+||||||||++|++||+.++.+|
T Consensus        13 i~G~~~~~~~l~~~~~~~~~~~~~~~~---~-----------------~~~~~~vll~G~~GtGKT~la~~la~~~~~~~   72 (268)
T 2r62_A           13 MAGNEEAKEEVVEIVDFLKYPERYANL---G-----------------AKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPF   72 (268)
T ss_dssp             SSSCTTTHHHHHHHHHHHHCHHHHHHH---S-----------------CCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCC
T ss_pred             hCCcHHHHHHHHHHHHHHHChHHHHHC---C-----------------CCCCceEEEECCCCCcHHHHHHHHHHHhCCCE
Confidence            899999999998876421 01111100   0                 11246799999999999999999999999999


Q ss_pred             EEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccc-ccccchHHHHHHHHHHHhCce
Q 012525          354 VIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI-SRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       354 v~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~-~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      +.+++.++.. .+.+.. +..++.+|..+..    ..++||||||||.|...+..... ..+.....+++.|+..|++..
T Consensus        73 ~~v~~~~~~~-~~~~~~-~~~~~~~~~~a~~----~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~  146 (268)
T 2r62_A           73 FSMGGSSFIE-MFVGLG-ASRVRDLFETAKK----QAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFG  146 (268)
T ss_dssp             CCCCSCTTTT-SCSSSC-SSSSSTTHHHHHH----SCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSS
T ss_pred             EEechHHHHH-hhcchH-HHHHHHHHHHHHh----cCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcc
Confidence            9999988774 355544 2333444544332    25789999999999887532211 111111225677787777432


Q ss_pred             eeeecceeeecCCeEEEecCCCC
Q 012525          433 TKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       433 v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      .        ...+.++|+|+|..
T Consensus       147 ~--------~~~~v~vi~ttn~~  161 (268)
T 2r62_A          147 S--------ENAPVIVLAATNRP  161 (268)
T ss_dssp             C--------SCSCCEEEECBSCC
T ss_pred             c--------CCCCEEEEEecCCc
Confidence            1        11257888888865

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.43  E-value=1.5e-13  Score=136.65  Aligned_cols=132  Identities=25%  Similarity=0.378  Sum_probs=94.6

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---C
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---N  350 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~  350 (461)
                      .++|++.+.+.+...+..                             ++....+|||+||||||||++|++|++..   +
T Consensus         3 ~iig~s~~~~~~~~~~~~-----------------------------~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~   53 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAM-----------------------------VAPSDATVLIHGDSGTGKELVARALHACSARSD   53 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHH-----------------------------HCSTTSCEEEESCTTSCHHHHHHHHHHHSSCSS
T ss_pred             CcEECCHHHHHHHHHHHH-----------------------------HhCCCCcEEEECCCCchHHHHHHHHHHhCcccC
Confidence            478888887777666631                             11234789999999999999999999965   5


Q ss_pred             CceEEecchhhhhcCcccccHHHHHHHHHH-----------hhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          351 VPFVIADATTLTQAGYVGEDVESILYKLLA-----------QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       351 ~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~-----------~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      .+|+.++|..+...     ..+   ..+|.           ...+.+..+++++||||||+.|...              
T Consensus        54 ~~~v~v~~~~~~~~-----l~~---~~lfg~~~g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~~~--------------  111 (304)
T 1ojl_A           54 RPLVTLNCAALNES-----LLE---SELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPL--------------  111 (304)
T ss_dssp             SCCCEEECSSCCHH-----HHH---HHHTCCCSSCCC---CCCCCHHHHHTTSEEEEESCTTCCHH--------------
T ss_pred             CCeEEEeCCCCChH-----HHH---HHhcCccccccCchhhhhcCHHHhcCCCEEEEeccccCCHH--------------
Confidence            78999999876531     001   11111           1122344457789999999999887              


Q ss_pred             HHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          420 VQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      +|..|+.+|+...+...........++.+|+|+|.++
T Consensus       112 ~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l  148 (304)
T 1ojl_A          112 MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDL  148 (304)
T ss_dssp             HHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCH
T ss_pred             HHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccH
Confidence            8999999999877654444444455889999999874

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.41  E-value=7.3e-13  Score=140.93  Aligned_cols=142  Identities=19%  Similarity=0.258  Sum_probs=91.4

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHH
Q 012525          265 KEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       265 ~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAra  344 (461)
                      ..+...+.+.|+|++.+++.+..++.                                 ...+|||+||||||||+||++
T Consensus        14 ~~l~~~l~~~ivGq~~~i~~l~~al~---------------------------------~~~~VLL~GpPGtGKT~LAra   60 (500)
T 3nbx_X           14 SRLSSSLEKGLYERSHAIRLCLLAAL---------------------------------SGESVFLLGPPGIAKSLIARR   60 (500)
T ss_dssp             HHHHHHHHTTCSSCHHHHHHHHHHHH---------------------------------HTCEEEEECCSSSSHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHh---------------------------------cCCeeEeecCchHHHHHHHHH
Confidence            45778888889999999988877662                                 136899999999999999999


Q ss_pred             HHHhcCC--ceEEecchhhhhcCcccc-cHHHHH-HHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          345 LARHVNV--PFVIADATTLTQAGYVGE-DVESIL-YKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       345 LA~~l~~--pfv~i~~s~l~~~g~vGe-~~e~~L-~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      ||+.+..  +|..+.+.......++|. ...... ...+....... ....+|||||||+++.++              +
T Consensus        61 La~~l~~~~~f~~~~~~~~t~~dL~G~~~~~~~~~~g~~~~~~~g~-l~~~~IL~IDEI~r~~~~--------------~  125 (500)
T 3nbx_X           61 LKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYERLTSGY-LPEAEIVFLDEIWKAGPA--------------I  125 (500)
T ss_dssp             GGGGBSSCCEEEEECCTTCCHHHHHCCBC----------CBCCTTS-GGGCSEEEEESGGGCCHH--------------H
T ss_pred             HHHHHhhhhHHHHHHHhcCCHHHhcCcccHHHHhhchhHHhhhccC-CCcceeeeHHhHhhhcHH--------------H
Confidence            9998843  555555532111112221 111100 11121111100 013569999999998887              8


Q ss_pred             HHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          421 QQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +++|+.+|+++.+.+.......+..+++++|.++
T Consensus       126 q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~l  159 (500)
T 3nbx_X          126 LNTLLTAINERQFRNGAHVEKIPMRLLVAASNEL  159 (500)
T ss_dssp             HHHHHHHHHSSEEECSSSEEECCCCEEEEEESSC
T ss_pred             HHHHHHHHHHHhccCCCCcCCcchhhhhhccccC
Confidence            9999999999888775445555556645555433

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.40  E-value=4e-14  Score=153.34  Aligned_cols=153  Identities=18%  Similarity=0.209  Sum_probs=99.5

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHH
Q 012525          264 PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       264 ~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAr  343 (461)
                      ...+...+...|+|++.+|+.|..++.            .+  .....   . .  .-.....||||+||||||||+||+
T Consensus       286 ~~~l~~~l~~~I~G~e~vk~al~~~l~------------~g--~~~~~---~-~--~~~r~~~~vLL~GppGtGKT~LAr  345 (595)
T 3f9v_A          286 RDRIISSIAPSIYGHWELKEALALALF------------GG--VPKVL---E-D--TRIRGDIHILIIGDPGTAKSQMLQ  345 (595)
T ss_dssp             GGTHHHHTSSTTSCCHHHHHHHTTTTT------------CC--CCEET---T-T--TEECCSCCEEEEESSCCTHHHHHH
T ss_pred             HHHHHHhhcchhcChHHHHHHHHHHHh------------CC--Ccccc---c-C--CCcCCCcceEEECCCchHHHHHHH
Confidence            345777888889999999987755541            00  00000   0 0  111223589999999999999999


Q ss_pred             HHHHhcCCceEEe----cchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          344 TLARHVNVPFVIA----DATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       344 aLA~~l~~pfv~i----~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                      ++|+.+...++..    .+..+..     ..........+....+.+..++++||||||||++...              
T Consensus       346 ~la~~~~r~~~~~~~~~~~~~l~~-----~~~~~~~~g~~~~~~G~l~~A~~gil~IDEid~l~~~--------------  406 (595)
T 3f9v_A          346 FISRVAPRAVYTTGKGSTAAGLTA-----AVVREKGTGEYYLEAGALVLADGGIAVIDEIDKMRDE--------------  406 (595)
T ss_dssp             SSSTTCSCEECCCTTCSTTTTSEE-----ECSSGGGTSSCSEEECHHHHHSSSEECCTTTTCCCSH--------------
T ss_pred             HHHHhCCCceecCCCccccccccc-----eeeeccccccccccCCeeEecCCCcEEeehhhhCCHh--------------
Confidence            9999997655442    2222221     1111111111111223344567899999999999888              


Q ss_pred             HHHHHHHHHhCceeeee--cceeeecCCeEEEecCCCC
Q 012525          420 VQQALLKMLEGTETKTF--AAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~--~~~r~~~rd~IiI~TsNid  455 (461)
                      .+++|+++||.+.+.+.  ......+.++.+|+|+|..
T Consensus       407 ~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~  444 (595)
T 3f9v_A          407 DRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPK  444 (595)
T ss_dssp             HHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCT
T ss_pred             HhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCc
Confidence            89999999998888765  2244556689999999975

>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=99.39  E-value=3.1e-13  Score=141.22  Aligned_cols=105  Identities=28%  Similarity=0.347  Sum_probs=80.9

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC--C
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN--V  351 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~--~  351 (461)
                      .|+||+++|+.+...+...    .     .+                 ...+.++||+||||||||++|+++|+.++  .
T Consensus        38 ~iiG~~~~~~~l~~~~~~~----~-----~~-----------------~~~~~~iLl~GppGtGKT~la~ala~~l~~~~   91 (456)
T 2c9o_A           38 GLVGQENAREACGVIVELI----K-----SK-----------------KMAGRAVLLAGPPGTGKTALALAIAQELGSKV   91 (456)
T ss_dssp             TEESCHHHHHHHHHHHHHH----H-----TT-----------------CCTTCEEEEECCTTSSHHHHHHHHHHHHCTTS
T ss_pred             hccCHHHHHHHHHHHHHHH----H-----hC-----------------CCCCCeEEEECCCcCCHHHHHHHHHHHhCCCc
Confidence            3899999999988776311    0     01                 01247899999999999999999999999  8


Q ss_pred             ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhc
Q 012525          352 PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAES  408 (461)
Q Consensus       352 pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~  408 (461)
                      +|+.++++++. ..++|+. +. +..+|..+.. .....++||||||||.+..+|..
T Consensus        92 ~~~~~~~~~~~-~~~~~~~-~~-~~~~f~~a~~-~~~~~~~il~iDEid~l~~~r~~  144 (456)
T 2c9o_A           92 PFCPMVGSEVY-STEIKKT-EV-LMENFRRAIG-LRIKETKEVYEGEVTELTPCETE  144 (456)
T ss_dssp             CEEEEEGGGGC-CSSSCHH-HH-HHHHHHHTEE-EEEEEEEEEEEEEEEEEEEC---
T ss_pred             eEEEEeHHHHH-HHhhhhh-HH-HHHHHHHHHh-hhhcCCcEEEEechhhcccccCC
Confidence            99999999988 4578776 44 8888887732 23347899999999999988754

>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=99.39  E-value=6.3e-13  Score=131.43  Aligned_cols=114  Identities=17%  Similarity=0.305  Sum_probs=70.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC-------ceEEecchhhhhcC----------------c----ccccHHHHH---
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV-------PFVIADATTLTQAG----------------Y----VGEDVESIL---  375 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~-------pfv~i~~s~l~~~g----------------~----vGe~~e~~L---  375 (461)
                      .+|||+||||||||++|++||+.++.       +|   ++.......                +    .+......+   
T Consensus        46 ~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~  122 (350)
T 1g8p_A           46 GGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPV---SSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGAL  122 (350)
T ss_dssp             CCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTT---CCSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEE
T ss_pred             ceEEEECCCCccHHHHHHHHHHhCccccccccccc---cccccccccchhhhhccccccCCCcccccCCCcchhhheeec
Confidence            57999999999999999999998863       21   111111000                0    011111111   


Q ss_pred             --HHHHHhh-----chhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc--eeeecCCe
Q 012525          376 --YKLLAQA-----EFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA--VSKVSRDN  446 (461)
Q Consensus       376 --~~lf~~a-----~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~--~r~~~rd~  446 (461)
                        ...+...     .+.+..++++||||||||.+...              +++.|+..|+.....+...  ....+.++
T Consensus       123 ~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~~~--------------~~~~Ll~~le~~~~~~~~~g~~~~~~~~~  188 (350)
T 1g8p_A          123 DIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDH--------------IVDLLLDVAQSGENVVERDGLSIRHPARF  188 (350)
T ss_dssp             CHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCHH--------------HHHHHHHHHHHSEEEECCTTCCEEEECCE
T ss_pred             hhhhhhcCCceeecCceeeecCCCEEEEeChhhCCHH--------------HHHHHHHHHhcCceEEEecceEEeeCCce
Confidence              1122221     12233456889999999999887              8999999999765333322  33444589


Q ss_pred             EEEecCCCCc
Q 012525          447 LYIKTSGLDS  456 (461)
Q Consensus       447 IiI~TsNid~  456 (461)
                      ++|+|+|...
T Consensus       189 ~li~~~n~~~  198 (350)
T 1g8p_A          189 VLVGSGNPEE  198 (350)
T ss_dssp             EEEEEECSCS
T ss_pred             EEEEEeCCCC
Confidence            9999999643

>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=99.38  E-value=4.7e-13  Score=129.29  Aligned_cols=111  Identities=28%  Similarity=0.321  Sum_probs=74.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccH---HHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDV---ESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~---e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      ..++||+||||||||++|+++|+.++.+|+.+++.+.    +.|...   ...++.+|..+.    ...++||||||||.
T Consensus        64 ~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~----~~g~~~~~~~~~~~~~~~~~~----~~~~~vl~iDEid~  135 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK----MIGFSETAKCQAMKKIFDDAY----KSQLSCVVVDDIER  135 (272)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGG----CTTCCHHHHHHHHHHHHHHHH----TSSEEEEEECCHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHH----hcCCchHHHHHHHHHHHHHHH----hcCCcEEEEEChhh
Confidence            4689999999999999999999999999999988753    233331   234455555432    23678999999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      |...+...    ......+++.|+..|++...        ...+.++|+|+|..
T Consensus       136 l~~~~~~~----~~~~~~~l~~L~~~~~~~~~--------~~~~~~ii~ttn~~  177 (272)
T 1d2n_A          136 LLDYVPIG----PRFSNLVLQALLVLLKKAPP--------QGRKLLIIGTTSRK  177 (272)
T ss_dssp             HTTCBTTT----TBCCHHHHHHHHHHTTCCCS--------TTCEEEEEEEESCH
T ss_pred             hhccCCCC----hhHHHHHHHHHHHHhcCccC--------CCCCEEEEEecCCh
Confidence            86553211    11223467777777764210        11246788888764

>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=99.37  E-value=2.7e-12  Score=122.51  Aligned_cols=137  Identities=30%  Similarity=0.397  Sum_probs=87.7

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++.+++.+...+.. +... ......+                . ..+.+++|+||||||||||+++||..+
T Consensus        14 ~~~~-i~g~~~~~~~l~~l~~~-~~~~-~~~~~~~----------------~-~~~~g~ll~G~~G~GKTtl~~~i~~~~   73 (254)
T 1ixz_A           14 TFKD-VAGAEEAKEELKEIVEF-LKNP-SRFHEMG----------------A-RIPKGVLLVGPPGVGKTHLARAVAGEA   73 (254)
T ss_dssp             CGGG-CCSCHHHHHHHHHHHHH-HHCH-HHHHHTT----------------C-CCCSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CHHH-hCCcHHHHHHHHHHHHH-HHCH-HHHHHcC----------------C-CCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            3455 89999999999887642 2110 0000000                0 113569999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+++.+++.++... +.+.. ...+..+|..+..    ..++++||||||.+...+..............++.|+..|+
T Consensus        74 ~~~~i~~~~~~~~~~-~~~~~-~~~i~~~~~~~~~----~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~  147 (254)
T 1ixz_A           74 RVPFITASGSDFVEM-FVGVG-AARVRDLFETAKR----HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMD  147 (254)
T ss_dssp             TCCEEEEEHHHHHHS-CTTHH-HHHHHHHHHHHTT----SSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHH
T ss_pred             CCCEEEeeHHHHHHH-HhhHH-HHHHHHHHHHHHh----cCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHh
Confidence            999999999887642 44443 4556666765432    25689999999988766432111112223457788888888


Q ss_pred             Cce
Q 012525          430 GTE  432 (461)
Q Consensus       430 g~~  432 (461)
                      +.+
T Consensus       148 g~~  150 (254)
T 1ixz_A          148 GFE  150 (254)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            654

>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=99.35  E-value=6.5e-13  Score=142.22  Aligned_cols=152  Identities=24%  Similarity=0.333  Sum_probs=93.3

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHH
Q 012525          264 PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       264 ~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAr  343 (461)
                      ..+..+.|++.++|++.+++.+...+...  .+..                       ...+.++||+||||||||+||+
T Consensus        72 ~~~~~~~l~~di~G~~~vk~~i~~~~~l~--~~~~-----------------------~~~g~~vll~Gp~GtGKTtlar  126 (543)
T 3m6a_A           72 LKEAGRLLDEEHHGLEKVKERILEYLAVQ--KLTK-----------------------SLKGPILCLAGPPGVGKTSLAK  126 (543)
T ss_dssp             TTTGGGTHHHHCSSCHHHHHHHHHHHHHH--HHSS-----------------------SCCSCEEEEESSSSSSHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHH--Hhcc-----------------------cCCCCEEEEECCCCCCHHHHHH
Confidence            44556778888999999999987765311  1100                       0134689999999999999999


Q ss_pred             HHHHhcCCceEEecchhhhhc--------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccccccc
Q 012525          344 TLARHVNVPFVIADATTLTQA--------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDV  415 (461)
Q Consensus       344 aLA~~l~~pfv~i~~s~l~~~--------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~  415 (461)
                      +||+.++.+|+.+++..+...        .|+|.. ...+...|..+.     ...+||||||||++..++..       
T Consensus       127 ~ia~~l~~~~~~i~~~~~~~~~~~~g~~~~~ig~~-~~~~~~~~~~a~-----~~~~vl~lDEid~l~~~~~~-------  193 (543)
T 3m6a_A          127 SIAKSLGRKFVRISLGGVRDESEIRGHRRTYVGAM-PGRIIQGMKKAG-----KLNPVFLLDEIDKMSSDFRG-------  193 (543)
T ss_dssp             HHHHHHTCEEEEECCCC---------------------CHHHHHHTTC-----SSSEEEEEEESSSCC------------
T ss_pred             HHHHhcCCCeEEEEecccchhhhhhhHHHHHhccC-chHHHHHHHHhh-----ccCCEEEEhhhhhhhhhhcc-------
Confidence            999999999999988765431        233322 222333343332     24569999999999887321       


Q ss_pred             chHHHHHHHHHHHhCceeeeecc---eeeec-CCeEEEecCCCCc
Q 012525          416 SGEGVQQALLKMLEGTETKTFAA---VSKVS-RDNLYIKTSGLDS  456 (461)
Q Consensus       416 s~~~v~~aLL~~LEg~~v~i~~~---~r~~~-rd~IiI~TsNid~  456 (461)
                         ..+++||++||..+......   ..... .+.++|+|+|...
T Consensus       194 ---~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~  235 (543)
T 3m6a_A          194 ---DPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLA  235 (543)
T ss_dssp             -------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTT
T ss_pred             ---CHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccc
Confidence               15789999998655433222   22222 3689999999753

>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=99.35  E-value=5.2e-12  Score=123.73  Aligned_cols=128  Identities=23%  Similarity=0.344  Sum_probs=91.5

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ++|++.+++.|...+......                          .....+|||+||+|||||++|+++|+.++.+|+
T Consensus        14 ~ig~~~~~~~l~~~l~~~~~~--------------------------~~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~   67 (324)
T 1hqc_A           14 YIGQERLKQKLRVYLEAAKAR--------------------------KEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLR   67 (324)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHH--------------------------CSCCCCCEEECCTTCCCHHHHHHHHHHHTCCEE
T ss_pred             hhCHHHHHHHHHHHHHHHHcc--------------------------CCCCCcEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            799999999888877421100                          012367999999999999999999999999999


Q ss_pred             EecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceee
Q 012525          355 IADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK  434 (461)
Q Consensus       355 ~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~  434 (461)
                      .+++..+..        ...+...+..     ..+.+++||||||+.+...              .++.|+..|+...+.
T Consensus        68 ~~~~~~~~~--------~~~l~~~l~~-----~~~~~~~l~lDEi~~l~~~--------------~~~~L~~~l~~~~~~  120 (324)
T 1hqc_A           68 VTSGPAIEK--------PGDLAAILAN-----SLEEGDILFIDEIHRLSRQ--------------AEEHLYPAMEDFVMD  120 (324)
T ss_dssp             EECTTTCCS--------HHHHHHHHTT-----TCCTTCEEEETTTTSCCHH--------------HHHHHHHHHHHSEEE
T ss_pred             EEeccccCC--------hHHHHHHHHH-----hccCCCEEEEECCcccccc--------------hHHHHHHHHHhhhhH
Confidence            998877642        2333333322     1246789999999999877              789999999977655


Q ss_pred             eecceee-------ecCCeEEEecCCCC
Q 012525          435 TFAAVSK-------VSRDNLYIKTSGLD  455 (461)
Q Consensus       435 i~~~~r~-------~~rd~IiI~TsNid  455 (461)
                      +......       ...++++|+++|..
T Consensus       121 ~v~~~~~~~~~~~~~~~~~~~i~~t~~~  148 (324)
T 1hqc_A          121 IVIGQGPAARTIRLELPRFTLIGATTRP  148 (324)
T ss_dssp             ECCSSSSSCCCEEEECCCCEEEEEESCC
T ss_pred             HhccccccccccccCCCCEEEEEeCCCc
Confidence            4432111       11257888888855

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.34  E-value=2e-12  Score=135.51  Aligned_cols=109  Identities=30%  Similarity=0.427  Sum_probs=77.0

Q ss_pred             HHHhhcCChHHHH---HHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHH
Q 012525          270 GLDKFVIGQEKAK---KVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       270 ~Ld~~VvGqd~aK---~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      .|++ |+||+.++   +.|...+..            +                   ...+|||+||||||||++|++||
T Consensus        24 ~l~~-ivGq~~~~~~~~~L~~~i~~------------~-------------------~~~~vLL~GppGtGKTtlAr~ia   71 (447)
T 3pvs_A           24 NLAQ-YIGQQHLLAAGKPLPRAIEA------------G-------------------HLHSMILWGPPGTGKTTLAEVIA   71 (447)
T ss_dssp             STTT-CCSCHHHHSTTSHHHHHHHH------------T-------------------CCCEEEEECSTTSSHHHHHHHHH
T ss_pred             CHHH-hCCcHHHHhchHHHHHHHHc------------C-------------------CCcEEEEECCCCCcHHHHHHHHH
Confidence            3455 89999998   666666631            0                   12579999999999999999999


Q ss_pred             HhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHH
Q 012525          347 RHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLK  426 (461)
Q Consensus       347 ~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~  426 (461)
                      +.++.+|+.+++....         ...++.++..+.......+++||||||||.+...              .++.||.
T Consensus        72 ~~~~~~f~~l~a~~~~---------~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~--------------~q~~LL~  128 (447)
T 3pvs_A           72 RYANADVERISAVTSG---------VKEIREAIERARQNRNAGRRTILFVDEVHRFNKS--------------QQDAFLP  128 (447)
T ss_dssp             HHTTCEEEEEETTTCC---------HHHHHHHHHHHHHHHHTTCCEEEEEETTTCC--------------------CCHH
T ss_pred             HHhCCCeEEEEeccCC---------HHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHH--------------HHHHHHH
Confidence            9999999998865432         2344555554444334557899999999999877              7889999


Q ss_pred             HHhCcee
Q 012525          427 MLEGTET  433 (461)
Q Consensus       427 ~LEg~~v  433 (461)
                      .||...+
T Consensus       129 ~le~~~v  135 (447)
T 3pvs_A          129 HIEDGTI  135 (447)
T ss_dssp             HHHTTSC
T ss_pred             HHhcCce
Confidence            9996543

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.31  E-value=1.2e-11  Score=120.09  Aligned_cols=150  Identities=27%  Similarity=0.364  Sum_probs=93.1

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ |+|++.+++.|...+.. +... .......                . ..+.+++|+||+|||||||+++||..+
T Consensus        38 ~~~~-i~g~~~~~~~l~~l~~~-~~~~-~~l~~~~----------------~-~~~~gvll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           38 TFKD-VAGAEEAKEELKEIVEF-LKNP-SRFHEMG----------------A-RIPKGVLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             CGGG-SSSCHHHHHHHHHHHHH-HHCH-HHHHHTT----------------C-CCCCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CHHH-hCChHHHHHHHHHHHHH-HHCH-HHHHHcC----------------C-CCCCeEEEECCCcChHHHHHHHHHHHc
Confidence            4555 89999999999887642 1110 0000000                0 113559999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ..+++.+++.++... +.+.. ...+..+|..+..    ..++++||||||.+...+..............++.++..|+
T Consensus        98 ~~~~i~~~~~~~~~~-~~~~~-~~~i~~~~~~~~~----~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~ls  171 (278)
T 1iy2_A           98 RVPFITASGSDFVEM-FVGVG-AARVRDLFETAKR----HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMD  171 (278)
T ss_dssp             TCCEEEEEHHHHHHS-TTTHH-HHHHHHHHHHHHT----SCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHT
T ss_pred             CCCEEEecHHHHHHH-HhhHH-HHHHHHHHHHHHh----cCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHh
Confidence            999999999887642 44433 4455666665432    25689999999988765432110111122346677888888


Q ss_pred             CceeeeecceeeecCCeEEEecCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +.+..         +..++++++|.
T Consensus       172 gg~~~---------~~~i~~a~t~~  187 (278)
T 1iy2_A          172 GFEKD---------TAIVVMAATNR  187 (278)
T ss_dssp             TCCTT---------CCEEEEEEESC
T ss_pred             CCCCC---------CCEEEEEecCC
Confidence            65421         23566666654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.29  E-value=1.2e-11  Score=109.98  Aligned_cols=117  Identities=26%  Similarity=0.363  Sum_probs=76.8

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-----  349 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-----  349 (461)
                      ++|++.+.+.+...+..                               ....++||+||+|||||++|+++++.+     
T Consensus        24 ~~g~~~~~~~l~~~l~~-------------------------------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~   72 (187)
T 2p65_A           24 VIGRDTEIRRAIQILSR-------------------------------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDV   72 (187)
T ss_dssp             CCSCHHHHHHHHHHHTS-------------------------------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCS
T ss_pred             hhcchHHHHHHHHHHhC-------------------------------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCC
Confidence            78999888877766520                               113679999999999999999999987     


Q ss_pred             -----CCceEEecchhhhhcC-cccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHH
Q 012525          350 -----NVPFVIADATTLTQAG-YVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQA  423 (461)
Q Consensus       350 -----~~pfv~i~~s~l~~~g-~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~a  423 (461)
                           +.+++.+++..+.... +.+ .....+..++.....   ...+.||||||+|.+...+........     +++.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~---~~~~~vl~iDe~~~l~~~~~~~~~~~~-----~~~~  143 (187)
T 2p65_A           73 PDSLKGRKLVSLDLSSLIAGAKYRG-DFEERLKSILKEVQD---AEGQVVMFIDEIHTVVGAGAVAEGALD-----AGNI  143 (187)
T ss_dssp             CTTTTTCEEEEECHHHHHHHCCSHH-HHHHHHHHHHHHHHH---TTTSEEEEETTGGGGSSSSSSCTTSCC-----THHH
T ss_pred             cchhcCCeEEEEeHHHhhcCCCchh-HHHHHHHHHHHHHHh---cCCceEEEEeCHHHhcccccccccchH-----HHHH
Confidence                 6788888887665321 222 223444444443321   125679999999999855321111111     6777


Q ss_pred             HHHHHhCc
Q 012525          424 LLKMLEGT  431 (461)
Q Consensus       424 LL~~LEg~  431 (461)
                      |+.+++..
T Consensus       144 l~~~~~~~  151 (187)
T 2p65_A          144 LKPMLARG  151 (187)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHhcC
Confidence            88888743

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.28  E-value=1.9e-11  Score=125.43  Aligned_cols=131  Identities=18%  Similarity=0.337  Sum_probs=104.2

Q ss_pred             CCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhhcCcccccHHHHHHHHHH-
Q 012525          305 SGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQAGYVGEDVESILYKLLA-  380 (461)
Q Consensus       305 ~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~-  380 (461)
                      .+.+..+..+.+.+..++....+|||+|++|||||++|++|+....   .+|+.++|+.+...        -.-..+|. 
T Consensus       140 ig~s~~m~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~--------~~~~elfg~  211 (387)
T 1ny5_A          140 VFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRD--------IFEAELFGY  211 (387)
T ss_dssp             CCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHH--------HHHHHHHCB
T ss_pred             hhccHHhhHHHHHHHHhcCCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHH--------HHHHHhcCC
Confidence            4567888888888888888999999999999999999999998764   69999999987632        11122332 


Q ss_pred             ----------hhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEe
Q 012525          381 ----------QAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIK  450 (461)
Q Consensus       381 ----------~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~  450 (461)
                                ...+.++.+++|+||||||+.|...              +|..|+++|+.+.+...........++.+|+
T Consensus       212 ~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~~--------------~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~  277 (387)
T 1ny5_A          212 EKGAFTGAVSSKEGFFELADGGTLFLDEIGELSLE--------------AQAKLLRVIESGKFYRLGGRKEIEVNVRILA  277 (387)
T ss_dssp             CTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCHH--------------HHHHHHHHHHHSEECCBTCCSBEECCCEEEE
T ss_pred             CCCCCCCcccccCCceeeCCCcEEEEcChhhCCHH--------------HHHHHHHHHhcCcEEeCCCCceeeccEEEEE
Confidence                      1234456678999999999999998              9999999999887765555555556899999


Q ss_pred             cCCCCcC
Q 012525          451 TSGLDSK  457 (461)
Q Consensus       451 TsNid~e  457 (461)
                      |||.+.+
T Consensus       278 at~~~l~  284 (387)
T 1ny5_A          278 ATNRNIK  284 (387)
T ss_dssp             EESSCHH
T ss_pred             eCCCCHH
Confidence            9998764

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.25  E-value=2.7e-11  Score=120.94  Aligned_cols=65  Identities=25%  Similarity=0.426  Sum_probs=47.5

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +++ ++|++.+++.+..++...     ..    +                 ...+.++||+||||||||++|+++|+.++
T Consensus        43 ~~~-ivG~~~~~~~l~~l~~~~-----~~----~-----------------~~~~~~vLl~GppGtGKT~la~~la~~l~   95 (368)
T 3uk6_A           43 SQG-MVGQLAARRAAGVVLEMI-----RE----G-----------------KIAGRAVLIAGQPGTGKTAIAMGMAQALG   95 (368)
T ss_dssp             ETT-EESCHHHHHHHHHHHHHH-----HT----T-----------------CCTTCEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             hhh-ccChHHHHHHHHHHHHHH-----Hc----C-----------------CCCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            444 899999999877655211     00    0                 01136899999999999999999999997


Q ss_pred             C--ceEEecchhhh
Q 012525          351 V--PFVIADATTLT  362 (461)
Q Consensus       351 ~--pfv~i~~s~l~  362 (461)
                      .  +|+.+++..+.
T Consensus        96 ~~~~~~~~~~~~~~  109 (368)
T 3uk6_A           96 PDTPFTAIAGSEIF  109 (368)
T ss_dssp             SSCCEEEEEGGGGS
T ss_pred             ccCCcccccchhhh
Confidence            5  78888776533

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.23  E-value=4.3e-11  Score=105.98  Aligned_cols=116  Identities=23%  Similarity=0.345  Sum_probs=75.6

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-----  349 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-----  349 (461)
                      ++|++..++.+...+..                               ....++||+||+|||||++|+++++.+     
T Consensus        24 ~~g~~~~~~~l~~~l~~-------------------------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~   72 (195)
T 1jbk_A           24 VIGRDEEIRRTIQVLQR-------------------------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEV   72 (195)
T ss_dssp             CCSCHHHHHHHHHHHTS-------------------------------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCS
T ss_pred             cccchHHHHHHHHHHhc-------------------------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCC
Confidence            78999888877776620                               123679999999999999999999986     


Q ss_pred             -----CCceEEecchhhhhc-CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHH
Q 012525          350 -----NVPFVIADATTLTQA-GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQA  423 (461)
Q Consensus       350 -----~~pfv~i~~s~l~~~-g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~a  423 (461)
                           +.+++.+++..+... .+.+. ....+..++....   ....+.||||||+|.+...+.. .....     +++.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~vl~iDe~~~l~~~~~~-~~~~~-----~~~~  142 (195)
T 1jbk_A           73 PEGLKGRRVLALDMGALVAGAKYRGE-FEERLKGVLNDLA---KQEGNVILFIDELHTMVGAGKA-DGAMD-----AGNM  142 (195)
T ss_dssp             CGGGTTCEEEEECHHHHHTTTCSHHH-HHHHHHHHHHHHH---HSTTTEEEEEETGGGGTT-------CCC-----CHHH
T ss_pred             chhhcCCcEEEeeHHHHhccCCcccc-HHHHHHHHHHHHh---hcCCCeEEEEeCHHHHhccCcc-cchHH-----HHHH
Confidence                 678888888876532 22222 2444555554322   1235679999999999865321 11111     5677


Q ss_pred             HHHHHhCc
Q 012525          424 LLKMLEGT  431 (461)
Q Consensus       424 LL~~LEg~  431 (461)
                      |+.+++..
T Consensus       143 l~~~~~~~  150 (195)
T 1jbk_A          143 LKPALARG  150 (195)
T ss_dssp             HHHHHHTT
T ss_pred             HHHhhccC
Confidence            77777744

>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=99.22  E-value=2.3e-11  Score=119.93  Aligned_cols=107  Identities=23%  Similarity=0.281  Sum_probs=76.5

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ ++|++.+++.|...+.            .+                  ..+..+||+||||||||++|+++|+.+
T Consensus        24 ~~~~-ivg~~~~~~~l~~~l~------------~~------------------~~~~~~L~~G~~G~GKT~la~~la~~l   72 (324)
T 3u61_B           24 TIDE-CILPAFDKETFKSITS------------KG------------------KIPHIILHSPSPGTGKTTVAKALCHDV   72 (324)
T ss_dssp             STTT-SCCCHHHHHHHHHHHH------------TT------------------CCCSEEEECSSTTSSHHHHHHHHHHHT
T ss_pred             CHHH-HhCcHHHHHHHHHHHH------------cC------------------CCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            4555 7999999998888773            00                  112456788889999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHh-hchhhhccCceEEEEcCccccc-hhhhccccccccchHHHHHHHHHH
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQ-AEFNVEAAQQGMVYIDEVDKIT-KKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~-a~~~v~~a~~gVLfIDEID~L~-~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      +.+++.+++++..         ...++..+.. +..........||||||+|.+. ..              .++.|+..
T Consensus        73 ~~~~~~i~~~~~~---------~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~~~--------------~~~~L~~~  129 (324)
T 3u61_B           73 NADMMFVNGSDCK---------IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAE--------------SQRHLRSF  129 (324)
T ss_dssp             TEEEEEEETTTCC---------HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGGHH--------------HHHHHHHH
T ss_pred             CCCEEEEcccccC---------HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCcHH--------------HHHHHHHH
Confidence            9999999986633         2233332222 1111112367899999999998 65              78999999


Q ss_pred             HhC
Q 012525          428 LEG  430 (461)
Q Consensus       428 LEg  430 (461)
                      |+.
T Consensus       130 le~  132 (324)
T 3u61_B          130 MEA  132 (324)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            984

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.20  E-value=1.3e-11  Score=126.05  Aligned_cols=133  Identities=26%  Similarity=0.392  Sum_probs=100.4

Q ss_pred             CCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC--ceEEecchhhhhcCcccccHHHHHHH----HH
Q 012525          306 GAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV--PFVIADATTLTQAGYVGEDVESILYK----LL  379 (461)
Q Consensus       306 ~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~--pfv~i~~s~l~~~g~vGe~~e~~L~~----lf  379 (461)
                      +.+..+.........++....+||++|++||||+++|+++++..+.  .|+.++|+.+.+.     ..++.+..    .|
T Consensus       133 g~s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~-----~~~~~lfg~~~g~~  207 (368)
T 3dzd_A          133 GEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQE-----LAESELFGHEKGAF  207 (368)
T ss_dssp             CCSHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTT-----THHHHHHEECSCSS
T ss_pred             ccchHHHHHHhhhhhhhccchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChH-----HHHHHhcCcccccc
Confidence            4556666666667777778889999999999999999999987754  3999999987642     12222211    01


Q ss_pred             ----HhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          380 ----AQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       380 ----~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                          ....+.++.+++++||||||+.|...              +|..||++|+.+.+...........++.+|++||.+
T Consensus       208 tga~~~~~g~~~~a~~gtlfldei~~l~~~--------------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~  273 (368)
T 3dzd_A          208 TGALTRKKGKLELADQGTLFLDEVGELDQR--------------VQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKN  273 (368)
T ss_dssp             SSCCCCEECHHHHTTTSEEEEETGGGSCHH--------------HHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESSC
T ss_pred             CCcccccCChHhhcCCCeEEecChhhCCHH--------------HHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCCC
Confidence                11234466678999999999999998              999999999988777655555555689999999987


Q ss_pred             cC
Q 012525          456 SK  457 (461)
Q Consensus       456 ~e  457 (461)
                      +.
T Consensus       274 l~  275 (368)
T 3dzd_A          274 LE  275 (368)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>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=99.19  E-value=1.4e-10  Score=104.97  Aligned_cols=103  Identities=26%  Similarity=0.373  Sum_probs=71.0

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-----  349 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-----  349 (461)
                      ++|++.+++.|...+..                               ....++||+||+|||||++|+++++.+     
T Consensus        19 ~~g~~~~~~~l~~~l~~-------------------------------~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~   67 (226)
T 2chg_A           19 VVGQDEVIQRLKGYVER-------------------------------KNIPHLLFSGPPGTGKTATAIALARDLFGENW   67 (226)
T ss_dssp             CCSCHHHHHHHHHHHHT-------------------------------TCCCCEEEECSTTSSHHHHHHHHHHHHHGGGG
T ss_pred             HcCcHHHHHHHHHHHhC-------------------------------CCCCeEEEECCCCCCHHHHHHHHHHHHhcccc
Confidence            78999999988877731                               012469999999999999999999876     


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhch--hhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHH
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEF--NVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM  427 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~--~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~  427 (461)
                      ...++.+++.....        ...+...+.....  ......+.||||||+|.+...              .++.|+.+
T Consensus        68 ~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~--------------~~~~l~~~  125 (226)
T 2chg_A           68 RDNFIEMNASDERG--------IDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTAD--------------AQAALRRT  125 (226)
T ss_dssp             GGGEEEEETTCTTC--------HHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHH--------------HHHHHHHH
T ss_pred             ccceEEeccccccC--------hHHHHHHHHHHhcccCCCccCceEEEEeChhhcCHH--------------HHHHHHHH
Confidence            34577777654332        1122222211111  122356789999999999876              67889998


Q ss_pred             HhC
Q 012525          428 LEG  430 (461)
Q Consensus       428 LEg  430 (461)
                      |+.
T Consensus       126 l~~  128 (226)
T 2chg_A          126 MEM  128 (226)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            884

>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=99.18  E-value=1.6e-11  Score=129.84  Aligned_cols=141  Identities=13%  Similarity=0.151  Sum_probs=100.5

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHH
Q 012525          264 PKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       264 ~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAr  343 (461)
                      ...+...+.. |+||+.+|+.|..++.             +  ....           .....||||.|+||| ||+||+
T Consensus       205 ~~~l~~sIap-I~G~e~vK~aLll~L~-------------G--G~~k-----------~rgdihVLL~G~PGt-KS~Lar  256 (506)
T 3f8t_A          205 LTTFARAIAP-LPGAEEVGKMLALQLF-------------S--CVGK-----------NSERLHVLLAGYPVV-CSEILH  256 (506)
T ss_dssp             HHHHHHHHCC-STTCHHHHHHHHHHHT-------------T--CCSS-----------GGGCCCEEEESCHHH-HHHHHH
T ss_pred             HHHHHHHhcc-cCCCHHHHHHHHHHHc-------------C--Cccc-----------cCCceeEEEECCCCh-HHHHHH
Confidence            4568888899 9999999998888772             0  0000           122358999999999 999999


Q ss_pred             HH-HHhcCCceEEec-ch---hhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          344 TL-ARHVNVPFVIAD-AT---TLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       344 aL-A~~l~~pfv~i~-~s---~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                      ++ ++.+....+... .+   .+... ....      .. +....+.+..++++|+|||||+++.++             
T Consensus       257 ~i~~~i~pR~~ft~g~~ss~~gLt~s-~r~~------tG-~~~~~G~l~LAdgGvl~lDEIn~~~~~-------------  315 (506)
T 3f8t_A          257 HVLDHLAPRGVYVDLRRTELTDLTAV-LKED------RG-WALRAGAAVLADGGILAVDHLEGAPEP-------------  315 (506)
T ss_dssp             HHHHHTCSSEEEEEGGGCCHHHHSEE-EEES------SS-EEEEECHHHHTTTSEEEEECCTTCCHH-------------
T ss_pred             HHHHHhCCCeEEecCCCCCccCceEE-EEcC------CC-cccCCCeeEEcCCCeeehHhhhhCCHH-------------
Confidence            99 887754322211 11   12211 1000      11 223345566678999999999999998             


Q ss_pred             HHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          419 GVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       419 ~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                       .+.+|++.||++++++. .. ..+.++.+|+|+|...
T Consensus       316 -~qsaLlEaMEe~~VtI~-G~-~lparf~VIAA~NP~~  350 (506)
T 3f8t_A          316 -HRWALMEAMDKGTVTVD-GI-ALNARCAVLAAINPGE  350 (506)
T ss_dssp             -HHHHHHHHHHHSEEEET-TE-EEECCCEEEEEECCCC
T ss_pred             -HHHHHHHHHhCCcEEEC-CE-EcCCCeEEEEEeCccc
Confidence             99999999999998877 44 7777999999999764

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.17  E-value=4.6e-11  Score=129.16  Aligned_cols=57  Identities=25%  Similarity=0.434  Sum_probs=45.0

Q ss_pred             hhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc----------eeeecCCeEEEecCCC
Q 012525          385 NVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA----------VSKVSRDNLYIKTSGL  454 (461)
Q Consensus       385 ~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~----------~r~~~rd~IiI~TsNi  454 (461)
                      .+..+++++||||||+.|.+.              +++.|++.|+...+.+...          ....+.++++|+|+|.
T Consensus       196 ~~~~a~~gvL~LDEi~~l~~~--------------~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~  261 (604)
T 3k1j_A          196 MIHRAHKGVLFIDEIATLSLK--------------MQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNL  261 (604)
T ss_dssp             HHHHTTTSEEEETTGGGSCHH--------------HHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECH
T ss_pred             eeeecCCCEEEEechhhCCHH--------------HHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCH
Confidence            345578899999999999877              8999999999887765533          2344558999999997


Q ss_pred             C
Q 012525          455 D  455 (461)
Q Consensus       455 d  455 (461)
                      +
T Consensus       262 ~  262 (604)
T 3k1j_A          262 D  262 (604)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=99.13  E-value=2.3e-10  Score=121.36  Aligned_cols=127  Identities=19%  Similarity=0.188  Sum_probs=80.7

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ |+|++.+++.|...+..............+              ........++||+||||||||++|+++|+++
T Consensus        37 ~~~d-liG~~~~~~~L~~~l~~~~~~~~~~~~~~g--------------~~~~~~~~~lLL~GppGtGKTtla~~la~~l  101 (516)
T 1sxj_A           37 NLQQ-VCGNKGSVMKLKNWLANWENSKKNSFKHAG--------------KDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL  101 (516)
T ss_dssp             SGGG-CCSCHHHHHHHHHHHHTHHHHHHTTTCCCC--------------TTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CHHH-hcCCHHHHHHHHHHHHHhHhhchhhccccC--------------ccCCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4555 899999999999888532211101111111              0000124689999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhh------chh--------hhccCceEEEEcCccccchhhhcccccccc
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQA------EFN--------VEAAQQGMVYIDEVDKITKKAESLNISRDV  415 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a------~~~--------v~~a~~gVLfIDEID~L~~~R~~~~~~~~~  415 (461)
                      +.+++.++++++...        ..+...+...      ...        .....+.||||||||.|.....        
T Consensus       102 ~~~~i~in~s~~~~~--------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~--------  165 (516)
T 1sxj_A          102 GYDILEQNASDVRSK--------TLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDR--------  165 (516)
T ss_dssp             TCEEEEECTTSCCCH--------HHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTST--------
T ss_pred             CCCEEEEeCCCcchH--------HHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhH--------
Confidence            999999999876532        1111111100      000        0124678999999999987521        


Q ss_pred             chHHHHHHHHHHHhC
Q 012525          416 SGEGVQQALLKMLEG  430 (461)
Q Consensus       416 s~~~v~~aLL~~LEg  430 (461)
                         +.+++|+++|+.
T Consensus       166 ---~~l~~L~~~l~~  177 (516)
T 1sxj_A          166 ---GGVGQLAQFCRK  177 (516)
T ss_dssp             ---THHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHh
Confidence               146788888874

>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=99.12  E-value=3.4e-10  Score=103.37  Aligned_cols=112  Identities=27%  Similarity=0.334  Sum_probs=70.0

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ++|++.+++.|...+..            +                  ..+..++|+||+|||||++|+.+++.+.....
T Consensus        25 ~~g~~~~~~~l~~~l~~------------~------------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~   74 (250)
T 1njg_A           25 VVGQEHVLTALANGLSL------------G------------------RIHHAYLFSGTRGVGKTSIARLLAKGLNCETG   74 (250)
T ss_dssp             CCSCHHHHHHHHHHHHH------------T------------------CCCSEEEEECSTTSCHHHHHHHHHHHHHCTTC
T ss_pred             HhCcHHHHHHHHHHHHc------------C------------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCC
Confidence            79999999988887731            0                  01246899999999999999999987743211


Q ss_pred             Ee--c------chhhhhc---Cc-----ccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          355 IA--D------ATTLTQA---GY-----VGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       355 ~i--~------~s~l~~~---g~-----vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                      ..  .      +..+...   .+     ........+..++..........++.+|||||+|.+...             
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~-------------  141 (250)
T 1njg_A           75 ITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH-------------  141 (250)
T ss_dssp             SCSSCCSCSHHHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHH-------------
T ss_pred             CCCCCCcccHHHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHH-------------
Confidence            00  0      0000000   00     001113344555554332222346789999999998776             


Q ss_pred             HHHHHHHHHHhC
Q 012525          419 GVQQALLKMLEG  430 (461)
Q Consensus       419 ~v~~aLL~~LEg  430 (461)
                       .++.|+..|+.
T Consensus       142 -~~~~l~~~l~~  152 (250)
T 1njg_A          142 -SFNALLKTLEE  152 (250)
T ss_dssp             -HHHHHHHHHHS
T ss_pred             -HHHHHHHHHhc
Confidence             78899999984

>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=99.08  E-value=3.5e-10  Score=110.06  Aligned_cols=108  Identities=29%  Similarity=0.375  Sum_probs=73.5

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +++ ++|++.+++.|...+..                               ....++||+||+|||||++|+++|+.+.
T Consensus        24 ~~~-~~g~~~~~~~l~~~l~~-------------------------------~~~~~~ll~G~~G~GKT~la~~l~~~l~   71 (327)
T 1iqp_A           24 LDD-IVGQEHIVKRLKHYVKT-------------------------------GSMPHLLFAGPPGVGKTTAALALARELF   71 (327)
T ss_dssp             TTT-CCSCHHHHHHHHHHHHH-------------------------------TCCCEEEEESCTTSSHHHHHHHHHHHHH
T ss_pred             HHH-hhCCHHHHHHHHHHHHc-------------------------------CCCCeEEEECcCCCCHHHHHHHHHHHhc
Confidence            444 89999999988877731                               0124699999999999999999999863


