Citrus Sinensis ID: 024550

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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------
Protein Sequence
MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAKEAEERAVQAEKKVLEISEE
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHcHHHHHHHccccccccEEcccccccHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHccccEEEEEEcccccccccHHHHHHHcccccccccccccccccccccccHHHHHHcccccccccEEEEEEccccccccccccccccccEEEEcccccHHHHHHHHHHHccccccccHHHHHHHcccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHcHHHHHHcccccccEEEEEcccccHHHHHHHHHHHcccccEEEEEcccHccHHHHHHHHHHHccccEEEEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccEEEEEEEccccccccHHHccccccccEEEEccccccHHHHHHHHHHccccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHcccEEcHHHHHHHHHHEHccccccEEcccc
Coil and Loop (DISEMBL)
MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRgyllygppgtgkSSLIAAMANYLKFDVYDLelsnllgnndLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDglwsscgderiIIFTTnhkerldpallrpgrmdmhinmshctpsgFKMLASnylgiaehpLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLEskkrandgseaKEAEERAVQAEKKVLEISEE
Flexible Loop (DISEMBL)
MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIfttnhkerldpaLLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAKEAEERAVQAEKKVLEISEE
Low Complexity Region (SEG)
mdfdmkkmimddLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAKEAEERAVQAEKKVLEISEE
Disordered region (IsUnstruct)
********IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEF*********************************
Disordered Region (DISOPRED)
***DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIE*******************************GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIE**********************************
Disordered Region (DISEMBL)
MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKK****************************
Disordered Region (DISPRO)
*****KKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIE************PDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAKEAEERAVQAEK********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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	266	2.2.26 [Sep-21-2011]
Q9P6Q3	449	Probable mitochondrial ch	yes	no	0.808	0.478	0.336	4e-32
Q54DY9	458	Probable mitochondrial ch	yes	no	0.654	0.379	0.368	6e-29
P32839	456	Mitochondrial chaperone B	yes	no	0.605	0.353	0.382	1e-27
Q7ZV60	420	Mitochondrial chaperone B	yes	no	0.590	0.373	0.402	4e-27
Q5E9H5	419	Mitochondrial chaperone B	yes	no	0.789	0.501	0.362	3e-25
Q7ZTL7	419	Mitochondrial chaperone B	N/A	no	0.586	0.372	0.384	4e-25
Q9Y276	419	Mitochondrial chaperone B	yes	no	0.703	0.446	0.352	3e-24
Q54HY8	421	Probable mitochondrial ch	no	no	0.650	0.410	0.372	1e-23
Q9CZP5	418	Mitochondrial chaperone B	yes	no	0.703	0.447	0.348	2e-23
Q5UR45	196	Putative AAA family ATPas	N/A	no	0.530	0.719	0.350	2e-16

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

 Score =  138 bits (348), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 132/247 (53%), Gaps = 32/247 (12%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           ++ ++KKMI DD+  FL+  ++Y   G  ++RGYLLYGPPG+GK+S + A+A  L +D+ 
Sbjct: 212 LESNVKKMITDDVHDFLRNSQWYDTRGIPYRRGYLLYGPPGSGKTSFLYALAGELDYDIC 271

Query: 61  DLELSNL-LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQ 119
            L L+   L ++ L H+L     K+++++ED+D   +      R R+    F        
Sbjct: 272 VLNLAEKGLTDDRLNHLLSNVPPKAVVLLEDVDSAFQ-----GRERSGEVGF-------- 318

Query: 120 KQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
              ++T SGLLN +DG+ SS  DERII  TTNH E+LDPAL+RPGR+D+   + + TP  
Sbjct: 319 -HANVTFSGLLNALDGVTSS--DERIIFMTTNHPEKLDPALVRPGRVDVKAYLGNATPEQ 375

Query: 180 FKMLASNYLG-------------IAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFA 226
            + + + + G               ++     ++ L    K +PAD  +  M  E P+  
Sbjct: 376 VREMFTRFYGHSPEMADDLSDIVCPKNTSMASLQGLFVMNKSSPADAVD--MAKELPDNP 433

Query: 227 LSGLIEF 233
            S    F
Sbjct: 434 PSTPFSF 440

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

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

 Score =  127 bits (320), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 70/190 (36%), Positives = 112/190 (58%), Gaps = 16/190 (8%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           +D    ++I+ D+++FL   ++Y   G  ++RGYLLYGPPGTGKSS I A+A  L+  + 
Sbjct: 211 LDKGKSELIIQDVKKFLNNSDWYNDRGIPYRRGYLLYGPPGTGKSSFITALAGELQLSIC 270

Query: 61  DLELSN-LLGNNDLRHILIATENKSILVVEDIDCCIEL--QDRLSRARAANPDFLIAGYE 117
            L L+   + +  L  +L     +SI+++EDID  I+    D  +++ +AN   + +G  
Sbjct: 271 ILNLAGKSVSDTSLNQLLATAPQRSIILLEDIDSAIQTGNHDLSAKSNSANAPSISSGGL 330

Query: 118 QQKQYH-----------ITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRM 166
           Q + Y+           +T SGLLN +DG+ +S G  RI+  TTNH E+LD  L+RPGR+
Sbjct: 331 QYQGYYGNPSVSSGGSALTFSGLLNALDGVAASEG--RILFMTTNHLEKLDKVLIRPGRV 388

Query: 167 DMHINMSHCT 176
           D+ I +  C+
Sbjct: 389 DLQIEIGLCS 398

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

Dictyostelium discoideum (taxid: 44689)

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

 Score =  123 bits (308), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 68/178 (38%), Positives = 105/178 (58%), Gaps = 17/178 (9%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           +D  +K+ I+DD+  F++  ++Y   G  ++RGYLLYGPPG+GK+S I A+A  L +++ 
Sbjct: 230 LDSGIKEGILDDVYDFMKNGKWYSDRGIPYRRGYLLYGPPGSGKTSFIQALAGELDYNIC 289

Query: 61  DLELS-NLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQ 119
            L LS N L ++ L H++     +SIL++EDID     + +                EQ 
Sbjct: 290 ILNLSENNLTDDRLNHLMNNMPERSILLLEDIDAAFNKRSQTG--------------EQG 335

Query: 120 KQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTP 177
               +T SGLLN +DG+ SS  +E I   TTNH E+LD A++RPGR+D  + + + TP
Sbjct: 336 FHSSVTFSGLLNALDGVTSS--EETITFMTTNHPEKLDAAIMRPGRIDYKVFVGNATP 391

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

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

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

 Score =  122 bits (305), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 68/169 (40%), Positives = 101/169 (59%), Gaps = 12/169 (7%)

Query: 9   IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL- 67
           I+DD++ F+   ++Y   G  ++RGYLLYGPPG GKSS I A+A  L + +  + LS+  
Sbjct: 201 IVDDVKEFIGNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELGYSICLMSLSDRS 260

Query: 68  LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
           L ++ L H+L     +SI+++ED+D     ++ L      NP         Q    +T S
Sbjct: 261 LSDDRLNHLLSVAPQQSIILLEDVDAAFVSRELLP---TENP------LAYQGMGRLTFS 311

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCT 176
           GLLN +DG+ SS  + RI+  TTN  ERLDPAL+RPGR+D+   + HC+
Sbjct: 312 GLLNALDGVASS--EARIVFMTTNFIERLDPALVRPGRVDLKQYVGHCS 358

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

Danio rerio (taxid: 7955)

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

 Score =  115 bits (288), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 87/240 (36%), Positives = 131/240 (54%), Gaps = 30/240 (12%)

Query: 9   IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV-YDLELSNL 67
           I+ D+  F+   ++Y   G  ++RGYLLYGPPG GKSS I A+A  L+  +       + 
Sbjct: 201 IVRDIREFIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELQHSICLLSLTDSS 260

Query: 68  LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAA-NPDFLIAGYEQQKQYHITL 126
           L ++ L H+L     +S++++ED+D        LSR  AA NP       + Q    +T 
Sbjct: 261 LSDDRLNHLLSVAPQQSLVLLEDVDAAF-----LSRDLAAENP------IKYQGLGRLTF 309

Query: 127 SGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF-KMLAS 185
           SGLLN +DG+ S+  + RI+  TTNH +RLDPAL+RPGR+DM   + HC+     +M   
Sbjct: 310 SGLLNALDGVAST--EARIVFMTTNHIDRLDPALIRPGRVDMKEYVGHCSRWQLTQMFQR 367

Query: 186 NYLG----IAEHPLFVEIEKLIATAKVTPADVAEQLM--RNEAPEFALSGLIEFLESKKR 239
            Y G    +AE+  F +   L AT +++PA V    M  +N+      +G I+  ES +R
Sbjct: 368 FYPGQATSLAEN--FAD-RVLQATTQISPAQVQGYFMLYKNDP-----AGAIQNAESLRR 419

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

Bos taurus (taxid: 9913)

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

 Score =  115 bits (287), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 65/169 (38%), Positives = 99/169 (58%), Gaps = 13/169 (7%)

Query: 9   IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV-YDLELSNL 67
           I+ D++ F++  ++Y   G  ++RGYLLYGPPG GKSS I A+A  L++ +       + 
Sbjct: 201 IVQDVKGFIENPKWYSDRGIPYRRGYLLYGPPGCGKSSFITALAGELEYSICLMSLSDSS 260

Query: 68  LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
           L ++ L H+L     +SI+++ED+D     +D        NP         Q    +T S
Sbjct: 261 LSDDRLNHLLSVAPQQSIILLEDVDAAFVSRD----LNKQNPT------AYQGMGRLTFS 310

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCT 176
           GLLN +DG+ S+  + RI+  TTNH +RLDPAL+RPGR+D+   + HCT
Sbjct: 311 GLLNALDGVAST--EARIVFMTTNHIDRLDPALIRPGRVDVKQYVGHCT 357

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

Xenopus laevis (taxid: 8355)

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

 Score =  112 bits (280), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 79/224 (35%), Positives = 118/224 (52%), Gaps = 37/224 (16%)

Query: 9   IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV-YDLELSNL 67
           I+ D++ F+   ++Y   G  ++RGYLLYGPPG GKSS I A+A  L+  +       + 
Sbjct: 201 IVRDVQEFIDNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSS 260

Query: 68  LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAA-NPDFLIAGYEQQKQYHITL 126
           L ++ L H+L     +S++++ED+D        LSR  A  NP       + Q    +T 
Sbjct: 261 LSDDRLNHLLSVAPQQSLVLLEDVDAAF-----LSRDLAVENP------VKYQGLGRLTF 309

Query: 127 SGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCT---------- 176
           SGLLN +DG+ S+  + RI+  TTNH +RLDPAL+RPGR+D+   + +C+          
Sbjct: 310 SGLLNALDGVAST--EARIVFMTTNHVDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQR 367

Query: 177 --PSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLM 218
             P     LA N+   AEH        L AT +++PA V    M
Sbjct: 368 FYPGQAPSLAENF---AEH-------VLRATNQISPAQVQGYFM 401

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

Homo sapiens (taxid: 9606)

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

 Score =  110 bits (275), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 69/185 (37%), Positives = 104/185 (56%), Gaps = 12/185 (6%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
           D+K  +++D++ F+  + +YR  G  ++RGYLLYG PG GKSSLI A+A  L  D+  + 
Sbjct: 194 DLKSKLIEDIKSFITNESWYRNRGIPYRRGYLLYGEPGNGKSSLINAIAGELNLDICIVS 253

Query: 64  LSNL-LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQY 122
           LS+  + +  + H+L     KSIL++EDID          ++   N D            
Sbjct: 254 LSSKDIDDKQINHLLNNAPPKSILLIEDIDAAF-------KSHRDNVDSNNN--NSNNNN 304

Query: 123 HITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKM 182
            +T SGLLN +DG+ S  G  RI+  TTN  E LD AL+R GR+D+ I +S+ T S    
Sbjct: 305 SLTYSGLLNALDGVASQEG--RILFMTTNKIELLDSALIREGRIDLKIKVSNATKSQAAQ 362

Query: 183 LASNY 187
           L +++
Sbjct: 363 LFTHF 367

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

Dictyostelium discoideum (taxid: 44689)

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

 Score =  109 bits (273), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 78/224 (34%), Positives = 118/224 (52%), Gaps = 37/224 (16%)

Query: 9   IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV-YDLELSNL 67
           I+ D+  F+   ++Y   G  ++RGYLLYGPPG GKSS I A+A  L+  +       + 
Sbjct: 201 IVKDIREFIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSS 260

Query: 68  LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAA-NPDFLIAGYEQQKQYHITL 126
           L ++ L H+L     +S++++ED+D        LSR  A  NP       + Q    +T 
Sbjct: 261 LSDDRLNHLLSVAPQQSLVLLEDVDAAF-----LSRDLAVENP------IKYQGLGRLTF 309

Query: 127 SGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCT---------- 176
           SGLLN +DG+ S+  + RI+  TTN+ +RLDPAL+RPGR+D+   + +C+          
Sbjct: 310 SGLLNALDGVAST--EARIVFMTTNYIDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQR 367

Query: 177 --PSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLM 218
             P     LA N+   AEH        L AT++++PA V    M
Sbjct: 368 FYPGQAPSLAENF---AEH-------VLKATSEISPAQVQGYFM 401

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

Mus musculus (taxid: 10090)

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

 Score = 86.7 bits (213), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 55/157 (35%), Positives = 93/157 (59%), Gaps = 16/157 (10%)

Query: 47  LIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENK-SILVVEDIDCCIE--------- 96
           +I A++ + K  ++ L L+N+  +N+L ++L A   K +ILV+EDIDC  E         
Sbjct: 1   MIKAISTHTKRHIHYLILNNIQDDNELINLLNAVNCKETILVLEDIDCASEAVKSRAKEE 60

Query: 97  --LQDRLSRARAANPDFLIAGY--EQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH 152
             + ++++  ++   + ++A    + +K   +TLSG+LN +DG+++S G  RI+I TTNH
Sbjct: 61  ETVVEKVTDDKSTLENKILADQLKKVEKVSKLTLSGILNSLDGIFNSEG--RIVIMTTNH 118

Query: 153 KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG 189
            E LDPAL+R GR+DM I  S+C       +  N+ G
Sbjct: 119 SEVLDPALIRRGRIDMQIEFSNCDRYQIAKMYENFYG 155

Acanthamoeba polyphaga (taxid: 5757)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	266
118486313	539	unknown [Populus trichocarpa]	0.939	0.463	0.703	1e-103
255543747	501	ATP binding protein, putative [Ricinus c	0.984	0.522	0.667	1e-101
224105359	457	predicted protein [Populus trichocarpa]	0.883	0.514	0.734	1e-100
225428416	494	PREDICTED: ATP-dependent zinc metallopro	0.951	0.512	0.676	1e-99
225428414	488	PREDICTED: ATP-dependent zinc metallopro	0.943	0.514	0.675	2e-99
255561048	528	ATP binding protein, putative [Ricinus c	0.947	0.477	0.660	2e-95
297738387	471	unnamed protein product [Vitis vinifera]	0.954	0.539	0.615	4e-93
359473572	543	PREDICTED: peroxisomal biogenesis factor	0.954	0.467	0.615	5e-93
224094843	461	predicted protein [Populus trichocarpa]	0.857	0.494	0.705	7e-92
297738388	479	unnamed protein product [Vitis vinifera]	0.932	0.517	0.614	1e-91

>gi|118486313|gb|ABK94998.1| unknown [Populus trichocarpa]

 Score =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 178/253 (70%), Positives = 213/253 (84%), Gaps = 3/253 (1%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD + K++IM+DLERF++R+EFYRRVGKAWKRGYLL+GPPGTGKSSLIAA+ANYLKFD+Y
Sbjct: 224 MDMEGKRVIMEDLERFVKRREFYRRVGKAWKRGYLLFGPPGTGKSSLIAAIANYLKFDIY 283

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N++LR++LI+TENKS+LVVEDIDC IELQDRL++ARA  P      Y Q  
Sbjct: 284 DLELTDLRTNSELRNLLISTENKSVLVVEDIDCSIELQDRLAQARAMMPSRHHPPYNQAN 343

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
           QY +TLSGLLNF+DGLWSSCGDERIIIFTTNHKERLDPALLRPGRMD+HI+MS+CTP GF
Sbjct: 344 QYQVTLSGLLNFVDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDVHIHMSYCTPCGF 403

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKK-- 238
           K+LASNYLG  EHPLF  +E LI  A+VTPA+V EQL+R E PE A++GLIEFLE K   
Sbjct: 404 KLLASNYLGFTEHPLFPCVEALIEKARVTPAEVGEQLLRYEEPESAITGLIEFLEDKSER 463

Query: 239 -RANDGSEAKEAE 250
            +  DG++    E
Sbjct: 464 LKREDGNKDSNGE 476

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543747|ref|XP_002512936.1| ATP binding protein, putative [Ricinus communis] gi|223547947|gb|EEF49439.1| ATP binding protein, putative [Ricinus communis]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 177/265 (66%), Positives = 219/265 (82%), Gaps = 3/265 (1%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD D+K++IM+DLERF++RKEFY+RVGKAWKRGYLL+GPPGTGKSSLIAAMANYLKFD+Y
Sbjct: 224 MDMDVKRVIMEDLERFVKRKEFYKRVGKAWKRGYLLFGPPGTGKSSLIAAMANYLKFDIY 283

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N+DLR +LI+T NKSILVVEDIDC IELQ+R++ ARA N      G+   +
Sbjct: 284 DLELTDLRTNSDLRRLLISTGNKSILVVEDIDCSIELQNRITEARALNAR---QGHGYVR 340

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
              +TLSGLLNF+DGLWSSCGDER+I+FTTNHKE+LDPALLRPGRMD+HI+MS+CTP GF
Sbjct: 341 DNQVTLSGLLNFVDGLWSSCGDERVIVFTTNHKEKLDPALLRPGRMDVHIHMSYCTPCGF 400

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA 240
           KMLA NYLGI EHPLF+EIE++I   KVTPA++ EQLM++E PE AL GL EFLE K   
Sbjct: 401 KMLAFNYLGITEHPLFLEIEEMIEITKVTPAEIGEQLMKSEEPEVALRGLTEFLEHKGTE 460

Query: 241 NDGSEAKEAEERAVQAEKKVLEISE 265
            +  + +E++ER  + E+  L  +E
Sbjct: 461 EEERKKRESDERIAKIEESGLAEAE 485

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105359|ref|XP_002313783.1| predicted protein [Populus trichocarpa] gi|222850191|gb|EEE87738.1| predicted protein [Populus trichocarpa]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 174/237 (73%), Positives = 206/237 (86%), Gaps = 2/237 (0%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD + K++IM+DLERF++R+EFYRRVGKAWKRGYLL+GPPGTGKSSLIAA+ANYLKFD+Y
Sbjct: 221 MDMEGKRVIMEDLERFVKRREFYRRVGKAWKRGYLLFGPPGTGKSSLIAAIANYLKFDIY 280

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N++LR++LI+TENKS+LVVEDIDC IELQDRL++ARA  P      Y Q  
Sbjct: 281 DLELTDLRTNSELRNLLISTENKSVLVVEDIDCSIELQDRLAQARAMMPSRHHPPYNQAN 340

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
           Q  +TLSGLLNF+DGLWSSCGDERIIIFTTNHKERLDPALLRPGRMD+HI+MS+CTP GF
Sbjct: 341 Q--VTLSGLLNFVDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDVHIHMSYCTPCGF 398

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESK 237
           K+LASNYLG  EHPLF  +E LI  A+VTPA+V EQL+R E PE A++GLIEFLE K
Sbjct: 399 KLLASNYLGFTEHPLFPCVEALIEKARVTPAEVGEQLLRYEEPESAITGLIEFLEDK 455

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428416|ref|XP_002283761.1| PREDICTED: ATP-dependent zinc metalloprotease FtsH-like isoform 2 [Vitis vinifera]

 Score =  368 bits (945), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 178/263 (67%), Positives = 213/263 (80%), Gaps = 10/263 (3%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD ++K+ +M+DLERF++RK FYR+VGKAWKRGYLL+GPPGTGKSSLIAAMANYL FD+Y
Sbjct: 215 MDSELKRTLMNDLERFVRRKGFYRKVGKAWKRGYLLFGPPGTGKSSLIAAMANYLNFDIY 274

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N++LR +LI+T N+SILVVEDIDC +ELQDRL++AR  NP        Q  
Sbjct: 275 DLELTDLRCNSELRKLLISTANRSILVVEDIDCSLELQDRLAQARMMNPHRY-----QTS 329

Query: 121 QYH----ITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCT 176
           Q H    +TLSGLLNFIDGLWSSCGDERII+FTTNHK++LDPALLRPGRMDMHINMS+CT
Sbjct: 330 QVHLSKSVTLSGLLNFIDGLWSSCGDERIIVFTTNHKDKLDPALLRPGRMDMHINMSYCT 389

Query: 177 PSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLES 236
           P GFKMLASNYL I  HPLF E+E LI  AKVTPA+V EQLM++E P+  L GLI FL  
Sbjct: 390 PCGFKMLASNYLEITNHPLFPEVEDLILEAKVTPAEVGEQLMKSEEPDITLEGLIRFLVE 449

Query: 237 KKRANDGSEAKEAEERAVQAEKK 259
           KK + D ++A+EAE  A +A  K
Sbjct: 450 KKES-DAAKAREAELEAARASDK 471

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428414|ref|XP_002283754.1| PREDICTED: ATP-dependent zinc metalloprotease FtsH-like isoform 1 [Vitis vinifera]

 Score =  368 bits (944), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 175/259 (67%), Positives = 212/259 (81%), Gaps = 8/259 (3%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD ++K+ +M+DLERF++RK FYR+VGKAWKRGYLL+GPPGTGKSSLIAAMANYL FD+Y
Sbjct: 215 MDSELKRTLMNDLERFVRRKGFYRKVGKAWKRGYLLFGPPGTGKSSLIAAMANYLNFDIY 274

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N++LR +LI+T N+SILVVEDIDC +ELQDRL++AR  NP        + +
Sbjct: 275 DLELTDLRCNSELRKLLISTANRSILVVEDIDCSLELQDRLAQARMMNP-------HRYQ 327

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
              +TLSGLLNFIDGLWSSCGDERII+FTTNHK++LDPALLRPGRMDMHINMS+CTP GF
Sbjct: 328 TSQVTLSGLLNFIDGLWSSCGDERIIVFTTNHKDKLDPALLRPGRMDMHINMSYCTPCGF 387

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA 240
           KMLASNYL I  HPLF E+E LI  AKVTPA+V EQLM++E P+  L GLI FL  KK +
Sbjct: 388 KMLASNYLEITNHPLFPEVEDLILEAKVTPAEVGEQLMKSEEPDITLEGLIRFLVEKKES 447

Query: 241 NDGSEAKEAEERAVQAEKK 259
            D ++A+EAE  A +A  K
Sbjct: 448 -DAAKAREAELEAARASDK 465

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561048|ref|XP_002521536.1| ATP binding protein, putative [Ricinus communis] gi|223539214|gb|EEF40807.1| ATP binding protein, putative [Ricinus communis]

 Score =  354 bits (908), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 171/259 (66%), Positives = 216/259 (83%), Gaps = 7/259 (2%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           +D  +K  I++DLERF++RK++YR+VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFD+Y
Sbjct: 224 LDAQLKGTILEDLERFVKRKDYYRKVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDIY 283

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL+ L  N++LR +LIAT N+SILVVEDIDC IE QDRL+ A AA      A Y  QK
Sbjct: 284 DLELTELRCNSELRKLLIATANRSILVVEDIDCTIEFQDRLAEANAAE---FHAHYPPQK 340

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
           Q  +TLSGLLNFIDGLWSSCGDERIIIFTTNHKE+LDPALLRPGRMD+H++MS+CTP GF
Sbjct: 341 Q--VTLSGLLNFIDGLWSSCGDERIIIFTTNHKEKLDPALLRPGRMDVHVHMSYCTPCGF 398

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA 240
           ++LA+NYLGI +H LF  IE LI TA+VTPA+VAEQL+R++  E  LS LI+FLE +K+ 
Sbjct: 399 RLLAANYLGIKDHHLFGRIEDLILTAQVTPAEVAEQLLRSDELETVLSELIQFLEVRKK- 457

Query: 241 NDGSEAKEAEERAVQAEKK 259
            + +E ++A+++ ++ ++K
Sbjct: 458 -EITEQEKADQKELRVDEK 475

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738387|emb|CBI27588.3| unnamed protein product [Vitis vinifera]

 Score =  347 bits (889), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 168/273 (61%), Positives = 210/273 (76%), Gaps = 19/273 (6%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD  +K+ ++ DL+RF++R++FY+RVGKAWKRGYLLYGPPGTGK+SLIAAMANYLKFDVY
Sbjct: 200 MDLKLKEDLIKDLDRFVRRRKFYKRVGKAWKRGYLLYGPPGTGKTSLIAAMANYLKFDVY 259

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N+ LR +L++T+N+SILV+EDIDC  ELQDR             AG   Q 
Sbjct: 260 DLELTSLQRNSQLRKLLVSTKNRSILVIEDIDCSTELQDRQ------------AGRYNQP 307

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
              +TLSGLLNFIDGLWSSCGDERII+FTTNHK+R+DPALLRPGRMDMHI+MS+CTP GF
Sbjct: 308 TTQLTLSGLLNFIDGLWSSCGDERIIVFTTNHKDRIDPALLRPGRMDMHIHMSYCTPYGF 367

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA 240
           K LASNYLG++ H LF EIE+LI   +VTPA++AE+LM++E  + AL GLIEFL+  K A
Sbjct: 368 KTLASNYLGVSNHRLFTEIERLITEVEVTPAEIAEELMKSEEADVALEGLIEFLKRAKIA 427

Query: 241 NDGS--EAKEAEE-----RAVQAEKKVLEISEE 266
            + S  E KE +E     R V   +KV+E   +
Sbjct: 428 ENKSNGEGKEVDEQGTERRDVVESEKVVETKRQ 460

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473572|ref|XP_002265232.2| PREDICTED: peroxisomal biogenesis factor 6-like [Vitis vinifera]

 Score =  346 bits (888), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 168/273 (61%), Positives = 210/273 (76%), Gaps = 19/273 (6%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD  +K+ ++ DL+RF++R++FY+RVGKAWKRGYLLYGPPGTGK+SLIAAMANYLKFDVY
Sbjct: 272 MDLKLKEDLIKDLDRFVRRRKFYKRVGKAWKRGYLLYGPPGTGKTSLIAAMANYLKFDVY 331

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N+ LR +L++T+N+SILV+EDIDC  ELQDR             AG   Q 
Sbjct: 332 DLELTSLQRNSQLRKLLVSTKNRSILVIEDIDCSTELQDRQ------------AGRYNQP 379

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
              +TLSGLLNFIDGLWSSCGDERII+FTTNHK+R+DPALLRPGRMDMHI+MS+CTP GF
Sbjct: 380 TTQLTLSGLLNFIDGLWSSCGDERIIVFTTNHKDRIDPALLRPGRMDMHIHMSYCTPYGF 439

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA 240
           K LASNYLG++ H LF EIE+LI   +VTPA++AE+LM++E  + AL GLIEFL+  K A
Sbjct: 440 KTLASNYLGVSNHRLFTEIERLITEVEVTPAEIAEELMKSEEADVALEGLIEFLKRAKIA 499

Query: 241 NDGS--EAKEAEE-----RAVQAEKKVLEISEE 266
            + S  E KE +E     R V   +KV+E   +
Sbjct: 500 ENKSNGEGKEVDEQGTERRDVVESEKVVETKRQ 532

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224094843|ref|XP_002310261.1| predicted protein [Populus trichocarpa] gi|222853164|gb|EEE90711.1| predicted protein [Populus trichocarpa]

 Score =  342 bits (878), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 165/234 (70%), Positives = 196/234 (83%), Gaps = 6/234 (2%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           +D   K  I++DLERF++R+++YR+VGKAWKRGYLLYGPPGTGKSSLIAAMANYL FD+Y
Sbjct: 223 LDTKDKDKILEDLERFVKRRDYYRKVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDIY 282

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL+ +  N+DLR +LIAT N+SILVVEDIDC IELQDR++  RA  P     GY  QK
Sbjct: 283 DLELTEVRCNSDLRKVLIATANRSILVVEDIDCTIELQDRIAEERA-TPGL---GYPPQK 338

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
           Q  +TLSGLLNFIDGLWSSCGDERII+FTTNH E+LDPALLRPGRMD+H++MS+CTP GF
Sbjct: 339 Q--VTLSGLLNFIDGLWSSCGDERIIVFTTNHIEKLDPALLRPGRMDVHVHMSYCTPCGF 396

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFL 234
           K LA+NYLGI +H LF EIE+LI TA+VTPA+VAEQLMR++  E  L  LIEFL
Sbjct: 397 KFLAANYLGIKDHVLFEEIEELIKTAEVTPAEVAEQLMRSDELETVLKELIEFL 450

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738388|emb|CBI27589.3| unnamed protein product [Vitis vinifera]

 Score =  342 bits (876), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 161/262 (61%), Positives = 205/262 (78%), Gaps = 14/262 (5%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY 60
           MD  +K+ ++ DL+RF++R++FY+RVGKAWKRGYLLYGPPGTGK+SLIAAMANYLKFDVY
Sbjct: 200 MDLKLKEDLIKDLDRFVRRRKFYKRVGKAWKRGYLLYGPPGTGKTSLIAAMANYLKFDVY 259

Query: 61  DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQK 120
           DLEL++L  N+ LR +L++T+N+SILV+EDIDC  ELQDR             AG   Q 
Sbjct: 260 DLELTSLQRNSQLRKLLVSTKNRSILVIEDIDCSTELQDRQ------------AGRYNQP 307

Query: 121 QYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF 180
              +TLSGLLNFIDGLWSSCGDERII+FTTNHK+R+DPALLRPGRMDMHI+MS+CTP GF
Sbjct: 308 TTQLTLSGLLNFIDGLWSSCGDERIIVFTTNHKDRIDPALLRPGRMDMHIHMSYCTPYGF 367

Query: 181 KMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA 240
           K LASNYLG++ H LF EIE+LI   +VTPA++AE+LM++E  + AL GLI FL+  K A
Sbjct: 368 KTLASNYLGVSNHRLFTEIERLITEVEVTPAEIAEELMKSEEADVALEGLIAFLKRAKSA 427

Query: 241 NDGS--EAKEAEERAVQAEKKV 260
            + S    K+ +E+ ++ +  V
Sbjct: 428 ENKSNCRGKKVDEQGIERQDVV 449

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	266
TAIR|locus:2077997	576	BCS1 "cytochrome BC1 synthesis	0.921	0.425	0.632	2.6e-79
TAIR|locus:2175986	505	AT5G17760 [Arabidopsis thalian	0.921	0.485	0.590	8.1e-76
TAIR|locus:2078007	451	AT3G50940 [Arabidopsis thalian	0.838	0.494	0.645	4.5e-75
TAIR|locus:1005716649	495	AT2G18193 [Arabidopsis thalian	0.812	0.436	0.640	1.9e-74
TAIR|locus:2053109	494	AT2G18190 [Arabidopsis thalian	0.857	0.461	0.618	7.5e-73
TAIR|locus:2175956	533	AT5G17740 [Arabidopsis thalian	0.917	0.457	0.576	1.8e-71
TAIR|locus:2175946	470	AT5G17730 [Arabidopsis thalian	0.815	0.461	0.602	2.4e-69
TAIR|locus:2095532	477	AT3G28600 [Arabidopsis thalian	0.894	0.498	0.518	8.5e-65
TAIR|locus:2115954	248	AT4G05380 [Arabidopsis thalian	0.868	0.931	0.543	8.5e-65
TAIR|locus:2037186	475	AT1G43910 [Arabidopsis thalian	0.936	0.524	0.521	1.1e-64

TAIR|locus:2077997 BCS1 "cytochrome BC1 synthesis" [Arabidopsis thaliana (taxid:3702)]

 Score = 797 (285.6 bits), Expect = 2.6e-79, P = 2.6e-79
 Identities = 158/250 (63%), Positives = 198/250 (79%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L++F++R++FY+RVGKAWKRGYLLYGPPGTGKSSLIAAMAN+L FD+YDLEL+ +  N++
Sbjct:   281 LDKFVKRRDFYKRVGKAWKRGYLLYGPPGTGKSSLIAAMANHLNFDIYDLELTAVNNNSE 340

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNF 132
             LR +LIAT N+SIL+VEDIDC +EL+DR S       D +    E  +   +TLSGLLNF
Sbjct:   341 LRRLLIATANRSILIVEDIDCSLELKDRTSDEPPRESDDI----EDPRYKKVTLSGLLNF 396

Query:   133 IDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE 192
             IDGLWSSCGDERIIIFTTN+KE+LD ALLRPGRMDMHI+MS+CTPS FK LA NYL I E
Sbjct:   397 IDGLWSSCGDERIIIFTTNYKEKLDAALLRPGRMDMHIHMSYCTPSTFKALALNYLEIKE 456

Query:   193 HPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAKEAEER 252
             H LF +IE+ I   +VTPA+VAEQLMRN++ +  L GLIEFL+ KK  N+  +AK  E++
Sbjct:   457 HRLFSKIEEGIEATEVTPAEVAEQLMRNDSVDKVLEGLIEFLKVKKIENEQDKAK-TEKQ 515

Query:   253 AVQAEKKVLE 262
              ++ +KK  E
Sbjct:   516 ELENKKKTKE 525

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0052542 "defense response by callose deposition" evidence=RCA

TAIR|locus:2175986 AT5G17760 [Arabidopsis thaliana (taxid:3702)]

 Score = 764 (274.0 bits), Expect = 8.1e-76, P = 8.1e-76
 Identities = 154/261 (59%), Positives = 198/261 (75%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L+RF++RKEFY+RVGKAWKRGYLLYGPPGTGKSSL+AAMANYLKFDVYDL+L++++ ++D
Sbjct:   235 LDRFIRRKEFYKRVGKAWKRGYLLYGPPGTGKSSLVAAMANYLKFDVYDLQLASVMRDSD 294

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQ-QKQYHITLSGLLN 131
             LR +L+AT N+SILV+EDIDC ++L +R+ +     P   + G  + + Q  +TLSGLLN
Sbjct:   295 LRRLLLATRNRSILVIEDIDCAVDLPNRIEQ-----P---VEGKNRGESQGPLTLSGLLN 346

Query:   132 FIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA 191
             FIDGLWSSCGDERIIIFTTNHK+RLDPALLRPGRMDMHI M HC+  GFK LASNYLG++
Sbjct:   347 FIDGLWSSCGDERIIIFTTNHKDRLDPALLRPGRMDMHIYMGHCSFQGFKTLASNYLGLS 406

Query:   192 E----HPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLES---KKRANDGS 244
             +    H LF EIE+LI    +TPA VAE+LM++E  + AL GL+  LE    K + ++  
Sbjct:   407 DAAMPHRLFPEIERLIDGEVMTPAQVAEELMKSEDADVALEGLVNVLEKMRLKSKESNPV 466

Query:   245 EAKEAEERAVQAEKKVLEISE 265
               K+ E R    E ++   +E
Sbjct:   467 MMKQKESRLEMEEMRLKSDTE 487

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM;IDA

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

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

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

 Score = 757 (271.5 bits), Expect = 4.5e-75, P = 4.5e-75
 Identities = 151/234 (64%), Positives = 191/234 (81%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L+RF+QRK FY RVGKAWKRGYLLYGPPGTGKSSLIAA+AN+L FD+YDL+L++L  N +
Sbjct:   229 LDRFVQRKGFYGRVGKAWKRGYLLYGPPGTGKSSLIAAIANHLNFDIYDLDLTSLNNNAE 288

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNF 132
             LR +L++T N+SILVVEDIDC IEL+DR +     N D L       K   +TLSGLLNF
Sbjct:   289 LRRLLMSTANRSILVVEDIDCSIELKDRSTDQE--NNDPL------HKT--VTLSGLLNF 338

Query:   133 IDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE 192
             +DGLWSSCG+ERII+FTTN++E+LDPALLRPGRMDMHI+MS+CTP+ FK+LASNYL I +
Sbjct:   339 VDGLWSSCGNERIIVFTTNYREKLDPALLRPGRMDMHIHMSYCTPAAFKVLASNYLEIQD 398

Query:   193 HPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEA 246
             H LF +IE+ I   +VTPA+VAEQLMR+++ +  L GL+EFL++KK+  D S+A
Sbjct:   399 HILFEQIEEFIREIEVTPAEVAEQLMRSDSVDKVLQGLVEFLKAKKQI-DNSKA 451

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

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

 Score = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 146/228 (64%), Positives = 184/228 (80%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             LERFL+RKEFY+RVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV+DLELS++  N +
Sbjct:   225 LERFLKRKEFYKRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVFDLELSSIYDNGE 284

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNF 132
             L+ +L++T N+SILV+EDIDC  E++DR     A N +      ++Q +  +TLSG+LNF
Sbjct:   285 LKRVLLSTTNRSILVIEDIDCNAEVRDR----EAENQE------DEQIKGKVTLSGILNF 334

Query:   133 IDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGI-- 190
             IDGLWSS GDERII+FTTNHKERLDPALLRPGRMD+HINMS+CT  GF+ L SNYLG+  
Sbjct:   335 IDGLWSSFGDERIIVFTTNHKERLDPALLRPGRMDVHINMSYCTGLGFRTLVSNYLGLDG 394

Query:   191 AEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKK 238
               HPL  EIE L+ + +VTPA++AE+LM+++  +  L G+I F+E +K
Sbjct:   395 LNHPLCEEIEALVDSTEVTPAELAEELMQDDDTDVVLRGVISFVEKRK 442

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:2053109 AT2G18190 [Arabidopsis thaliana (taxid:3702)]

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 149/241 (61%), Positives = 187/241 (77%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             +ERFL+R+EFY+RVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV+DLELS++  N  
Sbjct:   226 MERFLKRREFYKRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVFDLELSSIYENAQ 285

Query:    73 LRHILIATENKSILVVEDIDCC-IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLN 131
             L+ IL++T N+SILV+EDIDC   E+ DR +       ++    YE+     +TLSGLLN
Sbjct:   286 LKSILLSTTNRSILVIEDIDCSSAEVVDREA------DEY--QEYEEGYYGRVTLSGLLN 337

Query:   132 FIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA 191
             F+DGLWSS GDERII+FTTNHKERLDPALLRPGRMDMHINMS+CT  GF+ L SNYLG+ 
Sbjct:   338 FVDGLWSSFGDERIIVFTTNHKERLDPALLRPGRMDMHINMSYCTGLGFRTLVSNYLGLG 397

Query:   192 --EHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAKEA 249
                HPL  EIE LI + +VTPA++AE+LM+ +  +  L G++ F+E++K   + S+ KE 
Sbjct:   398 GLNHPLCEEIEALIDSTEVTPAELAEELMQEDDTDVVLRGVVSFVENRKV--EISKTKEL 455

Query:   250 E 250
             E
Sbjct:   456 E 456

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175956 AT5G17740 [Arabidopsis thaliana (taxid:3702)]

 Score = 723 (259.6 bits), Expect = 1.8e-71, P = 1.8e-71
 Identities = 151/262 (57%), Positives = 192/262 (73%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L+RF+ RK+FY+RVGKAWKRGYLLYGPPGTGKSSL+AAMANYLKFD+YDL+L+++ G+  
Sbjct:   227 LDRFVGRKDFYKRVGKAWKRGYLLYGPPGTGKSSLVAAMANYLKFDIYDLQLASVQGDAH 286

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSR-ARAANPDFLIAGYEQQKQYHITLSGLLN 131
             LR +L+AT N SIL++EDIDC ++L  RL      + P   +   +  K   +TLSGLLN
Sbjct:   287 LRSLLLATNNSSILLIEDIDCSVDLPTRLQPPTETSQP---LGAVQVSKP--LTLSGLLN 341

Query:   132 FIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA 191
              IDGLWSSCG+ERIIIFTTN+KE+LDPALLRPGRMDMHI M HC+  GFK LASNYLG++
Sbjct:   342 CIDGLWSSCGNERIIIFTTNNKEKLDPALLRPGRMDMHIYMGHCSFQGFKTLASNYLGLS 401

Query:   192 E-----HPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESK----KRAND 242
             +     HPL  +I+ LI    +TPA VAE+LM++E  + AL GL++ L+ K    K+ +D
Sbjct:   402 DENDDTHPLCPDIKHLIDGHVLTPAQVAEELMKDEDADAALEGLVKVLKRKRLEPKKCDD 461

Query:   243 GSEAK---EAEERAVQAEKKVL 261
              S+ K   E EE    AE  VL
Sbjct:   462 ESKMKKLKEGEEAIADAELAVL 483

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175946 AT5G17730 [Arabidopsis thaliana (taxid:3702)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 138/229 (60%), Positives = 175/229 (76%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L+RF++RK+FY+RVGK WKRGYLLYGPPGTGK+SL+AA+ANYLKFD+YDL+L+++  + D
Sbjct:   227 LDRFIRRKDFYKRVGKPWKRGYLLYGPPGTGKTSLVAAIANYLKFDIYDLQLASVREDAD 286

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNF 132
             LR +L+ T N SIL+VEDIDC ++L  RL   +    D      + +    +TLSGLL  
Sbjct:   287 LRRLLLGTTNSSILLVEDIDCAVDLHTRL---QPKTQD------DTKGSSMLTLSGLLTC 337

Query:   133 IDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE 192
             IDGLWSSCGDERI+IFTT HKERLDPALLRPGRMDMHI+M HC    FK LASNYLG++ 
Sbjct:   338 IDGLWSSCGDERIVIFTTTHKERLDPALLRPGRMDMHIHMGHCCFDVFKTLASNYLGLSH 397

Query:   193 ---HPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKK 238
                H L+ EIE+LI    +TPA VAE+LM+NE P+ AL GL++ L+ K+
Sbjct:   398 DDPHHLYPEIERLIKGEVLTPAQVAEELMKNEDPDVALEGLVKVLKRKR 446

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2095532 AT3G28600 [Arabidopsis thaliana (taxid:3702)]

 Score = 660 (237.4 bits), Expect = 8.5e-65, P = 8.5e-65
 Identities = 127/245 (51%), Positives = 178/245 (72%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L  F   KE+Y+++GKAWKRGYLL+GPPGTGKS++IAAMAN+L + +YDLEL+ +  N++
Sbjct:   220 LAAFSNGKEYYKKIGKAWKRGYLLHGPPGTGKSTMIAAMANHLNYSIYDLELTAIRNNSE 279

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRAR--AANPDFLIAGYEQQKQYHITLSGLL 130
             LR +L AT +KSI+V+EDIDC ++L  +  + +    + +    G E+ K + +TLSGLL
Sbjct:   280 LRKLLTATSSKSIIVIEDIDCSLDLTGKRKKEKNLMTSREDGEQGTEEDKSF-VTLSGLL 338

Query:   131 NFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGI 190
             NFIDG+WS+CG ERIIIFTTNH E+LDPAL+R GRMDMHI +S+C+   FK+LA NYL +
Sbjct:   339 NFIDGIWSACGQERIIIFTTNHFEKLDPALIRRGRMDMHIELSYCSFEAFKILAKNYLDL 398

Query:   191 AEHPLFVEIEKLIATAKVTPADVAEQLMRNEAP---EFALSGLIEFLESKKRANDGSEAK 247
               HPLF +IE L+   K+ PADVAE LM+       + +L  LI+ LE KK+ + G++  
Sbjct:   399 DTHPLFKKIESLLKETKIAPADVAENLMKKNTEIDADGSLKDLIQALEGKKKIH-GAQVD 457

Query:   248 EAEER 252
             E +++
Sbjct:   458 EPKDK 462

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2115954 AT4G05380 [Arabidopsis thaliana (taxid:3702)]

 Score = 660 (237.4 bits), Expect = 8.5e-65, P = 8.5e-65
 Identities = 130/239 (54%), Positives = 172/239 (71%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L+ F   K+F++ VG+AWKRGYLLYGPPGTGKSSL+AA+AN++ + +YDL++ ++  +  
Sbjct:    13 LDAFSNGKDFFKTVGRAWKRGYLLYGPPGTGKSSLVAAIANFMNYSIYDLQIQSVKDDAM 72

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYH----ITLSG 128
             LR IL +TEN+SIL++ED+DC     D  +  R  N D    G  Q K+      +TLSG
Sbjct:    73 LRQILTSTENRSILLIEDLDC--SGAD--TTCRKENKDETEYGENQNKKKKKDPKVTLSG 128

Query:   129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYL 188
             LLNF+DGLWSSC +ERIIIFTTNHKE+LDPALLRPGRMD+HI M +CTP  FK LA+ YL
Sbjct:   129 LLNFVDGLWSSCVEERIIIFTTNHKEKLDPALLRPGRMDVHILMDYCTPIVFKKLAALYL 188

Query:   189 GIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAK 247
              I EH LF  IEK+    K TPA++ E+LM ++ P+  L GL+EFLESKK   +  +++
Sbjct:   189 EIEEHELFDPIEKMFLEVKATPAEITEKLMVSKDPDVTLKGLVEFLESKKMTKESVDSE 247

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2037186 AT1G43910 [Arabidopsis thaliana (taxid:3702)]

 Score = 659 (237.0 bits), Expect = 1.1e-64, P = 1.1e-64
 Identities = 133/255 (52%), Positives = 180/255 (70%)