Q ss_pred             C-----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHH
Q 012525          351 V-----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALL  425 (461)
Q Consensus       351 ~-----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL  425 (461)
                      .     .++.+++++.....    .....+.....  ...+...+..||||||+|.+...              .+++|+
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~--~~~~~~~~~~vliiDe~~~l~~~--------------~~~~L~  131 (327)
T 1iqp_A           72 GENWRHNFLELNASDERGIN----VIREKVKEFAR--TKPIGGASFKIIFLDEADALTQD--------------AQQALR  131 (327)
T ss_dssp             GGGHHHHEEEEETTCHHHHH----TTHHHHHHHHH--SCCGGGCSCEEEEEETGGGSCHH--------------HHHHHH
T ss_pred             CCcccCceEEeeccccCchH----HHHHHHHHHHh--hCCcCCCCCeEEEEeCCCcCCHH--------------HHHHHH
Confidence            2     46777766543210    11112222111  11122356789999999999877              789999


Q ss_pred             HHHhC
Q 012525          426 KMLEG  430 (461)
Q Consensus       426 ~~LEg  430 (461)
                      +.|+.
T Consensus       132 ~~le~  136 (327)
T 1iqp_A          132 RTMEM  136 (327)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            99984

>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=99.07  E-value=1.6e-10  Score=114.14  Aligned_cols=107  Identities=25%  Similarity=0.358  Sum_probs=72.1

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +++ |+|++++++.|...+.            .                   ....++||+||||||||++|+++|+.+.
T Consensus        36 ~~~-i~g~~~~~~~l~~~l~------------~-------------------~~~~~~ll~G~~G~GKT~la~~la~~l~   83 (353)
T 1sxj_D           36 LDE-VTAQDHAVTVLKKTLK------------S-------------------ANLPHMLFYGPPGTGKTSTILALTKELY   83 (353)
T ss_dssp             TTT-CCSCCTTHHHHHHHTT------------C-------------------TTCCCEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHH-hhCCHHHHHHHHHHHh------------c-------------------CCCCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            444 8999999988877762            0                   0124699999999999999999999864


Q ss_pred             ------CceEEecchhhhhcCcccccHHHHHHHHHHhh-ch-----------hhhccCceEEEEcCccccchhhhccccc
Q 012525          351 ------VPFVIADATTLTQAGYVGEDVESILYKLLAQA-EF-----------NVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       351 ------~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a-~~-----------~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                            ..++.+++++....        ..++..+... ..           ........||||||+|.+...       
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~~-------  148 (353)
T 1sxj_D           84 GPDLMKSRILELNASDERGI--------SIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTAD-------  148 (353)
T ss_dssp             HHHHHTTSEEEECSSSCCCH--------HHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHH-------
T ss_pred             CCcccccceEEEccccccch--------HHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccCHH-------
Confidence                  35777777654211        1111111110 00           011235579999999999887       


Q ss_pred             cccchHHHHHHHHHHHhCc
Q 012525          413 RDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg~  431 (461)
                             .+++|++.|+..
T Consensus       149 -------~~~~Ll~~le~~  160 (353)
T 1sxj_D          149 -------AQSALRRTMETY  160 (353)
T ss_dssp             -------HHHHHHHHHHHT
T ss_pred             -------HHHHHHHHHHhc
Confidence                   789999999843

>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=99.03  E-value=2e-10  Score=111.40  Aligned_cols=109  Identities=28%  Similarity=0.379  Sum_probs=74.2

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ ++|++.+++.|...+..                               ....++||+||+|||||++|+++|+.+
T Consensus        15 ~~~~-~~g~~~~~~~l~~~l~~-------------------------------~~~~~~ll~G~~G~GKt~la~~l~~~l   62 (319)
T 2chq_A           15 TLDE-VVGQDEVIQRLKGYVER-------------------------------KNIPHLLFSGPPGTGKTATAIALARDL   62 (319)
T ss_dssp             SGGG-SCSCHHHHHHHHTTTTT-------------------------------TCCCCEEEESSSSSSHHHHHHHHHHHH
T ss_pred             CHHH-HhCCHHHHHHHHHHHhC-------------------------------CCCCeEEEECcCCcCHHHHHHHHHHHh
Confidence            3455 89999999988776620                               012469999999999999999999986


Q ss_pred             -----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHH
Q 012525          350 -----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQAL  424 (461)
Q Consensus       350 -----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aL  424 (461)
                           ..+++.+++++.....    .....+......  ..+....+.||||||+|.+...              .+++|
T Consensus        63 ~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~--~~~~~~~~~vliiDe~~~l~~~--------------~~~~L  122 (319)
T 2chq_A           63 FGENWRDNFIEMNASDERGID----VVRHKIKEFART--APIGGAPFKIIFLDEADALTAD--------------AQAAL  122 (319)
T ss_dssp             HTTCHHHHCEEEETTSTTCTT----TSSHHHHHHHHS--CCSSSCCCEEEEEETGGGSCHH--------------HHHTT
T ss_pred             cCCcccCCeEEEeCccccChH----HHHHHHHHHHhc--CCCCCCCceEEEEeCCCcCCHH--------------HHHHH
Confidence                 3467888877643211    111222222211  1122246789999999999877              78899


Q ss_pred             HHHHhC
Q 012525          425 LKMLEG  430 (461)
Q Consensus       425 L~~LEg  430 (461)
                      ++.|+.
T Consensus       123 ~~~le~  128 (319)
T 2chq_A          123 RRTMEM  128 (319)
T ss_dssp             GGGTSS
T ss_pred             HHHHHh
Confidence            999984

>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=99.01  E-value=8.7e-10  Score=109.61  Aligned_cols=107  Identities=28%  Similarity=0.369  Sum_probs=70.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +++ ++|++.+++.|...+..            +                  ..+..+||+||+|||||++|+++|+.+.
T Consensus        15 ~~~-~vg~~~~~~~L~~~l~~------------~------------------~~~~~~ll~G~~G~GKT~la~~la~~l~   63 (373)
T 1jr3_A           15 FAD-VVGQEHVLTALANGLSL------------G------------------RIHHAYLFSGTRGVGKTSIARLLAKGLN   63 (373)
T ss_dssp             TTT-SCSCHHHHHHHHHHHHH------------T------------------CCCSEEEEESCTTSSHHHHHHHHHHHHS
T ss_pred             hhh-ccCcHHHHHHHHHHHHh------------C------------------CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            344 89999999988887731            0                  0124589999999999999999999885


Q ss_pred             Cc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhh
Q 012525          351 VP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKA  406 (461)
Q Consensus       351 ~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R  406 (461)
                      ..                        ++.++...     ..+   ...++.++...........+.||||||+|.+... 
T Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~---~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~-  134 (373)
T 1jr3_A           64 CETGITATPCGVCDNCREIEQGRFVDLIEIDAAS-----RTK---VEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH-  134 (373)
T ss_dssp             CTTCSCSSCCSSSHHHHHHHTSCCSSCEEEETTC-----SCC---SSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHH-
T ss_pred             CCCCCCCCCCcccHHHHHHhccCCCceEEecccc-----cCC---HHHHHHHHHHHhhccccCCeEEEEEECcchhcHH-
Confidence            42                        12222111     001   1123344443332222345789999999999876 


Q ss_pred             hccccccccchHHHHHHHHHHHhC
Q 012525          407 ESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       407 ~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                   .+++|++.|+.
T Consensus       135 -------------~~~~Ll~~le~  145 (373)
T 1jr3_A          135 -------------SFNALLKTLEE  145 (373)
T ss_dssp             -------------HHHHHHHHHHS
T ss_pred             -------------HHHHHHHHHhc
Confidence                         78999999985

>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=99.00  E-value=6.8e-10  Score=107.81  Aligned_cols=106  Identities=20%  Similarity=0.287  Sum_probs=72.7

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      +++ ++|++.+++.|...+..                               ....++||+||+|||||++|+++++.+ 
T Consensus        20 ~~~-~~g~~~~~~~l~~~l~~-------------------------------~~~~~~ll~G~~G~GKt~la~~l~~~l~   67 (323)
T 1sxj_B           20 LSD-IVGNKETIDRLQQIAKD-------------------------------GNMPHMIISGMPGIGKTTSVHCLAHELL   67 (323)
T ss_dssp             GGG-CCSCTHHHHHHHHHHHS-------------------------------CCCCCEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHH-HHCCHHHHHHHHHHHHc-------------------------------CCCCeEEEECcCCCCHHHHHHHHHHHhc
Confidence            444 78999999988887620                               012459999999999999999999986 


Q ss_pred             ----CCceEEecchhhhhcCcccccHHHHHHHHHHhhc---hhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          350 ----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAE---FNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       350 ----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~---~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                          ...++.+++.+...        ...++.++....   ..+...+..||||||+|.+...              .++
T Consensus        68 ~~~~~~~~~~~~~~~~~~--------~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~--------------~~~  125 (323)
T 1sxj_B           68 GRSYADGVLELNASDDRG--------IDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAG--------------AQQ  125 (323)
T ss_dssp             GGGHHHHEEEECTTSCCS--------HHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHH--------------HHH
T ss_pred             CCcccCCEEEecCccccC--------hHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHH--------------HHH
Confidence                33567777654321        223333333211   1111234789999999999877              788


Q ss_pred             HHHHHHhC
Q 012525          423 ALLKMLEG  430 (461)
Q Consensus       423 aLL~~LEg  430 (461)
                      +|++.|+.
T Consensus       126 ~L~~~le~  133 (323)
T 1sxj_B          126 ALRRTMEL  133 (323)
T ss_dssp             TTHHHHHH
T ss_pred             HHHHHHhc
Confidence            99999984

>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=99.00  E-value=1.4e-09  Score=108.61  Aligned_cols=84  Identities=17%  Similarity=0.187  Sum_probs=61.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc------CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV------NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l------~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                      .++||+||+|+|||++|+++|+.+      ...|+.++++..    ..  . ...++.++..+..........|+||||+
T Consensus        19 ~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~----~~--~-id~ir~li~~~~~~p~~~~~kvviIdea   91 (305)
T 2gno_A           19 ISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE----NI--G-IDDIRTIKDFLNYSPELYTRKYVIVHDC   91 (305)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS----CB--C-HHHHHHHHHHHTSCCSSSSSEEEEETTG
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcC----CC--C-HHHHHHHHHHHhhccccCCceEEEeccH
Confidence            579999999999999999999864      336666665421    11  1 3345566655544333346789999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      |.|...              .+++||+.||+
T Consensus        92 d~lt~~--------------a~naLLk~LEe  108 (305)
T 2gno_A           92 ERMTQQ--------------AANAFLKALEE  108 (305)
T ss_dssp             GGBCHH--------------HHHHTHHHHHS
T ss_pred             HHhCHH--------------HHHHHHHHHhC
Confidence            999987              89999999995

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.99  E-value=1.8e-09  Score=107.66  Aligned_cols=107  Identities=25%  Similarity=0.362  Sum_probs=71.7

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ ++||+.+++.|...+..            +                   ...|++|+||+|||||++|+++|+.+
T Consensus        23 ~~~~-~~g~~~~~~~L~~~i~~------------g-------------------~~~~~ll~Gp~G~GKTtla~~la~~l   70 (340)
T 1sxj_C           23 TLDE-VYGQNEVITTVRKFVDE------------G-------------------KLPHLLFYGPPGTGKTSTIVALAREI   70 (340)
T ss_dssp             SGGG-CCSCHHHHHHHHHHHHT------------T-------------------CCCCEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cHHH-hcCcHHHHHHHHHHHhc------------C-------------------CCceEEEECCCCCCHHHHHHHHHHHH
Confidence            4555 79999999988877730            1                   11459999999999999999999987


Q ss_pred             CC-----ceEEecchhhhhcCcccccHHHHHHHHHHhhc--hhhhccCceEEEEcCccccchhhhccccccccchHHHHH
Q 012525          350 NV-----PFVIADATTLTQAGYVGEDVESILYKLLAQAE--FNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQ  422 (461)
Q Consensus       350 ~~-----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~--~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~  422 (461)
                      ..     .++.+++++..     +   ...++..+....  .........|++|||+|.|...              .++
T Consensus        71 ~~~~~~~~~~~~~~~~~~-----~---~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~~--------------~~~  128 (340)
T 1sxj_C           71 YGKNYSNMVLELNASDDR-----G---IDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNA--------------AQN  128 (340)
T ss_dssp             HTTSHHHHEEEECTTSCC-----S---HHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHH--------------HHH
T ss_pred             cCCCccceEEEEcCcccc-----c---HHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCHH--------------HHH
Confidence            43     35555554321     1   122232222111  1111134679999999999877              789


Q ss_pred             HHHHHHhC
Q 012525          423 ALLKMLEG  430 (461)
Q Consensus       423 aLL~~LEg  430 (461)
                      +|++.||.
T Consensus       129 ~L~~~le~  136 (340)
T 1sxj_C          129 ALRRVIER  136 (340)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhc
Confidence            99999984

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.97  E-value=4.2e-10  Score=118.16  Aligned_cols=114  Identities=28%  Similarity=0.366  Sum_probs=71.1

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      |++ |+|++..++.|...+..                               ....|+||+||||||||++|++||+.+ 
T Consensus       179 ld~-iiGr~~~i~~l~~~l~r-------------------------------~~~~~~LL~G~pG~GKT~la~~la~~l~  226 (468)
T 3pxg_A          179 LDP-VIGRSKEIQRVIEVLSR-------------------------------RTKNNPVLIGEPGVGKTAIAEGLAQQII  226 (468)
T ss_dssp             SCC-CCCCHHHHHHHHHHHHC-------------------------------SSSCEEEEESCTTTTTHHHHHHHHHHHH
T ss_pred             CCC-ccCcHHHHHHHHHHHhc-------------------------------cCCCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            454 89999999988777620                               124689999999999999999999986 


Q ss_pred             ---------CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          350 ---------NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       350 ---------~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                               +.+|+.+++.    ..|.|+. +..+..++..+..    ..++|||||    ....              +
T Consensus       227 ~~~~p~~l~~~~~~~l~~~----~~~~g~~-e~~~~~~~~~~~~----~~~~iLfiD----~~~~--------------a  279 (468)
T 3pxg_A          227 NNEVPEILRDKRVMTLDMG----TKYRGEF-EDRLKKVMDEIRQ----AGNIILFID----AAID--------------A  279 (468)
T ss_dssp             SSCSCTTTSSCCEECC---------------CTTHHHHHHHHHT----CCCCEEEEC----C------------------
T ss_pred             hCCCChhhcCCeEEEeeCC----ccccchH-HHHHHHHHHHHHh----cCCeEEEEe----Cchh--------------H
Confidence                     6788888887    2344443 4455666655432    367899999    1111              6


Q ss_pred             HHHHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          421 QQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      ++.|+..|+.+             ++++|+++|.+.
T Consensus       280 ~~~L~~~L~~g-------------~v~vI~at~~~e  302 (468)
T 3pxg_A          280 SNILKPSLARG-------------ELQCIGATTLDE  302 (468)
T ss_dssp             ----CCCTTSS-------------SCEEEEECCTTT
T ss_pred             HHHHHHhhcCC-------------CEEEEecCCHHH
Confidence            77888888744             356677776654

>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=98.96  E-value=1.1e-09  Score=109.25  Aligned_cols=63  Identities=22%  Similarity=0.272  Sum_probs=49.3

Q ss_pred             hhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc---
Q 012525          273 KFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---  349 (461)
Q Consensus       273 ~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l---  349 (461)
                      +.++|++..++.|...+.....        .                   ..+.+++|+||+|||||++|+++++.+   
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~--------~-------------------~~~~~vll~G~~G~GKT~la~~l~~~~~~~   72 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVK--------N-------------------EVKFSNLFLGLTGTGKTFVSKYIFNEIEEV   72 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHT--------T-------------------CCCCEEEEEECTTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHc--------C-------------------CCCCcEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            4489999999999887742110        0                   113679999999999999999999987   


Q ss_pred             --------CCceEEecchhhh
Q 012525          350 --------NVPFVIADATTLT  362 (461)
Q Consensus       350 --------~~pfv~i~~s~l~  362 (461)
                              +.+++.+++....
T Consensus        73 ~~~~~~~~~~~~~~i~~~~~~   93 (384)
T 2qby_B           73 KKEDEEYKDVKQAYVNCREVG   93 (384)
T ss_dssp             HHHSSSSTTCEEEEEEHHHHC
T ss_pred             hhhhcCCCCceEEEEECccCC
Confidence                    8899999987543

>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=98.95  E-value=1.2e-09  Score=122.43  Aligned_cols=121  Identities=24%  Similarity=0.338  Sum_probs=69.9

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++..++.+...+..                               ....++||+||||||||++|++||+.+
T Consensus       168 ~ld~-viGr~~~i~~l~~~l~~-------------------------------~~~~~vlL~G~pG~GKT~la~~la~~l  215 (854)
T 1qvr_A          168 KLDP-VIGRDEEIRRVIQILLR-------------------------------RTKNNPVLIGEPGVGKTAIVEGLAQRI  215 (854)
T ss_dssp             CSCC-CCSCHHHHHHHHHHHHC-------------------------------SSCCCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCcc-cCCcHHHHHHHHHHHhc-------------------------------CCCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            3444 79999888877776620                               123679999999999999999999987


Q ss_pred             ----------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          350 ----------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       350 ----------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                                +.+++.+++..+.. ..+.|+. +..+..++..+...   ..+.||||||+|.+.......      ...
T Consensus       216 ~~~~~p~~l~~~~~~~l~~~~l~~g~~~~g~~-~~~l~~~~~~~~~~---~~~~iL~IDEi~~l~~~~~~~------g~~  285 (854)
T 1qvr_A          216 VKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEF-EERLKAVIQEVVQS---QGEVILFIDELHTVVGAGKAE------GAV  285 (854)
T ss_dssp             HHTCSCTTSTTCEEEEECC-----------CH-HHHHHHHHHHHHTT---CSSEEEEECCC-------------------
T ss_pred             hcCCCchhhcCCeEEEeehHHhhccCccchHH-HHHHHHHHHHHHhc---CCCeEEEEecHHHHhccCCcc------chH
Confidence                      77899999987763 2345543 66777777654421   256799999999998653221      112


Q ss_pred             HHHHHHHHHHhCce
Q 012525          419 GVQQALLKMLEGTE  432 (461)
Q Consensus       419 ~v~~aLL~~LEg~~  432 (461)
                      .+.+.|+.+|+...
T Consensus       286 ~~~~~L~~~l~~~~  299 (854)
T 1qvr_A          286 DAGNMLKPALARGE  299 (854)
T ss_dssp             ------HHHHHTTC
T ss_pred             HHHHHHHHHHhCCC
Confidence            26778888887543

>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=98.95  E-value=1.5e-09  Score=119.65  Aligned_cols=121  Identities=26%  Similarity=0.383  Sum_probs=82.2

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..+++ |+|++..++.+...+..                               ..+.++||+||||||||++|++||+.
T Consensus       183 ~~~d~-~iGr~~~i~~l~~~l~~-------------------------------~~~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          183 GGIDP-LIGREKELERAIQVLCR-------------------------------RRKNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             TCSCC-CCSCHHHHHHHHHHHTS-------------------------------SSSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCC-ccCCHHHHHHHHHHHhc-------------------------------cCCCCeEEEcCCCCCHHHHHHHHHHH
Confidence            34555 89999998887776620                               12478999999999999999999987


Q ss_pred             c----------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccch
Q 012525          349 V----------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSG  417 (461)
Q Consensus       349 l----------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~  417 (461)
                      +          +..++.++...+.. ..+.|. .+..++.++.....    ..++||||||+|.+...+...     .+.
T Consensus       231 l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~-~e~~l~~~~~~~~~----~~~~iL~IDEi~~l~~~~~~~-----~~~  300 (758)
T 1r6b_X          231 IVQGDVPEVMADCTIYSLDIGSLLAGTKYRGD-FEKRFKALLKQLEQ----DTNSILFIDEIHTIIGAGAAS-----GGQ  300 (758)
T ss_dssp             HHHTCSCGGGTTCEEEECCCC---CCCCCSSC-HHHHHHHHHHHHSS----SSCEEEEETTTTTTTTSCCSS-----SCH
T ss_pred             HHhCCCChhhcCCEEEEEcHHHHhccccccch-HHHHHHHHHHHHHh----cCCeEEEEechHHHhhcCCCC-----cch
Confidence            7          55677777776653 234554 47777887765543    367899999999997653211     112


Q ss_pred             HHHHHHHHHHHhCc
Q 012525          418 EGVQQALLKMLEGT  431 (461)
Q Consensus       418 ~~v~~aLL~~LEg~  431 (461)
                      ..+.+.|..+|+..
T Consensus       301 ~~~~~~L~~~l~~~  314 (758)
T 1r6b_X          301 VDAANLIKPLLSSG  314 (758)
T ss_dssp             HHHHHHHSSCSSSC
T ss_pred             HHHHHHHHHHHhCC
Confidence            23566666666643

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.92  E-value=3.2e-09  Score=105.22  Aligned_cols=102  Identities=24%  Similarity=0.330  Sum_probs=66.7

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc----
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV----  349 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l----  349 (461)
                      .++|++..++.|...+..        ...                   .....+++|+||||||||++|+++++.+    
T Consensus        20 ~~~gr~~~~~~l~~~l~~--------~~~-------------------~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~   72 (387)
T 2v1u_A           20 VLPHREAELRRLAEVLAP--------ALR-------------------GEKPSNALLYGLTGTGKTAVARLVLRRLEARA   72 (387)
T ss_dssp             CCTTCHHHHHHHHHTTGG--------GTS-------------------SCCCCCEEECBCTTSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH--------HHc-------------------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHH
Confidence            479999998888776621        000                   1224789999999999999999999988    


Q ss_pred             -----CCceEEecchhhhhc---------------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          350 -----NVPFVIADATTLTQA---------------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       350 -----~~pfv~i~~s~l~~~---------------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                           +.+++.+++......               ...+......+..++....   ...++.||||||+|.+...
T Consensus        73 ~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~---~~~~~~vlilDEi~~l~~~  145 (387)
T 2v1u_A           73 SSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLS---RLRGIYIIVLDEIDFLPKR  145 (387)
T ss_dssp             HHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHT---TSCSEEEEEEETTTHHHHS
T ss_pred             hccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHh---ccCCeEEEEEccHhhhccc
Confidence                 788899987653311               0112222333333333221   1224669999999998765

>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=98.90  E-value=1.8e-09  Score=106.74  Aligned_cols=86  Identities=16%  Similarity=0.278  Sum_probs=56.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      ..+++|+||||||||+||+++++.+   +.+++.+++.++... +.... .......|...     ...+.|||||||+.
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~~~~~-~~~~~-~~~~~~~~~~~-----~~~~~vL~iDEi~~  109 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQA-MVEHL-KKGTINEFRNM-----YKSVDLLLLDDVQF  109 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHH-HHHHH-HHTCHHHHHHH-----HHTCSEEEEECGGG
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH-HHHHH-HcCcHHHHHHH-----hcCCCEEEEcCccc
Confidence            3679999999999999999999988   889999998876531 11110 00000111111     12467999999999


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHh
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +..++.            .++.|+..|+
T Consensus       110 l~~~~~------------~~~~l~~~l~  125 (324)
T 1l8q_A          110 LSGKER------------TQIEFFHIFN  125 (324)
T ss_dssp             GTTCHH------------HHHHHHHHHH
T ss_pred             ccCChH------------HHHHHHHHHH
Confidence            886421            4666666655

>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=98.88  E-value=1.2e-08  Score=102.13  Aligned_cols=86  Identities=16%  Similarity=0.205  Sum_probs=59.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQ  381 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~  381 (461)
                      +.+||+||+|||||++|+++|+.+...                        ++.++...-  ..  ... .+.++.++..
T Consensus        25 ~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~--~~--~~~-i~~ir~l~~~   99 (334)
T 1a5t_A           25 HALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG--KN--TLG-VDAVREVTEK   99 (334)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT--CS--SBC-HHHHHHHHHH
T ss_pred             eeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecccc--CC--CCC-HHHHHHHHHH
Confidence            459999999999999999999987643                        222222100  00  012 3445666655


Q ss_pred             hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       382 a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      ...........|+||||+|.|...              .+++||+.||+
T Consensus       100 ~~~~~~~~~~kvviIdead~l~~~--------------a~naLLk~lEe  134 (334)
T 1a5t_A          100 LNEHARLGGAKVVWVTDAALLTDA--------------AANALLKTLEE  134 (334)
T ss_dssp             TTSCCTTSSCEEEEESCGGGBCHH--------------HHHHHHHHHTS
T ss_pred             HhhccccCCcEEEEECchhhcCHH--------------HHHHHHHHhcC
Confidence            543333456789999999999887              78999999995

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.88  E-value=5e-09  Score=105.54  Aligned_cols=77  Identities=12%  Similarity=0.126  Sum_probs=53.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc----------CCceEEecchhhhhc---------Ccccc-----cHHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV----------NVPFVIADATTLTQA---------GYVGE-----DVESILYKLLA  380 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l----------~~pfv~i~~s~l~~~---------g~vGe-----~~e~~L~~lf~  380 (461)
                      +.+++|+||||||||++++.+++++          ...++.++|..+...         .+.|+     .....+..+|.
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            4789999999999999999999988          346788998764421         01111     12445666665


Q ss_pred             hhchhhhccCceEEEEcCccccc
Q 012525          381 QAEFNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       381 ~a~~~v~~a~~gVLfIDEID~L~  403 (461)
                      ....  ......||||||||.|.
T Consensus       125 ~~~~--~~~~~~ii~lDE~d~l~  145 (318)
T 3te6_A          125 NVPK--AKKRKTLILIQNPENLL  145 (318)
T ss_dssp             HSCG--GGSCEEEEEEECCSSSC
T ss_pred             Hhhh--ccCCceEEEEecHHHhh
Confidence            4311  12356799999999998

>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=98.86  E-value=7.4e-09  Score=103.58  Aligned_cols=108  Identities=31%  Similarity=0.497  Sum_probs=73.2

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ ++|++.+++.|...+.....+        +                  ....+++|+|||||||||||++||..+
T Consensus        23 ~l~~-~~g~~~~~~~l~~~i~~~~~~--------~------------------~~~~~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           23 SLDE-FIGQENVKKKLSLALEAAKMR--------G------------------EVLDHVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             SGGG-CCSCHHHHHHHHHHHHHHHHH--------T------------------CCCCCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             cHHH-ccCcHHHHHHHHHHHHHHHhc--------C------------------CCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            4555 689999988888777321100        0                  113679999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.++...+...+..        ...+..++..      .....|+||||++.+...              +++.|+..|+
T Consensus        76 ~~~~~~~sg~~~~~--------~~~l~~~~~~------~~~~~v~~iDE~~~l~~~--------------~~e~L~~~~~  127 (334)
T 1in4_A           76 QTNIHVTSGPVLVK--------QGDMAAILTS------LERGDVLFIDEIHRLNKA--------------VEELLYSAIE  127 (334)
T ss_dssp             TCCEEEEETTTCCS--------HHHHHHHHHH------CCTTCEEEEETGGGCCHH--------------HHHHHHHHHH
T ss_pred             CCCEEEEechHhcC--------HHHHHHHHHH------ccCCCEEEEcchhhcCHH--------------HHHHHHHHHH
Confidence            98876655543321        1222222221      124569999999998865              6778888887


Q ss_pred             Cce
Q 012525          430 GTE  432 (461)
Q Consensus       430 g~~  432 (461)
                      ...
T Consensus       128 ~~~  130 (334)
T 1in4_A          128 DFQ  130 (334)
T ss_dssp             TSC
T ss_pred             hcc
Confidence            543

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.86  E-value=1.1e-08  Score=92.54  Aligned_cols=102  Identities=14%  Similarity=0.139  Sum_probs=60.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc----CCceEEecchhhhhcCcccccHHHHHHHHHHhhch---hhhccCceEEEEc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEF---NVEAAQQGMVYID  397 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~---~v~~a~~gVLfID  397 (461)
                      +.+++|+||+|||||||+++|+..+    +..++.++..++...          +...+.....   .-...++.+||||
T Consensus        38 g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~llilD  107 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLIFR----------LKHLMDEGKDTKFLKTVLNSPVLVLD  107 (180)
T ss_dssp             CCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHHHHH----------HHHHHHHTCCSHHHHHHHTCSEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHHHHH----------HHHHhcCchHHHHHHHhcCCCEEEEe
Confidence            4779999999999999999999877    455666666555421          1111110000   0001256799999


Q ss_pred             CccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          398 EVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       398 EID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                      |++.....            ...+..|+.+|+...          .....+|.|||...+.
T Consensus       108 E~~~~~~~------------~~~~~~l~~ll~~~~----------~~~~~ii~tsn~~~~~  146 (180)
T 3ec2_A          108 DLGSERLS------------DWQRELISYIITYRY----------NNLKSTIITTNYSLQR  146 (180)
T ss_dssp             TCSSSCCC------------HHHHHHHHHHHHHHH----------HTTCEEEEECCCCSCC
T ss_pred             CCCCCcCC------------HHHHHHHHHHHHHHH----------HcCCCEEEEcCCChhH
Confidence            99843221            014556666665221          1234677788877654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.86  E-value=2e-09  Score=118.90  Aligned_cols=114  Identities=28%  Similarity=0.367  Sum_probs=72.1

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      +++ |+|++..++.|...+..                               ....|+||+||||||||++|++||+.+ 
T Consensus       179 ld~-iiG~~~~i~~l~~~l~~-------------------------------~~~~~vLL~G~pGtGKT~la~~la~~l~  226 (758)
T 3pxi_A          179 LDP-VIGRSKEIQRVIEVLSR-------------------------------RTKNNPVLIGEPGVGKTAIAEGLAQQII  226 (758)
T ss_dssp             SCC-CCCCHHHHHHHHHHHHC-------------------------------SSSCEEEEESCTTTTTHHHHHHHHHHHH
T ss_pred             CCC-ccCchHHHHHHHHHHhC-------------------------------CCCCCeEEECCCCCCHHHHHHHHHHHHh
Confidence            444 89999999988877720                               124789999999999999999999987 


Q ss_pred             ---------CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHH
Q 012525          350 ---------NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       350 ---------~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                               +..++.+++    ...|.|+. +..++.+|..+..    ..++|||||    ....              +
T Consensus       227 ~~~~p~~l~~~~~~~~~~----g~~~~G~~-e~~l~~~~~~~~~----~~~~iLfiD----~~~~--------------~  279 (758)
T 3pxi_A          227 NNEVPEILRDKRVMTLDM----GTKYRGEF-EDRLKKVMDEIRQ----AGNIILFID----AAID--------------A  279 (758)
T ss_dssp             SSCSCTTTSSCCEECC---------------CTTHHHHHHHHHT----CCCCEEEEC----C------------------
T ss_pred             cCCCChhhcCCeEEEecc----cccccchH-HHHHHHHHHHHHh----cCCEEEEEc----Cchh--------------H
Confidence                     677887777    23355543 5566777765543    478899999    1111              6


Q ss_pred             HHHHHHHHhCceeeeecceeeecCCeEEEecCCCCc
Q 012525          421 QQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~  456 (461)
                      ++.|+..|+..             ++++|+++|...
T Consensus       280 ~~~L~~~l~~~-------------~v~~I~at~~~~  302 (758)
T 3pxi_A          280 SNILKPSLARG-------------ELQCIGATTLDE  302 (758)
T ss_dssp             ----CCCTTSS-------------SCEEEEECCTTT
T ss_pred             HHHHHHHHhcC-------------CEEEEeCCChHH
Confidence            77888888743             356666666554

>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=98.85  E-value=9.2e-09  Score=107.23  Aligned_cols=86  Identities=17%  Similarity=0.276  Sum_probs=56.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      .+++|+||||||||+||++|++.+     +.+++.+++..+... +.... .......|....    ...+.|||||||+
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~~~~-~~~~~-~~~~~~~~~~~~----~~~~~vL~IDEi~  204 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLND-LVDSM-KEGKLNEFREKY----RKKVDILLIDDVQ  204 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHHHHH-HHHHH-HTTCHHHHHHHH----TTTCSEEEEECGG
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHH-HHHHH-HcccHHHHHHHh----cCCCCEEEEeCcc
Confidence            679999999999999999999988     788899888776421 11000 000000111110    1156799999999


Q ss_pred             ccchhhhccccccccchHHHHHHHHHHHh
Q 012525          401 KITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       401 ~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      .+..++.            .++.|+..|+
T Consensus       205 ~l~~~~~------------~q~~l~~~l~  221 (440)
T 2z4s_A          205 FLIGKTG------------VQTELFHTFN  221 (440)
T ss_dssp             GGSSCHH------------HHHHHHHHHH
T ss_pred             cccCChH------------HHHHHHHHHH
Confidence            9886411            5667777765

>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=98.84  E-value=1.4e-08  Score=101.13  Aligned_cols=113  Identities=15%  Similarity=0.209  Sum_probs=73.0

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCC--cEEEEccCCCchHHHHHHHHHhc--
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKS--NVLLMGPTGSGKTLLAKTLARHV--  349 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~--~VLL~GPPGTGKTtLAraLA~~l--  349 (461)
                      .++|++..++.|...+.....    .                       ..+.  +++|+||+|||||++++++++.+  
T Consensus        18 ~l~gr~~~~~~l~~~l~~~~~----~-----------------------~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~   70 (389)
T 1fnn_A           18 RLPHREQQLQQLDILLGNWLR----N-----------------------PGHHYPRATLLGRPGTGKTVTLRKLWELYKD   70 (389)
T ss_dssp             CCTTCHHHHHHHHHHHHHHHH----S-----------------------TTSSCCEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             CCCChHHHHHHHHHHHHHHHc----C-----------------------CCCCCCeEEEECCCCCCHHHHHHHHHHHHhh
Confidence            389999999998887742111    0                       0123  79999999999999999999988  


Q ss_pred             --CCceEEecchhhhhc-----------C----cccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          350 --NVPFVIADATTLTQA-----------G----YVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       350 --~~pfv~i~~s~l~~~-----------g----~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                        +..++.+++......           +    ..+......+..+.....   ....+.||||||++.+...       
T Consensus        71 ~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~---~~~~~~vlilDE~~~l~~~-------  140 (389)
T 1fnn_A           71 KTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLR---ERDLYMFLVLDDAFNLAPD-------  140 (389)
T ss_dssp             SCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHH---HTTCCEEEEEETGGGSCHH-------
T ss_pred             hcCeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHh---hcCCeEEEEEECccccchH-------
Confidence              567888887543310           0    011122222222221111   1134679999999998554       


Q ss_pred             cccchHHHHHHHHHHHhC
Q 012525          413 RDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg  430 (461)
                             .+..|+..++.
T Consensus       141 -------~~~~L~~~~~~  151 (389)
T 1fnn_A          141 -------ILSTFIRLGQE  151 (389)
T ss_dssp             -------HHHHHHHHTTC
T ss_pred             -------HHHHHHHHHHh
Confidence                   78899888874

>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=98.81  E-value=1.6e-08  Score=100.22  Aligned_cols=49  Identities=22%  Similarity=0.367  Sum_probs=36.4

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ ++|++.+++.|...+.           ..                   ....+++|+||+||||||++++||+.+
T Consensus        12 ~~~~-~vg~~~~~~~l~~~~~-----------~~-------------------~~~~~~ll~Gp~G~GKTtl~~~la~~l   60 (354)
T 1sxj_E           12 SLNA-LSHNEELTNFLKSLSD-----------QP-------------------RDLPHLLLYGPNGTGKKTRCMALLESI   60 (354)
T ss_dssp             SGGG-CCSCHHHHHHHHTTTT-----------CT-------------------TCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CHHH-hcCCHHHHHHHHHHHh-----------hC-------------------CCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3555 7899998887766551           00                   012459999999999999999999964

>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=98.77  E-value=2.6e-08  Score=92.01  Aligned_cols=77  Identities=19%  Similarity=0.283  Sum_probs=54.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      ..+++|+||||||||++|+++++.+.   .+++.+++.++... + .    ..    +.      ....+.||||||++.
T Consensus        52 ~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~~-~-~----~~----~~------~~~~~~vliiDe~~~  115 (242)
T 3bos_A           52 VQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASI-S-T----AL----LE------GLEQFDLICIDDVDA  115 (242)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGGGS-C-G----GG----GT------TGGGSSEEEEETGGG
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHH-H-H----HH----HH------hccCCCEEEEecccc
Confidence            37899999999999999999998774   67788888776632 1 0    00    00      013567999999998


Q ss_pred             cchhhhccccccccchHHHHHHHHHHHh
Q 012525          402 ITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       402 L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.....            .++.|+.+|+
T Consensus       116 ~~~~~~------------~~~~l~~~l~  131 (242)
T 3bos_A          116 VAGHPL------------WEEAIFDLYN  131 (242)
T ss_dssp             GTTCHH------------HHHHHHHHHH
T ss_pred             ccCCHH------------HHHHHHHHHH
Confidence            876511            3666777765

>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=98.77  E-value=2.1e-08  Score=99.16  Aligned_cols=117  Identities=17%  Similarity=0.289  Sum_probs=74.5

Q ss_pred             hcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc----
Q 012525          274 FVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV----  349 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l----  349 (461)
                      .++|++...+.|...+...        ..                   .....+++|+||+|||||+|++++++.+    
T Consensus        21 ~~~gr~~e~~~l~~~l~~~--------~~-------------------~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~   73 (386)
T 2qby_A           21 ELPHREDQIRKIASILAPL--------YR-------------------EEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKF   73 (386)
T ss_dssp             CCTTCHHHHHHHHHSSGGG--------GG-------------------TCCCCCEEEEECTTSSHHHHHHHHHHHHHHHT
T ss_pred             CCCChHHHHHHHHHHHHHH--------Hc-------------------CCCCCeEEEECCCCCCHHHHHHHHHHHHHHHh
Confidence            3799999988887766210        00                   0124679999999999999999999988    


Q ss_pred             --CCceEEecchhhhhc---------------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccc
Q 012525          350 --NVPFVIADATTLTQA---------------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNIS  412 (461)
Q Consensus       350 --~~pfv~i~~s~l~~~---------------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~  412 (461)
                        +.+++.+++......               ...+......+..++.....   ...+.||||||++.+.....     
T Consensus        74 ~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~---~~~~~vlilDE~~~l~~~~~-----  145 (386)
T 2qby_A           74 LGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRD---YGSQVVIVLDEIDAFVKKYN-----  145 (386)
T ss_dssp             CSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHT---CCSCEEEEEETHHHHHHSSC-----
T ss_pred             cCCceEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhc---cCCeEEEEEcChhhhhccCc-----
Confidence              788888887643210               01122223333333322211   12377999999999875410     


Q ss_pred             cccchHHHHHHHHHHHhC
Q 012525          413 RDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       413 ~~~s~~~v~~aLL~~LEg  430 (461)
                           ..++..|+..++.
T Consensus       146 -----~~~l~~l~~~~~~  158 (386)
T 2qby_A          146 -----DDILYKLSRINSE  158 (386)
T ss_dssp             -----STHHHHHHHHHHS
T ss_pred             -----CHHHHHHhhchhh
Confidence                 0167788888863

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.60  E-value=1.5e-08  Score=92.86  Aligned_cols=37  Identities=32%  Similarity=0.435  Sum_probs=31.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~  362 (461)
                      .+++|+||+|||||+||++|++.+   +.+++.+++.++.
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~   94 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELF   94 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHHH
Confidence            679999999999999999999977   5677777777654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.60  E-value=5e-08  Score=87.16  Aligned_cols=60  Identities=20%  Similarity=0.331  Sum_probs=45.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDK  401 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~  401 (461)
                      ...++|+||+|+|||+|+++++..+   +..++.++..++...     .        +        ..+..+|+|||++.
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~-----~--------~--------~~~~~lLilDE~~~   94 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLT-----D--------A--------AFEAEYLAVDQVEK   94 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCC-----G--------G--------GGGCSEEEEESTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHH-----H--------H--------HhCCCEEEEeCccc
Confidence            4679999999999999999999977   556777777665531     0        0        12456999999998


Q ss_pred             cchh
Q 012525          402 ITKK  405 (461)
Q Consensus       402 L~~~  405 (461)
                      +...
T Consensus        95 ~~~~   98 (149)
T 2kjq_A           95 LGNE   98 (149)
T ss_dssp             CCSH
T ss_pred             cChH
Confidence            7665

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.42  E-value=1.5e-07  Score=89.82  Aligned_cols=99  Identities=10%  Similarity=0.168  Sum_probs=58.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      .++||+||||||||++|.+||+.+...++.+..+.   ..+.           +..      .....||+|||++.-.- 
T Consensus        59 n~ili~GPPGtGKTt~a~ala~~l~g~i~~fans~---s~f~-----------l~~------l~~~kIiiLDEad~~~~-  117 (212)
T 1tue_A           59 NCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNST---SHFW-----------LEP------LTDTKVAMLDDATTTCW-  117 (212)
T ss_dssp             SEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCSS---SCGG-----------GGG------GTTCSSEEEEEECHHHH-
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeeeEEecc---chhh-----------hcc------cCCCCEEEEECCCchhH-
Confidence            57999999999999999999999865433221110   0000           000      01234899999994321 


Q ss_pred             hhccccccccchHHHHHHHHHHHhCceeeeecceee--ecCCeEEEecCCCCcC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSK--VSRDNLYIKTSGLDSK  457 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~--~~rd~IiI~TsNid~e  457 (461)
                                  +.+...+..+|||..+.+...-+.  .....-+|.|||++..
T Consensus       118 ------------~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~  159 (212)
T 1tue_A          118 ------------TYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPA  159 (212)
T ss_dssp             ------------HHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTT
T ss_pred             ------------HHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcc
Confidence                        124567888999986665433111  1123467788888654

>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=98.42  E-value=5.4e-07  Score=107.44  Aligned_cols=159  Identities=16%  Similarity=0.108  Sum_probs=85.2

Q ss_pred             HHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHh---------hhccCCCCCchhhhhccccc--cccccCCcEEEEccC
Q 012525          266 EICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHA---------NLKKGSGAEPKTAAAVDNDD--NVELEKSNVLLMGPT  334 (461)
Q Consensus       266 el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~---------~~~~g~~~s~~~~~~~~~~~--~~~~~~~~VLL~GPP  334 (461)
                      +....|++ |-|.+++|+.+.+++....+.-+..         ....-...+..+..+ |.+.  .-.+..+.+||+|||
T Consensus      1014 ~~~~~~~~-~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tG~~gl-D~~lg~GG~p~g~~~l~~G~~ 1091 (1706)
T 3cmw_A         1014 ASGSSTGS-MSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSL-DIALGAGGLPMGRIVEIYGPE 1091 (1706)
T ss_dssp             -----------CTTHHHHHHHHHHHHHHHHHHCGGGSEEGGGCGGGSCCEECCSCHHH-HHHTSSSSEETTSEEEEECST
T ss_pred             cCCceeee-cCCccHHHHHHHHHHHHHHhhccCcccchhchhhhhccccccccCchhH-HHHhccCCCCCCCEEEEEcCC
Confidence            33455555 7899999999988887554321110         000000000001000 0111  112334569999999


Q ss_pred             CCchHHHHHHHHHhc---CCceEEecchh----hhh-------cCcccc---cHHHHHHHHHHhhchhhhccCceEEEEc
Q 012525          335 GSGKTLLAKTLARHV---NVPFVIADATT----LTQ-------AGYVGE---DVESILYKLLAQAEFNVEAAQQGMVYID  397 (461)
Q Consensus       335 GTGKTtLAraLA~~l---~~pfv~i~~s~----l~~-------~g~vGe---~~e~~L~~lf~~a~~~v~~a~~gVLfID  397 (461)
                      |||||+||++++.+.   +.+.+.++...    +..       ..|+++   .-|..++.++..++.    ..+++||+|
T Consensus      1092 g~GKT~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~----~~~~~i~~d 1167 (1706)
T 3cmw_A         1092 SSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS----GAVDVIVVD 1167 (1706)
T ss_dssp             TSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH----TCCSEEEES
T ss_pred             CCChHHHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHh----cCCeEEEeC
Confidence            999999999999766   34544444433    221       235555   136777777765543    368899999


Q ss_pred             Cccccchhhhcc-cccc-c-cchHHHHHHHHHHHhC
Q 012525          398 EVDKITKKAESL-NISR-D-VSGEGVQQALLKMLEG  430 (461)
Q Consensus       398 EID~L~~~R~~~-~~~~-~-~s~~~v~~aLL~~LEg  430 (461)
                      ||++|.+.++.. +.+. + .-..++++++|..|++
T Consensus      1168 ~~~al~~~~~~~g~~~~~~~~~~~r~~~q~l~~~~~ 1203 (1706)
T 3cmw_A         1168 SVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAG 1203 (1706)
T ss_dssp             CGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHH
T ss_pred             chHhcCcccccccccccccccHHHHHHHHHHHHHHh
Confidence            999999986521 1111 1 2234467888888875

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.37  E-value=3.5e-08  Score=98.18  Aligned_cols=38  Identities=21%  Similarity=0.408  Sum_probs=31.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC----CceEEecchhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN----VPFVIADATTLT  362 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~----~pfv~i~~s~l~  362 (461)
                      ..+++|+||||||||+||++||+.+.    .+++.+.+.++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l~  193 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFA  193 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHHH
Confidence            36899999999999999999998664    677777776554

>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=98.35  E-value=7.4e-07  Score=110.23  Aligned_cols=115  Identities=16%  Similarity=0.135  Sum_probs=71.4

Q ss_pred             CCcEEEEccCCCchHHHH-HHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhh-c------hhh----hccCce
Q 012525          325 KSNVLLMGPTGSGKTLLA-KTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA-E------FNV----EAAQQG  392 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLA-raLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a-~------~~v----~~a~~g  392 (461)
                      .++|||+||||||||++| +++++..+..++.++++..+..        ..+...+... .      +.+    ...+..
T Consensus      1267 ~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infsa~ts~--------~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~ 1338 (2695)
T 4akg_A         1267 KRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTT--------EHILSALHRHTNYVTTSKGLTLLPKSDIKNL 1338 (2695)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECCTTCCH--------HHHHHHHHHHBCCEEETTTEEEEEBSSSSCE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEeecCCCH--------HHHHHHHHHHhhhccccCCccccCCCCCceE
Confidence            378999999999999999 5555555677888887766532        2233333221 1      101    123457


Q ss_pred             EEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc-eeeecCCeEEEecCCCC
Q 012525          393 MVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       393 VLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r~~~rd~IiI~TsNid  455 (461)
                      ||||||||....++-        +....+..|.++||.+.+..... ......++.+|+|+|..
T Consensus      1339 VlFiDEinmp~~d~y--------g~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp 1394 (2695)
T 4akg_A         1339 VLFCDEINLPKLDKY--------GSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPP 1394 (2695)
T ss_dssp             EEEEETTTCSCCCSS--------SCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCT
T ss_pred             EEEeccccccccccc--------CchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCC
Confidence            999999996443321        11126788888999554443322 22222478999999975

>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=98.26  E-value=1.9e-06  Score=106.58  Aligned_cols=105  Identities=19%  Similarity=0.204  Sum_probs=74.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      ..++++.||+|||||++++.||+.++.+++.++|++-..        ...+..+|..+..     .+..++||||+++..
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld--------~~~lg~~~~g~~~-----~Gaw~~~DE~nr~~~  711 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFD--------YQVLSRLLVGITQ-----IGAWGCFDEFNRLDE  711 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCC--------HHHHHHHHHHHHH-----HTCEEEEETTTSSCH
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCC--------hhHhhHHHHHHHh-----cCCEeeehhhhhcCh
Confidence            567899999999999999999999999999999997653        2333444433221     356999999999888


Q ss_pred             hhhccccccccchHHHHHHH-------HHHHhCceeeeecc--eeeecCCeEEEecCCCCc
Q 012525          405 KAESLNISRDVSGEGVQQAL-------LKMLEGTETKTFAA--VSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aL-------L~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~  456 (461)
                      +              +++.|       +..|......+...  ......++.++.|.|.+.
T Consensus       712 e--------------vLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy  758 (2695)
T 4akg_A          712 K--------------VLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGY  758 (2695)
T ss_dssp             H--------------HHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCS
T ss_pred             H--------------HHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCc
Confidence            7              55554       44444444333333  333334789999999763

>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=98.24  E-value=1.8e-06  Score=85.07  Aligned_cols=97  Identities=20%  Similarity=0.305  Sum_probs=56.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      ..+|+|+||||||||++|++||+.+.. +-.++...   ..+.           +..      ....-|+++||.. +..
T Consensus       104 ~n~~~l~GppgtGKt~~a~ala~~~~l-~G~vn~~~---~~f~-----------l~~------~~~k~i~l~Ee~~-~~~  161 (267)
T 1u0j_A          104 RNTIWLFGPATTGKTNIAEAIAHTVPF-YGCVNWTN---ENFP-----------FND------CVDKMVIWWEEGK-MTA  161 (267)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHSSC-EEECCTTC---SSCT-----------TGG------GSSCSEEEECSCC-EET
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhhhcc-cceeeccc---cccc-----------ccc------ccccEEEEecccc-chh
Confidence            356999999999999999999997644 22232211   1110           110      1133466666666 444


Q ss_pred             hhhccccccccchHHHHHHHHHHHhCceeeeeccee--eecCCeEEEecCCCCcC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVS--KVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r--~~~rd~IiI~TsNid~e  457 (461)
                      .              +++.|..+|+|..+.+....+  ......-+|.|+|.+..
T Consensus       162 d--------------~~~~lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~  202 (267)
T 1u0j_A          162 K--------------VVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMC  202 (267)
T ss_dssp             T--------------THHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTT
T ss_pred             H--------------HHHHHHHHhCCCcEEEecCcCCcccccCCCEEEEecCCcc
Confidence            4              567888899988777654422  11124566778887543

>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=98.10  E-value=6.4e-06  Score=82.56  Aligned_cols=61  Identities=23%  Similarity=0.230  Sum_probs=42.5

Q ss_pred             hcCChHHHHHHHHHHH-HHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEE--EccCCCchHHHHHHHHHhc-
Q 012525          274 FVIGQEKAKKVLSVAV-YNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLL--MGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       274 ~VvGqd~aK~~L~~al-~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL--~GPPGTGKTtLAraLA~~l-  349 (461)
                      .++|++...+.|...+ .....       .                  ......+++|  +||+|||||+|++.+++.+ 
T Consensus        23 ~l~gR~~el~~l~~~l~~~~~~-------~------------------~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~   77 (412)
T 1w5s_A           23 ELRVRRGEAEALARIYLNRLLS-------G------------------AGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVS   77 (412)
T ss_dssp             SCSSSCHHHHHHHHHHHHHHHT-------S------------------SCBCCEEEEEECTTCCSSSHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHhHHHhc-------C------------------CCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHH
Confidence            3789998888887766 31100       0                  0011357889  9999999999999999876 


Q ss_pred             --------CCceEEecch
Q 012525          350 --------NVPFVIADAT  359 (461)
Q Consensus       350 --------~~pfv~i~~s  359 (461)
                              +..++.+++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~   95 (412)
T 1w5s_A           78 EAAAKEGLTVKQAYVNAF   95 (412)
T ss_dssp             HHHHHTTCCEEEEEEEGG
T ss_pred             HHHhccCCceeEEEEECC
Confidence                    4466777763

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.05  E-value=3.1e-05  Score=75.33  Aligned_cols=51  Identities=20%  Similarity=0.292  Sum_probs=40.3

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ++|+++..+.|...+..                                 ...++|+||+|+|||+|++.+++.++  ++
T Consensus        14 ~~gR~~el~~L~~~l~~---------------------------------~~~v~i~G~~G~GKT~Ll~~~~~~~~--~~   58 (350)
T 2qen_A           14 IFDREEESRKLEESLEN---------------------------------YPLTLLLGIRRVGKSSLLRAFLNERP--GI   58 (350)
T ss_dssp             SCSCHHHHHHHHHHHHH---------------------------------CSEEEEECCTTSSHHHHHHHHHHHSS--EE
T ss_pred             cCChHHHHHHHHHHHhc---------------------------------CCeEEEECCCcCCHHHHHHHHHHHcC--cE
Confidence            78999988888777620                                 14689999999999999999999875  55


Q ss_pred             Eecchh
Q 012525          355 IADATT  360 (461)
Q Consensus       355 ~i~~s~  360 (461)
                      .+++..
T Consensus        59 ~~~~~~   64 (350)
T 2qen_A           59 LIDCRE   64 (350)
T ss_dssp             EEEHHH
T ss_pred             EEEeec
Confidence            565543

>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=98.02  E-value=1.3e-05  Score=81.05  Aligned_cols=74  Identities=18%  Similarity=0.265  Sum_probs=44.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC--ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV--PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~--pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      ...++|+||||||||+||..+|...+.  .|+.+...+.... +. ...+..+..++....    . .. +||||||+.+
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~-~~-~~le~~l~~i~~~l~----~-~~-LLVIDsI~aL  194 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSG-YN-TDFNVFVDDIARAML----Q-HR-VIVIDSLKNV  194 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTT-CB-CCHHHHHHHHHHHHH----H-CS-EEEEECCTTT
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhh-hh-cCHHHHHHHHHHHHh----h-CC-EEEEeccccc
Confidence            455799999999999999999986543  3555522222211 11 333555544443322    2 22 9999999998


Q ss_pred             chhh
Q 012525          403 TKKA  406 (461)
Q Consensus       403 ~~~R  406 (461)
                      ....
T Consensus       195 ~~~~  198 (331)
T 2vhj_A          195 IGAA  198 (331)
T ss_dssp             C---
T ss_pred             cccc
Confidence            6653

>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=97.78  E-value=4.7e-05  Score=74.12  Aligned_cols=35  Identities=23%  Similarity=0.428  Sum_probs=29.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATT  360 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~  360 (461)
                      ..++|+||+|+|||+|++.+++.+...++.+++..
T Consensus        31 ~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~   65 (357)
T 2fna_A           31 PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRK   65 (357)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGG
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchh
Confidence            36899999999999999999998876667776654

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=97.76  E-value=8.1e-05  Score=93.29  Aligned_cols=105  Identities=13%  Similarity=0.151  Sum_probs=71.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      ..+..+.||+|||||.+++.||+.++.+++.++|.+-.+        ...+..+|..+.     ..+...+||||+++..
T Consensus       604 ~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d--------~~~~g~i~~G~~-----~~GaW~cfDEfNrl~~  670 (3245)
T 3vkg_A          604 RMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFD--------LQAMSRIFVGLC-----QCGAWGCFDEFNRLEE  670 (3245)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCC--------HHHHHHHHHHHH-----HHTCEEEEETTTSSCH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCC--------HHHHHHHHhhHh-----hcCcEEEehhhhcCCH
Confidence            456689999999999999999999999999999987553        223333443222     1356789999999988


Q ss_pred             hhhccccccccchHHHHHHHHHHHh---------Cceeeee-cceeeecCCeEEEecCCCCc
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLE---------GTETKTF-AAVSKVSRDNLYIKTSGLDS  456 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LE---------g~~v~i~-~~~r~~~rd~IiI~TsNid~  456 (461)
                      +              +++.+.+.|.         ...+... ...-.....+.++.|.|.+.
T Consensus       671 ~--------------vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY  718 (3245)
T 3vkg_A          671 R--------------ILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGY  718 (3245)
T ss_dssp             H--------------HHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCG
T ss_pred             H--------------HHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCc
Confidence            7              5555554443         2233332 22223334789999999764

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=97.73  E-value=4.4e-05  Score=95.59  Aligned_cols=115  Identities=17%  Similarity=0.190  Sum_probs=71.4

Q ss_pred             CCcEEEEccCCCchHHHHHH-HHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHh----hc----hhhhc----cCc
Q 012525          325 KSNVLLMGPTGSGKTLLAKT-LARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQ----AE----FNVEA----AQQ  391 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAra-LA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~----a~----~~v~~----a~~  391 (461)
                      ..+|||+||||||||++++. +++..+.+++.++++..+..        ..+...+..    ..    +.+-.    .+.
T Consensus      1304 ~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tta--------~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~ 1375 (3245)
T 3vkg_A         1304 HRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTP--------ELLLKTFDHHCEYKRTPSGETVLRPTQLGKW 1375 (3245)
T ss_dssp             TCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCCH--------HHHHHHHHHHEEEEECTTSCEEEEESSTTCE
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCCH--------HHHHHHHhhcceEEeccCCCcccCCCcCCce
Confidence            37899999999999977654 55554667788888766542        233333321    11    11111    334


Q ss_pred             eEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecc-eeeecCCeEEEecCCCC
Q 012525          392 GMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA-VSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       392 gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~-~r~~~rd~IiI~TsNid  455 (461)
                      .|||||||+.-..+.-        +...+...|.++||.+.+.+... ......++.+|+|.|..
T Consensus      1376 ~VlFiDDiNmp~~D~y--------GtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp 1432 (3245)
T 3vkg_A         1376 LVVFCDEINLPSTDKY--------GTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPP 1432 (3245)
T ss_dssp             EEEEETTTTCCCCCTT--------SCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCT
T ss_pred             EEEEecccCCCCcccc--------ccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCC
Confidence            6999999996443311        11127788889999655555433 33333589999999864

>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=97.57  E-value=5.5e-05  Score=67.30  Aligned_cols=34  Identities=18%  Similarity=0.354  Sum_probs=30.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..|+|+|+||+||||+|++|++.++.+|+.++..
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~~D   37 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVD   37 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCeEEeccc
Confidence            4689999999999999999999999888876554

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.57  E-value=6.7e-05  Score=90.86  Aligned_cols=80  Identities=25%  Similarity=0.237  Sum_probs=49.2

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhh---cCccc-----------ccHHHHHHHHHHhhchh
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQ---AGYVG-----------EDVESILYKLLAQAEFN  385 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~---~g~vG-----------e~~e~~L~~lf~~a~~~  385 (461)
                      ..+.+++|+||||||||+||.+++.+.   +...+.++......   ....|           ...+..+..++.    .
T Consensus      1425 ~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~----l 1500 (2050)
T 3cmu_A         1425 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDA----L 1500 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHH----H
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHH----H
Confidence            457899999999999999999998754   33445555442210   00112           112333333322    2


Q ss_pred             hhccCceEEEEcCccccchhh
Q 012525          386 VEAAQQGMVYIDEVDKITKKA  406 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~R  406 (461)
                      +......+|||||++.+.+.+
T Consensus      1501 vr~~~~~lVVIDsi~al~p~~ 1521 (2050)
T 3cmu_A         1501 ARSGAVDVIVVDSVAALTPKA 1521 (2050)
T ss_dssp             HHHTCCSEEEESCGGGCCCHH
T ss_pred             HhcCCCCEEEEcChhHhcccc
Confidence            233467899999999888753

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.53  E-value=5.3e-05  Score=67.94  Aligned_cols=34  Identities=29%  Similarity=0.439  Sum_probs=30.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..|+|+|++|+||||+|+.||+.++.+|+..+..
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l~~~~i~~d~~   39 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLTKRILYDSDKE   39 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHCCCEEEHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCCEEEChHH
Confidence            5799999999999999999999999998876543

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=97.52  E-value=0.00031  Score=64.30  Aligned_cols=27  Identities=26%  Similarity=0.498  Sum_probs=23.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      .+.|.||+|+|||||++.|+..++..+
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            478999999999999999999876443

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.40  E-value=9.3e-05  Score=67.84  Aligned_cols=34  Identities=44%  Similarity=0.675  Sum_probs=30.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ...|+|.|++|+||||+++.||+.++.+|+..+.
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~d~   58 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKLNVPFIDLDW   58 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHTCCEEEHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCCCEEcchH
Confidence            4679999999999999999999999999886654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.38  E-value=0.0001  Score=65.31  Aligned_cols=33  Identities=30%  Similarity=0.482  Sum_probs=30.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .+|+|.|++|+||||+|+.||+.++.+|+..+.
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~id~D~   40 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVLDTDM   40 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEEChH
Confidence            579999999999999999999999999987654

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.36  E-value=0.0001  Score=65.76  Aligned_cols=32  Identities=38%  Similarity=0.687  Sum_probs=28.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|+|.|+||+||||+|+.||+.++.+|+..+.
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d~d~   37 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLDSDF   37 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEcccH
Confidence            58999999999999999999999998876543

>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=64.01  Aligned_cols=32  Identities=22%  Similarity=0.425  Sum_probs=28.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|+|.|++|+||||+|+.|++.++.+|+..+.
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~~~~i~~d~   34 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELKYPIIKGSS   34 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHCCCEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeeecCcc
Confidence            48899999999999999999999998876654

>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=97.34  E-value=0.00057  Score=71.02  Aligned_cols=24  Identities=33%  Similarity=0.598  Sum_probs=21.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++|.|++|||||+++.++++.+
T Consensus        46 ~~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           46 HHVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHH
Confidence            479999999999999999999876

>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=97.31  E-value=0.00014  Score=65.15  Aligned_cols=33  Identities=30%  Similarity=0.560  Sum_probs=29.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ..|+|+|+||+||||+|+.||+.++.+++..+.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~D~   35 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALGVGLLDTDV   35 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHTCCEEEHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEEeCch
Confidence            358999999999999999999999999876654

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.29  E-value=0.00036  Score=61.60  Aligned_cols=31  Identities=23%  Similarity=0.284  Sum_probs=25.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH-hcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR-HVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~-~l~~pfv~i  356 (461)
                      ..|+|.|+||+||||+|+.|++ .++..++..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~~~~~~~i~~   34 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNINR   34 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEECH
T ss_pred             eEEEEecCCCCCHHHHHHHHHhhcCCcEEecH
Confidence            3589999999999999999999 566555443

>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=97.28  E-value=0.00016  Score=64.74  Aligned_cols=34  Identities=35%  Similarity=0.553  Sum_probs=30.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ...|+|+|+||+||||+++.|++.++.+++..+.
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~d~   44 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSGLKYINVGD   44 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHCCEEEEHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhCCeEEEHHH
Confidence            4679999999999999999999999988876654

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.25  E-value=0.00018  Score=63.65  Aligned_cols=32  Identities=38%  Similarity=0.784  Sum_probs=27.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|+|+|++|+||||+++.||..++.+++..+
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id~d   36 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD   36 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEecc
Confidence            56899999999999999999999988766543

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=97.22  E-value=0.00021  Score=66.87  Aligned_cols=78  Identities=18%  Similarity=0.169  Sum_probs=43.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc--------C-CceEEecchhhhhcCcc----------cccHHH-HHHHHHHhhchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV--------N-VPFVIADATTLTQAGYV----------GEDVES-ILYKLLAQAEFN  385 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l--------~-~pfv~i~~s~l~~~g~v----------Ge~~e~-~L~~lf~~a~~~  385 (461)
                      ..+|++|+||||||++|..++...        + .+++..+..++.-. +.          ....+. ....++..+.  
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~-~~~~~~~k~~~~~~~~~~~~~~~~~~~~~--   82 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIP-HTYIETDAKKLPKSTDEQLSAHDMYEWIK--   82 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSC-CEEEECCTTTCSSCCSSCEEGGGHHHHTT--
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCcccc-ccccchhhhhccccCcccccHHHHHHHhh--
Confidence            457999999999999998875432        3 56655555544321 11          000000 0011121110  


Q ss_pred             hhccCceEEEEcCccccchhh
Q 012525          386 VEAAQQGMVYIDEVDKITKKA  406 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~R  406 (461)
                      ....++.||||||++.+.+.+
T Consensus        83 ~~~~~~~vliIDEAq~l~~~~  103 (199)
T 2r2a_A           83 KPENIGSIVIVDEAQDVWPAR  103 (199)
T ss_dssp             SGGGTTCEEEETTGGGTSBCC
T ss_pred             ccccCceEEEEEChhhhccCc
Confidence            122357899999999986553

>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=97.21  E-value=0.00018  Score=64.42  Aligned_cols=34  Identities=29%  Similarity=0.544  Sum_probs=29.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +..|+|.|+||+||||+|+.|++.++.+++..+.
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l~~~~i~~D~   38 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGLRLPLLSKDA   38 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHTCCEEEHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCeEecHHH
Confidence            3568999999999999999999999988776543

>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=97.21  E-value=0.00018  Score=65.11  Aligned_cols=34  Identities=26%  Similarity=0.416  Sum_probs=29.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh-cCCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH-VNVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~-l~~pfv~i~~  358 (461)
                      ...|+|+|++|+||||+++.||+. ++.+++.++.
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~l~g~~~id~d~   44 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAELDGFQHLEVGK   44 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTTEEEEEHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCCEEeeHHH
Confidence            467999999999999999999999 7888776653

>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=97.15  E-value=0.00024  Score=62.64  Aligned_cols=32  Identities=31%  Similarity=0.587  Sum_probs=28.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|+|.|++|+||||+|+.|++.++.+++..+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~d   34 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEEccc
Confidence            35899999999999999999999998877654

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=97.14  E-value=0.00027  Score=64.43  Aligned_cols=33  Identities=36%  Similarity=0.627  Sum_probs=29.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +..|+|.|+||+||||+|+.|++.++.+++.++
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l~~~~i~~d   52 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKLGIPQISTG   52 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            356999999999999999999999998887654

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.12  E-value=0.00025  Score=63.32  Aligned_cols=32  Identities=19%  Similarity=0.301  Sum_probs=28.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|+|.|+||+||||+|+.|++.++.+++..+
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~d   35 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKYGYTHLSAG   35 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEEeHH
Confidence            45899999999999999999999998776543

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.11  E-value=0.00026  Score=63.62  Aligned_cols=33  Identities=15%  Similarity=0.326  Sum_probs=29.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +..|+|.|++|+||||+|+.||+.++.+++..+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~d   41 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTG   41 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            356999999999999999999999998877654

>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=97.11  E-value=0.00027  Score=61.40  Aligned_cols=30  Identities=30%  Similarity=0.513  Sum_probs=26.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|+|.|+||+||||+|+.| +.++.+++.++
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~g~~~i~~~   32 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KERGAKVIVMS   32 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHTTCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCcEEEHh
Confidence            5889999999999999999 88888877653

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.10  E-value=0.0003  Score=67.54  Aligned_cols=32  Identities=41%  Similarity=0.501  Sum_probs=28.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .++|+||+|+||||||+.||+.++.+++..+.
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            47899999999999999999999998887755

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.10  E-value=0.00038  Score=63.54  Aligned_cols=33  Identities=33%  Similarity=0.681  Sum_probs=28.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ..|+|.|++|+||||+|+.|++.++..++..+.
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~d~   51 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEACGYPFIEGDA   51 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHHTCCEEEGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCEEEeCCc
Confidence            569999999999999999999999887776543

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.09  E-value=0.00031  Score=61.72  Aligned_cols=32  Identities=34%  Similarity=0.586  Sum_probs=28.2

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|+|.|++|+||||+|+.|++.++.+++..+.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d~   33 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDVDE   33 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEECcH
Confidence            48999999999999999999999988876543

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.09  E-value=0.00021  Score=63.86  Aligned_cols=32  Identities=28%  Similarity=0.505  Sum_probs=27.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|+|.|++|+||||+|+.|++.++.+++..+
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l~~~~i~~d   36 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQELGFKKLSTG   36 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTCEEECHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEecHH
Confidence            46899999999999999999999988776543

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=97.06  E-value=0.00033  Score=64.91  Aligned_cols=31  Identities=26%  Similarity=0.501  Sum_probs=28.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.|+||+||||+|+.||+.++.+++..
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            5689999999999999999999999887765

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=97.05  E-value=0.00095  Score=61.80  Aligned_cols=25  Identities=32%  Similarity=0.340  Sum_probs=22.0

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .+..++|+||+|+|||+|++.|+..
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~   47 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVT   47 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            3467899999999999999999984

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=97.04  E-value=0.00036  Score=64.24  Aligned_cols=31  Identities=26%  Similarity=0.548  Sum_probs=27.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|+|+|+||+||||+|+.|++.++.+++..+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~d   32 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKYGIPHISTG   32 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeHH
Confidence            4889999999999999999999988877653

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.03  E-value=0.00066  Score=62.30  Aligned_cols=23  Identities=26%  Similarity=0.286  Sum_probs=18.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .-++++||+|+||||++..++..
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~   26 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEI   26 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999998666543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.02  E-value=0.004  Score=56.70  Aligned_cols=25  Identities=24%  Similarity=0.352  Sum_probs=21.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|+||+|+|||||++.|+..+
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~   47 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKG   47 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4678899999999999999999644

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.01  E-value=0.00036  Score=62.79  Aligned_cols=32  Identities=19%  Similarity=0.360  Sum_probs=28.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|+|.|++|+||||+|+.|++.++.+++..+
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d   44 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKYGFTHLSTG   44 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            56899999999999999999999998776543

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.01  E-value=0.00041  Score=63.76  Aligned_cols=31  Identities=29%  Similarity=0.580  Sum_probs=27.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|+|.|+||+||||+|+.|++.++.+++..+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~d   32 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYEIPHISTG   32 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEeeHH
Confidence            4889999999999999999999998877553

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=97.00  E-value=0.00032  Score=62.56  Aligned_cols=32  Identities=19%  Similarity=0.234  Sum_probs=27.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC-----CceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN-----VPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~-----~pfv~i~  357 (461)
                      ..|+|.|++|+||||+++.|++.++     .+++.++
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~i~~~   40 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFG   40 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcCcceEEEehH
Confidence            4689999999999999999999887     6666543

>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=97.00  E-value=0.0015  Score=62.61  Aligned_cols=37  Identities=24%  Similarity=0.453  Sum_probs=30.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh---cCCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH---VNVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~---l~~pfv~i~~s~l~  362 (461)
                      ..|+|.|+||+||||+|+.|++.   .+.+++.++...+.
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~D~~~   44 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIR   44 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECTHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECchHHH
Confidence            45899999999999999999997   67777755655444

>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=96.99  E-value=0.00044  Score=62.10  Aligned_cols=36  Identities=39%  Similarity=0.495  Sum_probs=30.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTL  361 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l  361 (461)
                      ..++|.||+|+||||+++.|+...+...+.++..++
T Consensus        10 ~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~d~~   45 (191)
T 1zp6_A           10 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDL   45 (191)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTTHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhccCCCeEEEcccch
Confidence            568899999999999999999988777777776554

>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=96.98  E-value=0.00043  Score=65.05  Aligned_cols=33  Identities=30%  Similarity=0.477  Sum_probs=29.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ...|+|.|+||+||||+|+.||+.++.+++..+
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~d   48 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFCVCHLATG   48 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceecHH
Confidence            357999999999999999999999998877653

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.97  E-value=0.00041  Score=64.73  Aligned_cols=31  Identities=23%  Similarity=0.491  Sum_probs=28.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.|+||+||||+|+.||+.++.+++.+
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   38 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITTHFELKHLSS   38 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSSSEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCeEEec
Confidence            5699999999999999999999999887755

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=96.96  E-value=0.0013  Score=70.92  Aligned_cols=32  Identities=25%  Similarity=0.378  Sum_probs=25.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEe
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIA  356 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i  356 (461)
                      ...++|.|+||||||+++.+++..+   +..++.+
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~  238 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLC  238 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            4678999999999999999998755   4444443

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=96.96  E-value=0.0017  Score=59.16  Aligned_cols=35  Identities=26%  Similarity=0.213  Sum_probs=27.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      +.-++|+||+|+|||+|++.|+...+.+.+.++..
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~   54 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTE   54 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECC
Confidence            45689999999999999999998445566555543

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.96  E-value=0.00036  Score=62.05  Aligned_cols=29  Identities=38%  Similarity=0.523  Sum_probs=23.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ..|+|.|++|+||||+|+.|++.++.+++
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            56899999999999999999999999887

>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=96.95  E-value=0.00041  Score=61.80  Aligned_cols=32  Identities=25%  Similarity=0.371  Sum_probs=28.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|+|.|++|+||||+|+.|++.++.+++..+
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~d   38 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRDFGWVHLSAG   38 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEeeHH
Confidence            45899999999999999999999998776553

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.95  E-value=0.00035  Score=64.83  Aligned_cols=31  Identities=19%  Similarity=0.327  Sum_probs=27.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.|+||+||||+|+.||+.++.+++.+
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   36 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKYQLAHISA   36 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            5699999999999999999999999876554

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=96.93  E-value=0.00048  Score=64.00  Aligned_cols=31  Identities=23%  Similarity=0.465  Sum_probs=28.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.|+||+||||+|+.||+.++.+++..
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            4689999999999999999999999887765

>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=96.90  E-value=0.00061  Score=60.48  Aligned_cols=32  Identities=34%  Similarity=0.574  Sum_probs=27.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..++|.|++|+||||+++.|++.++..++..+
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~~d   40 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   40 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhhCcEEEeCc
Confidence            46899999999999999999999887666543

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.88  E-value=0.00056  Score=62.21  Aligned_cols=32  Identities=22%  Similarity=0.395  Sum_probs=28.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|+|+|++|+||||+|+.|++.++.+++..+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~d   47 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG   47 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeHH
Confidence            46899999999999999999999998777654

>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=96.85  E-value=0.0031  Score=59.74  Aligned_cols=34  Identities=32%  Similarity=0.402  Sum_probs=27.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      .+++|++|+|+|||.+|.+++..++.+.+.+..+
T Consensus       109 ~~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~  142 (237)
T 2fz4_A          109 KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (237)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESS
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCC
Confidence            3489999999999999999998887666655544

>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=96.83  E-value=0.00064  Score=62.79  Aligned_cols=30  Identities=20%  Similarity=0.420  Sum_probs=27.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+|.|+||+||||+|+.|++.++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~g~~~i~~   31 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            489999999999999999999999887766

>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=96.83  E-value=0.00047  Score=65.66  Aligned_cols=33  Identities=18%  Similarity=0.279  Sum_probs=28.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +..|+|.|+||+||||+|+.|++.++.+++.++
T Consensus        29 ~~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~~   61 (243)
T 3tlx_A           29 DGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTG   61 (243)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEEecH
Confidence            356999999999999999999999988776554

>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=96.78  E-value=0.00098  Score=59.57  Aligned_cols=37  Identities=27%  Similarity=0.478  Sum_probs=31.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~  362 (461)
                      ..|+|+|++|+||||+++.|++.+   +.+++.++...+.
T Consensus         6 ~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d~~~~~   45 (179)
T 2pez_A            6 CTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIR   45 (179)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEECChHHH
Confidence            568899999999999999999988   8888888765543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.78  E-value=0.00091  Score=61.20  Aligned_cols=31  Identities=35%  Similarity=0.577  Sum_probs=26.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      +..++|.|++|+||||+++.|++.++..++.
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~~g~~~i~   59 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADETGLEFAE   59 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHCCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCCeEEc
Confidence            4568899999999999999999999776554

>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=96.76  E-value=0.0029  Score=60.35  Aligned_cols=31  Identities=19%  Similarity=0.247  Sum_probs=23.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i  356 (461)
                      .-++++|++|+||||++..++..+   +..++.+
T Consensus        13 ~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~   46 (223)
T 2b8t_A           13 WIEFITGPMFAGKTAELIRRLHRLEYADVKYLVF   46 (223)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            457899999999999998887655   3444444

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.74  E-value=0.0011  Score=59.15  Aligned_cols=31  Identities=29%  Similarity=0.254  Sum_probs=27.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc---CCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV---NVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~  357 (461)
                      .|+|.|++|+||||+|+.|++.+   +.+++..+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d   35 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYR   35 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            37899999999999999999988   88887664

>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=96.74  E-value=0.00094  Score=62.67  Aligned_cols=29  Identities=31%  Similarity=0.535  Sum_probs=26.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      .|+|.||||+||+|.|+.||+.++.+++.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g~~~is   30 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKGFVHIS   30 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            47899999999999999999999887654

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.74  E-value=0.00091  Score=60.16  Aligned_cols=29  Identities=14%  Similarity=0.480  Sum_probs=25.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      .|+|.|++|+||||+++.|++.++..++.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~~~   30 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEIFK   30 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEEEC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcEEc
Confidence            48899999999999999999999886653

>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=96.74  E-value=0.003  Score=57.85  Aligned_cols=25  Identities=48%  Similarity=0.531  Sum_probs=21.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..-+.|.||+|+|||||++.|+..+
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568899999999999999999744

>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=96.72  E-value=0.001  Score=60.08  Aligned_cols=33  Identities=15%  Similarity=0.193  Sum_probs=27.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc-CCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV-NVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l-~~pfv~i~  357 (461)
                      +..|+|.|++|+||||+++.|++.+ +.+++.++
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~   37 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESIPANTIKYLN   37 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTSCGGGEEEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHCCCceEEEe
Confidence            3568999999999999999999998 46776554

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.70  E-value=0.0009  Score=63.88  Aligned_cols=37  Identities=27%  Similarity=0.445  Sum_probs=31.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTL  361 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l  361 (461)
                      +..|+|.|+||+||||+|+.|++.++..++.++...+
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            3568999999999999999999999866666676655

>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=96.69  E-value=0.00098  Score=61.44  Aligned_cols=30  Identities=27%  Similarity=0.473  Sum_probs=26.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..|.|.|++|+||||+++.|++.++.+++.
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g~~~~d   35 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQWHLLD   35 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            458899999999999999999999887664

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.64  E-value=0.00071  Score=60.19  Aligned_cols=24  Identities=17%  Similarity=0.300  Sum_probs=22.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .|+|.|+||+||||+|+.|++.++
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            489999999999999999999886

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.62  E-value=0.0011  Score=62.08  Aligned_cols=30  Identities=27%  Similarity=0.552  Sum_probs=26.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+|.|+||+||||+|+.|++.++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~lg~~~i~~   31 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKYSLAHIES   31 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEch
Confidence            389999999999999999999998776655

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.60  E-value=0.0013  Score=64.46  Aligned_cols=37  Identities=30%  Similarity=0.424  Sum_probs=29.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTL  361 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l  361 (461)
                      +..|+|.||||+||||+|+.|++.+...++.++...+
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~D~~   69 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTF   69 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEechHh
Confidence            3568999999999999999999988544566665433

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.60  E-value=0.0012  Score=62.64  Aligned_cols=30  Identities=20%  Similarity=0.413  Sum_probs=26.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      ++.|+|.||||+||+|+|+.||+.++.+.+
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            356788999999999999999999987655

>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=96.60  E-value=0.0015  Score=66.96  Aligned_cols=31  Identities=35%  Similarity=0.341  Sum_probs=26.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      +..++|+||+|+|||||+++|+..++..++.
T Consensus       169 ~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~  199 (377)
T 1svm_A          169 KRYWLFKGPIDSGKTTLAAALLELCGGKALN  199 (377)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCEEEC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcCCcEEE
Confidence            4678999999999999999999988765544

>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=96.59  E-value=0.0011  Score=60.21  Aligned_cols=31  Identities=26%  Similarity=0.379  Sum_probs=26.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|.|.|++|+||||+++.|++ ++.+++..+.
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~i~~d~   33 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYVLDADK   33 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEEEEHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEEEEccH
Confidence            488999999999999999999 8887766554

>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=96.57  E-value=0.0013  Score=59.41  Aligned_cols=31  Identities=32%  Similarity=0.599  Sum_probs=28.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|.|.|++|+||||+|+.||+.++.+++..+
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            5889999999999999999999998887654

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.55  E-value=0.00084  Score=61.11  Aligned_cols=29  Identities=21%  Similarity=0.190  Sum_probs=24.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      +..|+|.|++|+||||+++.|++.++.++
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~~   38 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNNN   38 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence            46689999999999999999999875543

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.54  E-value=0.0014  Score=63.39  Aligned_cols=34  Identities=35%  Similarity=0.541  Sum_probs=30.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ...|.|.|++|+||||+++.||+.++.+|+..+.
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg~~~~d~d~   81 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLGYTFFDCDT   81 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHTCEEEEHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCcEEeCcH
Confidence            3679999999999999999999999998876554

>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=96.53  E-value=0.0018  Score=59.18  Aligned_cols=37  Identities=27%  Similarity=0.359  Sum_probs=28.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTL  361 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l  361 (461)
                      +..|.|.||+|+||||++++|+..+   +...+.++...+
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d~d~~   64 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILDGDNV   64 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEecCchh
Confidence            3568899999999999999999988   444335555444

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.53  E-value=0.0013  Score=66.19  Aligned_cols=34  Identities=38%  Similarity=0.600  Sum_probs=30.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..|+|+||+|+|||+||+.||+.++..++.+|..
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds~   39 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALPCELISVDSA   39 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEEEEEECTT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCcEEeccch
Confidence            3589999999999999999999999888877653

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=96.52  E-value=0.0039  Score=63.06  Aligned_cols=77  Identities=22%  Similarity=0.234  Sum_probs=44.9

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhh------cCcc--------cccHHHHHHHHHHhhchhh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQ------AGYV--------GEDVESILYKLLAQAEFNV  386 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~------~g~v--------Ge~~e~~L~~lf~~a~~~v  386 (461)
                      ....++|+||||+|||+||..++..+   +...+.++......      .++.        ....+..+..    +...+
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~----~~~l~  135 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEI----ADMLV  135 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHH----HHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHH----HHHHH
Confidence            45678999999999999999998654   34555555432110      0110        0122222221    11112


Q ss_pred             hccCceEEEEcCccccch
Q 012525          387 EAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       387 ~~a~~gVLfIDEID~L~~  404 (461)
                      ...+..+||||++..+..
T Consensus       136 ~~~~~~lIVIDsl~~l~~  153 (349)
T 2zr9_A          136 RSGALDIIVIDSVAALVP  153 (349)
T ss_dssp             TTTCCSEEEEECGGGCCC
T ss_pred             hcCCCCEEEEcChHhhcc
Confidence            233577999999999884

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=96.52  E-value=0.0043  Score=63.21  Aligned_cols=77  Identities=21%  Similarity=0.192  Sum_probs=46.2

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc------Cc--------ccccHHHHHHHHHHhhchhh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA------GY--------VGEDVESILYKLLAQAEFNV  386 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~------g~--------vGe~~e~~L~~lf~~a~~~v  386 (461)
                      ....++|+||||+||||||..++..+   +..++.++.......      ++        .....+..+..+    ...+
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~----~~l~  135 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIV----DELV  135 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHH----HHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHH----HHHh
Confidence            35678899999999999999998764   445555555432110      00        011223332221    1112


Q ss_pred             hccCceEEEEcCccccch
Q 012525          387 EAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       387 ~~a~~gVLfIDEID~L~~  404 (461)
                      ......+++||++..+..
T Consensus       136 ~~~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          136 RSGVVDLIVVDSVAALVP  153 (356)
T ss_dssp             HTSCCSEEEEECTTTCCC
T ss_pred             hhcCCCeEEehHhhhhcC
Confidence            223567999999998876

>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=96.52  E-value=0.0014  Score=59.03  Aligned_cols=31  Identities=29%  Similarity=0.363  Sum_probs=27.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|.|.|++|+||||+++.|++. +.+++..+
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            56889999999999999999998 88877655

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.50  E-value=0.0087  Score=55.25  Aligned_cols=25  Identities=36%  Similarity=0.644  Sum_probs=20.9

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .+..++|+||||+|||++|..++..
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~   46 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWN   46 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3467899999999999999888754

>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=96.47  E-value=0.0015  Score=59.59  Aligned_cols=30  Identities=47%  Similarity=0.586  Sum_probs=25.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|.|.|++|+||||+++.|++ ++.+++..+
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~id~d   33 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPLVDAD   33 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcccchH
Confidence            478999999999999999998 888876544

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.47  E-value=0.01  Score=55.70  Aligned_cols=112  Identities=14%  Similarity=0.145  Sum_probs=61.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch---------hhhhc----------Cccccc-----HHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT---------TLTQA----------GYVGED-----VESILYK  377 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s---------~l~~~----------g~vGe~-----~e~~L~~  377 (461)
                      ...|++++.+|.||||+|-.+|-..   +..++.+...         .+...          +|....     .+.....
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~  107 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMA  107 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHH
Confidence            3679999999999999999988544   4444444211         11111          111111     1223344


Q ss_pred             HHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          378 LLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       378 lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      .+..+...+......+|+|||+..+..-       .-.    -.+.++++|+..           +...-+|.|.|..+.
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~~-------g~l----~~~ev~~~l~~R-----------p~~~~vIlTGr~ap~  165 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVAY-------DYL----PLEEVISALNAR-----------PGHQTVIITGRGCHR  165 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHHT-------TSS----CHHHHHHHHHTS-----------CTTCEEEEECSSCCH
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCccccC-------CCC----CHHHHHHHHHhC-----------cCCCEEEEECCCCcH
Confidence            4444544454556779999999754332       001    134566666622           234566667766544


Q ss_pred             c
Q 012525          458 T  458 (461)
Q Consensus       458 ~  458 (461)
                      +
T Consensus       166 ~  166 (196)
T 1g5t_A          166 D  166 (196)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=96.46  E-value=0.0021  Score=63.53  Aligned_cols=81  Identities=10%  Similarity=0.057  Sum_probs=52.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVD  400 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID  400 (461)
                      ...+||+||.|+||++.++.|++.+..    ++..+.   +..    ..++...    ...+..........||+|||++
T Consensus        18 ~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~---~~~----~~~~~~l----~~~~~~~plf~~~kvvii~~~~   86 (343)
T 1jr3_D           18 RAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFS---IDP----NTDWNAI----FSLCQAMSLFASRQTLLLLLPE   86 (343)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEE---CCT----TCCHHHH----HHHHHHHHHCCSCEEEEEECCS
T ss_pred             CcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEE---ecC----CCCHHHH----HHHhcCcCCccCCeEEEEECCC
Confidence            367899999999999999999886521    211111   110    1232332    2222221122456799999999


Q ss_pred             c-cchhhhccccccccchHHHHHHHHHHHhC
Q 012525          401 K-ITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       401 ~-L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      . +..+              .+++|++.||.
T Consensus        87 ~kl~~~--------------~~~aLl~~le~  103 (343)
T 1jr3_D           87 NGPNAA--------------INEQLLTLTGL  103 (343)
T ss_dssp             SCCCTT--------------HHHHHHHHHTT
T ss_pred             CCCChH--------------HHHHHHHHHhc
Confidence            8 8776              78999999994

>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=96.39  E-value=0.0023  Score=60.41  Aligned_cols=30  Identities=23%  Similarity=0.550  Sum_probs=26.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +..++|.||+|+||||+++.|++.++...+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg~~~~   56 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFGLQHL   56 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCCCE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEe
Confidence            467999999999999999999998877544

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=96.39  E-value=0.0053  Score=56.53  Aligned_cols=37  Identities=27%  Similarity=0.328  Sum_probs=29.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC----CceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN----VPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~----~pfv~i~~s~l~  362 (461)
                      ..|+|.|++|+||||+++.|++.++    .+++.++...+.
T Consensus        26 ~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~~d~~r   66 (211)
T 1m7g_A           26 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIR   66 (211)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEECChHHh
Confidence            5688999999999999999999774    456666654443

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=96.36  E-value=0.0011  Score=60.24  Aligned_cols=27  Identities=19%  Similarity=0.309  Sum_probs=23.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      +..|+|.|++|+||||+|+.|++.++.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            456899999999999999999997643

>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=96.35  E-value=0.0046  Score=61.33  Aligned_cols=37  Identities=30%  Similarity=0.343  Sum_probs=28.4

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---------CCceEEecch
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---------NVPFVIADAT  359 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---------~~pfv~i~~s  359 (461)
                      .....++|+|+||+|||+||..+|..+         +...+.++..
T Consensus       105 ~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e  150 (324)
T 2z43_A          105 ETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTE  150 (324)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESS
T ss_pred             CCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECC
Confidence            345678999999999999999999764         3455555554

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.34  E-value=0.002  Score=58.19  Aligned_cols=27  Identities=26%  Similarity=0.337  Sum_probs=24.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..|+|.|++|+||||+|+.|++.++..
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhc
Confidence            458999999999999999999988763

>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=96.33  E-value=0.0021  Score=59.55  Aligned_cols=32  Identities=22%  Similarity=0.333  Sum_probs=28.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|.|+|.+|+||||+++.|++.++.+++..+.
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vid~D~   45 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVVNVDR   45 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEEECcH
Confidence            37799999999999999999998988876554

>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=96.32  E-value=0.01  Score=64.09  Aligned_cols=25  Identities=24%  Similarity=0.372  Sum_probs=20.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...+++.|+||||||+++..+...+
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHH
Confidence            4679999999999999887776544

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.31  E-value=0.0019  Score=65.59  Aligned_cols=34  Identities=35%  Similarity=0.551  Sum_probs=29.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..|+|.||+|+|||+||..||+.++..++..|..
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~   74 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKM   74 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSS
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCcEEccccc
Confidence            4688999999999999999999998877765554

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.24  E-value=0.0028  Score=58.19  Aligned_cols=33  Identities=33%  Similarity=0.540  Sum_probs=29.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ..|.|.|++|+||||+++.|++.++.+++..+.
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~d~   36 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDTGA   36 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecCCh
Confidence            468999999999999999999999988876543

>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=96.24  E-value=0.003  Score=60.69  Aligned_cols=32  Identities=28%  Similarity=0.509  Sum_probs=27.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      +..|.|.||+|+||||+|+.||+.++.+++..
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg~~~~d~   40 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALGARYLDT   40 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCcccC
Confidence            35689999999999999999999998876643

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.24  E-value=0.0019  Score=65.96  Aligned_cols=30  Identities=33%  Similarity=0.577  Sum_probs=27.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      .+|+|+|++|+||||++++||+.++.+|+.
T Consensus        25 ~~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A           25 VCVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            469999999999999999999999888854

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.22  E-value=0.0028  Score=58.11  Aligned_cols=27  Identities=26%  Similarity=0.464  Sum_probs=24.0

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .+..|+|.||+|+||||+++.|++.+.
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            356799999999999999999999874

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.22  E-value=0.021  Score=59.60  Aligned_cols=33  Identities=30%  Similarity=0.320  Sum_probs=25.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~  357 (461)
                      +..|+|.|++|+||||++..||..+   +..+..++
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            5678899999999999999999766   44444443

>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=96.21  E-value=0.0027  Score=58.51  Aligned_cols=31  Identities=35%  Similarity=0.482  Sum_probs=26.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|.|.|++|+||||+++.|++ ++.+++..+
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-lg~~~id~D   35 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-LGINVIDAD   35 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-TTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-cCCEEEEcc
Confidence            4588999999999999999998 888777653

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.14  E-value=0.0039  Score=59.57  Aligned_cols=31  Identities=32%  Similarity=0.498  Sum_probs=26.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ...|.|.||+|+||||+++.||+.++..++.
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~Lg~~~~d   57 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAESLNWRLLD   57 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhcCCCcCC
Confidence            3568899999999999999999999876653

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.13  E-value=0.034  Score=58.25  Aligned_cols=75  Identities=17%  Similarity=0.177  Sum_probs=44.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc------------------CcccccHHHHHHHHHHhhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA------------------GYVGEDVESILYKLLAQAE  383 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~------------------g~vGe~~e~~L~~lf~~a~  383 (461)
                      +..|+|.|++|+||||++..||..+   +..+..+++......                  ...+.+....+...+..+.
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~~gvpv~~~~~~~dp~~i~~~al~~a~  179 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFK  179 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGGGTCEEECCTTCCCHHHHHHHHHHHHH
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHhcCCcEEecCCCCCHHHHHHHHHHHHH
Confidence            5678999999999999999999766   444444443221100                  0122343444444444332


Q ss_pred             hhhhccCceEEEEcCccccc
Q 012525          384 FNVEAAQQGMVYIDEVDKIT  403 (461)
Q Consensus       384 ~~v~~a~~gVLfIDEID~L~  403 (461)
                      .    ...-+||||..-.+.
T Consensus       180 ~----~~~DvVIIDTaGrl~  195 (443)
T 3dm5_A          180 S----KGVDIIIVDTAGRHK  195 (443)
T ss_dssp             H----TTCSEEEEECCCCSS
T ss_pred             h----CCCCEEEEECCCccc
Confidence            2    134589999886554

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=96.09  E-value=0.0037  Score=58.71  Aligned_cols=33  Identities=24%  Similarity=0.483  Sum_probs=28.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +..|.|.|++|+||||+++.|++.++.+++..+
T Consensus        16 ~~~i~i~G~~gsGKst~~~~l~~~lg~~~~d~d   48 (236)
T 1q3t_A           16 TIQIAIDGPASSGKSTVAKIIAKDFGFTYLDTG   48 (236)
T ss_dssp             CCEEEEECSSCSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCceecCC
Confidence            456899999999999999999999998776543

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=96.06  E-value=0.0026  Score=61.49  Aligned_cols=32  Identities=25%  Similarity=0.314  Sum_probs=25.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-CCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-NVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-~~pfv~i~  357 (461)
                      ..|+|.|+||+||||+|+.|++.+ +..++..+
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i~~D   35 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNINRD   35 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEECHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEeccc
Confidence            358999999999999999999964 65555444

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=96.05  E-value=0.011  Score=72.05  Aligned_cols=81  Identities=23%  Similarity=0.246  Sum_probs=48.7

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---Cccccc-----------HHHHHHHHHHhhch
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGED-----------VESILYKLLAQAEF  384 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~-----------~e~~L~~lf~~a~~  384 (461)
                      -....++||+||||||||+||.+++.+.   +.+.+.++..+..+.   ...|.+           .+..++ +....  
T Consensus      1078 i~~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~-i~~~l-- 1154 (2050)
T 3cmu_A         1078 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALE-ICDAL-- 1154 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHH-HHHHH--
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHH-HHHHH--
Confidence            3457889999999999999999987543   556666666543321   011110           011111 11111  


Q ss_pred             hhhccCceEEEEcCccccchhh
Q 012525          385 NVEAAQQGMVYIDEVDKITKKA  406 (461)
Q Consensus       385 ~v~~a~~gVLfIDEID~L~~~R  406 (461)
                       .....+.+|+|||+..|.+..
T Consensus      1155 -~~~~~~dlvVIDsl~~L~~~~ 1175 (2050)
T 3cmu_A         1155 -ARSGAVDVIVVDSVAALTPKA 1175 (2050)
T ss_dssp             -HHHTCCSEEEESCGGGCCCHH
T ss_pred             -HHhCCCCEEEECCcccccccc
Confidence             112357799999999997654

>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=96.05  E-value=0.0074  Score=54.45  Aligned_cols=23  Identities=43%  Similarity=0.655  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .++++.+|+|+|||+++..++..
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~   71 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKD   71 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHH
Confidence            57999999999999998877754

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=96.05  E-value=0.012  Score=59.78  Aligned_cols=36  Identities=28%  Similarity=0.301  Sum_probs=28.1

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ....++|+|+||+|||+||..+|..+   +.+++.++..
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E  100 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE  100 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            45678999999999999999998654   4566666653

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=96.05  E-value=0.004  Score=59.10  Aligned_cols=27  Identities=19%  Similarity=0.212  Sum_probs=24.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..|.|.|++|+||||+|+.|++.++.+
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~lg~~   49 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLLGQN   49 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhh
Confidence            458899999999999999999999876

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=96.03  E-value=0.0031  Score=57.59  Aligned_cols=32  Identities=41%  Similarity=0.521  Sum_probs=26.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc-CCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV-NVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l-~~pfv~i~  357 (461)
                      ..|.|.|++|+||||+|+.|++.+ +..++..+
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~~D   54 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKHLPNCSVISQD   54 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTSTTEEEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCcEEEeCC
Confidence            457899999999999999999988 66665544

>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=95.98  E-value=0.015  Score=59.94  Aligned_cols=25  Identities=36%  Similarity=0.325  Sum_probs=21.1

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHH
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ....-++|+||+|+|||||++.|+-
T Consensus       176 ~~Gei~~I~G~sGsGKTTLl~~la~  200 (400)
T 3lda_A          176 ETGSITELFGEFRTGKSQLCHTLAV  200 (400)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEEcCCCCChHHHHHHHHH
Confidence            3456788999999999999997764

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=95.93  E-value=0.0081  Score=60.52  Aligned_cols=27  Identities=44%  Similarity=0.457  Sum_probs=23.4

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-+.|+||+|+|||||++.++..+
T Consensus       129 ~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          129 ETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            345668899999999999999999876

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=95.86  E-value=0.02  Score=58.15  Aligned_cols=24  Identities=38%  Similarity=0.558  Sum_probs=21.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..++|.||+|+||||+.++|+..+
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~~  147 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDYL  147 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcc
Confidence            468999999999999999998866

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=95.84  E-value=0.016  Score=58.13  Aligned_cols=25  Identities=28%  Similarity=0.271  Sum_probs=22.0

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .+..++|+||||+|||+||..+|..
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~  145 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVT  145 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4566889999999999999999986

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=95.80  E-value=0.0058  Score=56.74  Aligned_cols=30  Identities=37%  Similarity=0.486  Sum_probs=27.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..|.|.|++|+|||++++.||+.++.+|+.
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            458899999999999999999999999985

>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=95.80  E-value=0.0053  Score=61.72  Aligned_cols=33  Identities=42%  Similarity=0.655  Sum_probs=28.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .-|+|.||+|+|||+||..||+.++..++.+|.
T Consensus        11 ~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds   43 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIELRKILPVELISVDS   43 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEEEEECCT
T ss_pred             cEEEEECCCccCHHHHHHHHHHhCCCcEEeccc
Confidence            457899999999999999999999877766654

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.79  E-value=0.0049  Score=55.28  Aligned_cols=37  Identities=32%  Similarity=0.322  Sum_probs=28.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTL  361 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l  361 (461)
                      +..|+|.|++|+||||+++.|++.+.   .+++.++...+
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~~d~~   52 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWA   52 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEeeHHHH
Confidence            35689999999999999999999874   33445554443