Query:    13 LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
             L+ F + K+F++ VG+AWKRGYLLYGPPGTGKSS++AA+AN++K+ +YDL++ ++  + +
Sbjct:   221 LDAFSKGKDFFKSVGRAWKRGYLLYGPPGTGKSSMVAAIANHMKYHIYDLQIQSVRDDGE 280

Query:    73 LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQ--KQYH--ITLSG 128
             LR IL +T+N+SIL++EDIDC  +   R    +         G  Q+  K++   I+LSG
Sbjct:   281 LREILTSTKNRSILLIEDIDCGADASRRRQSKKKEEDGGEDDGEPQKRKKKFEVGISLSG 340

Query:   129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYL 188
             LLNF+DGLWSSCG+E+IIIFTTNHKE+LDPALLRPGRMD+HI M +CTP  FK L + YL
Sbjct:   341 LLNFVDGLWSSCGEEKIIIFTTNHKEKLDPALLRPGRMDVHILMDNCTPFVFKKLVALYL 400

Query:   189 GIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRANDGSEAKE 248
                EH LF  IEKLI     TPA+V +QLM ++  + AL GL EFLE+KK    G ++  
Sbjct:   401 KTDEHVLFDPIEKLILEVSSTPAEVTQQLMASKNADIALKGLAEFLENKK-LKKGEDSSV 459

Query:   249 AEERAVQ-AEKKVLE 262
              EE  ++ AE K  E
Sbjct:   460 EEEGEIEDAETKEAE 474

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0005783 "endoplasmic reticulum" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	266
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	5e-20
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	2e-13
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	4e-13
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-12
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	5e-12
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	1e-11
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	4e-11
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	5e-11
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	2e-09
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	2e-09
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	4e-09
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	4e-09
smart00382	148	smart00382, AAA, ATPases associated with a variety	8e-09
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	1e-08
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	3e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	2e-04
COG1484	254	COG1484, DnaC, DNA replication protein [DNA replic	4e-04
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	5e-04
PRK08116	268	PRK08116, PRK08116, hypothetical protein; Validate	6e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	0.001
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	0.001
PRK08939	306	PRK08939, PRK08939, primosomal protein DnaI; Revie	0.002
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	0.002
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	0.002
TIGR04352	280	TIGR04352, HprK_rel_A, HprK-related kinase A	0.004
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.004

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

 Score = 83.0 bits (206), Expect = 5e-20
 Identities = 43/145 (29%), Positives = 66/145 (45%), Gaps = 26/145 (17%)

Query: 34  YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN------NDLRHIL--IATENKSI 85
            LLYGPPGTGK++L  A+A  L     ++  S L+          LR +          +
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60

Query: 86  LVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERI 145
           + +++I       D L+ +R +  D               ++ LL  +DG  +S   + I
Sbjct: 61  IFIDEI-------DALAGSRGSGGDSESRR---------VVNQLLTELDGF-TSSLSKVI 103

Query: 146 IIFTTNHKERLDPALLRPGRMDMHI 170
           +I  TN  ++LDPALLR GR D  I
Sbjct: 104 VIAATNRPDKLDPALLR-GRFDRII 127

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

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

 Score = 69.3 bits (169), Expect = 2e-13
 Identities = 76/273 (27%), Positives = 131/273 (47%), Gaps = 40/273 (14%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
           D  K  + +L  +L+    ++++G    +G L+ GPPGTGK+ L  A+A   K   + + 
Sbjct: 158 DEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTIS 217

Query: 64  LSNLL------GNNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAG 115
            S+ +      G + +R +    +  +  I+ +++ID        + R R A    L  G
Sbjct: 218 GSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDA-------VGRQRGAG---LGGG 267

Query: 116 YEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFT-TNHKERLDPALLRPGRMDMHINMSH 174
           +++++Q   TL+ +L  +DG     G+E II+   TN  + LDPALLRPGR D  + +  
Sbjct: 268 HDEREQ---TLNQMLVEMDGFE---GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGL 321

Query: 175 CTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTP----ADVAEQLMRNEAPEFALSG- 229
               G + +   ++     PL  +I+  I  A+ TP    AD+A   + NEA  FA  G 
Sbjct: 322 PDVRGREQILKVHM--RRVPLAPDIDAAI-IARGTPGFSGADLAN--LVNEAALFAARGN 376

Query: 230 -----LIEFLESKKRANDGSEAKEAEERAVQAE 257
                ++EF ++K +   G+E +       Q E
Sbjct: 377 KRVVSMVEFEKAKDKIMMGAERRSMVMTEAQKE 409

Length = 644

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

 Score = 68.5 bits (168), Expect = 4e-13
 Identities = 78/265 (29%), Positives = 124/265 (46%), Gaps = 42/265 (15%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           FL+    + ++G    +G LL GPPGTGK+ L  A+A       + +  S+       +G
Sbjct: 73  FLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVG 132

Query: 70  NNDLRHIL-IATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
            + +R +   A +N   I+ +++ID        + R R A    L  G ++++Q   TL+
Sbjct: 133 ASRVRDLFEQAKKNAPCIIFIDEIDA-------VGRQRGAG---LGGGNDEREQ---TLN 179

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG-FKMLASN 186
            LL  +DG  ++ G   I+I  TN  + LDPALLRPGR D  + +      G  ++L  +
Sbjct: 180 QLLVEMDGFGTNTG--VIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVH 237

Query: 187 YLGIAEHPLFVEIEKLIATAKVTP----ADVAEQLMRNEAPEFALSGLIEFLESKKRAND 242
                   L  +++ L A A+ TP    AD+A  L  NEA   A           K    
Sbjct: 238 AKNK---KLAPDVD-LKAVARRTPGFSGADLANLL--NEAALLA-------ARKNKTEIT 284

Query: 243 GSEAKEAEERAVQ-AEKKVLEISEE 266
            ++ +EA +R +   EKK   ISE+
Sbjct: 285 MNDIEEAIDRVIAGPEKKSRVISEK 309

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

 Score = 67.2 bits (164), Expect = 1e-12
 Identities = 51/172 (29%), Positives = 81/172 (47%), Gaps = 26/172 (15%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
           + K+ + + +E  L+R E +R++G    +G LLYGPPGTGK+ L  A+A   +     ++
Sbjct: 249 EAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVK 308

Query: 64  LSNLLG------NNDLRHIL--IATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAG 115
            S LL         ++R +         SI+ +++I       D L+  R  + D     
Sbjct: 309 GSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEI-------DSLASGRGPSEDGSGRR 361

Query: 116 YEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMD 167
              Q         LL  +DG+     +  ++I  TN  + LDPALLRPGR D
Sbjct: 362 VVGQ---------LLTELDGI--EKAEGVLVIAATNRPDDLDPALLRPGRFD 402

Length = 494

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

 Score = 65.5 bits (160), Expect = 5e-12
 Identities = 53/166 (31%), Positives = 78/166 (46%), Gaps = 23/166 (13%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           FL++ E +  VG    +G LL GPPGTGK+ L  A+A   +   + +  S        +G
Sbjct: 201 FLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVG 260

Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +    +  S  I+ +++ID        + R R A     I G     +   TL+
Sbjct: 261 AARVRDLFKKAKENSPCIVFIDEIDA-------VGRQRGAG----IGG--GNDEREQTLN 307

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMS 173
            LL  +DG   + G   I+I  TN  + LD ALLRPGR D  I +S
Sbjct: 308 QLLTEMDGFKGNKG--VIVIAATNRVDILDAALLRPGRFDRQITVS 351

Length = 638

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

 Score = 64.0 bits (156), Expect = 1e-11
 Identities = 60/171 (35%), Positives = 87/171 (50%), Gaps = 25/171 (14%)

Query: 9   IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL 68
           I + +E  L   E Y  +G    +G +LYGPPGTGK+ L  A+AN        +  S L+
Sbjct: 195 IKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELI 254

Query: 69  ------GNNDLRHIL-IATENK-SILVVEDIDCC-IELQDRLSRARAANPDFLIAGYEQQ 119
                 G   +R +  +A EN  SI+ +++ID    +  D  S            G E++
Sbjct: 255 QKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATS------------GGEKE 302

Query: 120 KQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            Q   T+  LLN +DG + S GD ++I+  TN  E LDPAL+RPGR+D  I
Sbjct: 303 IQR--TMLELLNQLDG-FDSRGDVKVIM-ATNRIESLDPALIRPGRIDRKI 349

Length = 438

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

 Score = 62.1 bits (151), Expect = 4e-11
 Identities = 58/176 (32%), Positives = 85/176 (48%), Gaps = 24/176 (13%)

Query: 4   DMKKM-IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL 62
           D++K  I + +E  L   E Y ++G    RG LLYGPPGTGK+ L  A+A++       +
Sbjct: 151 DIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRV 210

Query: 63  ELSNLL------GNNDLRHIL-IATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIA 114
             S  +      G   +R +  +A EN  SI+ ++++D          R  A       A
Sbjct: 211 VGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIAT-----KRFDAQTG----A 261

Query: 115 GYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
             E Q+     L  LLN +DG   +   +  +I  TN  + LDPALLRPGR+D  I
Sbjct: 262 DREVQR----ILLELLNQMDGFDQTTNVK--VIMATNRADTLDPALLRPGRLDRKI 311

Length = 398

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

 Score = 62.2 bits (151), Expect = 5e-11
 Identities = 56/176 (31%), Positives = 83/176 (47%), Gaps = 32/176 (18%)

Query: 6   KKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE-- 63
           K+ I + +E  ++  E +  +G    +G LLYGPPGTGK+ L  A+AN        +   
Sbjct: 187 KEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGP 246

Query: 64  --LSNLLGNND--LRHILI-ATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYE 117
             +S   G ++  LR I   A EN  SI+ +++ID           A A   + +    E
Sbjct: 247 EIMSKYYGESEERLREIFKEAEENAPSIIFIDEID-----------AIAPKREEVTGEVE 295

Query: 118 QQKQYHITLSGLLNFIDGLWSSCGDER---IIIFTTNHKERLDPALLRPGRMDMHI 170
           ++      ++ LL  +DGL       R   I+I  TN  + LDPAL RPGR D  I
Sbjct: 296 KR-----VVAQLLTLMDGL-----KGRGRVIVIGATNRPDALDPALRRPGRFDREI 341

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

>gnl|CDD|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 = 54.8 bits (132), Expect = 2e-09
 Identities = 36/149 (24%), Positives = 55/149 (36%), Gaps = 23/149 (15%)

Query: 31  KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVED 90
            +  LLYGPPGTGK++L  A+AN L                     L A++    LVV +
Sbjct: 19  PKNLLLYGPPGTGKTTLARAIANELFRPGAPF------------LYLNASDLLEGLVVAE 66

Query: 91  IDCCIELQDRLSRARAANPDFL----IAGYEQQKQYHITLSGLLNFIDGL--WSSCGDER 144
           +     ++     A  A P  L    I    +  Q     + LL  ++ L       +  
Sbjct: 67  LFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQ-----NALLRVLETLNDLRIDRENV 121

Query: 145 IIIFTTNHKERLDPALLRPGRMDMHINMS 173
            +I  TN     D       R+D+ I + 
Sbjct: 122 RVIGATNRPLLGDLDRALYDRLDIRIVIP 150

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

 Score = 57.3 bits (139), Expect = 2e-09
 Identities = 53/172 (30%), Positives = 76/172 (44%), Gaps = 43/172 (25%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
           L+  E +  +G    +G LLYGPPGTGK+ L  A+AN        +  S L+      G 
Sbjct: 171 LKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGA 230

Query: 71  NDLRHIL-IATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
             +R +  +A E   SI+ +++ID                    I      K++    SG
Sbjct: 231 RLVRELFELAREKAPSIIFIDEIDA-------------------IGA----KRFDSGTSG 267

Query: 129 ----------LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
                     LLN +DG +   G+ + +I  TN  + LDPALLRPGR D  I
Sbjct: 268 DREVQRTMLELLNQLDG-FDPRGNVK-VIMATNRPDILDPALLRPGRFDRKI 317

Length = 406

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

 Score = 56.6 bits (137), Expect = 4e-09
 Identities = 75/267 (28%), Positives = 115/267 (43%), Gaps = 46/267 (17%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------G 69
           FL+  + Y+ +G    +G LL GPPGTGK+ L  A+A       + +  S+ +      G
Sbjct: 168 FLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVG 227

Query: 70  NNDLRHILIATENK---SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITL 126
            + +R  L     K    I+ +++ID        + R R A       G ++++Q   TL
Sbjct: 228 ASRVRD-LFEQAKKNAPCIIFIDEID-------AVGRQRGAGL---GGGNDEREQ---TL 273

Query: 127 SGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG----FKM 182
           + LL  +DG      +  I+I  TN  + LDPALLRPGR D  I +      G     K+
Sbjct: 274 NQLLVEMDG--FGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKV 331

Query: 183 LASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMR--NEAPEFALSGLIEFLESKKRA 240
            A N          V+++K+   A+ TP      L    NEA   A           K+ 
Sbjct: 332 HAKN----KPLAEDVDLKKI---ARGTPGFSGADLANLLNEAALLA-------ARRNKKE 377

Query: 241 NDGSEAKEAEERAVQ-AEKKVLEISEE 266
               + +EA +R +   E+K   ISE 
Sbjct: 378 ITMRDIEEAIDRVIAGPERKSRVISEA 404

Length = 596

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

 Score = 56.0 bits (135), Expect = 4e-09
 Identities = 54/162 (33%), Positives = 77/162 (47%), Gaps = 23/162 (14%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
           L+  E +  VG    +G LLYGPPGTGK+ L  A+A+        +  S L+      G 
Sbjct: 142 LKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGA 201

Query: 71  NDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
             +R I    + K  SI+ +++ID           A AA         +++ Q   TL  
Sbjct: 202 RLVREIFELAKEKAPSIIFIDEID-----------AIAAKRTDSGTSGDREVQR--TLMQ 248

Query: 129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
           LL  +DG +   G+ ++I   TN  + LDPALLRPGR D  I
Sbjct: 249 LLAELDG-FDPRGNVKVIA-ATNRPDILDPALLRPGRFDRII 288

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

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

 Score = 53.1 bits (127), Expect = 8e-09
 Identities = 39/150 (26%), Positives = 55/150 (36%), Gaps = 15/150 (10%)

Query: 31  KRGYLLYGPPGTGKSSLIAAMANYLKFDVY-----DLELSNLLGNNDLRHILIATENKSI 85
               L+ GPPG+GK++L  A+A  L          D E       + L  I++  +  S 
Sbjct: 2   GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61

Query: 86  LVVEDIDCCIELQDRLSRARAANPDFLI---AGYEQQKQYHITLSGLLNFIDGLWSSCGD 142
                +         L+ AR   PD LI          +    L  L      L      
Sbjct: 62  SGELRLR------LALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEK 115

Query: 143 ERIIIFTTNHKERLDPALLRPGRMDMHINM 172
              +I TTN ++ L PALLR  R D  I +
Sbjct: 116 NLTVILTTNDEKDLGPALLRR-RFDRRIVL 144

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|200312 TIGR03689, pup_AAA, proteasome ATPase

 Score = 55.1 bits (133), Expect = 1e-08
 Identities = 61/184 (33%), Positives = 84/184 (45%), Gaps = 39/184 (21%)

Query: 9   IMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIA-AMANYLKFDVYDL----- 62
           I D +E      E YR  G    +G LLYGPPG GK +LIA A+AN L   +        
Sbjct: 194 IRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGK-TLIAKAVANSLAARIGAEGGGKS 252

Query: 63  --------ELSNLLGNNDLRHI-LI-------ATENKSILVVEDIDCCIELQDRLSRARA 106
                   EL N       R I LI       A+E + ++V  D     E+ D L R R 
Sbjct: 253 YFLNIKGPELLNKYVGETERQIRLIFQRAREKASEGRPVIVFFD-----EM-DSLFRTRG 306

Query: 107 ANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRM 166
                  +G     +  + +  LL  IDG+ S   D  I+I  +N ++ +DPA+LRPGR+
Sbjct: 307 -------SGVSSDVETTV-VPQLLAEIDGVESL--DNVIVIGASNREDMIDPAILRPGRL 356

Query: 167 DMHI 170
           D+ I
Sbjct: 357 DVKI 360

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

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

 Score = 54.1 bits (130), Expect = 3e-08
 Identities = 48/175 (27%), Positives = 81/175 (46%), Gaps = 25/175 (14%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
           ++K+ + + +E  L+  E + ++G    +G LL+GPPGTGK+ L  A+A     +   + 
Sbjct: 460 EVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVR 519

Query: 64  ----LSNLLGNND--LRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAG 115
               LS  +G ++  +R I       +  I+  ++ID        ++ AR A        
Sbjct: 520 GPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDA-------IAPARGAR------- 565

Query: 116 YEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
                     ++ LL  +DG+        ++I  TN  + LDPALLRPGR D  I
Sbjct: 566 -FDTSVTDRIVNQLLTEMDGIQELSN--VVVIAATNRPDILDPALLRPGRFDRLI 617

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 18/40 (45%), Positives = 26/40 (65%), Gaps = 5/40 (12%)

Query: 28 KAWKRGY-----LLYGPPGTGKSSLIAAMANYLKFDVYDL 62
          ++W +G      LLYGPPG GK+SL  A+AN   ++V +L
Sbjct: 31 ESWLKGKPKKALLLYGPPGVGKTSLAHALANDYGWEVIEL 70

Length = 482

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

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 65/244 (26%), Positives = 96/244 (39%), Gaps = 41/244 (16%)

Query: 32  RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE---LSNLLGNNDLRHILIATE----NKS 84
           +G LL+GPPGTGK+ L  A+AN     +       LS  +G ++LR   +  E      S
Sbjct: 19  KGVLLHGPPGTGKTLLARALANEGAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPS 78

Query: 85  ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDER 144
           I+ +++ID         + A   + D       Q +     ++ LL  +DGL      + 
Sbjct: 79  IIFIDEID---------ALAPKRSSD-------QGEVERRVVAQLLALMDGL---KRGQV 119

Query: 145 IIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA 204
           I+I  TN  + LDPA  RPGR D  I ++    +G        L I    +F+       
Sbjct: 120 IVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRL----EILQIHTRLMFLGPPGTGK 175

Query: 205 T-AKVTPADVAEQL--MRNEAPEFALSGLIEFLESKKRANDGSEAKEAEERAVQAEKKVL 261
           T A  T       L  +  EA    L   I+          G      E+   +A KKVL
Sbjct: 176 TLAARTVGKSGADLGALAKEAALRELRRAIDL--------VGEYIGVTEDDFEEALKKVL 227

Query: 262 EISE 265
               
Sbjct: 228 PSRG 231

Length = 494

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

 Score = 40.5 bits (95), Expect = 4e-04
 Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 6/55 (10%)

Query: 2   DFDMKKMI-MDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL 55
           DF+ +  I    LE      EF+ R         +L GPPG GK+ L  A+ N L
Sbjct: 80  DFEFQPGIDKKALEDLASLVEFFER-----GENLVLLGPPGVGKTHLAIAIGNEL 129

Length = 254

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

 Score = 40.5 bits (96), Expect = 5e-04
 Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)

Query: 35 LLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN-NDLRHIL 77
          +L+GPPGTGK++L   +A           LS +     DLR ++
Sbjct: 40 ILWGPPGTGKTTLARIIAGATDAPFE--ALSAVTSGVKDLREVI 81

Length = 413

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

 Score = 40.0 bits (94), Expect = 6e-04
 Identities = 14/28 (50%), Positives = 17/28 (60%)

Query: 28  KAWKRGYLLYGPPGTGKSSLIAAMANYL 55
           K    G LL+G  GTGK+ L A +AN L
Sbjct: 111 KKENVGLLLWGSVGTGKTYLAACIANEL 138

Length = 268

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

 Score = 39.8 bits (94), Expect = 0.001
 Identities = 18/37 (48%), Positives = 25/37 (67%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 53
           L++ E +  VG    +G LLYGPPGTGK+ L  A+A+
Sbjct: 151 LKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH 187

Length = 389

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

 Score = 39.4 bits (93), Expect = 0.001
 Identities = 22/46 (47%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 125 TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
           TL  LL  +DG +   G+ +II   TN  + LDPA+LRPGR D  I
Sbjct: 254 TLMQLLAEMDG-FDPRGNVKIIA-ATNRIDILDPAILRPGRFDRII 297

Length = 389

>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed

 Score = 38.7 bits (91), Expect = 0.002
 Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 14/101 (13%)

Query: 5   MKKMIMDDLERFLQRKEFYRRVGKA----WKRGYLLYGPPGTGKSSLIAAMANYLK---- 56
           +  + +DD +R          +         +G  LYG  G GKS L+AA+AN L     
Sbjct: 126 LADIDLDDRDRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGV 185

Query: 57  ------FDVYDLELSNLLGNNDLRHILIATENKSILVVEDI 91
                 F  +  EL N + +  ++  + A +   +L+++DI
Sbjct: 186 SSTLLHFPEFIRELKNSISDGSVKEKIDAVKEAPVLMLDDI 226

Length = 306

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

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 9/63 (14%)

Query: 36  LYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL-GNNDLRHILIATEN------KSILVV 88
           L+GPPGTGK++L   +A           LS +  G  DLR I+           ++IL +
Sbjct: 53  LWGPPGTGKTTLARLIAGTTNAAFE--ALSAVTSGVKDLREIIEEARKNRLLGRRTILFL 110

Query: 89  EDI 91
           ++I
Sbjct: 111 DEI 113

Length = 436

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

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG 69
           +  +L+  E   R G    +  L YGPPGTGK+ +  A+AN  K  +  ++ + L+G
Sbjct: 136 IMEYLENPE---RFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIG 189

Length = 368

>gnl|CDD|213965 TIGR04352, HprK_rel_A, HprK-related kinase A

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 14/69 (20%)

Query: 32  RGYLLYGPPGTGKSSLIAAMANYLK--------FDVYDLELSNLLGNNDLRHILIATENK 83
           R  +L  PPG+GKS+L AA+A  L+        F + DLE   LL     R   I+ +N+
Sbjct: 109 RALILPAPPGSGKSTLCAALA--LRGWRLLSDEFALLDLEDGLLLPL--PR--PISLKNE 162

Query: 84  SILVVEDID 92
           SI ++    
Sbjct: 163 SIDIIRAFA 171

A number of protein families resemble HPr kinase (see TIGR00679) but do not belong to that system. They include this family, which appears instead to be the marker for a different type of gene neighborhood, in which one of the conserved neighboring proteins resembles (but is distinct from) PqqD. Length = 280

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

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 13/39 (33%), Positives = 17/39 (43%)

Query: 20 KEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFD 58
           +  RR         LL GP GTGK+SL+  +   L   
Sbjct: 13 LDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVA 51

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	266
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.98
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.98
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.98
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.97
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.97
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.97
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.97
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.97
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.97
CHL00195	489	ycf46 Ycf46; Provisional	99.97
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.97
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.97
CHL00206	2281	ycf2 Ycf2; Provisional	99.97
CHL00176	638	ftsH cell division protein; Validated	99.96
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.96
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.96
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.96
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.96
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.95
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.93
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.93
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.93
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.93
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.93
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.89
PF00004	132	AAA: ATPase family associated with various cellula	99.85
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.84
CHL00181	287	cbbX CbbX; Provisional	99.83
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.82
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.81
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.8
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.8
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.78
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.78
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.78
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.78
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.78
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.78
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.74
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.69
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.69
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.69
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.69
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.68
PRK04195	482	replication factor C large subunit; Provisional	99.68
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.68
PRK06893	229	DNA replication initiation factor; Validated	99.67
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.67
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.66
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.65
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.65
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.65
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.65
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.64
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.64
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.64
PRK13342	413	recombination factor protein RarA; Reviewed	99.63
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.63
PLN03025	319	replication factor C subunit; Provisional	99.63
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.63
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.63
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.63
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.62
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.61
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.61
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.61
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.61
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.6
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.6
PRK10865	857	protein disaggregation chaperone; Provisional	99.6
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.6
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.6
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.59
KOG2028	554	consensus ATPase related to the helicase subunit o	99.59
PRK08084	235	DNA replication initiation factor; Provisional	99.59
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.58
PRK08727	233	hypothetical protein; Validated	99.58
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.58
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.58
PHA02544	316	44 clamp loader, small subunit; Provisional	99.58
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.58
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.57
CHL00095	821	clpC Clp protease ATP binding subunit	99.57
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.57
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.56
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.56
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.56
PRK05642	234	DNA replication initiation factor; Validated	99.56
PRK12422	445	chromosomal replication initiation protein; Provis	99.56
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.55
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.55
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.55
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.55
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.54
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.53
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.53
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.53
PRK06620	214	hypothetical protein; Validated	99.53
PRK12402	337	replication factor C small subunit 2; Reviewed	99.52
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.52
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.52
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.52
PRK13341	725	recombination factor protein RarA/unknown domain f	99.52
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.52
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.52
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.51
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.5
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.5
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.5
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.5
COG0714	329	MoxR-like ATPases [General function prediction onl	99.49
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.49
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.48
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.48
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.48
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.47
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.46
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.45
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.45
PRK10865	857	protein disaggregation chaperone; Provisional	99.45
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.45
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.45
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.44
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.44
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.44
PRK09087	226	hypothetical protein; Validated	99.44
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.44
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.42
PHA02244	383	ATPase-like protein	99.42
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.42
CHL00095	821	clpC Clp protease ATP binding subunit	99.41
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.38
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.37
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.36
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.36
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.36
PF07726	131	AAA_3: ATPase family associated with various cellu	99.36
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.36
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.35
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.34
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.34
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.32
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.31
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.31
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.28
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.28
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.26
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.25
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.25
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.25
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.24
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.24
PRK04132	846	replication factor C small subunit; Provisional	99.24
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.24
smart00382	148	AAA ATPases associated with a variety of cellular	99.23
PRK13531	498	regulatory ATPase RavA; Provisional	99.21
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.21
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	99.2
PRK08116	268	hypothetical protein; Validated	99.2
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.19
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.19
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.18
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	99.15
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	99.14
smart00350	509	MCM minichromosome maintenance proteins.	99.13
PRK08181	269	transposase; Validated	99.12
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.11
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.11
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.1
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	99.1
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.09
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.09
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	99.08
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.07
PRK08699	325	DNA polymerase III subunit delta'; Validated	99.07
PRK12377	248	putative replication protein; Provisional	99.06
PRK06526	254	transposase; Provisional	99.05
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	99.04
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.02
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	99.01
PRK06835	329	DNA replication protein DnaC; Validated	99.01
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.0
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.0
PRK08939	306	primosomal protein DnaI; Reviewed	99.0
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.99
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.98
PRK07952	244	DNA replication protein DnaC; Validated	98.98
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.97
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.96
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.95
COG2204	464	AtoC Response regulator containing CheY-like recei	98.93
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.92
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.92
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	98.91
PRK09862	506	putative ATP-dependent protease; Provisional	98.91
KOG1514	767	consensus Origin recognition complex, subunit 1, a	98.91
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	98.89
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	98.89
PF13173	128	AAA_14: AAA domain	98.89
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.88
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.86
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.86
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.86
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.85
PRK09183	259	transposase/IS protein; Provisional	98.85
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	98.85
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	98.85
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.83
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.82
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.81
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.8
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.79
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.79
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	98.78
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.78
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.76
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.74
PRK06921	266	hypothetical protein; Provisional	98.73
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.73
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.72
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.71
COG1485	367	Predicted ATPase [General function prediction only	98.71
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.66
PF05729	166	NACHT: NACHT domain	98.65
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.65
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.62
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.62
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.57
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.55
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	98.54
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.54
PRK15115	444	response regulator GlrR; Provisional	98.51
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.51
PHA02624	647	large T antigen; Provisional	98.51
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.46
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.46
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	98.41
PHA00729	226	NTP-binding motif containing protein	98.4
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.39
PHA02774	613	E1; Provisional	98.38
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.37
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	98.36
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	98.36
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	98.33
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	98.29
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	98.26
PRK00131	175	aroK shikimate kinase; Reviewed	98.24
PF14516	331	AAA_35: AAA-like domain	98.22
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	98.21
TIGR02237	209	recomb_radB DNA repair and recombination protein R	98.21
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.17
PRK07261	171	topology modulation protein; Provisional	98.17
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.16
COG4619	223	ABC-type uncharacterized transport system, ATPase	98.15
PRK08118	167	topology modulation protein; Reviewed	98.15
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.14
PRK00771	437	signal recognition particle protein Srp54; Provisi	98.12
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	98.12
PRK06581	263	DNA polymerase III subunit delta'; Validated	98.11
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	98.1
PRK13765	637	ATP-dependent protease Lon; Provisional	98.1
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	98.09
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	98.06
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.06
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	98.05
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	98.05
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	98.04
PRK13947	171	shikimate kinase; Provisional	98.04
KOG2383	467	consensus Predicted ATPase [General function predi	98.04
PRK03839	180	putative kinase; Provisional	98.03
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	98.03
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.03
PRK00625	173	shikimate kinase; Provisional	98.02
PRK05973	237	replicative DNA helicase; Provisional	98.01
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.0
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.99
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.99
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.99
PRK13949	169	shikimate kinase; Provisional	97.98
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.97
PRK06067	234	flagellar accessory protein FlaH; Validated	97.97
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	97.96
PLN03210	1153	Resistant to P. syringae 6; Provisional	97.96
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.96
PRK14532	188	adenylate kinase; Provisional	97.95
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	97.95
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.94
PF13479	213	AAA_24: AAA domain	97.94
COG1241	682	MCM2 Predicted ATPase involved in replication cont	97.94
PRK09376	416	rho transcription termination factor Rho; Provisio	97.93
PRK13948	182	shikimate kinase; Provisional	97.92
PRK14531	183	adenylate kinase; Provisional	97.92
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.91
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.91
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.91
PRK06217	183	hypothetical protein; Validated	97.91
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	97.9
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.9
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.9
PTZ00202	550	tuzin; Provisional	97.88
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.87
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.86
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.86
PRK11823	446	DNA repair protein RadA; Provisional	97.86
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.85
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.84
PRK14530	215	adenylate kinase; Provisional	97.84
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.84
PRK12608	380	transcription termination factor Rho; Provisional	97.83
PRK04841	903	transcriptional regulator MalT; Provisional	97.83
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	97.82
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.82
cd01128	249	rho_factor Transcription termination factor rho is	97.81
PRK05057	172	aroK shikimate kinase I; Reviewed	97.81
PRK06696	223	uridine kinase; Validated	97.8
PRK06762	166	hypothetical protein; Provisional	97.79
PRK13946	184	shikimate kinase; Provisional	97.79
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	97.78
PF13245	76	AAA_19: Part of AAA domain	97.78
PRK03731	171	aroL shikimate kinase II; Reviewed	97.77
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.77
PRK06547	172	hypothetical protein; Provisional	97.77
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	97.77
PLN02200	234	adenylate kinase family protein	97.76
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.75
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.75
PRK14528	186	adenylate kinase; Provisional	97.75
PTZ00088	229	adenylate kinase 1; Provisional	97.74
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.74
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	97.73
PRK02496	184	adk adenylate kinase; Provisional	97.72
TIGR00767	415	rho transcription termination factor Rho. Members	97.71
PRK00279	215	adk adenylate kinase; Reviewed	97.69
PRK14737	186	gmk guanylate kinase; Provisional	97.69
PRK14527	191	adenylate kinase; Provisional	97.69
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.69
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.68
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.68
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.68
PRK13695	174	putative NTPase; Provisional	97.67
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.67
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	97.66
PRK04040	188	adenylate kinase; Provisional	97.66
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	97.66
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.66
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	97.65
COG4178	604	ABC-type uncharacterized transport system, permeas	97.64
PLN02674	244	adenylate kinase	97.64
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.64
PRK04296	190	thymidine kinase; Provisional	97.62
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.61
PRK09354	349	recA recombinase A; Provisional	97.61
PRK10867	433	signal recognition particle protein; Provisional	97.61
PRK01184	184	hypothetical protein; Provisional	97.61
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	97.6
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	97.6
PLN02199	303	shikimate kinase	97.59
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.58
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	97.57
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.56
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.55
PRK04182	180	cytidylate kinase; Provisional	97.55
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.54
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.54
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.53
PRK14526	211	adenylate kinase; Provisional	97.53
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	97.52
PHA02530	300	pseT polynucleotide kinase; Provisional	97.5
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	97.5
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	97.5
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.5
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	97.5
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	97.5
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.5
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	97.49
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	97.49
PRK08233	182	hypothetical protein; Provisional	97.48
TIGR00959	428	ffh signal recognition particle protein. This mode	97.48
PRK15455	644	PrkA family serine protein kinase; Provisional	97.48
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.48
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.47
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.47
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	97.47
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	97.46
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	97.46
TIGR02236	310	recomb_radA DNA repair and recombination protein R	97.45
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	97.44
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	97.44
PRK00409	782	recombination and DNA strand exchange inhibitor pr	97.44
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	97.44
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.42
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.42
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	97.41
PLN02459	261	probable adenylate kinase	97.41
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.4
PRK12339	197	2-phosphoglycerate kinase; Provisional	97.4
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	97.39
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.38
PRK05541	176	adenylylsulfate kinase; Provisional	97.38
PRK04220	301	2-phosphoglycerate kinase; Provisional	97.38
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.37
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.37
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.37
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	97.37
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.36
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.36
PRK14529	223	adenylate kinase; Provisional	97.36
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	97.34
PRK04328	249	hypothetical protein; Provisional	97.34
PRK00889	175	adenylylsulfate kinase; Provisional	97.33
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.33
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.33
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.32
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	97.32
PTZ00494	664	tuzin-like protein; Provisional	97.31
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.31
TIGR00064	272	ftsY signal recognition particle-docking protein F	97.31
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	97.31
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.3
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	97.3
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	97.29
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	97.29
PRK12338	319	hypothetical protein; Provisional	97.28
PRK10416	318	signal recognition particle-docking protein FtsY;	97.28
PRK13808	333	adenylate kinase; Provisional	97.28
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.28
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	97.28
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.28
PRK05480	209	uridine/cytidine kinase; Provisional	97.28
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.27
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	97.27
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.26
PTZ00035	337	Rad51 protein; Provisional	97.26
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	97.24
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	97.23
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.22
PLN02165	334	adenylate isopentenyltransferase	97.22
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	97.21
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	97.21
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	97.21
PRK14730	195	coaE dephospho-CoA kinase; Provisional	97.21
PRK12337	475	2-phosphoglycerate kinase; Provisional	97.21
PRK09825	176	idnK D-gluconate kinase; Provisional	97.2
PRK08356	195	hypothetical protein; Provisional	97.2
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	97.2
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	97.2
COG4133	209	CcmA ABC-type transport system involved in cytochr	97.19
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	97.19
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	97.19
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	97.18
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.17
PRK14021	542	bifunctional shikimate kinase/3-dehydroquinate syn	97.17
PRK14974	336	cell division protein FtsY; Provisional	97.17
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	97.17
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.17
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	97.16
KOG0481	729	consensus DNA replication licensing factor, MCM5 c	97.16
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	97.16
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	97.16
cd03115	173	SRP The signal recognition particle (SRP) mediates	97.16
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	97.16
TIGR00235	207	udk uridine kinase. Model contains a number of lon	97.15
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	97.15
PRK00300	205	gmk guanylate kinase; Provisional	97.14
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	97.14
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	97.13
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	97.13
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.13
PRK06761	282	hypothetical protein; Provisional	97.12
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.12
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	97.11
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	97.11
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	97.11
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	97.11
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	97.11
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	97.1
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	97.1
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	97.1
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	97.1
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	97.09
PRK11545	163	gntK gluconate kinase 1; Provisional	97.09
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	97.09

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

Probab=100.00  E-value=4.4e-44  Score=305.41  Aligned_cols=223  Identities=26%  Similarity=0.342  Sum_probs=191.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      ++++++|.+.++.+|.+|++|..+|+.||+|+|||||||||||.+|+|+|+..++.|+.+..+.+.      +..-++++
T Consensus       157 ~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSElVqKYiGEGaRlVRel  236 (406)
T COG1222         157 DEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVREL  236 (406)
T ss_pred             HHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceEEEeccHHHHHHHhccchHHHHHH
Confidence            468899999999999999999999999999999999999999999999999999999999999876      34557788


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |.-+.  .||||||||||+++..+.+...+.             +.+.++++-+||+.|||+...  .++-||++||+++
T Consensus       237 F~lArekaPsIIFiDEIDAIg~kR~d~~t~g-------------DrEVQRTmleLL~qlDGFD~~--~nvKVI~ATNR~D  301 (406)
T COG1222         237 FELAREKAPSIIFIDEIDAIGAKRFDSGTSG-------------DREVQRTMLELLNQLDGFDPR--GNVKVIMATNRPD  301 (406)
T ss_pred             HHHHhhcCCeEEEEechhhhhcccccCCCCc-------------hHHHHHHHHHHHHhccCCCCC--CCeEEEEecCCcc
Confidence            87664  699999999999988665544332             478899999999999999765  6799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH-------cCCCHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM-------RNEAPEFA  226 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~-------~~~~~~~~  226 (266)
                      .|||||+|||||+..|+||+|+.+.|.+||+.|..+....-..+++.++.. .++|+++|..+|.       +.+.....
T Consensus       302 ~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt  381 (406)
T COG1222         302 ILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVT  381 (406)
T ss_pred             ccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeec
Confidence            999999999999999999999999999999999999877767777777775 5699999999983       34455556


Q ss_pred             HHHHHHHHHhhhhh
Q 024550          227 LSGLIEFLESKKRA  240 (266)
Q Consensus       227 ~~~~~~~~~~~~~~  240 (266)
                      .+++.+++++....
T Consensus       382 ~~DF~~Av~KV~~~  395 (406)
T COG1222         382 MEDFLKAVEKVVKK  395 (406)
T ss_pred             HHHHHHHHHHHHhc
Confidence            66666666665543

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

Probab=100.00  E-value=8.3e-43  Score=306.41  Aligned_cols=234  Identities=65%  Similarity=1.086  Sum_probs=212.0

Q ss_pred             CChHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHc
Q 024550            1 MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIAT   80 (266)
Q Consensus         1 l~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~   80 (266)
                      ||++.|++|++++..|+..++||.+.|.++.+|+|||||||||||+++.|+|+.++..++.++.+....+..++.++...
T Consensus       205 Md~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n~dLr~LL~~t  284 (457)
T KOG0743|consen  205 MDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLDSDLRHLLLAT  284 (457)
T ss_pred             cChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCcHHHHHHHHhC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999888899999999


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                      +..+||+|+|||+-+..+.+........         +......++++|||.+||+++.++...|||+|||+.+.|||||
T Consensus       285 ~~kSIivIEDIDcs~~l~~~~~~~~~~~---------~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPAL  355 (457)
T KOG0743|consen  285 PNKSILLIEDIDCSFDLRERRKKKKENF---------EGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPAL  355 (457)
T ss_pred             CCCcEEEEeecccccccccccccccccc---------cCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhh
Confidence            9999999999998876444433221110         0023457999999999999999999999999999999999999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCC-CCcHHHHHHHhhcCCCCHHHHHHHHHcCC-CHHHHHHHHHHHHHhhh
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAE-HPLFVEIEKLIATAKVTPADVAEQLMRNE-APEFALSGLIEFLESKK  238 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~-~~~~~~~~~l~~~~~~s~~~i~~~l~~~~-~~~~~~~~~~~~~~~~~  238 (266)
                      +||||++++|+|+.++.++.+.++..|++... ..+..+++.+......|||++++.++.+. +++.+++.+++++++.+
T Consensus       356 lRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h~L~~eie~l~~~~~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~~~~  435 (457)
T KOG0743|consen  356 LRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDHRLFDEIERLIEETEVTPAQVAEELMKNKNDADVALKGLVEALESKK  435 (457)
T ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCcchhHHHHHHhhcCccCHHHHHHHHhhccccHHHHHHHHHHHHHhhh
Confidence            99999999999999999999999999999975 88899999999999999999999999877 89999999999999998


Q ss_pred             hhccc
Q 024550          239 RANDG  243 (266)
Q Consensus       239 ~~~~~  243 (266)
                      ....+
T Consensus       436 ~~~~~  440 (457)
T KOG0743|consen  436 EKRNK  440 (457)
T ss_pred             hhhcc
Confidence            76433

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

Probab=100.00  E-value=1.7e-38  Score=288.80  Aligned_cols=198  Identities=26%  Similarity=0.364  Sum_probs=177.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++|.++++.+..++.++..|.++|+.+|+|||||||||||||++|+++|++.+.+|+.+....+.      ++..++++
T Consensus       440 E~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~sk~vGeSEr~ir~i  519 (693)
T KOG0730|consen  440 EELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFSKYVGESERAIREV  519 (693)
T ss_pred             HHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHHHHhcCchHHHHHHH
Confidence            678999999999999999999999999999999999999999999999999999999999988776      46779999


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |.++.  .|||+|+||||.+...|+..+                .+...+++++||+.|||+-..  .+++|||+||+|+
T Consensus       520 F~kAR~~aP~IiFfDEiDsi~~~R~g~~----------------~~v~~RVlsqLLtEmDG~e~~--k~V~ViAATNRpd  581 (693)
T KOG0730|consen  520 FRKARQVAPCIIFFDEIDALAGSRGGSS----------------SGVTDRVLSQLLTEMDGLEAL--KNVLVIAATNRPD  581 (693)
T ss_pred             HHHHhhcCCeEEehhhHHhHhhccCCCc----------------cchHHHHHHHHHHHccccccc--CcEEEEeccCChh
Confidence            99886  489999999999988554221                144578999999999998654  6799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .||+||+|||||+..|++|+||.+.|.+|++.++.+.......++..++.. .+||++||.++|.
T Consensus       582 ~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq  646 (693)
T KOG0730|consen  582 MIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQ  646 (693)
T ss_pred             hcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHH
Confidence            999999999999999999999999999999999999877777788888875 5699999999984

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

Probab=100.00  E-value=5.4e-38  Score=278.88  Aligned_cols=195  Identities=27%  Similarity=0.380  Sum_probs=169.4

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~   77 (266)
                      |.|+++. .+++||+.|..|.++|=..|+||||+||||||||.|||++|.+.++||+..+.+.+.      +...++++|
T Consensus       311 EAK~ELe-EiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdEm~VGvGArRVRdLF  389 (752)
T KOG0734|consen  311 EAKQELE-EIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMFVGVGARRVRDLF  389 (752)
T ss_pred             HHHHHHH-HHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhhhhhcccHHHHHHHH
Confidence            4555554 489999999999999999999999999999999999999999999999999998874      467889999


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..++  .||||||||||.+.+.+...+.                -....++++||..||++..+  .++|||++||.|+.
T Consensus       390 ~aAk~~APcIIFIDEiDavG~kR~~~~~----------------~y~kqTlNQLLvEmDGF~qN--eGiIvigATNfpe~  451 (752)
T KOG0734|consen  390 AAAKARAPCIIFIDEIDAVGGKRNPSDQ----------------HYAKQTLNQLLVEMDGFKQN--EGIIVIGATNFPEA  451 (752)
T ss_pred             HHHHhcCCeEEEEechhhhcccCCccHH----------------HHHHHHHHHHHHHhcCcCcC--CceEEEeccCChhh
Confidence            8775  5999999999999875543332                24578999999999999776  57999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      ||+||.|||||+++|.+|.||...|.+|+..|+.+....-..+..-++.. .+||++|++|++
T Consensus       452 LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlV  514 (752)
T KOG0734|consen  452 LDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLV  514 (752)
T ss_pred             hhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHH
Confidence            99999999999999999999999999999999988755545555556664 679999999988

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

Probab=100.00  E-value=5.4e-37  Score=276.14  Aligned_cols=197  Identities=22%  Similarity=0.356  Sum_probs=172.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      ++++.++..+++.++++++.|..+|+..|.|||||||||||||.+|+|+|++.|.+|+.+....+.      ++..++.+
T Consensus       517 ~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPELlNkYVGESErAVR~v  596 (802)
T KOG0733|consen  517 EEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPELLNKYVGESERAVRQV  596 (802)
T ss_pred             HHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHHHHHHHhhhHHHHHHHH
Confidence            468899999999999999999999999999999999999999999999999999999999988765      35678899


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|||||+||+|.|++.++....                ....+++|+||..|||+..+  .++.||++||+|+
T Consensus       597 FqRAR~saPCVIFFDEiDaL~p~R~~~~s----------------~~s~RvvNqLLtElDGl~~R--~gV~viaATNRPD  658 (802)
T KOG0733|consen  597 FQRARASAPCVIFFDEIDALVPRRSDEGS----------------SVSSRVVNQLLTELDGLEER--RGVYVIAATNRPD  658 (802)
T ss_pred             HHHhhcCCCeEEEecchhhcCcccCCCCc----------------hhHHHHHHHHHHHhcccccc--cceEEEeecCCCc
Confidence            98764  6999999999999987765442                34478999999999999776  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH--HHHHHHhhc---CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF--VEIEKLIAT---AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~--~~~~~l~~~---~~~s~~~i~~~l  217 (266)
                      .+|||++|||||+..++++.|+.++|..|++.+.+..+.++.  .+++.++..   .+||++|++.++
T Consensus       659 iIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLv  726 (802)
T KOG0733|consen  659 IIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALV  726 (802)
T ss_pred             ccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHH
Confidence            999999999999999999999999999999999986544443  345566654   579999999887

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

Probab=100.00  E-value=1.1e-35  Score=267.67  Aligned_cols=206  Identities=23%  Similarity=0.313  Sum_probs=172.7