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.79  E-value=0.0051  Score=55.47  Aligned_cols=25  Identities=28%  Similarity=0.450  Sum_probs=22.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..+.|.||+|+||||+++.|+..+
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3568899999999999999999877

>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=95.75  E-value=0.0069  Score=54.35  Aligned_cols=25  Identities=32%  Similarity=0.565  Sum_probs=21.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .++|.||+|+||||+++.|++..+.
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            4789999999999999999986643

>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=95.73  E-value=0.017  Score=58.85  Aligned_cols=78  Identities=23%  Similarity=0.278  Sum_probs=46.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc------Cc--------ccccHHHHHHHHHHhhchh
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA------GY--------VGEDVESILYKLLAQAEFN  385 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~------g~--------vGe~~e~~L~~lf~~a~~~  385 (461)
                      .....++|+|+||+|||+||..+|..+   +.+++.++.......      ++        .....+..+..+    ...
T Consensus        72 ~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l----~~l  147 (366)
T 1xp8_A           72 PRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIM----ELL  147 (366)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHH----HHH
T ss_pred             cCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHH----HHH
Confidence            345678899999999999999888654   445665555421110      00        001222222222    111


Q ss_pred             hhccCceEEEEcCccccch
Q 012525          386 VEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~  404 (461)
                      +......+||||.+..+..
T Consensus       148 ~~~~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          148 VRSGAIDVVVVDSVAALTP  166 (366)
T ss_dssp             HTTTCCSEEEEECTTTCCC
T ss_pred             HhcCCCCEEEEeChHHhcc
Confidence            2223567999999999875

>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=95.72  E-value=0.005  Score=63.42  Aligned_cols=32  Identities=19%  Similarity=0.194  Sum_probs=27.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      +.-|+|+|+||+||||+|+.|++.++..++..
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            45688999999999999999999987765543

>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=95.72  E-value=0.0065  Score=61.19  Aligned_cols=33  Identities=33%  Similarity=0.474  Sum_probs=27.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .-|+|.||+|+|||+||..||+.++..++..+.
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds   36 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNGEVISGDS   36 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTEEEEECCG
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCccceeecCc
Confidence            347899999999999999999998876665544

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=95.71  E-value=0.014  Score=62.16  Aligned_cols=36  Identities=25%  Similarity=0.444  Sum_probs=27.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC---ceEEecchh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV---PFVIADATT  360 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~---pfv~i~~s~  360 (461)
                      +..|+|+|.||+||||+|+.||+.++.   +...++..+
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~~L~~~~~d~~v~s~D~   73 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGE   73 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCCeEEecccH
Confidence            456889999999999999999998843   433444443

>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=95.71  E-value=0.0058  Score=56.38  Aligned_cols=26  Identities=23%  Similarity=0.446  Sum_probs=23.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +.-++|.||+|+|||||++.|++.+.
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            45688999999999999999998774

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.71  E-value=0.0064  Score=54.74  Aligned_cols=25  Identities=24%  Similarity=0.492  Sum_probs=22.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-+.|.||+|+|||||++.|++.+.
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            5688999999999999999998763

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.70  E-value=0.0058  Score=61.95  Aligned_cols=32  Identities=34%  Similarity=0.566  Sum_probs=27.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|+|.||+|+|||+||+.||+.++..++.+|.
T Consensus         9 lI~I~GptgSGKTtla~~La~~l~~~iis~Ds   40 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKKFNGEIISGDS   40 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTEEEEECCS
T ss_pred             eEEEECCCcCcHHHHHHHHHHHcCCceecccc
Confidence            58899999999999999999999876665554

>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=95.69  E-value=0.0051  Score=58.27  Aligned_cols=37  Identities=27%  Similarity=0.404  Sum_probs=28.8

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ++.....|+|.||+|+|||+||..|++... .++..+.
T Consensus        30 v~~~g~~ilI~GpsGsGKStLA~~La~~g~-~iIsdDs   66 (205)
T 2qmh_A           30 VDIYGLGVLITGDSGVGKSETALELVQRGH-RLIADDR   66 (205)
T ss_dssp             EEETTEEEEEECCCTTTTHHHHHHHHTTTC-EEEESSE
T ss_pred             EEECCEEEEEECCCCCCHHHHHHHHHHhCC-eEEecch
Confidence            344467799999999999999999999876 5544443

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.66  E-value=0.0054  Score=56.40  Aligned_cols=26  Identities=38%  Similarity=0.567  Sum_probs=22.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +..|.|.||+|+|||||+++|+..+.
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            35678999999999999999999874

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.57  E-value=0.0076  Score=54.37  Aligned_cols=25  Identities=28%  Similarity=0.594  Sum_probs=22.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.-+.|.||+|+|||||++.|+..+
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhC
Confidence            3557899999999999999999875

>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=95.56  E-value=0.021  Score=57.14  Aligned_cols=25  Identities=40%  Similarity=0.624  Sum_probs=23.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..++|.||+|+|||||+++|+..+.
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~  196 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIP  196 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCc
Confidence            6799999999999999999998874

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.55  E-value=0.0066  Score=55.35  Aligned_cols=30  Identities=40%  Similarity=0.483  Sum_probs=25.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC--CceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN--VPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~--~pfv~  355 (461)
                      ..+.|.||+|+|||||++.|+..++  ..++.
T Consensus         7 ~~i~i~G~~GsGKSTl~~~l~~~~~~~i~~v~   38 (211)
T 3asz_A            7 FVIGIAGGTASGKTTLAQALARTLGERVALLP   38 (211)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHGGGEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCeEEEe
Confidence            4578999999999999999999887  55443

>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=95.53  E-value=0.0064  Score=59.19  Aligned_cols=31  Identities=29%  Similarity=0.386  Sum_probs=26.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      ..|.|.|++|+||||+|+.|+ .++.+++..+
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~lg~~~id~D  106 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NLGAYIIDSD  106 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HHTCEEEEHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HCCCcEEehh
Confidence            458899999999999999999 5787776553

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.43  E-value=0.023  Score=52.34  Aligned_cols=35  Identities=37%  Similarity=0.457  Sum_probs=25.1

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHh----cCCceEEec
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARH----VNVPFVIAD  357 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~----l~~pfv~i~  357 (461)
                      ..+.-++|.|+||+|||++|..+|..    .+.+++.++
T Consensus        28 ~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s   66 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVT   66 (251)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            34567899999999999999877642    244555444

>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=95.42  E-value=0.044  Score=57.02  Aligned_cols=27  Identities=30%  Similarity=0.546  Sum_probs=23.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      +..|+|+|.||+||||+++.|++.++.
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~~   65 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLNF   65 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            356899999999999999999998753

>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=95.39  E-value=0.014  Score=57.26  Aligned_cols=26  Identities=27%  Similarity=0.256  Sum_probs=22.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .....++|+|+||+|||++|..+|..
T Consensus        96 ~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           96 ESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34567899999999999999999865

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=95.39  E-value=0.059  Score=53.51  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=22.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.|++|+||||++..||..+
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~l  128 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKMF  128 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHHH
Confidence            4568899999999999999999766

>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=95.24  E-value=0.015  Score=53.90  Aligned_cols=24  Identities=33%  Similarity=0.632  Sum_probs=21.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.|+|.||+|+|||||++.|.+..
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            458999999999999999998765

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=95.23  E-value=0.012  Score=64.21  Aligned_cols=38  Identities=26%  Similarity=0.456  Sum_probs=32.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLT  362 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~  362 (461)
                      +..|+|+|.+|+||||+|++|++.+   +.+++.++...+.
T Consensus        52 g~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lDgD~iR   92 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNIR   92 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEESHHHHT
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEechHHhh
Confidence            3568999999999999999999998   8899888765543

>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=95.16  E-value=0.017  Score=69.38  Aligned_cols=82  Identities=20%  Similarity=0.212  Sum_probs=48.6

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc---CcccccH-------HHHHHHHHHhhchhhhcc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA---GYVGEDV-------ESILYKLLAQAEFNVEAA  389 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~---g~vGe~~-------e~~L~~lf~~a~~~v~~a  389 (461)
                      ..+..++|+|+||+|||+||..+|..+   +.+++.++.......   ...|.+.       +..+..++......+...
T Consensus       730 ~~G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS~Ees~~ql~A~~lGvd~~~L~i~~~~~leei~~~l~~lv~~~  809 (1706)
T 3cmw_A          730 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSG  809 (1706)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHT
T ss_pred             CCCceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEeccchHHHHHHHHcCCChhheEEecCCcHHHHHHHHHHHHHcc
Confidence            456789999999999999999998755   345666665432210   0011000       001122222222222334


Q ss_pred             CceEEEEcCccccch
Q 012525          390 QQGMVYIDEVDKITK  404 (461)
Q Consensus       390 ~~gVLfIDEID~L~~  404 (461)
                      ...+||||++..+..
T Consensus       810 ~~~lVVIDsLq~l~~  824 (1706)
T 3cmw_A          810 AVDVIVVDSVAALTP  824 (1706)
T ss_dssp             CCSEEEESCSTTCCC
T ss_pred             CCCEEEEechhhhcc
Confidence            678999999999885

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.14  E-value=0.011  Score=54.12  Aligned_cols=25  Identities=40%  Similarity=0.630  Sum_probs=21.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..+.|.||+|+|||||++.|+..+
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3568999999999999999999865

>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=95.01  E-value=0.0062  Score=55.35  Aligned_cols=23  Identities=26%  Similarity=0.473  Sum_probs=21.4

Q ss_pred             EEEEccCCCchHHHHHHHHHhcC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |+|.|++|+||||+++.|++.+.
T Consensus         3 I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            78999999999999999999874

>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=94.98  E-value=0.013  Score=60.89  Aligned_cols=31  Identities=32%  Similarity=0.507  Sum_probs=26.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|+|.||+|+|||+||..||+.++..++.++
T Consensus         4 ~i~i~GptgsGKttla~~La~~~~~~iis~D   34 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKFNGEVINSD   34 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHTEEEEECC
T ss_pred             EEEEECcchhhHHHHHHHHHHHCCCeEeecC
Confidence            4789999999999999999999987666544

>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=94.95  E-value=0.069  Score=56.52  Aligned_cols=44  Identities=20%  Similarity=0.175  Sum_probs=33.4

Q ss_pred             CChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          276 IGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       276 vGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      +|.+..++.|...+...       ..                     .....|.|+|+.|+|||+||+.+++
T Consensus       131 ~GR~~~~~~l~~~L~~~-------~~---------------------~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEM-------CD---------------------LDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCCHHHHHHHHHHHHHH-------TT---------------------SSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcc-------cC---------------------CCceEEEEEcCCCCCHHHHHHHHHH
Confidence            59999999888877310       00                     0125688999999999999999996

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.86  E-value=0.16  Score=53.88  Aligned_cols=34  Identities=26%  Similarity=0.302  Sum_probs=26.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      +..|+|.|++|+||||++..||..+   +..+..+++
T Consensus       101 ~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          101 QNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             -EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            4578999999999999999999765   455554444

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=94.85  E-value=0.024  Score=51.82  Aligned_cols=31  Identities=26%  Similarity=0.335  Sum_probs=25.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i  356 (461)
                      .-|.|.|++|+||||+++.|+..+   +.+++.+
T Consensus        23 ~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~   56 (201)
T 1rz3_A           23 LVLGIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEe
Confidence            457899999999999999999876   4455444

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=94.84  E-value=0.016  Score=55.03  Aligned_cols=30  Identities=23%  Similarity=0.338  Sum_probs=27.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..|.|.|++|||||++|+.||+.++.+|+.
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            457899999999999999999999998875

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=94.84  E-value=0.034  Score=56.23  Aligned_cols=76  Identities=18%  Similarity=0.288  Sum_probs=44.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc-----CCceEEecchhhhhc------Cc--------ccccHHHH-HHHHHHhhchhh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATTLTQA------GY--------VGEDVESI-LYKLLAQAEFNV  386 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~l~~~------g~--------vGe~~e~~-L~~lf~~a~~~v  386 (461)
                      -++|+||||+|||+||..++..+     +..++.++...-...      ++        .....+.. +. +.... ..+
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~-i~~~l-~~i  107 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRID-MVNQL-DAI  107 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHH-HHHHH-HTC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHH-HHHHH-HHh
Confidence            58999999999999987776443     445666665431110      11        01122333 22 11111 012


Q ss_pred             hccCceEEEEcCccccch
Q 012525          387 EAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       387 ~~a~~gVLfIDEID~L~~  404 (461)
                      ....+.+|+||-|..|..
T Consensus       108 ~~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          108 ERGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             CTTCCEEEEEECSTTCBC
T ss_pred             hccCceEEEEeccccccc
Confidence            344678999999999975

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=94.76  E-value=0.046  Score=57.34  Aligned_cols=23  Identities=30%  Similarity=0.288  Sum_probs=19.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .-.++.|+||||||++...+++.
T Consensus       162 ~v~~I~G~aGsGKTt~I~~~~~~  184 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEILSRVNF  184 (446)
T ss_dssp             EEEEEEECTTSCHHHHHHHHCCT
T ss_pred             cEEEEEcCCCCCHHHHHHHHhcc
Confidence            45789999999999998877753

>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=94.73  E-value=0.031  Score=56.03  Aligned_cols=26  Identities=31%  Similarity=0.442  Sum_probs=22.8

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..++|.||+|+||||+++.||..+
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35678899999999999999999866

>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=94.73  E-value=0.022  Score=60.11  Aligned_cols=24  Identities=33%  Similarity=0.605  Sum_probs=20.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..++|+|++|+|||+|+..|+...
T Consensus       152 q~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          152 GKIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             CEEEEECCSSSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCccHHHHHHHhhh
Confidence            568999999999999999887654

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.71  E-value=0.017  Score=54.43  Aligned_cols=27  Identities=19%  Similarity=0.218  Sum_probs=23.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      .-|-|.||.|+|||||++.|+..++..
T Consensus        26 ~iigI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           26 FLIGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhchh
Confidence            457799999999999999999987653

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.70  E-value=0.048  Score=53.91  Aligned_cols=25  Identities=28%  Similarity=0.494  Sum_probs=22.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.||.|+||||+++.||..+
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4568899999999999999999865

>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=94.68  E-value=0.019  Score=52.59  Aligned_cols=25  Identities=28%  Similarity=0.549  Sum_probs=22.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.-+.|.||+|+|||||+++|+..+
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3557899999999999999999876

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=94.67  E-value=0.02  Score=53.42  Aligned_cols=25  Identities=32%  Similarity=0.526  Sum_probs=22.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..+.|.||+|+|||||++.|+..+
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4668899999999999999999876

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=94.65  E-value=0.059  Score=49.88  Aligned_cols=31  Identities=19%  Similarity=0.155  Sum_probs=23.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i  356 (461)
                      .-.+++|++|+||||.+..++..+   +..++.+
T Consensus         9 ~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~   42 (191)
T 1xx6_A            9 WVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVF   42 (191)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            347899999999999888777655   4444444

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=94.63  E-value=0.018  Score=55.23  Aligned_cols=30  Identities=23%  Similarity=0.524  Sum_probs=26.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .+-|.|+||+||||+|+.|++.++.+++..
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            366899999999999999999999887755

>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=94.61  E-value=0.021  Score=53.44  Aligned_cols=26  Identities=19%  Similarity=0.524  Sum_probs=23.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +.-++|.||+|+|||||+++|++...
T Consensus        19 g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           19 RKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            46688999999999999999998764

>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=94.60  E-value=0.13  Score=60.55  Aligned_cols=28  Identities=29%  Similarity=0.439  Sum_probs=24.1

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..+..+.|.||+|+|||||+++|.+.+.
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            3456788999999999999999998774

>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=94.53  E-value=0.075  Score=56.07  Aligned_cols=22  Identities=32%  Similarity=0.560  Sum_probs=19.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHH
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraL  345 (461)
                      .+..++|.||+|+|||||++.+
T Consensus        38 ~Ge~~~l~G~nGsGKSTL~~~~   59 (525)
T 1tf7_A           38 IGRSTLVSGTSGTGKTLFSIQF   59 (525)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHH
Confidence            4577899999999999999994

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=94.48  E-value=0.021  Score=53.97  Aligned_cols=31  Identities=23%  Similarity=0.429  Sum_probs=25.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC--CceEE
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN--VPFVI  355 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~--~pfv~  355 (461)
                      +.-|+|.|++|+||||+++.|++.+.  ..++.
T Consensus        26 g~~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~   58 (229)
T 4eaq_A           26 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIM   58 (229)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHTTTSCEEE
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHhcCCCcee
Confidence            35688999999999999999999886  34443

>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=94.26  E-value=0.11  Score=58.70  Aligned_cols=45  Identities=22%  Similarity=0.351  Sum_probs=34.1

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ++|.++..+.|...+...                             ....+.|.|+|+.|+|||+||+.+++.
T Consensus       126 ~vgR~~~~~~l~~~l~~~-----------------------------~~~~~~v~i~G~gG~GKTtLa~~~~~~  170 (1249)
T 3sfz_A          126 FVTRKKLVHAIQQKLWKL-----------------------------NGEPGWVTIYGMAGCGKSVLAAEAVRD  170 (1249)
T ss_dssp             CCCCHHHHHHHHHHHHTT-----------------------------TTSCEEEEEECSTTSSHHHHHHHHTCC
T ss_pred             eccHHHHHHHHHHHHhhc-----------------------------cCCCCEEEEEeCCCCCHHHHHHHHhcC
Confidence            689999998888877300                             001245789999999999999998864

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=94.23  E-value=0.058  Score=53.02  Aligned_cols=25  Identities=28%  Similarity=0.547  Sum_probs=22.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-|.|.|++|+||||||+.|++.+.
T Consensus        32 ~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           32 LFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4578999999999999999998775

>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=94.22  E-value=0.028  Score=52.96  Aligned_cols=26  Identities=23%  Similarity=0.438  Sum_probs=23.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +.-+.|.||+|+|||||.++|+..+.
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCC
Confidence            46688999999999999999998764

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=94.20  E-value=0.019  Score=61.22  Aligned_cols=26  Identities=12%  Similarity=0.051  Sum_probs=24.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      ..|+|+|.+|+||||+|++||+.++.
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            67999999999999999999999975

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.20  E-value=0.069  Score=54.32  Aligned_cols=26  Identities=27%  Similarity=0.491  Sum_probs=22.8

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..++|.||.|+||||+++.||..+
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhc
Confidence            34578899999999999999999866

>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=94.19  E-value=0.028  Score=50.39  Aligned_cols=24  Identities=33%  Similarity=0.494  Sum_probs=22.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.|.||.|+|||||.++|+..+
T Consensus        34 e~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           34 IMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            457899999999999999999987

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=94.18  E-value=0.026  Score=60.79  Aligned_cols=37  Identities=24%  Similarity=0.322  Sum_probs=30.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC----CceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN----VPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~----~pfv~i~~s~l~  362 (461)
                      ..|+|.|.+|+||||+|++|++.++    .+++.++...+.
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD~D~ir  437 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVR  437 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEEHHHHH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEECcHHHH
Confidence            5689999999999999999999886    677777765543

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.15  E-value=0.012  Score=57.65  Aligned_cols=25  Identities=16%  Similarity=0.385  Sum_probs=19.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-|.|.|++|+||||+|+.|++.++
T Consensus         6 ~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            6 PIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             CEEEEESCC---CCTHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3478999999999999999999876

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=94.14  E-value=0.024  Score=50.61  Aligned_cols=19  Identities=53%  Similarity=0.805  Sum_probs=17.1

Q ss_pred             CcEEEEccCCCchHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAra  344 (461)
                      .-+.|.||+|+|||||+++
T Consensus        10 ei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A           10 SLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EEEEEECCTTSCHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            4578999999999999995

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=94.11  E-value=0.07  Score=53.17  Aligned_cols=25  Identities=28%  Similarity=0.368  Sum_probs=22.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.|++|+||||++..||..+
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~LA~~l  129 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAKMANYY  129 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568899999999999999999765

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=94.09  E-value=0.15  Score=48.38  Aligned_cols=32  Identities=16%  Similarity=0.052  Sum_probs=23.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~  357 (461)
                      .-.+++|++|+||||.+..++..+   +..++.+.
T Consensus        29 ~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k   63 (214)
T 2j9r_A           29 WIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFK   63 (214)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE
Confidence            345689999999999887777544   55555554

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=93.92  E-value=0.021  Score=53.07  Aligned_cols=25  Identities=32%  Similarity=0.515  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHH-Hhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLA-RHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA-~~l  349 (461)
                      +.-+.|.||+|+|||||++.|+ ..+
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3567899999999999999999 765

>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=93.91  E-value=0.061  Score=57.22  Aligned_cols=25  Identities=36%  Similarity=0.496  Sum_probs=22.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.|++|+|||||++.||..+
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHh
Confidence            4568899999999999999999866

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.82  E-value=0.036  Score=51.02  Aligned_cols=23  Identities=39%  Similarity=0.651  Sum_probs=21.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.|.||+|+|||||++.|+..+
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            48899999999999999999876

>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=93.82  E-value=0.017  Score=54.92  Aligned_cols=25  Identities=16%  Similarity=0.345  Sum_probs=22.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-|+|.|++|+||||+++.|++.+.
T Consensus        25 ~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           25 KKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            5688999999999999999999983

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=93.73  E-value=0.035  Score=53.64  Aligned_cols=25  Identities=32%  Similarity=0.553  Sum_probs=22.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...++|.||+|+||||+.++|+..+
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHHhC
Confidence            4568899999999999999999865

>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=93.70  E-value=0.035  Score=53.24  Aligned_cols=26  Identities=35%  Similarity=0.544  Sum_probs=22.3

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ....++|+||+|+|||||++.++..+
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            45678999999999999999998643

>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=93.69  E-value=0.3  Score=52.77  Aligned_cols=35  Identities=23%  Similarity=0.473  Sum_probs=27.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc-------CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV-------NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l-------~~pfv~i~~s  359 (461)
                      ..|+|+.|.+|+|||++.+.|...+       .+.|+.+|..
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpK  255 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPK  255 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSS
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCC
Confidence            4899999999999999999876543       1346777654

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=93.64  E-value=0.17  Score=47.41  Aligned_cols=34  Identities=21%  Similarity=0.332  Sum_probs=24.9

Q ss_pred             CcEEEEccCCCchH-HHHHHHHHhc--CCceEEecch
Q 012525          326 SNVLLMGPTGSGKT-LLAKTLARHV--NVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKT-tLAraLA~~l--~~pfv~i~~s  359 (461)
                      .-.+++|++|+||| .|.+++.+..  +..++.+...
T Consensus        21 ~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~   57 (195)
T 1w4r_A           21 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYA   57 (195)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEET
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccc
Confidence            34689999999999 8888887644  4555555533

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=93.60  E-value=0.039  Score=54.93  Aligned_cols=25  Identities=28%  Similarity=0.667  Sum_probs=23.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..+.|+||+|+|||||+++|+..+
T Consensus       126 Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          126 KNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHhhhc
Confidence            4678899999999999999999987

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=93.54  E-value=0.072  Score=54.51  Aligned_cols=34  Identities=32%  Similarity=0.402  Sum_probs=27.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ..+||.+|+|+|||.++-.++..++...+.+-.+
T Consensus       109 ~~~ll~~~TGsGKT~~~l~~i~~~~~~~Lvl~P~  142 (472)
T 2fwr_A          109 KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (472)
T ss_dssp             TEEEEECCTTSCHHHHHHHHHHHHCSCEEEEESS
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEECC
Confidence            3489999999999999988888777766655554

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=93.52  E-value=0.058  Score=56.88  Aligned_cols=44  Identities=23%  Similarity=0.311  Sum_probs=33.5

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ++|.+...+.|...+..       .                      ....+.|+|+|++|+|||+||+.+++
T Consensus       126 ~vGR~~~l~~L~~~L~~-------~----------------------~~~~~~v~I~G~~GiGKTtLa~~~~~  169 (591)
T 1z6t_A          126 FVTRKKLVNAIQQKLSK-------L----------------------KGEPGWVTIHGMAGCGKSVLAAEAVR  169 (591)
T ss_dssp             CCCCHHHHHHHHHHHTT-------S----------------------TTSCEEEEEECCTTSSHHHHHHHHHC
T ss_pred             ecccHHHHHHHHHHHhc-------c----------------------cCCCceEEEEcCCCCCHHHHHHHHHh
Confidence            68999999888887720       0                      01124688999999999999999875

>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=93.44  E-value=0.047  Score=50.44  Aligned_cols=32  Identities=22%  Similarity=0.304  Sum_probs=27.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEecchh
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATT  360 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~  360 (461)
                      +|++|++|+|||++|+.++.. +.+.+++....
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~~   33 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATSQ   33 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECCC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecCC
Confidence            789999999999999999988 77776666543

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=93.40  E-value=0.044  Score=53.86  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=22.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-|.|.|++|+|||||++.|+..+.
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4577999999999999999999875

>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=93.37  E-value=0.057  Score=47.86  Aligned_cols=28  Identities=21%  Similarity=0.399  Sum_probs=23.4

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..+.-.+|+||.|+|||+|+++|+-.+.
T Consensus        24 ~~~g~~~i~G~NGsGKStll~ai~~~l~   51 (182)
T 3kta_A           24 FSKGFTAIVGANGSGKSNIGDAILFVLG   51 (182)
T ss_dssp             CCSSEEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             cCCCcEEEECCCCCCHHHHHHHHHHHHc
Confidence            3345678999999999999999998764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.35  E-value=0.042  Score=51.47  Aligned_cols=25  Identities=20%  Similarity=0.324  Sum_probs=22.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..|+|.|.+|+||||+++.|++.+.
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            4589999999999999999999984

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=93.30  E-value=0.045  Score=52.77  Aligned_cols=26  Identities=15%  Similarity=0.267  Sum_probs=22.3

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-++|.|+||+|||||++.||..+
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34568899999999999999998755

>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=93.27  E-value=0.1  Score=61.39  Aligned_cols=28  Identities=29%  Similarity=0.534  Sum_probs=23.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..+..|-|.|++|+|||||+++|.+...
T Consensus      1103 ~~Ge~vaIVG~SGsGKSTL~~lL~rl~~ 1130 (1321)
T 4f4c_A         1103 EPGQTLALVGPSGCGKSTVVALLERFYD 1130 (1321)
T ss_dssp             CTTCEEEEECSTTSSTTSHHHHHTTSSC
T ss_pred             CCCCEEEEECCCCChHHHHHHHHhcCcc
Confidence            3456788999999999999999998663

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.13  E-value=0.038  Score=59.37  Aligned_cols=37  Identities=27%  Similarity=0.412  Sum_probs=28.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC----CceEEecchhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN----VPFVIADATTL  361 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~----~pfv~i~~s~l  361 (461)
                      +..+.|+|++|+|||||+++||..+.    ..+..++...+
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~L~~~~G~~i~~lDgD~~  409 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAARLMEMGGRCVTLLDGDIV  409 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHHHHTTCSSCEEEESSHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHHhhcccCCceEEEECCcHH
Confidence            35688999999999999999999885    23444555544

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=93.10  E-value=0.048  Score=54.11  Aligned_cols=25  Identities=20%  Similarity=0.228  Sum_probs=22.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.-|.|.||+|+|||||++.|+..+
T Consensus        90 g~ivgI~G~sGsGKSTL~~~L~gll  114 (312)
T 3aez_A           90 PFIIGVAGSVAVGKSTTARVLQALL  114 (312)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCchHHHHHHHHHhhc
Confidence            3557799999999999999999876

>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=93.03  E-value=0.055  Score=53.55  Aligned_cols=26  Identities=35%  Similarity=0.436  Sum_probs=22.9

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..++|.||+|+||||+++.||..+
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            35678899999999999999999766

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=93.03  E-value=0.059  Score=50.92  Aligned_cols=31  Identities=35%  Similarity=0.408  Sum_probs=27.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .|-|+|..||||||+++.|++ ++.+++..|.
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            378999999999999999998 8998877665

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=92.91  E-value=0.052  Score=50.37  Aligned_cols=28  Identities=29%  Similarity=0.455  Sum_probs=24.0

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ++.....|||.|++|+||||+|.+|.+.
T Consensus        12 v~v~G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           12 LVIDKMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEETTEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEECCEEEEEEcCCCCCHHHHHHHHHHc
Confidence            4455688999999999999999999874

>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=92.85  E-value=0.14  Score=53.27  Aligned_cols=25  Identities=28%  Similarity=0.563  Sum_probs=22.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.||+|+|||+|++.|++.+
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHH
Confidence            4679999999999999999999865

>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=92.79  E-value=0.047  Score=51.80  Aligned_cols=28  Identities=32%  Similarity=0.427  Sum_probs=23.5

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -..+..+.|.||.|+|||||.++|+..+
T Consensus        28 i~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           28 IKEGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            3345678899999999999999999755

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=92.71  E-value=0.099  Score=56.54  Aligned_cols=21  Identities=29%  Similarity=0.593  Sum_probs=15.6

Q ss_pred             cEEEEccCCCchHHHH-HHHHH
Q 012525          327 NVLLMGPTGSGKTLLA-KTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLA-raLA~  347 (461)
                      -.|+.||||||||+++ .+|+.
T Consensus       207 ~~lI~GPPGTGKT~ti~~~I~~  228 (646)
T 4b3f_X          207 LAIIHGPPGTGKTTTVVEIILQ  228 (646)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHHHHHHHHHH
Confidence            3689999999999754 44443

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=92.71  E-value=0.062  Score=50.37  Aligned_cols=25  Identities=36%  Similarity=0.470  Sum_probs=22.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-|+|.|++|+||||+++.|++.+.
T Consensus         7 ~~i~~eG~~gsGKsT~~~~l~~~l~   31 (213)
T 4edh_A            7 LFVTLEGPEGAGKSTNRDYLAERLR   31 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            4588999999999999999998773

>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=92.66  E-value=0.2  Score=48.36  Aligned_cols=22  Identities=32%  Similarity=0.234  Sum_probs=18.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .++++.+|+|+|||+++-..+-
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~   66 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLI   66 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHH
Confidence            5799999999999998765543

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=92.63  E-value=0.058  Score=51.33  Aligned_cols=25  Identities=20%  Similarity=0.267  Sum_probs=19.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.-|+|.|++|+||||+++.|++.+
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568899999999999999999877

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=92.63  E-value=0.094  Score=50.28  Aligned_cols=33  Identities=24%  Similarity=0.208  Sum_probs=25.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      .+|+|.|++||||||+|-.+|..+   +..++.++.
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            569999999999999998888765   555544443

>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=92.59  E-value=0.048  Score=51.79  Aligned_cols=27  Identities=30%  Similarity=0.420  Sum_probs=23.2

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345678899999999999999999765

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.59  E-value=0.058  Score=54.42  Aligned_cols=25  Identities=40%  Similarity=0.620  Sum_probs=23.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..++|.||+|+|||||+++|+..+.
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            6799999999999999999998774

>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=92.54  E-value=0.063  Score=54.51  Aligned_cols=24  Identities=33%  Similarity=0.595  Sum_probs=21.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..++|.||+|+||||++++|+..+
T Consensus       137 ~~i~ivG~~GsGKTTll~~l~~~~  160 (372)
T 2ewv_A          137 GLILVTGPTGSGKSTTIASMIDYI  160 (372)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhc
Confidence            568999999999999999999866

>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=92.52  E-value=0.2  Score=55.74  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=18.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .++++.||+|+|||+++..+..
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~  131 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVL  131 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            5699999999999997666643

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.42  E-value=0.052  Score=51.08  Aligned_cols=26  Identities=31%  Similarity=0.368  Sum_probs=22.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..+.|.||.|+|||||.++|+..+
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            44567899999999999999999765

>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=92.42  E-value=0.07  Score=52.49  Aligned_cols=26  Identities=35%  Similarity=0.484  Sum_probs=22.8

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..++|.|++|+||||++..||..+
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l  129 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAIS  129 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            45678999999999999999999755

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=92.40  E-value=0.07  Score=53.44  Aligned_cols=25  Identities=16%  Similarity=0.254  Sum_probs=22.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-|.|.||+|+||||+++.|+..+.
T Consensus        93 ~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           93 YIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3577999999999999999999875

>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=92.39  E-value=0.065  Score=53.70  Aligned_cols=27  Identities=33%  Similarity=0.517  Sum_probs=23.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..+.|.||+|+|||||+++|+..+...
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            568899999999999999999987543

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=92.38  E-value=0.36  Score=44.69  Aligned_cols=19  Identities=47%  Similarity=0.616  Sum_probs=16.0

Q ss_pred             CCcEEEEccCCCchHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAr  343 (461)
                      ..++++..|+|+|||+.+-
T Consensus        66 ~~~~l~~a~TGsGKT~~~~   84 (245)
T 3dkp_A           66 GRELLASAPTGSGKTLAFS   84 (245)
T ss_dssp             TCCEEEECCTTSCHHHHHH
T ss_pred             CCCEEEECCCCCcHHHHHH
Confidence            3679999999999998643

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=92.37  E-value=0.075  Score=48.48  Aligned_cols=24  Identities=25%  Similarity=0.224  Sum_probs=21.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.|.|++|+|||||+..|++.+
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l   28 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAA   28 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhh
Confidence            347899999999999999999876

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=92.34  E-value=0.11  Score=48.89  Aligned_cols=28  Identities=21%  Similarity=0.284  Sum_probs=24.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      +.-|+|.|++|+||||+++.|++.+...
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l~~~   32 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKLQPN   32 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHHCSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            3568999999999999999999999763

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=92.29  E-value=0.29  Score=48.52  Aligned_cols=32  Identities=34%  Similarity=0.449  Sum_probs=24.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc----CCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV----NVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~  358 (461)
                      +++|..|+|+|||+.+-+++...    +...+.+-.
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P   60 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAP   60 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECS
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEEC
Confidence            69999999999999988776554    444444444

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=92.21  E-value=0.078  Score=50.70  Aligned_cols=25  Identities=16%  Similarity=0.368  Sum_probs=22.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.-|+|.|++|+||||+++.|++.+
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568999999999999999999877

>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=92.18  E-value=0.13  Score=50.61  Aligned_cols=34  Identities=29%  Similarity=0.357  Sum_probs=25.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      +..++|.|++|+||||++..||..+   +..+..+++
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~  134 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGA  134 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEec
Confidence            5678899999999999999999766   444444443

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.17  E-value=0.064  Score=50.07  Aligned_cols=23  Identities=48%  Similarity=0.631  Sum_probs=20.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..+.|.||.|+|||||+++|+..
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            55789999999999999999975

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=92.16  E-value=0.081  Score=44.83  Aligned_cols=22  Identities=27%  Similarity=0.504  Sum_probs=19.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .|+|.|++|+|||+|...+...
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            5899999999999999999864

>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=92.07  E-value=0.067  Score=51.33  Aligned_cols=27  Identities=30%  Similarity=0.572  Sum_probs=22.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        31 ~~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           31 NKGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             eCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            345668899999999999999999755

>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=92.06  E-value=0.077  Score=50.72  Aligned_cols=25  Identities=44%  Similarity=0.647  Sum_probs=22.2

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .+..+.|.||.|+|||||.++|+..
T Consensus        28 ~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4566889999999999999999986

>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=92.04  E-value=0.067  Score=50.27  Aligned_cols=27  Identities=37%  Similarity=0.487  Sum_probs=23.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        33 ~~Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           33 EKGNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             ETTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345678899999999999999999765

>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=92.04  E-value=0.086  Score=47.99  Aligned_cols=24  Identities=29%  Similarity=0.346  Sum_probs=21.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .-++|.|++|+|||||++.|.+.+
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhc
Confidence            457899999999999999998765

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.03  E-value=0.066  Score=51.66  Aligned_cols=27  Identities=19%  Similarity=0.336  Sum_probs=22.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        30 ~~Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           30 RAGDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345567899999999999999999765

>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=92.00  E-value=0.063  Score=50.67  Aligned_cols=27  Identities=26%  Similarity=0.333  Sum_probs=23.4

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        32 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           32 ERGQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            345678899999999999999999866

>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=91.98  E-value=0.08  Score=51.23  Aligned_cols=27  Identities=41%  Similarity=0.534  Sum_probs=23.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        44 ~~Ge~~~l~G~NGsGKSTLlk~l~Gl~   70 (267)
T 2zu0_C           44 HPGEVHAIMGPNGSGKSTLSATLAGRE   70 (267)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTCT
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            345668899999999999999999863

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=91.97  E-value=0.089  Score=47.18  Aligned_cols=23  Identities=35%  Similarity=0.612  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.|+..
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            45899999999999999999875

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=91.95  E-value=0.082  Score=47.35  Aligned_cols=24  Identities=33%  Similarity=0.560  Sum_probs=21.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|+|.|++|+|||||.+.|+...
T Consensus        30 ~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           30 FKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            458999999999999999999754

>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=91.93  E-value=0.062  Score=51.39  Aligned_cols=27  Identities=30%  Similarity=0.473  Sum_probs=23.2

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        33 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           33 KQGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345678899999999999999999765

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=91.92  E-value=0.049  Score=49.43  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=21.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .+.|.|++|+|||||++.|+..+.
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            478999999999999999998763

>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=91.88  E-value=0.063  Score=52.42  Aligned_cols=27  Identities=19%  Similarity=0.306  Sum_probs=23.2

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-+.|.||.|+|||||.++|+..+
T Consensus        32 ~~Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           32 KRGEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            345668899999999999999999765

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=91.86  E-value=0.083  Score=50.39  Aligned_cols=24  Identities=38%  Similarity=0.713  Sum_probs=21.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.|.||.|+|||||.++|+..+
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            567899999999999999999765

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.85  E-value=0.066  Score=51.96  Aligned_cols=26  Identities=35%  Similarity=0.486  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..+.|.||.|+|||||.++|+..+
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            44668899999999999999999765

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=91.85  E-value=0.073  Score=56.53  Aligned_cols=25  Identities=24%  Similarity=0.376  Sum_probs=23.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .+++|.||+|+||||++++|+..+.
T Consensus       261 ~~i~I~GptGSGKTTlL~aL~~~i~  285 (511)
T 2oap_1          261 FSAIVVGETASGKTTTLNAIMMFIP  285 (511)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5699999999999999999998874

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=91.84  E-value=0.16  Score=44.70  Aligned_cols=24  Identities=33%  Similarity=0.580  Sum_probs=21.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|+|.|++|+|||+|...|....
T Consensus        49 ~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           49 PSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            579999999999999999998643

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=91.81  E-value=0.071  Score=51.67  Aligned_cols=27  Identities=30%  Similarity=0.534  Sum_probs=23.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||+++|+..+
T Consensus        35 ~~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           35 ASGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             ETTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            345678899999999999999999755

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=91.80  E-value=0.1  Score=44.46  Aligned_cols=23  Identities=13%  Similarity=0.352  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...|...
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            45899999999999999999863

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.79  E-value=0.1  Score=47.10  Aligned_cols=25  Identities=32%  Similarity=0.577  Sum_probs=22.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...|+|.|++|+|||+|..+|....
T Consensus        12 ~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           12 QPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3679999999999999999998754

>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=91.76  E-value=0.078  Score=53.98  Aligned_cols=26  Identities=31%  Similarity=0.506  Sum_probs=22.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        29 ~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           29 PGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            34567899999999999999999755

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=91.76  E-value=0.39  Score=44.50  Aligned_cols=23  Identities=26%  Similarity=0.560  Sum_probs=20.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|..+|..
T Consensus        29 ~~~i~lvG~~g~GKStlin~l~g   51 (239)
T 3lxx_A           29 QLRIVLVGKTGAGKSATGNSILG   51 (239)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHcC
Confidence            35699999999999999999985

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=91.75  E-value=0.084  Score=51.22  Aligned_cols=23  Identities=35%  Similarity=0.661  Sum_probs=20.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ++.|.||+|+|||||.++|+...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58899999999999999999754

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=91.74  E-value=0.07  Score=51.41  Aligned_cols=27  Identities=41%  Similarity=0.524  Sum_probs=23.3

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        44 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           44 PSGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            345678899999999999999999765

>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=91.73  E-value=0.075  Score=50.50  Aligned_cols=26  Identities=35%  Similarity=0.454  Sum_probs=22.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..+.|.||.|+|||||.++|+..+
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            45668899999999999999999755

>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=91.69  E-value=0.072  Score=50.65  Aligned_cols=27  Identities=30%  Similarity=0.504  Sum_probs=22.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           26 QPNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345568899999999999999999755

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.69  E-value=0.068  Score=52.22  Aligned_cols=27  Identities=30%  Similarity=0.368  Sum_probs=23.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        45 ~~Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           45 AKGDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            345668899999999999999999765

>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=91.66  E-value=0.077  Score=51.43  Aligned_cols=26  Identities=35%  Similarity=0.580  Sum_probs=22.7

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..+.|.||.|+|||||.++|+..+
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            45668899999999999999999765

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=91.64  E-value=0.09  Score=53.38  Aligned_cols=27  Identities=41%  Similarity=0.532  Sum_probs=23.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-+.|.||+|+|||||.++||...
T Consensus        39 ~~Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           39 REGEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            345667899999999999999999765

>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=91.62  E-value=0.1  Score=44.02  Aligned_cols=23  Identities=26%  Similarity=0.520  Sum_probs=20.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|++.|++|+|||+|...+...
T Consensus         4 ~~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            4 YKLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999999864

>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=91.54  E-value=0.32  Score=50.57  Aligned_cols=26  Identities=38%  Similarity=0.438  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..++|.|++|+||||++..||..+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l  122 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYY  122 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45668899999999999999999766

>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=91.51  E-value=0.11  Score=43.86  Aligned_cols=23  Identities=26%  Similarity=0.489  Sum_probs=20.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...+...
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            45999999999999999998753

>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=91.49  E-value=0.086  Score=50.64  Aligned_cols=26  Identities=31%  Similarity=0.505  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..+.|.||.|+|||||.++|+..+
T Consensus        25 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34568899999999999999999765

>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=91.45  E-value=0.12  Score=43.84  Aligned_cols=23  Identities=26%  Similarity=0.511  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...+...
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            46999999999999999999853

>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=91.42  E-value=0.67  Score=48.35  Aligned_cols=36  Identities=8%  Similarity=0.021  Sum_probs=27.2

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc----CCceEEecch
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADAT  359 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~s  359 (461)
                      ...-++|.|+||+|||++|..+|..+    +.+++.++..
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E  280 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLE  280 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESS
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEecc
Confidence            34568899999999999999998754    3456655543

>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=91.41  E-value=0.096  Score=53.78  Aligned_cols=26  Identities=35%  Similarity=0.592  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        28 ~Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           28 EGEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHcCC
Confidence            34567899999999999999999765

>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=91.40  E-value=0.11  Score=53.92  Aligned_cols=25  Identities=36%  Similarity=0.525  Sum_probs=22.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..++|.||+|+||||+.++|+..+.
T Consensus       168 gii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          168 GIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             CeEEEECCCCCCHHHHHHHHHhhcC
Confidence            4589999999999999999999875

>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=91.40  E-value=0.085  Score=50.86  Aligned_cols=27  Identities=30%  Similarity=0.460  Sum_probs=23.1

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        39 ~~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           39 EEGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            345668899999999999999999765

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=91.31  E-value=0.1  Score=53.18  Aligned_cols=26  Identities=38%  Similarity=0.571  Sum_probs=22.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           28 DGEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            34567899999999999999999765

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.30  E-value=0.088  Score=50.82  Aligned_cols=27  Identities=37%  Similarity=0.493  Sum_probs=22.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        31 ~~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           31 NEGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            345667899999999999999999755

>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=91.29  E-value=0.12  Score=43.89  Aligned_cols=23  Identities=17%  Similarity=0.414  Sum_probs=20.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      -.|+|.|++|+|||+|..++...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            4 IKLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999998753

>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=91.25  E-value=0.1  Score=53.04  Aligned_cols=26  Identities=38%  Similarity=0.488  Sum_probs=22.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           28 DGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            34567899999999999999999765

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=91.23  E-value=0.11  Score=49.20  Aligned_cols=27  Identities=30%  Similarity=0.315  Sum_probs=23.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      +.-|+|.|++|+||||+++.|++.+..
T Consensus        21 ~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           21 SMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            355889999999999999999987644

>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=91.20  E-value=0.13  Score=43.92  Aligned_cols=23  Identities=30%  Similarity=0.463  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      -.|+|.|++|+|||+|.+.+...
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46999999999999999999864

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=91.20  E-value=0.081  Score=50.82  Aligned_cols=27  Identities=22%  Similarity=0.288  Sum_probs=23.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        29 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           29 NKGDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             ETTCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            345668899999999999999999765

>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=91.19  E-value=0.1  Score=53.24  Aligned_cols=26  Identities=31%  Similarity=0.546  Sum_probs=22.4

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        36 ~Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           36 DGEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            34567899999999999999999755

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=91.15  E-value=0.13  Score=44.32  Aligned_cols=23  Identities=30%  Similarity=0.434  Sum_probs=20.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|...+..
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            46799999999999999999975

>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=91.14  E-value=0.1  Score=53.16  Aligned_cols=26  Identities=31%  Similarity=0.556  Sum_probs=22.7

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHcCC
Confidence            44667899999999999999999765

>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=91.07  E-value=0.12  Score=44.31  Aligned_cols=22  Identities=45%  Similarity=0.619  Sum_probs=19.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.|..
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~   26 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAG   26 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCccHHHHHHHHhc
Confidence            4599999999999999999874

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=91.06  E-value=0.11  Score=55.72  Aligned_cols=38  Identities=24%  Similarity=0.291  Sum_probs=29.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC---CceEEecchhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN---VPFVIADATTLT  362 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~---~pfv~i~~s~l~  362 (461)
                      +..|+|+|++|+||||+|+.|++.++   .++..++...+.
T Consensus       372 ~~~I~l~G~~GsGKSTia~~La~~L~~~G~~~~~ld~D~ir  412 (546)
T 2gks_A          372 GFCVWLTGLPCAGKSTIAEILATMLQARGRKVTLLDGDVVR  412 (546)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECHHHHH
T ss_pred             ceEEEccCCCCCCHHHHHHHHHHHhhhcCCeEEEECchHhh
Confidence            35688999999999999999999774   455666655443

>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=91.05  E-value=0.1  Score=46.19  Aligned_cols=21  Identities=43%  Similarity=0.763  Sum_probs=19.4

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|.+.++.
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            489999999999999999986

>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=90.99  E-value=0.13  Score=43.84  Aligned_cols=23  Identities=30%  Similarity=0.380  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
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            46999999999999999999853

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=90.94  E-value=0.13  Score=48.24  Aligned_cols=24  Identities=21%  Similarity=0.419  Sum_probs=21.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .-|+|.|++|+||||+++.|++.+
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            458899999999999999999877

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=90.92  E-value=0.13  Score=44.65  Aligned_cols=22  Identities=23%  Similarity=0.427  Sum_probs=19.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.|+.
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~   25 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTG   25 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            3589999999999999999986

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=90.91  E-value=0.48  Score=48.46  Aligned_cols=22  Identities=32%  Similarity=0.658  Sum_probs=18.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .++++..|+|+|||..+-..+.
T Consensus        20 ~~~l~~~~tGsGKT~~~~~~~~   41 (555)
T 3tbk_A           20 KNTIICAPTGCGKTFVSLLICE   41 (555)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEeCCCChHHHHHHHHHH
Confidence            6799999999999998766654

>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=90.88  E-value=0.14  Score=44.16  Aligned_cols=23  Identities=30%  Similarity=0.554  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...+...
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            56999999999999999988753

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=90.87  E-value=0.13  Score=43.90  Aligned_cols=22  Identities=27%  Similarity=0.474  Sum_probs=19.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            3589999999999999999985

>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=90.86  E-value=0.14  Score=44.15  Aligned_cols=22  Identities=32%  Similarity=0.522  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~   29 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVT   29 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999999975

>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=90.85  E-value=0.14  Score=44.57  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=20.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~   33 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTD   33 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999999986

>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=90.84  E-value=0.14  Score=43.44  Aligned_cols=22  Identities=23%  Similarity=0.475  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|..+|..
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999999985

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=90.82  E-value=0.42  Score=48.97  Aligned_cols=17  Identities=29%  Similarity=0.204  Sum_probs=15.6

Q ss_pred             CcEEEEccCCCchHHHH
Q 012525          326 SNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLA  342 (461)
                      .++|+.+|+|+|||+++
T Consensus         3 ~~~lv~a~TGsGKT~~~   19 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRRV   19 (431)
T ss_dssp             CEEEEECCTTSCTTTTH
T ss_pred             CEEEEEcCCCCCHHHHH
Confidence            67999999999999976

>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=90.77  E-value=0.13  Score=43.73  Aligned_cols=22  Identities=32%  Similarity=0.594  Sum_probs=19.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~   25 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVE   25 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            4589999999999999999975

>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=90.77  E-value=0.15  Score=43.52  Aligned_cols=22  Identities=32%  Similarity=0.542  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus         8 ~~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            8 MRILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999999975