Q ss_pred             HHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHHHH
Q 024550            6 KKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHILIA   79 (266)
Q Consensus         6 ~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~~~   79 (266)
                      ..++.+. ..++.+++.|..+|+.||+|+|||||||||||+||+++|+++++||+.+++..+.      ++..++++|..
T Consensus       199 ~~el~~l-i~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApeivSGvSGESEkkiRelF~~  277 (802)
T KOG0733|consen  199 LAELCEL-IIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVSGVSGESEKKIRELFDQ  277 (802)
T ss_pred             HHHHHHH-HHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchhhhcccCcccHHHHHHHHHH
Confidence            3444444 4458999999999999999999999999999999999999999999999988776      36789999999


Q ss_pred             cc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC--CCceEEEEecCCCCC
Q 024550           80 TE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC--GDERIIIFTTNHKER  155 (266)
Q Consensus        80 ~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~--~~~~ivi~ttn~~~~  155 (266)
                      +.  .|||+||||||.+.+.+.....                .-..+++.+||..||++....  +.+|+||+|||+|+.
T Consensus       278 A~~~aPcivFiDeIDAI~pkRe~aqr----------------eMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDs  341 (802)
T KOG0733|consen  278 AKSNAPCIVFIDEIDAITPKREEAQR----------------EMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDS  341 (802)
T ss_pred             HhccCCeEEEeecccccccchhhHHH----------------HHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcc
Confidence            86  4999999999999987766443                233679999999999876553  467999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHcCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMRNEAPEFALSGL  230 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~~~~~~~~~~~~  230 (266)
                      ||++|.|+|||+..|.+..|+..+|.+|++.+.........-++..++.. .+|-++|+..++  ++....+++++
T Consensus       342 lDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~--~~Aa~vAikR~  415 (802)
T KOG0733|consen  342 LDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALC--REAAFVAIKRI  415 (802)
T ss_pred             cCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHH--HHHHHHHHHHH
Confidence            99999999999999999999999999999999987766666667777663 569999998887  22344444443

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

Probab=100.00  E-value=3.7e-35  Score=240.43  Aligned_cols=200  Identities=30%  Similarity=0.442  Sum_probs=174.8

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~   77 (266)
                      -+|+++.+.+..+|.+.++|.+.|+.||+|+|+|||||||||+|++++|+.....|+.+..+.+.      ++..+++.|
T Consensus       162 ~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~firvvgsefvqkylgegprmvrdvf  241 (408)
T KOG0727|consen  162 VQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEGPRMVRDVF  241 (408)
T ss_pred             hhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHHHHHHHhccCcHHHHHHH
Confidence            37899999999999999999999999999999999999999999999999999999999998876      456678888


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      .-++  .|+|+||||+|.+...  +++....           .+.+.+.++-+||+.|+++...  .++-+|++||+.+.
T Consensus       242 rlakenapsiifideidaiatk--rfdaqtg-----------adrevqril~ellnqmdgfdq~--~nvkvimatnradt  306 (408)
T KOG0727|consen  242 RLAKENAPSIIFIDEIDAIATK--RFDAQTG-----------ADREVQRILIELLNQMDGFDQT--TNVKVIMATNRADT  306 (408)
T ss_pred             HHHhccCCcEEEeehhhhHhhh--hcccccc-----------ccHHHHHHHHHHHHhccCcCcc--cceEEEEecCcccc
Confidence            6664  5899999999999763  3333322           2467788999999999999765  67999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      +||+|+||||++..|+||.|+..+++-+|..+.++.......+++.++.. ...|+++|..+|.
T Consensus       307 ldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicq  370 (408)
T KOG0727|consen  307 LDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQ  370 (408)
T ss_pred             cCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHH
Confidence            99999999999999999999999999999999888877777788887776 4599999998873

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

Probab=100.00  E-value=5.1e-35  Score=273.06  Aligned_cols=218  Identities=29%  Similarity=0.396  Sum_probs=180.4

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      ++.|++|++ ++.||+.|+.|.++|...|+|+||+||||||||.||+|+|.+.|+||+.++.+++.      ..+.++++
T Consensus       317 deAK~El~E-~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE~~~g~~asrvr~l  395 (774)
T KOG0731|consen  317 DEAKEELME-FVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEMFVGVGASRVRDL  395 (774)
T ss_pred             HHHHHHHHH-HHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHHHHhcccchHHHHHH
Confidence            467788777 68999999999999999999999999999999999999999999999999999886      46778999


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..++  .|||+||||||.+...+...            .....+.+...++++||..||++...  .++||+++||+++
T Consensus       396 f~~ar~~aP~iifideida~~~~r~G~------------~~~~~~~e~e~tlnQll~emDgf~~~--~~vi~~a~tnr~d  461 (774)
T KOG0731|consen  396 FPLARKNAPSIIFIDEIDAVGRKRGGK------------GTGGGQDEREQTLNQLLVEMDGFETS--KGVIVLAATNRPD  461 (774)
T ss_pred             HHHhhccCCeEEEeccccccccccccc------------ccCCCChHHHHHHHHHHHHhcCCcCC--CcEEEEeccCCcc
Confidence            98876  49999999999997644310            01122466688999999999999665  6799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCC-cHHHHHHHhh-cCCCCHHHHHHHHH-------cCCCHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHP-LFVEIEKLIA-TAKVTPADVAEQLM-------RNEAPEF  225 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~-~~~~~~~l~~-~~~~s~~~i~~~l~-------~~~~~~~  225 (266)
                      .||+||+|||||+..|.++.|+...|..|+..++...... ...++..++. ..+|+++||++++.       ++.....
T Consensus       462 ~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r~~~~~i  541 (774)
T KOG0731|consen  462 ILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCNEAALLAARKGLREI  541 (774)
T ss_pred             ccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHHhccCcc
Confidence            9999999999999999999999999999999999877654 3445555555 46799999999872       2334444


Q ss_pred             HHHHHHHHHH
Q 024550          226 ALSGLIEFLE  235 (266)
Q Consensus       226 ~~~~~~~~~~  235 (266)
                      ...++..+++
T Consensus       542 ~~~~~~~a~~  551 (774)
T KOG0731|consen  542 GTKDLEYAIE  551 (774)
T ss_pred             chhhHHHHHH
Confidence            5556666666

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

Probab=100.00  E-value=6.5e-34  Score=232.85  Aligned_cols=199  Identities=26%  Similarity=0.365  Sum_probs=169.4

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~   77 (266)
                      .+.++|.+-+..+.++|++|..+|+..|+|+|||||||||||.+++++|....+.|+.++.+.+.      +...++++|
T Consensus       154 ~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht~c~firvsgselvqk~igegsrmvrelf  233 (404)
T KOG0728|consen  154 KQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKYIGEGSRMVRELF  233 (404)
T ss_pred             HHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhcceEEEEechHHHHHHHhhhhHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999999998876      234567777


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..+.  .|+|+|+||||++...+.+.+..             .+.+.+.+.-+|||.++++-.+  .++-+|++||+.+-
T Consensus       234 vmarehapsiifmdeidsigs~r~e~~~g-------------gdsevqrtmlellnqldgfeat--knikvimatnridi  298 (404)
T KOG0728|consen  234 VMAREHAPSIIFMDEIDSIGSSRVESGSG-------------GDSEVQRTMLELLNQLDGFEAT--KNIKVIMATNRIDI  298 (404)
T ss_pred             HHHHhcCCceEeeecccccccccccCCCC-------------ccHHHHHHHHHHHHhccccccc--cceEEEEecccccc
Confidence            6664  59999999999998755443322             2466788889999999999655  67999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      ||+||+||||++..|+||.|+.+.|.+|++.+..+....-..++..++.+ .+.|++++...|
T Consensus       299 ld~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~vc  361 (404)
T KOG0728|consen  299 LDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKGVC  361 (404)
T ss_pred             ccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhhhh
Confidence            99999999999999999999999999999988877654444566666665 568899988877

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

Probab=100.00  E-value=2.2e-33  Score=258.41  Aligned_cols=200  Identities=25%  Similarity=0.372  Sum_probs=171.6

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++|++|++-+..+|+++++|.. |+.++.|||||||||||||.+|+|+|.++...|+.+...++.      ++.+++++
T Consensus       678 eevK~eIldTIqlPL~hpeLfss-glrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGPELLNMYVGqSE~NVR~V  756 (953)
T KOG0736|consen  678 EEVKTEILDTIQLPLKHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGPELLNMYVGQSEENVREV  756 (953)
T ss_pred             HHHHHHHHHHhcCcccChhhhhc-cccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCHHHHHHHhcchHHHHHHH
Confidence            57999999999999999999875 788889999999999999999999999999999999987765      57889999


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |.+++  .|||||+||+|++++.|.+.+.+              .+-..+++++||.+||++.......++||++||+|+
T Consensus       757 FerAR~A~PCVIFFDELDSlAP~RG~sGDS--------------GGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPD  822 (953)
T KOG0736|consen  757 FERARSAAPCVIFFDELDSLAPNRGRSGDS--------------GGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPD  822 (953)
T ss_pred             HHHhhccCCeEEEeccccccCccCCCCCCc--------------cccHHHHHHHHHHHhhcccCCCCCceEEEecCCCcc
Confidence            99986  59999999999999866554422              245578999999999999876778899999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCH-HHHHHHHHHhhCCCCCCcHHHHHHHhhc--CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTP-SGFKMLASNYLGIAEHPLFVEIEKLIAT--AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~-~~~~~i~~~~~~~~~~~~~~~~~~l~~~--~~~s~~~i~~~l  217 (266)
                      .|||+|+|||||+.-+++..++. +.+..+++....+....-..++.+++.+  ..||++|+-.+|
T Consensus       823 LLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TGADlYsLC  888 (953)
T KOG0736|consen  823 LLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTGADLYSLC  888 (953)
T ss_pred             ccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCchhHHHHHH
Confidence            99999999999999999977765 5567888877777666656667777775  569999998876

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

Probab=100.00  E-value=4.1e-33  Score=228.99  Aligned_cols=188  Identities=21%  Similarity=0.336  Sum_probs=162.5

Q ss_pred             HHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHHHHcc--
Q 024550           10 MDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHILIATE--   81 (266)
Q Consensus        10 ~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~~~~~--   81 (266)
                      -..+..||..|+.|..|.   |+++|||||||||||++|+++|++.++|++.+.+..+.+      ...+++++..+.  
T Consensus       133 crli~~yLenPe~Fg~WA---PknVLFyGppGTGKTm~Akalane~kvp~l~vkat~liGehVGdgar~Ihely~rA~~~  209 (368)
T COG1223         133 CRLIMEYLENPERFGDWA---PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKA  209 (368)
T ss_pred             HHHHHHHhhChHHhcccC---cceeEEECCCCccHHHHHHHHhcccCCceEEechHHHHHHHhhhHHHHHHHHHHHHHhc
Confidence            455889999999999988   789999999999999999999999999999999988763      355777777765  


Q ss_pred             cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccccc
Q 024550           82 NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALL  161 (266)
Q Consensus        82 ~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~  161 (266)
                      .|||+||||+|.++-.+.....               .++...++|.||..||+..++  .+++.|++||+|+.||+++.
T Consensus       210 aPcivFiDE~DAiaLdRryQel---------------RGDVsEiVNALLTelDgi~en--eGVvtIaaTN~p~~LD~aiR  272 (368)
T COG1223         210 APCIVFIDELDAIALDRRYQEL---------------RGDVSEIVNALLTELDGIKEN--EGVVTIAATNRPELLDPAIR  272 (368)
T ss_pred             CCeEEEehhhhhhhhhhhHHHh---------------cccHHHHHHHHHHhccCcccC--CceEEEeecCChhhcCHHHH
Confidence            5999999999999875544332               255678999999999999755  67999999999999999999


Q ss_pred             CCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHc
Q 024550          162 RPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMR  219 (266)
Q Consensus       162 r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~  219 (266)
                      +  ||...|+|.+|+.++|.+|++.|......+....+..+++. -++|++||.+.++.
T Consensus       273 s--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikekvlK  329 (368)
T COG1223         273 S--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLK  329 (368)
T ss_pred             h--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHHHHH
Confidence            9  99999999999999999999999999888877777777775 45999999987753

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

Probab=100.00  E-value=1.1e-32  Score=247.35  Aligned_cols=201  Identities=27%  Similarity=0.399  Sum_probs=163.9

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +.+|+++.+.+..++.++++|..+|+++|+|+|||||||||||++++++|+.++.+++.+.++.+.      +...+..+
T Consensus       151 ~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l~~k~~ge~~~~lr~l  230 (398)
T PTZ00454        151 DIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDV  230 (398)
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHHHHhcchhHHHHHHH
Confidence            467899999999999999999999999999999999999999999999999999999999876553      23446666


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..|+||||||+|.++..+.....             ..+......+..+++.++++...  .+++||+|||+++
T Consensus       231 f~~A~~~~P~ILfIDEID~i~~~r~~~~~-------------~~d~~~~r~l~~LL~~ld~~~~~--~~v~VI~aTN~~d  295 (398)
T PTZ00454        231 FRLARENAPSIIFIDEVDSIATKRFDAQT-------------GADREVQRILLELLNQMDGFDQT--TNVKVIMATNRAD  295 (398)
T ss_pred             HHHHHhcCCeEEEEECHhhhccccccccC-------------CccHHHHHHHHHHHHHhhccCCC--CCEEEEEecCCch
Confidence            6554  46899999999999763321110             01133456778888888877543  5689999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .+|++++|||||+..|+|+.|+.++|..||+.++...+.....++..++.. .+||++||..++.
T Consensus       296 ~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~  360 (398)
T PTZ00454        296 TLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQ  360 (398)
T ss_pred             hCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999987655544556666654 5799999999883

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

Probab=100.00  E-value=1.5e-33  Score=231.88  Aligned_cols=199  Identities=25%  Similarity=0.337  Sum_probs=168.9

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~   77 (266)
                      .+.+++.+.++.++.+++.|..+|+.||+|+|+|||||||||.+||++|...+..|+.+....+.      +..-+++.|
T Consensus       178 kQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQLVQMfIGdGAkLVRDAF  257 (424)
T KOG0652|consen  178 KQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQMFIGDGAKLVRDAF  257 (424)
T ss_pred             HHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcchHHHhhhhcchHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999998887766554      223356666


Q ss_pred             HHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      .-+  +.|+|+||||+|.+...+.....+.             +.+.++++-+|||.++++.+.  ..+-||++||+.+-
T Consensus       258 aLAKEkaP~IIFIDElDAIGtKRfDSek~G-------------DREVQRTMLELLNQLDGFss~--~~vKviAATNRvDi  322 (424)
T KOG0652|consen  258 ALAKEKAPTIIFIDELDAIGTKRFDSEKAG-------------DREVQRTMLELLNQLDGFSSD--DRVKVIAATNRVDI  322 (424)
T ss_pred             HHhhccCCeEEEEechhhhccccccccccc-------------cHHHHHHHHHHHHhhcCCCCc--cceEEEeecccccc
Confidence            555  4699999999999987554433322             467788999999999999665  67999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcC-CCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATA-KVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~-~~s~~~i~~~l  217 (266)
                      |||+|+|+||++..|+||.|+.+.|..|++.+..+........+++++..+ .|++++...+|
T Consensus       323 LDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTddFNGAQcKAVc  385 (424)
T KOG0652|consen  323 LDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTDDFNGAQCKAVC  385 (424)
T ss_pred             cCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhcccccCchhheeee
Confidence            999999999999999999999999999999999888777777777787754 48888877666

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

Probab=100.00  E-value=1.5e-33  Score=234.88  Aligned_cols=200  Identities=29%  Similarity=0.379  Sum_probs=167.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++.++|.+.+..+|.+|++|...|+.||+|++|||+||||||.||+++|+.....|+.+-.+.+.      ++.-++++
T Consensus       191 e~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvGseLiQkylGdGpklvRql  270 (440)
T KOG0726|consen  191 ESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVREL  270 (440)
T ss_pred             HHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhhhHHHHHHHhccchHHHHHH
Confidence            467899999999999999999999999999999999999999999999999999999998887765      24456677


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |.-+.  .|+|+||||||++...+=+..+.             ...+.++++-+|||.++++.++  ..+-||++||+.+
T Consensus       271 F~vA~e~apSIvFiDEIdAiGtKRyds~Sg-------------gerEiQrtmLELLNQldGFdsr--gDvKvimATnrie  335 (440)
T KOG0726|consen  271 FRVAEEHAPSIVFIDEIDAIGTKRYDSNSG-------------GEREIQRTMLELLNQLDGFDSR--GDVKVIMATNRIE  335 (440)
T ss_pred             HHHHHhcCCceEEeehhhhhccccccCCCc-------------cHHHHHHHHHHHHHhccCcccc--CCeEEEEeccccc
Confidence            76553  69999999999997643222111             1356677888999999999776  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhh-cCCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~-~~~~s~~~i~~~l  217 (266)
                      .|||+|+||||++..|+|+.||...+++||..+.+.....-...++.++. +..+|++||..+|
T Consensus       336 ~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAic  399 (440)
T KOG0726|consen  336 TLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAIC  399 (440)
T ss_pred             ccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHH
Confidence            99999999999999999999999999999998887765444455655554 5679999999887

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

Probab=99.98  E-value=3.8e-32  Score=249.75  Aligned_cols=199  Identities=27%  Similarity=0.381  Sum_probs=169.3

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      ++.|.++.+ ++.||+.|..|..+|...|+|+||+||||||||+||+++|.+.++||+.++.+++.      +.+.++++
T Consensus       156 dEakeel~E-iVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FVemfVGvGAsRVRdL  234 (596)
T COG0465         156 DEAKEELSE-LVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDL  234 (596)
T ss_pred             HHHHHHHHH-HHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCceeccchhhhhhhcCCCcHHHHHH
Confidence            456777666 78999999999999999999999999999999999999999999999999999886      46788999


Q ss_pred             HHHccc--CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATEN--KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~~--~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.+  |||+||||||.+...+...             ....+.+.+.+++++|..||++..+  .+++++++||+|+
T Consensus       235 F~qAkk~aP~IIFIDEiDAvGr~Rg~g-------------~GggnderEQTLNQlLvEmDGF~~~--~gviviaaTNRpd  299 (596)
T COG0465         235 FEQAKKNAPCIIFIDEIDAVGRQRGAG-------------LGGGNDEREQTLNQLLVEMDGFGGN--EGVIVIAATNRPD  299 (596)
T ss_pred             HHHhhccCCCeEEEehhhhcccccCCC-------------CCCCchHHHHHHHHHHhhhccCCCC--CceEEEecCCCcc
Confidence            998864  9999999999997633221             1122455678999999999999643  6799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      -+|+||+|||||+..|.++.||...|.+|++.+..........++..++.. .+|+++++.+++
T Consensus       300 VlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~  363 (596)
T COG0465         300 VLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLL  363 (596)
T ss_pred             cchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccchHhhhH
Confidence            999999999999999999999999999999988877655544555555553 579999999998

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.98  E-value=1.6e-31  Score=240.59  Aligned_cols=223  Identities=25%  Similarity=0.331  Sum_probs=171.9

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++++.+.+..++.++..|..+|+.+++++|||||||||||++|+++|++++.+++.++++.+..      ...++.+
T Consensus       137 ~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~~l~~~~~g~~~~~i~~~  216 (389)
T PRK03992        137 EEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVREL  216 (389)
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCCEEEeehHHHhHhhccchHHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999999999999887642      3445666


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|+||||||+|.++..+......             ........+..++..+++....  .+++||+|||+++
T Consensus       217 f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~-------------~~~~~~~~l~~lL~~ld~~~~~--~~v~VI~aTn~~~  281 (389)
T PRK03992        217 FELAREKAPSIIFIDEIDAIAAKRTDSGTS-------------GDREVQRTLMQLLAEMDGFDPR--GNVKIIAATNRID  281 (389)
T ss_pred             HHHHHhcCCeEEEEechhhhhcccccCCCC-------------ccHHHHHHHHHHHHhccccCCC--CCEEEEEecCChh
Confidence            76553  58999999999997643221110             0123345666777777776433  4689999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHc-------CCCHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMR-------NEAPEFA  226 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~-------~~~~~~~  226 (266)
                      .+|++++|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+|+++||..++..       .......
T Consensus       282 ~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~eA~~~a~~~~~~~i~  361 (389)
T PRK03992        282 ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEVT  361 (389)
T ss_pred             hCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCCCCcC
Confidence            999999999999999999999999999999999876654433445555553 56999999988742       2223345


Q ss_pred             HHHHHHHHHhhhhh
Q 024550          227 LSGLIEFLESKKRA  240 (266)
Q Consensus       227 ~~~~~~~~~~~~~~  240 (266)
                      .+++.++++..+..
T Consensus       362 ~~d~~~A~~~~~~~  375 (389)
T PRK03992        362 MEDFLKAIEKVMGK  375 (389)
T ss_pred             HHHHHHHHHHHhcc
Confidence            56666666655443

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

Probab=99.98  E-value=1.1e-31  Score=231.20  Aligned_cols=197  Identities=22%  Similarity=0.286  Sum_probs=161.6

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC-----hhhHH-HH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG-----NNDLR-HI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~-----~~~l~-~~   76 (266)
                      ++.|+-+.++++.++..|++|+-+-. |.+|+|++||||||||+||+|+|.+++..|+.|+.+.+.+     ...+. -+
T Consensus       218 ~~AK~lL~EAVvlPi~mPe~F~Girr-PWkgvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstltSKwRGeSEKlvRlL  296 (491)
T KOG0738|consen  218 HEAKKLLKEAVVLPIWMPEFFKGIRR-PWKGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKWRGESEKLVRLL  296 (491)
T ss_pred             HHHHHHHHHHHhhhhhhHHHHhhccc-ccceeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhhhhhccchHHHHHHH
Confidence            46788899999999999999986444 5579999999999999999999999999999999998874     23444 44


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC--CceEEEEecCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG--DERIIIFTTNH  152 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~--~~~ivi~ttn~  152 (266)
                      |..+.  .|++|||||||.|+..+...               ...+...+..++||..|||......  ..|+|+++||.
T Consensus       297 FemARfyAPStIFiDEIDslcs~RG~s---------------~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~  361 (491)
T KOG0738|consen  297 FEMARFYAPSTIFIDEIDSLCSQRGGS---------------SEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNF  361 (491)
T ss_pred             HHHHHHhCCceeehhhHHHHHhcCCCc---------------cchhHHHHHHHHHHHHhhccccccccceeEEEEeccCC
Confidence            44443  59999999999999755332               1235667889999999998754432  23778899999


Q ss_pred             CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          153 KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       153 ~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      |+.||.||+|  ||...|++|+|+.+.|..+++..+..........++.++.. .+||++||.++|
T Consensus       362 PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvC  425 (491)
T KOG0738|consen  362 PWDIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVC  425 (491)
T ss_pred             CcchHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHH
Confidence            9999999999  99999999999999999999999987655555566666665 569999999998

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

Probab=99.97  E-value=3.5e-31  Score=227.50  Aligned_cols=212  Identities=21%  Similarity=0.297  Sum_probs=180.6

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhC-CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh------hhHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVG-KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN------NDLRH   75 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~-~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~------~~l~~   75 (266)
                      +++++++++.+..++.++++|...+ ..+++|||||||||||||++|+++|++.|.+|+.++.+.+++.      ..+..
T Consensus        98 e~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~KWfgE~eKlv~A  177 (386)
T KOG0737|consen   98 EEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTSKWFGEAQKLVKA  177 (386)
T ss_pred             HHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccchhhHHHHHHHHHH
Confidence            4688999999999999999997443 5578999999999999999999999999999999999988742      22344


Q ss_pred             HHHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC
Q 024550           76 ILIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK  153 (266)
Q Consensus        76 ~~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~  153 (266)
                      +|.-+.  +|+||||||+|.+.+.+...                +.+....+.++|...+||+....+..++|+|+||+|
T Consensus       178 vFslAsKl~P~iIFIDEvds~L~~R~s~----------------dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP  241 (386)
T KOG0737|consen  178 VFSLASKLQPSIIFIDEVDSFLGQRRST----------------DHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRP  241 (386)
T ss_pred             HHhhhhhcCcceeehhhHHHHHhhcccc----------------hHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCC
Confidence            444443  69999999999998866221                235567788899999999998877789999999999


Q ss_pred             CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHcCCCHHHHHHHHHH
Q 024550          154 ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMRNEAPEFALSGLIE  232 (266)
Q Consensus       154 ~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~~~~~~~~~~~~~~  232 (266)
                      ..+|.|++|  |+...++++.|+..+|.+|++-++..+......++.+++.. .|||+.||.++|     ...++..+.+
T Consensus       242 ~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSDLkelC-----~~Aa~~~ire  314 (386)
T KOG0737|consen  242 FDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSDLKELC-----RLAALRPIRE  314 (386)
T ss_pred             ccHHHHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHHHHHHH-----HHHhHhHHHH
Confidence            999999999  99999999999999999999999999887777777777775 569999999998     6777788888


Q ss_pred             HHHhh
Q 024550          233 FLESK  237 (266)
Q Consensus       233 ~~~~~  237 (266)
                      .++..
T Consensus       315 ~~~~~  319 (386)
T KOG0737|consen  315 LLVSE  319 (386)
T ss_pred             HHHhc
Confidence            87775

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

Probab=99.97  E-value=4.7e-31  Score=241.26  Aligned_cols=213  Identities=24%  Similarity=0.330  Sum_probs=179.4

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++|+.+.+-+..+-+-+..|....++.+.|||||||||||||++|.++|..++..|+.+....+.      ++..++.+
T Consensus       673 ~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fisvKGPElL~KyIGaSEq~vR~l  752 (952)
T KOG0735|consen  673 FEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFISVKGPELLSKYIGASEQNVRDL  752 (952)
T ss_pred             HHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEEecCHHHHHHHhcccHHHHHHH
Confidence            467888888888899999999999999999999999999999999999999999999999877665      46789999


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|||||+||+|++++.|...+                .+-..+.++++|..|||.-.  -.++.|+|+|.+|+
T Consensus       753 F~rA~~a~PCiLFFDEfdSiAPkRGhDs----------------TGVTDRVVNQlLTelDG~Eg--l~GV~i~aaTsRpd  814 (952)
T KOG0735|consen  753 FERAQSAKPCILFFDEFDSIAPKRGHDS----------------TGVTDRVVNQLLTELDGAEG--LDGVYILAATSRPD  814 (952)
T ss_pred             HHHhhccCCeEEEeccccccCcccCCCC----------------CCchHHHHHHHHHhhccccc--cceEEEEEecCCcc
Confidence            98875  699999999999988553322                24557899999999998733  36799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHcCCCHHHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMRNEAPEFALSGLIEF  233 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~~~~~~~~~~~~~~~  233 (266)
                      .+||||+||||++..++.+.|+..+|.+|+...........+.+++-++.. .+||++|+..++.     ..-+..+-+|
T Consensus       815 liDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll~-----~A~l~avh~~  889 (952)
T KOG0735|consen  815 LIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLLY-----NAQLAAVHEI  889 (952)
T ss_pred             ccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHHH-----HHHHHHHHHH
Confidence            999999999999999999999999999999987776666666777777775 5699999999883     3334455555


Q ss_pred             HHhhh
Q 024550          234 LESKK  238 (266)
Q Consensus       234 ~~~~~  238 (266)
                      +.+..
T Consensus       890 l~~~~  894 (952)
T KOG0735|consen  890 LKRED  894 (952)
T ss_pred             HHhcC
Confidence            55544

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

Probab=99.97  E-value=1.5e-31  Score=220.85  Aligned_cols=199  Identities=24%  Similarity=0.299  Sum_probs=164.7

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~   77 (266)
                      ++...+.+-+..++.+++.|-.+|+.||+|+|+|||||||||..||++|+..+.-|+.+-.+.+.      +...++++|
T Consensus       184 eqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdacfirvigselvqkyvgegarmvrelf  263 (435)
T KOG0729|consen  184 EQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELF  263 (435)
T ss_pred             HHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCceEEeehhHHHHHHHhhhhHHHHHHHH
Confidence            56677888899999999999999999999999999999999999999999999999999988776      234567888


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..+.  ..|++|+||||.+.+.+-...             ...+.+.+.++-++++.|+++..+  .++-++++||+|+.
T Consensus       264 ~martkkaciiffdeidaiggarfddg-------------~ggdnevqrtmleli~qldgfdpr--gnikvlmatnrpdt  328 (435)
T KOG0729|consen  264 EMARTKKACIIFFDEIDAIGGARFDDG-------------AGGDNEVQRTMLELINQLDGFDPR--GNIKVLMATNRPDT  328 (435)
T ss_pred             HHhcccceEEEEeeccccccCccccCC-------------CCCcHHHHHHHHHHHHhccCCCCC--CCeEEEeecCCCCC
Confidence            7764  579999999999987442221             123466788888999999999766  56899999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      |||+|+||||++..++|..|+.+.|..|++.+.......-....+.++.- ..-|+++|..++
T Consensus       329 ldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcpnstgaeirsvc  391 (435)
T KOG0729|consen  329 LDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPNSTGAEIRSVC  391 (435)
T ss_pred             cCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCCCCcchHHHHHH
Confidence            99999999999999999999999999999988877655544444333332 237888888877

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

Probab=99.97  E-value=2.1e-30  Score=234.15  Aligned_cols=199  Identities=28%  Similarity=0.384  Sum_probs=160.0

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~   77 (266)
                      ++++++.+.+..++.++.+|..+|+.+++++|||||||||||++|+++|++++.+++.+..+.+..      ...+..+|
T Consensus       190 ~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~seL~~k~~Ge~~~~vr~lF  269 (438)
T PTZ00361        190 QQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELF  269 (438)
T ss_pred             HHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEecchhhhhhcchHHHHHHHHH
Confidence            567888888889999999999999999999999999999999999999999999999998877642      23356666


Q ss_pred             HHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..+  ..|+||||||||.++..+......             ........+..+++.++++...  .++.||+|||+++.
T Consensus       270 ~~A~~~~P~ILfIDEID~l~~kR~~~~sg-------------g~~e~qr~ll~LL~~Ldg~~~~--~~V~VI~ATNr~d~  334 (438)
T PTZ00361        270 RVAEENAPSIVFIDEIDAIGTKRYDATSG-------------GEKEIQRTMLELLNQLDGFDSR--GDVKVIMATNRIES  334 (438)
T ss_pred             HHHHhCCCcEEeHHHHHHHhccCCCCCCc-------------ccHHHHHHHHHHHHHHhhhccc--CCeEEEEecCChHH
Confidence            554  368999999999997533211110             0123345667788888877543  46899999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhh-cCCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~-~~~~s~~~i~~~l  217 (266)
                      +|++++|||||+..|+|+.|+.++|.+||+.++.........++..++. ..++|+++|..++
T Consensus       335 LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~  397 (438)
T PTZ00361        335 LDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAIC  397 (438)
T ss_pred             hhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHH
Confidence            9999999999999999999999999999999987765444445555554 4579999999887

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.97  E-value=1.4e-30  Score=241.73  Aligned_cols=220  Identities=24%  Similarity=0.366  Sum_probs=172.5

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++|.++.+ +..++.++..|...|..+++|+|||||||||||++++++|++++.+++.++++.+.      +...+..+
T Consensus        61 ~~~k~~l~~-~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~~~~g~~~~~l~~~  139 (495)
T TIGR01241        61 DEAKEELME-IVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDL  139 (495)
T ss_pred             HHHHHHHHH-HHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHHHHHhcccHHHHHHH
Confidence            456666665 56679999999999999999999999999999999999999999999999987653      34567788


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|+||||||+|.++..+.....             ..+.....+++.++..|+++...  .+++||+|||+++
T Consensus       140 f~~a~~~~p~Il~iDEid~l~~~r~~~~~-------------~~~~~~~~~~~~lL~~~d~~~~~--~~v~vI~aTn~~~  204 (495)
T TIGR01241       140 FEQAKKNAPCIIFIDEIDAVGRQRGAGLG-------------GGNDEREQTLNQLLVEMDGFGTN--TGVIVIAATNRPD  204 (495)
T ss_pred             HHHHHhcCCCEEEEechhhhhhccccCcC-------------CccHHHHHHHHHHHhhhccccCC--CCeEEEEecCChh
Confidence            87763  5899999999999864432100             01123356788899999987554  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHc-------CCCHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMR-------NEAPEFA  226 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~-------~~~~~~~  226 (266)
                      .+|++++|||||+..|+++.|+.++|.+|++.++.........++..++.. .+||++||.+++..       .......
T Consensus       205 ~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~~~i~  284 (495)
T TIGR01241       205 VLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEIT  284 (495)
T ss_pred             hcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            999999999999999999999999999999999977654444556666665 45999999988742       1233345


Q ss_pred             HHHHHHHHHhhh
Q 024550          227 LSGLIEFLESKK  238 (266)
Q Consensus       227 ~~~~~~~~~~~~  238 (266)
                      .+++..+++...
T Consensus       285 ~~~l~~a~~~~~  296 (495)
T TIGR01241       285 MNDIEEAIDRVI  296 (495)
T ss_pred             HHHHHHHHHHHh
Confidence            666666666553

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.97  E-value=2e-30  Score=250.72  Aligned_cols=198  Identities=25%  Similarity=0.345  Sum_probs=165.5

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++|+.+.+.+..++..+..|..+|+.+++|+|||||||||||++|+++|++++.+|+.++++.+.      ++..++.+
T Consensus       459 ~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~~~vGese~~i~~~  538 (733)
T TIGR01243       459 EEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREI  538 (733)
T ss_pred             HHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhhcccCcHHHHHHHH
Confidence            467888999999999999999999999999999999999999999999999999999999987654      24567888


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|+||||||+|.+++.+....               ........++.|+..|++....  .+++||+|||+|+
T Consensus       539 f~~A~~~~p~iifiDEid~l~~~r~~~~---------------~~~~~~~~~~~lL~~ldg~~~~--~~v~vI~aTn~~~  601 (733)
T TIGR01243       539 FRKARQAAPAIIFFDEIDAIAPARGARF---------------DTSVTDRIVNQLLTEMDGIQEL--SNVVVIAATNRPD  601 (733)
T ss_pred             HHHHHhcCCEEEEEEChhhhhccCCCCC---------------CccHHHHHHHHHHHHhhcccCC--CCEEEEEeCCChh
Confidence            87764  589999999999986332111               0123356888899999987543  5799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|++++|||||+..|+++.|+.++|.+||+.+..........++..++.. .+||++||.+++
T Consensus       602 ~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~  665 (733)
T TIGR01243       602 ILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVC  665 (733)
T ss_pred             hCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999999999999999999988876654444556666664 469999999877

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.97  E-value=3.3e-30  Score=235.99  Aligned_cols=200  Identities=20%  Similarity=0.259  Sum_probs=155.4

Q ss_pred             HHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHHHHc--ccCCeeeeecchhh
Q 024550           23 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHILIAT--ENKSILVVEDIDCC   94 (266)
Q Consensus        23 ~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~~~~--~~~~vl~iDeid~l   94 (266)
                      ...+|+++++|+|||||||||||++|+++|++++.+++.++++.+.      +...++.+|..+  ..||||||||||.+
T Consensus       251 ~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~l~~~~vGese~~l~~~f~~A~~~~P~IL~IDEID~~  330 (489)
T CHL00195        251 ASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKA  330 (489)
T ss_pred             HHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHHhcccccChHHHHHHHHHHHHHhcCCcEEEehhhhhh
Confidence            4567999999999999999999999999999999999999987654      245677787654  46999999999998


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSH  174 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~  174 (266)
                      +..+...               .+......+++.++..|+..    ..+++||+|||+++.||++++|+|||+..|+++.
T Consensus       331 ~~~~~~~---------------~d~~~~~rvl~~lL~~l~~~----~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~l  391 (489)
T CHL00195        331 FSNSESK---------------GDSGTTNRVLATFITWLSEK----KSPVFVVATANNIDLLPLEILRKGRFDEIFFLDL  391 (489)
T ss_pred             hccccCC---------------CCchHHHHHHHHHHHHHhcC----CCceEEEEecCChhhCCHHHhCCCcCCeEEEeCC
Confidence            7522111               11233456677777777643    3569999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCc--HHHHHHHhhc-CCCCHHHHHHHHHc------CCCHHHHHHHHHHHHHhhhhhc
Q 024550          175 CTPSGFKMLASNYLGIAEHPL--FVEIEKLIAT-AKVTPADVAEQLMR------NEAPEFALSGLIEFLESKKRAN  241 (266)
Q Consensus       175 p~~~~~~~i~~~~~~~~~~~~--~~~~~~l~~~-~~~s~~~i~~~l~~------~~~~~~~~~~~~~~~~~~~~~~  241 (266)
                      |+.++|.+||+.++.......  ..++..++.. .+||++||.+++..      .+......+++..+++.....+
T Consensus       392 P~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~~~A~~~~~~lt~~dl~~a~~~~~Pls  467 (489)
T CHL00195        392 PSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYEKREFTTDDILLALKQFIPLA  467 (489)
T ss_pred             cCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCCc
Confidence            999999999999998754321  3455666664 57999999988743      2334456677777777776653

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

Probab=99.97  E-value=1.2e-29  Score=235.74  Aligned_cols=198  Identities=29%  Similarity=0.411  Sum_probs=168.0

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      ++.|+.+.+.+..++..++.|...++.+++|+|||||||||||++|+++|.+++.+|+.+..+++.+      +..++.+
T Consensus       248 ~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~sk~vGesek~ir~~  327 (494)
T COG0464         248 EEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIREL  327 (494)
T ss_pred             HHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHHHhccccchHHHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999999999999887663      5678899


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||+|.++..++....                .....++++++..|++....  .++++|+|||+|+
T Consensus       328 F~~A~~~~p~iiFiDEiDs~~~~r~~~~~----------------~~~~r~~~~lL~~~d~~e~~--~~v~vi~aTN~p~  389 (494)
T COG0464         328 FEKARKLAPSIIFIDEIDSLASGRGPSED----------------GSGRRVVGQLLTELDGIEKA--EGVLVIAATNRPD  389 (494)
T ss_pred             HHHHHcCCCcEEEEEchhhhhccCCCCCc----------------hHHHHHHHHHHHHhcCCCcc--CceEEEecCCCcc
Confidence            98876  6999999999999874432211                12257899999999987554  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc--HHHHHHHhh-cCCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL--FVEIEKLIA-TAKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~--~~~~~~l~~-~~~~s~~~i~~~l~  218 (266)
                      .+|++++|||||+..|+|+.|+..+|.+||..++......+  ..++..++. ..+|+++||..++.
T Consensus       390 ~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~  456 (494)
T COG0464         390 DLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVR  456 (494)
T ss_pred             ccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHH
Confidence            99999999999999999999999999999999998665432  334455555 45699999999883

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.97  E-value=7.7e-30  Score=233.46  Aligned_cols=194  Identities=27%  Similarity=0.390  Sum_probs=148.5

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCc----------EEEEeCCccc----
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFD----------VYDLELSNLL----   68 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~----------~~~i~~~~~~----   68 (266)
                      +++++++.+.+..++.++++|..+|+++++|+|||||||||||++++++|+.++.+          |+.+....+.    
T Consensus       188 ~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~eLl~kyv  267 (512)
T TIGR03689       188 DSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGPELLNKYV  267 (512)
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEeccchhhccccc
Confidence            35778899999999999999999999999999999999999999999999998654          3334433332    


Q ss_pred             --ChhhHHHHHHHcc------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC
Q 024550           69 --GNNDLRHILIATE------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC  140 (266)
Q Consensus        69 --~~~~l~~~~~~~~------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~  140 (266)
                        +...++.+|..+.      .++||||||+|.++..+....               +......+++.|++.|+++... 
T Consensus       268 Gete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~---------------s~d~e~~il~~LL~~LDgl~~~-  331 (512)
T TIGR03689       268 GETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGV---------------SSDVETTVVPQLLSELDGVESL-  331 (512)
T ss_pred             chHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCc---------------cchHHHHHHHHHHHHhcccccC-
Confidence              1234556665442      589999999999986432110               0112245778999999988554 


Q ss_pred             CCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          141 GDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       141 ~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                       .+++||+|||+++.||++++|||||+..|+|+.|+.++|.+||+.++... .++..+   +....+++.+++..++
T Consensus       332 -~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~~-l~l~~~---l~~~~g~~~a~~~al~  403 (512)
T TIGR03689       332 -DNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTDS-LPLDAD---LAEFDGDREATAAALI  403 (512)
T ss_pred             -CceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhcc-CCchHH---HHHhcCCCHHHHHHHH
Confidence             56999999999999999999999999999999999999999999998653 233333   3334566666666554

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.