>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=90.75  E-value=0.15  Score=43.33  Aligned_cols=22  Identities=23%  Similarity=0.534  Sum_probs=19.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+++..
T Consensus         4 ~ki~v~G~~~~GKssli~~l~~   25 (167)
T 1c1y_A            4 YKLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            3589999999999999999986

>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=0.092  Score=53.13  Aligned_cols=26  Identities=35%  Similarity=0.627  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        25 ~Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHcCC
Confidence            34567899999999999999999765

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=90.65  E-value=0.18  Score=50.36  Aligned_cols=24  Identities=29%  Similarity=0.448  Sum_probs=21.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|.|.|+||+|||||+..|+..+
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            568899999999999999998765

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=90.64  E-value=0.14  Score=44.81  Aligned_cols=22  Identities=23%  Similarity=0.427  Sum_probs=20.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.|+.
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~   29 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTG   29 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4699999999999999999986

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=90.63  E-value=0.12  Score=53.10  Aligned_cols=27  Identities=37%  Similarity=0.476  Sum_probs=23.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-+.|.||+|+|||||.++|+..+
T Consensus        45 ~~Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           45 SPGQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            345678899999999999999999754

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=90.62  E-value=0.23  Score=53.31  Aligned_cols=23  Identities=39%  Similarity=0.625  Sum_probs=19.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .++|+.+|+|+|||..+..++..
T Consensus        23 ~~~ll~~~TGsGKTl~~~~~i~~   45 (699)
T 4gl2_A           23 KNIIICLPTGCGKTRVAVYIAKD   45 (699)
T ss_dssp             CCEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHH
Confidence            67999999999999988777654

>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=90.62  E-value=0.14  Score=43.70  Aligned_cols=21  Identities=43%  Similarity=0.716  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|...+..
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            489999999999999999863

>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=90.55  E-value=0.16  Score=43.23  Aligned_cols=21  Identities=29%  Similarity=0.472  Sum_probs=19.2

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|...+..
T Consensus         2 ki~~~G~~~~GKssl~~~l~~   22 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKL   22 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            489999999999999999975

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=90.52  E-value=0.1  Score=48.63  Aligned_cols=24  Identities=33%  Similarity=0.445  Sum_probs=21.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.-|.|.|+.|+||||+++.|+..
T Consensus        20 g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           20 PFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhc
Confidence            345889999999999999999987

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=90.52  E-value=0.41  Score=49.69  Aligned_cols=35  Identities=26%  Similarity=0.413  Sum_probs=27.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc----CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~s  359 (461)
                      +..|+|.|++|+||||++-.||..+    +..+..+++.
T Consensus       100 ~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D  138 (433)
T 2xxa_A          100 PAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSAD  138 (433)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            4678899999999999999998655    5555555554

>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=90.51  E-value=0.16  Score=43.68  Aligned_cols=23  Identities=22%  Similarity=0.475  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.|...
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            56999999999999999999863

>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=90.46  E-value=0.16  Score=43.99  Aligned_cols=22  Identities=27%  Similarity=0.528  Sum_probs=20.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.|..
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~   40 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMY   40 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHhh
Confidence            5699999999999999999985

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=90.43  E-value=0.13  Score=49.88  Aligned_cols=25  Identities=36%  Similarity=0.735  Sum_probs=22.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..+.|.||.|+|||||.++|+..+
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            5678899999999999999999876

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=90.41  E-value=0.14  Score=53.57  Aligned_cols=25  Identities=32%  Similarity=0.519  Sum_probs=22.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.||.|+|||||+|.|+..+
T Consensus       138 Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          138 GPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             CCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCcc
Confidence            3568999999999999999999754

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=90.35  E-value=0.16  Score=43.88  Aligned_cols=22  Identities=32%  Similarity=0.546  Sum_probs=19.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~   28 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQ   28 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHG
T ss_pred             EEEEEECcCCCCHHHHHHHHHh
Confidence            4699999999999999999974

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=90.32  E-value=0.24  Score=49.78  Aligned_cols=26  Identities=31%  Similarity=0.417  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...|+++.|++|+|||++++.++..+
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~   59 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLRE   59 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHH
Confidence            45799999999999999999997643

>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=90.30  E-value=0.15  Score=55.09  Aligned_cols=23  Identities=39%  Similarity=0.691  Sum_probs=18.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..+++.||||||||+++..+...
T Consensus       196 ~~~li~GppGTGKT~~~~~~i~~  218 (624)
T 2gk6_A          196 PLSLIQGPPGTGKTVTSATIVYH  218 (624)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999987666543

>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=90.29  E-value=0.14  Score=43.66  Aligned_cols=22  Identities=41%  Similarity=0.694  Sum_probs=19.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -.|+|.|++|+|||+|.+.+..
T Consensus         3 ~ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            3 YKVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             CEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHcC
Confidence            3589999999999999998863

>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=90.28  E-value=0.17  Score=44.52  Aligned_cols=23  Identities=26%  Similarity=0.520  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|.+|+|||+|+..|+..
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46999999999999999999864

>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=90.19  E-value=0.16  Score=43.72  Aligned_cols=23  Identities=22%  Similarity=0.468  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.++|...
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            56999999999999999999864

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=90.19  E-value=0.52  Score=51.70  Aligned_cols=21  Identities=38%  Similarity=0.533  Sum_probs=17.2

Q ss_pred             cCCcEEEEccCCCchHHHHHH
Q 012525          324 EKSNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAra  344 (461)
                      ..+.+|+.||+|+|||+.|-.
T Consensus       154 ~rk~vlv~apTGSGKT~~al~  174 (677)
T 3rc3_A          154 QRKIIFHSGPTNSGKTYHAIQ  174 (677)
T ss_dssp             CCEEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHH
Confidence            456899999999999996533

>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=90.17  E-value=0.17  Score=44.18  Aligned_cols=24  Identities=33%  Similarity=0.342  Sum_probs=21.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|+|.|++|+|||+|.+.+....
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            569999999999999999887654

>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=90.15  E-value=0.17  Score=43.92  Aligned_cols=23  Identities=26%  Similarity=0.535  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      -.|+|.|++|+|||+|..+|...
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            45999999999999999999863

>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=90.14  E-value=0.16  Score=43.58  Aligned_cols=22  Identities=23%  Similarity=0.375  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~   36 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMY   36 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999999975

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=90.13  E-value=0.16  Score=43.77  Aligned_cols=22  Identities=32%  Similarity=0.545  Sum_probs=19.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|..+|..
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            4699999999999999999864

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=90.12  E-value=0.15  Score=46.28  Aligned_cols=24  Identities=42%  Similarity=0.609  Sum_probs=21.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..++|.|.+|+|||||+..|+..+
T Consensus        31 ~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           31 VAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            568999999999999999998875

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=90.11  E-value=0.17  Score=44.06  Aligned_cols=23  Identities=22%  Similarity=0.465  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|..+|...
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            46999999999999999999864

>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=89.99  E-value=0.092  Score=53.17  Aligned_cols=26  Identities=27%  Similarity=0.498  Sum_probs=22.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++||...
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34567899999999999999999755

>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=89.98  E-value=0.18  Score=44.49  Aligned_cols=22  Identities=41%  Similarity=0.640  Sum_probs=20.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~   47 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTR   47 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            5699999999999999999986

>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=89.95  E-value=0.18  Score=43.53  Aligned_cols=23  Identities=26%  Similarity=0.611  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...+...
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            46999999999999999999753

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=89.93  E-value=0.091  Score=52.21  Aligned_cols=27  Identities=30%  Similarity=0.614  Sum_probs=23.4

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||+|+|||||+++|+..+
T Consensus        78 ~~Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           78 MPGQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             CTTCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCchHHHHHHHHHcCC
Confidence            345678899999999999999999866

>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=89.90  E-value=0.19  Score=43.79  Aligned_cols=23  Identities=22%  Similarity=0.446  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...+...
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            56899999999999999999864

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=89.89  E-value=0.12  Score=50.78  Aligned_cols=27  Identities=26%  Similarity=0.333  Sum_probs=23.2

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||.|+|||||.++|+..+
T Consensus        62 ~~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           62 ERGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            345678899999999999999999765

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=89.87  E-value=0.6  Score=47.96  Aligned_cols=22  Identities=41%  Similarity=0.709  Sum_probs=18.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .++++..|+|+|||..+-..+.
T Consensus        23 ~~~l~~~~tGsGKT~~~~~~~~   44 (556)
T 4a2p_A           23 KNALICAPTGSGKTFVSILICE   44 (556)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEcCCCChHHHHHHHHHH
Confidence            5799999999999998766654

>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=89.83  E-value=0.14  Score=53.13  Aligned_cols=34  Identities=38%  Similarity=0.506  Sum_probs=26.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      +..|+|.|++|+||||++..||..+   +..++.+++
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~  135 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAA  135 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEec
Confidence            4679999999999999999999866   234444444

>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=89.82  E-value=0.19  Score=43.36  Aligned_cols=22  Identities=36%  Similarity=0.543  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~   32 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKD   32 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            5699999999999999999975

>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=89.75  E-value=0.18  Score=43.90  Aligned_cols=23  Identities=26%  Similarity=0.525  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
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            56999999999999999999753

>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=89.74  E-value=0.18  Score=44.35  Aligned_cols=23  Identities=26%  Similarity=0.547  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
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            45899999999999999999864

>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=89.66  E-value=0.2  Score=43.38  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=19.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.+..
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~   27 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTT   27 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999999975

>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=89.66  E-value=0.79  Score=49.84  Aligned_cols=19  Identities=53%  Similarity=0.690  Sum_probs=17.0

Q ss_pred             CCcEEEEccCCCchHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAr  343 (461)
                      ..++++.+|+|+|||+++.
T Consensus        39 ~~~~lv~apTGsGKT~~~~   57 (720)
T 2zj8_A           39 GKNALISIPTASGKTLIAE   57 (720)
T ss_dssp             TCEEEEECCGGGCHHHHHH
T ss_pred             CCcEEEEcCCccHHHHHHH
Confidence            4789999999999999883

>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=89.65  E-value=0.29  Score=45.68  Aligned_cols=32  Identities=31%  Similarity=0.478  Sum_probs=24.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc--CCceEEec
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV--NVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l--~~pfv~i~  357 (461)
                      ..+++.|.+|+||||++..||..+  +..+..++
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            457899999999999999999765  44444444

>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=89.64  E-value=0.17  Score=44.05  Aligned_cols=22  Identities=23%  Similarity=0.446  Sum_probs=19.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .|+|.|++|+|||+|...+...
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            4899999999999999998753

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=89.62  E-value=0.69  Score=50.75  Aligned_cols=35  Identities=20%  Similarity=0.210  Sum_probs=22.1

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      ....+++.+|+|+|||+.+-...-.-+...+.+..
T Consensus       231 ~~~~vlv~ApTGSGKT~a~~l~ll~~g~~vLVl~P  265 (666)
T 3o8b_A          231 SFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNP  265 (666)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHHTTCCEEEEES
T ss_pred             cCCeEEEEeCCchhHHHHHHHHHHHCCCeEEEEcc
Confidence            45679999999999997654433333333343333

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=89.50  E-value=0.17  Score=44.43  Aligned_cols=23  Identities=30%  Similarity=0.485  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.++|+..
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45899999999999999999864

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=89.50  E-value=0.21  Score=43.90  Aligned_cols=23  Identities=35%  Similarity=0.553  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|..+|...
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46999999999999999999863

>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=89.50  E-value=0.24  Score=56.36  Aligned_cols=23  Identities=26%  Similarity=0.444  Sum_probs=20.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..-++|+||.|+||||+.|.++.
T Consensus       673 g~i~~ItGPNGaGKSTlLr~i~~  695 (918)
T 3thx_B          673 ERVMIITGPNMGGKSSYIKQVAL  695 (918)
T ss_dssp             CCEEEEESCCCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCchHHHHHHHHH
Confidence            45688999999999999999874

>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=89.47  E-value=0.2  Score=44.66  Aligned_cols=22  Identities=32%  Similarity=0.536  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.+..
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999999986

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=89.44  E-value=0.21  Score=49.11  Aligned_cols=35  Identities=20%  Similarity=0.237  Sum_probs=25.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEec
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIAD  357 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~  357 (461)
                      ..+.-++|.|+||+|||++|..+|..+   +.+++.++
T Consensus        66 ~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s  103 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  103 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            334568999999999999999998644   34555444

>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=89.44  E-value=0.19  Score=44.19  Aligned_cols=24  Identities=21%  Similarity=0.387  Sum_probs=21.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ...|+|.|++|+|||+|...|...
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            467999999999999999999753

>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=89.40  E-value=0.47  Score=53.07  Aligned_cols=25  Identities=20%  Similarity=0.389  Sum_probs=21.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .+..++|+||.|+||||+.|.|+..
T Consensus       606 ~g~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          606 QRRMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHH
Confidence            3456889999999999999999864

>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=89.38  E-value=0.24  Score=56.35  Aligned_cols=23  Identities=17%  Similarity=0.302  Sum_probs=20.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      +.-++|+||.|+||||+.|.++-
T Consensus       662 g~i~~ItGpNGsGKSTlLr~ial  684 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQTGV  684 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35688999999999999999954

>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=89.36  E-value=0.21  Score=46.41  Aligned_cols=23  Identities=30%  Similarity=0.549  Sum_probs=21.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhcC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |.|.|..|+||||+++.|++.+.
T Consensus         5 I~~EG~dGsGKsTq~~~L~~~L~   27 (205)
T 4hlc_A            5 ITFEGPEGSGKTTVINEVYHRLV   27 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Confidence            78999999999999999999883

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=89.33  E-value=0.3  Score=50.81  Aligned_cols=27  Identities=26%  Similarity=0.383  Sum_probs=23.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..+.|.||+|+|||||.+.|+......
T Consensus       158 q~~~IvG~sGsGKSTLl~~Iag~~~~~  184 (438)
T 2dpy_A          158 QRMGLFAGSGVGKSVLLGMMARYTRAD  184 (438)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcccCCC
Confidence            568899999999999999999988543

>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=89.31  E-value=0.22  Score=43.59  Aligned_cols=23  Identities=26%  Similarity=0.533  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|..+|...
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            56999999999999999999763

>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=89.28  E-value=0.22  Score=43.86  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...|...
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            56999999999999999999753

>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=89.27  E-value=0.22  Score=44.11  Aligned_cols=22  Identities=27%  Similarity=0.528  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        15 ~ki~v~G~~~~GKSsli~~l~~   36 (206)
T 2bov_A           15 HKVIMVGSGGVGKSALTLQFMY   36 (206)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            5699999999999999999975

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=89.22  E-value=0.31  Score=49.11  Aligned_cols=27  Identities=15%  Similarity=0.289  Sum_probs=23.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      ..+.|.||+|+|||||.+.|+..+...
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~~~~~   98 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNGASAD   98 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            568899999999999999999988643

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=89.21  E-value=0.2  Score=50.09  Aligned_cols=25  Identities=24%  Similarity=0.308  Sum_probs=21.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...+.|.|+||+|||||.++|+..+
T Consensus        55 g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           55 AIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhh
Confidence            3568899999999999999999755

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=89.18  E-value=0.21  Score=45.49  Aligned_cols=24  Identities=42%  Similarity=0.596  Sum_probs=21.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|+|.|.+|+|||+|+..++...
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            458899999999999999998765

>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=89.15  E-value=0.26  Score=42.62  Aligned_cols=23  Identities=22%  Similarity=0.291  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
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            56999999999999999998753

>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=89.05  E-value=0.23  Score=44.09  Aligned_cols=23  Identities=30%  Similarity=0.563  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...|...
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            9 LKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            56999999999999999999763

>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=89.02  E-value=0.21  Score=52.68  Aligned_cols=25  Identities=40%  Similarity=0.624  Sum_probs=21.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.|++|+|||||++.++...
T Consensus       281 G~i~~i~G~~GsGKSTLl~~l~g~~  305 (525)
T 1tf7_A          281 DSIILATGATGTGKTLLVSRFVENA  305 (525)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3668899999999999999998654

>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=89.02  E-value=0.23  Score=44.07  Aligned_cols=23  Identities=22%  Similarity=0.439  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
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            56999999999999999999863

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=89.01  E-value=0.42  Score=45.52  Aligned_cols=32  Identities=25%  Similarity=0.247  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHH-HHHHHHHhc--CCceEEec
Q 012525          326 SNVLLMGPTGSGKTL-LAKTLARHV--NVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GPPGTGKTt-LAraLA~~l--~~pfv~i~  357 (461)
                      .-.+++|+.|+|||| |.+.+.+..  +..++.+.
T Consensus        29 ~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~k   63 (219)
T 3e2i_A           29 WIECITGSMFSGKSEELIRRLRRGIYAKQKVVVFK   63 (219)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEEE
Confidence            346799999999999 555554433  44444443

>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=89.00  E-value=0.22  Score=43.22  Aligned_cols=22  Identities=18%  Similarity=0.380  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
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            5699999999999999999984

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=88.97  E-value=0.2  Score=43.80  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...|...
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            56999999999999999998754

>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=88.94  E-value=0.24  Score=43.61  Aligned_cols=22  Identities=23%  Similarity=0.455  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        21 ~ki~v~G~~~~GKSsli~~l~~   42 (189)
T 1z06_A           21 FKIIVIGDSNVGKTCLTYRFCA   42 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            5699999999999999999875

>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=88.86  E-value=0.25  Score=43.72  Aligned_cols=22  Identities=27%  Similarity=0.483  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~   43 (191)
T 2a5j_A           22 FKYIIIGDTGVGKSCLLLQFTD   43 (191)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999999975

>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=88.84  E-value=0.25  Score=43.69  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=20.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|...|..
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~   44 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIAS   44 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHc
Confidence            35699999999999999999985

>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=88.83  E-value=0.2  Score=45.05  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        30 ~ki~vvG~~~vGKSsli~~l~~   51 (201)
T 2hup_A           30 FKLVLVGDASVGKTCVVQRFKT   51 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhh
Confidence            5699999999999999999975

>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=88.83  E-value=0.23  Score=49.68  Aligned_cols=28  Identities=32%  Similarity=0.468  Sum_probs=23.7

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +...+..|+|.|++|+|||++|.+|.+.
T Consensus       140 v~~~g~~vl~~G~sG~GKSt~a~~l~~~  167 (314)
T 1ko7_A          140 VDVYGVGVLITGDSGIGKSETALELIKR  167 (314)
T ss_dssp             EEETTEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEECCEEEEEEeCCCCCHHHHHHHHHhc
Confidence            3445678999999999999999999874

>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=88.81  E-value=0.25  Score=43.83  Aligned_cols=22  Identities=27%  Similarity=0.545  Sum_probs=19.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus        22 ~ki~vvG~~~vGKTsLi~~l~~   43 (187)
T 3c5c_A           22 VNLAILGRRGAGKSALTVKFLT   43 (187)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCcHHHHHHHHHh
Confidence            4699999999999999988875

>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=88.79  E-value=0.22  Score=44.28  Aligned_cols=22  Identities=27%  Similarity=0.404  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~   30 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYAD   30 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999999875

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=88.77  E-value=0.57  Score=50.31  Aligned_cols=23  Identities=39%  Similarity=0.494  Sum_probs=18.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .++|+..|+|+|||+.....+-.
T Consensus        60 ~d~lv~~pTGsGKTl~~~lpal~   82 (591)
T 2v1x_A           60 KEVFLVMPTGGGKSLCYQLPALC   82 (591)
T ss_dssp             CCEEEECCTTSCTTHHHHHHHHT
T ss_pred             CCEEEEECCCChHHHHHHHHHHH
Confidence            56999999999999876655533

>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=88.75  E-value=0.25  Score=44.07  Aligned_cols=23  Identities=22%  Similarity=0.411  Sum_probs=20.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|...|..
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~   50 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCK   50 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHH
T ss_pred             CeEEEEECcCCCCHHHHHHHHHh
Confidence            35799999999999999999975

>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=88.74  E-value=0.23  Score=44.03  Aligned_cols=23  Identities=30%  Similarity=0.501  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...|...
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            56999999999999999999753

>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=88.73  E-value=0.25  Score=43.84  Aligned_cols=23  Identities=26%  Similarity=0.304  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      -.|+|.|++|+|||+|...+...
T Consensus        21 ~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           21 LKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            56999999999999999877753

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=88.71  E-value=0.22  Score=50.86  Aligned_cols=27  Identities=19%  Similarity=0.246  Sum_probs=22.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-+.|.||+|+|||||.++|+...
T Consensus        52 ~~Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           52 PAGQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             cCCCEEEEEcCCCchHHHHHHHHhcCC
Confidence            345667899999999999999999765

>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=88.71  E-value=0.23  Score=43.85  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=21.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -.|+|.|++|+|||+|...|...-
T Consensus        24 ~ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           24 FKLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCcCHHHHHHHHhcCC
Confidence            569999999999999999998643

>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=88.70  E-value=0.25  Score=43.64  Aligned_cols=23  Identities=22%  Similarity=0.404  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            56999999999999999999864

>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=88.69  E-value=0.13  Score=46.18  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=20.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ...|+|.|++|+|||||.++|+..
T Consensus        26 ~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           26 GIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            356899999999999999988754

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=88.64  E-value=0.25  Score=45.41  Aligned_cols=28  Identities=25%  Similarity=0.406  Sum_probs=23.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEE
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVI  355 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~  355 (461)
                      |.|.|.-|+||||.++.|++.+   +.+++.
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~   33 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVIL   33 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEE
Confidence            6799999999999999999877   445443

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=88.63  E-value=0.61  Score=52.04  Aligned_cols=22  Identities=45%  Similarity=0.552  Sum_probs=18.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .++|+.||+|+|||.++-..+-
T Consensus       390 ~~~Ll~a~TGSGKTlvall~il  411 (780)
T 1gm5_A          390 MNRLLQGDVGSGKTVVAQLAIL  411 (780)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHH
T ss_pred             CcEEEEcCCCCCHHHHHHHHHH
Confidence            5899999999999998865543

>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=88.55  E-value=0.19  Score=43.47  Aligned_cols=23  Identities=22%  Similarity=0.290  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...+...
T Consensus         8 ~ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            8 LRLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEEECCGGGCHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46999999999999999999863

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=88.55  E-value=1.9  Score=50.00  Aligned_cols=21  Identities=38%  Similarity=0.425  Sum_probs=17.5

Q ss_pred             CcEEEEccCCCchHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA  346 (461)
                      .++|++||+|+|||.+|-..|
T Consensus       625 ~d~ll~~~TGsGKT~val~aa  645 (1151)
T 2eyq_A          625 MDRLVCGDVGFGKTEVAMRAA  645 (1151)
T ss_dssp             CEEEEECCCCTTTHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHH
Confidence            479999999999999875444

>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=88.44  E-value=0.3  Score=54.36  Aligned_cols=24  Identities=29%  Similarity=0.416  Sum_probs=21.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +..++|+||.|+||||+.|.++..
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            567889999999999999999864

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=88.42  E-value=0.25  Score=44.14  Aligned_cols=24  Identities=29%  Similarity=0.389  Sum_probs=21.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ...|+|.|.+|+|||+|..+|...
T Consensus        24 ~~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           24 YRKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEEECCCCcCHHHHHHHHHhC
Confidence            356999999999999999999863

>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=88.39  E-value=0.25  Score=43.43  Aligned_cols=22  Identities=27%  Similarity=0.519  Sum_probs=20.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|..+|..
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHc
Confidence            5699999999999999999976

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=88.35  E-value=0.27  Score=50.85  Aligned_cols=35  Identities=23%  Similarity=0.302  Sum_probs=26.4

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc----CCceEEecc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADA  358 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~  358 (461)
                      .+.-++|.|+||+|||+++..+|..+    +.+++.++.
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~  240 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSL  240 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEES
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC
Confidence            34568899999999999999998744    445555443

>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=88.34  E-value=0.28  Score=43.04  Aligned_cols=26  Identities=27%  Similarity=0.461  Sum_probs=21.8

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-.+|+||.|+|||++..+|.-.+
T Consensus        22 ~~g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           22 KEGINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             CSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            34457899999999999999998655

>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=88.32  E-value=0.26  Score=44.07  Aligned_cols=22  Identities=32%  Similarity=0.549  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~   30 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSD   30 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999999975

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=88.27  E-value=0.28  Score=43.76  Aligned_cols=22  Identities=32%  Similarity=0.594  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|..+|..
T Consensus        21 ~~i~v~G~~~~GKSsli~~l~~   42 (213)
T 3cph_A           21 MKILLIGDSGVGKSCLLVRFVE   42 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            5699999999999999999985

>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=88.25  E-value=0.21  Score=49.90  Aligned_cols=28  Identities=36%  Similarity=0.385  Sum_probs=23.5

Q ss_pred             cccccCCcEEEEccCCCchHHHHHHHHH
Q 012525          320 NVELEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       320 ~~~~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -++..+..|||.|++|+|||++|..|.+
T Consensus       142 ~v~~~g~gvli~G~sG~GKStlal~l~~  169 (312)
T 1knx_A          142 LLEVFGVGVLLTGRSGIGKSECALDLIN  169 (312)
T ss_dssp             EEEETTEEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEECCEEEEEEcCCCCCHHHHHHHHHH
Confidence            3445578899999999999999988865

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=88.16  E-value=0.26  Score=43.06  Aligned_cols=22  Identities=27%  Similarity=0.486  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus        19 ~~i~v~G~~~~GKssl~~~l~~   40 (186)
T 1ksh_A           19 LRLLMLGLDNAGKTTILKKFNG   40 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999999875

>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=88.09  E-value=0.29  Score=43.98  Aligned_cols=23  Identities=43%  Similarity=0.492  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|...+...
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            56999999999999999999863

>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=88.05  E-value=0.19  Score=43.62  Aligned_cols=22  Identities=32%  Similarity=0.579  Sum_probs=19.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      ...|+|.|++|+|||+|...+.
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            3579999999999999998886

>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=88.00  E-value=0.27  Score=55.00  Aligned_cols=24  Identities=38%  Similarity=0.700  Sum_probs=19.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ...+++.||||||||+++..++..
T Consensus       371 ~~~~lI~GppGTGKT~ti~~~i~~  394 (800)
T 2wjy_A          371 RPLSLIQGPPGTGKTVTSATIVYH  394 (800)
T ss_dssp             SSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            456889999999999987666553

>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=87.99  E-value=0.28  Score=48.02  Aligned_cols=26  Identities=38%  Similarity=0.438  Sum_probs=22.4

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..+.|.|++|+||||++..||..+
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~  122 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYY  122 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45668899999999999999999765

>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=87.86  E-value=0.28  Score=44.56  Aligned_cols=23  Identities=26%  Similarity=0.547  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
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            56999999999999999999864

>1dek_A Deoxynucleoside monophosphate kinase; transferase, phosphotransferase; HET: DGP; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1 PDB: 1del_A*

Probab=87.83  E-value=0.25  Score=47.48  Aligned_cols=27  Identities=22%  Similarity=0.230  Sum_probs=23.9

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |.|+|.+|+||||+|+.|++.++.+++
T Consensus         4 i~ltG~~~sGK~tv~~~l~~~~g~~~~   30 (241)
T 1dek_A            4 IFLSGVKRSGKDTTADFIMSNYSAVKY   30 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEEC
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCeEE
Confidence            679999999999999999998876653

>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=87.77  E-value=0.21  Score=44.00  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=20.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ...|+|.|++|+|||+|...|...
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~   44 (190)
T 2h57_A           21 EVHVLCLGLDNSGKTTIINKLKPS   44 (190)
T ss_dssp             CEEEEEEECTTSSHHHHHHHTSCG
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            356999999999999999998754

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=87.76  E-value=0.25  Score=44.35  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=19.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.+..
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999999864

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=87.73  E-value=0.29  Score=44.41  Aligned_cols=23  Identities=30%  Similarity=0.600  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
T Consensus        27 ~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           27 FKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            56999999999999999998753

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=87.73  E-value=0.94  Score=45.27  Aligned_cols=24  Identities=29%  Similarity=0.519  Sum_probs=21.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|.|.|+||+|||||..+|...+
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            458899999999999999998754

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=87.68  E-value=1  Score=48.23  Aligned_cols=22  Identities=32%  Similarity=0.658  Sum_probs=19.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .++++.+|+|+|||+.+-.++.
T Consensus        29 ~~~iv~~~TGsGKTl~~~~~i~   50 (696)
T 2ykg_A           29 KNTIICAPTGCGKTFVSLLICE   50 (696)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEcCCCchHHHHHHHHHH
Confidence            6799999999999998876664

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=87.66  E-value=0.3  Score=43.08  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=20.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
T Consensus        19 ~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           19 LKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            57999999999999999999864

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=87.66  E-value=0.29  Score=43.06  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=20.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|...|..
T Consensus        17 ~~ki~v~G~~~~GKSsl~~~l~~   39 (199)
T 4bas_A           17 KLQVVMCGLDNSGKTTIINQVKP   39 (199)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            36799999999999999998864

>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=87.58  E-value=0.31  Score=43.91  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        26 ~ki~vvG~~~~GKSsLi~~l~~   47 (217)
T 2f7s_A           26 IKLLALGDSGVGKTTFLYRYTD   47 (217)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999999875

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=87.58  E-value=0.25  Score=43.23  Aligned_cols=22  Identities=23%  Similarity=0.439  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...|..
T Consensus        22 ~~i~v~G~~~~GKSsli~~l~~   43 (181)
T 2h17_A           22 HKVIIVGLDNAGKTTILYQFSM   43 (181)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999999975

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=87.55  E-value=0.29  Score=42.97  Aligned_cols=22  Identities=23%  Similarity=0.439  Sum_probs=20.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.+..
T Consensus        17 ~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           17 HKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999999984

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=87.54  E-value=0.3  Score=43.41  Aligned_cols=22  Identities=32%  Similarity=0.596  Sum_probs=19.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.|..
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            4699999999999999999864

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=87.49  E-value=0.32  Score=43.16  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=20.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|...+..
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~   42 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTT   42 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            35699999999999999998874

>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=87.46  E-value=0.28  Score=43.22  Aligned_cols=23  Identities=43%  Similarity=0.618  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|.+.+...
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            56999999999999999998754

>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=87.44  E-value=0.28  Score=46.72  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=20.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|++|+|||+|..+|...
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            46899999999999999999753

>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=87.39  E-value=0.19  Score=43.68  Aligned_cols=22  Identities=32%  Similarity=0.526  Sum_probs=9.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~   30 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSE   30 (183)
T ss_dssp             EEEEEECCCCC-----------
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999998864

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=87.38  E-value=0.39  Score=48.39  Aligned_cols=35  Identities=17%  Similarity=0.151  Sum_probs=26.0

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      ...-++|.|+||+|||++|..+|..+   +.+++.++.
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSl   82 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSL   82 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            34568899999999999999998754   455544433

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=87.24  E-value=0.32  Score=43.71  Aligned_cols=23  Identities=22%  Similarity=0.483  Sum_probs=20.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|...|..
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~   47 (207)
T 2fv8_A           25 RKKLVVVGDGACGKTCLLIVFSK   47 (207)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECcCCCCHHHHHHHHhc
Confidence            35799999999999999999986

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=87.19  E-value=0.31  Score=43.65  Aligned_cols=22  Identities=27%  Similarity=0.560  Sum_probs=19.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|.+.|..
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~   47 (200)
T 2o52_A           26 FKFLVIGSAGTGKSCLLHQFIE   47 (200)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            5699999999999999999874

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=87.11  E-value=0.27  Score=48.14  Aligned_cols=23  Identities=26%  Similarity=0.472  Sum_probs=19.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      -.|+|.|++|+|||||.+.|+..
T Consensus        19 ~~I~lvG~nG~GKSTLl~~L~g~   41 (301)
T 2qnr_A           19 FTLMVVGESGLGKSTLINSLFLT   41 (301)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHC-
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            45799999999999999998753

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=87.06  E-value=1  Score=52.05  Aligned_cols=21  Identities=33%  Similarity=0.444  Sum_probs=17.7

Q ss_pred             CcEEEEccCCCchHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA  346 (461)
                      .++|+.+|+|+|||+++...+
T Consensus       200 ~dvLV~ApTGSGKTlva~l~i  220 (1108)
T 3l9o_A          200 ESVLVSAHTSAGKTVVAEYAI  220 (1108)
T ss_dssp             CCEEEECCSSSHHHHHHHHHH
T ss_pred             CCEEEECCCCCChHHHHHHHH
Confidence            679999999999999875444

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=87.04  E-value=0.91  Score=46.68  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.2

Q ss_pred             cCCcEEEEccCCCchHH
Q 012525          324 EKSNVLLMGPTGSGKTL  340 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTt  340 (461)
                      ....+++.+|+|+|||+
T Consensus        18 ~~~~~lv~a~TGsGKT~   34 (451)
T 2jlq_A           18 KKRLTIMDLHPGAGKTK   34 (451)
T ss_dssp             TTCEEEECCCTTSSCCT
T ss_pred             cCCeEEEECCCCCCHhh
Confidence            34556999999999998

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=87.03  E-value=0.34  Score=43.35  Aligned_cols=23  Identities=22%  Similarity=0.498  Sum_probs=20.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|.+|+|||+|...+..
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~   47 (201)
T 2gco_A           25 RKKLVIVGDGACGKTCLLIVFSK   47 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            35799999999999999999986

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=86.96  E-value=0.32  Score=48.39  Aligned_cols=25  Identities=16%  Similarity=0.331  Sum_probs=21.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ...|.|.|++|+||||++..|+..+
T Consensus        56 ~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           56 TLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3568899999999999999998754

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=86.90  E-value=0.37  Score=47.24  Aligned_cols=25  Identities=28%  Similarity=0.449  Sum_probs=21.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      ..-+.|.||+|+|||||.++|+ ...
T Consensus       165 G~i~~l~G~sG~GKSTLln~l~-~~~  189 (302)
T 2yv5_A          165 GFICILAGPSGVGKSSILSRLT-GEE  189 (302)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHH-SCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHH-Hhh
Confidence            4567899999999999999999 653

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=86.87  E-value=0.35  Score=43.37  Aligned_cols=22  Identities=18%  Similarity=0.238  Sum_probs=20.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|...+..
T Consensus        10 ~ki~i~G~~~~GKTsli~~l~~   31 (212)
T 2j0v_A           10 IKCVTVGDGAVGKTCMLICYTS   31 (212)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999999985

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=86.81  E-value=0.29  Score=43.97  Aligned_cols=21  Identities=43%  Similarity=0.688  Sum_probs=19.1

Q ss_pred             CcEEEEccCCCchHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA  346 (461)
                      ..|+|.|++|+|||+|.+.+.
T Consensus        24 ~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           24 FKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHTC
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            468999999999999999985

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=86.76  E-value=0.44  Score=48.45  Aligned_cols=35  Identities=37%  Similarity=0.545  Sum_probs=25.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      ...|+++.|++|+|||++++.+...+   +..++.+|.
T Consensus        52 ~~~h~~i~G~tGsGKs~~~~~li~~~~~~g~~viv~Dp   89 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDP   89 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEE
T ss_pred             CcceEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeC
Confidence            35899999999999999987766433   444554443

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=86.72  E-value=0.39  Score=44.66  Aligned_cols=22  Identities=36%  Similarity=0.520  Sum_probs=18.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      ...+++.||+|+|||++...+.
T Consensus        76 g~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           76 NSVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCcHHhHHHHH
Confidence            4779999999999998665553

>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=86.71  E-value=0.32  Score=43.33  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=20.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|+|.|++|+|||+|...+..
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            35699999999999999998863

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=86.65  E-value=0.3  Score=50.81  Aligned_cols=21  Identities=43%  Similarity=0.608  Sum_probs=19.6

Q ss_pred             EEEEccCCCchHHHHHHHHHh
Q 012525          328 VLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|.|++|+|||||.++|+..
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            889999999999999999875

---

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	461
d1um8a_	364	c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 2	2e-60
d1g41a_	443	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	1e-55
d1g41a_	443	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	4e-05
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	4e-44
d1r6bx3	315	c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, A	8e-19
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	2e-15
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	4e-15
d1qvra3	315	c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus	1e-14
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	2e-12
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	2e-09
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	5e-09
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	2e-08
d1kaga_	169	c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia	8e-07
d1lw7a2	192	c.37.1.1 (A:220-411) Transcriptional regulator Nad	1e-06
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	4e-06
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	8e-06
d1rkba_	173	c.37.1.1 (A:) Adenylate kinase {Human (Homo sapien	1e-05
d1ny5a2	247	c.37.1.20 (A:138-384) Transcriptional activator si	2e-05
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	2e-05
d1zp6a1	176	c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {	3e-05
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	3e-05
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	3e-05
d1qhxa_	178	c.37.1.3 (A:) Chloramphenicol phosphotransferase {	3e-05
d1e6ca_	170	c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chr	8e-05
d1viaa_	161	c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobact	8e-05
d1g8pa_	333	c.37.1.20 (A:) ATPase subunit of magnesium chelata	8e-05
d2iyva1	165	c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycoba	8e-05
d1y63a_	174	c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishma	9e-05
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	1e-04
d1knqa_	171	c.37.1.17 (A:) Gluconate kinase {Escherichia coli	3e-04
d1c4oa1	408	c.37.1.19 (A:2-409) Nucleotide excision repair enz	4e-04
d2cdna1	181	c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium	5e-04
d1t5la1	413	c.37.1.19 (A:2-414) Nucleotide excision repair enz	6e-04
d1qvra2	387	c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus	6e-04
d1akya1	180	c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Bak	6e-04
d2bdta1	176	c.37.1.25 (A:1-176) Hypothetical protein BH3686 {B	8e-04
d1zaka1	189	c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Mai	0.001
d2ak3a1	189	c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow	0.002
d1e4va1	179	c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Esc	0.002
d1zina1	182	c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bac	0.002
d1ak2a1	190	c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Co	0.002
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	0.002
d1s3ga1	182	c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bac	0.003
d1qf9a_	194	c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoi	0.003
d3adka_	194	c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [	0.004

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]} Length = 364

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

 Score =  200 bits (508), Expect = 2e-60
 Identities = 98/177 (55%), Positives = 138/177 (77%), Gaps = 1/177 (0%)

Query: 259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
             +P PKE+   LD +VIGQE+AKKV SVAVYNHYKR+     K        +   +++ 
Sbjct: 3   SYIPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSF-KEKLKKQDNQDSNVELEHL 61

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
           + VEL KSN+LL+GPTGSGKTL+A+TLA+H+++P  I+DAT+LT+AGYVGEDVE+IL +L
Sbjct: 62  EEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRL 121

Query: 379 LAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKT 435
           L  +++NV+ AQ+G+V+IDE+DKI++ +E+ +I+RDVSGEGVQQALLK++EG+    
Sbjct: 122 LQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNI 178

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 443

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score =  188 bits (479), Expect = 1e-55
 Identities = 50/180 (27%), Positives = 80/180 (44%), Gaps = 28/180 (15%)

Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LD+ +IGQ  AK+ +++A+ N ++R+                         E
Sbjct: 4   TPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQL-----------------QEPLRHE 46

Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L   A
Sbjct: 47  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA 106

Query: 383 EFNVEAAQQGMVY-----------IDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT 431
              V   +                +D +    K       + D      Q    K+ EG 
Sbjct: 107 MKLVRQQEIAKNRARAEDVAEERILDALLPPAKNQWGEVENHDSHSSTRQAFRKKLREGQ 166

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 443

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 43.2 bits (101), Expect = 4e-05
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNL 447
             Q G+V+IDE+DKI KK E      DVS EGVQ+ LL ++EG+   T   + K      
Sbjct: 247 VEQNGIVFIDEIDKICKKGE--YSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILF 304

Query: 448 YIKTSGLDSKT 458
               +   ++ 
Sbjct: 305 IASGAFQVARP 315

>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 =  154 bits (391), Expect = 4e-44
 Identities = 70/191 (36%), Positives = 108/191 (56%), Gaps = 29/191 (15%)

Query: 263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVE 322
           TP+EI   LD+ +IGQ  AK+ +++A+ N ++R+      +                  E
Sbjct: 4   TPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRH-----------------E 46

Query: 323 LEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQA 382
           +   N+L++GPTG GKT +A+ LA+  N PF+  +AT  T+ GYVG++V+SI+  L   A
Sbjct: 47  VTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA 106

Query: 383 EFNVEAAQQ-GMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSK 441
              ++A +Q G+V+IDE+DKI KK E      DVS EGVQ+ LL ++EG+          
Sbjct: 107 GGAIDAVEQNGIVFIDEIDKICKKGE--YSGADVSREGVQRDLLPLVEGS---------T 155

Query: 442 VSRDNLYIKTS 452
           VS  +  +KT 
Sbjct: 156 VSTKHGMVKTD 166

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 315

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

 Score = 84.5 bits (208), Expect = 8e-19
 Identities = 33/165 (20%), Positives = 57/165 (34%), Gaps = 28/165 (16%)

Query: 259 EDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDND 318
            D  T K +   L   V GQ+KA + L+ A+      + H +   GS             
Sbjct: 8   SDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGS------------- 54

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVES----I 374
                     L  GPTG GKT +   L++ + +  +  D +   +   V   + +    +
Sbjct: 55  ---------FLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYV 105

Query: 375 LYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG 419
            +         V      ++ +DE++K        NI   V   G
Sbjct: 106 GFDQGGLLTDAVIKHPHAVLLLDEIEKAHPD--VFNILLQVMDNG 148

>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 = 73.7 bits (181), Expect = 2e-15
 Identities = 42/161 (26%), Positives = 66/161 (40%), Gaps = 25/161 (15%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           V G E+AK+ L   V    + + + +     GA                    VLL+GP 
Sbjct: 11  VAGAEEAKEELKEIV----EFLKNPSRFHEMGARIPK---------------GVLLVGPP 51

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV 394
           G GKT LA+ +A    VPF+ A  +   +  +VG    + +  L   A    +     +V
Sbjct: 52  GVGKTHLARAVAGEARVPFITASGSDFVE-MFVGVG-AARVRDLFETA----KRHAPCIV 105

Query: 395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKT 435
           +IDE+D + +K  S     +   E     LL  ++G E  T
Sbjct: 106 FIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDT 146

>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 = 72.6 bits (178), Expect = 4e-15
 Identities = 36/160 (22%), Positives = 67/160 (41%), Gaps = 25/160 (15%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           V G ++AK+ ++  V    + +   +  +  G +                   VL++GP 
Sbjct: 14  VAGCDEAKEEVAELV----EYLREPSRFQKLGGKIPK---------------GVLMVGPP 54

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV 394
           G+GKTLLAK +A    VPF     +   +  +VG    S +  +  QA    + A   ++
Sbjct: 55  GTGKTLLAKAIAGEAKVPFFTISGSDFVE-MFVGVG-ASRVRDMFEQA----KKAAPCII 108

Query: 395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK 434
           +IDE+D + ++  +         E     +L  ++G E  
Sbjct: 109 FIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGN 148

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 315

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

 Score = 72.4 bits (177), Expect = 1e-14
 Identities = 39/180 (21%), Positives = 66/180 (36%), Gaps = 45/180 (25%)

Query: 254 GSNLGEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAA 313
              L  +      + + L K V+GQ++A + ++ A+      +   N   GS        
Sbjct: 4   SKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGS-------- 55

Query: 314 AVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQ------- 363
                          L +GPTG GKT LAKTLA  +       +  D T   +       
Sbjct: 56  --------------FLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRL 101

Query: 364 ----AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG 419
                GYVG +    L + + +  ++V       +  DE++K     +  NI   +  +G
Sbjct: 102 IGAPPGYVGYEEGGQLTEAVRRRPYSV-------ILFDEIEKAHP--DVFNILLQILDDG 152

>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 = 65.5 bits (158), Expect = 2e-12
 Identities = 16/106 (15%), Positives = 38/106 (35%), Gaps = 2/106 (1%)

Query: 322 ELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQ 381
            L     L++G   +GK+ + K     +N+P++  D     +  Y+    +  L +L  +
Sbjct: 26  GLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYI--SYKDFLLELQKE 83

Query: 382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM 427
               V+     +  +  +  I      +  + +         LL+ 
Sbjct: 84  INKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLES 129

>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 = 57.0 bits (137), Expect = 2e-09
 Identities = 16/107 (14%), Positives = 35/107 (32%), Gaps = 4/107 (3%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEF 384
           K   L  GP  SGKT LA  L        +  +         +G  ++  L  +    + 
Sbjct: 154 KRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFL-VVFEDVKG 212

Query: 385 NVEAAQQGM--VYIDEVDKITKKAE-SLNISRDVSGEGVQQALLKML 428
               ++       I+ +D +    + S+ ++ +      +  +    
Sbjct: 213 TGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPG 259

>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 = 54.6 bits (130), Expect = 5e-09
 Identities = 27/133 (20%), Positives = 51/133 (38%), Gaps = 39/133 (29%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
            IGQE+ K+ L V +     R                          +    ++LL GP 
Sbjct: 11  YIGQERLKQKLRVYLEAAKAR--------------------------KEPLEHLLLFGPP 44

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV 394
           G GKT LA  +A  + V   +     + + G +   + + L +               ++
Sbjct: 45  GLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEE-------------GDIL 91

Query: 395 YIDEVDKITKKAE 407
           +IDE+ +++++AE
Sbjct: 92  FIDEIHRLSRQAE 104

>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 = 53.9 bits (129), Expect = 2e-08
 Identities = 19/160 (11%), Positives = 38/160 (23%), Gaps = 26/160 (16%)

Query: 270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVL 329
            +       ++  +   V +                         V            V+
Sbjct: 83  VVQVENGFMKQGHRGWLVDLTGELVGCSPV---------------VAEFGGHRYASGMVI 127

Query: 330 LMGPTGSGKTLLAKTLARHVN--VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           + G   SGKT L   L   +     +          +GY  +     +  +         
Sbjct: 128 VTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPL-SGYNTDF-NVFVDDIARAML---- 181

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKM 427
             Q  ++ ID +  +   A   N +      G    L  +
Sbjct: 182 --QHRVIVIDSLKNVIGAAGG-NTTSGGISRGAFDLLSDI 218

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]} Length = 169

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]

 Score = 46.7 bits (109), Expect = 8e-07
 Identities = 13/31 (41%), Positives = 22/31 (70%)

Query: 324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFV 354
           EK N+ L+GP G+GK+ + + LA+ +N+ F 
Sbjct: 1   EKRNIFLVGPMGAGKSTIGRQLAQQLNMEFY 31

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]} Length = 192

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]

 Score = 47.0 bits (110), Expect = 1e-06
 Identities = 11/61 (18%), Positives = 18/61 (29%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNV 386
            V ++G   SGK++L   LA   N                 G++           A  + 
Sbjct: 9   TVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREFVFEKLGGDEQAMQYSDYPQMALGHQ 68

Query: 387 E 387
            
Sbjct: 69  R 69

>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 = 46.1 bits (108), Expect = 4e-06
 Identities = 24/124 (19%), Positives = 44/124 (35%), Gaps = 4/124 (3%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
            LL G  GSGKT L   +        ++ D  T  Q     +++  +  K + +      
Sbjct: 35  FLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKH----V 90

Query: 388 AAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNL 447
                 +    + +++ +  +L I        V      ML+    +T   V  V + N 
Sbjct: 91  TPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINS 150

Query: 448 YIKT 451
           Y+ T
Sbjct: 151 YLGT 154

>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 = 45.2 bits (106), Expect = 8e-06
 Identities = 37/160 (23%), Positives = 58/160 (36%), Gaps = 24/160 (15%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           + G E  K+ L   V    +   H +     G  P                  VL  GP 
Sbjct: 9   IGGLEDVKRELQELVQYPVE---HPDKFLKFGMTPS---------------KGVLFYGPP 50

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV 394
           G GKTLLAK +A      F+      L    + GE  E+ + ++  +A          ++
Sbjct: 51  GCGKTLLAKAIANECQANFISIKGPELLT-MWFGES-EANVREIFDKARQA----APCVL 104

Query: 395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETK 434
           + DE+D I K           + + V   +L  ++G  TK
Sbjct: 105 FFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK 144

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]} Length = 173

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]

 Score = 43.4 bits (101), Expect = 1e-05
 Identities = 19/94 (20%), Positives = 30/94 (31%), Gaps = 4/94 (4%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVE----SILYKLLAQA 382
           N+LL G  G GKT L K LA    + ++        +  Y G D E     +    +   
Sbjct: 6   NILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDE 65

Query: 383 EFNVEAAQQGMVYIDEVDKITKKAESLNISRDVS 416
             N       +V     D   ++   +       
Sbjct: 66  LDNQMREGGVIVDYHGCDFFPERWFHIVFVLRTD 99

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 43.7 bits (103), Expect = 2e-05
 Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 24/113 (21%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEF 384
           +  VL+ G +G GK ++A+ +  H            L  A    +  E+ L+     A  
Sbjct: 23  ECPVLITGESGVGKEVVARLI--HKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFT 80