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.97  E-value=1e-29  Score=252.71  Aligned_cols=177  Identities=18%  Similarity=0.172  Sum_probs=138.3

Q ss_pred             CHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh----------------------------
Q 024550           19 RKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN----------------------------   70 (266)
Q Consensus        19 ~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~----------------------------   70 (266)
                      .+....++|..+|+|+||+||||||||+||+++|.++++||+.++++++...                            
T Consensus      1618 ~kP~slrLGl~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~ 1697 (2281)
T CHL00206       1618 GKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDL 1697 (2281)
T ss_pred             CcCHHHHcCCCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhccccccccccccccccccccccccccccc
Confidence            3456678899999999999999999999999999999999999998776521                            


Q ss_pred             ---------------------hhHHHHHHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhh
Q 024550           71 ---------------------NDLRHILIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS  127 (266)
Q Consensus        71 ---------------------~~l~~~~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (266)
                                           ..++.+|..+  ..||||||||||.++..                      .....+++
T Consensus      1698 ~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~~----------------------ds~~ltL~ 1755 (2281)
T CHL00206       1698 DTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVN----------------------ESNYLSLG 1755 (2281)
T ss_pred             chhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCCC----------------------ccceehHH
Confidence                                 0145566655  46999999999999751                      11123578


Q ss_pred             hhhhhhhccccC-CCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH---HHHHHHh
Q 024550          128 GLLNFIDGLWSS-CGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF---VEIEKLI  203 (266)
Q Consensus       128 ~ll~~l~~~~~~-~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~---~~~~~l~  203 (266)
                      .|++.|++.... ...+++||||||+|+.|||||+|||||+..|+++.|+.++|.+++...+...+..+.   .++..++
T Consensus      1756 qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA 1835 (2281)
T CHL00206       1756 LLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFG 1835 (2281)
T ss_pred             HHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHH
Confidence            899999976432 235799999999999999999999999999999999999999988754432222221   2345555


Q ss_pred             hc-CCCCHHHHHHHH
Q 024550          204 AT-AKVTPADVAEQL  217 (266)
Q Consensus       204 ~~-~~~s~~~i~~~l  217 (266)
                      .. .|||++||++++
T Consensus      1836 ~~T~GfSGADLanLv 1850 (2281)
T CHL00206       1836 SITMGSNARDLVALT 1850 (2281)
T ss_pred             HhCCCCCHHHHHHHH
Confidence            54 579999999987

>CHL00176 ftsH cell division protein; Validated

Probab=99.96  E-value=3.8e-29  Score=235.57  Aligned_cols=218  Identities=25%  Similarity=0.360  Sum_probs=169.0

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~   77 (266)
                      +.++++ ..+..++..+..|..+|...++++|||||||||||++|+++|.+++.+++.++++.+.      +...++.+|
T Consensus       190 ~~k~~l-~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~~~~~g~~~~~vr~lF  268 (638)
T CHL00176        190 EAKEEF-EEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLF  268 (638)
T ss_pred             HHHHHH-HHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHHHHhhhhhHHHHHHHH
Confidence            455555 4467889999999999999999999999999999999999999999999999988764      234566777


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..+.  .||||||||+|.++..+.....             ..+.....+++.++..+++....  .+++||+|||+++.
T Consensus       269 ~~A~~~~P~ILfIDEID~l~~~r~~~~~-------------~~~~e~~~~L~~LL~~~dg~~~~--~~ViVIaaTN~~~~  333 (638)
T CHL00176        269 KKAKENSPCIVFIDEIDAVGRQRGAGIG-------------GGNDEREQTLNQLLTEMDGFKGN--KGVIVIAATNRVDI  333 (638)
T ss_pred             HHHhcCCCcEEEEecchhhhhcccCCCC-------------CCcHHHHHHHHHHHhhhccccCC--CCeeEEEecCchHh
Confidence            7654  5899999999999753321100             11233456788899999887543  56999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHc-------CCCHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMR-------NEAPEFAL  227 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~-------~~~~~~~~  227 (266)
                      +|++++|||||+..|+|+.|+.++|.+|++.++..........+..++.. .+||++||.+++..       ........
T Consensus       334 LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~~~~~It~  413 (638)
T CHL00176        334 LDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATITM  413 (638)
T ss_pred             hhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCcCH
Confidence            99999999999999999999999999999999987544445566667665 45999999988732       22223345


Q ss_pred             HHHHHHHHhh
Q 024550          228 SGLIEFLESK  237 (266)
Q Consensus       228 ~~~~~~~~~~  237 (266)
                      +++..++.+.
T Consensus       414 ~dl~~Ai~rv  423 (638)
T CHL00176        414 KEIDTAIDRV  423 (638)
T ss_pred             HHHHHHHHHH
Confidence            5555555543

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

Probab=99.96  E-value=2e-30  Score=216.87  Aligned_cols=207  Identities=19%  Similarity=0.265  Sum_probs=168.3

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~   77 (266)
                      ..|+.+.+.+..+++-|.+|.-- ..|.+|||||||||||||+||+++|.+.+..|+.++.+++++      +.-+..+|
T Consensus       140 ~AKeALKEAVILPIKFPqlFtGk-R~PwrgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLvSKWmGESEkLVknLF  218 (439)
T KOG0739|consen  140 GAKEALKEAVILPIKFPQLFTGK-RKPWRGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKNLF  218 (439)
T ss_pred             hHHHHHHhheeecccchhhhcCC-CCcceeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHHHHHHhccHHHHHHHHH
Confidence            46788899999999999988653 345579999999999999999999999999999999998873      33456777


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..+.  .|+||||||||.+++.++....                ....++..+||..|.+.-.. ..+++|+++||-|+.
T Consensus       219 emARe~kPSIIFiDEiDslcg~r~enEs----------------easRRIKTEfLVQMqGVG~d-~~gvLVLgATNiPw~  281 (439)
T KOG0739|consen  219 EMARENKPSIIFIDEIDSLCGSRSENES----------------EASRRIKTEFLVQMQGVGND-NDGVLVLGATNIPWV  281 (439)
T ss_pred             HHHHhcCCcEEEeehhhhhccCCCCCch----------------HHHHHHHHHHHHhhhccccC-CCceEEEecCCCchh
Confidence            6654  5999999999999987665543                44577889999999987543 457999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhc-CCCCHHHHHHHHHcCCCHHHHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIAT-AKVTPADVAEQLMRNEAPEFALSGLIEF  233 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~-~~~s~~~i~~~l~~~~~~~~~~~~~~~~  233 (266)
                      ||+|++|  ||...|++|+|+...|..+|+.+++.-...+. .++..+... .+||++||.-.+     ++..++.+.+.
T Consensus       282 LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivV-----rDalmePvRkv  354 (439)
T KOG0739|consen  282 LDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVV-----RDALMEPVRKV  354 (439)
T ss_pred             HHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEe-----hhhhhhhHHHh
Confidence            9999999  99999999999999999999999998877765 567777775 469999987554     34444444443


Q ss_pred             HH
Q 024550          234 LE  235 (266)
Q Consensus       234 ~~  235 (266)
                      -.
T Consensus       355 qs  356 (439)
T KOG0739|consen  355 QS  356 (439)
T ss_pred             hh
Confidence            33

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

Probab=99.96  E-value=3.7e-30  Score=216.19  Aligned_cols=198  Identities=27%  Similarity=0.337  Sum_probs=161.9

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      .++..++++-+..++..+.++.+.|+.+|.+++||||||||||.+++++|+.+|++++.+..+.+.+      ..-+++.
T Consensus       138 ~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~lv~kyiGEsaRlIRem  217 (388)
T KOG0651|consen  138 FYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKYIGESARLIRDM  217 (388)
T ss_pred             HHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhcCCceEEeeHhhhhhhhcccHHHHHHHH
Confidence            3567788888999999999999999999999999999999999999999999999999999988763      2346777


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|||||+||||++.+.+.....             ..+...+.++-.|++.|+++..-  .++-+|+|||+|+
T Consensus       218 f~yA~~~~pciifmdeiDAigGRr~se~T-------------s~dreiqrTLMeLlnqmdgfd~l--~rVk~ImatNrpd  282 (388)
T KOG0651|consen  218 FRYAREVIPCIIFMDEIDAIGGRRFSEGT-------------SSDREIQRTLMELLNQMDGFDTL--HRVKTIMATNRPD  282 (388)
T ss_pred             HHHHhhhCceEEeehhhhhhccEEecccc-------------chhHHHHHHHHHHHHhhccchhc--ccccEEEecCCcc
Confidence            87765  5899999999999875522222             22467788889999999988554  5688999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCC---CCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA---EHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~---~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .|+|+|+||||++..+++|.|+...|..|++.+-...   +.-..+.+..+..  +|+++++.+.+
T Consensus       283 tLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d--~f~gad~rn~~  346 (388)
T KOG0651|consen  283 TLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVD--GFNGADLRNVC  346 (388)
T ss_pred             ccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHh--ccChHHHhhhc
Confidence            9999999999999999999999999998877655433   2222344444444  58999977766

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

Probab=99.96  E-value=1e-28  Score=214.32  Aligned_cols=166  Identities=17%  Similarity=0.120  Sum_probs=131.5

Q ss_pred             HHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHHHHcc-------cCCeeeee
Q 024550           23 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHILIATE-------NKSILVVE   89 (266)
Q Consensus        23 ~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~~~~~-------~~~vl~iD   89 (266)
                      +...|+.+|++++||||||||||++|+++|+++|.+++.++..++.+      +..++++|..+.       .|||||||
T Consensus       140 l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFID  219 (413)
T PLN00020        140 LALPNIKVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFIN  219 (413)
T ss_pred             hhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEe
Confidence            34468899999999999999999999999999999999999988773      467888887664       59999999


Q ss_pred             cchhhHHHhHHHhhhhhcCCcccccccccccc-chhhhhhhhhhhhcc--------c--cCCCCceEEEEecCCCCCCcc
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQ-YHITLSGLLNFIDGL--------W--SSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ll~~l~~~--------~--~~~~~~~ivi~ttn~~~~ld~  158 (266)
                      |||.+++.+....                ... ...+...|++.+|+.        +  .....+++||+|||+|+.||+
T Consensus       220 EIDA~~g~r~~~~----------------~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDp  283 (413)
T PLN00020        220 DLDAGAGRFGTTQ----------------YTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYA  283 (413)
T ss_pred             hhhhcCCCCCCCC----------------cchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCH
Confidence            9999987442110                111 123346788887752        2  122456899999999999999


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCC
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAK  207 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~  207 (266)
                      +|+|||||+..+  ..|+.++|.+|++.++...+.. ..++..++..+.
T Consensus       284 ALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~-~~dv~~Lv~~f~  329 (413)
T PLN00020        284 PLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVS-REDVVKLVDTFP  329 (413)
T ss_pred             hHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCC-HHHHHHHHHcCC
Confidence            999999999864  5899999999999999887544 577888877643

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.96  E-value=9.4e-29  Score=221.36  Aligned_cols=200  Identities=27%  Similarity=0.336  Sum_probs=156.1

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++++.+.+..++.++..|..+|+.+++|+|||||||||||++++++|+.++.+++.+....+..      ...+..+
T Consensus       128 ~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~~~~l~~~~~g~~~~~i~~~  207 (364)
T TIGR01242       128 EEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREI  207 (364)
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEecchHHHHHHhhhHHHHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999999999887665432      2234555


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..|+||||||+|.++..+.....             ..+......+..++..+++....  .++.||+|||+++
T Consensus       208 f~~a~~~~p~il~iDEiD~l~~~~~~~~~-------------~~~~~~~~~l~~ll~~ld~~~~~--~~v~vI~ttn~~~  272 (364)
T TIGR01242       208 FELAKEKAPSIIFIDEIDAIAAKRTDSGT-------------SGDREVQRTLMQLLAELDGFDPR--GNVKVIAATNRPD  272 (364)
T ss_pred             HHHHHhcCCcEEEhhhhhhhccccccCCC-------------CccHHHHHHHHHHHHHhhCCCCC--CCEEEEEecCChh
Confidence            5544  35899999999998753321110             00123345667777777765333  4689999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|++++|||||+..|+|+.|+.++|.+|++.+..........++..++.. .+++++||..++
T Consensus       273 ~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~  336 (364)
T TIGR01242       273 ILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAIC  336 (364)
T ss_pred             hCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999999999999999999998866543332344555554 469999999886

Many proteins may score above the trusted cutoff because an internal

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.95  E-value=4.1e-27  Score=223.71  Aligned_cols=198  Identities=24%  Similarity=0.380  Sum_probs=157.5

Q ss_pred             HHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHHH
Q 024550            5 MKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHILI   78 (266)
Q Consensus         5 ~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~~   78 (266)
                      .+..+ ..+..++..+..+..++...++|+||+||||||||+++++++++++.+++.++++.+.      +...++.+|.
T Consensus       160 ~~~~l-~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~~~~g~~~~~~~~~f~  238 (644)
T PRK10733        160 AKEEV-AELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFE  238 (644)
T ss_pred             HHHHH-HHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHHhhhcccHHHHHHHHH
Confidence            34443 4466778888888888888899999999999999999999999999999999987654      2345667776


Q ss_pred             Hcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC
Q 024550           79 ATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL  156 (266)
Q Consensus        79 ~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l  156 (266)
                      .+.  .||||||||+|.++..+.....             ........+++.+|..|+++...  .++++|+|||+|+.+
T Consensus       239 ~a~~~~P~IifIDEiD~l~~~r~~~~~-------------g~~~~~~~~ln~lL~~mdg~~~~--~~vivIaaTN~p~~l  303 (644)
T PRK10733        239 QAKKAAPCIIFIDEIDAVGRQRGAGLG-------------GGHDEREQTLNQMLVEMDGFEGN--EGIIVIAATNRPDVL  303 (644)
T ss_pred             HHHhcCCcEEEehhHhhhhhccCCCCC-------------CCchHHHHHHHHHHHhhhcccCC--CCeeEEEecCChhhc
Confidence            653  6899999999999764322110             11233456889999999988554  569999999999999


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      |++++|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+||++||.+++.
T Consensus       304 D~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~  366 (644)
T PRK10733        304 DPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  366 (644)
T ss_pred             CHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999977654434445556554 5799999999983

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.93  E-value=2.6e-25  Score=215.23  Aligned_cols=197  Identities=28%  Similarity=0.385  Sum_probs=157.9

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      .++++.+.+.+..++.++..|..+|+.+++++|||||||||||++++++|++++.+++.+++..+.+      ...+..+
T Consensus       184 ~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~~~~~g~~~~~l~~l  263 (733)
T TIGR01243       184 KEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREI  263 (733)
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHhcccccHHHHHHHHH
Confidence            3567888888888999999999999999999999999999999999999999999999999876542      3456777


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .++||||||+|.+++.+....                ......+++.|+..|++....  ..+++|++||+++
T Consensus       264 f~~a~~~~p~il~iDEid~l~~~r~~~~----------------~~~~~~~~~~Ll~~ld~l~~~--~~vivI~atn~~~  325 (733)
T TIGR01243       264 FKEAEENAPSIIFIDEIDAIAPKREEVT----------------GEVEKRVVAQLLTLMDGLKGR--GRVIVIGATNRPD  325 (733)
T ss_pred             HHHHHhcCCcEEEeehhhhhcccccCCc----------------chHHHHHHHHHHHHhhccccC--CCEEEEeecCChh
Confidence            76653  579999999999976332110                011245677888888877543  5689999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|+++.|+|||+..|+++.|+.++|.+|++.+...........+..++.. .+|+++++..++
T Consensus       326 ~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~  389 (733)
T TIGR01243       326 ALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALA  389 (733)
T ss_pred             hcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHH
Confidence            999999999999999999999999999999988766543333345555553 569999998875

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

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

Probab=99.93  E-value=3.9e-25  Score=201.89  Aligned_cols=192  Identities=26%  Similarity=0.378  Sum_probs=164.9

Q ss_pred             HHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHHHHH
Q 024550            6 KKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHILIA   79 (266)
Q Consensus         6 ~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~~~~   79 (266)
                      .+.+.+.+..++..+..+...|+++|+++|+|||||||||.+++++|++.++.++.+++..+.      +++.++..|..
T Consensus       193 ~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~peli~k~~gEte~~LR~~f~~  272 (693)
T KOG0730|consen  193 LSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGPELISKFPGETESNLRKAFAE  272 (693)
T ss_pred             HHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHhCceeEecccHHHHHhcccchHHHHHHHHHH
Confidence            456677788899999999999999999999999999999999999999999999999988765      45778999987


Q ss_pred             cc--c-CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC
Q 024550           80 TE--N-KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL  156 (266)
Q Consensus        80 ~~--~-~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l  156 (266)
                      +.  + |+++||||+|.+++.+....                 ....++..+++..|++....  ..+++|++||+|+.|
T Consensus       273 a~k~~~psii~IdEld~l~p~r~~~~-----------------~~e~Rv~sqlltL~dg~~~~--~~vivl~atnrp~sl  333 (693)
T KOG0730|consen  273 ALKFQVPSIIFIDELDALCPKREGAD-----------------DVESRVVSQLLTLLDGLKPD--AKVIVLAATNRPDSL  333 (693)
T ss_pred             HhccCCCeeEeHHhHhhhCCcccccc-----------------hHHHHHHHHHHHHHhhCcCc--CcEEEEEecCCcccc
Confidence            64  3 89999999999987443322                 12356788889999988533  579999999999999


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      |+++.| |||+..+++..|+..+|..|++.+..+.+.....++..++.. ++|.++|+...+
T Consensus       334 d~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~  394 (693)
T KOG0730|consen  334 DPALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALC  394 (693)
T ss_pred             Chhhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHH
Confidence            999999 999999999999999999999999998877755666666664 779999999988

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

Probab=99.93  E-value=1.2e-25  Score=199.48  Aligned_cols=197  Identities=22%  Similarity=0.264  Sum_probs=165.0

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      .+.|+.+.+.++.++.+++.|..+-- +.+++||.||||||||+|++++|.+.+..|+.++++.+.+      +..++.+
T Consensus       159 ~~~k~~l~e~vi~p~lr~d~F~glr~-p~rglLLfGPpgtGKtmL~~aiAsE~~atff~iSassLtsK~~Ge~eK~vral  237 (428)
T KOG0740|consen  159 EDAKQSLKEAVILPLLRPDLFLGLRE-PVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSLTSKYVGESEKLVRAL  237 (428)
T ss_pred             hhHHHHhhhhhhhcccchHhhhcccc-ccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHhhhhccChHHHHHHHH
Confidence            46788999999999999999876543 4569999999999999999999999999999999998874      2345666


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |.-+  .+|+|+||||+|.++..++...                ......+..++|..+++.......++++|+|||.|+
T Consensus       238 f~vAr~~qPsvifidEidslls~Rs~~e----------------~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~  301 (428)
T KOG0740|consen  238 FKVARSLQPSVIFIDEIDSLLSKRSDNE----------------HESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPW  301 (428)
T ss_pred             HHHHHhcCCeEEEechhHHHHhhcCCcc----------------cccchhhhhHHHhhhccccCCCCCeEEEEecCCCch
Confidence            6444  4799999999999998663322                244567888899999988887778999999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .+|.+++|  ||...+++|.|+.+.|..+|..++......+ ..+++.++.. .+||..||...|.
T Consensus       302 e~Dea~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~k  365 (428)
T KOG0740|consen  302 ELDEAARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCK  365 (428)
T ss_pred             HHHHHHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHH
Confidence            99999999  9999999999999999999999998885444 3677777774 5699999999884

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

Probab=99.93  E-value=3.9e-26  Score=203.41  Aligned_cols=201  Identities=21%  Similarity=0.360  Sum_probs=155.7

Q ss_pred             CChHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCc-EEEEeCCccc------ChhhH
Q 024550            1 MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFD-VYDLELSNLL------GNNDL   73 (266)
Q Consensus         1 l~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~-~~~i~~~~~~------~~~~l   73 (266)
                      ||.|.-+--++++...+-.|+...++|++.-+|+|||||||||||.+||.+.+-++.. --.++...+.      ++.++
T Consensus       226 Ld~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPeIL~KYVGeSE~Nv  305 (744)
T KOG0741|consen  226 LDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPEILNKYVGESEENV  305 (744)
T ss_pred             chHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHHHHHHhhcccHHHH
Confidence            4455555556777777778899999999999999999999999999999999999642 2334443332      46789


Q ss_pred             HHHHHHcc----------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCc
Q 024550           74 RHILIATE----------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDE  143 (266)
Q Consensus        74 ~~~~~~~~----------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~  143 (266)
                      +.+|..+.          .-.||++||||++|..|.....              +.+-...++++||..||+.-.-  ++
T Consensus       306 R~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g--------------~TGVhD~VVNQLLsKmDGVeqL--NN  369 (744)
T KOG0741|consen  306 RKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAG--------------STGVHDTVVNQLLSKMDGVEQL--NN  369 (744)
T ss_pred             HHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCC--------------CCCccHHHHHHHHHhcccHHhh--hc
Confidence            99998763          2369999999999985433221              1244567899999999988554  67


Q ss_pred             eEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCC----CCcHHHHHHHhhcC-CCCHHHHHHHH
Q 024550          144 RIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE----HPLFVEIEKLIATA-KVTPADVAEQL  217 (266)
Q Consensus       144 ~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~----~~~~~~~~~l~~~~-~~s~~~i~~~l  217 (266)
                      ++||+-||+.+.+|.||+|||||..++++.+||+..|.+|++.+.....    ...+.++.++++.+ .||+++|..++
T Consensus       370 ILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEleglV  448 (744)
T KOG0741|consen  370 ILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGAELEGLV  448 (744)
T ss_pred             EEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHH
Confidence            9999999999999999999999999999999999999999987776542    22234455555543 49999998877

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

Probab=99.93  E-value=4e-25  Score=211.98  Aligned_cols=197  Identities=24%  Similarity=0.296  Sum_probs=160.2

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCccc------Chh
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNLL------GNN   71 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~~------~~~   71 (266)
                      .++++++.+-+..+|..++.|..+++.||+|+|||||||||||+.|+++|..+.     ..|+.-..++..      .+.
T Consensus       271 ~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkgaD~lskwvgEaER  350 (1080)
T KOG0732|consen  271 ENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKGADCLSKWVGEAER  350 (1080)
T ss_pred             HHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcCchhhccccCcHHH
Confidence            357889999999999999999999999999999999999999999999999883     333333333322      256


Q ss_pred             hHHHHHHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEe
Q 024550           72 DLRHILIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFT  149 (266)
Q Consensus        72 ~l~~~~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~t  149 (266)
                      .+.-+|..+.  +|.|+|+||||.+++.++.--                ......+++.||..|+|+..+  ..+++|+|
T Consensus       351 qlrllFeeA~k~qPSIIffdeIdGlapvrSskq----------------Eqih~SIvSTLLaLmdGldsR--gqVvvigA  412 (1080)
T KOG0732|consen  351 QLRLLFEEAQKTQPSIIFFDEIDGLAPVRSSKQ----------------EQIHASIVSTLLALMDGLDSR--GQVVVIGA  412 (1080)
T ss_pred             HHHHHHHHHhccCceEEeccccccccccccchH----------------HHhhhhHHHHHHHhccCCCCC--CceEEEcc
Confidence            6778887764  699999999999988653321                133356888999999999776  56999999


Q ss_pred             cCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhc-CCCCHHHHHHHH
Q 024550          150 TNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEI-EKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       150 tn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~-~~~s~~~i~~~l  217 (266)
                      ||+|+.+|++|+|||||+..++|+.|+.+.|.+|+..+-.+...++...+ ..++.. .+|.++|+..++
T Consensus       413 TnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLC  482 (1080)
T KOG0732|consen  413 TNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALC  482 (1080)
T ss_pred             cCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHH
Confidence            99999999999999999999999999999999999999988876665544 444443 569999977766

>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=99.89  E-value=1.1e-21  Score=160.56  Aligned_cols=165  Identities=19%  Similarity=0.226  Sum_probs=110.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDF  111 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~  111 (266)
                      .++|||||||+||||||+.+|++++.++..++...+....++..++.....+.||||||||.+-...++.-....++..+
T Consensus        51 ~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i~k~~dl~~il~~l~~~~ILFIDEIHRlnk~~qe~LlpamEd~~i  130 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAIEKAGDLAAILTNLKEGDILFIDEIHRLNKAQQEILLPAMEDGKI  130 (233)
T ss_dssp             -EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC--SCHHHHHHHHT--TT-EEEECTCCC--HHHHHHHHHHHHCSEE
T ss_pred             ceEEEECCCccchhHHHHHHHhccCCCeEeccchhhhhHHHHHHHHHhcCCCcEEEEechhhccHHHHHHHHHHhccCeE
Confidence            47999999999999999999999999999999887777788888888888999999999999865444333322221111


Q ss_pred             ccccccccccchhhhhhhhhhhhccccC------CCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHH
Q 024550          112 LIAGYEQQKQYHITLSGLLNFIDGLWSS------CGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLAS  185 (266)
Q Consensus       112 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~------~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~  185 (266)
                                         ..+-+....      .-.+..+|+||++...|.+.|..  ||+...++..++.++..+|+.
T Consensus       131 -------------------diiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrd--RFgi~~~l~~Y~~~el~~Iv~  189 (233)
T PF05496_consen  131 -------------------DIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRD--RFGIVLRLEFYSEEELAKIVK  189 (233)
T ss_dssp             -------------------EEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCT--TSSEEEE----THHHHHHHHH
T ss_pred             -------------------EEEeccccccceeeccCCCceEeeeeccccccchhHHh--hcceecchhcCCHHHHHHHHH
Confidence                               000000000      00347899999999999999999  999999999999999999999


Q ss_pred             HhhCCCCCCcHHHHHH-HhhcCCCCHHHHHHHH
Q 024550          186 NYLGIAEHPLFVEIEK-LIATAKVTPADVAEQL  217 (266)
Q Consensus       186 ~~~~~~~~~~~~~~~~-l~~~~~~s~~~i~~~l  217 (266)
                      +.....+..+.++... ++.....||+=..++|
T Consensus       190 r~a~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll  222 (233)
T PF05496_consen  190 RSARILNIEIDEDAAEEIARRSRGTPRIANRLL  222 (233)
T ss_dssp             HCCHCTT-EE-HHHHHHHHHCTTTSHHHHHHHH
T ss_pred             HHHHHhCCCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            9998888888766654 4555557776544444

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=99.85  E-value=3.3e-21  Score=147.59  Aligned_cols=123  Identities=33%  Similarity=0.539  Sum_probs=97.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHHHHc--cc-CCeeeeecchhhHHHhHHHhhh
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHILIAT--EN-KSILVVEDIDCCIELQDRLSRA  104 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~~~~--~~-~~vl~iDeid~l~~~~~~~~~~  104 (266)
                      +||+||||||||++++.+|+.++.+++.+++..+.+      ...+..+|..+  .. ++||||||+|.+....+.    
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~~~----   76 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKSQP----   76 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHCST----
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccccc----
Confidence            689999999999999999999999999999998862      34566667665  23 799999999999863300    


Q ss_pred             hhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCC
Q 024550          105 RAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSH  174 (266)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~  174 (266)
                                  .........+..+++.++..... ..+++||+|||.++.++++++| +||+..|++|.
T Consensus        77 ------------~~~~~~~~~~~~L~~~l~~~~~~-~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   77 ------------SSSSFEQRLLNQLLSLLDNPSSK-NSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             ------------SSSHHHHHHHHHHHHHHHTTTTT-SSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             ------------ccccccccccceeeecccccccc-cccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence                        11234456777888888876543 3469999999999999999997 79999999874

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 ....

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

Probab=99.84  E-value=6.2e-20  Score=153.30  Aligned_cols=170  Identities=20%  Similarity=0.195  Sum_probs=128.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDF  111 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~  111 (266)
                      -.+|||||||.||||+|..+|+++|+++...+...+....++..++.....+.|||||||+.+.+...+.-++..++-.+
T Consensus        53 DHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK~gDlaaiLt~Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf~l  132 (332)
T COG2255          53 DHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEEVLYPAMEDFRL  132 (332)
T ss_pred             CeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccccChhhHHHHHhcCCcCCeEEEehhhhcChhHHHHhhhhhhheeE
Confidence            36999999999999999999999999999999999999999999999999999999999999977555444333222111


Q ss_pred             ccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCC
Q 024550          112 LIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA  191 (266)
Q Consensus       112 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~  191 (266)
                      .+........  .+     ..++      =.+..+|++|.+...|...|..  ||+....+..++.++..+|+.+.....
T Consensus       133 DI~IG~gp~A--rs-----v~ld------LppFTLIGATTr~G~lt~PLrd--RFGi~~rlefY~~~eL~~Iv~r~a~~l  197 (332)
T COG2255         133 DIIIGKGPAA--RS-----IRLD------LPPFTLIGATTRAGMLTNPLRD--RFGIIQRLEFYTVEELEEIVKRSAKIL  197 (332)
T ss_pred             EEEEccCCcc--ce-----Eecc------CCCeeEeeeccccccccchhHH--hcCCeeeeecCCHHHHHHHHHHHHHHh
Confidence            1000000000  00     0000      0357899999999999999999  999999999999999999999999888


Q ss_pred             CCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          192 EHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       192 ~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      +..+.++. ..++.....||+ |++.|
T Consensus       198 ~i~i~~~~a~eIA~rSRGTPR-IAnRL  223 (332)
T COG2255         198 GIEIDEEAALEIARRSRGTPR-IANRL  223 (332)
T ss_pred             CCCCChHHHHHHHHhccCCcH-HHHHH
Confidence            87776554 455555666665 55555

>CHL00181 cbbX CbbX; Provisional

Probab=99.83  E-value=2.9e-19  Score=154.55  Aligned_cols=170  Identities=19%  Similarity=0.285  Sum_probs=117.8

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCc---eeEEecCCCCChHHHHHHHHHHcC-------CcEEEEeCCcccC---
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKR---GYLLYGPPGTGKSSLIAAMANYLK-------FDVYDLELSNLLG---   69 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~---~iLl~GppGtGKT~la~ala~~~~-------~~~~~i~~~~~~~---   69 (266)
                      +++|++|.+. ..++.....+...|+.++.   +++|+||||||||++|+++|..+.       .+++.++...+.+   
T Consensus        29 ~~vK~~i~e~-~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~l~~~~~  107 (287)
T CHL00181         29 APVKTRIREI-AALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDLVGQYI  107 (287)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHHHHHHHh
Confidence            3566666664 4555566777778876542   489999999999999999998762       3578888665432   


Q ss_pred             ---hhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEE
Q 024550           70 ---NNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERII  146 (266)
Q Consensus        70 ---~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~iv  146 (266)
                         ......++..+ .++||||||++.+......                  .......+..|+..|+...    ..++|
T Consensus       108 g~~~~~~~~~l~~a-~ggVLfIDE~~~l~~~~~~------------------~~~~~e~~~~L~~~me~~~----~~~~v  164 (287)
T CHL00181        108 GHTAPKTKEVLKKA-MGGVLFIDEAYYLYKPDNE------------------RDYGSEAIEILLQVMENQR----DDLVV  164 (287)
T ss_pred             ccchHHHHHHHHHc-cCCEEEEEccchhccCCCc------------------cchHHHHHHHHHHHHhcCC----CCEEE
Confidence               22334455544 5689999999988531100                  0112345666777776532    45677


Q ss_pred             EEecCCC-----CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHH
Q 024550          147 IFTTNHK-----ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVE  198 (266)
Q Consensus       147 i~ttn~~-----~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~  198 (266)
                      |++++..     -.++|+|.+  ||+..|+|+.|+.+++.+|+..++......+..+
T Consensus       165 I~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~  219 (287)
T CHL00181        165 IFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPE  219 (287)
T ss_pred             EEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChh
Confidence            7776532     134699999  9999999999999999999999998766555443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.82  E-value=5.5e-19  Score=151.39  Aligned_cols=169  Identities=18%  Similarity=0.268  Sum_probs=115.0

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCC---ceeEEecCCCCChHHHHHHHHHHc-------CCcEEEEeCCcccC----
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWK---RGYLLYGPPGTGKSSLIAAMANYL-------KFDVYDLELSNLLG----   69 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~---~~iLl~GppGtGKT~la~ala~~~-------~~~~~~i~~~~~~~----   69 (266)
                      ++|+.|.+. ..++.........|..++   .+++||||||||||++|+++|+.+       ..+++.++++++.+    
T Consensus        13 ~vk~~i~~~-~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~~l~~~~~g   91 (261)
T TIGR02881        13 EVKALIKEI-YAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERADLVGEYIG   91 (261)
T ss_pred             HHHHHHHHH-HHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHHHhhhhhcc
Confidence            456666554 455555555556676533   358999999999999999999875       24677777766543    


Q ss_pred             --hhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEE
Q 024550           70 --NNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIII  147 (266)
Q Consensus        70 --~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi  147 (266)
                        ...+..+|..+ .++||||||+|.|.....                   .......+..++..|+..    ...+++|
T Consensus        92 ~~~~~~~~~~~~a-~~~VL~IDE~~~L~~~~~-------------------~~~~~~~i~~Ll~~~e~~----~~~~~vi  147 (261)
T TIGR02881        92 HTAQKTREVIKKA-LGGVLFIDEAYSLARGGE-------------------KDFGKEAIDTLVKGMEDN----RNEFVLI  147 (261)
T ss_pred             chHHHHHHHHHhc-cCCEEEEechhhhccCCc-------------------cchHHHHHHHHHHHHhcc----CCCEEEE
Confidence              23445666554 478999999998852000                   011133566677777754    2345566


Q ss_pred             EecCCC-----CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH
Q 024550          148 FTTNHK-----ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEI  199 (266)
Q Consensus       148 ~ttn~~-----~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~  199 (266)
                      +++...     ..++|+|.+  ||+..|+||.++.+++.+|++.++......+.++.
T Consensus       148 la~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a  202 (261)
T TIGR02881       148 LAGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEEA  202 (261)
T ss_pred             ecCCcchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHH
Confidence            555432     236889999  99999999999999999999999976655554443

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

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.81  E-value=8.1e-19  Score=151.79  Aligned_cols=170  Identities=18%  Similarity=0.293  Sum_probs=120.1

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCC---CceeEEecCCCCChHHHHHHHHHHcC-------CcEEEEeCCcccC----
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAW---KRGYLLYGPPGTGKSSLIAAMANYLK-------FDVYDLELSNLLG----   69 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~---~~~iLl~GppGtGKT~la~ala~~~~-------~~~~~i~~~~~~~----   69 (266)
                      ++|+++.+ +..++..+..+...|+..   +.+++|+||||||||++|+++|..+.       .+++.+++.++..    
T Consensus        29 ~vk~~i~e-~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~~~~~g  107 (284)
T TIGR02880        29 PVKTRIRE-IAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIG  107 (284)
T ss_pred             HHHHHHHH-HHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHHhHhhcc
Confidence            45666655 455577777888888764   34799999999999999999998773       3688888765532    


Q ss_pred             --hhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEE
Q 024550           70 --NNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIII  147 (266)
Q Consensus        70 --~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi  147 (266)
                        ...+..+|..+ .++||||||++.+......                  .......++.|+..|+..    ..++++|
T Consensus       108 ~~~~~~~~~~~~a-~~gvL~iDEi~~L~~~~~~------------------~~~~~~~~~~Ll~~le~~----~~~~~vI  164 (284)
T TIGR02880       108 HTAPKTKEILKRA-MGGVLFIDEAYYLYRPDNE------------------RDYGQEAIEILLQVMENQ----RDDLVVI  164 (284)
T ss_pred             cchHHHHHHHHHc-cCcEEEEechhhhccCCCc------------------cchHHHHHHHHHHHHhcC----CCCEEEE
Confidence              23344555554 4699999999988531100                  011234566777777643    2457777


Q ss_pred             EecCCC--C---CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH
Q 024550          148 FTTNHK--E---RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEI  199 (266)
Q Consensus       148 ~ttn~~--~---~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~  199 (266)
                      ++++..  +   .++|+|.+  ||...|+||.++.+++..|+..++......+..+.
T Consensus       165 ~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a  219 (284)
T TIGR02880       165 LAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEA  219 (284)
T ss_pred             EeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHH
Confidence            776532  2   24899999  99999999999999999999999988665554433

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.

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

Probab=99.80  E-value=3.5e-19  Score=155.22  Aligned_cols=141  Identities=19%  Similarity=0.252  Sum_probs=106.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC-----hhhHHHHHHHc---ccCCeeeeecchhhHHHhHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG-----NNDLRHILIAT---ENKSILVVEDIDCCIELQDRL  101 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~-----~~~l~~~~~~~---~~~~vl~iDeid~l~~~~~~~  101 (266)
                      |=++|+||||||||||++|+.||...|..+-.....++..     -..++.+|+=+   ..+-+|||||.|.++-.+...
T Consensus       383 pfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnkt  462 (630)
T KOG0742|consen  383 PFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKT  462 (630)
T ss_pred             hhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCccccchHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchh
Confidence            4467999999999999999999999998876666555542     24466666533   457899999999987543322


Q ss_pred             hhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHH
Q 024550          102 SRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFK  181 (266)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~  181 (266)
                      -               .+......+|.||-.--..    +..++++.+||+|..+|.++-.  |++..|+||+|..++|.
T Consensus       463 y---------------mSEaqRsaLNAlLfRTGdq----SrdivLvlAtNrpgdlDsAV~D--Ride~veFpLPGeEERf  521 (630)
T KOG0742|consen  463 Y---------------MSEAQRSALNALLFRTGDQ----SRDIVLVLATNRPGDLDSAVND--RIDEVVEFPLPGEEERF  521 (630)
T ss_pred             h---------------hcHHHHHHHHHHHHHhccc----ccceEEEeccCCccchhHHHHh--hhhheeecCCCChHHHH
Confidence            1               1233445566655443222    3568889999999999999999  99999999999999999


Q ss_pred             HHHHHhhCCC
Q 024550          182 MLASNYLGIA  191 (266)
Q Consensus       182 ~i~~~~~~~~  191 (266)
                      +|+..|+.+.
T Consensus       522 kll~lYlnky  531 (630)
T KOG0742|consen  522 KLLNLYLNKY  531 (630)
T ss_pred             HHHHHHHHHH
Confidence            9999888543

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

Probab=99.80  E-value=3.6e-19  Score=164.03  Aligned_cols=218  Identities=17%  Similarity=0.246  Sum_probs=150.0

Q ss_pred             CChHHH--HHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh--------
Q 024550            1 MDFDMK--KMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN--------   70 (266)
Q Consensus         1 l~~~~~--~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~--------   70 (266)
                      ||++|.  .++.+.+.+|+....+..   -..++-+.|+||||+|||++++++|..+|..|++++...+.+.        
T Consensus       409 LdeDHYgm~dVKeRILEfiAV~kLrg---s~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHRR  485 (906)
T KOG2004|consen  409 LDEDHYGMEDVKERILEFIAVGKLRG---SVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRR  485 (906)
T ss_pred             hcccccchHHHHHHHHHHHHHHhhcc---cCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhcccce
Confidence            455554  566777777777665533   2234458899999999999999999999999999999887642        


Q ss_pred             -------hhHHHHHHHc-ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCC
Q 024550           71 -------NDLRHILIAT-ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGD  142 (266)
Q Consensus        71 -------~~l~~~~~~~-~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  142 (266)
                             ..+.+.+.+. ..+.+++|||+|.+..       ....+|...++-..+.++....+..+|+.--.+     .
T Consensus       486 TYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~-------g~qGDPasALLElLDPEQNanFlDHYLdVp~DL-----S  553 (906)
T KOG2004|consen  486 TYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGS-------GHQGDPASALLELLDPEQNANFLDHYLDVPVDL-----S  553 (906)
T ss_pred             eeeccCChHHHHHHHhhCCCCceEEeehhhhhCC-------CCCCChHHHHHHhcChhhccchhhhccccccch-----h
Confidence                   2333444444 3688999999999863       112223333334444555566666666665555     5


Q ss_pred             ceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHcCCC
Q 024550          143 ERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEA  222 (266)
Q Consensus       143 ~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~~~~  222 (266)
                      .++||||.|..+.+|++|+.  |+ ..|+++-+..++..+|.++|+-..-   ..++.---.....+-..+.. +..+++
T Consensus       554 kVLFicTAN~idtIP~pLlD--RM-EvIelsGYv~eEKv~IA~~yLip~a---~~~~gl~~e~v~is~~al~~-lI~~Yc  626 (906)
T KOG2004|consen  554 KVLFICTANVIDTIPPPLLD--RM-EVIELSGYVAEEKVKIAERYLIPQA---LKDCGLKPEQVKISDDALLA-LIERYC  626 (906)
T ss_pred             heEEEEeccccccCChhhhh--hh-heeeccCccHHHHHHHHHHhhhhHH---HHHcCCCHHhcCccHHHHHH-HHHHHH
Confidence            69999999999999999999  99 4599999999999999999984321   00110000111233333333 344667


Q ss_pred             HHHHHHHHHHHHHhhhhh
Q 024550          223 PEFALSGLIEFLESKKRA  240 (266)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~  240 (266)
                      .+..++.+.+.++...++
T Consensus       627 rEaGVRnLqk~iekI~Rk  644 (906)
T KOG2004|consen  627 REAGVRNLQKQIEKICRK  644 (906)
T ss_pred             HHHhHHHHHHHHHHHHHH
Confidence            888899888888887776

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.78  E-value=6.1e-18  Score=149.58  Aligned_cols=160  Identities=19%  Similarity=0.209  Sum_probs=121.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANP  109 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~  109 (266)
                      ++.++|||||||||||++++++|++++..+..++...+.....+..++.....++||||||+|.+.......        
T Consensus        50 ~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~~~~~~l~~~l~~l~~~~vl~IDEi~~l~~~~~e~--------  121 (328)
T PRK00080         50 ALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEI--------  121 (328)
T ss_pred             CCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccccChHHHHHHHHhcccCCEEEEecHhhcchHHHHH--------
Confidence            355799999999999999999999999998887776665666677777777889999999999885422111        


Q ss_pred             ccccccccccccchhhhhhhhhhhhccc---------c-----CCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCC
Q 024550          110 DFLIAGYEQQKQYHITLSGLLNFIDGLW---------S-----SCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHC  175 (266)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~-----~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p  175 (266)
                                         +...++...         .     ..-.++.+|++||++..++++|.+  ||+..+.|+.|
T Consensus       122 -------------------l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~  180 (328)
T PRK00080        122 -------------------LYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRD--RFGIVQRLEFY  180 (328)
T ss_pred             -------------------HHHHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHH--hcCeeeecCCC
Confidence                               111111100         0     001246789999999999999999  99999999999


Q ss_pred             CHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHHH
Q 024550          176 TPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQLM  218 (266)
Q Consensus       176 ~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l~  218 (266)
                      +.+++.+|+.......+..... .+..++...+.+|+.+...+.
T Consensus       181 ~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~  224 (328)
T PRK00080        181 TVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLR  224 (328)
T ss_pred             CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHH
Confidence            9999999999998887766654 456667777778877766663

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

Probab=99.78  E-value=9.2e-18  Score=139.16  Aligned_cols=190  Identities=20%  Similarity=0.247  Sum_probs=142.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIA   79 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~   79 (266)
                      +.+|+.+.+....|+...         +..++||||++|||||++++++..++   |..++++.-..+..-..+...+..
T Consensus        33 e~Qk~~l~~Nt~~Fl~G~---------pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~L~~l~~l~~~l~~  103 (249)
T PF05673_consen   33 ERQKEALIENTEQFLQGL---------PANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKEDLGDLPELLDLLRD  103 (249)
T ss_pred             HHHHHHHHHHHHHHHcCC---------CCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHHhccHHHHHHHHhc
Confidence            356777777777777553         35689999999999999999999877   788999999888877778788877


Q ss_pred             cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           80 TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                      .+.+-|||+||+-.                          .........|...|+|..+..+.+++|.+|+|+...++..
T Consensus       104 ~~~kFIlf~DDLsF--------------------------e~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~  157 (249)
T PF05673_consen  104 RPYKFILFCDDLSF--------------------------EEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPES  157 (249)
T ss_pred             CCCCEEEEecCCCC--------------------------CCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccchh
Confidence            78899999998762                          3334456778888898888888999999999975444322


Q ss_pred             ccC---------------------CCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHH
Q 024550          160 LLR---------------------PGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLM  218 (266)
Q Consensus       160 l~r---------------------~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~  218 (266)
                      +..                     ..||+..|.|..|+.++..+|+..++...+.....+-        +....+...+.
T Consensus       158 ~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~--------l~~~Al~wa~~  229 (249)
T PF05673_consen  158 FSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEE--------LRQEALQWALR  229 (249)
T ss_pred             hhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH--------HHHHHHHHHHH
Confidence            211                     1299999999999999999999999988776665322        22233555555


Q ss_pred             cCCCHHHHHHHHHHHHH
Q 024550          219 RNEAPEFALSGLIEFLE  235 (266)
Q Consensus       219 ~~~~~~~~~~~~~~~~~  235 (266)
                      ++...-.++.++..++.
T Consensus       230 rg~RSGRtA~QF~~~l~  246 (249)
T PF05673_consen  230 RGGRSGRTARQFIDDLA  246 (249)
T ss_pred             cCCCCHHHHHHHHHHHh
Confidence            55555555566665554

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.78  E-value=1e-17  Score=146.67  Aligned_cols=158  Identities=20%  Similarity=0.233  Sum_probs=116.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPD  110 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~  110 (266)
                      +.+++||||||||||++++++|++++.++..++.........+...+.....+.+|||||++.+......          
T Consensus        30 ~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vl~iDEi~~l~~~~~e----------   99 (305)
T TIGR00635        30 LDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEE----------   99 (305)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcCchhHHHHHHhcccCCEEEEehHhhhCHHHHH----------
Confidence            4569999999999999999999999998887776655555566677777778899999999988642211          


Q ss_pred             cccccccccccchhhhhhhhhhhhccc--------------cCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCC
Q 024550          111 FLIAGYEQQKQYHITLSGLLNFIDGLW--------------SSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCT  176 (266)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~ll~~l~~~~--------------~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~  176 (266)
                                       .+++.++...              .....++++|++||++..+++++.+  ||+..+.++.|+
T Consensus       100 -----------------~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~s--R~~~~~~l~~l~  160 (305)
T TIGR00635       100 -----------------LLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRD--RFGIILRLEFYT  160 (305)
T ss_pred             -----------------HhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHh--hcceEEEeCCCC
Confidence                             1122211100              0111347899999999999999999  999999999999


Q ss_pred             HHHHHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          177 PSGFKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       177 ~~~~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+++.+++.......+.....+ +..++...+.+|+.+.+.+
T Consensus       161 ~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll  202 (305)
T TIGR00635       161 VEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLL  202 (305)
T ss_pred             HHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHH
Confidence            9999999998887666555443 4566666666676665544

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

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

Probab=99.78  E-value=7.1e-19  Score=149.18  Aligned_cols=146  Identities=21%  Similarity=0.352  Sum_probs=114.3

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccC------hhhHHHHHHHcc-----cCC--e
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLG------NNDLRHILIATE-----NKS--I   85 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~------~~~l~~~~~~~~-----~~~--v   85 (266)
                      +.+.+-+||+||||||||+|++++|..+         ...++++++..+.+      ...+..+|.+..     +++  .
T Consensus       174 It~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVf  253 (423)
T KOG0744|consen  174 ITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVF  253 (423)
T ss_pred             eeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEE
Confidence            3455679999999999999999999987         46788899887763      344556665432     233  4


Q ss_pred             eeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCc
Q 024550           86 LVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGR  165 (266)
Q Consensus        86 l~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~R  165 (266)
                      ++|||++++...|.......            ...+.-+.++.+|..||.+...  .++++++|+|-.+.+|-||..  |
T Consensus       254 vLIDEVESLa~aR~s~~S~~------------EpsDaIRvVNalLTQlDrlK~~--~NvliL~TSNl~~siD~AfVD--R  317 (423)
T KOG0744|consen  254 VLIDEVESLAAARTSASSRN------------EPSDAIRVVNALLTQLDRLKRY--PNVLILATSNLTDSIDVAFVD--R  317 (423)
T ss_pred             EEeHHHHHHHHHHHhhhcCC------------CCchHHHHHHHHHHHHHHhccC--CCEEEEeccchHHHHHHHhhh--H
Confidence            55999999988664332211            1245568899999999988665  569999999999999999999  9


Q ss_pred             ceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          166 MDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       166 f~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      -+.+.++.+|+...+.+|++..+.
T Consensus       318 ADi~~yVG~Pt~~ai~~Ilkscie  341 (423)
T KOG0744|consen  318 ADIVFYVGPPTAEAIYEILKSCIE  341 (423)
T ss_pred             hhheeecCCccHHHHHHHHHHHHH
Confidence            999999999999999999987763

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

Probab=99.78  E-value=4.7e-18  Score=157.26  Aligned_cols=208  Identities=18%  Similarity=0.207  Sum_probs=132.2

Q ss_pred             HHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChh---------------
Q 024550            7 KMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNN---------------   71 (266)
Q Consensus         7 ~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~---------------   71 (266)
                      ..+.+.+.+||....+....   ...-++|+||||+|||+|++++|+.+|..|+.++...+.+++               
T Consensus       329 ekVKeRIlEyLAV~~l~~~~---kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHRRTYIGamPG  405 (782)
T COG0466         329 EKVKERILEYLAVQKLTKKL---KGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPG  405 (782)
T ss_pred             hhHHHHHHHHHHHHHHhccC---CCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhccccccccccCCh
Confidence            45566667777666544322   123588999999999999999999999999999999887532               


Q ss_pred             hHHHHHHHc-ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEec
Q 024550           72 DLRHILIAT-ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTT  150 (266)
Q Consensus        72 ~l~~~~~~~-~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~tt  150 (266)
                      .+.+.+.++ ..+.|++|||||.+...       ..-+|...++-..+.++.......+|+.--.+     ..|+||+|+
T Consensus       406 rIiQ~mkka~~~NPv~LLDEIDKm~ss-------~rGDPaSALLEVLDPEQN~~F~DhYLev~yDL-----S~VmFiaTA  473 (782)
T COG0466         406 KIIQGMKKAGVKNPVFLLDEIDKMGSS-------FRGDPASALLEVLDPEQNNTFSDHYLEVPYDL-----SKVMFIATA  473 (782)
T ss_pred             HHHHHHHHhCCcCCeEEeechhhccCC-------CCCChHHHHHhhcCHhhcCchhhccccCccch-----hheEEEeec
Confidence            233333333 46899999999998641       11112212222223333333333344332233     469999999


Q ss_pred             CCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHH--HHh-hcCCCCHHHHHHHHHcCCCHHHHH
Q 024550          151 NHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIE--KLI-ATAKVTPADVAEQLMRNEAPEFAL  227 (266)
Q Consensus       151 n~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~--~l~-~~~~~s~~~i~~~l~~~~~~~~~~  227 (266)
                      |..+.+|.+|+.  |+ .+|+++-++.++..+|.++|+=..      .+.  .+- ....++...|..++ +.+.++..+
T Consensus       474 Nsl~tIP~PLlD--RM-EiI~lsgYt~~EKl~IAk~~LiPk------~~~~~gL~~~el~i~d~ai~~iI-~~YTREAGV  543 (782)
T COG0466         474 NSLDTIPAPLLD--RM-EVIRLSGYTEDEKLEIAKRHLIPK------QLKEHGLKKGELTITDEAIKDII-RYYTREAGV  543 (782)
T ss_pred             CccccCChHHhc--ce-eeeeecCCChHHHHHHHHHhcchH------HHHHcCCCccceeecHHHHHHHH-HHHhHhhhh
Confidence            999999999999  99 569999999999999999988321      111  011 11224444444433 344555555


Q ss_pred             HHHHHHHHhhhh
Q 024550          228 SGLIEFLESKKR  239 (266)
Q Consensus       228 ~~~~~~~~~~~~  239 (266)
                      +.+..-+...-+
T Consensus       544 R~LeR~i~ki~R  555 (782)
T COG0466         544 RNLEREIAKICR  555 (782)
T ss_pred             hHHHHHHHHHHH
Confidence            555555444433

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

Probab=99.78  E-value=4.3e-18  Score=148.54  Aligned_cols=122  Identities=28%  Similarity=0.398  Sum_probs=98.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcc------cCCeeeeecchhhHHHhHHHhhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATE------NKSILVVEDIDCCIELQDRLSRA  104 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~------~~~vl~iDeid~l~~~~~~~~~~  104 (266)
                      -.+++|||||||||||+|+.+|..++.+|..+++... +...++.++..+.      +..|||||||+.+-         
T Consensus        48 l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~~-gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfn---------  117 (436)
T COG2256          48 LHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTS-GVKDLREIIEEARKNRLLGRRTILFLDEIHRFN---------  117 (436)
T ss_pred             CceeEEECCCCCCHHHHHHHHHHhhCCceEEeccccc-cHHHHHHHHHHHHHHHhcCCceEEEEehhhhcC---------
Confidence            3569999999999999999999999999999997665 5567888887763      37999999999773         


Q ss_pred             hhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEec--CCCCCCcccccCCCcceeEEEcCCCCHHHHHH
Q 024550          105 RAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTT--NHKERLDPALLRPGRMDMHINMSHCTPSGFKM  182 (266)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~tt--n~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~  182 (266)
                                        +..+..||-.++.      ..+++|++|  |+.-.++++|++  |+ .++.+...+.++..+
T Consensus       118 ------------------K~QQD~lLp~vE~------G~iilIGATTENPsF~ln~ALlS--R~-~vf~lk~L~~~di~~  170 (436)
T COG2256         118 ------------------KAQQDALLPHVEN------GTIILIGATTENPSFELNPALLS--RA-RVFELKPLSSEDIKK  170 (436)
T ss_pred             ------------------hhhhhhhhhhhcC------CeEEEEeccCCCCCeeecHHHhh--hh-heeeeecCCHHHHHH
Confidence                              3344567777774      347778755  455678999999  87 568999999999999


Q ss_pred             HHHHhhC
Q 024550          183 LASNYLG  189 (266)
Q Consensus       183 i~~~~~~  189 (266)
                      ++.+.+.
T Consensus       171 ~l~ra~~  177 (436)
T COG2256         171 LLKRALL  177 (436)
T ss_pred             HHHHHHh
Confidence            9988443

>TIGR00763 lon ATP-dependent protease La

Probab=99.74  E-value=3.1e-17  Score=159.68  Aligned_cols=132  Identities=25%  Similarity=0.276  Sum_probs=96.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC---------------hhhHHHHHHHc-ccCCeeeeecchhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG---------------NNDLRHILIAT-ENKSILVVEDIDCC   94 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~---------------~~~l~~~~~~~-~~~~vl~iDeid~l   94 (266)
                      +..++|+||||||||++|+++|+.++.+++.+++.....               ...+...|..+ ..+.|++|||||.+
T Consensus       347 ~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~g~i~~~l~~~~~~~~villDEidk~  426 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNPLFLLDEIDKI  426 (775)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCCCCchHHHHHHHhCcCCCEEEEechhhc
Confidence            346999999999999999999999999999998765432               12344455443 34569999999998


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc-----ccc------CCCCceEEEEecCCCCCCcccccCC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG-----LWS------SCGDERIIIFTTNHKERLDPALLRP  163 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~-----~~~------~~~~~~ivi~ttn~~~~ld~al~r~  163 (266)
                      ....                       .....+.|+..|+.     +..      ....+++||+|||.++.++++|++ 
T Consensus       427 ~~~~-----------------------~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~L~~-  482 (775)
T TIGR00763       427 GSSF-----------------------RGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPLLD-  482 (775)
T ss_pred             CCcc-----------------------CCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCchhCCHHHhC-
Confidence            6310                       00112334444331     000      011468899999999999999999 


Q ss_pred             CcceeEEEcCCCCHHHHHHHHHHhh
Q 024550          164 GRMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       164 ~Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                       ||. .|+|+.|+.+++.+|++.++
T Consensus       483 -R~~-vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       483 -RME-VIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             -Cee-EEecCCCCHHHHHHHHHHHH
Confidence             995 69999999999999998887

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.

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

Probab=99.69  E-value=3.2e-16  Score=145.73  Aligned_cols=170  Identities=18%  Similarity=0.228  Sum_probs=128.5

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHHHHcc--cCCeeeeecchhhHHHhH
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHILIATE--NKSILVVEDIDCCIELQD   99 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~~~~~--~~~vl~iDeid~l~~~~~   99 (266)
                      +.....+||+|+||||||++++++|+++|.++++++|.++..      +..+..+|.++.  +|+|||+-++|.+...++
T Consensus       428 ~~~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~d  507 (953)
T KOG0736|consen  428 LTLNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQD  507 (953)
T ss_pred             cccceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCC
Confidence            334456999999999999999999999999999999998873      456778887764  799999999998863111


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhh-ccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHH
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID-GLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPS  178 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~-~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~  178 (266)
                      .                   +.....+..+-..+. ........+++||+||+..+.+++.+.+  .|.+.|.++.|+.+
T Consensus       508 g-------------------ged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~  566 (953)
T KOG0736|consen  508 G-------------------GEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEE  566 (953)
T ss_pred             C-------------------chhHHHHHHHHHHHhcccccCCCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHH
Confidence            1                   111222222222222 1122234679999999999999999999  99999999999999


Q ss_pred             HHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          179 GFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       179 ~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      +|.+|++.|+.............++.+ .+|+.+++..+..
T Consensus       567 qRl~iLq~y~~~~~~n~~v~~k~~a~~t~gfs~~~L~~l~~  607 (953)
T KOG0736|consen  567 QRLEILQWYLNHLPLNQDVNLKQLARKTSGFSFGDLEALVA  607 (953)
T ss_pred             HHHHHHHHHHhccccchHHHHHHHHHhcCCCCHHHHHHHhc
Confidence            999999999987765555555566665 5699999988764

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.69  E-value=3.7e-16  Score=141.95  Aligned_cols=153  Identities=13%  Similarity=0.267  Sum_probs=109.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHHc------
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIAT------   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~~------   80 (266)
                      ++.+|||||||||||++|+.+|+.+++.                        +++++...-.+...++.+....      
T Consensus        40 ~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~  119 (484)
T PRK14956         40 GHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMG  119 (484)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhhcccHHHHHHHHHHHHhhhhc
Confidence            4579999999999999999999998763                        4455543322333444443322      


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                      ....|++|||+|.+..                           ...+.||..|+.    .+..++||.+|+.+..+++++
T Consensus       120 g~~KV~IIDEah~Ls~---------------------------~A~NALLKtLEE----Pp~~viFILaTte~~kI~~TI  168 (484)
T PRK14956        120 GKYKVYIIDEVHMLTD---------------------------QSFNALLKTLEE----PPAHIVFILATTEFHKIPETI  168 (484)
T ss_pred             CCCEEEEEechhhcCH---------------------------HHHHHHHHHhhc----CCCceEEEeecCChhhccHHH
Confidence            2356999999998742                           245667777764    345688999999999999999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++  || ..+.|..++.++..+.+++....++..... .+..++...+.++++..++|
T Consensus       169 ~S--RC-q~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~Gd~RdAL~lL  223 (484)
T PRK14956        169 LS--RC-QDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLSFM  223 (484)
T ss_pred             Hh--hh-heeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCChHHHHHHHH
Confidence            99  98 569999999999999898888777665543 33445555556666655554

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.69  E-value=7e-16  Score=141.66  Aligned_cols=154  Identities=17%  Similarity=0.278  Sum_probs=108.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++++|||||||||||++|+++|+.+++                        .++.++++.-.+...++.+....     
T Consensus        35 l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~~~gid~iR~i~~~~~~~p~  114 (472)
T PRK14962         35 ISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAASNRGIDEIRKIRDAVGYRPM  114 (472)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcccCCHHHHHHHHHHHhhChh
Confidence            4567999999999999999999999865                        46666665433334445444332     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.+..                           ..++.|+..++..    +..+++|++|+.+..++++
T Consensus       115 ~~~~kVvIIDE~h~Lt~---------------------------~a~~~LLk~LE~p----~~~vv~Ilattn~~kl~~~  163 (472)
T PRK14962        115 EGKYKVYIIDEVHMLTK---------------------------EAFNALLKTLEEP----PSHVVFVLATTNLEKVPPT  163 (472)
T ss_pred             cCCeEEEEEEChHHhHH---------------------------HHHHHHHHHHHhC----CCcEEEEEEeCChHhhhHH
Confidence             2357999999998842                           1345667777643    3457777777778899999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  || ..+.|+.++.++...++.......+..+.. .+..++...+.+.+.+.+.+
T Consensus       164 L~S--R~-~vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~GdlR~aln~L  219 (472)
T PRK14962        164 IIS--RC-QVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTML  219 (472)
T ss_pred             Hhc--Cc-EEEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence            999  88 479999999999999998888766655544 34445554555555555444

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.69  E-value=6.7e-16  Score=145.58  Aligned_cols=154  Identities=15%  Similarity=0.261  Sum_probs=112.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+|||||+|||||++++.+|+.+++                        .+++++..+-.+...++.++....    
T Consensus        37 L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~  116 (830)
T PRK07003         37 LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPV  116 (830)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEEecccccccHHHHHHHHHHHHhccc
Confidence            3567999999999999999999998865                        345555543333344555555432    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|+||||+|.|..                           ...+.||+.|+.-    +..++||.+||.+..|.+.
T Consensus       117 ~gr~KVIIIDEah~LT~---------------------------~A~NALLKtLEEP----P~~v~FILaTtd~~KIp~T  165 (830)
T PRK07003        117 DARFKVYMIDEVHMLTN---------------------------HAFNAMLKTLEEP----PPHVKFILATTDPQKIPVT  165 (830)
T ss_pred             cCCceEEEEeChhhCCH---------------------------HHHHHHHHHHHhc----CCCeEEEEEECChhhccch
Confidence              357999999998842                           2456677777753    3468899999999999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..+.|..++.++..+.+++++..++..+..+ +..++.....+.++..+++
T Consensus       166 IrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~GsmRdALsLL  221 (830)
T PRK07003        166 VLS--RC-LQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALSLT  221 (830)
T ss_pred             hhh--he-EEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  99 6799999999999999999888776665443 3444444556666555553

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.68  E-value=3e-16  Score=146.09  Aligned_cols=153  Identities=16%  Similarity=0.293  Sum_probs=114.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCC-----------------------------cEEEEeCCcccChhhHHHHHHHc-
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKF-----------------------------DVYDLELSNLLGNNDLRHILIAT-   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~-----------------------------~~~~i~~~~~~~~~~l~~~~~~~-   80 (266)
                      ++.+||+||+|||||++++.+|+.+++                             .+++++..+-.+-..+++++... 
T Consensus        38 pHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~  117 (700)
T PRK12323         38 HHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAV  117 (700)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHH
Confidence            567999999999999999999999976                             34455544333344555555442 


Q ss_pred             -----ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           81 -----ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        81 -----~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                           .+..|++|||+|.|..                           ...|.||+.|+.    .+..++||.+||.++.
T Consensus       118 ~~P~~gr~KViIIDEah~Ls~---------------------------~AaNALLKTLEE----PP~~v~FILaTtep~k  166 (700)
T PRK12323        118 YAPTAGRFKVYMIDEVHMLTN---------------------------HAFNAMLKTLEE----PPEHVKFILATTDPQK  166 (700)
T ss_pred             hchhcCCceEEEEEChHhcCH---------------------------HHHHHHHHhhcc----CCCCceEEEEeCChHh
Confidence                 2357999999998732                           245667777664    3456899999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      |.+++++  || ..+.|+.++.++..+.+..++..++.....+ +..++...+.++++..+++
T Consensus       167 LlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~Gs~RdALsLL  226 (700)
T PRK12323        167 IPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALSLT  226 (700)
T ss_pred             hhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999999  98 6799999999999999888887766555443 4555666677777776665

>PRK04195 replication factor C large subunit; Provisional

Probab=99.68  E-value=2.5e-15  Score=139.34  Aligned_cols=155  Identities=18%  Similarity=0.265  Sum_probs=110.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHc--------ccCCeeeeecchhhHHHhHHHh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIAT--------ENKSILVVEDIDCCIELQDRLS  102 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~--------~~~~vl~iDeid~l~~~~~~~~  102 (266)
                      ++++|||||||||||++|+++|++++.+++.+++++......+..+....        ..+.+|+|||+|.+..      
T Consensus        39 ~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~r~~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~------  112 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDEVDGIHG------  112 (482)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEcccccccHHHHHHHHHHhhccCcccCCCCeEEEEecCccccc------
Confidence            67899999999999999999999999999999998776544444443322        2467999999998853      


Q ss_pred             hhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc-cccCCCcceeEEEcCCCCHHHHH
Q 024550          103 RARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP-ALLRPGRMDMHINMSHCTPSGFK  181 (266)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~-al~r~~Rf~~~i~~~~p~~~~~~  181 (266)
                                       .........+++.++.      .+..+|+++|.+..++. .+.+  |+ ..|.|+.|+..++.
T Consensus       113 -----------------~~d~~~~~aL~~~l~~------~~~~iIli~n~~~~~~~k~Lrs--r~-~~I~f~~~~~~~i~  166 (482)
T PRK04195        113 -----------------NEDRGGARAILELIKK------AKQPIILTANDPYDPSLRELRN--AC-LMIEFKRLSTRSIV  166 (482)
T ss_pred             -----------------ccchhHHHHHHHHHHc------CCCCEEEeccCccccchhhHhc--cc-eEEEecCCCHHHHH
Confidence                             1111233455555553      23456678888887776 5665  55 67999999999999


Q ss_pred             HHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          182 MLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       182 ~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .++..++...+.... ..+..++...+...+.+.+.|
T Consensus       167 ~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ain~L  203 (482)
T PRK04195        167 PVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDL  203 (482)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999998877766554 445555655555555554444

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.68  E-value=2.4e-15  Score=128.88  Aligned_cols=128  Identities=23%  Similarity=0.196  Sum_probs=91.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHH---------------------------------HHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLR---------------------------------HILI   78 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~---------------------------------~~~~   78 (266)
                      ..+||+||||||||++|+++|..+|.+++.+++..-.....+.                                 .++.
T Consensus        22 ~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~~  101 (262)
T TIGR02640        22 YPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLTL  101 (262)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCchHHH
Confidence            4699999999999999999999999999999887543322110                                 1112


Q ss_pred             HcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-c-----------CCCCceEE
Q 024550           79 ATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-S-----------SCGDERII  146 (266)
Q Consensus        79 ~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~-----------~~~~~~iv  146 (266)
                      ....+.+|+|||++.+.+                           .+.+.|+..|+... .           ....+..+
T Consensus       102 A~~~g~~lllDEi~r~~~---------------------------~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frv  154 (262)
T TIGR02640       102 AVREGFTLVYDEFTRSKP---------------------------ETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRV  154 (262)
T ss_pred             HHHcCCEEEEcchhhCCH---------------------------HHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEE
Confidence            234578999999997643                           23344444443211 0           01135678


Q ss_pred             EEecCCC-----CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          147 IFTTNHK-----ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       147 i~ttn~~-----~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      |+|+|..     ..++++|++  || ..+.++.|+.++..+|+...++
T Consensus       155 IaTsN~~~~~g~~~l~~aL~~--R~-~~i~i~~P~~~~e~~Il~~~~~  199 (262)
T TIGR02640       155 IFTSNPVEYAGVHETQDALLD--RL-ITIFMDYPDIDTETAILRAKTD  199 (262)
T ss_pred             EEeeCCccccceecccHHHHh--hc-EEEECCCCCHHHHHHHHHHhhC
Confidence            9999975     356899999  98 6799999999999999998764

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).

>PRK06893 DNA replication initiation factor; Validated

Probab=99.67  E-value=8.3e-16  Score=129.17  Aligned_cols=158  Identities=16%  Similarity=0.195  Sum_probs=102.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAAN  108 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~  108 (266)
                      ..++||||||||||+|++++|+++   +....+++.....  ......+....+..+|+|||++.+.+            
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~~--~~~~~~~~~~~~~dlLilDDi~~~~~------------  105 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQ--YFSPAVLENLEQQDLVCLDDLQAVIG------------  105 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHhh--hhhHHHHhhcccCCEEEEeChhhhcC------------
Confidence            358999999999999999999986   3445555543221  11224455566778999999998753            


Q ss_pred             CccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc---ccccCCCcceeEEEcCCCCHHHHHHHHH
Q 024550          109 PDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD---PALLRPGRMDMHINMSHCTPSGFKMLAS  185 (266)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld---~al~r~~Rf~~~i~~~~p~~~~~~~i~~  185 (266)
                                .......+..+++.+.   .. +..+++++++..|..++   +.|.++.+++..+.++.|+.+++.+|++
T Consensus       106 ----------~~~~~~~l~~l~n~~~---~~-~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~  171 (229)
T PRK06893        106 ----------NEEWELAIFDLFNRIK---EQ-GKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQ  171 (229)
T ss_pred             ----------ChHHHHHHHHHHHHHH---Hc-CCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHH
Confidence                      1111223334444332   21 12234455556666554   7899844556789999999999999999


Q ss_pred             HhhCCCCCCcHHHHH-HHhhcCCCCHHHHHHHH
Q 024550          186 NYLGIAEHPLFVEIE-KLIATAKVTPADVAEQL  217 (266)
Q Consensus       186 ~~~~~~~~~~~~~~~-~l~~~~~~s~~~i~~~l  217 (266)
                      +.....+..+.++.. .++....-+.+.+...+
T Consensus       172 ~~a~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l  204 (229)
T PRK06893        172 RNAYQRGIELSDEVANFLLKRLDRDMHTLFDAL  204 (229)
T ss_pred             HHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHH
Confidence            888766666655544 44555556666666554

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

Probab=99.67  E-value=2.5e-16  Score=152.57  Aligned_cols=134  Identities=20%  Similarity=0.250  Sum_probs=98.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHHcc--cCCeeeee
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIATE--NKSILVVE   89 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~~~--~~~vl~iD   89 (266)
                      ...+++||||||||||++++++|..+          +..++.+++..+...        ..+..++..+.  .++|||||
T Consensus       202 ~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiD  281 (731)
T TIGR02639       202 KKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFID  281 (731)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEe
Confidence            35679999999999999999999987          778899887766532        46777777653  48899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-----CCCcccccCCC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-----ERLDPALLRPG  164 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-----~~ld~al~r~~  164 (266)
                      |+|.+.+.....                  .......+.|...+..      ..+.+|++||..     -..|++|.|  
T Consensus       282 Eih~l~~~g~~~------------------~~~~~~~~~L~~~l~~------g~i~~IgaTt~~e~~~~~~~d~al~r--  335 (731)
T TIGR02639       282 EIHTIVGAGATS------------------GGSMDASNLLKPALSS------GKLRCIGSTTYEEYKNHFEKDRALSR--  335 (731)
T ss_pred             cHHHHhccCCCC------------------CccHHHHHHHHHHHhC------CCeEEEEecCHHHHHHHhhhhHHHHH--
Confidence            999997522110                  0001122333344432      468899999863     346999999  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      ||. .|+++.|+.+++.+|++.....
T Consensus       336 Rf~-~i~v~~p~~~~~~~il~~~~~~  360 (731)
T TIGR02639       336 RFQ-KIDVGEPSIEETVKILKGLKEK  360 (731)
T ss_pred             hCc-eEEeCCCCHHHHHHHHHHHHHH
Confidence            996 6999999999999999866643

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=1.5e-15  Score=141.71  Aligned_cols=154  Identities=14%  Similarity=0.246  Sum_probs=114.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++.+||+||||||||++|+++|+.+++                        .++.++.++-.+...++.++...     
T Consensus        36 l~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~  115 (702)
T PRK14960         36 LHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPT  115 (702)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhhhh
Confidence            3578999999999999999999999865                        45566655444445566665543     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.|..                           ...+.|+..|+.-    +..+.||.+|+.+..+++.
T Consensus       116 ~gk~KV~IIDEVh~LS~---------------------------~A~NALLKtLEEP----P~~v~FILaTtd~~kIp~T  164 (702)
T PRK14960        116 QGRFKVYLIDEVHMLST---------------------------HSFNALLKTLEEP----PEHVKFLFATTDPQKLPIT  164 (702)
T ss_pred             cCCcEEEEEechHhcCH---------------------------HHHHHHHHHHhcC----CCCcEEEEEECChHhhhHH
Confidence             2357999999998742                           2445677777643    3457788888888888999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..++|..++.++..+.+.+.+..++..... .+..++...+.+.+++.+.+
T Consensus       165 IlS--RC-q~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~GdLRdALnLL  220 (702)
T PRK14960        165 VIS--RC-LQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDALSLT  220 (702)
T ss_pred             HHH--hh-heeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            998  88 669999999999999999998887766654 44556666667777776664

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

Probab=99.65  E-value=2.7e-15  Score=145.32  Aligned_cols=132  Identities=22%  Similarity=0.224  Sum_probs=94.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChh---------------hHHHHHHHcc-cCCeeeeecchhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNN---------------DLRHILIATE-NKSILVVEDIDCC   94 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~---------------~l~~~~~~~~-~~~vl~iDeid~l   94 (266)
                      ...++|+||||||||++++.+|..++.+++.+++.......               .+...+.... .+.|++|||+|.+
T Consensus       349 g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~G~~~~~l~~~~~~~~villDEidk~  428 (784)
T PRK10787        349 GPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKM  428 (784)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccchhccCCCCCcHHHHHHHhcCCCCCEEEEEChhhc
Confidence            34699999999999999999999999999999887654321               2222333332 4679999999988


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc-----cc------CCCCceEEEEecCCCCCCcccccCC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL-----WS------SCGDERIIIFTTNHKERLDPALLRP  163 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----~~------~~~~~~ivi~ttn~~~~ld~al~r~  163 (266)
                      ....                       .....+.|+..++.-     ..      ..-.+++||+|+|.. .++++|++ 
T Consensus       429 ~~~~-----------------------~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~-  483 (784)
T PRK10787        429 SSDM-----------------------RGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLD-  483 (784)
T ss_pred             cccc-----------------------CCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhc-
Confidence            5411                       011233444444420     00      011468999999987 59999999 


Q ss_pred             CcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          164 GRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       164 ~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                       ||. .|.++.++.++..+|+++++-
T Consensus       484 -R~~-ii~~~~~t~eek~~Ia~~~L~  507 (784)
T PRK10787        484 -RME-VIRLSGYTEDEKLNIAKRHLL  507 (784)
T ss_pred             -cee-eeecCCCCHHHHHHHHHHhhh
Confidence             995 699999999999999999983

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=1.8e-15  Score=140.25  Aligned_cols=154  Identities=16%  Similarity=0.287  Sum_probs=113.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+|||||||||||++|+++|+.+++.                        +++++.++-.+-..++.+.....    
T Consensus        37 l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~  116 (509)
T PRK14958         37 LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPT  116 (509)
T ss_pred             CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccc
Confidence            36679999999999999999999999653                        56666654445555666655432    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        +..|++|||+|.|..                           ...+.|+..|+.-    +..++||.+|+.+..+.+.
T Consensus       117 ~~~~kV~iIDE~~~ls~---------------------------~a~naLLk~LEep----p~~~~fIlattd~~kl~~t  165 (509)
T PRK14958        117 KGRFKVYLIDEVHMLSG---------------------------HSFNALLKTLEEP----PSHVKFILATTDHHKLPVT  165 (509)
T ss_pred             cCCcEEEEEEChHhcCH---------------------------HHHHHHHHHHhcc----CCCeEEEEEECChHhchHH
Confidence              346999999998742                           2356677777753    3457788888888899989


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..++|..++.++....+...+..++..... .+..++...+.+++++.+.+
T Consensus       166 I~S--Rc-~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lL  221 (509)
T PRK14958        166 VLS--RC-LQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLL  221 (509)
T ss_pred             HHH--Hh-hhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence            999  88 668999999999888888888777666543 34455555566666666655

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.65  E-value=1.3e-14  Score=118.79  Aligned_cols=190  Identities=19%  Similarity=0.229  Sum_probs=138.4

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHc
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIAT   80 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~   80 (266)
                      .+|+.+.+...+|+...         |..++||||..|||||++++|+-.++   |..+++++-.++.+-..+...+...
T Consensus        67 ~qk~~L~~NT~~F~~G~---------pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k~dl~~Lp~l~~~Lr~~  137 (287)
T COG2607          67 RQKEALVRNTEQFAEGL---------PANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDKEDLATLPDLVELLRAR  137 (287)
T ss_pred             HHHHHHHHHHHHHHcCC---------cccceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcHHHHhhHHHHHHHHhcC
Confidence            35566666666665443         34579999999999999999999888   6789999999888878888888888


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                      .++.|||+||+-.                          .+.......|-..|+|-.+..+.+|+|.+|+|+...|+..+
T Consensus       138 ~~kFIlFcDDLSF--------------------------e~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~  191 (287)
T COG2607         138 PEKFILFCDDLSF--------------------------EEGDDAYKALKSALEGGVEGRPANVLFYATSNRRHLLPEDM  191 (287)
T ss_pred             CceEEEEecCCCC--------------------------CCCchHHHHHHHHhcCCcccCCCeEEEEEecCCcccccHhh
Confidence            9999999999863                          33345666777888988888888999999999865543221


Q ss_pred             c--------------------CCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHcC
Q 024550          161 L--------------------RPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRN  220 (266)
Q Consensus       161 ~--------------------r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~~  220 (266)
                      .                    -+.||+..+.|+.++.++..+|+.+|....+.....+--        -...+.+...++
T Consensus       192 ~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e~l--------~~eAl~WAt~rg  263 (287)
T COG2607         192 KDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDEEL--------HAEALQWATTRG  263 (287)
T ss_pred             hhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHHHH--------HHHHHHHHHhcC
Confidence            1                    123999999999999999999999999887766643221        122245555554


Q ss_pred             CCHHHHHHHHHHHHHh
Q 024550          221 EAPEFALSGLIEFLES  236 (266)
Q Consensus       221 ~~~~~~~~~~~~~~~~  236 (266)
                      .+.=..+.++...+..
T Consensus       264 ~RSGR~A~QF~~~~~g  279 (287)
T COG2607         264 GRSGRVAWQFIRDLAG  279 (287)
T ss_pred             CCccHhHHHHHHHHHh
Confidence            4333444444444433

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.65  E-value=1.2e-15  Score=149.07  Aligned_cols=132  Identities=18%  Similarity=0.231  Sum_probs=93.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccC--------hhhHHHHHHHcc---cCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLG--------NNDLRHILIATE---NKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~--------~~~l~~~~~~~~---~~~vl~iD   89 (266)
                      ..+++|+||||||||++++.+|..+          +.+++.++++.+..        ...+..++....   .++|||||
T Consensus       208 ~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfID  287 (852)
T TIGR03345       208 QNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFID  287 (852)
T ss_pred             cCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEe
Confidence            4579999999999999999999986          35577777766542        145666776553   57899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-----CCCcccccCCC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-----ERLDPALLRPG  164 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-----~~ld~al~r~~  164 (266)
                      |+|.+.+.++..                  . ....-+-|+..+.    .  ..+.+|+||+..     -.+|++|.|  
T Consensus       288 Eih~l~~~g~~~------------------~-~~d~~n~Lkp~l~----~--G~l~~IgaTT~~e~~~~~~~d~AL~r--  340 (852)
T TIGR03345       288 EAHTLIGAGGQA------------------G-QGDAANLLKPALA----R--GELRTIAATTWAEYKKYFEKDPALTR--  340 (852)
T ss_pred             ChHHhccCCCcc------------------c-cccHHHHhhHHhh----C--CCeEEEEecCHHHHhhhhhccHHHHH--
Confidence            999997522110                  0 0111122333333    2  468899988864     347999999  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      ||. .|.++.|+.++...|++.+...
T Consensus       341 Rf~-~i~v~eps~~~~~~iL~~~~~~  365 (852)
T TIGR03345       341 RFQ-VVKVEEPDEETAIRMLRGLAPV  365 (852)
T ss_pred             hCe-EEEeCCCCHHHHHHHHHHHHHh
Confidence            995 7999999999999997655543

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.64  E-value=5.4e-15  Score=132.38  Aligned_cols=154  Identities=15%  Similarity=0.223  Sum_probs=108.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+||+||||||||++|+++|+.+++                        .++.++.........++.+.....    
T Consensus        37 ~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~  116 (363)
T PRK14961         37 IHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPS  116 (363)
T ss_pred             CCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcc
Confidence            4567999999999999999999998863                        233444332223344555544421    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|++|||+|.+..                           ...+.++..++.-    +..+.+|.+|+.++.+.++
T Consensus       117 ~~~~kviIIDEa~~l~~---------------------------~a~naLLk~lEe~----~~~~~fIl~t~~~~~l~~t  165 (363)
T PRK14961        117 KSRFKVYLIDEVHMLSR---------------------------HSFNALLKTLEEP----PQHIKFILATTDVEKIPKT  165 (363)
T ss_pred             cCCceEEEEEChhhcCH---------------------------HHHHHHHHHHhcC----CCCeEEEEEcCChHhhhHH
Confidence              346999999998732                           2345577776643    3456777778888889999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  || ..++|+.|+.++...++...+...+..... .+..++...+.+++++.+.+
T Consensus       166 I~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l  221 (363)
T PRK14961        166 ILS--RC-LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLL  221 (363)
T ss_pred             HHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            998  88 679999999999999999888777655544 44555556667777666655

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.64  E-value=4.3e-15  Score=142.49  Aligned_cols=154  Identities=17%  Similarity=0.273  Sum_probs=110.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++.+|||||||||||++|+++|+.+++.                        +++++..+..+...++.+....     
T Consensus        37 l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~  116 (944)
T PRK14949         37 LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPS  116 (944)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhh
Confidence            36678999999999999999999999764                        1223332222223344444332     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|+||||+|.|.                           ...++.||..|+.-    +..++||++|+.+..|.+.
T Consensus       117 ~gk~KViIIDEAh~LT---------------------------~eAqNALLKtLEEP----P~~vrFILaTTe~~kLl~T  165 (944)
T PRK14949        117 RGRFKVYLIDEVHMLS---------------------------RSSFNALLKTLEEP----PEHVKFLLATTDPQKLPVT  165 (944)
T ss_pred             cCCcEEEEEechHhcC---------------------------HHHHHHHHHHHhcc----CCCeEEEEECCCchhchHH
Confidence             135699999999873                           33567778887753    3457788888888889999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..+.|+.++.++....+.+.+...+.... ..+..++...+.+++++.+++
T Consensus       166 IlS--RC-q~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~Gd~R~ALnLL  221 (944)
T PRK14949        166 VLS--RC-LQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDALSLT  221 (944)
T ss_pred             HHH--hh-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  88 67999999999999999888876655554 344555666667777777665

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

Probab=99.64  E-value=1.9e-15  Score=136.41  Aligned_cols=141  Identities=22%  Similarity=0.267  Sum_probs=93.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh--------hhHHHHHHH------cccCCeeeeecchhhHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN--------NDLRHILIA------TENKSILVVEDIDCCIE   96 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~--------~~l~~~~~~------~~~~~vl~iDeid~l~~   96 (266)
                      ..++||+||||||||++|+++|..++.+|+.+++..+...        ..+..++..      ...++||||||||.+..
T Consensus       108 ~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~  187 (412)
T PRK05342        108 KSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIAR  187 (412)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhcc
Confidence            4679999999999999999999999999999998876531        112232222      23689999999999965


Q ss_pred             HhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc---------CCCCceEEEEecCCCC-------------
Q 024550           97 LQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS---------SCGDERIIIFTTNHKE-------------  154 (266)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~---------~~~~~~ivi~ttn~~~-------------  154 (266)
                      .....+.             ..+.....+++.||+.|++...         ......++|.|+|-.-             
T Consensus       188 ~~~~~~~-------------~~d~s~~~vQ~~LL~~Leg~~~~v~~~gg~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~  254 (412)
T PRK05342        188 KSENPSI-------------TRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNILFICGGAFDGLEKII  254 (412)
T ss_pred             ccCCCCc-------------CCCcccHHHHHHHHHHHhcCeEEeCCCCCcCcCCCCeEEeccCCceeeecccccCcHHHH
Confidence            2110000             0011223467788888875421         1112345555655400             


Q ss_pred             ---------------------------------------CCcccccCCCcceeEEEcCCCCHHHHHHHHHH
Q 024550          155 ---------------------------------------RLDPALLRPGRMDMHINMSHCTPSGFKMLASN  186 (266)
Q Consensus       155 ---------------------------------------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~  186 (266)
                                                             .+.|+|+.  |++..+.|...+.++..+|+..
T Consensus       255 ~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEflg--Rld~iv~f~~L~~~~L~~Il~~  323 (412)
T PRK05342        255 KQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFIG--RLPVVATLEELDEEALVRILTE  323 (412)
T ss_pred             HHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHhC--CCCeeeecCCCCHHHHHHHHHH
Confidence                                                   13455565  9999999999999999988874

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.63  E-value=8.2e-15  Score=133.43  Aligned_cols=150  Identities=23%  Similarity=0.307  Sum_probs=104.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcc------cCCeeeeecchhhHHHhHHHhhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATE------NKSILVVEDIDCCIELQDRLSRA  104 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~------~~~vl~iDeid~l~~~~~~~~~~  104 (266)
                      ..+++||||||||||++|+++|+.++.+++.+++... +...+..++....      .+.||||||+|.+..        
T Consensus        36 ~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~~-~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~--------  106 (413)
T PRK13342         36 LSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTS-GVKDLREVIEEARQRRSAGRRTILFIDEIHRFNK--------  106 (413)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCCEEEEecccc-cHHHHHHHHHHHHHhhhcCCceEEEEechhhhCH--------
Confidence            3479999999999999999999999999999988654 3344555554432      578999999998742        


Q ss_pred             hhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEec--CCCCCCcccccCCCcceeEEEcCCCCHHHHHH
Q 024550          105 RAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTT--NHKERLDPALLRPGRMDMHINMSHCTPSGFKM  182 (266)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~tt--n~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~  182 (266)
                                         ...+.|+..++.      ..+++|++|  |....+++++++  || ..+.|+.++.++...
T Consensus       107 -------------------~~q~~LL~~le~------~~iilI~att~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~  158 (413)
T PRK13342        107 -------------------AQQDALLPHVED------GTITLIGATTENPSFEVNPALLS--RA-QVFELKPLSEEDIEQ  158 (413)
T ss_pred             -------------------HHHHHHHHHhhc------CcEEEEEeCCCChhhhccHHHhc--cc-eeeEeCCCCHHHHHH
Confidence                               123345555553      246666654  344578999999  88 679999999999999


Q ss_pred             HHHHhhCCC--CC-CcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          183 LASNYLGIA--EH-PLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       183 i~~~~~~~~--~~-~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++.+.+...  +. .+. +.+..++...+.+++.+.+.+
T Consensus       159 lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~L  197 (413)
T PRK13342        159 LLKRALEDKERGLVELDDEALDALARLANGDARRALNLL  197 (413)
T ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            999877542  11 233 334444554455555555544

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.63  E-value=6.1e-15  Score=136.13  Aligned_cols=154  Identities=16%  Similarity=0.287  Sum_probs=111.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC----------------------------cEEEEeCCcccChhhHHHHHHHcc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF----------------------------DVYDLELSNLLGNNDLRHILIATE   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~----------------------------~~~~i~~~~~~~~~~l~~~~~~~~   81 (266)
                      .++++||+||||||||++|+++|+.+++                            .+++++..+-.+...++.++..+.
T Consensus        42 i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~  121 (507)
T PRK06645         42 LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAE  121 (507)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHH
Confidence            3568999999999999999999999865                            233444433334455666665542


Q ss_pred             ------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           82 ------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        82 ------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                            ...|++|||+|.+..                           ..++.|+..++.    .+..++||++|+.++.
T Consensus       122 ~~P~~~~~KVvIIDEa~~Ls~---------------------------~a~naLLk~LEe----pp~~~vfI~aTte~~k  170 (507)
T PRK06645        122 YKPLQGKHKIFIIDEVHMLSK---------------------------GAFNALLKTLEE----PPPHIIFIFATTEVQK  170 (507)
T ss_pred             hccccCCcEEEEEEChhhcCH---------------------------HHHHHHHHHHhh----cCCCEEEEEEeCChHH
Confidence                  457999999997732                           235567777664    2356788888888889


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++++.+  || ..++|+.++.++...++...+..++..+.. .+..++...+.+++++.+.+
T Consensus       171 I~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~L  230 (507)
T PRK06645        171 IPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSIL  230 (507)
T ss_pred             hhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999999  88 579999999999999999999887766553 34455555556666655544

>PLN03025 replication factor C subunit; Provisional

Probab=99.63  E-value=7.4e-15  Score=129.42  Aligned_cols=151  Identities=19%  Similarity=0.243  Sum_probs=106.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC-----cEEEEeCCcccChhhHHHHHHH---c------ccCCeeeeecchhhHHHh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF-----DVYDLELSNLLGNNDLRHILIA---T------ENKSILVVEDIDCCIELQ   98 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~-----~~~~i~~~~~~~~~~l~~~~~~---~------~~~~vl~iDeid~l~~~~   98 (266)
                      ++|||||||||||++++++|+++..     .+++++.++..+...++..+..   .      ....|++|||+|.+..  
T Consensus        36 ~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~sd~~~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~--  113 (319)
T PLN03025         36 NLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTS--  113 (319)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecccccccHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCH--
Confidence            5999999999999999999999732     3566666655444444443322   1      1357999999998843  


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHH
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPS  178 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~  178 (266)
                                               ...+.|+..++..    +....+|.+||.+..+.+++.+  || ..+.|+.|+.+
T Consensus       114 -------------------------~aq~aL~~~lE~~----~~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~~~  161 (319)
T PLN03025        114 -------------------------GAQQALRRTMEIY----SNTTRFALACNTSSKIIEPIQS--RC-AIVRFSRLSDQ  161 (319)
T ss_pred             -------------------------HHHHHHHHHHhcc----cCCceEEEEeCCccccchhHHH--hh-hcccCCCCCHH
Confidence                                     1234455555532    2335677788888888899999  87 57999999999


Q ss_pred             HHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          179 GFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       179 ~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +....+......++..+. +.+..++...+.+.+.+.+.+
T Consensus       162 ~l~~~L~~i~~~egi~i~~~~l~~i~~~~~gDlR~aln~L  201 (319)
T PLN03025        162 EILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALNNL  201 (319)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999999988887776654 445556666666666666555

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

Probab=99.63  E-value=3.8e-15  Score=137.67  Aligned_cols=174  Identities=20%  Similarity=0.275  Sum_probs=126.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcccCh--hhH----HHHHHHc--ccCCeeeeecchhhHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNLLGN--NDL----RHILIAT--ENKSILVVEDIDCCIEL   97 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~~~~--~~l----~~~~~~~--~~~~vl~iDeid~l~~~   97 (266)
                      .+.++||+||+|||||.|++++++++    .+++..++|+.+...  ..+    ..+|..+  ..|+|+++|++|.++..
T Consensus       430 ~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~  509 (952)
T KOG0735|consen  430 RHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYAPSIIVLDDLDCLASA  509 (952)
T ss_pred             ccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchhHHHHHHHHHHHHHHHHhhCCcEEEEcchhhhhcc
Confidence            34579999999999999999999988    466778899888643  223    3344444  46999999999999861


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCH
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTP  177 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~  177 (266)
                      .+..              ..++......+..+++.+-..+...+..+.||+|.+..+.+++.|.+|++|..++.++.|+.
T Consensus       510 s~~e--------------~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~  575 (952)
T KOG0735|consen  510 SSNE--------------NGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAV  575 (952)
T ss_pred             Cccc--------------CCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcch
Confidence            1110              11223444566666655544333334557899999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhCCCCCC-cHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          178 SGFKMLASNYLGIAEHP-LFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       178 ~~~~~i~~~~~~~~~~~-~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|.+|++..++..... ...++..++.+ .||.+.|+.-+.
T Consensus       576 ~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifV  617 (952)
T KOG0735|consen  576 TRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFV  617 (952)
T ss_pred             hHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHH
Confidence            99999999999776422 23455555554 458888876654

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.63  E-value=7e-15  Score=138.60  Aligned_cols=154  Identities=15%  Similarity=0.274  Sum_probs=111.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+||+||+|||||++|+.+|+.+++                        .+++++..+-.+...++.+.....    
T Consensus        37 l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~  116 (647)
T PRK07994         37 LHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPA  116 (647)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhhh
Confidence            3567999999999999999999999876                        234455443223344555544321    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|++|||+|.|.                           ....+.||+.|+.    .+..++||.+|+.+..|.+.
T Consensus       117 ~g~~KV~IIDEah~Ls---------------------------~~a~NALLKtLEE----Pp~~v~FIL~Tt~~~kLl~T  165 (647)
T PRK07994        117 RGRFKVYLIDEVHMLS---------------------------RHSFNALLKTLEE----PPEHVKFLLATTDPQKLPVT  165 (647)
T ss_pred             cCCCEEEEEechHhCC---------------------------HHHHHHHHHHHHc----CCCCeEEEEecCCccccchH
Confidence              35699999999874                           2356778887775    34567888888889999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..++|+.++.++....+.+.+..++..... .+..++...+.+++++.+++
T Consensus       166 I~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~Gs~R~Al~ll  221 (647)
T PRK07994        166 ILS--RC-LQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLARAADGSMRDALSLT  221 (647)
T ss_pred             HHh--hh-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  98 779999999999999998888666555443 34445555666777666655

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

Probab=99.63  E-value=6.5e-15  Score=141.78  Aligned_cols=172  Identities=13%  Similarity=0.262  Sum_probs=112.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHH---------------HH---HcccCCeeeeecchh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHI---------------LI---ATENKSILVVEDIDC   93 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~---------------~~---~~~~~~vl~iDeid~   93 (266)
                      ..+||+||||||||++|+++|..++.+++.++++.+.....+..+               +.   .....+||||||||.
T Consensus       489 ~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~LiG~~~gyvg~~~~g~L~~~v~~~p~sVlllDEiek  568 (758)
T PRK11034        489 GSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEK  568 (758)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHcCCCCCcccccccchHHHHHHhCCCcEEEeccHhh
Confidence            359999999999999999999999999999999877532222221               11   123568999999998


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCCC-------------
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHK-------------  153 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~-------------  153 (266)
                      +.+                           .+.+.|++.|+.-.-+.       -.+.+||+|||.-             
T Consensus       569 a~~---------------------------~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~g~~~  621 (758)
T PRK11034        569 AHP---------------------------DVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIH  621 (758)
T ss_pred             hhH---------------------------HHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcccCccc
Confidence            753                           24566667666321111       1357899999832             


Q ss_pred             ------------CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHcCC
Q 024550          154 ------------ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNE  221 (266)
Q Consensus       154 ------------~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~~~  221 (266)
                                  ..+.|.|+.  |++.+|.|+.++.++..+|+..++....    ..+...--...++..-+..++....
T Consensus       622 ~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~~~~l~~I~~~~l~~~~----~~l~~~~i~l~~~~~~~~~l~~~~~  695 (758)
T PRK11034        622 QDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIVELQ----AQLDQKGVSLEVSQEARDWLAEKGY  695 (758)
T ss_pred             chhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCCHHHHHHHHHHHHHHHH----HHHHHCCCCceECHHHHHHHHHhCC
Confidence                        125678888  9999999999999999999987774321    1111111123355555544444444