Query: 385 N--------VEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE 429
                     E A  G +++DE+ +++ +               Q  LL+++E
Sbjct: 81  GAVSSKEGFFELADGGTLFLDEIGELSLE--------------AQAKLLRVIE 119

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 43.6 bits (102), Expect = 2e-05
 Identities = 36/155 (23%), Positives = 58/155 (37%), Gaps = 28/155 (18%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           V+GQE     L+  +     RI+HA L  G+    KT+ A        L     +   P 
Sbjct: 14  VVGQEHVLTALANGLSL--GRIHHAYLFSGTRGVGKTSIA--RLLAKGLNCETGITATPC 69

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV 394
           G           R V++  +  DA + T+     + ++++ Y   A+  F V        
Sbjct: 70  GVCDNCREIEQGRFVDL--IEIDAASRTKVEDTRDLLDNVQYAP-ARGRFKV-------Y 119

Query: 395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE 429
            IDEV  +++ +                ALLK LE
Sbjct: 120 LIDEVHMLSRHS--------------FNALLKTLE 140

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]} Length = 176

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]

 Score = 42.6 bits (99), Expect = 3e-05
 Identities = 14/34 (41%), Positives = 19/34 (55%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTL 361
           +LL G  GSGK+ +A+ LA    VP V   +  L
Sbjct: 7   LLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDL 40

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.2 bits (100), Expect = 3e-05
 Identities = 14/74 (18%), Positives = 22/74 (29%), Gaps = 14/74 (18%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           V G + +   L   + N      ++    G                        +L GP 
Sbjct: 16  VCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVF--------------RAAMLYGPP 61

Query: 335 GSGKTLLAKTLARH 348
           G GKT  A  +A+ 
Sbjct: 62  GIGKTTAAHLVAQE 75

>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 = 43.0 bits (100), Expect = 3e-05
 Identities = 25/91 (27%), Positives = 32/91 (35%), Gaps = 26/91 (28%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
            IGQE  KK LS+A+     R     L                         +VLL GP 
Sbjct: 11  FIGQENVKKKLSLALEAAKMR--GEVL------------------------DHVLLAGPP 44

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAG 365
           G GKT LA  +A  +     +     L + G
Sbjct: 45  GLGKTTLAHIIASELQTNIHVTSGPVLVKQG 75

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]} Length = 178

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]

 Score = 42.3 bits (98), Expect = 3e-05
 Identities = 9/61 (14%), Positives = 25/61 (40%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           ++L G + +GK+ + + L   +  P++     +L +A  +         +  A    ++ 
Sbjct: 6   IILNGGSSAGKSGIVRCLQSVLPEPWLAFGVDSLIEAMPLKMQSAEGGIEFDADGGVSIG 65

Query: 388 A 388
            
Sbjct: 66  P 66

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]} Length = 170

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]

 Score = 41.1 bits (95), Expect = 8e-05
 Identities = 9/30 (30%), Positives = 15/30 (50%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFV 354
              + ++G  G G T + + LAR +   FV
Sbjct: 2   TEPIFMVGARGCGMTTVGRELARALGYEFV 31

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]} Length = 161

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]

 Score = 40.7 bits (94), Expect = 8e-05
 Identities = 12/31 (38%), Positives = 23/31 (74%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
           N++ +G  GSGK+ LA+ LA+ +++ F+ +D
Sbjct: 2   NIVFIGFMGSGKSTLARALAKDLDLVFLDSD 32

>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 = 42.2 bits (98), Expect = 8e-05
 Identities = 14/72 (19%), Positives = 22/72 (30%), Gaps = 31/72 (43%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           ++GQE  K  L +            +   G                       VL+ G  
Sbjct: 9   IVGQEDMKLALLLTA---------VDPGIG----------------------GVLVFGDR 37

Query: 335 GSGKTLLAKTLA 346
           G+GK+   + LA
Sbjct: 38  GTGKSTAVRALA 49

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]} Length = 165

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]

 Score = 40.7 bits (94), Expect = 8e-05
 Identities = 9/28 (32%), Positives = 17/28 (60%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFV 354
             +L+G  GSGK+ + + LA+ + V  +
Sbjct: 3   KAVLVGLPGSGKSTIGRRLAKALGVGLL 30

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]} Length = 174

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]

 Score = 40.8 bits (94), Expect = 9e-05
 Identities = 9/31 (29%), Positives = 18/31 (58%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
           N+L+ G  G+GKT +A+ +A  ++    +  
Sbjct: 7   NILITGTPGTGKTSMAEMIAAELDGFQHLEV 37

>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 = 41.5 bits (96), Expect = 1e-04
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVE 387
           VLL GP  SGKT LA  +A   N PF+   +      G+        + K+      +  
Sbjct: 43  VLLEGPPHSGKTALAAKIAEESNFPFIKICSPD-KMIGFSETAKCQAMKKIF----DDAY 97

Query: 388 AAQQGMVYIDEVDKITKK 405
            +Q   V +D+++++   
Sbjct: 98  KSQLSCVVVDDIERLLDY 115

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]} Length = 171

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]

 Score = 39.2 bits (90), Expect = 3e-04
 Identities = 10/29 (34%), Positives = 18/29 (62%)

Query: 328 VLLMGPTGSGKTLLAKTLARHVNVPFVIA 356
            +LMG +GSGK+ +A  +A  ++  F+  
Sbjct: 9   YVLMGVSGSGKSAVASEVAHQLHAAFLDG 37

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 408

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 40.2 bits (93), Expect = 4e-04
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESIL 375
           + +   +  V L+G TG+GKT+    +   +  P ++  A     A  +  +   + 
Sbjct: 22  EALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVL-APNKILAAQLAAEFRELF 77

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]} Length = 181

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]

 Score = 38.7 bits (89), Expect = 5e-04
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
            VLL+GP G+GK   A  LA  + +P +   
Sbjct: 2   RVLLLGPPGAGKGTQAVKLAEKLGIPQISTG 32

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 413

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 39.7 bits (92), Expect = 6e-04
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 1/80 (1%)

Query: 319 DNVELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKL 378
           D +     +  L+G TG+GKT     +   VN P ++  A   T AG +  +++      
Sbjct: 25  DGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVI-AHNKTLAGQLYSELKEFFPHN 83

Query: 379 LAQAEFNVEAAQQGMVYIDE 398
             +   +     Q   Y+ +
Sbjct: 84  AVEYFVSYYDYAQPEAYVPQ 103

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 387

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

 Score = 39.7 bits (92), Expect = 6e-04
 Identities = 28/128 (21%), Positives = 50/128 (39%), Gaps = 21/128 (16%)

Query: 324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT--------TLTQAGYVGEDVE 372
            K+N +L+G  G GKT + + LA+ +   +VP  +             L  A Y GE  E
Sbjct: 42  TKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEE 101

Query: 373 SILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTE 432
               +L A  +  V++  + +++IDE+         +   +          L   L   E
Sbjct: 102 ----RLKAVIQEVVQSQGEVILFIDELH------TVVGAGKAEGAVDAGNMLKPALARGE 151

Query: 433 TKTFAAVS 440
            +   A +
Sbjct: 152 LRLIGATT 159

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 180

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]

 Score = 38.4 bits (88), Expect = 6e-04
 Identities = 8/31 (25%), Positives = 14/31 (45%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
            ++L+GP G+GK   A  L    +   +   
Sbjct: 4   RMVLIGPPGAGKGTQAPNLQERFHAAHLATG 34

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]} Length = 176

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]

 Score = 38.1 bits (87), Expect = 8e-04
 Identities = 10/31 (32%), Positives = 15/31 (48%)

Query: 325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVI 355
           K   ++ GP G GK+   K LA  ++    I
Sbjct: 2   KKLYIITGPAGVGKSTTCKRLAAQLDNSAYI 32

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]} Length = 189

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]

 Score = 37.9 bits (87), Expect = 0.001
 Identities = 5/28 (17%), Positives = 11/28 (39%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFV 354
            V++ G   SGK    + +     +  +
Sbjct: 5   KVMISGAPASGKGTQCELIKTKYQLAHI 32

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]} Length = 189

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]

 Score = 37.1 bits (85), Expect = 0.002
 Identities = 7/28 (25%), Positives = 14/28 (50%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFV 354
              +MG  GSGK  ++  + +H  +  +
Sbjct: 8   RAAIMGAPGSGKGTVSSRITKHFELKHL 35

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]} Length = 179

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]

 Score = 37.2 bits (85), Expect = 0.002
 Identities = 6/28 (21%), Positives = 14/28 (50%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFV 354
            ++L+G   +GK   A+ +     +P +
Sbjct: 2   RIILLGAPVAGKGTQAQFIMEKYGIPQI 29

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]} Length = 182

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]

 Score = 37.2 bits (85), Expect = 0.002
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
           N++LMG  G+GK   A+ +     +P +   
Sbjct: 2   NLVLMGLPGAGKGTQAEKIVAAYGIPHISTG 32

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]} Length = 190

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]

 Score = 36.8 bits (84), Expect = 0.002
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFV 354
             +L+GP G+GK   A  LA++  V  +
Sbjct: 5   RAVLLGPPGAGKGTQAPKLAKNFCVCHL 32

>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 = 37.3 bits (85), Expect = 0.002
 Identities = 31/154 (20%), Positives = 54/154 (35%), Gaps = 31/154 (20%)

Query: 275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPT 334
           V G  K    +   V    +   H  L K  G +P                  +LL GP 
Sbjct: 6   VGGCRKQLAQIKEMVELPLR---HPALFKAIGVKPP---------------RGILLYGPP 47

Query: 335 GSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV 394
           G+GKTL+A+ +A      F + +   +        +         A+           ++
Sbjct: 48  GTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPA------II 101

Query: 395 YIDEVDKITKKAESLNISRDVSGEGVQQALLKML 428
           +IDE+D I  K       R+ +   V++ ++  L
Sbjct: 102 FIDELDAIAPK-------REKTHGEVERRIVSQL 128

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]} Length = 182

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]

 Score = 36.4 bits (83), Expect = 0.003
 Identities = 9/28 (32%), Positives = 14/28 (50%)

Query: 327 NVLLMGPTGSGKTLLAKTLARHVNVPFV 354
           N++LMG  G+GK   A  +      P +
Sbjct: 2   NIVLMGLPGAGKGTQADRIVEKYGTPHI 29

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]} Length = 194

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]

 Score = 36.5 bits (83), Expect = 0.003
 Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 3/38 (7%)

Query: 323 LEKSN---VLLMGPTGSGKTLLAKTLARHVNVPFVIAD 357
           +EKS    V ++G  GSGK      + R      + A 
Sbjct: 1   MEKSKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAG 38

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]} Length = 194

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]

 Score = 36.1 bits (82), Expect = 0.004
 Identities = 8/34 (23%), Positives = 18/34 (52%), Gaps = 1/34 (2%)

Query: 322 ELEKSNVL-LMGPTGSGKTLLAKTLARHVNVPFV 354
           +L+KS ++ ++G  GSGK    + + +      +
Sbjct: 4   KLKKSKIIFVVGGPGSGKGTQCEKIVQKYGYTHL 37

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	461
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.92
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.89
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.85
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.8
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.8
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.79
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.72
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.72
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.69
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.69
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.62
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.61
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.58
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.58
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.32
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.31
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.28
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.27
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.27
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.25
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.06
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.04
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.99
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.96
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.96
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.84
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	98.74
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.73
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.7
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.61
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.51
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.35
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.22
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.21
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.04
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.03
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.97
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.92
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.88
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.86
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.85
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.8
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.66
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.62
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.61
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.56
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.55
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.55
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.54
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.53
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.46
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.46
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.4
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.37
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.37
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.34
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.3
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.26
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.26
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.25
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.24
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.22
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.21
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.2
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.18
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.06
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.03
d1okkd2	207	GTPase domain of the signal recognition particle r	96.69
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.66
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.64
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	96.58
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.58
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.58
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.57
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.34
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.29
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.27
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	96.27
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.24
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.23
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.19
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.11
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.06
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.0
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	95.9
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	95.85
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.76
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.71
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	95.69
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.56
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	95.37
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.33
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.31
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	95.27
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.12
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	95.11
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.91
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.78
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	94.74
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.6
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	94.41
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.36
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.34
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.28
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	94.27
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	94.19
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.13
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	94.08
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.02
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	93.98
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.96
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	93.89
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	93.78
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	93.74
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.64
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	93.11
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	92.95
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	92.93
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	92.88
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	92.86
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	92.86
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.76
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	92.66
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	92.65
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	92.64
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	92.64
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	92.64
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	92.63
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.61
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.6
d2fh5b1	207	Signal recognition particle receptor beta-subunit	92.43
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.39
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.35
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	92.34
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	92.19
d2awna2	232	Maltose transport protein MalK, N-terminal domain	92.12
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	92.01
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	91.84
d1g2912	240	Maltose transport protein MalK, N-terminal domain	91.79
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	91.75
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.72
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	91.61
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	91.52
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	91.44
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	91.33
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	91.3
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	91.22
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	91.21
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	91.21
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	91.13
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	91.09
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.07
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	90.95
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	90.95
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	90.91
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	90.9
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	90.85
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	90.77
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	90.77
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	90.7
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	90.67
d1nrjb_	209	Signal recognition particle receptor beta-subunit	90.63
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.59
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	90.55
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.29
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	90.27
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	90.24
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	90.21
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	90.12
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	90.07
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	90.03
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.97
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.79
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	89.69
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	89.59
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	89.57
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	89.5
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	89.45
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	89.42
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	89.42
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	89.42
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	89.41
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	89.38
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	89.21
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	89.2
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	89.03
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	88.97
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	88.87
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	88.86
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	88.71
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	88.7
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	88.65
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	88.62
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	88.6
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	88.59
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	88.44
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	88.35
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	88.32
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	88.28
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.2
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	88.06
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	88.05
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	87.88
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	87.83
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	87.81
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	87.74
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	87.57
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	87.52
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	87.52
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	87.49
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.46
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	87.45
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	87.41
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	87.39
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	87.35
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	86.8
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	86.7
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	86.67
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	86.57
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	86.23
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.2
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	85.94
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	85.91
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	85.61
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	85.43
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	85.22
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	84.91
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	84.72
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	84.68
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	84.18
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	83.92
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	83.77
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	83.27
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	82.89
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	81.88
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	81.69
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	81.07
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	80.52
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	80.15

>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=99.92  E-value=3.8e-25  Score=224.36  Aligned_cols=196  Identities=52%  Similarity=0.800  Sum_probs=133.2

Q ss_pred             CCCCCCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCc
Q 012525          258 GEDLPTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSG  337 (461)
Q Consensus       258 ~~~l~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTG  337 (461)
                      ...+|||+++...|+++||||++||+++..++++||+|+......+.. ..................+.++||.||+|||
T Consensus         2 ~~~~~tP~ei~~~L~~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~-~~~~~~~~~~~~~~~~~p~~niLfiGPTGvG   80 (364)
T d1um8a_           2 LSYIPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQ-DNQDSNVELEHLEEVELSKSNILLIGPTGSG   80 (364)
T ss_dssp             CSCCCCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHH-CSHHHHHHHHHHHHTTCCCCCEEEECCTTSS
T ss_pred             CCCCCCHHHHHHHhCCeecChHHHHHHHHHHHHHHHHHHHHHHHhhcc-ccccccccccccccccCCCcceeeeCCCCcc
Confidence            457899999999999999999999999999999999987643221100 0000111111122234567999999999999


Q ss_pred             hHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccch
Q 012525          338 KTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSG  417 (461)
Q Consensus       338 KTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~  417 (461)
                      ||.|||+||+.++.+|+.++++.+.+.+|+|.+.+..+..++..+...+..++.+|++||||+++.+.........+++.
T Consensus        81 KTElAk~LA~~~~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~  160 (364)
T d1um8a_          81 KTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSG  160 (364)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------C
T ss_pred             HHHHHHHHHhhcccceeehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhccccccccccccccc
Confidence            99999999999999999999999999999999999999999999888888889999999999998876444444556777


Q ss_pred             HHHHHHHHHHHhCceeeeecc-eeeecC-CeEEEecCCC
Q 012525          418 EGVQQALLKMLEGTETKTFAA-VSKVSR-DNLYIKTSGL  454 (461)
Q Consensus       418 ~~v~~aLL~~LEg~~v~i~~~-~r~~~r-d~IiI~TsNi  454 (461)
                      ..+++.||++||++..++... .+.... +.++|.|+|+
T Consensus       161 ~~V~~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i  199 (364)
T d1um8a_         161 EGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDI  199 (364)
T ss_dssp             HHHHHHHHHHHHCCEEC---------------CEECTTC
T ss_pred             hHHHHhhhhhhcCceeccCCCCCCcCCcceeEEEeehhh
Confidence            889999999999887765544 444444 7899999997

>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=99.89  E-value=1.3e-23  Score=207.76  Aligned_cols=155  Identities=43%  Similarity=0.706  Sum_probs=123.7

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .+|+++.+.|++.|+||++||++|..+|++|++++....                 .......+.++||+||||||||+|
T Consensus         3 ~~p~~i~~~L~~~ViGQd~A~~~l~~av~~~~~r~~~~~-----------------~~~~~~~~~~iLl~GPpG~GKT~l   65 (309)
T d1ofha_           3 MTPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQE-----------------PLRHEVTPKNILMIGPTGVGKTEI   65 (309)
T ss_dssp             CCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCH-----------------HHHHHCCCCCEEEECCTTSSHHHH
T ss_pred             CCHHHHHHHhcCcccChHHHHHHHHHHHHHHHHHhccCC-----------------CCccCCCCceEEEECCCCCCHHHH
Confidence            489999999999999999999999999988877642110                 001122458899999999999999


Q ss_pred             HHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhc-cCceEEEEcCccccchhhhccccccccchHHH
Q 012525          342 AKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEA-AQQGMVYIDEVDKITKKAESLNISRDVSGEGV  420 (461)
Q Consensus       342 AraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~-a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v  420 (461)
                      |++||+.++.+|+.++++++.+.++++...++.+..+|..+...... .+++||||||||++++.+..  ...+++.+++
T Consensus        66 AkalA~~~~~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~--~~~~~~~~gv  143 (309)
T d1ofha_          66 ARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEY--SGADVSREGV  143 (309)
T ss_dssp             HHHHHHHHTCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSC--CSSHHHHHHH
T ss_pred             HHHHhhccccchhcccccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccC--cccchhhhHH
Confidence            99999999999999999999877666666588899999887765432 35799999999999986432  2344556678


Q ss_pred             HHHHHHHHhCceeee
Q 012525          421 QQALLKMLEGTETKT  435 (461)
Q Consensus       421 ~~aLL~~LEg~~v~i  435 (461)
                      ++.||++||+..++.
T Consensus       144 ~~~LL~~~dg~~~~~  158 (309)
T d1ofha_         144 QRDLLPLVEGSTVST  158 (309)
T ss_dssp             HHHHHHHHHCCEEEE
T ss_pred             HHHhhHHhcCCEEec
Confidence            999999999887653

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.85  E-value=4.2e-22  Score=206.56  Aligned_cols=154  Identities=32%  Similarity=0.461  Sum_probs=98.4

Q ss_pred             CCHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHH
Q 012525          262 PTPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLL  341 (461)
Q Consensus       262 ~t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtL  341 (461)
                      .||+++...||++||||++||++|..+|++||+++.....                 ...+..++||||.||||||||+|
T Consensus         3 ltP~~i~~~Ld~yVvGQ~~AKk~lsvav~nhyrR~~~~~~-----------------~~~ei~ksNILliGPTGvGKTlL   65 (443)
T d1g41a_           3 MTPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEP-----------------LRHEVTPKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCHHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHSCTT-----------------TTTTCCCCCEEEECCTTSSHHHH
T ss_pred             CCHHHHHHHhcCcccCcHHHHHHHHHHHHHHHHHhhcccc-----------------cccccccccEEEECCCCCCHHHH
Confidence            3899999999999999999999999999999999864221                 12245689999999999999999


Q ss_pred             HHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEE-----------EEcCccccchhhhccc
Q 012525          342 AKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMV-----------YIDEVDKITKKAESLN  410 (461)
Q Consensus       342 AraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVL-----------fIDEID~L~~~R~~~~  410 (461)
                      ||+||+.+++||+.++|+.+++.||+|+++++.++.++..+...+..+..+++           ++|+++..........
T Consensus        66 Ar~LAk~l~VPFv~~daT~fTeaGYvG~DVesii~~L~~~a~~~v~~~e~~~V~~~~~~~~~e~~~d~l~~~~~~~~~~~  145 (443)
T d1g41a_          66 ARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAMKLVRQQEIAKNRARAEDVAEERILDALLPPAKNQWGEV  145 (443)
T ss_dssp             HHHHHHHTTCCEEEEEGGGGC----CCCCTHHHHHHHHHHHHHHHHHHHHHSCC--------------------------
T ss_pred             HHHHHHHhCCCEEEeecceeeecceeecchhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccc
Confidence            99999999999999999999999999999999999999888777666555555           6788777665543333


Q ss_pred             cccccchHHHHHHHHHHHhCce
Q 012525          411 ISRDVSGEGVQQALLKMLEGTE  432 (461)
Q Consensus       411 ~~~~~s~~~v~~aLL~~LEg~~  432 (461)
                      ...+.+.+..+..++.+++|..
T Consensus       146 ~~~~~~~~~~~~~~~~L~~G~~  167 (443)
T d1g41a_         146 ENHDSHSSTRQAFRKKLREGQL  167 (443)
T ss_dssp             ----------------------
T ss_pred             ccccchhhhhHHHHHHHhcCCc
Confidence            4455666667777777777654

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.80  E-value=9.5e-20  Score=174.93  Aligned_cols=149  Identities=28%  Similarity=0.383  Sum_probs=107.4

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHH-HHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNH-YKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~-~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .|++ |+|++++|+.|.+.+... ....++.   .+                 ...+.+|||+||||||||++|++||++
T Consensus         7 ~~~d-i~G~~~~k~~l~~~i~~l~~~~~~~~---~g-----------------~~~~~giLl~GppGtGKT~la~aia~~   65 (247)
T d1ixza_           7 TFKD-VAGAEEAKEELKEIVEFLKNPSRFHE---MG-----------------ARIPKGVLLVGPPGVGKTHLARAVAGE   65 (247)
T ss_dssp             CGGG-CCSCHHHHHHHHHHHHHHHCHHHHHH---TT-----------------CCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cHHH-HccHHHHHHHHHHHHHHHHCHHHHHH---cC-----------------CCCCceEEEecCCCCChhHHHHHHHHH
Confidence            4565 999999999998876421 0111111   11                 122478999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++.+|+.++++++.. +|+|+. +..++.+|..+...    .++||||||||.+..+|+............+++.||..|
T Consensus        66 ~~~~~~~i~~~~l~~-~~~g~~-~~~l~~~f~~a~~~----~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~  139 (247)
T d1ixza_          66 ARVPFITASGSDFVE-MFVGVG-AARVRDLFETAKRH----APCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEM  139 (247)
T ss_dssp             TTCCEEEEEHHHHHH-SCTTHH-HHHHHHHHHHHTTS----SSEEEEEETHHHHHC---------CHHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEhHHhhh-ccccHH-HHHHHHHHHHHHHc----CCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHh
Confidence            999999999999985 688877 77888999877543    789999999999998876555544445566899999999


Q ss_pred             hCceeeeecceeeecCCeEEEecCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      ++...         ...+++|+|||.
T Consensus       140 d~~~~---------~~~vivi~tTn~  156 (247)
T d1ixza_         140 DGFEK---------DTAIVVMAATNR  156 (247)
T ss_dssp             HTCCT---------TCCEEEEEEESC
T ss_pred             hCCCC---------CCCEEEEEeCCC
Confidence            85431         124688888873

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.80  E-value=1.4e-19  Score=174.82  Aligned_cols=150  Identities=24%  Similarity=0.342  Sum_probs=114.6

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++.+|+.|.+.|.  +.  .+.....               ......++++||+||||||||++|++||+++
T Consensus        10 t~~D-i~Gl~~~k~~l~e~v~--~~--~~~~~~~---------------~~g~~~~~~iLL~GppGtGKT~la~~iA~~~   69 (256)
T d1lv7a_          10 TFAD-VAGCDEAKEEVAELVE--YL--REPSRFQ---------------KLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA   69 (256)
T ss_dssp             CGGG-SCSCHHHHHHTHHHHH--HH--HCGGGC--------------------CCCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CHHH-HhchHHHHHHHHHHHH--HH--HCHHHHH---------------HcCCCCCCeEEeeCCCCCCccHHHHHHHHHc
Confidence            3555 9999999999988773  11  1111100               0011235789999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+++.++++++.. .|+|+. +..++.+|..+...    .++||||||||.+...|+....+.+.....+++.||..||
T Consensus        70 ~~~~~~i~~~~l~~-~~~g~~-~~~l~~~f~~A~~~----~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d  143 (256)
T d1lv7a_          70 KVPFFTISGSDFVE-MFVGVG-ASRVRDMFEQAKKA----APCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMD  143 (256)
T ss_dssp             TCCEEEECSCSSTT-SCCCCC-HHHHHHHHHHHHTT----CSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEhHHhhh-cchhHH-HHHHHHHHHHHHHc----CCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhh
Confidence            99999999999984 699998 78899999877643    8899999999999988776665555556678899999999


Q ss_pred             CceeeeecceeeecCCeEEEecCCC
Q 012525          430 GTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       430 g~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +....         ...++|+|||.
T Consensus       144 ~~~~~---------~~v~vIatTn~  159 (256)
T d1lv7a_         144 GFEGN---------EGIIVIAATNR  159 (256)
T ss_dssp             TCCSS---------SCEEEEEEESC
T ss_pred             CCCCC---------CCEEEEEeCCC
Confidence            55321         25788888884

>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=99.79  E-value=9.7e-20  Score=180.41  Aligned_cols=153  Identities=22%  Similarity=0.322  Sum_probs=116.4

Q ss_pred             CHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHH
Q 012525          263 TPKEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       263 t~~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLA  342 (461)
                      ..+++.+.|+++|+||++|++.|.+++..++..+...                      ..+..++||+||+|||||.||
T Consensus        12 ~l~~l~~~L~~~viGQ~~a~~~v~~~v~~~~~~l~~~----------------------~~p~~~~lf~Gp~GvGKT~la   69 (315)
T d1r6bx3          12 TLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHE----------------------HKPVGSFLFAGPTGVGKTEVT   69 (315)
T ss_dssp             HHHHHHHHHTTTSCSCHHHHHHHHHHHHHHHTTCSCT----------------------TSCSEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHHHhCCeecChHHHHHHHHHHHHHHHccCCCC----------------------CCCceEEEEECCCcchhHHHH
Confidence            4678999999999999999999999996554332111                      012346899999999999999


Q ss_pred             HHHHHhcCCceEEecchhhhhcC-----------cccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhcccc
Q 012525          343 KTLARHVNVPFVIADATTLTQAG-----------YVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNI  411 (461)
Q Consensus       343 raLA~~l~~pfv~i~~s~l~~~g-----------~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~  411 (461)
                      ++||+.++.+|+.++++++.+.+           |+|......+...+       .....+|++|||||++.+.      
T Consensus        70 k~la~~l~~~~i~~d~s~~~~~~~~~~l~g~~~gy~g~~~~~~l~~~~-------~~~~~~vvl~DeieKa~~~------  136 (315)
T d1r6bx3          70 VQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAV-------IKHPHAVLLLDEIEKAHPD------  136 (315)
T ss_dssp             HHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHH-------HHCSSEEEEEETGGGSCHH------
T ss_pred             HHHHhhccCCeeEeccccccchhhhhhhcccCCCccccccCChhhHHH-------HhCccchhhhcccccccch------
Confidence            99999999999999999887643           33333223333332       2346789999999999988      


Q ss_pred             ccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          412 SRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       412 ~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                              +++.||++||++.++.........++.|+|+|+|++...
T Consensus       137 --------V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~  175 (315)
T d1r6bx3         137 --------VFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRE  175 (315)
T ss_dssp             --------HHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-
T ss_pred             --------HhhhhHHhhccceecCCCCCccCccceEEEeccchhhHH
Confidence                    999999999988877554433334499999999988654

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=1.4e-17  Score=159.77  Aligned_cols=145  Identities=26%  Similarity=0.414  Sum_probs=108.8

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHH--HHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYK--RIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~k--ri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +++ |+|++.+|+.|++.+....+  ..+..   .+                 ...+++|||+||||||||++|+++|++
T Consensus         3 ~~d-v~G~~~~k~~l~~~i~~~l~~~~~~~~---~g-----------------~~~~~giLL~GppGtGKT~l~~ala~~   61 (258)
T d1e32a2           3 YDD-VGGCRKQLAQIKEMVELPLRHPALFKA---IG-----------------VKPPRGILLYGPPGTGKTLIARAVANE   61 (258)
T ss_dssp             GGG-CCSCSHHHHHHHHHHHHHHHCHHHHHH---CC-----------------CCCCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhh-hccHHHHHHHHHHHHHHHhcCHHHHHh---CC-----------------CCCCceeEEecCCCCCchHHHHHHHHH
Confidence            455 99999999999998753322  12211   11                 123578999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHH
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKML  428 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~L  428 (461)
                      ++.+|+.++++++.. .++|+. +..++.+|..+...    .++||||||+|.+..+|+...   ......+.+.++..+
T Consensus        62 ~~~~~~~i~~~~l~~-~~~g~~-~~~l~~~f~~A~~~----~p~il~iDeid~l~~~r~~~~---~~~~~~~~~~~~~~~  132 (258)
T d1e32a2          62 TGAFFFLINGPEIMS-KLAGES-ESNLRKAFEEAEKN----APAIIFIDELDAIAPKREKTH---GEVERRIVSQLLTLM  132 (258)
T ss_dssp             TTCEEEEECHHHHTT-SCTTHH-HHHHHHHHHHHHHT----CSEEEEESSGGGTCCHHHHCC---CTTHHHHHHHHHHHH
T ss_pred             hCCeEEEEEchhhcc-cccccH-HHHHHHHHHHHHhc----CCeEEEehhhhhhccCCCCCC---CchHHHHHHHhcccc
Confidence            999999999999984 478777 77888899877654    789999999999999876532   223345777888877


Q ss_pred             hCceeeeecceeeecCCeEEEecCCC
Q 012525          429 EGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       429 Eg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      +....         ..+.++|+|||.
T Consensus       133 ~~~~~---------~~~vlvi~tTn~  149 (258)
T d1e32a2         133 DGLKQ---------RAHVIVMAATNR  149 (258)
T ss_dssp             HTCCC---------SSCEEEEEEESC
T ss_pred             ccccc---------cCCccEEEeCCC
Confidence            74321         125688888874

>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=99.72  E-value=4.3e-18  Score=168.74  Aligned_cols=151  Identities=27%  Similarity=0.356  Sum_probs=106.6

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHH
Q 012525          265 KEICKGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKT  344 (461)
Q Consensus       265 ~el~~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAra  344 (461)
                      ..+.+.|++.|+||++|++.|..++..++..+.     ..                 ..+...+||+||+|||||.+|+.
T Consensus        15 ~~l~~~L~~~v~GQ~~ai~~v~~~i~~~~~~l~-----~~-----------------~kp~~~~lf~Gp~G~GKt~lak~   72 (315)
T d1qvra3          15 LRLEEELHKRVVGQDEAIRAVADAIRRARAGLK-----DP-----------------NRPIGSFLFLGPTGVGKTELAKT   72 (315)
T ss_dssp             HSHHHHHHHHSCSCHHHHHHHHHHHHHHGGGCS-----CS-----------------SSCSEEEEEBSCSSSSHHHHHHH
T ss_pred             HHHHHHhcCeEeCHHHHHHHHHHHHHHHhcCCC-----CC-----------------CCCceEEEEECCCcchHHHHHHH
Confidence            358899999999999999999888843221110     00                 01123678999999999999999


Q ss_pred             HHHhc---CCceEEecchhhhh-----------cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccc
Q 012525          345 LARHV---NVPFVIADATTLTQ-----------AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLN  410 (461)
Q Consensus       345 LA~~l---~~pfv~i~~s~l~~-----------~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~  410 (461)
                      ||+.+   +.+|+.++++++..           .+|+|......+.+.+.       ....+||||||||++.++     
T Consensus        73 la~~l~~~~~~~~~~~~~~~~~~~~~~~L~g~~~gyvG~~~~~~l~~~~~-------~~p~~Vvl~DEieK~~~~-----  140 (315)
T d1qvra3          73 LAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVR-------RRPYSVILFDEIEKAHPD-----  140 (315)
T ss_dssp             HHHHHHSSGGGEEEECTTTCCSSGGGGGC--------------CHHHHHH-------HCSSEEEEESSGGGSCHH-----
T ss_pred             HHHHhcCCCcceEEEeccccccchhhhhhcCCCCCCcCcccCChHHHHHH-------hCCCcEEEEehHhhcCHH-----
Confidence            99988   67899999987664           25666554444544433       346789999999999998     


Q ss_pred             cccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcCc
Q 012525          411 ISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSKT  458 (461)
Q Consensus       411 ~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e~  458 (461)
                               +++.|+++|+++.+..........++.++|+|+|++.+.
T Consensus       141 ---------v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~  179 (315)
T d1qvra3         141 ---------VFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPL  179 (315)
T ss_dssp             ---------HHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHH
T ss_pred             ---------HHHHHHHHhccCceeCCCCcEecCcceEEEEecccChHH
Confidence                     999999999988776443333333489999999998643

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=1.1e-17  Score=161.38  Aligned_cols=151  Identities=25%  Similarity=0.353  Sum_probs=109.6

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      |++ |+|++++|+.|.+.+.....+- +.....+                 ...+++|||+||||||||++|++||++++
T Consensus         6 f~d-i~G~~~~k~~l~~~i~~~l~~~-~~~~~~g-----------------~~~~~giLL~Gp~GtGKT~l~~ala~~~~   66 (265)
T d1r7ra3           6 WED-IGGLEDVKRELQELVQYPVEHP-DKFLKFG-----------------MTPSKGVLFYGPPGCGKTLLAKAIANECQ   66 (265)
T ss_dssp             CSS-CSSSSCCCCHHHHHTHHHHHCH-HHHHHCC-----------------CCCCCEEEEBCCTTSSHHHHHHHHHHHTT
T ss_pred             HHH-hcCHHHHHHHHHHHHHHHhhCH-HHHHhCC-----------------CCCCCeEEEECCCCCcchhHHHHHHHHhC
Confidence            444 8999999999999885433210 0111111                 12347899999999999999999999999


Q ss_pred             CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          351 VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       351 ~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      .+|+.++++++.. .+.|.. +..++.+|..+...    .++||||||+|.+..+|+....+.....+++.+.|+..|++
T Consensus        67 ~~~~~~~~~~l~~-~~~~~~-~~~l~~~f~~A~~~----~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~  140 (265)
T d1r7ra3          67 ANFISIKGPELLT-MWFGES-EANVREIFDKARQA----APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDG  140 (265)
T ss_dssp             CEEEEECHHHHHT-SCTTTH-HHHHHHHHHHHHHT----CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC-
T ss_pred             CcEEEEEHHHhhh-ccccch-HHHHHHHHHHHHhc----CCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhC
Confidence            9999999999884 477755 78888999877644    78999999999999987654444444455578888888874


Q ss_pred             ceeeeecceeeecCCeEEEecCCCC
Q 012525          431 TETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       431 ~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ....         .+.++|+|||.-
T Consensus       141 ~~~~---------~~v~vi~ttn~~  156 (265)
T d1r7ra3         141 MSTK---------KNVFIIGATNRP  156 (265)
T ss_dssp             --------------CCEEEECCBSC
T ss_pred             cCCC---------CCEEEEEeCCCc
Confidence            4211         146889998843

>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=99.69  E-value=1.4e-17  Score=159.22  Aligned_cols=113  Identities=27%  Similarity=0.338  Sum_probs=85.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      .++|||+||||||||++|++||++++.+|+.++++++. .++.+......++.+|..+...    +++||||||||++..
T Consensus        40 ~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~-~g~~~~~~~~~i~~if~~A~~~----~p~il~iDEid~l~~  114 (246)
T d1d2na_          40 LVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKM-IGFSETAKCQAMKKIFDDAYKS----QLSCVVVDDIERLLD  114 (246)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGC-TTCCHHHHHHHHHHHHHHHHTS----SEEEEEECCHHHHTT
T ss_pred             CeEEEEECcCCCCHHHHHHHHhhccccccccccccccc-ccccccchhhhhhhhhhhhhhc----ccceeehhhhhhHhh
Confidence            36799999999999999999999999999999998765 3566666567788899877644    789999999999887


Q ss_pred             hhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCC
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGL  454 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNi  454 (461)
                      .+..   +.. ....+.++|+.+|++....        ..+.++|+|||.
T Consensus       115 ~~~~---~~~-~~~~~~~~ll~~l~~~~~~--------~~~v~vi~tTn~  152 (246)
T d1d2na_         115 YVPI---GPR-FSNLVLQALLVLLKKAPPQ--------GRKLLIIGTTSR  152 (246)
T ss_dssp             CBTT---TTB-CCHHHHHHHHHHTTCCCST--------TCEEEEEEEESC
T ss_pred             hccc---ccc-hhHHHHHHHHHHhcCCCcc--------ccceeeeeccCC
Confidence            6432   111 2345788999999854211        124678888884

>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=99.62  E-value=1.3e-16  Score=158.66  Aligned_cols=112  Identities=17%  Similarity=0.164  Sum_probs=84.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC--CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN--VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~--~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      +.++||+||||||||+||++||.+++  .+|+.++.+++.. +|+|+. +..++.+|..+.      +++||||||||.+
T Consensus       123 ~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~-~~~G~~-e~~~~~~f~~a~------~~~ilf~DEid~~  194 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLS-GYNTDF-NVFVDDIARAML------QHRVIVIDSLKNV  194 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSST-TCBCCH-HHHHHHHHHHHH------HCSEEEEECCTTT
T ss_pred             CceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhh-cccchH-HHHHHHHHHHHh------hccEEEeehhhhh
Confidence            44566699999999999999999986  6899999999994 699988 889999998875      3679999999999


Q ss_pred             chhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCC
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLD  455 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid  455 (461)
                      ..+|......  ...+++++.||..||+....         .++++|+|||.+
T Consensus       195 ~~~r~~~~~~--~~~~r~v~~lL~e~dg~~~~---------~~v~viaatN~~  236 (321)
T d1w44a_         195 IGAAGGNTTS--GGISRGAFDLLSDIGAMAAS---------RGCVVIASLNPT  236 (321)
T ss_dssp             C-------------CCHHHHHHHHHHHHHHHH---------HTCEEEEECCCC
T ss_pred             ccccccCCCC--CcchhhhhhhhhhccccccC---------CCeEEEEeCCCc
Confidence            9987543222  22345899999999965421         258999999964

>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=99.61  E-value=2.6e-15  Score=139.73  Aligned_cols=132  Identities=26%  Similarity=0.387  Sum_probs=91.9

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+||+.+|+.|..++.....+        +                  ....|+||+||||||||++|++||+++
T Consensus         7 ~~~d-ivGqe~~~~~l~~~i~~~~~~--------~------------------~~~~~~L~~GPpGtGKT~lA~~la~~~   59 (238)
T d1in4a2           7 SLDE-FIGQENVKKKLSLALEAAKMR--------G------------------EVLDHVLLAGPPGLGKTTLAHIIASEL   59 (238)
T ss_dssp             SGGG-CCSCHHHHHHHHHHHHHHHHH--------T------------------CCCCCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             cHHH-cCChHHHHHHHHHHHHHHHhc--------C------------------CCCCeEEEECCCCCcHHHHHHHHHhcc
Confidence            5666 899999999999988543221        0                  123689999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.+++.++..+....        ..+...+..      ..++.++||||+|++...              .++.|+..|+
T Consensus        60 ~~~~~~~~~~~~~~~--------~~~~~~~~~------~~~~~~~~ide~~~~~~~--------------~~~~l~~~~~  111 (238)
T d1in4a2          60 QTNIHVTSGPVLVKQ--------GDMAAILTS------LERGDVLFIDEIHRLNKA--------------VEELLYSAIE  111 (238)
T ss_dssp             TCCEEEEETTTCCSH--------HHHHHHHHH------CCTTCEEEEETGGGCCHH--------------HHHHHHHHHH
T ss_pred             CCCcccccCcccccH--------HHHHHHHHh------hccCCchHHHHHHHhhhH--------------HHhhccccee
Confidence            999999887766531        222333322      235679999999999877              7889999998


Q ss_pred             Cceeeeecc------eee-ecCCeEEEecCCCCc
Q 012525          430 GTETKTFAA------VSK-VSRDNLYIKTSGLDS  456 (461)
Q Consensus       430 g~~v~i~~~------~r~-~~rd~IiI~TsNid~  456 (461)
                      ...+.....      ... ...++++|+++|...
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~  145 (238)
T d1in4a2         112 DFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSG  145 (238)
T ss_dssp             TSCCCC---------------CCCEEEEEESCGG
T ss_pred             eeeeeeeecCcccccccccCCCCeEEEEecCCCc
Confidence            655433221      111 122678887777653

>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=99.58  E-value=1.3e-15  Score=149.90  Aligned_cols=139  Identities=22%  Similarity=0.299  Sum_probs=93.3

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcCC---
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVNV---  351 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~---  351 (461)
                      |+||+.+|+.|..++.                               .....||||+||||||||+|||+++..+..   
T Consensus         9 I~Gq~~~kral~laa~-------------------------------~~~~h~vLl~G~pG~GKT~lar~~~~iLp~~~~   57 (333)
T d1g8pa_           9 IVGQEDMKLALLLTAV-------------------------------DPGIGGVLVFGDRGTGKSTAVRALAALLPEIEA   57 (333)
T ss_dssp             SCSCHHHHHHHHHHHH-------------------------------CGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEE
T ss_pred             ccCcHHHHHHHHHHHh-------------------------------ccCCCeEEEECCCCccHHHHHHHHHHhCCCchh
Confidence            9999999998776552                               012368999999999999999999987621   


Q ss_pred             ------------------------------ceEEecchhhhhcCccc-ccHHHHHHH-HHHhhchhhhccCceEEEEcCc
Q 012525          352 ------------------------------PFVIADATTLTQAGYVG-EDVESILYK-LLAQAEFNVEAAQQGMVYIDEV  399 (461)
Q Consensus       352 ------------------------------pfv~i~~s~l~~~g~vG-e~~e~~L~~-lf~~a~~~v~~a~~gVLfIDEI  399 (461)
                                                    +++...... .....+| .+....+.. ......+.+..++++|+|||||
T Consensus        58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi  136 (333)
T d1g8pa_          58 VEGCPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGV-SEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDEC  136 (333)
T ss_dssp             ETTCTTCCSSGGGSCTTCCCSCCCEEEECCCEEEECTTC-CHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTG
T ss_pred             hccCccccCccccccchhhccccCcccccCceeeccCCC-CcccccCcchhhhccccCcceeeccccccccccEeecccH
Confidence                                          111111000 0000111 121111111 1112234566678999999999


Q ss_pred             cccchhhhccccccccchHHHHHHHHHHHhCceeeeecc--eeeecCCeEEEecCCCCcCcC
Q 012525          400 DKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAA--VSKVSRDNLYIKTSGLDSKTL  459 (461)
Q Consensus       400 D~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~--~r~~~rd~IiI~TsNid~e~l  459 (461)
                      +++.++              ++++|++.||++++.+...  ....+.++++|+|+|.....+
T Consensus       137 ~~~~~~--------------~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l  184 (333)
T d1g8pa_         137 NLLEDH--------------IVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDL  184 (333)
T ss_dssp             GGSCHH--------------HHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCC
T ss_pred             HHHHHH--------------HHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCcccccc
Confidence            999998              9999999999888887533  566677999999999887643

>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=99.58  E-value=9.4e-15  Score=136.17  Aligned_cols=112  Identities=26%  Similarity=0.442  Sum_probs=82.0

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+||+++|+.|..++..+..        +.                  ....|+||+||||||||++|+++|+++
T Consensus         7 ~~dd-ivGq~~~~~~L~~~i~~~~~--------~~------------------~~~~~~Ll~GPpG~GKTtla~~la~~~   59 (239)
T d1ixsb2           7 TLDE-YIGQERLKQKLRVYLEAAKA--------RK------------------EPLEHLLLFGPPGLGKTTLAHVIAHEL   59 (239)
T ss_dssp             SGGG-SCSCHHHHHHHHHHHHHHTT--------SS------------------SCCCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CHHH-hCCHHHHHHHHHHHHHHHHh--------cC------------------CCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            5676 79999999999988842210        00                  124789999999999999999999999


Q ss_pred             CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHh
Q 012525          350 NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       350 ~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      +.++..++.+.....        ..........     .....|+||||+|++...              .+..|+..|+
T Consensus        60 ~~~~~~~~~~~~~~~--------~~~~~~~~~~-----~~~~~i~~iDe~~~~~~~--------------~~~~l~~~~e  112 (239)
T d1ixsb2          60 GVNLRVTSGPAIEKP--------GDLAAILANS-----LEEGDILFIDEIHRLSRQ--------------AEEHLYPAME  112 (239)
T ss_dssp             TCCEEEEETTTCCSH--------HHHHHHHHTT-----CCTTCEEEEETGGGCCHH--------------HHHHHHHHHH
T ss_pred             CCCeEeccCCccccc--------hhhHHHHHhh-----ccCCCeeeeecccccchh--------------HHHhhhhhhh
Confidence            999999988776531        1112222111     124579999999999887              7889999998


Q ss_pred             Cceeee
Q 012525          430 GTETKT  435 (461)
Q Consensus       430 g~~v~i  435 (461)
                      ......
T Consensus       113 ~~~~~~  118 (239)
T d1ixsb2         113 DFVMDI  118 (239)
T ss_dssp             HSEEEE
T ss_pred             hhhhhh
Confidence            654433

>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=99.32  E-value=3.3e-12  Score=119.81  Aligned_cols=108  Identities=29%  Similarity=0.374  Sum_probs=75.0

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ ++||+++++.|...+.+            +                  ..++.+||+||||||||++|+++++.+
T Consensus        10 ~~~d-lig~~~~~~~L~~~i~~------------~------------------~~~~~~Ll~Gp~G~GKtt~a~~~~~~l   58 (239)
T d1njfa_          10 TFAD-VVGQEHVLTALANGLSL------------G------------------RIHHAYLFSGTRGVGKTSIARLLAKGL   58 (239)
T ss_dssp             SGGG-SCSCHHHHHHHHHHHHT------------T------------------CCCSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CHHH-ccChHHHHHHHHHHHHc------------C------------------CCCeeEEEECCCCCcHHHHHHHHHHHh
Confidence            5666 89999999998887731            0                  113458999999999999999999987


Q ss_pred             CCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          350 NVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       350 ~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ...                        ++.++..+..       . ...++.++..........+..|+||||+|.|...
T Consensus        59 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-------~-i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~  130 (239)
T d1njfa_          59 NCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRT-------K-VEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH  130 (239)
T ss_dssp             HCTTCSCSSCCSCSHHHHHHHHTCCTTEEEEETTCSS-------S-HHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHH
T ss_pred             cCccccccCccccchHHHHHHcCCCCeEEEecchhcC-------C-HHHHHHHHHHHHhccccCCCEEEEEECcccCCHH
Confidence            432                        2222222111       1 2345566655443333345569999999999887


Q ss_pred             hhccccccccchHHHHHHHHHHHhC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                                    .+++|++.||.
T Consensus       131 --------------~q~~Llk~lE~  141 (239)
T d1njfa_         131 --------------SFNALLKTLEE  141 (239)
T ss_dssp             --------------HHHHHHHHHHS
T ss_pred             --------------HHHHHHHHHhc
Confidence                          89999999994

>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=99.31  E-value=9.9e-13  Score=121.59  Aligned_cols=110  Identities=28%  Similarity=0.363  Sum_probs=77.2

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+++ |+|++++++.|..++..                               ....|+||+||||||||++|++||+++
T Consensus        22 ~~~d-iig~~~~~~~l~~~i~~-------------------------------~~~~~lll~Gp~G~GKTtla~~iak~l   69 (231)
T d1iqpa2          22 RLDD-IVGQEHIVKRLKHYVKT-------------------------------GSMPHLLFAGPPGVGKTTAALALAREL   69 (231)
T ss_dssp             STTT-CCSCHHHHHHHHHHHHH-------------------------------TCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CHHH-ccCcHHHHHHHHHHHHc-------------------------------CCCCeEEEECCCCCcHHHHHHHHHHHH
Confidence            4555 89999999999888731                               012579999999999999999999987


Q ss_pred             C-----CceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHH
Q 012525          350 N-----VPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQAL  424 (461)
Q Consensus       350 ~-----~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aL  424 (461)
                      .     .+++++++++.....    ............  .........||+|||+|.+...              .++.|
T Consensus        70 ~~~~~~~~~~e~n~s~~~~~~----~~~~~~~~~~~~--~~~~~~~~~iilide~d~~~~~--------------~~~~l  129 (231)
T d1iqpa2          70 FGENWRHNFLELNASDERGIN----VIREKVKEFART--KPIGGASFKIIFLDEADALTQD--------------AQQAL  129 (231)
T ss_dssp             HGGGHHHHEEEEETTCHHHHH----TTHHHHHHHHHS--CCGGGCSCEEEEEETGGGSCHH--------------HHHHH
T ss_pred             HhcccCCCeeEEecCcccchh----HHHHHHHHHHhh--hhccCCCceEEeehhhhhcchh--------------HHHHH
Confidence            4     367788877655321    111111211111  1122346789999999999888              78999


Q ss_pred             HHHHhCc
Q 012525          425 LKMLEGT  431 (461)
Q Consensus       425 L~~LEg~  431 (461)
                      +..|+..
T Consensus       130 l~~l~~~  136 (231)
T d1iqpa2         130 RRTMEMF  136 (231)
T ss_dssp             HHHHHHT
T ss_pred             hhhcccC
Confidence            9999843

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.28  E-value=2.4e-12  Score=122.58  Aligned_cols=115  Identities=19%  Similarity=0.358  Sum_probs=83.7

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHh-----------hchhh
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQ-----------AEFNV  386 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~-----------a~~~v  386 (461)
                      ++....+|||+|++|||||++|++|+...   ..+++.+++..+...        .....+|..           ..+.+
T Consensus        19 ~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~--------~~~~~lfg~~~~~~~~~~~~~~g~l   90 (247)
T d1ny5a2          19 ISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRD--------IFEAELFGYEKGAFTGAVSSKEGFF   90 (247)
T ss_dssp             HTTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHH--------HHHHHHHCBCTTSSTTCCSCBCCHH
T ss_pred             HhCCCCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhc--------ccHHHhcCcccCCcCCcccccCCHH
Confidence            34456789999999999999999999866   347889998876642        222233321           12235


Q ss_pred             hccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCceeeeecceeeecCCeEEEecCCCCcC
Q 012525          387 EAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       387 ~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~~~rd~IiI~TsNid~e  457 (461)
                      ..+++|+|||||||.|...              .|..|+++|+..++...........++.+|++++.+.+
T Consensus        91 ~~a~gGtL~l~~i~~L~~~--------------~Q~~L~~~l~~~~~~~~~~~~~~~~~~RlI~~s~~~l~  147 (247)
T d1ny5a2          91 ELADGGTLFLDEIGELSLE--------------AQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIK  147 (247)
T ss_dssp             HHTTTSEEEEESGGGCCHH--------------HHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHH
T ss_pred             HccCCCEEEEeChHhCCHH--------------HHHHHHHHHHhCCEEECCCCCceecCeEEEEecCCCHH
Confidence            5678899999999999988              89999999997766554444444447788888887653

>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=99.27  E-value=3.1e-12  Score=117.70  Aligned_cols=110  Identities=25%  Similarity=0.297  Sum_probs=73.0

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.|++ |+||+++++.|...+.+                               ....|+||+||||||||++|++||++
T Consensus        11 ~~~~d-ivg~~~~~~~L~~~i~~-------------------------------~~~~~lLl~Gp~G~GKttl~~~la~~   58 (227)
T d1sxjc2          11 ETLDE-VYGQNEVITTVRKFVDE-------------------------------GKLPHLLFYGPPGTGKTSTIVALARE   58 (227)
T ss_dssp             SSGGG-CCSCHHHHHHHHHHHHT-------------------------------TCCCCEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCHHH-ccCcHHHHHHHHHHHHc-------------------------------CCCCeEEEECCCCCChhHHHHHHHHH
Confidence            35666 89999999999887731                               01247999999999999999999998


Q ss_pred             cCC-----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHH
Q 012525          349 VNV-----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQA  423 (461)
Q Consensus       349 l~~-----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~a  423 (461)
                      +..     .++.++.++...     ..........+ .....+......||||||+|.+...              .++.
T Consensus        59 l~~~~~~~~~~e~~~~~~~~-----~~~~~~~~~~~-~~~~~~~~~~~kiiiiDe~d~~~~~--------------~~~~  118 (227)
T d1sxjc2          59 IYGKNYSNMVLELNASDDRG-----IDVVRNQIKDF-ASTRQIFSKGFKLIILDEADAMTNA--------------AQNA  118 (227)
T ss_dssp             HHTTSHHHHEEEECTTSCCS-----HHHHHTHHHHH-HHBCCSSSCSCEEEEETTGGGSCHH--------------HHHH
T ss_pred             hhcCCCcceeEEecccccCC-----eeeeecchhhc-cccccccCCCeEEEEEeccccchhh--------------HHHH
Confidence            753     244555444321     11111111111 1111222334569999999999888              8999


Q ss_pred             HHHHHhC
Q 012525          424 LLKMLEG  430 (461)
Q Consensus       424 LL~~LEg  430 (461)
                      |+..|+.
T Consensus       119 Ll~~le~  125 (227)
T d1sxjc2         119 LRRVIER  125 (227)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhhh
Confidence            9999984

>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=99.27  E-value=2.2e-12  Score=119.09  Aligned_cols=111  Identities=23%  Similarity=0.283  Sum_probs=76.2

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.+++ |+||+++++.|...+.+                               ....|+||+||||||||++|+++|++
T Consensus        12 ~~~~d-~ig~~~~~~~L~~~~~~-------------------------------~~~~~~ll~Gp~G~GKTt~a~~la~~   59 (224)
T d1sxjb2          12 QVLSD-IVGNKETIDRLQQIAKD-------------------------------GNMPHMIISGMPGIGKTTSVHCLAHE   59 (224)
T ss_dssp             SSGGG-CCSCTHHHHHHHHHHHS-------------------------------CCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCHHH-hcCCHHHHHHHHHHHHc-------------------------------CCCCeEEEECCCCCCchhhHHHHHHH
Confidence            35666 79999999998887730                               01257999999999999999999998


Q ss_pred             cCC-----ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHHHHHH
Q 012525          349 VNV-----PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQA  423 (461)
Q Consensus       349 l~~-----pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~a  423 (461)
                      ++.     .++++++++....     ..-......+.............|+||||+|.+...              .+++
T Consensus        60 l~~~~~~~~~~~~n~~~~~~~-----~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~--------------~~~~  120 (224)
T d1sxjb2          60 LLGRSYADGVLELNASDDRGI-----DVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAG--------------AQQA  120 (224)
T ss_dssp             HHGGGHHHHEEEECTTSCCSH-----HHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHH--------------HHHT
T ss_pred             HhccccccccccccccccCCc-----eehhhHHHHHHHhhccCCCcceEEEEEecccccchh--------------HHHH
Confidence            864     3666666654421     101111112222222223345669999999999988              8899


Q ss_pred             HHHHHhC
Q 012525          424 LLKMLEG  430 (461)
Q Consensus       424 LL~~LEg  430 (461)
                      |+..|+.
T Consensus       121 ll~~~e~  127 (224)
T d1sxjb2         121 LRRTMEL  127 (224)
T ss_dssp             THHHHHH
T ss_pred             Hhhhccc
Confidence            9999984

>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=99.25  E-value=9.4e-12  Score=115.64  Aligned_cols=114  Identities=18%  Similarity=0.201  Sum_probs=72.6

Q ss_pred             HHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          269 KGLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       269 ~~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      +.+++ |+|++++++.|...+..............              .........++||+||||||||++|++||++
T Consensus        11 ~~~~d-lig~~~~~~~L~~~l~~~~~~~~~~~~~~--------------~~~~~~~~~~lll~GPpG~GKTt~a~~la~~   75 (253)
T d1sxja2          11 TNLQQ-VCGNKGSVMKLKNWLANWENSKKNSFKHA--------------GKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE   75 (253)
T ss_dssp             SSGGG-CCSCHHHHHHHHHHHHTHHHHHHTTTCCC--------------CTTSTTSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCHHH-hcCCHHHHHHHHHHHHhhhhcchhhhhhh--------------cccCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            34666 89999999999998854322211111000              0111122468999999999999999999999


Q ss_pred             cCCceEEecchhhhhcCcccccHHHHHHHHHHh--------------hchhhhccCceEEEEcCccccchh
Q 012525          349 VNVPFVIADATTLTQAGYVGEDVESILYKLLAQ--------------AEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       349 l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~--------------a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ++..++.++.+++...        ..+...+..              ........+..++++||+|.+...
T Consensus        76 ~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~  138 (253)
T d1sxja2          76 LGYDILEQNASDVRSK--------TLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGG  138 (253)
T ss_dssp             TTCEEEEECTTSCCCH--------HHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTT
T ss_pred             HHhhhhccccccchhh--------HHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccc
Confidence            9999999988765531        111111110              001112245679999999998876

>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=99.06  E-value=2.3e-10  Score=105.74  Aligned_cols=124  Identities=24%  Similarity=0.337  Sum_probs=86.1

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|+. ++|++..++.|...+.                               ...+.|++|.||||+|||++++.||+.+
T Consensus        20 ~ld~-~igRd~Ei~~l~~iL~-------------------------------r~~k~n~lLvG~pGVGKTalv~~LA~ri   67 (195)
T d1jbka_          20 KLDP-VIGRDEEIRRTIQVLQ-------------------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRI   67 (195)
T ss_dssp             CSCC-CCSCHHHHHHHHHHHT-------------------------------SSSSCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCC-CcCcHHHHHHHHHHHh-------------------------------ccCCCCeEEEecCCcccHHHHHHHHHHH
Confidence            3454 8999999988887772                               1224789999999999999999999754


Q ss_pred             ----------CCceEEecchhhhhc-CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          350 ----------NVPFVIADATTLTQA-GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       350 ----------~~pfv~i~~s~l~~~-g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                                +..++.++...+... +|.|+ .+..+..++.+...   ...+.||||||++.+...-.+ ..+.+    
T Consensus        68 ~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~-~E~rl~~il~e~~~---~~~~iILfIDeih~l~~~g~~-~g~~d----  138 (195)
T d1jbka_          68 INGEVPEGLKGRRVLALDMGALVAGAKYRGE-FEERLKGVLNDLAK---QEGNVILFIDELHTMVGAGKA-DGAMD----  138 (195)
T ss_dssp             HHTCSCGGGTTCEEEEECHHHHHTTTCSHHH-HHHHHHHHHHHHHH---STTTEEEEEETGGGGTT-------CCC----
T ss_pred             HhCCCCHHHcCceEEEeeHHHHhccCCccHH-HHHHHHHHHHHHhc---CCCcEEEEcchHHHHhcCCCC-CCccc----
Confidence                      467999999987742 34443 47777777765422   124569999999999765221 11122    


Q ss_pred             HHHHHHHHHHhCceeee
Q 012525          419 GVQQALLKMLEGTETKT  435 (461)
Q Consensus       419 ~v~~aLL~~LEg~~v~i  435 (461)
                       +-+.|..+|+.+.+.+
T Consensus       139 -~~~~Lkp~L~rg~l~~  154 (195)
T d1jbka_         139 -AGNMLKPALARGELHC  154 (195)
T ss_dssp             -CHHHHHHHHHTTSCCE
T ss_pred             -HHHHHHHHHhCCCceE
Confidence             5688888999665543

>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=99.04  E-value=6.3e-11  Score=108.66  Aligned_cols=110  Identities=25%  Similarity=0.345  Sum_probs=69.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++++++.|...+..                               ....++||+||||||||++++++|+++
T Consensus        10 ~~~d-iig~~~~~~~l~~~i~~-------------------------------~~~~~lll~Gp~G~GKTtl~~~i~~~l   57 (237)
T d1sxjd2          10 NLDE-VTAQDHAVTVLKKTLKS-------------------------------ANLPHMLFYGPPGTGKTSTILALTKEL   57 (237)
T ss_dssp             STTT-CCSCCTTHHHHHHHTTC-------------------------------TTCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CHHH-ccCcHHHHHHHHHHHHc-------------------------------CCCCeEEEECCCCCChHHHHHHHHHHH
Confidence            4566 79999999888776620                               012569999999999999999999986


Q ss_pred             ------CCceEEecchhhhhcCcccccHHHHHHHHHHhhc--------hhhhccCceEEEEcCccccchhhhcccccccc
Q 012525          350 ------NVPFVIADATTLTQAGYVGEDVESILYKLLAQAE--------FNVEAAQQGMVYIDEVDKITKKAESLNISRDV  415 (461)
Q Consensus       350 ------~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~--------~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~  415 (461)
                            ....+.++.............    +........        .........||||||+|.+...          
T Consensus        58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~----------  123 (237)
T d1sxjd2          58 YGPDLMKSRILELNASDERGISIVREK----VKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTAD----------  123 (237)
T ss_dssp             HHHHHHTTSEEEECSSSCCCHHHHTTH----HHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHH----------
T ss_pred             cCCcccccchhheeccccccchHHHHH----HHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCHH----------
Confidence                  344555555443311111111    111111000        0111234459999999999887          


Q ss_pred             chHHHHHHHHHHHh
Q 012525          416 SGEGVQQALLKMLE  429 (461)
Q Consensus       416 s~~~v~~aLL~~LE  429 (461)
                          .++.|+..++
T Consensus       124 ----~~~~l~~~~~  133 (237)
T d1sxjd2         124 ----AQSALRRTME  133 (237)
T ss_dssp             ----HHHHHHHHHH
T ss_pred             ----HHHHHhhccc
Confidence                7888888887

>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=98.99  E-value=5.4e-10  Score=107.81  Aligned_cols=125  Identities=26%  Similarity=0.385  Sum_probs=87.8

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|+. ++|.++..+.|...+.                               ...+.|+||.||||+|||++++.||+.+
T Consensus        16 ~ld~-~igRd~Ei~~l~~iL~-------------------------------r~~k~n~lLVG~~GvGKTalv~~la~ri   63 (268)
T d1r6bx2          16 GIDP-LIGREKELERAIQVLC-------------------------------RRRKNNPLLVGESGVGKTAIAEGLAWRI   63 (268)
T ss_dssp             CSCC-CCSCHHHHHHHHHHHT-------------------------------SSSSCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCc-ccChHHHHHHHHHHHh-------------------------------cCccCCcEEECCCCCcHHHHHHHHHHHH
Confidence            4554 8999999998888772                               1224789999999999999999999754


Q ss_pred             ----------CCceEEecchhhhhc-CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchH
Q 012525          350 ----------NVPFVIADATTLTQA-GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGE  418 (461)
Q Consensus       350 ----------~~pfv~i~~s~l~~~-g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~  418 (461)
                                +..++.++...+... +|.|+ .+..+..++.....    ..+.||||||++.|...-++.     .++.
T Consensus        64 ~~~~vp~~l~~~~i~~l~~~~liag~~~~g~-~e~r~~~i~~~~~~----~~~iIlfiDeih~l~~~g~~~-----g~~~  133 (268)
T d1r6bx2          64 VQGDVPEVMADCTIYSLDIGSLLAGTKYRGD-FEKRFKALLKQLEQ----DTNSILFIDEIHTIIGAGAAS-----GGQV  133 (268)
T ss_dssp             HHTCSCGGGTTCEEEECCCC---CCCCCSSC-HHHHHHHHHHHHSS----SSCEEEEETTTTTTTTSCCSS-----SCHH
T ss_pred             HhCCcccccccceeEEeeechHhccCccchh-HHHHHHHHHHHhhc----cCCceEEecchHHHhcCCCCC-----Cccc
Confidence                      457889999877753 45554 48888888876543    367899999999998752211     1122


Q ss_pred             HHHHHHHHHHhCceeeee
Q 012525          419 GVQQALLKMLEGTETKTF  436 (461)
Q Consensus       419 ~v~~aLL~~LEg~~v~i~  436 (461)
                      .+.+.|..+|+.+.+.+.
T Consensus       134 d~a~~Lkp~L~rg~i~vI  151 (268)
T d1r6bx2         134 DAANLIKPLLSSGKIRVI  151 (268)
T ss_dssp             HHHHHHSSCSSSCCCEEE
T ss_pred             cHHHHhhHHHhCCCCeEE
Confidence            366777778886655433

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.96  E-value=1.7e-10  Score=106.78  Aligned_cols=49  Identities=22%  Similarity=0.361  Sum_probs=38.1

Q ss_pred             HHHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          270 GLDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       270 ~Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .|++ |+|++++++.|...+..           .                   ....++||+||||||||++|+++|+.+
T Consensus         9 ~~~d-iig~~~~~~~L~~~~~~-----------~-------------------~~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2           9 SLNA-LSHNEELTNFLKSLSDQ-----------P-------------------RDLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             SGGG-CCSCHHHHHHHHTTTTC-----------T-------------------TCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CHHH-ccCcHHHHHHHHHHHHc-----------C-------------------CCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            4566 89999998888765510           0                   112579999999999999999999986

>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=98.96  E-value=2.2e-09  Score=98.67  Aligned_cols=87  Identities=16%  Similarity=0.219  Sum_probs=58.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc------------------------eEEecchhhhhcCcccccHHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP------------------------FVIADATTLTQAGYVGEDVESILYKLLAQ  381 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p------------------------fv~i~~s~l~~~g~vGe~~e~~L~~lf~~  381 (461)
                      +.+||+||+|+|||++|+.+|+.+...                        ++.+....-.  ...  . ...++.+...
T Consensus        25 h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~--~~i--~-~~~ir~l~~~   99 (207)
T d1a5ta2          25 HALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGK--NTL--G-VDAVREVTEK   99 (207)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTC--SSB--C-HHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcc--ccc--c-cchhhHHhhh
Confidence            559999999999999999999977321                        1111111000  001  1 3445555554


Q ss_pred             hchhhhccCceEEEEcCccccchhhhccccccccchHHHHHHHHHHHhCc
Q 012525          382 AEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       382 a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      ........+..|++|||+|.|...              .+++||+.||+.
T Consensus       100 ~~~~~~~~~~kviIide~d~l~~~--------------a~n~Llk~lEep  135 (207)
T d1a5ta2         100 LNEHARLGGAKVVWVTDAALLTDA--------------AANALLKTLEEP  135 (207)
T ss_dssp             TTSCCTTSSCEEEEESCGGGBCHH--------------HHHHHHHHHTSC
T ss_pred             hhhccccCccceEEechhhhhhhh--------------hhHHHHHHHHhh
Confidence            444334456779999999999998              899999999953

>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=98.84  E-value=4.1e-09  Score=106.39  Aligned_cols=124  Identities=23%  Similarity=0.338  Sum_probs=71.4

Q ss_pred             HHhhcCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhc-
Q 012525          271 LDKFVIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV-  349 (461)
Q Consensus       271 Ld~~VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l-  349 (461)
                      ||. ++|.+..++.|...|.                               ...+.|+||.|+||+|||.|++.||+.+ 
T Consensus        21 ld~-~~gr~~ei~~~~~~L~-------------------------------r~~k~n~llvG~~GvGKtaiv~~la~~i~   68 (387)
T d1qvra2          21 LDP-VIGRDEEIRRVIQILL-------------------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIV   68 (387)
T ss_dssp             SCC-CCSCHHHHHHHHHHHH-------------------------------CSSCCCCEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCC-CcCcHHHHHHHHHHHh-------------------------------cCCCCCCeEECCCCCCHHHHHHHHHHHHH
Confidence            444 8999999998888873                               1224789999999999999999999754 


Q ss_pred             ---------CCceEEecchhhhh-cCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchhhhccccccccchHH
Q 012525          350 ---------NVPFVIADATTLTQ-AGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKKAESLNISRDVSGEG  419 (461)
Q Consensus       350 ---------~~pfv~i~~s~l~~-~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~R~~~~~~~~~s~~~  419 (461)
                               +..++.++...+.. .+|.|+- +..+..++......   ..+.||||||++.+...-.+      .++..
T Consensus        69 ~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~-e~r~~~i~~~~~~~---~~~~ilfide~h~l~~~g~~------~g~~d  138 (387)
T d1qvra2          69 KGDVPEGLKGKRIVSLQMGSLLAGAKYRGEF-EERLKAVIQEVVQS---QGEVILFIDELHTVVGAGKA------EGAVD  138 (387)
T ss_dssp             HTCSCTTSTTCEEEEECC-----------CH-HHHHHHHHHHHHTT---CSSEEEEECCC--------------------
T ss_pred             hCCCCHHHcCceEEEeeHhhhhcccCcchhH-HHHHHHHHHHhccC---CCceEEEeccHHHHhcCCCC------CCccc
Confidence                     34688999987775 3455554 77777777654321   23568999999999865211      11122


Q ss_pred             HHHHHHHHHhCceeeee
Q 012525          420 VQQALLKMLEGTETKTF  436 (461)
Q Consensus       420 v~~aLL~~LEg~~v~i~  436 (461)
                      +.+.|..+|..+.+.++
T Consensus       139 ~a~~Lkp~L~rg~~~~I  155 (387)
T d1qvra2         139 AGNMLKPALARGELRLI  155 (387)
T ss_dssp             -----HHHHHTTCCCEE
T ss_pred             HHHHHHHHHhCCCccee
Confidence            67888899987665543

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.74  E-value=1.1e-08  Score=93.68  Aligned_cols=85  Identities=18%  Similarity=0.208  Sum_probs=62.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC------ceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV------PFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDE  398 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~------pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDE  398 (461)
                      ..++||+||+|+|||++|+.+++.+..      +|+.+....-    -.+   -+.++.+...........+.-|++|||
T Consensus        15 ~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~----~I~---Id~IR~i~~~~~~~~~~~~~KviIId~   87 (198)
T d2gnoa2          15 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE----NIG---IDDIRTIKDFLNYSPELYTRKYVIVHD   87 (198)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS----CBC---HHHHHHHHHHHTSCCSSSSSEEEEETT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcC----CCC---HHHHHHHHHHHhhCcccCCCEEEEEeC
Confidence            478999999999999999999987732      4666665311    111   344555555544443445667999999


Q ss_pred             ccccchhhhccccccccchHHHHHHHHHHHhC
Q 012525          399 VDKITKKAESLNISRDVSGEGVQQALLKMLEG  430 (461)
Q Consensus       399 ID~L~~~R~~~~~~~~~s~~~v~~aLL~~LEg  430 (461)
                      +|.|...              .+++||+.||+
T Consensus        88 ad~l~~~--------------aqNaLLK~LEE  105 (198)
T d2gnoa2          88 CERMTQQ--------------AANAFLKALEE  105 (198)
T ss_dssp             GGGBCHH--------------HHHHTHHHHHS
T ss_pred             ccccchh--------------hhhHHHHHHhC
Confidence            9999998              89999999995

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=98.73  E-value=1e-08  Score=102.55  Aligned_cols=86  Identities=22%  Similarity=0.188  Sum_probs=56.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      ++.+||+||||||||++|++||+.++.+|+.+++++.....+++..                  ....+.+||+++....
T Consensus       154 ~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~~l~~~------------------~~~~~~l~d~~~~~~~  215 (362)
T d1svma_         154 KRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVA------------------IDQFLVVFEDVKGTGG  215 (362)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHHHHGGG------------------TTCSCEEETTCCCSTT
T ss_pred             cCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHHHHHhH------------------HHHHHHHHHHHHHhhh
Confidence            3679999999999999999999999999999998876642111111                  1334567788876654


Q ss_pred             hhhccccccccchHHHHHHHHHHHhCc
Q 012525          405 KAESLNISRDVSGEGVQQALLKMLEGT  431 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~aLL~~LEg~  431 (461)
                      .+....  .....+ -.+.|+..++|.
T Consensus       216 ~~~~~~--~~~~~D-eiD~l~~~~dg~  239 (362)
T d1svma_         216 ESRDLP--SGQGIN-NLDNLRDYLDGS  239 (362)
T ss_dssp             TTTTCC--CCSHHH-HHHTTHHHHHCS
T ss_pred             hccCCC--CeEEEe-hHhhcccccCCc
Confidence            432211  111111 244566677764

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.70  E-value=6.3e-08  Score=88.55  Aligned_cols=103  Identities=17%  Similarity=0.201  Sum_probs=62.8

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHhcC----
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHVN----  350 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l~----  350 (461)
                      ++|++..++.|..++......       .                  ...+.++||+||||||||++|++|++.+.    
T Consensus        18 l~~Re~ei~~l~~~l~~~l~~-------~------------------~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~   72 (276)
T d1fnna2          18 LPHREQQLQQLDILLGNWLRN-------P------------------GHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT   72 (276)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHS-------T------------------TSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC
T ss_pred             CCCHHHHHHHHHHHHHHHHhC-------C------------------CCCCCceEEECCCCCCHHHHHHHHHHHHhcccC
Confidence            689999998888887422110       0                  02247899999999999999999999874    


Q ss_pred             CceEEecchhhhhc---------------CcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          351 VPFVIADATTLTQA---------------GYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       351 ~pfv~i~~s~l~~~---------------g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      ..++.+++......               ...+......+..+.....   ......++++|++|.+...
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~d~~~~~  139 (276)
T d1fnna2          73 ARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLR---ERDLYMFLVLDDAFNLAPD  139 (276)
T ss_dssp             CEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHH---HTTCCEEEEEETGGGSCHH
T ss_pred             CcEEEecchhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHh---hcccccccchhHHHHhhhh
Confidence            34555555432210               1122222222222222221   1224567889999988776

>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=98.61  E-value=8.6e-08  Score=88.52  Aligned_cols=85  Identities=16%  Similarity=0.318  Sum_probs=51.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCcccc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKI  402 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L  402 (461)
                      ..++|+||+|||||+|++++++++   +..++.++..++... +............+..    +  ..-.+|+||+||.+
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~----~--~~~dll~iDDi~~i  109 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQA-MVEHLKKGTINEFRNM----Y--KSVDLLLLDDVQFL  109 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHH-HHHHHHHTCHHHHHHH----H--HTCSEEEEECGGGG
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHHHHH-HHHHHHccchhhHHHH----H--hhccchhhhhhhhh
Confidence            348999999999999999999877   446667777665531 0000000001111111    1  13458999999998


Q ss_pred             chhhhccccccccchHHHHHHHHHHHh
Q 012525          403 TKKAESLNISRDVSGEGVQQALLKMLE  429 (461)
Q Consensus       403 ~~~R~~~~~~~~~s~~~v~~aLL~~LE  429 (461)
                      ..+..            .+.+|..+++
T Consensus       110 ~~~~~------------~~~~lf~lin  124 (213)
T d1l8qa2         110 SGKER------------TQIEFFHIFN  124 (213)
T ss_dssp             TTCHH------------HHHHHHHHHH
T ss_pred             cCchH------------HHHHHHHHHH
Confidence            76522            5666666665

>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=98.51  E-value=5.8e-08  Score=89.60  Aligned_cols=39  Identities=31%  Similarity=0.427  Sum_probs=36.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQ  363 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~  363 (461)
                      +.+|||+||||||||+||++||++++.+|+.++++++..
T Consensus        32 P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~~~   70 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQ   70 (273)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHHHH
Confidence            567999999999999999999999999999999988764

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.35  E-value=3.6e-07  Score=83.79  Aligned_cols=23  Identities=39%  Similarity=0.385  Sum_probs=20.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +++|+||||||||++++++++.+
T Consensus        48 ~l~l~GppGtGKT~l~~~l~~~l   70 (287)
T d1w5sa2          48 IYGSIGRVGIGKTTLAKFTVKRV   70 (287)
T ss_dssp             EEECTTCCSSSHHHHHHHHHHHH
T ss_pred             EEEeECCCCCCHHHHHHHHHHHH
Confidence            46778999999999999999876

>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=98.22  E-value=1.6e-06  Score=74.85  Aligned_cols=25  Identities=28%  Similarity=0.581  Sum_probs=22.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      +|+|.||+|+|||||++.|+..+..
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCC
Confidence            4899999999999999999997754

>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=98.21  E-value=3.4e-07  Score=76.73  Aligned_cols=35  Identities=37%  Similarity=0.745  Sum_probs=30.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      +++|+|.|||||||||+|++||+.++.+|+..+..
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L~~~~id~~~~   36 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQE   36 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCEEEEHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCeEeechh
Confidence            36799999999999999999999999999865544

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=98.04  E-value=1.1e-06  Score=75.03  Aligned_cols=37  Identities=24%  Similarity=0.332  Sum_probs=32.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~  362 (461)
                      +.|+|.|+|||||||||++||+.++.+++......+.
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~~~~~~   44 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREFV   44 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTCEEECCTTHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEeeehHHHh
Confidence            6799999999999999999999999999877765443

>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=98.03  E-value=9.1e-06  Score=73.65  Aligned_cols=38  Identities=21%  Similarity=0.426  Sum_probs=32.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQ  363 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~  363 (461)
                      ++++|+||+|+|||+|++.+++.++..+..+++.....
T Consensus        30 ~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~~~   67 (283)
T d2fnaa2          30 PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEE   67 (283)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTT
T ss_pred             CEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccccc
Confidence            67999999999999999999999988888777765443

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=97.97  E-value=1.7e-06  Score=73.72  Aligned_cols=33  Identities=36%  Similarity=0.590  Sum_probs=29.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .+|+|+|||||||||+|+.||+.++.+++.++.
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l~~~~i~~~~   37 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKSGLKYINVGD   37 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHCCEEEEHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHCCcEEechH
Confidence            579999999999999999999999999886554

>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=97.92  E-value=2.6e-06  Score=72.95  Aligned_cols=38  Identities=37%  Similarity=0.429  Sum_probs=33.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLT  362 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~  362 (461)
                      +.-|+|.|||||||||+|++|++.++.+++.++...+.
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~d~~~   41 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLW   41 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTTHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCEEEecHHHHH
Confidence            45688999999999999999999999999998876544

>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=97.88  E-value=3.2e-06  Score=73.59  Aligned_cols=32  Identities=38%  Similarity=0.687  Sum_probs=29.6

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +|+|.|+||+||||++++||+.++.+|+.++.
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~~~~~d~d~   33 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLDLVFLDSDF   33 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEecCc
Confidence            68999999999999999999999999997654

>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=97.86  E-value=3.8e-06  Score=72.93  Aligned_cols=32  Identities=31%  Similarity=0.574  Sum_probs=29.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +|+|+|+||+||||+++.||+.++.+|+..+.
T Consensus         3 ~IvliG~~G~GKSTig~~La~~l~~~fiD~D~   34 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRRLAKALGVGLLDTDV   34 (165)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHTCCEEEHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCeEeecc
Confidence            47888999999999999999999999987664

>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=97.85  E-value=3.7e-06  Score=73.34  Aligned_cols=33  Identities=30%  Similarity=0.561  Sum_probs=29.7

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .+|+|+|+||+||||+|+.||+.++.+|+..+.
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~D~   35 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDTDI   35 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEehhh
Confidence            468899999999999999999999999987653

>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=97.80  E-value=7.7e-06  Score=69.56  Aligned_cols=33  Identities=18%  Similarity=0.365  Sum_probs=29.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +-|+|+|+||+||||+|++||+.++.+++.++.
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~~   36 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCeEEeec
Confidence            568999999999999999999999988877654

>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=97.66  E-value=1.3e-05  Score=68.48  Aligned_cols=33  Identities=33%  Similarity=0.533  Sum_probs=28.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      +-++|+|+|||||||+|++||+.++.+++..+.
T Consensus         7 ~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d~   39 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDF   39 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEEGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeechhh
Confidence            447889999999999999999999988776554

>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=97.62  E-value=1.8e-05  Score=67.45  Aligned_cols=27  Identities=33%  Similarity=0.578  Sum_probs=24.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      +.+|+|+||||+||||+|+.||+.++.
T Consensus         5 ~~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            467999999999999999999999975

>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=97.61  E-value=1.6e-05  Score=67.08  Aligned_cols=28  Identities=29%  Similarity=0.469  Sum_probs=25.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      -|+|.||||+||||+|+.||+.++..++
T Consensus         4 lI~i~G~~GsGKTTva~~L~~~~~~~~~   31 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLAAQLDNSAY   31 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSSEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            4899999999999999999999987644

>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=97.56  E-value=1.7e-05  Score=67.34  Aligned_cols=24  Identities=38%  Similarity=0.621  Sum_probs=22.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +||+|+||||||||||++.+++.+
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            689999999999999999999877

>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=97.55  E-value=9.3e-06  Score=68.99  Aligned_cols=27  Identities=30%  Similarity=0.412  Sum_probs=23.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      +..|+|+|+||+||||+|++||+.++.
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            356889999999999999999998853

>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=97.55  E-value=4.3e-05  Score=70.15  Aligned_cols=99  Identities=10%  Similarity=0.143  Sum_probs=59.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITK  404 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~  404 (461)
                      ...++|+|||.||||++|.+|++.++..++....+  . +.             |.-+    ......|+++||+.....
T Consensus        53 kn~i~~~GP~~TGKS~f~~sl~~~l~G~vis~~N~--~-s~-------------F~Lq----~l~~~kv~l~dD~t~~~~  112 (205)
T d1tuea_          53 KNCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNS--T-SH-------------FWLE----PLTDTKVAMLDDATTTCW  112 (205)
T ss_dssp             CSEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCS--S-SC-------------GGGG----GGTTCSSEEEEEECHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHhCCEEEeccCC--C-CC-------------cccc----cccCCeEEEEeccccchH
Confidence            36689999999999999999999986533221111  0 00             1000    011345889999876555


Q ss_pred             hhhccccccccchHHHHHH-HHHHHhCceeeeecce--eeecCCeEEEecCCCCcC
Q 012525          405 KAESLNISRDVSGEGVQQA-LLKMLEGTETKTFAAV--SKVSRDNLYIKTSGLDSK  457 (461)
Q Consensus       405 ~R~~~~~~~~~s~~~v~~a-LL~~LEg~~v~i~~~~--r~~~rd~IiI~TsNid~e  457 (461)
                      .              ..+. |..+++|..+.+....  .......-+|.|+|.++.
T Consensus       113 ~--------------~~d~~lK~ll~G~~vsvd~KhK~~vqi~~pPliITsN~~~~  154 (205)
T d1tuea_         113 T--------------YFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPA  154 (205)
T ss_dssp             H--------------HHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTT
T ss_pred             H--------------HHHHHHHhccCCCeeeeecccCCcccccCCCEEEEcCCCCC
Confidence            4              5566 5668898877766551  111122235678888764

>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=97.54  E-value=2.2e-05  Score=67.97  Aligned_cols=31  Identities=29%  Similarity=0.546  Sum_probs=27.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      +|+|.||||+||||+|+.||+.++.+++...
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~~~~~i~~~   32 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAYGIPHISTG   32 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceechh
Confidence            4899999999999999999999998877543

>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=97.53  E-value=1.6e-05  Score=70.07  Aligned_cols=32  Identities=19%  Similarity=0.311  Sum_probs=28.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      |..|+|.||||+||||+|+.||+.++.+++.+
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~~~~~is~   34 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKYQLAHISA   34 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHCCcEEeh
Confidence            46799999999999999999999999887644

>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=97.46  E-value=3.1e-05  Score=67.61  Aligned_cols=30  Identities=40%  Similarity=0.697  Sum_probs=27.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      +|+|.||||+||||+|+.||+.++..++.+
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            589999999999999999999999887755

>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=97.46  E-value=3.4e-05  Score=67.85  Aligned_cols=31  Identities=32%  Similarity=0.518  Sum_probs=27.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.||||+||||+|+.||+.++..++.+
T Consensus         4 ~riil~G~pGSGKsT~a~~La~~~g~~~i~~   34 (190)
T d1ak2a1           4 VRAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   34 (190)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            4588999999999999999999998877654

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.40  E-value=0.0002  Score=62.64  Aligned_cols=24  Identities=33%  Similarity=0.600  Sum_probs=21.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      -|+|+|.||+||||+|++||+.++
T Consensus         4 li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999998774

>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=4.1e-05  Score=67.38  Aligned_cols=31  Identities=26%  Similarity=0.382  Sum_probs=27.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|+||||+||||+|+.||+.++..++..
T Consensus         7 ~iI~i~G~pGSGKsT~a~~La~~~g~~~i~~   37 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            4578999999999999999999998876544

>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=97.37  E-value=5.1e-05  Score=66.30  Aligned_cols=30  Identities=30%  Similarity=0.558  Sum_probs=27.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+|.||||+||||+|+.||+.++.+++.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~g~~~is~   31 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKYGTPHIST   31 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceeeH
Confidence            489999999999999999999999987754

>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=97.34  E-value=1.5e-05  Score=69.24  Aligned_cols=28  Identities=29%  Similarity=0.393  Sum_probs=24.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      +..|+|+|+||+||||+|++||+.++..
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            3567899999999999999999988653

>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=97.30  E-value=6e-05  Score=66.52  Aligned_cols=31  Identities=23%  Similarity=0.406  Sum_probs=27.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.||||+||||+|+.||+.++..++..
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            4588999999999999999999998877654

>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=97.26  E-value=6.8e-05  Score=65.60  Aligned_cols=31  Identities=26%  Similarity=0.521  Sum_probs=27.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      .|+|.||||+||||+|+.||+.++.+++...
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~g~~~i~~~   34 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERFHAAHLATG   34 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceEecc
Confidence            4889999999999999999999998776553

>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=97.26  E-value=7.3e-05  Score=65.00  Aligned_cols=30  Identities=20%  Similarity=0.420  Sum_probs=26.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      .|+|.||||+||||+|+.||+.++..++..
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~~~~~i~~   31 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceech
Confidence            488999999999999999999998877654

>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=97.25  E-value=7.4e-05  Score=66.55  Aligned_cols=31  Identities=23%  Similarity=0.490  Sum_probs=27.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.||||+||||+|+.||+.++.+++.+
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~~g~~~is~   37 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKHFELKHLSS   37 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHBCCEEEEH
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHHCCeEEcH
Confidence            5689999999999999999999999877644

>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=97.24  E-value=8.5e-05  Score=65.18  Aligned_cols=30  Identities=17%  Similarity=0.294  Sum_probs=26.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      ..|+|.||||+||||+|+.||+.++..++.
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~g~~~i~   31 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKYGYTHLS   31 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCceEc
Confidence            358999999999999999999999876653

>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=97.22  E-value=0.00021  Score=62.80  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=25.9

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      .+.-|||+|+||+||||+|+.+++..+..++
T Consensus        13 ~p~liil~G~pGsGKST~a~~l~~~~~~~~i   43 (172)
T d1yj5a2          13 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHV   43 (172)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHTGGGTCEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhcCCEEE
Confidence            3566899999999999999999988775443

>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=97.21  E-value=8.7e-05  Score=65.54  Aligned_cols=31  Identities=16%  Similarity=0.336  Sum_probs=27.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      ..|+|.||||+||||+|+.||+.++.+++..
T Consensus         9 ~iI~l~G~pGSGKsT~a~~La~~~g~~~is~   39 (194)
T d3adka_           9 KIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   39 (194)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeeEec
Confidence            5588999999999999999999998876543

>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=97.20  E-value=9.8e-05  Score=65.25  Aligned_cols=29  Identities=28%  Similarity=0.485  Sum_probs=25.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      -|++.||||+||+|+|+.||+.++.+++.
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            57788999999999999999999987763

>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=97.18  E-value=0.00012  Score=65.29  Aligned_cols=29  Identities=28%  Similarity=0.560  Sum_probs=25.9

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      .|.+.||||+||||+|+.||+.++.+++.
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg~~~is   33 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFGFTYLD   33 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            36688999999999999999999998765

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.06  E-value=0.00084  Score=55.53  Aligned_cols=34  Identities=21%  Similarity=0.261  Sum_probs=25.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecch
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADAT  359 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s  359 (461)
                      ...+|.+|+|+|||+++-.++...+..++.+...
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcCh
Confidence            5679999999999999876666666655554444

>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=0.00022  Score=59.40  Aligned_cols=34  Identities=24%  Similarity=0.321  Sum_probs=25.0

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCceEEecchhh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTL  361 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l  361 (461)
                      -|+|+|+||+||||+|+.|++... .++.++..++
T Consensus         4 lIii~G~pGsGKTTla~~L~~~~~-~~~~~~~d~~   37 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIAKNP-GFYNINRDDY   37 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHST-TEEEECHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCC-CCEEechHHH
Confidence            378999999999999999876553 2444554444

>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=96.69  E-value=0.0046  Score=56.18  Aligned_cols=26  Identities=35%  Similarity=0.436  Sum_probs=21.4

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..++|.||+|+||||.+-.||..+
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~   30 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYY   30 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            35678999999999999877777655

>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=96.66  E-value=0.0014  Score=59.16  Aligned_cols=38  Identities=26%  Similarity=0.319  Sum_probs=32.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc----CCceEEecchhhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADATTLTQ  363 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~s~l~~  363 (461)
                      ..|+|+|.||+||||||++|++.+    +.+++.++...+..
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~iR~   66 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRF   66 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchHHHH
Confidence            568999999999999999999765    56788888877664

>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=96.64  E-value=0.00047  Score=58.32  Aligned_cols=25  Identities=20%  Similarity=0.308  Sum_probs=22.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +-|+|.|+||+||||+++.|++.++
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~   26 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLR   26 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3489999999999999999999874

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=96.58  E-value=0.0023  Score=59.93  Aligned_cols=46  Identities=20%  Similarity=0.229  Sum_probs=34.3

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhhhhccccccccccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          275 VIGQEKAKKVLSVAVYNHYKRIYHANLKKGSGAEPKTAAAVDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       275 VvGqd~aK~~L~~al~~~~kri~~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ++|++..++.|...+....                            ......|.|+|..|+||||||+.+++.
T Consensus        22 ~~gR~~~~~~i~~~L~~~~----------------------------~~~~~~v~I~GmgGiGKTtLA~~v~~~   67 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEMC----------------------------DLDSFFLFLHGRAGSGKSVIASQALSK   67 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHHT----------------------------TSSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eeCcHHHHHHHHHHHHhcc----------------------------CCCceEEEEECCCCCCHHHHHHHHHHh
Confidence            6789988888887773110                            001245789999999999999999875

>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=96.58  E-value=0.00054  Score=57.52  Aligned_cols=23  Identities=30%  Similarity=0.355  Sum_probs=21.2

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.|+|++|+|||||++.|++.+
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l   26 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPAL   26 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            57899999999999999999876

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.58  E-value=0.0012  Score=59.07  Aligned_cols=27  Identities=37%  Similarity=0.618  Sum_probs=23.1

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-++|+|+||+|||++|..+|..+
T Consensus        24 ~~gsl~li~G~pGsGKT~l~~qia~~~   50 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTLLVSRFVENA   50 (242)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            445778999999999999999998765

>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=96.57  E-value=0.0054  Score=55.93  Aligned_cols=77  Identities=23%  Similarity=0.380  Sum_probs=43.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc------------------CcccccHHHHHHHHHHhhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA------------------GYVGEDVESILYKLLAQAE  383 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~------------------g~vGe~~e~~L~~lf~~a~  383 (461)
                      +..|+|.||+|+||||.+-.||..+   +..+..+.+......                  ...+.+....++.....+.
T Consensus         9 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~a~   88 (211)
T d2qy9a2           9 PFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAAK   88 (211)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHHHHHH
Confidence            3557899999999999887778655   344444443322210                  0112233344444333222


Q ss_pred             hhhhccCceEEEEcCccccchh
Q 012525          384 FNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       384 ~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      .    ...-+||||=.-+...+
T Consensus        89 ~----~~~d~ilIDTaGr~~~d  106 (211)
T d2qy9a2          89 A----RNIDVLIADTAGRLQNK  106 (211)
T ss_dssp             H----TTCSEEEECCCCCGGGH
T ss_pred             H----cCCCEEEeccCCCcccc
Confidence            1    13458999988765554

>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=96.34  E-value=0.0037  Score=50.25  Aligned_cols=19  Identities=26%  Similarity=0.104  Sum_probs=16.2

Q ss_pred             CCcEEEEccCCCchHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAr  343 (461)
                      ..+++|..|+|+|||.+|-
T Consensus         7 ~~~~il~~~tGsGKT~~~~   25 (140)
T d1yksa1           7 GMTTVLDFHPGAGKTRRFL   25 (140)
T ss_dssp             TCEEEECCCTTSSTTTTHH
T ss_pred             CCcEEEEcCCCCChhHHHH
Confidence            4789999999999997663

>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=96.29  E-value=0.00091  Score=56.80  Aligned_cols=24  Identities=17%  Similarity=0.308  Sum_probs=21.8

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      |+|.|++|+||||+++.||+.++.
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            689999999999999999998853

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=96.27  E-value=0.0055  Score=59.87  Aligned_cols=21  Identities=29%  Similarity=0.455  Sum_probs=17.1

Q ss_pred             CCcEEEEccCCCchHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraL  345 (461)
                      .+-++|.||||||||+++..+
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~  183 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKL  183 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHH
T ss_pred             CCeEEEEcCCCCCceehHHHH
Confidence            456889999999999987544

>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=96.27  E-value=0.0059  Score=57.34  Aligned_cols=92  Identities=17%  Similarity=0.308  Sum_probs=53.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhhhcCcccccHHHHHHHHHHhhchhhhccCceEEEEcCccccchh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLTQAGYVGEDVESILYKLLAQAEFNVEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~~~g~vGe~~e~~L~~lf~~a~~~v~~a~~gVLfIDEID~L~~~  405 (461)
                      .-++|+||++||||+++.+|++.++. +..++.+.   .     .        |..+    ......++++||... ...
T Consensus       105 n~~~l~G~~~tGKS~f~~~i~~~lg~-~~~~~~~~---~-----~--------f~l~----~l~~k~~~~~~e~~~-~~~  162 (267)
T d1u0ja_         105 NTIWLFGPATTGKTNIAEAIAHTVPF-YGCVNWTN---E-----N--------FPFN----DCVDKMVIWWEEGKM-TAK  162 (267)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSSC-EEECCTTC---S-----S--------CTTG----GGSSCSEEEECSCCE-ETT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHhcc-hhhccccC---C-----C--------cccc----ccCCCEEEEEeCCCc-ccc
Confidence            45789999999999999999999954 32222111   0     0        1001    112455889999874 222


Q ss_pred             hhccccccccchHHHHHHHHHHHhCceeeeecceee--ecC-CeEEEecCC
Q 012525          406 AESLNISRDVSGEGVQQALLKMLEGTETKTFAAVSK--VSR-DNLYIKTSG  453 (461)
Q Consensus       406 R~~~~~~~~~s~~~v~~aLL~~LEg~~v~i~~~~r~--~~r-d~IiI~TsN  453 (461)
                                    ..+.|..++.|..+.+....+.  .-. ..++|.|.|
T Consensus       163 --------------~~~~~K~l~gGd~i~v~~K~k~~~~~~~~p~li~s~n  199 (267)
T d1u0ja_         163 --------------VVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNT  199 (267)
T ss_dssp             --------------THHHHHHHHTTCCEEC------CCEECCCCEEEEESS
T ss_pred             --------------HHHHHHHhcCCCceEeecccCCCcEeeCCeEEEEeCC
Confidence                          3456778888888776655211  112 455555555

>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=96.24  E-value=0.0094  Score=53.97  Aligned_cols=25  Identities=40%  Similarity=0.420  Sum_probs=20.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..++|.||+|+||||.+-.||..+
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~~~   34 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLALYY   34 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3457889999999999888787655

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.23  E-value=0.0016  Score=57.55  Aligned_cols=25  Identities=40%  Similarity=0.639  Sum_probs=22.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .|+|+||+|+|||||++.|++....
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~   26 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSS   26 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCC
Confidence            4899999999999999999987754

>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=96.19  E-value=0.0018  Score=56.85  Aligned_cols=25  Identities=32%  Similarity=0.595  Sum_probs=22.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +.|+|+||+|+|||+|++.|++...
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~   26 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC
Confidence            4589999999999999999998764

>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=96.11  E-value=0.01  Score=54.10  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=20.2

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..|+|.||+|+||||.+-.||..+
T Consensus        11 p~vi~lvGptGvGKTTTiAKLAa~~   35 (213)
T d1vmaa2          11 PFVIMVVGVNGTGKTTSCGKLAKMF   35 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4567899999999999877777654

>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=96.06  E-value=0.014  Score=53.91  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=25.6

Q ss_pred             cccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          318 DDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       318 ~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +...-..+..+.|.||+|+|||||+++|+..+
T Consensus        22 isl~i~~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          22 INLSIKQGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             EEEEEETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             eEEEEcCCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            33333446778999999999999999999866

>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=96.00  E-value=0.0061  Score=55.52  Aligned_cols=25  Identities=32%  Similarity=0.432  Sum_probs=16.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..|+|.||+|+||||.+-.||..+
T Consensus        12 p~vi~lvGptGvGKTTTiAKLA~~~   36 (211)
T d1j8yf2          12 PYVIMLVGVQGTGKATTAGKLAYFY   36 (211)
T ss_dssp             SEEEEEECSCCC----HHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568899999999999877777654