Q ss_pred             CHHHHHHHHHHHHHh
Q 024550          222 APEFALSGLIEFLES  236 (266)
Q Consensus       222 ~~~~~~~~~~~~~~~  236 (266)
                      ++...++.+..+++.
T Consensus       696 ~~~~GAR~l~r~i~~  710 (758)
T PRK11034        696 DRAMGARPMARVIQD  710 (758)
T ss_pred             CCCCCCchHHHHHHH
Confidence            554444444444443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.62  E-value=8.3e-15  Score=134.34  Aligned_cols=154  Identities=12%  Similarity=0.183  Sum_probs=116.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC------------------------CcEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK------------------------FDVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~------------------------~~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++++||+||||+|||++|+.+|+.++                        ..+++++.++-.+...++.+.....    
T Consensus        34 i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~~vddIR~Iie~~~~~P~  113 (491)
T PRK14964         34 IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPI  113 (491)
T ss_pred             CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCCCHHHHHHHHHHHHhccc
Confidence            367899999999999999999998653                        3457777765555566776665542    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        +..|++|||+|.+..                           ...+.|+..|+.-    +..+++|.+|+.+..+.++
T Consensus       114 ~~~~KVvIIDEah~Ls~---------------------------~A~NaLLK~LEeP----p~~v~fIlatte~~Kl~~t  162 (491)
T PRK14964        114 SSKFKVYIIDEVHMLSN---------------------------SAFNALLKTLEEP----APHVKFILATTEVKKIPVT  162 (491)
T ss_pred             cCCceEEEEeChHhCCH---------------------------HHHHHHHHHHhCC----CCCeEEEEEeCChHHHHHH
Confidence              457999999997732                           2456677777753    3557888888888899999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  || ..++|..++.++....+...+..++..+.. .+..++...+.+.+++.+.+
T Consensus       163 I~S--Rc-~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslL  218 (491)
T PRK14964        163 IIS--RC-QRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLL  218 (491)
T ss_pred             HHH--hh-eeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  88 569999999999999999988887776654 34455556666766666555

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.61  E-value=1e-14  Score=137.11  Aligned_cols=154  Identities=15%  Similarity=0.284  Sum_probs=111.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC-----------------------------cEEEEeCCcccChhhHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF-----------------------------DVYDLELSNLLGNNDLRHILIAT   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~-----------------------------~~~~i~~~~~~~~~~l~~~~~~~   80 (266)
                      .++.+|||||+|||||++++++|+.+++                             .++.++..+-.+-..++.++...
T Consensus        37 l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~  116 (618)
T PRK14951         37 LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQA  116 (618)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHH
Confidence            3567999999999999999999999865                             23444443333334555655543


Q ss_pred             c------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           81 E------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        81 ~------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      .      ...|++|||+|.|..                           ...+.|+..|+.    .+..++||.+|+.+.
T Consensus       117 ~~~p~~g~~KV~IIDEvh~Ls~---------------------------~a~NaLLKtLEE----PP~~~~fIL~Ttd~~  165 (618)
T PRK14951        117 VYKPVQGRFKVFMIDEVHMLTN---------------------------TAFNAMLKTLEE----PPEYLKFVLATTDPQ  165 (618)
T ss_pred             HhCcccCCceEEEEEChhhCCH---------------------------HHHHHHHHhccc----CCCCeEEEEEECCch
Confidence            2      346999999998742                           234566766664    335577888888888


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+.+.+++  || ..++|+.++.++....+...+..++.....+ +..++...+.+.+++.+.+
T Consensus       166 kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s~GslR~al~lL  226 (618)
T PRK14951        166 KVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLT  226 (618)
T ss_pred             hhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            88889999  88 6799999999999999998888777666543 4555666666776666654

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

Probab=99.61  E-value=5.8e-15  Score=132.79  Aligned_cols=189  Identities=21%  Similarity=0.229  Sum_probs=116.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh--------hhHHHHHHH------cccCCeeeeecchhhHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN--------NDLRHILIA------TENKSILVVEDIDCCIE   96 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~--------~~l~~~~~~------~~~~~vl~iDeid~l~~   96 (266)
                      ..++||+||||||||++|+++|..++.++..+++..+...        ..+...+..      ...++||||||+|.+..
T Consensus       116 ~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~  195 (413)
T TIGR00382       116 KSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISR  195 (413)
T ss_pred             CceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhccccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhch
Confidence            3579999999999999999999999999999888766421        112333222      23578999999999875


Q ss_pred             HhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC----C-----CCceEEEEecCCC--------------
Q 024550           97 LQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS----C-----GDERIIIFTTNHK--------------  153 (266)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~----~-----~~~~ivi~ttn~~--------------  153 (266)
                      ..+..+..             .+.....+++.||+.|++....    .     ..+.++|.|+|-.              
T Consensus       196 ~~~~~s~~-------------~dvsg~~vq~~LL~iLeG~~~~v~~~~gr~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~  262 (413)
T TIGR00382       196 KSENPSIT-------------RDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKII  262 (413)
T ss_pred             hhcccccc-------------ccccchhHHHHHHHHhhccceecccCCCccccCCCeEEEEcCCceeeecccccChHHHH
Confidence            32211110             0122235677788888765421    1     1345777787751              


Q ss_pred             -------------C-----------------------CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH
Q 024550          154 -------------E-----------------------RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV  197 (266)
Q Consensus       154 -------------~-----------------------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~  197 (266)
                                   +                       .+.|+|+.  |++.++.|...+.+++.+|+......    +..
T Consensus       263 ~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEflg--Rld~Iv~f~pL~~~~L~~Il~~~~n~----l~k  336 (413)
T TIGR00382       263 KKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIG--RLPVIATLEKLDEEALIAILTKPKNA----LVK  336 (413)
T ss_pred             HHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHhC--CCCeEeecCCCCHHHHHHHHHHHHHH----HHH
Confidence                         0                       13455666  99999999999999998887754311    112


Q ss_pred             HHHHHhh----cCCCCHHHHHHHHHcCCCHHHHHHHHHHHHHhhh
Q 024550          198 EIEKLIA----TAKVTPADVAEQLMRNEAPEFALSGLIEFLESKK  238 (266)
Q Consensus       198 ~~~~l~~----~~~~s~~~i~~~l~~~~~~~~~~~~~~~~~~~~~  238 (266)
                      ++.....    ...++...+..+...+.++...++.+...+++.-
T Consensus       337 q~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~Lr~iie~~l  381 (413)
T TIGR00382       337 QYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLL  381 (413)
T ss_pred             HHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchHHHHHHHHhh
Confidence            2222221    1235666555555545555555555555555443

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.61  E-value=3.9e-15  Score=137.02  Aligned_cols=157  Identities=15%  Similarity=0.251  Sum_probs=108.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccCh-------hhHHHHHHHcccCCeeeeecchhhHHHhH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGN-------NDLRHILIATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~-------~~l~~~~~~~~~~~vl~iDeid~l~~~~~   99 (266)
                      ..++||||||||||+|++++++++     +..++++++..+...       .....+........+|+|||++.+.+.. 
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~-  227 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGKE-  227 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcCCH-
Confidence            459999999999999999999987     566888887765421       1122333344567899999999875311 


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC---CcccccCCCcce--eEEEcCC
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER---LDPALLRPGRMD--MHINMSH  174 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~---ld~al~r~~Rf~--~~i~~~~  174 (266)
                                              .....++..++...+.  ...++|+++..|..   +++++.+  ||.  ..+++..
T Consensus       228 ------------------------~~~~~l~~~~n~l~~~--~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~  279 (450)
T PRK00149        228 ------------------------RTQEEFFHTFNALHEA--GKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVDIEP  279 (450)
T ss_pred             ------------------------HHHHHHHHHHHHHHHC--CCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEEecC
Confidence                                    1122344444433332  23466666666644   6788998  885  6899999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          175 CTPSGFKMLASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       175 p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      |+.++|..|++......+..+.++. ..++....-+.+++...+
T Consensus       280 pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~~l  323 (450)
T PRK00149        280 PDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEGAL  323 (450)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHHHH
Confidence            9999999999999887666665544 555556667777766665

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.61  E-value=1.6e-14  Score=121.01  Aligned_cols=157  Identities=17%  Similarity=0.211  Sum_probs=102.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARA  106 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~  106 (266)
                      .+..++|+||||||||++++++++.+   +.+++.+++..+..  .....+.......+|+|||+|.+...         
T Consensus        37 ~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~~--~~~~~~~~~~~~~lLvIDdi~~l~~~---------  105 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQ--ADPEVLEGLEQADLVCLDDVEAIAGQ---------  105 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHHH--hHHHHHhhcccCCEEEEeChhhhcCC---------
Confidence            35679999999999999999999877   46788888877643  22344444556679999999987420         


Q ss_pred             cCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc---ccccCCCcc--eeEEEcCCCCHHHHH
Q 024550          107 ANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD---PALLRPGRM--DMHINMSHCTPSGFK  181 (266)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld---~al~r~~Rf--~~~i~~~~p~~~~~~  181 (266)
                                   ...   ...+...++.....  ...+|++++..+..++   +.|.+  ||  ...|.++.|+.+++.
T Consensus       106 -------------~~~---~~~L~~~l~~~~~~--~~~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~  165 (226)
T TIGR03420       106 -------------PEW---QEALFHLYNRVREA--GGRLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKI  165 (226)
T ss_pred             -------------hHH---HHHHHHHHHHHHHc--CCeEEEECCCChHHCCcccHHHHH--HHhcCeeEecCCCCHHHHH
Confidence                         011   12233333322211  2244444444444332   67777  66  478999999999999


Q ss_pred             HHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          182 MLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       182 ~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+++.+....+..+..+ +..++.....+++++.+++
T Consensus       166 ~~l~~~~~~~~~~~~~~~l~~L~~~~~gn~r~L~~~l  202 (226)
T TIGR03420       166 AALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALL  202 (226)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHH
Confidence            99988776555555443 4555555556777766664

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.60  E-value=6.1e-15  Score=134.06  Aligned_cols=157  Identities=15%  Similarity=0.229  Sum_probs=107.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccCh-------hhHHHHHHHcccCCeeeeecchhhHHHhH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGN-------NDLRHILIATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~-------~~l~~~~~~~~~~~vl~iDeid~l~~~~~   99 (266)
                      ..++||||||||||+|++++++++     +..++++++..+...       ..............+|+|||++.+.+.  
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~--  214 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAGK--  214 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcCC--
Confidence            458999999999999999999987     567888887665321       112222233445689999999987531  


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC---CCcccccCCCcce--eEEEcCC
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE---RLDPALLRPGRMD--MHINMSH  174 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~---~ld~al~r~~Rf~--~~i~~~~  174 (266)
                                          .   .....++..++.....  ...++|+++..|.   .+++.+.+  ||.  ..+.++.
T Consensus       215 --------------------~---~~~~~l~~~~n~~~~~--~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~  267 (405)
T TIGR00362       215 --------------------E---RTQEEFFHTFNALHEN--GKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVDIEP  267 (405)
T ss_pred             --------------------H---HHHHHHHHHHHHHHHC--CCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEEeCC
Confidence                                0   1122344444433322  2345665655664   35688888  775  6899999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          175 CTPSGFKMLASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       175 p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      |+.++|..|++..+...+..+.++. ..++....-+.+++...+
T Consensus       268 pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~r~l~~~l  311 (405)
T TIGR00362       268 PDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEGAL  311 (405)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            9999999999999988777665554 555666667777776665

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).

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.60  E-value=8.5e-15  Score=137.79  Aligned_cols=154  Identities=15%  Similarity=0.273  Sum_probs=114.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++++||+||+|||||++|+++|+.+++.                        +++++...-.+...++.++..+     
T Consensus        37 l~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~  116 (709)
T PRK08691         37 LHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPT  116 (709)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhh
Confidence            46789999999999999999999987542                        3444444333444566666543     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.+.                           ....+.|+..|+.-    +..+.||.+|+.+..+.+.
T Consensus       117 ~gk~KVIIIDEad~Ls---------------------------~~A~NALLKtLEEP----p~~v~fILaTtd~~kL~~T  165 (709)
T PRK08691        117 AGKYKVYIIDEVHMLS---------------------------KSAFNAMLKTLEEP----PEHVKFILATTDPHKVPVT  165 (709)
T ss_pred             hCCcEEEEEECccccC---------------------------HHHHHHHHHHHHhC----CCCcEEEEEeCCccccchH
Confidence             245799999999763                           12356677777753    3457788888889999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..+.|+.++.++....+.+.+...+..+.. .+..++...+.+.+++.+.+
T Consensus       166 IrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~GslRdAlnLL  221 (709)
T PRK08691        166 VLS--RC-LQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLL  221 (709)
T ss_pred             HHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHH
Confidence            998  98 668999999999999999999888776654 44556666667777777766

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.60  E-value=7.9e-15  Score=143.79  Aligned_cols=132  Identities=19%  Similarity=0.240  Sum_probs=95.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHHc---ccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIAT---ENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~~---~~~~vl~iD   89 (266)
                      ..+++|+||||||||++++++|..+          +.+++.++...+...        ..+..+|...   ..++|||||
T Consensus       199 ~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfID  278 (857)
T PRK10865        199 KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFID  278 (857)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEe
Confidence            4579999999999999999999988          778888888776532        2466666543   357899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccCCC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLRPG  164 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r~~  164 (266)
                      |+|.+.+..+..                  +. ....+.|...+.    +  +.+.+|++|+..+     .+|+++.|  
T Consensus       279 Eih~l~~~~~~~------------------~~-~d~~~~lkp~l~----~--g~l~~IgaTt~~e~r~~~~~d~al~r--  331 (857)
T PRK10865        279 ELHTMVGAGKAD------------------GA-MDAGNMLKPALA----R--GELHCVGATTLDEYRQYIEKDAALER--  331 (857)
T ss_pred             cHHHhccCCCCc------------------cc-hhHHHHhcchhh----c--CCCeEEEcCCCHHHHHHhhhcHHHHh--
Confidence            999997532110                  00 111222223322    2  4688999998775     47999999  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      ||. .|.++.|+.+++..|++.+...
T Consensus       332 Rf~-~i~v~eP~~~~~~~iL~~l~~~  356 (857)
T PRK10865        332 RFQ-KVFVAEPSVEDTIAILRGLKER  356 (857)
T ss_pred             hCC-EEEeCCCCHHHHHHHHHHHhhh
Confidence            996 5899999999999999877644

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.60  E-value=1.4e-14  Score=135.46  Aligned_cols=157  Identities=18%  Similarity=0.241  Sum_probs=105.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCccc-ChhhHH-HH----------------------
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLL-GNNDLR-HI----------------------   76 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~-~~~~l~-~~----------------------   76 (266)
                      +..+|||||||||||++|++++..+          +.+|+.++|.... +...+. .+                      
T Consensus        86 ~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~  165 (531)
T TIGR02902        86 PQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQ  165 (531)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEccccccCCccccchhhcCCcccchhccccccccCCccc
Confidence            4579999999999999999998653          3678999986421 111110 00                      


Q ss_pred             ----HHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc---------------
Q 024550           77 ----LIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW---------------  137 (266)
Q Consensus        77 ----~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------------  137 (266)
                          ......+++|||||++.|...                           .++.|+..|+...               
T Consensus       166 ~~~G~l~~a~gG~L~IdEI~~L~~~---------------------------~q~~LL~~Le~~~~~~~~~~~~~~~~~~  218 (531)
T TIGR02902       166 PKPGAVTRAHGGVLFIDEIGELHPV---------------------------QMNKLLKVLEDRKVFLDSAYYNSENPNI  218 (531)
T ss_pred             ccCchhhccCCcEEEEechhhCCHH---------------------------HHHHHHHHHHhCeeeeccccccccCccc
Confidence                011234689999999988542                           2233333332100               


Q ss_pred             ---------c-CCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCC
Q 024550          138 ---------S-SCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAK  207 (266)
Q Consensus       138 ---------~-~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~  207 (266)
                               . ...+.+++++||+.|+.+++++++  || ..|.|+.++.+++..|+++++...+..+.++...++..+.
T Consensus       219 ~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrs--R~-~~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~  295 (531)
T TIGR02902       219 PSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRS--RC-VEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYA  295 (531)
T ss_pred             ccchhhhcccCcccceEEEEEecCCcccCChHHhh--hh-heeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhh
Confidence                     0 001224566677889999999999  98 5799999999999999999998777666655555555555


Q ss_pred             CCHHHHHHHH
Q 024550          208 VTPADVAEQL  217 (266)
Q Consensus       208 ~s~~~i~~~l  217 (266)
                      .+.+++.+++
T Consensus       296 ~n~Rel~nll  305 (531)
T TIGR02902       296 SNGREAVNIV  305 (531)
T ss_pred             hhHHHHHHHH
Confidence            6777777766

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.60  E-value=1.6e-14  Score=141.91  Aligned_cols=133  Identities=20%  Similarity=0.235  Sum_probs=93.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHHc---ccCCeeee
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIAT---ENKSILVV   88 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~~---~~~~vl~i   88 (266)
                      ...+++|+||||||||++++.+|..+          +.+++.++...+...        ..+..++...   ..++||||
T Consensus       193 ~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfI  272 (852)
T TIGR03346       193 TKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFI  272 (852)
T ss_pred             CCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEe
Confidence            34579999999999999999999986          677888887765422        2456666554   35799999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccCC
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLRP  163 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r~  163 (266)
                      ||+|.+.+..+..                  + .....+.|...+    ..  ..+.+|++|+..+     .+|+++.| 
T Consensus       273 DEih~l~~~g~~~------------------~-~~d~~~~Lk~~l----~~--g~i~~IgaTt~~e~r~~~~~d~al~r-  326 (852)
T TIGR03346       273 DELHTLVGAGKAE------------------G-AMDAGNMLKPAL----AR--GELHCIGATTLDEYRKYIEKDAALER-  326 (852)
T ss_pred             ccHHHhhcCCCCc------------------c-hhHHHHHhchhh----hc--CceEEEEeCcHHHHHHHhhcCHHHHh-
Confidence            9999987521110                  0 011122222222    12  4588899888663     47999999 


Q ss_pred             CcceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          164 GRMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       164 ~Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                       ||. .|.++.|+.+++..|++.+...
T Consensus       327 -Rf~-~i~v~~p~~~~~~~iL~~~~~~  351 (852)
T TIGR03346       327 -RFQ-PVFVDEPTVEDTISILRGLKER  351 (852)
T ss_pred             -cCC-EEEeCCCCHHHHHHHHHHHHHH
Confidence             995 5899999999999999877544

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.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=2.3e-14  Score=133.14  Aligned_cols=154  Identities=18%  Similarity=0.270  Sum_probs=110.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++.+|||||||||||++|+.+|+.+++                        .+++++.....+...++.++...     
T Consensus        37 l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~  116 (546)
T PRK14957         37 VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPS  116 (546)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeecccccCHHHHHHHHHHHHhhhh
Confidence            3567999999999999999999998864                        34445543333333444444332     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.+.                           ....+.|+..|+.-    +..++||++|+.+..+.++
T Consensus       117 ~g~~kViIIDEa~~ls---------------------------~~a~naLLK~LEep----p~~v~fIL~Ttd~~kil~t  165 (546)
T PRK14957        117 QGRYKVYLIDEVHMLS---------------------------KQSFNALLKTLEEP----PEYVKFILATTDYHKIPVT  165 (546)
T ss_pred             cCCcEEEEEechhhcc---------------------------HHHHHHHHHHHhcC----CCCceEEEEECChhhhhhh
Confidence             245799999999773                           22456777777753    3457777777778888888


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..++|..++.++....+...+..++..... .+..++...+.+.+++.+.+
T Consensus       166 I~S--Rc-~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia~~s~GdlR~alnlL  221 (546)
T PRK14957        166 ILS--RC-IQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLL  221 (546)
T ss_pred             HHH--he-eeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            998  88 679999999999998888888777655543 34556666667777776665

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=3.5e-14  Score=131.49  Aligned_cols=154  Identities=18%  Similarity=0.286  Sum_probs=108.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC-----------------------cEEEEeCCcccChhhHHHHHHHc------
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF-----------------------DVYDLELSNLLGNNDLRHILIAT------   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~-----------------------~~~~i~~~~~~~~~~l~~~~~~~------   80 (266)
                      .++.+|||||||||||++|+++|+.+.+                       .++.++.....+...++.+....      
T Consensus        35 l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~  114 (504)
T PRK14963         35 LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLR  114 (504)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhcccc
Confidence            4567899999999999999999998853                       14555554333333444443322      


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                      ..+.|++|||+|.+.                           ...++.|+..++.-    +..+++|.+|+.+..+.+.+
T Consensus       115 ~~~kVVIIDEad~ls---------------------------~~a~naLLk~LEep----~~~t~~Il~t~~~~kl~~~I  163 (504)
T PRK14963        115 GGRKVYILDEAHMMS---------------------------KSAFNALLKTLEEP----PEHVIFILATTEPEKMPPTI  163 (504)
T ss_pred             CCCeEEEEECccccC---------------------------HHHHHHHHHHHHhC----CCCEEEEEEcCChhhCChHH
Confidence            246799999999663                           22456677777653    34577888888889999999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+  ||. .+.|+.|+.++....+...+...+..... .+..++...+.+.+.+.+.|
T Consensus       164 ~S--Rc~-~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~L  218 (504)
T PRK14963        164 LS--RTQ-HFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLL  218 (504)
T ss_pred             hc--ceE-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99  884 69999999999999999988877766543 34555555555666555444

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.59  E-value=4.2e-14  Score=127.21  Aligned_cols=153  Identities=18%  Similarity=0.259  Sum_probs=102.4

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHcCCc-----------------------EEEEeCCc-ccChhhHHHHHHHcc
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFD-----------------------VYDLELSN-LLGNNDLRHILIATE   81 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~-----------------------~~~i~~~~-~~~~~~l~~~~~~~~   81 (266)
                      .+...++++||+||||+|||++|+++|..+.+.                       ++.+.+.. ..+...++.++....
T Consensus        31 ~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~  110 (394)
T PRK07940         31 AGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHPDVRVVAPEGLSIGVDEVRELVTIAA  110 (394)
T ss_pred             cCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHH
Confidence            344467889999999999999999999987553                       22333221 123344566655432


Q ss_pred             ------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           82 ------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        82 ------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                            ...|++|||+|.+..                           ...+.|+..|+.    ++.+.++|.+|+.++.
T Consensus       111 ~~p~~~~~kViiIDead~m~~---------------------------~aanaLLk~LEe----p~~~~~fIL~a~~~~~  159 (394)
T PRK07940        111 RRPSTGRWRIVVIEDADRLTE---------------------------RAANALLKAVEE----PPPRTVWLLCAPSPED  159 (394)
T ss_pred             hCcccCCcEEEEEechhhcCH---------------------------HHHHHHHHHhhc----CCCCCeEEEEECChHH
Confidence                  346999999998842                           133567777764    2345666666666899


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQ  216 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~  216 (266)
                      +.+++++  || ..+.|+.|+.++...++....+.    .......++...+.++.....+
T Consensus       160 llpTIrS--Rc-~~i~f~~~~~~~i~~~L~~~~~~----~~~~a~~la~~s~G~~~~A~~l  213 (394)
T PRK07940        160 VLPTIRS--RC-RHVALRTPSVEAVAEVLVRRDGV----DPETARRAARASQGHIGRARRL  213 (394)
T ss_pred             ChHHHHh--hC-eEEECCCCCHHHHHHHHHHhcCC----CHHHHHHHHHHcCCCHHHHHHH
Confidence            9999999  88 67999999999988877643321    1234445555555666544333

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

Probab=99.59  E-value=6.8e-15  Score=127.06  Aligned_cols=121  Identities=25%  Similarity=0.376  Sum_probs=90.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCc---EEEEeCCcccChhhHHHHHHHcc-------cCCeeeeecchhhHHHhHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFD---VYDLELSNLLGNNDLRHILIATE-------NKSILVVEDIDCCIELQDRL  101 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~---~~~i~~~~~~~~~~l~~~~~~~~-------~~~vl~iDeid~l~~~~~~~  101 (266)
                      .+++||||||||||+||+.+++....+   |+++++... +...++.+|....       +++|||||||+.+-      
T Consensus       163 pSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a-~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFN------  235 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNA-KTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFN------  235 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhhcCCCceEEEEEecccc-chHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhh------
Confidence            359999999999999999999998776   666665544 4567888887753       58999999999763      


Q ss_pred             hhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEec--CCCCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          102 SRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTT--NHKERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~tt--n~~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                           +..+..||-.++.      ..+++|++|  |+.-.|+.+|++  || .++.+...+.+.
T Consensus       236 ---------------------ksQQD~fLP~VE~------G~I~lIGATTENPSFqln~aLlS--RC-~VfvLekL~~n~  285 (554)
T KOG2028|consen  236 ---------------------KSQQDTFLPHVEN------GDITLIGATTENPSFQLNAALLS--RC-RVFVLEKLPVNA  285 (554)
T ss_pred             ---------------------hhhhhcccceecc------CceEEEecccCCCccchhHHHHh--cc-ceeEeccCCHHH
Confidence                                 2233456666553      347788755  444578999999  87 457788888888


Q ss_pred             HHHHHHHhhC
Q 024550          180 FKMLASNYLG  189 (266)
Q Consensus       180 ~~~i~~~~~~  189 (266)
                      ...|+.+-+.
T Consensus       286 v~~iL~raia  295 (554)
T KOG2028|consen  286 VVTILMRAIA  295 (554)
T ss_pred             HHHHHHHHHH
Confidence            8888887553

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.59  E-value=1.5e-14  Score=122.09  Aligned_cols=157  Identities=18%  Similarity=0.186  Sum_probs=100.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC---CcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAA  107 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~  107 (266)
                      ...++||||||||||++++++++.+.   ..+.++++.....  ...+.+....+-.+|+|||++.+.+           
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~~--~~~~~~~~~~~~dlliiDdi~~~~~-----------  111 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRAW--FVPEVLEGMEQLSLVCIDNIECIAG-----------  111 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHhh--hhHHHHHHhhhCCEEEEeChhhhcC-----------
Confidence            35799999999999999999998763   4455555544321  1223333334457899999998743           


Q ss_pred             CCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC---CcccccCCCcce--eEEEcCCCCHHHHHH
Q 024550          108 NPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER---LDPALLRPGRMD--MHINMSHCTPSGFKM  182 (266)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~---ld~al~r~~Rf~--~~i~~~~p~~~~~~~  182 (266)
                                 .......+..+++.+-.   . +...+++++++.|..   +.+.|.+  ||.  .++.+..|+.+++.+
T Consensus       112 -----------~~~~~~~lf~l~n~~~e---~-g~~~li~ts~~~p~~l~~~~~~L~S--Rl~~g~~~~l~~~~~~~~~~  174 (235)
T PRK08084        112 -----------DELWEMAIFDLYNRILE---S-GRTRLLITGDRPPRQLNLGLPDLAS--RLDWGQIYKLQPLSDEEKLQ  174 (235)
T ss_pred             -----------CHHHHHHHHHHHHHHHH---c-CCCeEEEeCCCChHHcCcccHHHHH--HHhCCceeeecCCCHHHHHH
Confidence                       11222233344444322   1 112455556666655   5789999  775  889999999999999


Q ss_pred             HHHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          183 LASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       183 i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      ++++.....+..+.++. ..++....-+.+.+...+
T Consensus       175 ~l~~~a~~~~~~l~~~v~~~L~~~~~~d~r~l~~~l  210 (235)
T PRK08084        175 ALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMTL  210 (235)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHhhcCCHHHHHHHH
Confidence            99886665555555544 444445555666665554

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=1.5e-14  Score=134.89  Aligned_cols=154  Identities=16%  Similarity=0.299  Sum_probs=110.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+||+||||+|||++|+.+|+.+++.                        ++.++.+.-.+-..++.++..+.    
T Consensus        37 ~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p~  116 (527)
T PRK14969         37 LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAPT  116 (527)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCcc
Confidence            35679999999999999999999998652                        34444433223344555554432    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        +..|++|||+|.+..                           ...+.|+..++.-    +..++||.+|+.++.+.+.
T Consensus       117 ~~~~kVvIIDEad~ls~---------------------------~a~naLLK~LEep----p~~~~fIL~t~d~~kil~t  165 (527)
T PRK14969        117 RGRFKVYIIDEVHMLSK---------------------------SAFNAMLKTLEEP----PEHVKFILATTDPQKIPVT  165 (527)
T ss_pred             cCCceEEEEcCcccCCH---------------------------HHHHHHHHHHhCC----CCCEEEEEEeCChhhCchh
Confidence              346999999997732                           2456677777753    3457788888888888888


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..++|+.++.++....+.+.+..++..... .+..++...+.+++++.+.+
T Consensus       166 I~S--Rc-~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        166 VLS--RC-LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             HHH--HH-HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            998  88 679999999999998888888776655543 34555666667777666665

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=2.6e-14  Score=133.93  Aligned_cols=154  Identities=22%  Similarity=0.331  Sum_probs=110.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC--------------------------cEEEEeCCcccChhhHHHHHHHc---
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF--------------------------DVYDLELSNLLGNNDLRHILIAT---   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~--------------------------~~~~i~~~~~~~~~~l~~~~~~~---   80 (266)
                      .++.+|||||+|||||++|+++|+.+++                          .+++++.+...+-..++.+....   
T Consensus        34 ~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~  113 (584)
T PRK14952         34 INHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYA  113 (584)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhh
Confidence            4567999999999999999999998864                          23444443333333444443222   


Q ss_pred             ---ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc
Q 024550           81 ---ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD  157 (266)
Q Consensus        81 ---~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld  157 (266)
                         ....|++|||+|.|..                           ...+.||..|+.-    +..++||.+|+.+..+.
T Consensus       114 P~~~~~KVvIIDEah~Lt~---------------------------~A~NALLK~LEEp----p~~~~fIL~tte~~kll  162 (584)
T PRK14952        114 PAQSRYRIFIVDEAHMVTT---------------------------AGFNALLKIVEEP----PEHLIFIFATTEPEKVL  162 (584)
T ss_pred             hhcCCceEEEEECCCcCCH---------------------------HHHHHHHHHHhcC----CCCeEEEEEeCChHhhH
Confidence               2467999999998742                           2456677777753    35688888888889999


Q ss_pred             ccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          158 PALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       158 ~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      +++.+  || ..++|..++.++..+.+..++...+..+..+. ..++...+.+++++.+.|
T Consensus       163 ~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~GdlR~aln~L  220 (584)
T PRK14952        163 PTIRS--RT-HHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGGGSPRDTLSVL  220 (584)
T ss_pred             HHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999  87 67999999999999999988888776665443 444455556666555554

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

Probab=99.58  E-value=6.1e-15  Score=141.96  Aligned_cols=133  Identities=24%  Similarity=0.325  Sum_probs=91.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccC--------hhhHHHHHHHc--ccCCeeeeec
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLG--------NNDLRHILIAT--ENKSILVVED   90 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~--------~~~l~~~~~~~--~~~~vl~iDe   90 (266)
                      ..++||+||||||||++++++|...          +..++.++...+..        ...+..++...  ..++||||||
T Consensus       207 ~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDE  286 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDE  286 (758)
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEecc
Confidence            4579999999999999999999875          55666665554432        22345555443  3578999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccCCCc
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLRPGR  165 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r~~R  165 (266)
                      +|.+++.....                  .....    +.+.|......  ..+.+|++||.++     ..|++|.|  |
T Consensus       287 Ih~L~g~g~~~------------------~g~~d----~~nlLkp~L~~--g~i~vIgATt~~E~~~~~~~D~AL~r--R  340 (758)
T PRK11034        287 IHTIIGAGAAS------------------GGQVD----AANLIKPLLSS--GKIRVIGSTTYQEFSNIFEKDRALAR--R  340 (758)
T ss_pred             HHHHhccCCCC------------------CcHHH----HHHHHHHHHhC--CCeEEEecCChHHHHHHhhccHHHHh--h
Confidence            99997522110                  00011    11222222222  5688999998764     46999999  9


Q ss_pred             ceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          166 MDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       166 f~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      |. .|.++.|+.+++..|++.+...
T Consensus       341 Fq-~I~v~ePs~~~~~~IL~~~~~~  364 (758)
T PRK11034        341 FQ-KIDITEPSIEETVQIINGLKPK  364 (758)
T ss_pred             Cc-EEEeCCCCHHHHHHHHHHHHHH
Confidence            95 7999999999999999876543

>PRK08727 hypothetical protein; Validated

Probab=99.58  E-value=1.6e-14  Score=121.70  Aligned_cols=154  Identities=18%  Similarity=0.177  Sum_probs=100.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAAN  108 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~  108 (266)
                      ..++||||+|||||+++++++..+   +....+++...+.  ..+...+....+..+|+|||++.+...           
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~~--~~~~~~~~~l~~~dlLiIDDi~~l~~~-----------  108 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAA--GRLRDALEALEGRSLVALDGLESIAGQ-----------  108 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHhh--hhHHHHHHHHhcCCEEEEeCcccccCC-----------
Confidence            459999999999999999998765   5566666655442  234456666677889999999987431           


Q ss_pred             CccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC---cccccCCCcc--eeEEEcCCCCHHHHHHH
Q 024550          109 PDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL---DPALLRPGRM--DMHINMSHCTPSGFKML  183 (266)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l---d~al~r~~Rf--~~~i~~~~p~~~~~~~i  183 (266)
                                 ......+..+++.+..   .  ...+|+.+.+.|..+   +++|.+  ||  ...+.++.|+.+++..+
T Consensus       109 -----------~~~~~~lf~l~n~~~~---~--~~~vI~ts~~~p~~l~~~~~dL~S--Rl~~~~~~~l~~~~~e~~~~i  170 (233)
T PRK08727        109 -----------REDEVALFDFHNRARA---A--GITLLYTARQMPDGLALVLPDLRS--RLAQCIRIGLPVLDDVARAAV  170 (233)
T ss_pred             -----------hHHHHHHHHHHHHHHH---c--CCeEEEECCCChhhhhhhhHHHHH--HHhcCceEEecCCCHHHHHHH
Confidence                       1112233344444322   1  223444444566554   689999  86  57899999999999999


Q ss_pred             HHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHH
Q 024550          184 ASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQ  216 (266)
Q Consensus       184 ~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~  216 (266)
                      ++++....+..+..+. ..++....-+...+.+.
T Consensus       171 L~~~a~~~~l~l~~e~~~~La~~~~rd~r~~l~~  204 (233)
T PRK08727        171 LRERAQRRGLALDEAAIDWLLTHGERELAGLVAL  204 (233)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHH
Confidence            9987655555554443 34444444444444333

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.58  E-value=2.5e-14  Score=124.38  Aligned_cols=136  Identities=18%  Similarity=0.187  Sum_probs=94.0

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHH------------------HH-HHcccCCeeee
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRH------------------IL-IATENKSILVV   88 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~------------------~~-~~~~~~~vl~i   88 (266)
                      +..++.+||.||||||||++++.+|..++.+++.+++.......++..                  .+ .....++++++
T Consensus        61 l~~~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~~g~illl  140 (327)
T TIGR01650        61 FAYDRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQHNVALCF  140 (327)
T ss_pred             HhcCCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHhCCeEEEe
Confidence            334667999999999999999999999999999999876553211110                  01 11245788999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhh-----hhc--cccCCCCceEEEEecCCCC-------
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNF-----IDG--LWSSCGDERIIIFTTNHKE-------  154 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~-----l~~--~~~~~~~~~ivi~ttn~~~-------  154 (266)
                      ||+|...+                        .....++.+|+.     +.+  -.-.....+.+|+|+|..+       
T Consensus       141 DEin~a~p------------------------~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~  196 (327)
T TIGR01650       141 DEYDAGRP------------------------DVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGL  196 (327)
T ss_pred             chhhccCH------------------------HHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcc
Confidence            99997643                        111222333321     000  0001224578999999753       


Q ss_pred             -----CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          155 -----RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       155 -----~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                           .++.|++.  ||.+++.+.+|+.++-.+|+.....
T Consensus       197 y~Gt~~l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~~  234 (327)
T TIGR01650       197 YHGTQQINQAQMD--RWSIVTTLNYLEHDNEAAIVLAKAK  234 (327)
T ss_pred             eeeeecCCHHHHh--heeeEeeCCCCCHHHHHHHHHhhcc
Confidence                 46899999  9988899999999999999887653

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=4.1e-14  Score=132.90  Aligned_cols=154  Identities=17%  Similarity=0.251  Sum_probs=110.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+|||||+|||||++|+.+|+.+++                        .++.++.+...+...++.+...+.    
T Consensus        37 ~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~  116 (559)
T PRK05563         37 ISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPS  116 (559)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcc
Confidence            4667999999999999999999998853                        455565544334445566655432    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|++|||+|.|..                           ...+.|+..++.    ++..+++|.+|+.++.++++
T Consensus       117 ~~~~kViIIDE~~~Lt~---------------------------~a~naLLKtLEe----pp~~~ifIlatt~~~ki~~t  165 (559)
T PRK05563        117 EAKYKVYIIDEVHMLST---------------------------GAFNALLKTLEE----PPAHVIFILATTEPHKIPAT  165 (559)
T ss_pred             cCCeEEEEEECcccCCH---------------------------HHHHHHHHHhcC----CCCCeEEEEEeCChhhCcHH
Confidence              357999999998732                           245567776664    24567888888889999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..+.|+.|+.++....+...+...+..... .+..++...+.+++++.+.+
T Consensus       166 I~S--Rc-~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G~~R~al~~L  221 (559)
T PRK05563        166 ILS--RC-QRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSIL  221 (559)
T ss_pred             HHh--Hh-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  88 468999999999999999888777665553 34445555556666655554

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.58  E-value=3e-14  Score=125.32  Aligned_cols=123  Identities=19%  Similarity=0.210  Sum_probs=87.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHH----HHc---ccCCeeeeecchhhHHHhHHHhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHIL----IAT---ENKSILVVEDIDCCIELQDRLSR  103 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~----~~~---~~~~vl~iDeid~l~~~~~~~~~  103 (266)
                      ++.+|||||||+|||++++++++.++.+++.+++.. .....++..+    ...   ..+.||+|||+|.+..       
T Consensus        43 ~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~~~~-~~~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~-------  114 (316)
T PHA02544         43 PNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSD-CRIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGL-------  114 (316)
T ss_pred             CeEEEeeCcCCCCHHHHHHHHHHHhCccceEeccCc-ccHHHHHHHHHHHHHhhcccCCCeEEEEECcccccC-------
Confidence            456777999999999999999999999999999887 2222222211    111   3578999999997721       


Q ss_pred             hhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHH
Q 024550          104 ARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKML  183 (266)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i  183 (266)
                                      ..   ....+...++..    +....+|+|||.+..+++++.+  ||. .+.|+.|+.+++..+
T Consensus       115 ----------------~~---~~~~L~~~le~~----~~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~~~~i  168 (316)
T PHA02544        115 ----------------AD---AQRHLRSFMEAY----SKNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEEQIEM  168 (316)
T ss_pred             ----------------HH---HHHHHHHHHHhc----CCCceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHHHHHH
Confidence                            01   112233334432    2456788899999999999999  984 689999999998877


Q ss_pred             HHHh
Q 024550          184 ASNY  187 (266)
Q Consensus       184 ~~~~  187 (266)
                      +..+
T Consensus       169 l~~~  172 (316)
T PHA02544        169 MKQM  172 (316)
T ss_pred             HHHH
Confidence            6544

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=99.58  E-value=1.6e-14  Score=120.51  Aligned_cols=156  Identities=19%  Similarity=0.262  Sum_probs=102.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccC-------hhhHHHHHHHcccCCeeeeecchhhHHHhHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLG-------NNDLRHILIATENKSILVVEDIDCCIELQDR  100 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~-------~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~  100 (266)
                      .++||||+|+|||+|++++++++     +..++++++..+..       ...+..+........+|+|||++.+.+.   
T Consensus        36 ~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~~---  112 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAGK---  112 (219)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTTH---
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcCc---
Confidence            58999999999999999999875     56788888776542       1233445566678899999999988541   


Q ss_pred             HhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC---CcccccCCCcce--eEEEcCCC
Q 024550          101 LSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER---LDPALLRPGRMD--MHINMSHC  175 (266)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~---ld~al~r~~Rf~--~~i~~~~p  175 (266)
                                         ...+..+..+++.+.   ..  .+.+|+++...|..   +++.|.+  ||.  ..+.+..|
T Consensus       113 -------------------~~~q~~lf~l~n~~~---~~--~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~p  166 (219)
T PF00308_consen  113 -------------------QRTQEELFHLFNRLI---ES--GKQLILTSDRPPSELSGLLPDLRS--RLSWGLVVELQPP  166 (219)
T ss_dssp             -------------------HHHHHHHHHHHHHHH---HT--TSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEEEE---
T ss_pred             -------------------hHHHHHHHHHHHHHH---hh--CCeEEEEeCCCCccccccChhhhh--hHhhcchhhcCCC
Confidence                               112233344444443   22  34666666666654   4677888  665  68999999


Q ss_pred             CHHHHHHHHHHhhCCCCCCcHHHHHHHhh-cCCCCHHHHHHHH
Q 024550          176 TPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQL  217 (266)
Q Consensus       176 ~~~~~~~i~~~~~~~~~~~~~~~~~~l~~-~~~~s~~~i~~~l  217 (266)
                      +.+.|..|+.++....+..+.+++..++. ...-+.+++..++
T Consensus       167 d~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~~~r~L~~~l  209 (219)
T PF00308_consen  167 DDEDRRRILQKKAKERGIELPEEVIEYLARRFRRDVRELEGAL  209 (219)
T ss_dssp             -HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTSSHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcCCHHHHHHHH
Confidence            99999999999999888888777655444 4556777776665

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.57  E-value=3.7e-14  Score=137.59  Aligned_cols=152  Identities=18%  Similarity=0.274  Sum_probs=105.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC--------------------------cEEEEeCCcccChhhHHHHHHHc---
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF--------------------------DVYDLELSNLLGNNDLRHILIAT---   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~--------------------------~~~~i~~~~~~~~~~l~~~~~~~---   80 (266)
                      .++.+|||||+|||||++++.+|+.+++                          .++.++.....+...++.+....   
T Consensus        36 i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~  115 (824)
T PRK07764         36 INHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFA  115 (824)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhc
Confidence            3567999999999999999999999964                          23444443322333444433221   


Q ss_pred             ---ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc
Q 024550           81 ---ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD  157 (266)
Q Consensus        81 ---~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld  157 (266)
                         ....|+||||+|.|..                           ...+.||+.|+..    +..++||++|+.++.|.
T Consensus       116 p~~~~~KV~IIDEad~lt~---------------------------~a~NaLLK~LEEp----P~~~~fIl~tt~~~kLl  164 (824)
T PRK07764        116 PAESRYKIFIIDEAHMVTP---------------------------QGFNALLKIVEEP----PEHLKFIFATTEPDKVI  164 (824)
T ss_pred             hhcCCceEEEEechhhcCH---------------------------HHHHHHHHHHhCC----CCCeEEEEEeCChhhhh
Confidence               2467999999998842                           3456777887754    35688888888888899


Q ss_pred             ccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHH
Q 024550          158 PALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAE  215 (266)
Q Consensus       158 ~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~  215 (266)
                      ++|.+  || ..+.|..++.++...++..++..++..+..+ +..++...+.+..++.+
T Consensus       165 ~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~  220 (824)
T PRK07764        165 GTIRS--RT-HHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLS  220 (824)
T ss_pred             HHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            99999  88 6799999999999999998887766555433 33444444444444433

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.57  E-value=8.1e-14  Score=136.67  Aligned_cols=133  Identities=23%  Similarity=0.255  Sum_probs=93.3

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccC--------hhhHHHHHHHcc--cCCeee
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLG--------NNDLRHILIATE--NKSILV   87 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~--------~~~l~~~~~~~~--~~~vl~   87 (266)
                      ...+++++|+||||||||++++.+|..+          +.+++.++...+..        ...+..++..+.  .++|||
T Consensus       197 r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILf  276 (821)
T CHL00095        197 RRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQENNNIILV  276 (821)
T ss_pred             ccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEE
Confidence            3456689999999999999999999987          47889998776542        235667776543  478999


Q ss_pred             eecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccC
Q 024550           88 VEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLR  162 (266)
Q Consensus        88 iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r  162 (266)
                      |||+|.+.+.....                  +. ....+-|...+.    .  ..+.+|++|+..+     ..|++|.+
T Consensus       277 iDEih~l~~~g~~~------------------g~-~~~a~lLkp~l~----r--g~l~~IgaTt~~ey~~~ie~D~aL~r  331 (821)
T CHL00095        277 IDEVHTLIGAGAAE------------------GA-IDAANILKPALA----R--GELQCIGATTLDEYRKHIEKDPALER  331 (821)
T ss_pred             EecHHHHhcCCCCC------------------Cc-ccHHHHhHHHHh----C--CCcEEEEeCCHHHHHHHHhcCHHHHh
Confidence            99999997522100                  00 111222223333    2  4588888888653     46899999


Q ss_pred             CCcceeEEEcCCCCHHHHHHHHHHhh
Q 024550          163 PGRMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                        ||. .|.++.|+.++...|++...
T Consensus       332 --Rf~-~I~v~ep~~~e~~aILr~l~  354 (821)
T CHL00095        332 --RFQ-PVYVGEPSVEETIEILFGLR  354 (821)
T ss_pred             --cce-EEecCCCCHHHHHHHHHHHH
Confidence              995 58999999999888876543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.57  E-value=1.1e-13  Score=124.19  Aligned_cols=132  Identities=17%  Similarity=0.159  Sum_probs=88.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC---------CcEEEEeCCcccChhh--------------------------HHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK---------FDVYDLELSNLLGNND--------------------------LRH   75 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~---------~~~~~i~~~~~~~~~~--------------------------l~~   75 (266)
                      +.+++||||||||||++++++++.+.         ..+++++|....+...                          +..
T Consensus        40 ~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  119 (365)
T TIGR02928        40 PSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRR  119 (365)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHH
Confidence            45799999999999999999998763         5678888865543111                          111


Q ss_pred             HHHH---cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC
Q 024550           76 ILIA---TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH  152 (266)
Q Consensus        76 ~~~~---~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~  152 (266)
                      ++..   ..++.||+|||+|.+..                        .....+..++...+ .....+.++.+|+++|.
T Consensus       120 l~~~l~~~~~~~vlvIDE~d~L~~------------------------~~~~~L~~l~~~~~-~~~~~~~~v~lI~i~n~  174 (365)
T TIGR02928       120 LYKELNERGDSLIIVLDEIDYLVG------------------------DDDDLLYQLSRARS-NGDLDNAKVGVIGISND  174 (365)
T ss_pred             HHHHHHhcCCeEEEEECchhhhcc------------------------CCcHHHHhHhcccc-ccCCCCCeEEEEEEECC
Confidence            1111   23467999999998852                        01112333333211 11122246788899988


Q ss_pred             CC---CCcccccCCCcce-eEEEcCCCCHHHHHHHHHHhhC
Q 024550          153 KE---RLDPALLRPGRMD-MHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       153 ~~---~ld~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      ++   .+++.+.+  ||. ..|+|+.++.++...|+...+.
T Consensus       175 ~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       175 LKFRENLDPRVKS--SLCEEEIIFPPYDAEELRDILENRAE  213 (365)
T ss_pred             cchHhhcCHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHH
Confidence            75   57788887  775 6799999999999999998875

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=3.3e-14  Score=133.99  Aligned_cols=154  Identities=14%  Similarity=0.230  Sum_probs=111.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+|||||+|+|||++++.+|+.+++.                        +++++.....+...++.+.....    
T Consensus        37 ~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~  116 (576)
T PRK14965         37 VAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKYLPS  116 (576)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCeeeeeccCccCHHHHHHHHHHHHhccc
Confidence            46779999999999999999999998642                        44555443333445555554432    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|++|||+|.+..                           ...+.|+..|+.-    +..++||.+|+.+..|.++
T Consensus       117 ~~~~KVvIIdev~~Lt~---------------------------~a~naLLk~LEep----p~~~~fIl~t~~~~kl~~t  165 (576)
T PRK14965        117 RSRYKIFIIDEVHMLST---------------------------NAFNALLKTLEEP----PPHVKFIFATTEPHKVPIT  165 (576)
T ss_pred             cCCceEEEEEChhhCCH---------------------------HHHHHHHHHHHcC----CCCeEEEEEeCChhhhhHH
Confidence              356999999997732                           2456777777753    3568888888999999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..++|..++.++....+..++...+..+. ..+..++...+.+.+++.+.+
T Consensus       166 I~S--Rc-~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a~G~lr~al~~L  221 (576)
T PRK14965        166 ILS--RC-QRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTL  221 (576)
T ss_pred             HHH--hh-hhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  88 56999999999999888888877766554 344455555666666555554

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.56  E-value=4.5e-14  Score=131.57  Aligned_cols=154  Identities=18%  Similarity=0.299  Sum_probs=109.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++++||+||||+|||++|+++|+.+.+                        .++.++.+...+-..++.+.....    
T Consensus        37 l~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~  116 (605)
T PRK05896         37 LTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPT  116 (605)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchh
Confidence            3578999999999999999999998753                        344455443333344555544322    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|++|||+|.+..                           ...+.|+..|+.-    +..+++|++|+.+..+.++
T Consensus       117 ~~~~KVIIIDEad~Lt~---------------------------~A~NaLLKtLEEP----p~~tvfIL~Tt~~~KLl~T  165 (605)
T PRK05896        117 TFKYKVYIIDEAHMLST---------------------------SAWNALLKTLEEP----PKHVVFIFATTEFQKIPLT  165 (605)
T ss_pred             hCCcEEEEEechHhCCH---------------------------HHHHHHHHHHHhC----CCcEEEEEECCChHhhhHH
Confidence              356999999998732                           1345677777642    3457888888889999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++  || ..++|+.|+.++....+...+...+.... ..+..++...+.+++++.+.+
T Consensus       166 I~S--Rc-q~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS~GdlR~AlnlL  221 (605)
T PRK05896        166 IIS--RC-QRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSIL  221 (605)
T ss_pred             HHh--hh-hhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence            999  88 46999999999999999888877665443 444555666666777666655

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.56  E-value=6.1e-14  Score=125.27  Aligned_cols=154  Identities=19%  Similarity=0.317  Sum_probs=109.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++.+|||||||+|||++++++++.+.+                        .++.++.....+...++.++..+.    
T Consensus        35 ~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~  114 (355)
T TIGR02397        35 IAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPS  114 (355)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeeccccCCHHHHHHHHHHHhcCcc
Confidence            3567999999999999999999998743                        244444433223334555555432    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|++|||+|.+..                           ...+.++..++..    +..+++|.+|+.+..+.++
T Consensus       115 ~~~~~vviidea~~l~~---------------------------~~~~~Ll~~le~~----~~~~~lIl~~~~~~~l~~~  163 (355)
T TIGR02397       115 SGKYKVYIIDEVHMLSK---------------------------SAFNALLKTLEEP----PEHVVFILATTEPHKIPAT  163 (355)
T ss_pred             cCCceEEEEeChhhcCH---------------------------HHHHHHHHHHhCC----ccceeEEEEeCCHHHHHHH
Confidence              346999999997732                           2345566766542    3457777888888888889


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  || ..++|+.|+.++...++..++...+..+. ..+..++...+.+++.+.+.+
T Consensus       164 l~s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       164 ILS--RC-QRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             HHh--he-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHH
Confidence            998  88 57999999999999999998877776655 444555666666777666655

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=99.56  E-value=4.9e-14  Score=118.80  Aligned_cols=155  Identities=18%  Similarity=0.202  Sum_probs=100.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAAN  108 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~  108 (266)
                      ..++||||+|||||+|++++++++   +..+++++..++...  ...+.....+..+|+|||++.+.+            
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~~~--~~~~~~~~~~~d~LiiDDi~~~~~------------  111 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDR--GPELLDNLEQYELVCLDDLDVIAG------------  111 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHHhh--hHHHHHhhhhCCEEEEechhhhcC------------
Confidence            568999999999999999999765   567778887666432  223444445567999999997743            


Q ss_pred             CccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC---CcccccCCCcc--eeEEEcCCCCHHHHHHH
Q 024550          109 PDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER---LDPALLRPGRM--DMHINMSHCTPSGFKML  183 (266)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~---ld~al~r~~Rf--~~~i~~~~p~~~~~~~i  183 (266)
                                .......+..++|.   ..+.  ...++++++..|..   +.+.|.+  ||  +..+.+..|+.+++..+
T Consensus       112 ----------~~~~~~~Lf~l~n~---~~~~--g~~ilits~~~p~~l~~~~~~L~S--Rl~~gl~~~l~~~~~e~~~~i  174 (234)
T PRK05642        112 ----------KADWEEALFHLFNR---LRDS--GRRLLLAASKSPRELPIKLPDLKS--RLTLALVFQMRGLSDEDKLRA  174 (234)
T ss_pred             ----------ChHHHHHHHHHHHH---HHhc--CCEEEEeCCCCHHHcCccCccHHH--HHhcCeeeecCCCCHHHHHHH
Confidence                      11112233334443   3222  34666766665643   3688999  87  47889999999999999


Q ss_pred             HHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          184 ASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       184 ~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      ++......+..+.++. ..++....-+.+.+...+
T Consensus       175 l~~ka~~~~~~l~~ev~~~L~~~~~~d~r~l~~~l  209 (234)
T PRK05642        175 LQLRASRRGLHLTDEVGHFILTRGTRSMSALFDLL  209 (234)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            9865544444454443 344444555566555543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.56  E-value=3.1e-14  Score=130.15  Aligned_cols=157  Identities=17%  Similarity=0.218  Sum_probs=104.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh-------hhHHHHHHHcccCCeeeeecchhhHHHhHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN-------NDLRHILIATENKSILVVEDIDCCIELQDRL  101 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~-------~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~  101 (266)
                      ..++||||||+|||+|++++++.+   +..++++++..+...       ......-.......+|+|||++.+.+.    
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k----  217 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSGK----  217 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcCC----
Confidence            469999999999999999999976   677888887654321       111111122456789999999987430    


Q ss_pred             hhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC---CCcccccCCCcc--eeEEEcCCCC
Q 024550          102 SRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE---RLDPALLRPGRM--DMHINMSHCT  176 (266)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~---~ld~al~r~~Rf--~~~i~~~~p~  176 (266)
                                        ......+..+++.+   ...  ...+|+++++.|.   .++++|.+  ||  +..+.++.|+
T Consensus       218 ------------------~~~qeelf~l~N~l---~~~--~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd  272 (445)
T PRK12422        218 ------------------GATQEEFFHTFNSL---HTE--GKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLT  272 (445)
T ss_pred             ------------------hhhHHHHHHHHHHH---HHC--CCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCC
Confidence                              11122222333333   221  2345555555553   56789999  88  4899999999


Q ss_pred             HHHHHHHHHHhhCCCCCCcHHHHHH-HhhcCCCCHHHHHHHH
Q 024550          177 PSGFKMLASNYLGIAEHPLFVEIEK-LIATAKVTPADVAEQL  217 (266)
Q Consensus       177 ~~~~~~i~~~~~~~~~~~~~~~~~~-l~~~~~~s~~~i~~~l  217 (266)
                      .+++..|++......+..+..+... ++....-+.+++.+.+
T Consensus       273 ~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~dir~L~g~l  314 (445)
T PRK12422        273 KEGLRSFLERKAEALSIRIEETALDFLIEALSSNVKSLLHAL  314 (445)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            9999999999988877777666555 5555556666666554

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.55  E-value=8.5e-14  Score=132.15  Aligned_cols=154  Identities=16%  Similarity=0.267  Sum_probs=108.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcE---------------------EEEeCCcccChhhHHHHHHHcc------c
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDV---------------------YDLELSNLLGNNDLRHILIATE------N   82 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~---------------------~~i~~~~~~~~~~l~~~~~~~~------~   82 (266)
                      .++.+|||||+|+|||++|+++|+.+.+.-                     +.++...-.+...++.+...+.      .
T Consensus        39 l~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~  118 (725)
T PRK07133         39 ISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSK  118 (725)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCC
Confidence            467799999999999999999999886531                     2222221112333555544432      4


Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccC
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLR  162 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r  162 (266)
                      ..|++|||+|.|..                           ...+.|+..|+.-    +..+++|.+|+.++.|++++++
T Consensus       119 ~KV~IIDEa~~LT~---------------------------~A~NALLKtLEEP----P~~tifILaTte~~KLl~TI~S  167 (725)
T PRK07133        119 YKIYIIDEVHMLSK---------------------------SAFNALLKTLEEP----PKHVIFILATTEVHKIPLTILS  167 (725)
T ss_pred             CEEEEEEChhhCCH---------------------------HHHHHHHHHhhcC----CCceEEEEEcCChhhhhHHHHh
Confidence            57999999998742                           2456677777742    4567888888889999999999


Q ss_pred             CCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          163 PGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                        || ..+.|..|+.++....+...+...+..... .+..++...+.+++++...+
T Consensus       168 --Rc-q~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~GslR~AlslL  220 (725)
T PRK07133        168 --RV-QRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIA  220 (725)
T ss_pred             --hc-eeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence              88 479999999999999988887766655443 35556666667777665554

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.55  E-value=8.1e-14  Score=130.49  Aligned_cols=153  Identities=15%  Similarity=0.271  Sum_probs=107.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHH---c---
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIA---T---   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~---~---   80 (266)
                      ++.+||+||||||||++|+.+|+.+++.                        +++++...-.+...++.+...   .   
T Consensus        38 ~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~  117 (624)
T PRK14959         38 APAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPME  117 (624)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCceEEEecccccCHHHHHHHHHHHHhhhhc
Confidence            5689999999999999999999999753                        445544322222333333221   1   


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                      ....|++|||+|.+..                           ...+.|+..|+.-    ...++||++||.+..+.+.+
T Consensus       118 g~~kVIIIDEad~Lt~---------------------------~a~naLLk~LEEP----~~~~ifILaTt~~~kll~TI  166 (624)
T PRK14959        118 GRYKVFIIDEAHMLTR---------------------------EAFNALLKTLEEP----PARVTFVLATTEPHKFPVTI  166 (624)
T ss_pred             CCceEEEEEChHhCCH---------------------------HHHHHHHHHhhcc----CCCEEEEEecCChhhhhHHH
Confidence            2457999999998742                           2346677777652    34588888899888888899


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+  || ..|.|+.++.++...++...+...+..+.. .+..++...+.+.+++.+.+
T Consensus       167 ~S--Rc-q~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~~s~GdlR~Al~lL  221 (624)
T PRK14959        167 VS--RC-QHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLL  221 (624)
T ss_pred             Hh--hh-hccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            98  88 468999999999999998887776655543 34445555556666555544

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

Probab=99.55  E-value=1.5e-14  Score=122.42  Aligned_cols=152  Identities=18%  Similarity=0.235  Sum_probs=103.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCc------EEEEeCCcccChhhH-------HHHHHHc--------ccCCeeeeec
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFD------VYDLELSNLLGNNDL-------RHILIAT--------ENKSILVVED   90 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~------~~~i~~~~~~~~~~l-------~~~~~~~--------~~~~vl~iDe   90 (266)
                      ..+|||||||||||+.++++|.+++.+      +.+.+.++..+.+-.       ..+....        +..-|++|||
T Consensus        58 p~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDE  137 (346)
T KOG0989|consen   58 PHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDE  137 (346)
T ss_pred             ceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEec
Confidence            369999999999999999999999662      233344443322111       1111111        1236999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEE
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI  170 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i  170 (266)
                      .|.|.                           ...++.|.+.|+..    +..+.||..||+++.|+..+.+  ||. .+
T Consensus       138 cdsmt---------------------------sdaq~aLrr~mE~~----s~~trFiLIcnylsrii~pi~S--RC~-Kf  183 (346)
T KOG0989|consen  138 CDSMT---------------------------SDAQAALRRTMEDF----SRTTRFILICNYLSRIIRPLVS--RCQ-KF  183 (346)
T ss_pred             hhhhh---------------------------HHHHHHHHHHHhcc----ccceEEEEEcCChhhCChHHHh--hHH-Hh
Confidence            99885                           33566777888874    2458899999999999999999  995 57


Q ss_pred             EcCCCCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          171 NMSHCTPSGFKMLASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       171 ~~~~p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      .|+....+.....++.+-..++.....+. ..++...+.+-++....|
T Consensus       184 rFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~GdLR~Ait~L  231 (346)
T KOG0989|consen  184 RFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISDGDLRRAITTL  231 (346)
T ss_pred             cCCCcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence            88888888777778878888877776544 444443334444333333

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

Probab=99.55  E-value=1.7e-13  Score=132.92  Aligned_cols=172  Identities=16%  Similarity=0.258  Sum_probs=113.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhh-------------------HHHHHHHcccCCeeeeecchh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND-------------------LRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~-------------------l~~~~~~~~~~~vl~iDeid~   93 (266)
                      .+||+||||||||++|+++|..++.+++.++++.+.....                   +...+ .....+||+|||+|.
T Consensus       486 ~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~~~~lig~~~gyvg~~~~~~l~~~~-~~~p~~VvllDEiek  564 (731)
T TIGR02639       486 SFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQGGLLTEAV-RKHPHCVLLLDEIEK  564 (731)
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhcccHHHHhcCCCCCcccchhhHHHHHH-HhCCCeEEEEechhh
Confidence            4899999999999999999999999999999887643211                   22221 124579999999997


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCCCC------------
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHKE------------  154 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~~------------  154 (266)
                      +.+                           ...+.|++.|+...-+.       -.+.+||+|||...            
T Consensus       565 a~~---------------------------~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~  617 (731)
T TIGR02639       565 AHP---------------------------DIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGS  617 (731)
T ss_pred             cCH---------------------------HHHHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccCCcch
Confidence            743                           24556666666421111       13578999998531            


Q ss_pred             -------------CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHcCC
Q 024550          155 -------------RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNE  221 (266)
Q Consensus       155 -------------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~~~  221 (266)
                                   .+.|.|+.  ||+.+|.|...+.++..+|+..++....    ..+...-....++...+..++....
T Consensus       618 ~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~----~~l~~~~~~l~i~~~a~~~La~~~~  691 (731)
T TIGR02639       618 ENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLSEEVLEKIVQKFVDELS----KQLNEKNIKLELTDDAKKYLAEKGY  691 (731)
T ss_pred             hhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCCHHHHHHHHHHHHHHHH----HHHHhCCCeEEeCHHHHHHHHHhCC
Confidence                         24677777  9999999999999999999998885321    1111100012355554444444445


Q ss_pred             CHHHHHHHHHHHHHhhh
Q 024550          222 APEFALSGLIEFLESKK  238 (266)
Q Consensus       222 ~~~~~~~~~~~~~~~~~  238 (266)
                      ++...++.+..+++..-
T Consensus       692 ~~~~GaR~l~r~i~~~~  708 (731)
T TIGR02639       692 DEEFGARPLARVIQEEI  708 (731)
T ss_pred             CcccCchHHHHHHHHHh
Confidence            56566666666655543

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=1.1e-13  Score=130.33  Aligned_cols=154  Identities=14%  Similarity=0.248  Sum_probs=110.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcE-----------------------------EEEeCCcccChhhHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDV-----------------------------YDLELSNLLGNNDLRHILIAT   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~-----------------------------~~i~~~~~~~~~~l~~~~~~~   80 (266)
                      .++++|||||+|+|||++|+++|+.+++..                             ++++..+..+-..++.++..+
T Consensus        45 i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~  124 (598)
T PRK09111         45 IAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESV  124 (598)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHH
Confidence            366899999999999999999999886532                             223322222334555555443


Q ss_pred             c------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           81 E------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        81 ~------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      .      ...|++|||+|.+.                           ....+.|+..|+.-    +..++||.+|+.++
T Consensus       125 ~~~P~~a~~KVvIIDEad~Ls---------------------------~~a~naLLKtLEeP----p~~~~fIl~tte~~  173 (598)
T PRK09111        125 RYRPVSARYKVYIIDEVHMLS---------------------------TAAFNALLKTLEEP----PPHVKFIFATTEIR  173 (598)
T ss_pred             HhchhcCCcEEEEEEChHhCC---------------------------HHHHHHHHHHHHhC----CCCeEEEEEeCChh
Confidence            2      45799999999773                           22456677777753    34577777888888


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+.+.+.+  || ..++|+.|+.++...++...+...+..+. +.+..++...+.++.++.+.+
T Consensus       174 kll~tI~S--Rc-q~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~L  234 (598)
T PRK09111        174 KVPVTVLS--RC-QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLL  234 (598)
T ss_pred             hhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            88888998  88 56999999999999999998888776665 344555555666666665554

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.53  E-value=1.6e-13  Score=126.61  Aligned_cols=154  Identities=19%  Similarity=0.304  Sum_probs=105.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++.+|||||+|+|||++|+.+|+.+++                        .++.++.+.-.+...++.+....     
T Consensus        37 i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~  116 (486)
T PRK14953         37 VSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPI  116 (486)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcc
Confidence            3567999999999999999999998863                        23334333222233344443332     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.+..                           ...+.|+..++.-    +..+++|.+|+.++.++++
T Consensus       117 ~~~~KVvIIDEad~Lt~---------------------------~a~naLLk~LEep----p~~~v~Il~tt~~~kl~~t  165 (486)
T PRK14953        117 KGKYKVYIIDEAHMLTK---------------------------EAFNALLKTLEEP----PPRTIFILCTTEYDKIPPT  165 (486)
T ss_pred             cCCeeEEEEEChhhcCH---------------------------HHHHHHHHHHhcC----CCCeEEEEEECCHHHHHHH
Confidence             2357999999997732                           1345566666642    3456777777778888889


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  ||. .+.|+.|+.++...++..++...+..... .+..++...+.+.+++.+.+
T Consensus       166 I~S--Rc~-~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~G~lr~al~~L  221 (486)
T PRK14953        166 ILS--RCQ-RFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLL  221 (486)
T ss_pred             HHH--hce-EEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            998  884 69999999999999999888877765543 34455555566666665555

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.53  E-value=3.2e-13  Score=113.36  Aligned_cols=152  Identities=14%  Similarity=0.163  Sum_probs=99.2

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhh
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRAR  105 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~  105 (266)
                      .....++|+||+|||||++++++++.+   +.+++.+++..+..      .+.......+|+|||+|.+..         
T Consensus        40 ~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~~~------~~~~~~~~~~liiDdi~~l~~---------  104 (227)
T PRK08903         40 VADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPLL------AFDFDPEAELYAVDDVERLDD---------  104 (227)
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHhHH------HHhhcccCCEEEEeChhhcCc---------
Confidence            345679999999999999999999876   66788888765531      123344578999999997632         


Q ss_pred             hcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC-C--CCCcccccCCCcc--eeEEEcCCCCHHHH
Q 024550          106 AANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH-K--ERLDPALLRPGRM--DMHINMSHCTPSGF  180 (266)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~-~--~~ld~al~r~~Rf--~~~i~~~~p~~~~~  180 (266)
                                     .   ....+...++.....  ...++|.+++. +  ..+.+.|.+  ||  ...+.++.|+..++
T Consensus       105 ---------------~---~~~~L~~~~~~~~~~--~~~~vl~~~~~~~~~~~l~~~L~s--r~~~~~~i~l~pl~~~~~  162 (227)
T PRK08903        105 ---------------A---QQIALFNLFNRVRAH--GQGALLVAGPAAPLALPLREDLRT--RLGWGLVYELKPLSDADK  162 (227)
T ss_pred             ---------------h---HHHHHHHHHHHHHHc--CCcEEEEeCCCCHHhCCCCHHHHH--HHhcCeEEEecCCCHHHH
Confidence                           1   112233334332221  23334444443 3  234577777  76  57899999999999


Q ss_pred             HHHHHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          181 KMLASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       181 ~~i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      ..++..+....+..+..+. ..++.....++.++.+++
T Consensus       163 ~~~l~~~~~~~~v~l~~~al~~L~~~~~gn~~~l~~~l  200 (227)
T PRK08903        163 IAALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALL  200 (227)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHH
Confidence            8998887766666665544 444444456666666654

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

Probab=99.53  E-value=1.2e-13  Score=131.18  Aligned_cols=190  Identities=18%  Similarity=0.255  Sum_probs=131.1

Q ss_pred             HhhCHHHHHHhCCCCC----ceeEEecCCCCChHHHHHHHHHHcC---CcEEEEeCCcccChhhHHHHHHH---------
Q 024550           16 FLQRKEFYRRVGKAWK----RGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLELSNLLGNNDLRHILIA---------   79 (266)
Q Consensus        16 ~l~~~~~~~~~~~~~~----~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~~~~~~~~~~l~~~~~~---------   79 (266)
                      -+...-...+.|+..|    .++||.||.|+|||.+|++||..+.   ..++.++++.++....+..++..         
T Consensus       502 avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLIGaPPGYVGyee  581 (786)
T COG0542         502 AVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEE  581 (786)
T ss_pred             HHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHhCCCCCCceecc
Confidence            3333344445565543    3589999999999999999999996   78999999999865555544422         


Q ss_pred             ---------cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC-------Cc
Q 024550           80 ---------TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG-------DE  143 (266)
Q Consensus        80 ---------~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~-------~~  143 (266)
                               .+..+||++|||+..                           ...+++-||+.||.-.-+.+       .+
T Consensus       582 GG~LTEaVRr~PySViLlDEIEKA---------------------------HpdV~nilLQVlDdGrLTD~~Gr~VdFrN  634 (786)
T COG0542         582 GGQLTEAVRRKPYSVILLDEIEKA---------------------------HPDVFNLLLQVLDDGRLTDGQGRTVDFRN  634 (786)
T ss_pred             ccchhHhhhcCCCeEEEechhhhc---------------------------CHHHHHHHHHHhcCCeeecCCCCEEecce
Confidence                     124689999999954                           35578889999984433332       24


Q ss_pred             eEEEEecCCC----------------------------CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc
Q 024550          144 RIIIFTTNHK----------------------------ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL  195 (266)
Q Consensus       144 ~ivi~ttn~~----------------------------~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~  195 (266)
                      .+||+|||--                            ..+.|.|+.  |++.+|.|...+.+...+|+..++....   
T Consensus       635 tiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~L~~l~---  709 (786)
T COG0542         635 TIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQLNRLA---  709 (786)
T ss_pred             eEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHHHHHHH---
Confidence            6899999931                            123677777  9999999999999999999998884321   


Q ss_pred             HHHHHHHhhcCCCCHHHHHHHHHcCCCHHHHHHHHHHHHHhhh
Q 024550          196 FVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKK  238 (266)
Q Consensus       196 ~~~~~~l~~~~~~s~~~i~~~l~~~~~~~~~~~~~~~~~~~~~  238 (266)
                       ..+..---...++..-...+.-.+.++....+.+..+++..-
T Consensus       710 -~~L~~~~i~l~~s~~a~~~l~~~gyd~~~GARpL~R~Iq~~i  751 (786)
T COG0542         710 -KRLAERGITLELSDEAKDFLAEKGYDPEYGARPLRRAIQQEI  751 (786)
T ss_pred             -HHHHhCCceEEECHHHHHHHHHhccCCCcCchHHHHHHHHHH
Confidence             222110111236666666666666777777777777666543

>PRK06620 hypothetical protein; Validated

Probab=99.53  E-value=1.4e-13  Score=114.41  Aligned_cols=141  Identities=18%  Similarity=0.259  Sum_probs=93.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDF  111 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~  111 (266)
                      +.++||||||||||++++++++..+..++  +.... .    .. +  .....+|+|||+|.+.                
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~~~~--~~~~~-~----~~-~--~~~~d~lliDdi~~~~----------------   98 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNAYII--KDIFF-N----EE-I--LEKYNAFIIEDIENWQ----------------   98 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCCEEc--chhhh-c----hh-H--HhcCCEEEEeccccch----------------
Confidence            67999999999999999999998875332  21111 1    11 1  1345799999999441                


Q ss_pred             ccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC--CcccccCCCcce--eEEEcCCCCHHHHHHHHHHh
Q 024550          112 LIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER--LDPALLRPGRMD--MHINMSHCTPSGFKMLASNY  187 (266)
Q Consensus       112 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~--ld~al~r~~Rf~--~~i~~~~p~~~~~~~i~~~~  187 (266)
                                 ...+..++|.+...     ...++|+++..|..  + ++|++  |+.  .++.+..|+.+.+..++.+.
T Consensus        99 -----------~~~lf~l~N~~~e~-----g~~ilits~~~p~~l~l-~~L~S--Rl~~gl~~~l~~pd~~~~~~~l~k~  159 (214)
T PRK06620         99 -----------EPALLHIFNIINEK-----QKYLLLTSSDKSRNFTL-PDLSS--RIKSVLSILLNSPDDELIKILIFKH  159 (214)
T ss_pred             -----------HHHHHHHHHHHHhc-----CCEEEEEcCCCccccch-HHHHH--HHhCCceEeeCCCCHHHHHHHHHHH
Confidence                       11333444544432     34677777766654  4 78888  775  57999999999999999988


Q ss_pred             hCCCCCCcHHHHH-HHhhcCCCCHHHHHHHH
Q 024550          188 LGIAEHPLFVEIE-KLIATAKVTPADVAEQL  217 (266)
Q Consensus       188 ~~~~~~~~~~~~~-~l~~~~~~s~~~i~~~l  217 (266)
                      +...+..+.++.. .++....-+.+.+.+.+
T Consensus       160 ~~~~~l~l~~ev~~~L~~~~~~d~r~l~~~l  190 (214)
T PRK06620        160 FSISSVTISRQIIDFLLVNLPREYSKIIEIL  190 (214)
T ss_pred             HHHcCCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence            8766666655543 44444555666655554

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.52  E-value=3.5e-13  Score=119.45  Aligned_cols=151  Identities=15%  Similarity=0.222  Sum_probs=98.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCcccCh--------------------------hhHHHHHHHc-
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNLLGN--------------------------NDLRHILIAT-   80 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~~~~--------------------------~~l~~~~~~~-   80 (266)
                      ++|||||||||||++++++++++.     .+++.+++..+...                          ..++.+.... 
T Consensus        38 ~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (337)
T PRK12402         38 HLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYA  117 (337)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhcCcccccceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHH
Confidence            699999999999999999999884     34567776654210                          0111111111 


Q ss_pred             ------ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           81 ------ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        81 ------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                            ....+|+|||+|.+..                           ...+.|...++...    ....+|.+++.+.
T Consensus       118 ~~~~~~~~~~vlilDe~~~l~~---------------------------~~~~~L~~~le~~~----~~~~~Il~~~~~~  166 (337)
T PRK12402        118 SYRPLSADYKTILLDNAEALRE---------------------------DAQQALRRIMEQYS----RTCRFIIATRQPS  166 (337)
T ss_pred             hcCCCCCCCcEEEEeCcccCCH---------------------------HHHHHHHHHHHhcc----CCCeEEEEeCChh
Confidence                  2356999999997742                           11223444444321    2244555666666


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+.+.+.+  |+ ..+.|+.|+.++...++..+....+..+. +.+..++...+.+.+++.+.+
T Consensus       167 ~~~~~L~s--r~-~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l  227 (337)
T PRK12402        167 KLIPPIRS--RC-LPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTL  227 (337)
T ss_pred             hCchhhcC--Cc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            77788888  77 56999999999999999998877766554 344555555556666655555

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=3.6e-13  Score=120.96  Aligned_cols=154  Identities=15%  Similarity=0.260  Sum_probs=105.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------EEEEeCCcccChhhHHHHHHHc------ccCCeeeeecc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------VYDLELSNLLGNNDLRHILIAT------ENKSILVVEDI   91 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------~~~i~~~~~~~~~~l~~~~~~~------~~~~vl~iDei   91 (266)
                      .++++|||||||+|||++++++++.+..+            ++.++.....+...+..++..+      ....|++|||+
T Consensus        38 ~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~  117 (367)
T PRK14970         38 LAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEV  117 (367)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHHHHHHHHHHhhccccCCcEEEEEeCh
Confidence            35689999999999999999999987542            2223322222234555555533      23569999999


Q ss_pred             hhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEE
Q 024550           92 DCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHIN  171 (266)
Q Consensus        92 d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~  171 (266)
                      |.+..                           ..++.++..++..    +...++|.+|+.+..+.+++.+  |+. .++
T Consensus       118 ~~l~~---------------------------~~~~~ll~~le~~----~~~~~~Il~~~~~~kl~~~l~s--r~~-~v~  163 (367)
T PRK14970        118 HMLSS---------------------------AAFNAFLKTLEEP----PAHAIFILATTEKHKIIPTILS--RCQ-IFD  163 (367)
T ss_pred             hhcCH---------------------------HHHHHHHHHHhCC----CCceEEEEEeCCcccCCHHHHh--cce-eEe
Confidence            97632                           1345566666542    2346677777778888899998  774 589


Q ss_pred             cCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          172 MSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       172 ~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      |+.|+.++...++.......+..+. +.+..++...+.+.+.+.+.+
T Consensus       164 ~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~l  210 (367)
T PRK14970        164 FKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIF  210 (367)
T ss_pred             cCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            9999999999999888877776554 444555665666666665554

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.52  E-value=2.9e-13  Score=124.12  Aligned_cols=154  Identities=15%  Similarity=0.201  Sum_probs=107.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc-------------------------EEEEeCCcccChhhHHHHHHHc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD-------------------------VYDLELSNLLGNNDLRHILIAT----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~-------------------------~~~i~~~~~~~~~~l~~~~~~~----   80 (266)
                      .++.+|||||||+|||++|+++|+.+.+.                         ++.++.....+...++.+....    
T Consensus        38 i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d~~~i~g~~~~gid~ir~i~~~l~~~~  117 (451)
T PRK06305         38 AAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLDVLEIDGASHRGIEDIRQINETVLFTP  117 (451)
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCceEEeeccccCCHHHHHHHHHHHHhhh
Confidence            35679999999999999999999988542                         3344432222223333332221    


Q ss_pred             --ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           81 --ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        81 --~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                        ....|++|||+|.+..                           ...+.|+..++.-    +..+++|++||.+..+.+
T Consensus       118 ~~~~~kvvIIdead~lt~---------------------------~~~n~LLk~lEep----~~~~~~Il~t~~~~kl~~  166 (451)
T PRK06305        118 SKSRYKIYIIDEVHMLTK---------------------------EAFNSLLKTLEEP----PQHVKFFLATTEIHKIPG  166 (451)
T ss_pred             hcCCCEEEEEecHHhhCH---------------------------HHHHHHHHHhhcC----CCCceEEEEeCChHhcch
Confidence              3568999999998732                           1345677777753    345777888888889999


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++.+  || ..++|+.++.++....+...+...+.... +.+..++...+.+.+.+.+.+
T Consensus       167 tI~s--Rc-~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        167 TILS--RC-QKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             HHHH--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999  88 46999999999999988888877665554 345556666666666665554

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=2.7e-13  Score=128.44  Aligned_cols=153  Identities=16%  Similarity=0.262  Sum_probs=107.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc--------------------------EEEEeCCcccChhhHHHHHHHcc---
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD--------------------------VYDLELSNLLGNNDLRHILIATE---   81 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~--------------------------~~~i~~~~~~~~~~l~~~~~~~~---   81 (266)
                      .+++|||||+|+|||++|+++|+.+++.                          +++++.........+++++..+.   
T Consensus        38 ~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p  117 (620)
T PRK14948         38 APAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAP  117 (620)
T ss_pred             CceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhCh
Confidence            4579999999999999999999998652                          33444333223445666665442   


Q ss_pred             ---cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           82 ---NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        82 ---~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                         ...|++|||+|.|.                           ....+.||..|+.-    +..++||++|+.+..+.+
T Consensus       118 ~~~~~KViIIDEad~Lt---------------------------~~a~naLLK~LEeP----p~~tvfIL~t~~~~~llp  166 (620)
T PRK14948        118 VQARWKVYVIDECHMLS---------------------------TAAFNALLKTLEEP----PPRVVFVLATTDPQRVLP  166 (620)
T ss_pred             hcCCceEEEEECccccC---------------------------HHHHHHHHHHHhcC----CcCeEEEEEeCChhhhhH
Confidence               35799999999873                           22456778877742    345788888888888989


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++.+  || ..++|+.++.++....+.......+..+. ..+..++...+.+.+++.+.+
T Consensus       167 TIrS--Rc-~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G~lr~A~~lL  223 (620)
T PRK14948        167 TIIS--RC-QRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDAESLL  223 (620)
T ss_pred             HHHh--he-eEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999  88 56899999999888877777766555544 344455555555555555444

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.52  E-value=2.2e-13  Score=130.80  Aligned_cols=149  Identities=21%  Similarity=0.294  Sum_probs=99.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHH-------cccCCeeeeecchhhHHHhHHHhhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIA-------TENKSILVVEDIDCCIELQDRLSRA  104 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~-------~~~~~vl~iDeid~l~~~~~~~~~~  104 (266)
                      .++|||||||||||++|+++|+.++.+++.+++... +...+...+..       .....+|||||+|.+..        
T Consensus        53 ~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~~~-~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~--------  123 (725)
T PRK13341         53 GSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVLA-GVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNK--------  123 (725)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhcCcceeehhhhh-hhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCH--------
Confidence            469999999999999999999999999988887643 22233333322       23467999999998742        


Q ss_pred             hhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecC--CCCCCcccccCCCcceeEEEcCCCCHHHHHH
Q 024550          105 RAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTN--HKERLDPALLRPGRMDMHINMSHCTPSGFKM  182 (266)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn--~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~  182 (266)
                                         ...+.|+..++.      ..+++|++|+  ....+++++++  |+ ..+.|+.++.+++..
T Consensus       124 -------------------~qQdaLL~~lE~------g~IiLI~aTTenp~~~l~~aL~S--R~-~v~~l~pLs~edi~~  175 (725)
T PRK13341        124 -------------------AQQDALLPWVEN------GTITLIGATTENPYFEVNKALVS--RS-RLFRLKSLSDEDLHQ  175 (725)
T ss_pred             -------------------HHHHHHHHHhcC------ceEEEEEecCCChHhhhhhHhhc--cc-cceecCCCCHHHHHH
Confidence                               122344554443      2466666553  33568899999  76 459999999999999


Q ss_pred             HHHHhhC-------CCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          183 LASNYLG-------IAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       183 i~~~~~~-------~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++++++.       .....+.++ +..++.....+.+++.+.+
T Consensus       176 IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~L  218 (725)
T PRK13341        176 LLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNAL  218 (725)
T ss_pred             HHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            9998886       233334333 3445554445555555544

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.52  E-value=6.9e-13  Score=126.42  Aligned_cols=139  Identities=22%  Similarity=0.330  Sum_probs=92.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccChh-----------------------hHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGNN-----------------------DLRHIL   77 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~~-----------------------~l~~~~   77 (266)
                      ...++|+|+||||||++++.+..++          .+.+++++|..+.+..                       .+..+|
T Consensus       781 nnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF  860 (1164)
T PTZ00112        781 NQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLF  860 (1164)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHH
Confidence            3446799999999999999998766          2567899996654321                       122333


Q ss_pred             HHc----ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC-
Q 024550           78 IAT----ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH-  152 (266)
Q Consensus        78 ~~~----~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~-  152 (266)
                      ...    ....||+|||||.|...                        ...++-.|++...    ..+..++||+++|. 
T Consensus       861 ~~L~k~~r~v~IIILDEID~L~kK------------------------~QDVLYnLFR~~~----~s~SKLiLIGISNdl  912 (1164)
T PTZ00112        861 NQNKKDNRNVSILIIDEIDYLITK------------------------TQKVLFTLFDWPT----KINSKLVLIAISNTM  912 (1164)
T ss_pred             hhhhcccccceEEEeehHhhhCcc------------------------HHHHHHHHHHHhh----ccCCeEEEEEecCch
Confidence            322    12469999999988531                        1223333333322    22356889999985 


Q ss_pred             --CCCCcccccCCCccee-EEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH
Q 024550          153 --KERLDPALLRPGRMDM-HINMSHCTPSGFKMLASNYLGIAEHPLFVEI  199 (266)
Q Consensus       153 --~~~ld~al~r~~Rf~~-~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~  199 (266)
                        +..+++.+.+  ||.. .|.|++++.+++..|+...+......+.++.
T Consensus       913 DLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdA  960 (1164)
T PTZ00112        913 DLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTA  960 (1164)
T ss_pred             hcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHH
Confidence              5667788888  6654 4889999999999999988875433333333

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.52  E-value=9e-14  Score=129.69  Aligned_cols=156  Identities=14%  Similarity=0.173  Sum_probs=105.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccCh-------hhHHHHHHHcccCCeeeeecchhhHHHhHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGN-------NDLRHILIATENKSILVVEDIDCCIELQDR  100 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~-------~~l~~~~~~~~~~~vl~iDeid~l~~~~~~  100 (266)
                      .++|||++|||||+|+.++++++     +..++++++..+...       ..+..+........+|+||||+.+.+.   
T Consensus       316 pL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gk---  392 (617)
T PRK14086        316 PLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDK---  392 (617)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCC---
Confidence            49999999999999999999987     467788887665421       112222233456789999999988531   


Q ss_pred             HhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC---CCCcccccCCCcc--eeEEEcCCC
Q 024550          101 LSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK---ERLDPALLRPGRM--DMHINMSHC  175 (266)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~---~~ld~al~r~~Rf--~~~i~~~~p  175 (266)
                                         ......+..+++.+.   ..  ...+||++...|   ..+++.|.+  ||  +..+++..|
T Consensus       393 -------------------e~tqeeLF~l~N~l~---e~--gk~IIITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~P  446 (617)
T PRK14086        393 -------------------ESTQEEFFHTFNTLH---NA--NKQIVLSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPP  446 (617)
T ss_pred             -------------------HHHHHHHHHHHHHHH---hc--CCCEEEecCCChHhhhhccHHHHh--hhhcCceEEcCCC
Confidence                               111222333444433   22  234444443344   356789999  66  688899999


Q ss_pred             CHHHHHHHHHHhhCCCCCCcHHHHHHHh-hcCCCCHHHHHHHH
Q 024550          176 TPSGFKMLASNYLGIAEHPLFVEIEKLI-ATAKVTPADVAEQL  217 (266)
Q Consensus       176 ~~~~~~~i~~~~~~~~~~~~~~~~~~l~-~~~~~s~~~i~~~l  217 (266)
                      +.+.|..|++..+...+..+..++..++ .+..-+.+++..++
T Consensus       447 D~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~LegaL  489 (617)
T PRK14086        447 ELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELEGAL  489 (617)
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHHHHH
Confidence            9999999999999888877776665544 44556667666655

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.51  E-value=7.6e-14  Score=127.71  Aligned_cols=158  Identities=17%  Similarity=0.296  Sum_probs=104.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccCh-------hhHHHHHHHc-ccCCeeeeecchhhHHHh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGN-------NDLRHILIAT-ENKSILVVEDIDCCIELQ   98 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~-------~~l~~~~~~~-~~~~vl~iDeid~l~~~~   98 (266)
                      .+++||||||||||+|++++++++     +..++++++.++...       ..+....... ..+.+|+|||++.+.+..
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~~~  210 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIGKT  210 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcCcH
Confidence            459999999999999999999986     456788887665321       1122222222 257899999999875310


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC---CcccccCCCcc--eeEEEcC
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER---LDPALLRPGRM--DMHINMS  173 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~---ld~al~r~~Rf--~~~i~~~  173 (266)
                                               .....++..+......  ...++|++.+.|..   +.+.+.+  ||  +..+.+.
T Consensus       211 -------------------------~~q~elf~~~n~l~~~--~k~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~i~  261 (440)
T PRK14088        211 -------------------------GVQTELFHTFNELHDS--GKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLE  261 (440)
T ss_pred             -------------------------HHHHHHHHHHHHHHHc--CCeEEEECCCCHHHHHHHHHHHhh--HHhcCceEeeC
Confidence                                     0112233333333322  23555555566654   5678888  66  4789999


Q ss_pred             CCCHHHHHHHHHHhhCCCCCCcHHHHH-HHhhcCCCCHHHHHHHHH
Q 024550          174 HCTPSGFKMLASNYLGIAEHPLFVEIE-KLIATAKVTPADVAEQLM  218 (266)
Q Consensus       174 ~p~~~~~~~i~~~~~~~~~~~~~~~~~-~l~~~~~~s~~~i~~~l~  218 (266)
                      .|+.+.|..|++......+..+.++.. .++....-+.+++...+.
T Consensus       262 ~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~  307 (440)
T PRK14088        262 PPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAII  307 (440)
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHHHH
Confidence            999999999999998877666665554 445555667777776663

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.50  E-value=3.2e-13  Score=126.56  Aligned_cols=154  Identities=16%  Similarity=0.211  Sum_probs=108.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++.+|||||||+|||++|+++|+.+++.                        ++.++...-.+-..++.+....     
T Consensus        37 i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~  116 (563)
T PRK06647         37 IANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPA  116 (563)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchh
Confidence            35679999999999999999999998642                        3334333222233444444322     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.+.                           ....+.|+..++.    ++..+++|++|+.+..+.++
T Consensus       117 ~~~~KVvIIDEa~~Ls---------------------------~~a~naLLK~LEe----pp~~~vfI~~tte~~kL~~t  165 (563)
T PRK06647        117 SSRYRVYIIDEVHMLS---------------------------NSAFNALLKTIEE----PPPYIVFIFATTEVHKLPAT  165 (563)
T ss_pred             cCCCEEEEEEChhhcC---------------------------HHHHHHHHHhhcc----CCCCEEEEEecCChHHhHHH
Confidence             245799999999773                           2245567777664    34568888888888899999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  ||. .++|..++.++...++.......+..+.. .+..++...+.+++++.+.+
T Consensus       166 I~S--Rc~-~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~GdlR~alslL  221 (563)
T PRK06647        166 IKS--RCQ-HFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDAYTLF  221 (563)
T ss_pred             HHH--hce-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  884 68999999999999998888766655544 34445555666666666554

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=3.9e-13  Score=126.88  Aligned_cols=155  Identities=12%  Similarity=0.216  Sum_probs=107.2

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCc--------------------------------EEEEeCCcccChhhHHHH
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFD--------------------------------VYDLELSNLLGNNDLRHI   76 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~--------------------------------~~~i~~~~~~~~~~l~~~   76 (266)
                      ..++++||+||+|||||++|+.+|+.+++.                                ++.++.....+...++.+
T Consensus        36 ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l  115 (620)
T PRK14954         36 RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQL  115 (620)
T ss_pred             CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHH
Confidence            346679999999999999999999999762                                122222222223445554