>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=95.90  E-value=0.012  Score=54.76  Aligned_cols=33  Identities=30%  Similarity=0.372  Sum_probs=25.8

Q ss_pred             ccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          317 NDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       317 ~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+...-..+..+.|.||+|+|||||+++|+..+
T Consensus        33 ~isl~i~~Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          33 NINLKIPAGKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             EEEEEECTTCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             ceEEEEcCCCEEEEECCCCChHHHHHHHHhccc
Confidence            333333446778999999999999999998765

>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=95.85  E-value=0.012  Score=52.34  Aligned_cols=33  Identities=30%  Similarity=0.389  Sum_probs=26.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADA  358 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~  358 (461)
                      .+.+|..|+|+|||.+|-.++..++.+.+.+-.
T Consensus        86 ~~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p  118 (206)
T d2fz4a1          86 KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVP  118 (206)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             CCcEEEeCCCCCceehHHhHHHHhcCceeEEEc
Confidence            346788899999999999999888877655544

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.76  E-value=0.0077  Score=52.48  Aligned_cols=24  Identities=29%  Similarity=0.465  Sum_probs=20.2

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHH
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA  346 (461)
                      ..+.-++|+|+||+|||++|..++
T Consensus        24 ~~G~~~~I~G~~G~GKT~la~~~~   47 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKTLFSIQFL   47 (242)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHH
Confidence            456778999999999999997665

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.71  E-value=0.011  Score=56.94  Aligned_cols=27  Identities=37%  Similarity=0.544  Sum_probs=24.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      ..+||+.|++|+||||+.++|...+..
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i~~  192 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFIPK  192 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCT
T ss_pred             CCCEEEEeeccccchHHHHHHhhhccc
Confidence            378999999999999999999988743

>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=95.69  E-value=0.0024  Score=54.54  Aligned_cols=24  Identities=33%  Similarity=0.403  Sum_probs=21.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      |-+.|++|+||||||+.|++.++.
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            559999999999999999987753

>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=95.56  E-value=0.0041  Score=53.86  Aligned_cols=24  Identities=29%  Similarity=0.587  Sum_probs=21.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .-|+|.||+|+|||||++.|.+..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            458899999999999999999876

>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=95.37  E-value=0.03  Score=52.09  Aligned_cols=32  Identities=22%  Similarity=0.288  Sum_probs=25.1

Q ss_pred             cccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          318 DDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       318 ~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +...-..+..+.|.|++|+|||||+++|+..+
T Consensus        37 isl~i~~Ge~vaivG~sGsGKSTLl~ll~gl~   68 (255)
T d2hyda1          37 INLSIEKGETVAFVGMSGGGKSTLINLIPRFY   68 (255)
T ss_dssp             EEEEECTTCEEEEECSTTSSHHHHHTTTTTSS
T ss_pred             eEEEEcCCCEEEEECCCCCcHHHHHHHHHhcC
Confidence            33333445778999999999999999998755

>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=95.33  E-value=0.013  Score=54.92  Aligned_cols=78  Identities=22%  Similarity=0.236  Sum_probs=45.3

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc------Cc------c--cccHHHHHHHHHHhhchhh
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA------GY------V--GEDVESILYKLLAQAEFNV  386 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~------g~------v--Ge~~e~~L~~lf~~a~~~v  386 (461)
                      ...-++|+||||+|||+||-.++..+   +...+.++...-...      +.      +  -...|..+..+    ....
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i----~~l~  128 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEIC----DALA  128 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHH----HHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHH----HHHH
Confidence            34668899999999999998887654   445565655421110      10      0  01223332221    1122


Q ss_pred             hccCceEEEEcCccccchh
Q 012525          387 EAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       387 ~~a~~gVLfIDEID~L~~~  405 (461)
                      ...+..+|+||-|..+.+.
T Consensus       129 ~~~~~~liViDSi~al~~~  147 (263)
T d1u94a1         129 RSGAVDVIVVDSVAALTPK  147 (263)
T ss_dssp             HHTCCSEEEEECGGGCCCH
T ss_pred             hcCCCCEEEEECccccccc
Confidence            2345679999999988753

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.31  E-value=0.005  Score=52.03  Aligned_cols=27  Identities=30%  Similarity=0.281  Sum_probs=22.5

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ....-++|+||||+|||++|..+|..+
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            345678999999999999999888654

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.27  E-value=0.022  Score=51.13  Aligned_cols=23  Identities=30%  Similarity=0.443  Sum_probs=18.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ++++++..|+|+|||+++-..+.
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~   80 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSL   80 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHH
T ss_pred             CCCEEEEecCCChHHHHHHHHHH
Confidence            46799999999999987765554

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.12  E-value=0.0056  Score=53.97  Aligned_cols=24  Identities=21%  Similarity=0.331  Sum_probs=21.9

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      |-|.|++|+||||+|+.|++.++.
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhch
Confidence            669999999999999999998865

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=95.11  E-value=0.033  Score=50.37  Aligned_cols=25  Identities=36%  Similarity=0.566  Sum_probs=21.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..-++|+|++|+|||+|+-.||..+
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            5678899999999999998888643

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.91  E-value=0.0053  Score=53.89  Aligned_cols=26  Identities=35%  Similarity=0.309  Sum_probs=21.7

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHh
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ....-++|+|+||||||++|..+|..
T Consensus        32 ~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          32 ETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             ESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            34567999999999999999888753

>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=94.78  E-value=0.021  Score=53.56  Aligned_cols=79  Identities=23%  Similarity=0.271  Sum_probs=47.1

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchhhhhc------Cc--------ccccHHHHHHHHHHhhchh
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATTLTQA------GY--------VGEDVESILYKLLAQAEFN  385 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~l~~~------g~--------vGe~~e~~L~~lf~~a~~~  385 (461)
                      ...+-+.|+||+|||||+||..++..+   +..++.++...-...      +.        .-...|..+.-    ....
T Consensus        55 p~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~----~~~l  130 (268)
T d1xp8a1          55 PRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEI----MELL  130 (268)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHH----HHHH
T ss_pred             cCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHH----HHHH
Confidence            345667899999999999998887654   455666665421111      00        11122333221    1222


Q ss_pred             hhccCceEEEEcCccccchh
Q 012525          386 VEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~  405 (461)
                      +......+|+||-+..+.+.
T Consensus       131 ~~~~~~~liIiDSi~al~~r  150 (268)
T d1xp8a1         131 VRSGAIDVVVVDSVAALTPR  150 (268)
T ss_dssp             HTTTCCSEEEEECTTTCCCS
T ss_pred             HhcCCCcEEEEecccccccH
Confidence            23345679999999988864

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.74  E-value=0.026  Score=48.72  Aligned_cols=22  Identities=50%  Similarity=0.742  Sum_probs=18.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .++|+..|+|+|||+++-.++.
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEeCCCCcHHHHHHHHHH
Confidence            5789999999999997766654

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.60  E-value=0.0094  Score=52.65  Aligned_cols=28  Identities=25%  Similarity=0.178  Sum_probs=23.0

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -....-++|+|+||+|||++|..+|...
T Consensus        34 ip~G~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          34 IESMAITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             BCSSEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            3445678999999999999999998643

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.41  E-value=0.011  Score=50.08  Aligned_cols=22  Identities=27%  Similarity=0.264  Sum_probs=20.0

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +-+.|++|+|||||++.|++++
T Consensus         4 i~I~G~~gSGKTTli~~l~~~L   25 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVAAA   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHH
Confidence            5599999999999999999876

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.36  E-value=0.01  Score=52.69  Aligned_cols=27  Identities=44%  Similarity=0.457  Sum_probs=22.4

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ....-++|+||||+|||++|-.+|...
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            445678999999999999999887644

>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=94.34  E-value=0.014  Score=50.85  Aligned_cols=24  Identities=25%  Similarity=0.524  Sum_probs=21.3

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.|+|.||+|+|||+|++.|.+..
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhC
Confidence            458999999999999999998764

>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=94.28  E-value=0.046  Score=47.62  Aligned_cols=19  Identities=58%  Similarity=0.772  Sum_probs=16.8

Q ss_pred             CCcEEEEccCCCchHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAK  343 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAr  343 (461)
                      ..++++..|+|+|||++|.
T Consensus        40 ~~~~il~apTGsGKT~~a~   58 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAE   58 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHHH
Confidence            4789999999999999874

>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=94.27  E-value=0.031  Score=52.46  Aligned_cols=79  Identities=23%  Similarity=0.271  Sum_probs=45.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchh-hhhc-----C-----c---ccccHHHHHHHHHHhhchh
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATT-LTQA-----G-----Y---VGEDVESILYKLLAQAEFN  385 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~-l~~~-----g-----~---vGe~~e~~L~~lf~~a~~~  385 (461)
                      ...+-+.|+||+|+|||++|..++...   +...+.++... +...     +     +   .-...|..+.    .+...
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~----~~~~l  133 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALE----IADML  133 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHH----HHHHH
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHH----HHHHH
Confidence            345667899999999999997776543   45556665543 1110     0     0   0112233222    11222


Q ss_pred             hhccCceEEEEcCccccchh
Q 012525          386 VEAAQQGMVYIDEVDKITKK  405 (461)
Q Consensus       386 v~~a~~gVLfIDEID~L~~~  405 (461)
                      +......+|+||-+..+.+.
T Consensus       134 ~~~~~~~liIiDSi~al~~~  153 (269)
T d1mo6a1         134 IRSGALDIVVIDSVAALVPR  153 (269)
T ss_dssp             HHTTCEEEEEEECSTTCCCH
T ss_pred             HhcCCCCEEEEecccccccH
Confidence            23345679999999998864

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=94.19  E-value=0.014  Score=50.79  Aligned_cols=26  Identities=31%  Similarity=0.436  Sum_probs=23.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .-|+|.|+-|+|||+++|.+++.++.
T Consensus        34 ~ii~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          34 IMVYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             eEEEEecCCCccHHHHHHHHHhhccc
Confidence            34889999999999999999999976

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.13  E-value=0.0092  Score=51.59  Aligned_cols=27  Identities=33%  Similarity=0.386  Sum_probs=23.8

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCCce
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNVPF  353 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~pf  353 (461)
                      -|.|.|+.|+||||+++.|++.++...
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~~~~   37 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKNDIC   37 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTTTEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcE
Confidence            478999999999999999999986543

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=94.08  E-value=0.082  Score=48.00  Aligned_cols=19  Identities=26%  Similarity=0.181  Sum_probs=16.0

Q ss_pred             cccCCcEEEEccCCCchHH
Q 012525          322 ELEKSNVLLMGPTGSGKTL  340 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTt  340 (461)
                      ...++++|+.+|+|+|||+
T Consensus         6 ~~~~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTT
T ss_pred             hhcCCcEEEEECCCCCHHH
Confidence            3456889999999999996

>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=94.02  E-value=0.013  Score=51.08  Aligned_cols=28  Identities=25%  Similarity=0.226  Sum_probs=23.2

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -....-++|.|+||+|||++|..+|..+
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3445678999999999999999998644

>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=93.98  E-value=0.016  Score=50.07  Aligned_cols=28  Identities=29%  Similarity=0.379  Sum_probs=22.7

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEe
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIA  356 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i  356 (461)
                      |-|+|++|+||||+|+.|. ..+.+++..
T Consensus         6 IgitG~~gSGKstva~~l~-~~g~~~~~~   33 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALLR-SWGYPVLDL   33 (191)
T ss_dssp             EEEEECTTSCHHHHHHHHH-HTTCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHH-HCCCeEEEc
Confidence            5589999999999999995 577766543

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=93.96  E-value=0.022  Score=56.10  Aligned_cols=26  Identities=35%  Similarity=0.492  Sum_probs=22.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      .-|||.||+|+||||+..++-+.++.
T Consensus       159 GliLvtGpTGSGKSTTl~~~l~~~~~  184 (401)
T d1p9ra_         159 GIILVTGPTGSGKSTTLYAGLQELNS  184 (401)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHCC
T ss_pred             ceEEEEcCCCCCccHHHHHHhhhhcC
Confidence            44889999999999999999887753

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=93.89  E-value=0.018  Score=50.91  Aligned_cols=33  Identities=27%  Similarity=0.427  Sum_probs=26.1

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +......|||.|++|+|||++|-.|.+. +..++
T Consensus        10 v~~~g~gvl~~G~sG~GKStlal~l~~~-g~~lv   42 (176)
T d1kkma_          10 VDIYGLGVLITGDSGVGKSETALELVQR-GHRLI   42 (176)
T ss_dssp             EEETTEEEEEECCTTSCHHHHHHHHHHT-TCEEE
T ss_pred             EEECCEEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            3445688999999999999999888875 55444

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=93.78  E-value=0.18  Score=45.97  Aligned_cols=36  Identities=31%  Similarity=0.265  Sum_probs=24.9

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh-c--CCceEEecchh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH-V--NVPFVIADATT  360 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~-l--~~pfv~i~~s~  360 (461)
                      +.+.||+|.+|+|||.++-..+.. +  +...+.+-.+.
T Consensus        76 ~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~  114 (233)
T d2eyqa3          76 AMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTT  114 (233)
T ss_dssp             CCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSH
T ss_pred             ccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHH
Confidence            367899999999999998655543 3  44455444443

>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=93.74  E-value=0.051  Score=49.64  Aligned_cols=24  Identities=21%  Similarity=0.382  Sum_probs=21.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .+.++|+||...|||++.|+++-.
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~   64 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALI   64 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHHH
Confidence            466899999999999999999853

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=93.64  E-value=0.019  Score=46.99  Aligned_cols=20  Identities=30%  Similarity=0.491  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|...|..
T Consensus         3 ivlvG~~~vGKSsLi~~l~~   22 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKL   22 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            89999999999999999874

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=93.11  E-value=0.024  Score=50.18  Aligned_cols=33  Identities=39%  Similarity=0.463  Sum_probs=25.5

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +......|||.|++|+|||++|-.|.+. +..++
T Consensus        11 v~~~g~gvli~G~sG~GKS~lal~l~~~-G~~lv   43 (177)
T d1knxa2          11 LEVFGVGVLLTGRSGIGKSECALDLINK-NHLFV   43 (177)
T ss_dssp             EEETTEEEEEEESSSSSHHHHHHHHHTT-TCEEE
T ss_pred             EEECCEEEEEEcCCCCCHHHHHHHHHHc-CCcee
Confidence            3445678999999999999999888764 44444

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=92.95  E-value=0.026  Score=49.66  Aligned_cols=22  Identities=41%  Similarity=0.699  Sum_probs=20.1

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      |++.|++|+|||||.+.|.+.+
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Confidence            7899999999999999998755

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=92.93  E-value=0.023  Score=51.79  Aligned_cols=21  Identities=33%  Similarity=0.534  Sum_probs=16.3

Q ss_pred             CcEEEEccCCCchHHHH-HHHH
Q 012525          326 SNVLLMGPTGSGKTLLA-KTLA  346 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLA-raLA  346 (461)
                      .++|+.|+||||||+++ ..++
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~   36 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIA   36 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHHHHHH
Confidence            56899999999999754 4333

>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=92.88  E-value=0.025  Score=49.66  Aligned_cols=24  Identities=21%  Similarity=0.419  Sum_probs=21.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .-|+|.|+.|+||||+++.|++.+
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            348899999999999999999876

>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=92.86  E-value=0.028  Score=48.72  Aligned_cols=29  Identities=21%  Similarity=0.341  Sum_probs=23.8

Q ss_pred             EEEEccCCCchHHHHHHHHHhc---CCceEEe
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV---NVPFVIA  356 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l---~~pfv~i  356 (461)
                      |.|.|..|+||||+++.|++.+   +.+++.+
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~   34 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATL   34 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            7889999999999999999876   4455443

>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=92.86  E-value=0.028  Score=50.24  Aligned_cols=25  Identities=24%  Similarity=0.470  Sum_probs=21.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      .-++|.||+|+|||+|.+.|.+...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            3478999999999999999988753

>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=92.76  E-value=0.015  Score=51.38  Aligned_cols=25  Identities=16%  Similarity=0.306  Sum_probs=22.5

Q ss_pred             cEEEEccCCCchHHHHHHHHHhcCC
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      -|.|.|+-|+||||+++.|++.+..
T Consensus         4 ~I~ieG~dGsGKST~~~~L~~~l~~   28 (241)
T d1p5zb_           4 KISIEGNIAAGKSTFVNILKQLCED   28 (241)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhc
Confidence            4889999999999999999998853

>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=92.66  E-value=0.16  Score=47.19  Aligned_cols=36  Identities=31%  Similarity=0.315  Sum_probs=25.3

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecchh
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADATT  360 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s~  360 (461)
                      +.+-||.|..|+|||.+|-..+..+   +...+.+-.++
T Consensus       104 ~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~  142 (264)
T d1gm5a3         104 PMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTS  142 (264)
T ss_dssp             CCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCH
T ss_pred             cceeeeeccccccccHHHHHHHHHHHhcccceeEEeehH
Confidence            4567999999999999986665433   45555555543

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=92.65  E-value=0.032  Score=48.95  Aligned_cols=33  Identities=30%  Similarity=0.426  Sum_probs=25.4

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      +......|||.|++|+|||++|-.+.+. +..++
T Consensus        11 v~~~g~gvli~G~sg~GKS~la~~l~~~-g~~li   43 (169)
T d1ko7a2          11 VDVYGVGVLITGDSGIGKSETALELIKR-GHRLV   43 (169)
T ss_dssp             EEETTEEEEEEESTTSSHHHHHHHHHHT-TCEEE
T ss_pred             EEECCEEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            3445688999999999999999887765 44343

>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=92.64  E-value=0.076  Score=48.18  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=21.0

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHH
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ....-++|+||...|||++.|+++-
T Consensus        33 ~~~~~~iiTGpN~~GKSt~lk~i~l   57 (224)
T d1ewqa2          33 MAHELVLITGPNMAGKSTFLRQTAL   57 (224)
T ss_dssp             ESSCEEEEESCSSSSHHHHHHHHHH
T ss_pred             eCCcEEEEECCCccccchhhhhhHH
Confidence            3345589999999999999999875

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.028  Score=50.11  Aligned_cols=30  Identities=17%  Similarity=0.241  Sum_probs=24.1

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc---CCceEEe
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV---NVPFVIA  356 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i  356 (461)
                      =|.|.|+.|+||||+++.|++.+   +.+++.+
T Consensus         5 lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~   37 (209)
T d1nn5a_           5 LIVLEGVDRAGKSTQSRKLVEALCAAGHRAELL   37 (209)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            37788999999999999999976   4455443

>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=92.64  E-value=0.035  Score=48.86  Aligned_cols=29  Identities=48%  Similarity=0.646  Sum_probs=23.8

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEEec
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVIAD  357 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~i~  357 (461)
                      |-|+|.+|+||||+|+.|. .+|.+++..|
T Consensus         5 IgITG~igSGKStv~~~l~-~~G~~vidaD   33 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT-DLGVPLVDAD   33 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH-TTTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HCCCeEEEch
Confidence            4589999999999999886 5788776544

>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=92.63  E-value=0.052  Score=49.81  Aligned_cols=23  Identities=26%  Similarity=0.486  Sum_probs=20.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .-+|+|.|.+|+|||+|..+|..
T Consensus        32 ~l~I~LvG~tg~GKSSliN~ilg   54 (257)
T d1h65a_          32 SLTILVMGKGGVGKSSTVNSIIG   54 (257)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCcHHHHHHHHhC
Confidence            35799999999999999999974

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.61  E-value=0.038  Score=49.04  Aligned_cols=27  Identities=19%  Similarity=0.215  Sum_probs=23.9

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVP  352 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~p  352 (461)
                      .-|+|.|.-|+||||+++.|++.+...
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l~~~   29 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTYPEW   29 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCTTS
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhhc
Confidence            458899999999999999999998653

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.60  E-value=0.033  Score=45.10  Aligned_cols=20  Identities=35%  Similarity=0.569  Sum_probs=18.7

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|+|++|||+|...|..
T Consensus         3 I~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999876

>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=92.43  E-value=0.035  Score=48.28  Aligned_cols=22  Identities=45%  Similarity=0.536  Sum_probs=19.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ++|+|.|++++|||+|..+|..
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999999875

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=92.39  E-value=0.036  Score=45.34  Aligned_cols=21  Identities=33%  Similarity=0.589  Sum_probs=19.2

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|.+++..
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999998875

>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=92.35  E-value=0.025  Score=50.47  Aligned_cols=29  Identities=34%  Similarity=0.423  Sum_probs=23.9

Q ss_pred             ccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          321 VELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       321 ~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .-..+.-+.|.||.|+|||||.++|+..+
T Consensus        23 ~i~~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          23 TIEKGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             EEETTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhccc
Confidence            33445668899999999999999999765

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=92.34  E-value=0.033  Score=51.39  Aligned_cols=17  Identities=41%  Similarity=0.616  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCchHHHH
Q 012525          326 SNVLLMGPTGSGKTLLA  342 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLA  342 (461)
                      .++|+.|+||||||+++
T Consensus        25 g~~lV~g~aGSGKTt~l   41 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVL   41 (318)
T ss_dssp             SCEEEEECTTSCHHHHH
T ss_pred             CCEEEEecCCccHHHHH
Confidence            56999999999999764

>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=92.19  E-value=0.041  Score=48.56  Aligned_cols=27  Identities=33%  Similarity=0.532  Sum_probs=22.3

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      |-|+|.+|+||||+|+.|. .+|.+++.
T Consensus         6 IgitG~igSGKStv~~~l~-~~G~~vid   32 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFA-DLGINVID   32 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HTTCEEEE
T ss_pred             EEEECCCcCCHHHHHHHHH-HCCCcEEE
Confidence            5699999999999999886 56776554

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.12  E-value=0.036  Score=50.96  Aligned_cols=27  Identities=33%  Similarity=0.546  Sum_probs=22.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-+.|.||+|+|||||.+.|+...
T Consensus        24 ~~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhcCC
Confidence            344668899999999999999999755

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.01  E-value=0.057  Score=48.02  Aligned_cols=30  Identities=20%  Similarity=0.280  Sum_probs=25.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEE
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVI  355 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~  355 (461)
                      .-|.|.|+-|+||||+++.|++.+......
T Consensus         4 k~I~iEG~DGsGKST~~~~L~~~L~~~~~~   33 (214)
T d1tmka_           4 KLILIEGLDRTGKTTQCNILYKKLQPNCKL   33 (214)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHTTTSEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHhCCEE
Confidence            448899999999999999999998654443

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=91.84  E-value=0.034  Score=46.26  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=19.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|++|+|||+|..+|..
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4599999999999999988854

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=91.79  E-value=0.04  Score=50.85  Aligned_cols=26  Identities=31%  Similarity=0.556  Sum_probs=22.5

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+-|.||+|+|||||+++|+...
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            34667899999999999999999755

>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=91.75  E-value=0.035  Score=50.91  Aligned_cols=27  Identities=33%  Similarity=0.476  Sum_probs=22.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+.|.||+|+|||||.+.|+...
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCcchhhHhccCCC
Confidence            345678899999999999999998654

>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=91.72  E-value=0.042  Score=45.76  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=19.1

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|.+.|..
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~   24 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNG   24 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            489999999999999999865

>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=91.61  E-value=0.045  Score=50.59  Aligned_cols=24  Identities=38%  Similarity=0.713  Sum_probs=20.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .-+.|.||.|+|||||.+.|+..+
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCChHHHHHHHHHcCC
Confidence            345689999999999999999766

>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=91.52  E-value=0.079  Score=50.48  Aligned_cols=26  Identities=19%  Similarity=0.285  Sum_probs=22.5

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +--|-+.|++|+||||+|+.|+..+.
T Consensus        80 P~iIGIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          80 PYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEEeCCCCCCCcHHHHHHHHHHh
Confidence            34566999999999999999999874

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.44  E-value=0.037  Score=51.21  Aligned_cols=30  Identities=30%  Similarity=0.333  Sum_probs=24.5

Q ss_pred             cccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          320 NVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       320 ~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..-..+..+.|.||+|+|||||+++|...+
T Consensus        35 l~i~~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          35 FTLRPGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             EEECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EEEcCCCEEEEECCCCCcHHHHHHHHhccc
Confidence            333445678899999999999999998765

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=91.33  E-value=0.035  Score=51.14  Aligned_cols=34  Identities=24%  Similarity=0.339  Sum_probs=25.9

Q ss_pred             cccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          316 DNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       316 ~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.+...-..+..+.|.||+|+|||||+++|+..+
T Consensus        19 ~~isl~i~~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          19 RDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EEEEEEECTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             eeeEEEEcCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3333333445678899999999999999999765

>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=91.30  E-value=0.05  Score=48.39  Aligned_cols=27  Identities=22%  Similarity=0.230  Sum_probs=23.2

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCCceE
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNVPFV  354 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~pfv  354 (461)
                      |-|+|..||||||+|+.|++.++...+
T Consensus         4 IgiTG~igSGKsTva~~l~e~~g~~~i   30 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNYSAVKY   30 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEEC
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCeEE
Confidence            679999999999999999998775433

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=91.22  E-value=0.041  Score=50.83  Aligned_cols=26  Identities=19%  Similarity=0.285  Sum_probs=22.3

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+-|.||+|+|||||++.|+...
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCc
Confidence            34667899999999999999998655

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.21  E-value=0.057  Score=45.65  Aligned_cols=20  Identities=30%  Similarity=0.564  Sum_probs=18.3

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|||||+|+..+..
T Consensus         6 ivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            89999999999999998874

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.21  E-value=0.043  Score=51.62  Aligned_cols=35  Identities=26%  Similarity=0.250  Sum_probs=26.9

Q ss_pred             ccccccccccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          315 VDNDDNVELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       315 ~~~~~~~~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.+...-..+..+.|.||+|+|||||+++|+..+
T Consensus        52 L~~isl~i~~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          52 LKNINLNIEKGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             EEEEEEEECTTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             EeCeEEEEcCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            33444444456778899999999999999999866

>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=91.13  E-value=0.059  Score=45.04  Aligned_cols=20  Identities=15%  Similarity=0.444  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|+..+..
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999988875

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=91.09  E-value=0.1  Score=49.89  Aligned_cols=34  Identities=24%  Similarity=0.383  Sum_probs=25.2

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc-----CCceEEecchh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV-----NVPFVIADATT  360 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l-----~~pfv~i~~s~  360 (461)
                      .|=|.|+||+|||||...|.+.+     ..-++.++.+.
T Consensus        53 ~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss   91 (323)
T d2qm8a1          53 RVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSS   91 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGG
T ss_pred             EEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeeccccc
Confidence            36699999999999999998754     23455555543

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=91.07  E-value=0.085  Score=43.92  Aligned_cols=22  Identities=23%  Similarity=0.439  Sum_probs=19.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|.+|+|||+|...|..
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999998875

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.95  E-value=0.22  Score=46.80  Aligned_cols=22  Identities=32%  Similarity=0.733  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHHhc
Q 012525          328 VLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      |-|.|++|+||||||..|.+.+
T Consensus        30 IGi~G~qGSGKSTl~~~l~~~L   51 (286)
T d1odfa_          30 IFFSGPQGSGKSFTSIQIYNHL   51 (286)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHHHH
Confidence            4488999999999999887654

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=90.95  E-value=0.7  Score=39.59  Aligned_cols=25  Identities=32%  Similarity=0.430  Sum_probs=19.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.++++.-|+|+|||.++....-..
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~~~~   64 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPALLL   64 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEcCCCCCCcchhhhhhhhc
Confidence            4689999999999999875554433

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=90.91  E-value=0.057  Score=49.79  Aligned_cols=26  Identities=31%  Similarity=0.546  Sum_probs=22.4

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+-|.||+|+|||||.+.|+..+
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            34567899999999999999999765

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=90.90  E-value=0.064  Score=45.15  Aligned_cols=20  Identities=30%  Similarity=0.478  Sum_probs=18.7

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|...+..
T Consensus         8 i~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            89999999999999998875

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.85  E-value=0.065  Score=44.86  Aligned_cols=20  Identities=25%  Similarity=0.569  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|++.+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998875

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.77  E-value=0.067  Score=44.75  Aligned_cols=21  Identities=29%  Similarity=0.588  Sum_probs=19.1

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -|+|.|.+|+|||+|...+..
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998875

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.77  E-value=0.062  Score=45.77  Aligned_cols=20  Identities=30%  Similarity=0.504  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|++.+..
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            89999999999999988874

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=90.70  E-value=0.064  Score=45.03  Aligned_cols=21  Identities=33%  Similarity=0.586  Sum_probs=18.9

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|.++|..
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            389999999999999999974

>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=90.67  E-value=0.1  Score=50.00  Aligned_cols=24  Identities=17%  Similarity=0.343  Sum_probs=20.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..|=+.|+||+|||||..+|++.+
T Consensus        55 ~~IgitG~pGaGKSTLi~~l~~~~   78 (327)
T d2p67a1          55 LRLGVTGTPGAGKSTFLEAFGMLL   78 (327)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEeeCCCCCCHHHHHHHHHHHH
Confidence            346799999999999999998754

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.63  E-value=0.071  Score=45.71  Aligned_cols=23  Identities=35%  Similarity=0.619  Sum_probs=20.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHHh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      ..|+|.|+|++|||+|..+|...
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999754

>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=90.59  E-value=0.071  Score=44.51  Aligned_cols=21  Identities=33%  Similarity=0.452  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|...+..
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~   24 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIAS   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            489999999999999998875

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.55  E-value=0.071  Score=44.64  Aligned_cols=20  Identities=35%  Similarity=0.449  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|.+.+..
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998875

>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=90.29  E-value=0.092  Score=50.54  Aligned_cols=35  Identities=37%  Similarity=0.545  Sum_probs=25.4

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc---CCceEEecc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADA  358 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~  358 (461)
                      ..+|+++.|++|+|||++++.+...+   +.+++.+|.
T Consensus        49 ~~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~   86 (433)
T d1e9ra_          49 EPRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDP   86 (433)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEE
T ss_pred             ccceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeC
Confidence            35899999999999999987665432   445555544

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.27  E-value=0.072  Score=44.79  Aligned_cols=20  Identities=35%  Similarity=0.747  Sum_probs=18.8

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|.+.+..
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999886

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.24  E-value=0.059  Score=50.06  Aligned_cols=27  Identities=19%  Similarity=0.336  Sum_probs=22.9

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+..+-|.||+|+|||||+++|+...
T Consensus        26 ~~GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          26 RAGDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            345667899999999999999998755

>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=90.21  E-value=0.057  Score=49.48  Aligned_cols=26  Identities=35%  Similarity=0.627  Sum_probs=22.4

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.-+.|.||+|+|||||.++|+...
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            34567899999999999999999765

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.12  E-value=0.082  Score=44.39  Aligned_cols=21  Identities=24%  Similarity=0.542  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -|+|.|.+|+|||+|+..+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999884

>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=90.07  E-value=0.043  Score=50.76  Aligned_cols=26  Identities=27%  Similarity=0.498  Sum_probs=22.6

Q ss_pred             cCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          324 EKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       324 ~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+..+.|.||+|+|||||.+.|+...
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            35678899999999999999999754

>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=90.03  E-value=0.085  Score=43.79  Aligned_cols=20  Identities=25%  Similarity=0.534  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|.+.+..
T Consensus         5 v~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998875

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.97  E-value=0.079  Score=44.54  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -|+|.|.+|+|||+|.+.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999998875

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.79  E-value=0.081  Score=44.30  Aligned_cols=20  Identities=30%  Similarity=0.547  Sum_probs=18.2

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|...+..
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            89999999999999988774

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.69  E-value=0.093  Score=44.34  Aligned_cols=21  Identities=38%  Similarity=0.695  Sum_probs=18.8

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|++.+..
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998865

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.59  E-value=0.095  Score=44.04  Aligned_cols=20  Identities=25%  Similarity=0.498  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|.+.+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            89999999999999998875

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.57  E-value=0.089  Score=43.97  Aligned_cols=21  Identities=29%  Similarity=0.580  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|...+..
T Consensus         5 Ki~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999998875

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.50  E-value=0.096  Score=44.51  Aligned_cols=20  Identities=35%  Similarity=0.659  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|||||+|+..+..
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998875

>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=89.45  E-value=0.092  Score=43.59  Aligned_cols=20  Identities=25%  Similarity=0.446  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|++.+..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998874

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.42  E-value=0.093  Score=43.76  Aligned_cols=20  Identities=35%  Similarity=0.664  Sum_probs=18.6

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |++.|.+|+|||+|.+.+..
T Consensus         5 i~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999998875

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.42  E-value=0.1  Score=43.77  Aligned_cols=20  Identities=35%  Similarity=0.652  Sum_probs=18.3

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|...+..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            89999999999999998864

>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=89.42  E-value=0.078  Score=44.42  Aligned_cols=22  Identities=45%  Similarity=0.640  Sum_probs=19.1

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -.|+|.|++|+|||+|...|..
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4599999999999999988753

>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=89.41  E-value=0.093  Score=43.80  Aligned_cols=21  Identities=19%  Similarity=0.401  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|.+.+..
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998875

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.38  E-value=0.093  Score=44.33  Aligned_cols=21  Identities=24%  Similarity=0.518  Sum_probs=18.9

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|.+.+..
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999988875

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=89.21  E-value=0.092  Score=44.11  Aligned_cols=21  Identities=24%  Similarity=0.458  Sum_probs=19.1

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|+|++|||+|..+|..
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999974

>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=89.20  E-value=0.098  Score=43.96  Aligned_cols=20  Identities=30%  Similarity=0.627  Sum_probs=18.5

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|++.+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998874

>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=89.03  E-value=0.17  Score=45.59  Aligned_cols=34  Identities=15%  Similarity=0.173  Sum_probs=25.0

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc----CCceEEecc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV----NVPFVIADA  358 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l----~~pfv~i~~  358 (461)
                      +.-++|.|+||+|||+++..+|..+    +.+++.++.
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~   72 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee
Confidence            4568899999999999998887432    456555543

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.97  E-value=0.1  Score=44.02  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=19.3

Q ss_pred             cEEEEccCCCchHHHHHHHHHh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      -|+|.|.+|+|||+|...+...
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999888763

>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=88.87  E-value=0.096  Score=44.85  Aligned_cols=22  Identities=23%  Similarity=0.445  Sum_probs=19.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|+|.||+|||||..+|..
T Consensus        24 ~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          24 PEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHhcC
Confidence            3599999999999999999973

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.86  E-value=0.12  Score=43.26  Aligned_cols=21  Identities=33%  Similarity=0.534  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|.+.+..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998875

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=88.71  E-value=0.1  Score=42.94  Aligned_cols=21  Identities=33%  Similarity=0.544  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++++|||+|..+|..
T Consensus         3 kI~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999974

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.70  E-value=0.12  Score=43.27  Aligned_cols=20  Identities=40%  Similarity=0.630  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|++.+..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998865

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.65  E-value=0.11  Score=43.65  Aligned_cols=20  Identities=45%  Similarity=0.782  Sum_probs=18.3

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|++.+..
T Consensus         4 i~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCcCHHHHHHHHhC
Confidence            78999999999999998865

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=88.62  E-value=0.12  Score=43.39  Aligned_cols=21  Identities=29%  Similarity=0.556  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -|+|.|.+|+|||+|.+.+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998875

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.60  E-value=0.12  Score=43.39  Aligned_cols=21  Identities=33%  Similarity=0.591  Sum_probs=18.7

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|...+..
T Consensus         8 KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999988865

>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=88.59  E-value=0.12  Score=43.71  Aligned_cols=20  Identities=45%  Similarity=0.723  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|+|||+|++.+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998874

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.44  E-value=0.13  Score=42.96  Aligned_cols=21  Identities=24%  Similarity=0.589  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|.+.+..
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            389999999999999998875

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=88.35  E-value=1.7  Score=39.90  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=18.8

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhc
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      .+.+|.-|+|+|||.+|-++++.+
T Consensus       129 ~~~il~~pTGsGKT~i~~~i~~~~  152 (282)
T d1rifa_         129 RRRILNLPTSAGRSLIQALLARYY  152 (282)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CCceeEEEcccCccHHHHHHHHHh
Confidence            346777899999999998887543

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.32  E-value=0.13  Score=43.42  Aligned_cols=21  Identities=29%  Similarity=0.610  Sum_probs=19.1

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|.+.+..
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998875

>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=88.28  E-value=0.1  Score=47.86  Aligned_cols=27  Identities=33%  Similarity=0.409  Sum_probs=22.8

Q ss_pred             ccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          323 LEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       323 ~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ..+.-+-|.||.|+|||||.++|+..+
T Consensus        30 ~~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          30 PRGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            345667899999999999999998655

>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=88.06  E-value=0.089  Score=44.29  Aligned_cols=22  Identities=27%  Similarity=0.448  Sum_probs=19.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -.|+|.|++|+|||+|.+.+..
T Consensus        13 ~kIvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          13 MRILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             EEEEEEEETTSSHHHHHHHTTC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4599999999999999998864

>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=88.05  E-value=0.25  Score=44.45  Aligned_cols=35  Identities=17%  Similarity=0.295  Sum_probs=27.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      ++-+++.|-=|+||||+|-+||..+   +..++.+++.
T Consensus         8 p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1           8 PPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            4668899999999999998888766   5566555543

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.88  E-value=0.14  Score=43.38  Aligned_cols=21  Identities=24%  Similarity=0.377  Sum_probs=18.9

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -|+|.|.+|+|||+|.+.+..
T Consensus         7 KivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999988875

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.83  E-value=0.15  Score=42.60  Aligned_cols=21  Identities=19%  Similarity=0.463  Sum_probs=18.4

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|...+..
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999988764

>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=87.81  E-value=0.12  Score=47.73  Aligned_cols=28  Identities=29%  Similarity=0.529  Sum_probs=23.2

Q ss_pred             cccCCcEEEEccCCCchHHHHHHHHHhc
Q 012525          322 ELEKSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       322 ~~~~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -..+.-+-|.||.|+|||||+++|+..+
T Consensus        27 v~~Gei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          27 VNKGDVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            3445667899999999999999998755

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=87.74  E-value=0.13  Score=43.31  Aligned_cols=21  Identities=29%  Similarity=0.396  Sum_probs=19.4

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|.++|..
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~   27 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLG   27 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999985

>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=87.57  E-value=1.4  Score=36.46  Aligned_cols=31  Identities=29%  Similarity=0.537  Sum_probs=22.5

Q ss_pred             EEEccCCCchHH-HHHHHHH--hcCCceEEecch
Q 012525          329 LLMGPTGSGKTL-LAKTLAR--HVNVPFVIADAT  359 (461)
Q Consensus       329 LL~GPPGTGKTt-LAraLA~--~l~~pfv~i~~s  359 (461)
                      +++||.-+|||+ |.+.+.+  ..+..++.+...
T Consensus         6 ~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~   39 (139)
T d2b8ta1           6 FITGPMFAGKTAELIRRLHRLEYADVKYLVFKPK   39 (139)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEc
Confidence            689999999999 6677643  446666655554

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=87.52  E-value=0.1  Score=44.25  Aligned_cols=21  Identities=33%  Similarity=0.588  Sum_probs=18.5

Q ss_pred             CcEEEEccCCCchHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLA  346 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA  346 (461)
                      -.|+|.|++|+|||+|.+.+.
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTC
T ss_pred             EEEEEECCCCCCHHHHHHHHh
Confidence            459999999999999988774

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.52  E-value=0.14  Score=44.00  Aligned_cols=20  Identities=35%  Similarity=0.637  Sum_probs=18.4

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|...+..
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            89999999999999998875

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.49  E-value=0.14  Score=42.70  Aligned_cols=22  Identities=23%  Similarity=0.370  Sum_probs=19.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|+|.|.|++|||+|..+|.+
T Consensus         6 ~~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           6 GFIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            3489999999999999999974

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.45  E-value=0.15  Score=43.50  Aligned_cols=21  Identities=29%  Similarity=0.591  Sum_probs=18.9

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -|+|.|.+|+|||+|.+.+.+
T Consensus         4 KivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999988876

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.41  E-value=0.16  Score=42.65  Aligned_cols=21  Identities=24%  Similarity=0.509  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|...+..
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            488999999999999998875

>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=87.39  E-value=0.091  Score=44.30  Aligned_cols=20  Identities=35%  Similarity=0.612  Sum_probs=8.6

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|.+|||||+|.+.+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999987764

>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=87.35  E-value=0.14  Score=48.34  Aligned_cols=23  Identities=17%  Similarity=0.408  Sum_probs=17.7

Q ss_pred             cEEEEccCCCchHHHHHHHHHhc
Q 012525          327 NVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      -|-+.|++|+||||++++|.+.+
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~   28 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIF   28 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH
Confidence            36699999999999999999876

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.80  E-value=0.17  Score=43.21  Aligned_cols=21  Identities=29%  Similarity=0.425  Sum_probs=19.0

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|.+|+|||+|.+.+..
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            489999999999999988875

>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=86.70  E-value=0.12  Score=47.38  Aligned_cols=25  Identities=28%  Similarity=0.486  Sum_probs=21.6

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +..+-|.||.|+|||||.++|+..+
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4456699999999999999999766

>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=86.67  E-value=0.17  Score=43.29  Aligned_cols=20  Identities=25%  Similarity=0.383  Sum_probs=18.2

Q ss_pred             EEEEccCCCchHHHHHHHHH
Q 012525          328 VLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~  347 (461)
                      |+|.|++|+|||+|...+..
T Consensus         6 vvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999988765

>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=86.57  E-value=0.25  Score=42.03  Aligned_cols=32  Identities=19%  Similarity=0.162  Sum_probs=24.7

Q ss_pred             CcEEEEcc-CCCchHHHHHHHHHhc---CCceEEec
Q 012525          326 SNVLLMGP-TGSGKTLLAKTLARHV---NVPFVIAD  357 (461)
Q Consensus       326 ~~VLL~GP-PGTGKTtLAraLA~~l---~~pfv~i~  357 (461)
                      +.++++|- +|+||||++-.||..+   +..++.++
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            34789999 5999999999888766   55555555

>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=86.23  E-value=0.15  Score=46.26  Aligned_cols=25  Identities=32%  Similarity=0.525  Sum_probs=21.4

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      +.-+-|.||.|+|||||.++|+...
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHTSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            4567799999999999999999743

>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=86.20  E-value=0.18  Score=42.65  Aligned_cols=19  Identities=37%  Similarity=0.679  Sum_probs=17.7

Q ss_pred             cEEEEccCCCchHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTL  345 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraL  345 (461)
                      .|+|.|.+|+|||+|.+.+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3899999999999999998

>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=85.94  E-value=0.15  Score=43.04  Aligned_cols=21  Identities=33%  Similarity=0.512  Sum_probs=18.9

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|.|.|.|++|||+|..+|.+
T Consensus         3 ~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999963

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=85.91  E-value=0.11  Score=43.16  Aligned_cols=23  Identities=26%  Similarity=0.367  Sum_probs=19.8

Q ss_pred             CCcEEEEccCCCchHHHHHHHHH
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ...|.|.|.|++|||+|.++|..
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            45699999999999999988843

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=85.61  E-value=0.2  Score=42.07  Aligned_cols=22  Identities=23%  Similarity=0.392  Sum_probs=19.5

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -.|.|.|.+++|||+|..+|..
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
Confidence            3589999999999999999874

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.43  E-value=0.14  Score=43.19  Aligned_cols=21  Identities=33%  Similarity=0.567  Sum_probs=17.6

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|++|+|||+|...+..
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC-
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999887654

>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=85.22  E-value=0.2  Score=47.98  Aligned_cols=26  Identities=23%  Similarity=0.321  Sum_probs=23.0

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCC
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      -.|.|.|+-|+||||+++.|++.++.
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEEEECCccCCHHHHHHHHHHHhcc
Confidence            45889999999999999999998853

>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=84.91  E-value=0.19  Score=42.40  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=18.7

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|.|.|+|++|||+|..+|..
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            488999999999999999853

>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=84.72  E-value=0.07  Score=44.15  Aligned_cols=26  Identities=19%  Similarity=0.254  Sum_probs=21.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhcC
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHVN  350 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l~  350 (461)
                      +.-.+|+|+.|+|||++..||.-.+.
T Consensus        24 ~~~tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          24 ELVTTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc
Confidence            34467899999999999999987663

>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=84.68  E-value=0.24  Score=45.00  Aligned_cols=25  Identities=20%  Similarity=0.306  Sum_probs=21.1

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV  349 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l  349 (461)
                      ....+|.|++|+|||||..+|....
T Consensus        95 ~kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          95 GKISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             CCeEEEECCCCCCHHHHHHhhcchh
Confidence            4668899999999999999996433

>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=84.18  E-value=0.094  Score=43.09  Aligned_cols=21  Identities=24%  Similarity=0.480  Sum_probs=19.1

Q ss_pred             EEEEccCCCchHHHHHHHHHh
Q 012525          328 VLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~  348 (461)
                      |.|.|.|++|||+|..+|...
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            889999999999999999753

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=83.92  E-value=0.44  Score=42.71  Aligned_cols=35  Identities=26%  Similarity=0.450  Sum_probs=25.7

Q ss_pred             CCcEEEEccCCCchHHHHHHHHHhc---CCceEEecch
Q 012525          325 KSNVLLMGPTGSGKTLLAKTLARHV---NVPFVIADAT  359 (461)
Q Consensus       325 ~~~VLL~GPPGTGKTtLAraLA~~l---~~pfv~i~~s  359 (461)
                      .+-|++.|-=|+||||+|-.||..+   +..++.+++.
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            3557788999999999877777654   5566665554

>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=83.27  E-value=0.31  Score=40.84  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=19.4

Q ss_pred             cEEEEccCCCchHHHHHHHHHh
Q 012525          327 NVLLMGPTGSGKTLLAKTLARH  348 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~~  348 (461)
                      .|+|.|..|+|||+|.+.+...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999999653

>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=82.89  E-value=0.3  Score=43.07  Aligned_cols=22  Identities=32%  Similarity=0.543  Sum_probs=19.2

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      ..|||.|..|+|||+|.+.+..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4589999999999999998863

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.88  E-value=0.4  Score=40.69  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=19.4

Q ss_pred             CcEEEEccCCCchHHHHHHHHH
Q 012525          326 SNVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~  347 (461)
                      -.|++.|.+|+|||+|...+..
T Consensus         6 ~ki~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           6 LRLGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4589999999999999988865

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=81.69  E-value=1.4  Score=36.65  Aligned_cols=31  Identities=16%  Similarity=0.278  Sum_probs=20.2

Q ss_pred             EEEEccCCCchHHHH-HHHH--HhcCCceEEecc
Q 012525          328 VLLMGPTGSGKTLLA-KTLA--RHVNVPFVIADA  358 (461)
Q Consensus       328 VLL~GPPGTGKTtLA-raLA--~~l~~pfv~i~~  358 (461)
                      -|++||.-+|||+-. +.+.  +..+..++.+..
T Consensus        10 ~lI~GpMfSGKTteLi~~~~~~~~~g~~vl~i~~   43 (141)
T d1xx6a1          10 EVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKP   43 (141)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEEeccccHHHHHHHHHHHHhhhcCCcEEEEEe
Confidence            367899999999854 4442  344666555544

>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=81.07  E-value=0.31  Score=46.57  Aligned_cols=24  Identities=33%  Similarity=0.522  Sum_probs=22.2

Q ss_pred             EEEEccCCCchHHHHHHHHHhcCC
Q 012525          328 VLLMGPTGSGKTLLAKTLARHVNV  351 (461)
Q Consensus       328 VLL~GPPGTGKTtLAraLA~~l~~  351 (461)
                      |.|.|+-|+||||+++.|++.+..
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~~   31 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhh
Confidence            789999999999999999998854

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=80.52  E-value=0.43  Score=39.69  Aligned_cols=21  Identities=33%  Similarity=0.583  Sum_probs=18.5

Q ss_pred             cEEEEccCCCchHHHHHHHHH
Q 012525          327 NVLLMGPTGSGKTLLAKTLAR  347 (461)
Q Consensus       327 ~VLL~GPPGTGKTtLAraLA~  347 (461)
                      .|+|.|..|+|||+|.+.+-.
T Consensus         4 KivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            389999999999999988753

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=80.15  E-value=3.2  Score=40.37  Aligned_cols=37  Identities=27%  Similarity=0.443  Sum_probs=32.6

Q ss_pred             CcEEEEccCCCchHHHHHHHHHhcCCceEEecchhhh
Q 012525          326 SNVLLMGPTGSGKTLLAKTLARHVNVPFVIADATTLT  362 (461)
Q Consensus       326 ~~VLL~GPPGTGKTtLAraLA~~l~~pfv~i~~s~l~  362 (461)
                      +..+|.|-+|+|||+++-.+++..+.|++.+......
T Consensus        32 ~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~~~   68 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTL   68 (413)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSHHH
T ss_pred             CcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCHHH
Confidence            5689999999999999999999999998888776555