Q ss_pred             HHHc------ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEec
Q 024550           77 LIAT------ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTT  150 (266)
Q Consensus        77 ~~~~------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~tt  150 (266)
                      ....      ...-|++|||+|.+..                           ...+.|+..|+.-    +...++|.+|
T Consensus       116 ~e~~~~~P~~~~~KVvIIdEad~Lt~---------------------------~a~naLLK~LEeP----p~~tv~IL~t  164 (620)
T PRK14954        116 RENVRYGPQKGRYRVYIIDEVHMLST---------------------------AAFNAFLKTLEEP----PPHAIFIFAT  164 (620)
T ss_pred             HHHHHhhhhcCCCEEEEEeChhhcCH---------------------------HHHHHHHHHHhCC----CCCeEEEEEe
Confidence            4433      2457999999997732                           2345677777753    3446777777


Q ss_pred             CCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          151 NHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       151 n~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+..+.+++.+  |+ ..++|..++.++....+...+...+..+. +.+..++...+.+.+++.+.+
T Consensus       165 ~~~~kLl~TI~S--Rc-~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal~~La~~s~Gdlr~al~eL  229 (620)
T PRK14954        165 TELHKIPATIAS--RC-QRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSIL  229 (620)
T ss_pred             CChhhhhHHHHh--hc-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence            778888899998  87 67999999999999888888877665554 445556666666666665543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=1.8e-13  Score=123.91  Aligned_cols=154  Identities=12%  Similarity=0.208  Sum_probs=105.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc--------------------------------EEEEeCCcccChhhHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD--------------------------------VYDLELSNLLGNNDLRHIL   77 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~--------------------------------~~~i~~~~~~~~~~l~~~~   77 (266)
                      .++.+|||||||+|||++|+++|+.+.+.                                ++.++.....+...++.+.
T Consensus        37 ~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~  116 (397)
T PRK14955         37 VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLR  116 (397)
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHH
Confidence            46679999999999999999999999662                                2223222222234455444


Q ss_pred             HHc------ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecC
Q 024550           78 IAT------ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTN  151 (266)
Q Consensus        78 ~~~------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn  151 (266)
                      ...      ....|++|||+|.+..                           ...+.|+..++.-    +...++|.+|+
T Consensus       117 ~~~~~~p~~~~~kvvIIdea~~l~~---------------------------~~~~~LLk~LEep----~~~t~~Il~t~  165 (397)
T PRK14955        117 ENVRYGPQKGRYRVYIIDEVHMLSI---------------------------AAFNAFLKTLEEP----PPHAIFIFATT  165 (397)
T ss_pred             HHHhhchhcCCeEEEEEeChhhCCH---------------------------HHHHHHHHHHhcC----CCCeEEEEEeC
Confidence            443      2357999999997732                           2345567776642    34566777777


Q ss_pred             CCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          152 HKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       152 ~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+..+.+++.+  |+. .++|+.++.++....+...+...+..+. +.+..++...+.+...+.+.+
T Consensus       166 ~~~kl~~tl~s--R~~-~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g~lr~a~~~L  229 (397)
T PRK14955        166 ELHKIPATIAS--RCQ-RFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSIL  229 (397)
T ss_pred             ChHHhHHHHHH--HHH-HhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            77888889988  874 6999999999999888888877665554 444556666666676666544

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.50  E-value=5.2e-13  Score=123.65  Aligned_cols=154  Identities=18%  Similarity=0.265  Sum_probs=112.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHc-----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      .++.+|||||+|+|||++|+++|+.+.+                        .++.++.+.-.+-..++.+....     
T Consensus        35 l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas~~gId~IRelie~~~~~P~  114 (535)
T PRK08451         35 LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPS  114 (535)
T ss_pred             CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEeccccccCHHHHHHHHHHHhhCcc
Confidence            4667899999999999999999998742                        24444443322334566655442     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.+.                           ....+.|+..|+.-    +..+.||.+|+.+..+.++
T Consensus       115 ~~~~KVvIIDEad~Lt---------------------------~~A~NALLK~LEEp----p~~t~FIL~ttd~~kL~~t  163 (535)
T PRK08451        115 MARFKIFIIDEVHMLT---------------------------KEAFNALLKTLEEP----PSYVKFILATTDPLKLPAT  163 (535)
T ss_pred             cCCeEEEEEECcccCC---------------------------HHHHHHHHHHHhhc----CCceEEEEEECChhhCchH
Confidence             234699999999773                           23456677777753    3456777777888999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  |+ ..++|..++.++....+...+...+.... ..+..++...+.+++++.+.+
T Consensus       164 I~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~GdlR~alnlL  219 (535)
T PRK08451        164 ILS--RT-QHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLL  219 (535)
T ss_pred             HHh--hc-eeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence            999  87 57999999999999999988888776664 445566666677777777766

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

Probab=99.49  E-value=2.1e-13  Score=120.71  Aligned_cols=131  Identities=25%  Similarity=0.257  Sum_probs=91.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHH--HH----------ccc---C---Ceeeeecc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHIL--IA----------TEN---K---SILVVEDI   91 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~--~~----------~~~---~---~vl~iDei   91 (266)
                      ....+||.||||||||++++++|..++.+++.++|.......++...+  ..          .+.   .   +|+++|||
T Consensus        42 ~~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEI  121 (329)
T COG0714          42 AGGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEI  121 (329)
T ss_pred             cCCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEecc
Confidence            456799999999999999999999999999999999766544432111  10          011   1   39999999


Q ss_pred             hhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc-------cc-cCCCCceEEEEecC-----CCCCCcc
Q 024550           92 DCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG-------LW-SSCGDERIIIFTTN-----HKERLDP  158 (266)
Q Consensus        92 d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~-------~~-~~~~~~~ivi~ttn-----~~~~ld~  158 (266)
                      +...                           ..+.+.|+..|+.       .. ...+.+.++|+|+|     ....+++
T Consensus       122 nra~---------------------------p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~e  174 (329)
T COG0714         122 NRAP---------------------------PEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPE  174 (329)
T ss_pred             ccCC---------------------------HHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCH
Confidence            9653                           3355556655543       11 22235678888889     4467899


Q ss_pred             cccCCCcceeEEEcCCCCHH-HHHHHHHHhhC
Q 024550          159 ALLRPGRMDMHINMSHCTPS-GFKMLASNYLG  189 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~-~~~~i~~~~~~  189 (266)
                      ++++  ||.+.+.++.|+.+ +...+..+.-.
T Consensus       175 A~ld--Rf~~~~~v~yp~~~~e~~~i~~~~~~  204 (329)
T COG0714         175 ALLD--RFLLRIYVDYPDSEEEERIILARVGG  204 (329)
T ss_pred             HHHh--hEEEEEecCCCCchHHHHHHHHhCcc
Confidence            9999  99999999999554 44444444443

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.49  E-value=2e-13  Score=125.19  Aligned_cols=158  Identities=13%  Similarity=0.218  Sum_probs=105.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccCh---------hhHHHHHHHcccCCeeeeecchhhHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGN---------NDLRHILIATENKSILVVEDIDCCIEL   97 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~---------~~l~~~~~~~~~~~vl~iDeid~l~~~   97 (266)
                      ..++||||+|||||+|++++++++     +..++++++..+...         ..+...........+|+|||++.+.+ 
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~-  220 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLSY-  220 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHhccCCEEEEeccccccC-
Confidence            459999999999999999999965     467778887665421         11222333345678999999998743 


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC---CCcccccCCCcc--eeEEEc
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE---RLDPALLRPGRM--DMHINM  172 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~---~ld~al~r~~Rf--~~~i~~  172 (266)
                                           .......+..+++.+...     ...+|+++...|.   .+++.|.+  ||  +.++.+
T Consensus       221 ---------------------k~~~~e~lf~l~N~~~~~-----~k~iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~~L  272 (450)
T PRK14087        221 ---------------------KEKTNEIFFTIFNNFIEN-----DKQLFFSSDKSPELLNGFDNRLIT--RFNMGLSIAI  272 (450)
T ss_pred             ---------------------CHHHHHHHHHHHHHHHHc-----CCcEEEECCCCHHHHhhccHHHHH--HHhCCceecc
Confidence                                 111223344444444322     2334444444553   45788998  76  588999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCC--CcHH-HHHHHhhcCCCCHHHHHHHHH
Q 024550          173 SHCTPSGFKMLASNYLGIAEH--PLFV-EIEKLIATAKVTPADVAEQLM  218 (266)
Q Consensus       173 ~~p~~~~~~~i~~~~~~~~~~--~~~~-~~~~l~~~~~~s~~~i~~~l~  218 (266)
                      ..|+.+++.+|+++.+...+.  .+.+ .+..++....-+++.+..+|.
T Consensus       273 ~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~  321 (450)
T PRK14087        273 QKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVS  321 (450)
T ss_pred             CCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHH
Confidence            999999999999999876553  3444 445556667778888877763

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.48  E-value=1.7e-12  Score=117.64  Aligned_cols=131  Identities=20%  Similarity=0.218  Sum_probs=88.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccChh--------------------hHHHHH-------H
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGNN--------------------DLRHIL-------I   78 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~~--------------------~l~~~~-------~   78 (266)
                      +.+++||||||||||++++.+++.+     +..+++++|....+..                    ....++       .
T Consensus        55 ~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~  134 (394)
T PRK00411         55 PLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLD  134 (394)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHH
Confidence            4569999999999999999999877     5778888886543210                    111111       1


Q ss_pred             HcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC---CC
Q 024550           79 ATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK---ER  155 (266)
Q Consensus        79 ~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~---~~  155 (266)
                      ....+.||+|||+|.+..                       ......+..+++.++...   +.++.+|+++|..   +.
T Consensus       135 ~~~~~~viviDE~d~l~~-----------------------~~~~~~l~~l~~~~~~~~---~~~v~vI~i~~~~~~~~~  188 (394)
T PRK00411        135 ERDRVLIVALDDINYLFE-----------------------KEGNDVLYSLLRAHEEYP---GARIGVIGISSDLTFLYI  188 (394)
T ss_pred             hcCCEEEEEECCHhHhhc-----------------------cCCchHHHHHHHhhhccC---CCeEEEEEEECCcchhhh
Confidence            122457999999998851                       111224445555444331   2357788888765   35


Q ss_pred             CcccccCCCcce-eEEEcCCCCHHHHHHHHHHhhC
Q 024550          156 LDPALLRPGRMD-MHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       156 ld~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      +++.+.+  ||. ..|.|+.++.++...|+...+.
T Consensus       189 l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~  221 (394)
T PRK00411        189 LDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVE  221 (394)
T ss_pred             cCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHH
Confidence            6777776  553 5789999999999999988774

>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=99.48  E-value=5.3e-14  Score=108.99  Aligned_cols=105  Identities=32%  Similarity=0.412  Sum_probs=70.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHH---------------HcccCCeeeeecchhhHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILI---------------ATENKSILVVEDIDCCIEL   97 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~---------------~~~~~~vl~iDeid~l~~~   97 (266)
                      +++|+||||||||++++.+|..++.+++.++++...+...+...+.               ...++++++|||++.... 
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~a~~-   79 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINRAPP-   79 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG--H-
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcccCCH-
Confidence            4899999999999999999999999999999998776544332111               112578999999996532 


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc----------ccCCC-----CceEEEEecCCCC----CCcc
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL----------WSSCG-----DERIIIFTTNHKE----RLDP  158 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~----------~~~~~-----~~~ivi~ttn~~~----~ld~  158 (266)
                                                .++..++..++.-          .....     .+..+|+|+|...    .+++
T Consensus        80 --------------------------~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~  133 (139)
T PF07728_consen   80 --------------------------EVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSP  133 (139)
T ss_dssp             --------------------------HHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCH
T ss_pred             --------------------------HHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCH
Confidence                                      1222222222210          00001     1489999999887    8999


Q ss_pred             cccCCCcc
Q 024550          159 ALLRPGRM  166 (266)
Q Consensus       159 al~r~~Rf  166 (266)
                      +|++  ||
T Consensus       134 al~~--Rf  139 (139)
T PF07728_consen  134 ALLD--RF  139 (139)
T ss_dssp             HHHT--T-
T ss_pred             HHHh--hC
Confidence            9999  87

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>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=99.48  E-value=6.3e-13  Score=102.50  Aligned_cols=115  Identities=31%  Similarity=0.411  Sum_probs=78.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHH-----------HHHHcccCCeeeeecchhhH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRH-----------ILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~-----------~~~~~~~~~vl~iDeid~l~   95 (266)
                      ..+.++++||||||||++++.++..+   +.+++.+++...........           .......+.+|++||++.+.
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~~   97 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLS   97 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhhh
Confidence            35679999999999999999999998   88999999887654322221           11223468999999999772


Q ss_pred             HHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC--CCCceEEEEecCCCC--CCcccccCCCcceeEEE
Q 024550           96 ELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS--CGDERIIIFTTNHKE--RLDPALLRPGRMDMHIN  171 (266)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~--~~~~~ivi~ttn~~~--~ld~al~r~~Rf~~~i~  171 (266)
                      .                           .....++..+......  ...++.+|+++|...  .+++.+.+  ||+..+.
T Consensus        98 ~---------------------------~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~  148 (151)
T cd00009          98 R---------------------------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIV  148 (151)
T ss_pred             H---------------------------HHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccEee
Confidence            2                           0112233333322211  124577888888776  67788888  9987777


Q ss_pred             cC
Q 024550          172 MS  173 (266)
Q Consensus       172 ~~  173 (266)
                      ++
T Consensus       149 ~~  150 (151)
T cd00009         149 IP  150 (151)
T ss_pred             cC
Confidence            76

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.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.47  E-value=4.6e-13  Score=122.74  Aligned_cols=153  Identities=15%  Similarity=0.279  Sum_probs=110.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE------------------------EEEeCCcccChhhHHHHHHHcc-----
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV------------------------YDLELSNLLGNNDLRHILIATE-----   81 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~------------------------~~i~~~~~~~~~~l~~~~~~~~-----   81 (266)
                      .+++||+||.|||||++||.+|+.+++.-                        ++++..+-.+-.+++.+.....     
T Consensus        38 ~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~  117 (515)
T COG2812          38 AHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSE  117 (515)
T ss_pred             hhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCcc
Confidence            46799999999999999999999986542                        2222222223345566655542     


Q ss_pred             -cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           82 -NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        82 -~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                       +.-|.+|||+|.|.                           ....+.||..++    .++..++||.+|..++.++..+
T Consensus       118 ~ryKVyiIDEvHMLS---------------------------~~afNALLKTLE----EPP~hV~FIlATTe~~Kip~TI  166 (515)
T COG2812         118 GRYKVYIIDEVHMLS---------------------------KQAFNALLKTLE----EPPSHVKFILATTEPQKIPNTI  166 (515)
T ss_pred             ccceEEEEecHHhhh---------------------------HHHHHHHhcccc----cCccCeEEEEecCCcCcCchhh
Confidence             45799999999874                           335566777666    4566799999999999999999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhcCCCCHHHHHHHH
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEI-EKLIATAKVTPADVAEQL  217 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~i~~~l  217 (266)
                      ++  || ..+.|...+.++....+..++..++.....+. ..++.....|.+|...+|
T Consensus       167 lS--Rc-q~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~Gs~RDalslL  221 (515)
T COG2812         167 LS--RC-QRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLL  221 (515)
T ss_pred             hh--cc-ccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCCChhhHHHHH
Confidence            99  98 56999999999999999999998877665443 334444445555544443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.46  E-value=1.2e-12  Score=124.01  Aligned_cols=153  Identities=16%  Similarity=0.281  Sum_probs=106.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc-------------------------EEEEeCCcccChhhHHHHHHHc-----
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD-------------------------VYDLELSNLLGNNDLRHILIAT-----   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~-------------------------~~~i~~~~~~~~~~l~~~~~~~-----   80 (266)
                      ++.+|||||+|+|||++++.+|+.+++.                         ++.++.....+...++.+....     
T Consensus        38 ~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~  117 (585)
T PRK14950         38 AHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPA  117 (585)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcc
Confidence            5678999999999999999999988532                         2333433223334444444332     


Q ss_pred             -ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           81 -ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                       ....|++|||+|.|..                           ...+.|+..++.-    +...+||.+++..+.+.+.
T Consensus       118 ~~~~kVvIIDEa~~L~~---------------------------~a~naLLk~LEep----p~~tv~Il~t~~~~kll~t  166 (585)
T PRK14950        118 LARYKVYIIDEVHMLST---------------------------AAFNALLKTLEEP----PPHAIFILATTEVHKVPAT  166 (585)
T ss_pred             cCCeEEEEEeChHhCCH---------------------------HHHHHHHHHHhcC----CCCeEEEEEeCChhhhhHH
Confidence             2457999999997732                           2355677777653    2457777777878888888


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  || ..+.|+.++..+...++..++...+..+.. .+..++...+.++.++.+.+
T Consensus       167 I~S--R~-~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~Gdlr~al~~L  222 (585)
T PRK14950        167 ILS--RC-QRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLL  222 (585)
T ss_pred             HHh--cc-ceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            888  87 468999999999999888888777655543 34555656666777666655

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.45  E-value=1.7e-12  Score=105.77  Aligned_cols=124  Identities=20%  Similarity=0.311  Sum_probs=88.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcc-cChhhHHHHHHHcc---
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNL-LGNNDLRHILIATE---   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~-~~~~~l~~~~~~~~---   81 (266)
                      .++.+|||||+|+|||++++.+++.+...                        +..+..... .+...++.+...+.   
T Consensus        13 ~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~~   92 (188)
T TIGR00678        13 LAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTP   92 (188)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccCc
Confidence            45679999999999999999999987542                        333333221 12334544444332   


Q ss_pred             ---cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           82 ---NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        82 ---~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                         ...|++|||+|.+..                           ...+.|+..|+.-    +...++|.+|+.+..+.+
T Consensus        93 ~~~~~kviiide~~~l~~---------------------------~~~~~Ll~~le~~----~~~~~~il~~~~~~~l~~  141 (188)
T TIGR00678        93 QESGRRVVIIEDAERMNE---------------------------AAANALLKTLEEP----PPNTLFILITPSPEKLLP  141 (188)
T ss_pred             ccCCeEEEEEechhhhCH---------------------------HHHHHHHHHhcCC----CCCeEEEEEECChHhChH
Confidence               357999999998742                           2345577777652    345677777888899999


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHh
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNY  187 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~  187 (266)
                      ++.+  |+ ..++|+.|+.++...++...
T Consensus       142 ~i~s--r~-~~~~~~~~~~~~~~~~l~~~  167 (188)
T TIGR00678       142 TIRS--RC-QVLPFPPLSEEALLQWLIRQ  167 (188)
T ss_pred             HHHh--hc-EEeeCCCCCHHHHHHHHHHc
Confidence            9999  87 57999999999998888776

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.45  E-value=1.7e-12  Score=123.04  Aligned_cols=154  Identities=14%  Similarity=0.251  Sum_probs=111.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC-------------------------cEEEEeCCcccChhhHHHHHHHcc---
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF-------------------------DVYDLELSNLLGNNDLRHILIATE---   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~-------------------------~~~~i~~~~~~~~~~l~~~~~~~~---   81 (266)
                      .++.+|||||+|+|||++++.+|+.+.+                         .++.+++....+...++.+...+.   
T Consensus        38 l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~~ld~~~~~~vd~Ir~li~~~~~~P  117 (614)
T PRK14971         38 LAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLIEQVRIPP  117 (614)
T ss_pred             CCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhCc
Confidence            4667999999999999999999998753                         344454443323345555554432   


Q ss_pred             ---cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           82 ---NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        82 ---~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                         ..-|++|||+|.+.                           ....+.|+..|+.-    +...++|.+|+.+..+.+
T Consensus       118 ~~~~~KVvIIdea~~Ls---------------------------~~a~naLLK~LEep----p~~tifIL~tt~~~kIl~  166 (614)
T PRK14971        118 QIGKYKIYIIDEVHMLS---------------------------QAAFNAFLKTLEEP----PSYAIFILATTEKHKILP  166 (614)
T ss_pred             ccCCcEEEEEECcccCC---------------------------HHHHHHHHHHHhCC----CCCeEEEEEeCCchhchH
Confidence               35699999999773                           22456677777753    345777777777788999


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++.+  || ..++|..++.++....+...+...+..... .+..++...+.+.+++.+.+
T Consensus       167 tI~S--Rc-~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~L  223 (614)
T PRK14971        167 TILS--RC-QIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIF  223 (614)
T ss_pred             HHHh--hh-heeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            9999  88 559999999999999998888777766654 45666666677777666554

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.45  E-value=1.7e-12  Score=127.57  Aligned_cols=172  Identities=15%  Similarity=0.265  Sum_probs=109.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHH---------------H---HcccCCeeeeecc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHIL---------------I---ATENKSILVVEDI   91 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~---------------~---~~~~~~vl~iDei   91 (266)
                      .+||+||+|||||++|+++|..+   +.+++.++++.+........++               .   .....+||+|||+
T Consensus       600 ~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEi  679 (857)
T PRK10865        600 SFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEV  679 (857)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeeh
Confidence            58999999999999999999987   4578889888765322222221               1   1224589999999


Q ss_pred             hhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCCC-----------
Q 024550           92 DCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHK-----------  153 (266)
Q Consensus        92 d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~-----------  153 (266)
                      +.+.+                           ...+.|++.++.-.-..       -.+.+||+|||..           
T Consensus       680 eka~~---------------------------~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~  732 (857)
T PRK10865        680 EKAHP---------------------------DVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGEL  732 (857)
T ss_pred             hhCCH---------------------------HHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhcccc
Confidence            97642                           24556666665321111       1346789999862           


Q ss_pred             --------------CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHc
Q 024550          154 --------------ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMR  219 (266)
Q Consensus       154 --------------~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~  219 (266)
                                    ..+.|+|+.  |++.++.|.+++.+...+|+..++....    ..+...-....+++..+..+...
T Consensus       733 ~~~~~~~~~~~~~~~~f~PELln--Rld~iivF~PL~~edl~~Iv~~~L~~l~----~rl~~~gi~l~is~~al~~L~~~  806 (857)
T PRK10865        733 DYAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHPLGEQHIASIAQIQLQRLY----KRLEERGYEIHISDEALKLLSEN  806 (857)
T ss_pred             chHHHHHHHHHHHcccccHHHHH--hCCeeEecCCCCHHHHHHHHHHHHHHHH----HHHHhCCCcCcCCHHHHHHHHHc
Confidence                          124578888  9999999999999999999988884421    11111101123555555544444


Q ss_pred             CCCHHHHHHHHHHHHHhh
Q 024550          220 NEAPEFALSGLIEFLESK  237 (266)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~  237 (266)
                      +.++...++.+..+++..
T Consensus       807 gy~~~~GARpL~r~I~~~  824 (857)
T PRK10865        807 GYDPVYGARPLKRAIQQQ  824 (857)
T ss_pred             CCCccCChHHHHHHHHHH
Confidence            556555555555555544

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.45  E-value=2.3e-12  Score=115.07  Aligned_cols=87  Identities=18%  Similarity=0.278  Sum_probs=59.8

Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC------CCceEEEEecC---
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC------GDERIIIFTTN---  151 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~------~~~~ivi~ttn---  151 (266)
                      .+.+|+||||||.++....  +.             ..+....-++..||..+++..-..      ...++||++.-   
T Consensus       246 e~~GIVfiDEiDKIa~~~~--~~-------------~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~  310 (441)
T TIGR00390       246 EQSGIIFIDEIDKIAKKGE--SS-------------GADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQL  310 (441)
T ss_pred             HcCCEEEEEchhhhcccCC--CC-------------CCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCC
Confidence            3578999999999985321  00             112333457777888887643221      14567777553   


Q ss_pred             -CCCCCcccccCCCcceeEEEcCCCCHHHHHHHH
Q 024550          152 -HKERLDPALLRPGRMDMHINMSHCTPSGFKMLA  184 (266)
Q Consensus       152 -~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~  184 (266)
                       .|.+|-|.|.-  ||...+.+..++.++...|+
T Consensus       311 ~kp~DlIPEl~G--R~Pi~v~L~~L~~edL~rIL  342 (441)
T TIGR00390       311 AKPSDLIPELQG--RFPIRVELQALTTDDFERIL  342 (441)
T ss_pred             CChhhccHHHhC--ccceEEECCCCCHHHHHHHh
Confidence             45667788887  99999999999999987776

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

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

Probab=99.45  E-value=1.1e-12  Score=117.16  Aligned_cols=86  Identities=17%  Similarity=0.241  Sum_probs=59.7

Q ss_pred             cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC------CCceEEEEecC----
Q 024550           82 NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC------GDERIIIFTTN----  151 (266)
Q Consensus        82 ~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~------~~~~ivi~ttn----  151 (266)
                      +.+|+||||||.++.....  .             ..+....-++..||..++|..-..      ...++||++--    
T Consensus       249 ~~GIVfiDEiDKIa~~~~~--~-------------~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~  313 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGS--S-------------GPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVS  313 (443)
T ss_pred             cCCEEEEEcchhhcccCCC--C-------------CCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCC
Confidence            5789999999999863211  0             112333457777888887632211      14567777543    


Q ss_pred             CCCCCcccccCCCcceeEEEcCCCCHHHHHHHH
Q 024550          152 HKERLDPALLRPGRMDMHINMSHCTPSGFKMLA  184 (266)
Q Consensus       152 ~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~  184 (266)
                      .|.+|-|.|.-  ||...+.+..++.++...|+
T Consensus       314 kp~DlIPEl~G--R~Pi~v~L~~L~~~dL~~IL  344 (443)
T PRK05201        314 KPSDLIPELQG--RFPIRVELDALTEEDFVRIL  344 (443)
T ss_pred             ChhhccHHHhC--ccceEEECCCCCHHHHHHHh
Confidence            45667788887  99999999999999987776

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.44  E-value=8.1e-12  Score=110.04  Aligned_cols=149  Identities=18%  Similarity=0.247  Sum_probs=102.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCc---ccChhhHHHHHHHcc-
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSN---LLGNNDLRHILIATE-   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~---~~~~~~l~~~~~~~~-   81 (266)
                      .++++||+||+|+|||++|+++|+.+.+                        .++.+....   ..+-..++++..... 
T Consensus        21 ~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~~~~  100 (328)
T PRK05707         21 HPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSFVVQ  100 (328)
T ss_pred             cceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHHHhh
Confidence            4668999999999999999999998854                        344444321   123345555544332 


Q ss_pred             -----cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC
Q 024550           82 -----NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL  156 (266)
Q Consensus        82 -----~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l  156 (266)
                           ..-|++||++|.|-                           ....+.||+.|+.    ++.+.+||.+|+.++.+
T Consensus       101 ~~~~~~~kv~iI~~a~~m~---------------------------~~aaNaLLK~LEE----Pp~~~~fiL~t~~~~~l  149 (328)
T PRK05707        101 TAQLGGRKVVLIEPAEAMN---------------------------RNAANALLKSLEE----PSGDTVLLLISHQPSRL  149 (328)
T ss_pred             ccccCCCeEEEECChhhCC---------------------------HHHHHHHHHHHhC----CCCCeEEEEEECChhhC
Confidence                 35688999999874                           3355778887775    34578999999999999


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAE  215 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~  215 (266)
                      .+++++  || ..+.|+.|+.++....+....+..   ...+...++...+.+|.....
T Consensus       150 l~TI~S--Rc-~~~~~~~~~~~~~~~~L~~~~~~~---~~~~~~~~l~la~Gsp~~A~~  202 (328)
T PRK05707        150 LPTIKS--RC-QQQACPLPSNEESLQWLQQALPES---DERERIELLTLAGGSPLRALQ  202 (328)
T ss_pred             cHHHHh--hc-eeeeCCCcCHHHHHHHHHHhcccC---ChHHHHHHHHHcCCCHHHHHH
Confidence            999999  98 459999999999888777654211   123333444444555554443

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.44  E-value=2.7e-12  Score=121.92  Aligned_cols=182  Identities=16%  Similarity=0.197  Sum_probs=100.4

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccC-hhhHH----------------HHHH---
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLG-NNDLR----------------HILI---   78 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~-~~~l~----------------~~~~---   78 (266)
                      +.+..++|+||||||||++|++++...          +.+++.+++..+.. ...+.                ..+.   
T Consensus       173 ~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~g  252 (615)
T TIGR02903       173 PFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETG  252 (615)
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcC
Confidence            445679999999999999999998655          35788888876521 11110                0011   


Q ss_pred             ---------HcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEE-
Q 024550           79 ---------ATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIF-  148 (266)
Q Consensus        79 ---------~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~-  148 (266)
                               ....+++|||||++.|.......-...-....+.+.+...+.........+...++.   .....+++|+ 
T Consensus       253 l~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~---~~~~~~VLI~a  329 (615)
T TIGR02903       253 VPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEE---GAPADFVLIGA  329 (615)
T ss_pred             CCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecceeccCCcccchhhhhhccc---CccceEEEEEe
Confidence                     012468999999998854222111100000000000000000000000001011111   1112355555 


Q ss_pred             ecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHH
Q 024550          149 TTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQ  216 (266)
Q Consensus       149 ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~  216 (266)
                      ||+.+..++++|.+  ||. .+.|+.++.+++..|+++++...+..+..+...++......++...+.
T Consensus       330 Tt~~~~~l~~aLrS--R~~-~i~~~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~  394 (615)
T TIGR02903       330 TTRDPEEINPALRS--RCA-EVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNI  394 (615)
T ss_pred             ccccccccCHHHHh--cee-EEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHH
Confidence            55678889999999  986 578999999999999999887655445555555555544444444443

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.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.44  E-value=3.9e-12  Score=109.86  Aligned_cols=88  Identities=15%  Similarity=0.161  Sum_probs=64.2

Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC----------
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH----------  152 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~----------  152 (266)
                      |+||||||++.|.                           -...+.|-..|+.-..     .++|.+||+          
T Consensus       292 pGVLFIDEvHmLD---------------------------IE~FsFlnrAlEse~a-----PIii~AtNRG~~kiRGTd~  339 (450)
T COG1224         292 PGVLFIDEVHMLD---------------------------IECFSFLNRALESELA-----PIIILATNRGMTKIRGTDI  339 (450)
T ss_pred             cceEEEechhhhh---------------------------HHHHHHHHHHhhcccC-----cEEEEEcCCceeeecccCC
Confidence            6899999998773                           1233344455554322     466777774          


Q ss_pred             --CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc
Q 024550          153 --KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT  205 (266)
Q Consensus       153 --~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~  205 (266)
                        |..+|..|+.  |+ ..|...+++.++.+.|++.....+...+.++.-+++..
T Consensus       340 ~sPhGIP~DlLD--Rl-lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~  391 (450)
T COG1224         340 ESPHGIPLDLLD--RL-LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTD  391 (450)
T ss_pred             cCCCCCCHhhhh--he-eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHh
Confidence              6788999999  98 77999999999999999999988887777665544443

>PRK09087 hypothetical protein; Validated

Probab=99.44  E-value=1.6e-12  Score=108.92  Aligned_cols=143  Identities=13%  Similarity=0.117  Sum_probs=91.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFL  112 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~  112 (266)
                      .++||||+|+|||||+++++...+..+  ++...+. .    +.+.... ..+|+|||++.+..                
T Consensus        46 ~l~l~G~~GsGKThLl~~~~~~~~~~~--i~~~~~~-~----~~~~~~~-~~~l~iDDi~~~~~----------------  101 (226)
T PRK09087         46 VVVLAGPVGSGKTHLASIWREKSDALL--IHPNEIG-S----DAANAAA-EGPVLIEDIDAGGF----------------  101 (226)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhcCCEE--ecHHHcc-h----HHHHhhh-cCeEEEECCCCCCC----------------
Confidence            499999999999999999998876653  3332221 1    1111212 26889999996521                


Q ss_pred             cccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC---CcccccCCCcce--eEEEcCCCCHHHHHHHHHHh
Q 024550          113 IAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER---LDPALLRPGRMD--MHINMSHCTPSGFKMLASNY  187 (266)
Q Consensus       113 ~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~---ld~al~r~~Rf~--~~i~~~~p~~~~~~~i~~~~  187 (266)
                               ....+..+++.+..   .  ...++|+++..|..   ..+.|.+  ||.  .++++..|+.+.+.++++++
T Consensus       102 ---------~~~~lf~l~n~~~~---~--g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l~~pd~e~~~~iL~~~  165 (226)
T PRK09087        102 ---------DETGLFHLINSVRQ---A--GTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEIGEPDDALLSQVIFKL  165 (226)
T ss_pred             ---------CHHHHHHHHHHHHh---C--CCeEEEECCCChHHhccccccHHH--HHhCCceeecCCCCHHHHHHHHHHH
Confidence                     11223334444332   2  34566666655542   3678888  764  88999999999999999999


Q ss_pred             hCCCCCCcHHHHH-HHhhcCCCCHHHHHH
Q 024550          188 LGIAEHPLFVEIE-KLIATAKVTPADVAE  215 (266)
Q Consensus       188 ~~~~~~~~~~~~~-~l~~~~~~s~~~i~~  215 (266)
                      +...+..+.++.. .++....-+.+.+..
T Consensus       166 ~~~~~~~l~~ev~~~La~~~~r~~~~l~~  194 (226)
T PRK09087        166 FADRQLYVDPHVVYYLVSRMERSLFAAQT  194 (226)
T ss_pred             HHHcCCCCCHHHHHHHHHHhhhhHHHHHH
Confidence            9887766665553 344444444444443

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.44  E-value=3.2e-12  Score=112.36  Aligned_cols=151  Identities=16%  Similarity=0.173  Sum_probs=99.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCcccChhhHHHHHH----Hc----ccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNLLGNNDLRHILI----AT----ENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~~~~~~l~~~~~----~~----~~~~vl~iDeid~l~~~~~   99 (266)
                      .++||||||||||++++++++.+.     ..++.++++.......+...+.    ..    ..+.+++|||+|.+..   
T Consensus        40 ~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~---  116 (319)
T PRK00440         40 HLLFAGPPGTGKTTAALALARELYGEDWRENFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS---  116 (319)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCccccceEEeccccccchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH---
Confidence            589999999999999999999873     3445555443322222222221    11    1246999999998742   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                              .....|+..++..    .....+|.++|.+..+.+++.+  |+. .++|+.|+.++
T Consensus       117 ------------------------~~~~~L~~~le~~----~~~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~~e  165 (319)
T PRK00440        117 ------------------------DAQQALRRTMEMY----SQNTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKKEA  165 (319)
T ss_pred             ------------------------HHHHHHHHHHhcC----CCCCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCHHH
Confidence                                    1123344444432    2335667777887888888888  875 59999999999


Q ss_pred             HHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          180 FKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       180 ~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ...++..++...+..+. ..+..++...+.+++.+.+.+
T Consensus       166 i~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l  204 (319)
T PRK00440        166 VAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINAL  204 (319)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999998887776554 444555555555655555544

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.42  E-value=2.6e-12  Score=126.45  Aligned_cols=129  Identities=20%  Similarity=0.363  Sum_probs=92.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHH---------------HH---HcccCCeeeeec
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHI---------------LI---ATENKSILVVED   90 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~---------------~~---~~~~~~vl~iDe   90 (266)
                      ..+||+||+|||||++|+++|..+   +.+++.++++.+........+               +.   .....+||+|||
T Consensus       596 ~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDe  675 (852)
T TIGR03346       596 GSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDE  675 (852)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchHHHhcCCCCCccCcccccHHHHHHHcCCCcEEEEec
Confidence            459999999999999999999987   468899998876543222211               11   123468999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCCCC---------
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHKE---------  154 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~~---------  154 (266)
                      |+.+.                           ....+.|++.|+.-.-..       -.+.+||+|||...         
T Consensus       676 ieka~---------------------------~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~~~  728 (852)
T TIGR03346       676 VEKAH---------------------------PDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGG  728 (852)
T ss_pred             cccCC---------------------------HHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhccc
Confidence            99764                           235566777775321111       13578999999621         


Q ss_pred             ----------------CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          155 ----------------RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       155 ----------------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                                      .+.|.|+.  |++.++.|.+++.+....|+..++.
T Consensus       729 ~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL~~e~l~~I~~l~L~  777 (852)
T TIGR03346       729 DDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPLGREQIARIVEIQLG  777 (852)
T ss_pred             ccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCcCHHHHHHHHHHHHH
Confidence                            13467777  9999999999999999999887774

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.

>PHA02244 ATPase-like protein

Probab=99.42  E-value=8.7e-13  Score=116.07  Aligned_cols=119  Identities=21%  Similarity=0.312  Sum_probs=79.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCc----cc----ChhhH--HHHHHHcccCCeeeeecchhhHHHhHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSN----LL----GNNDL--RHILIATENKSILVVEDIDCCIELQDR  100 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~----~~----~~~~l--~~~~~~~~~~~vl~iDeid~l~~~~~~  100 (266)
                      +..+||+||||||||++|+++|..++.+++.++...    +.    ....+  ..++.....+++|+|||++.+.+... 
T Consensus       119 ~~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~~~GgvLiLDEId~a~p~vq-  197 (383)
T PHA02244        119 NIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAFKKGGLFFIDEIDASIPEAL-  197 (383)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHhhcCCEEEEeCcCcCCHHHH-
Confidence            446999999999999999999999999999887431    10    00111  13333456789999999997743111 


Q ss_pred             HhhhhhcCCccccccccccccchhhhhhhh-----hhhhccccCCCCceEEEEecCCC-----------CCCcccccCCC
Q 024550          101 LSRARAANPDFLIAGYEQQKQYHITLSGLL-----NFIDGLWSSCGDERIIIFTTNHK-----------ERLDPALLRPG  164 (266)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll-----~~l~~~~~~~~~~~ivi~ttn~~-----------~~ld~al~r~~  164 (266)
                                             ..++.++     ..+.+.. ....++.+|+|+|.+           ..+++++++  
T Consensus       198 -----------------------~~L~~lLd~r~l~l~g~~i-~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllD--  251 (383)
T PHA02244        198 -----------------------IIINSAIANKFFDFADERV-TAHEDFRVISAGNTLGKGADHIYVARNKIDGATLD--  251 (383)
T ss_pred             -----------------------HHHHHHhccCeEEecCcEE-ecCCCEEEEEeeCCCccCcccccCCCcccCHHHHh--
Confidence                                   1111111     1111111 123467899999973           567999999  


Q ss_pred             cceeEEEcCCCCH
Q 024550          165 RMDMHINMSHCTP  177 (266)
Q Consensus       165 Rf~~~i~~~~p~~  177 (266)
                      || ..|+|+.|+.
T Consensus       252 RF-v~I~~dyp~~  263 (383)
T PHA02244        252 RF-APIEFDYDEK  263 (383)
T ss_pred             hc-EEeeCCCCcH
Confidence            99 5699999984

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

Probab=99.42  E-value=1e-11  Score=110.82  Aligned_cols=129  Identities=19%  Similarity=0.269  Sum_probs=91.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc-----EEEEeCCcccChhhH-------------------------HHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD-----VYDLELSNLLGNNDL-------------------------RHILIAT   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~-----~~~i~~~~~~~~~~l-------------------------~~~~~~~   80 (266)
                      |.++++|||||||||.+++.++.++..+     +++++|....+...+                         .+.+...
T Consensus        42 p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~  121 (366)
T COG1474          42 PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKK  121 (366)
T ss_pred             CccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhc
Confidence            4469999999999999999999988544     889999877643221                         1112222


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC---CCCc
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK---ERLD  157 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~---~~ld  157 (266)
                      ....|++|||+|.|..                       .. ...+-.|+..    .......+.+|+.+|..   +.++
T Consensus       122 ~~~~IvvLDEid~L~~-----------------------~~-~~~LY~L~r~----~~~~~~~v~vi~i~n~~~~~~~ld  173 (366)
T COG1474         122 GKTVIVILDEVDALVD-----------------------KD-GEVLYSLLRA----PGENKVKVSIIAVSNDDKFLDYLD  173 (366)
T ss_pred             CCeEEEEEcchhhhcc-----------------------cc-chHHHHHHhh----ccccceeEEEEEEeccHHHHHHhh
Confidence            3467999999999964                       11 1233333333    22224567899999875   5778


Q ss_pred             ccccCCCcce-eEEEcCCCCHHHHHHHHHHhhC
Q 024550          158 PALLRPGRMD-MHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       158 ~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      +.+.+  +++ ..|.||+++.+|...|+.....
T Consensus       174 ~rv~s--~l~~~~I~F~pY~a~el~~Il~~R~~  204 (366)
T COG1474         174 PRVKS--SLGPSEIVFPPYTAEELYDILRERVE  204 (366)
T ss_pred             hhhhh--ccCcceeeeCCCCHHHHHHHHHHHHH
Confidence            88887  554 4599999999999999987775

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.41  E-value=4.6e-12  Score=124.39  Aligned_cols=172  Identities=19%  Similarity=0.247  Sum_probs=107.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHH----------------HHH--HcccCCeeeeecc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRH----------------ILI--ATENKSILVVEDI   91 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~----------------~~~--~~~~~~vl~iDei   91 (266)
                      .+||+||+|||||++|+++|..+   ..+++.++++.+.....+..                +..  ...+.+|++|||+
T Consensus       541 ~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDei  620 (821)
T CHL00095        541 SFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEI  620 (821)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccHHHhcCCCCcccCcCccchHHHHHHhCCCeEEEECCh
Confidence            48999999999999999999988   35788888877643222211                111  1234589999999


Q ss_pred             hhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC-------CCCceEEEEecCCCCC---------
Q 024550           92 DCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS-------CGDERIIIFTTNHKER---------  155 (266)
Q Consensus        92 d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-------~~~~~ivi~ttn~~~~---------  155 (266)
                      |.+.+                           ...+.|++.|+.-.-+       ...+.+||+|||....         
T Consensus       621 eka~~---------------------------~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~~~~~~  673 (821)
T CHL00095        621 EKAHP---------------------------DIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGL  673 (821)
T ss_pred             hhCCH---------------------------HHHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHhhcccc
Confidence            97643                           3456666666632110       0145789999884311         


Q ss_pred             ----------------------------CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCC
Q 024550          156 ----------------------------LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAK  207 (266)
Q Consensus       156 ----------------------------ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~  207 (266)
                                                  +.|.|+.  |++.+|.|...+.++..+|+...+....    ..+...--...
T Consensus       674 gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln--Rid~ii~F~pL~~~~l~~Iv~~~l~~l~----~rl~~~~i~l~  747 (821)
T CHL00095        674 GFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN--RLDEIIVFRQLTKNDVWEIAEIMLKNLF----KRLNEQGIQLE  747 (821)
T ss_pred             CCcccccccccccHHHHHHHHHHHHHHhcCHHHhc--cCCeEEEeCCCCHHHHHHHHHHHHHHHH----HHHHHCCcEEE
Confidence                                        2356777  9999999999999999999988874321    11111000123


Q ss_pred             CCHHHHHHHHHcCCCHHHHHHHHHHHHHhh
Q 024550          208 VTPADVAEQLMRNEAPEFALSGLIEFLESK  237 (266)
Q Consensus       208 ~s~~~i~~~l~~~~~~~~~~~~~~~~~~~~  237 (266)
                      +++..+..+...+.++...++.+..+++..
T Consensus       748 ~~~~~~~~La~~~~~~~~GAR~l~r~i~~~  777 (821)
T CHL00095        748 VTERIKTLLIEEGYNPLYGARPLRRAIMRL  777 (821)
T ss_pred             ECHHHHHHHHHhcCCCCCChhhHHHHHHHH
Confidence            555544444443445555555555555443

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.38  E-value=5.9e-11  Score=104.37  Aligned_cols=151  Identities=17%  Similarity=0.217  Sum_probs=102.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC--------cEEEEeCC--cccChhhHHHHHHHc------ccCCeeeeecchh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF--------DVYDLELS--NLLGNNDLRHILIAT------ENKSILVVEDIDC   93 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~--------~~~~i~~~--~~~~~~~l~~~~~~~------~~~~vl~iDeid~   93 (266)
                      .++.+|||||+|+|||++|+++|+.+.+        .++.+...  ...+...++.+....      ...-|++||++|.
T Consensus        25 ~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~  104 (313)
T PRK05564         25 FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEK  104 (313)
T ss_pred             CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHHHHHHHHhcCcccCCceEEEEechhh
Confidence            4668999999999999999999997733        23334331  111234455555432      2357999999997


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcC
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMS  173 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~  173 (266)
                      +.                           ....+.|+..++.    ++...++|.+|+.++.+.+++.+  || ..++|+
T Consensus       105 m~---------------------------~~a~naLLK~LEe----pp~~t~~il~~~~~~~ll~TI~S--Rc-~~~~~~  150 (313)
T PRK05564        105 MT---------------------------EQAQNAFLKTIEE----PPKGVFIILLCENLEQILDTIKS--RC-QIYKLN  150 (313)
T ss_pred             cC---------------------------HHHHHHHHHHhcC----CCCCeEEEEEeCChHhCcHHHHh--hc-eeeeCC
Confidence            73                           2245677777774    34567777777888999999999  88 579999


Q ss_pred             CCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          174 HCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       174 ~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .|+.++....+...+..   .....+..++...+.++..+....
T Consensus       151 ~~~~~~~~~~l~~~~~~---~~~~~~~~l~~~~~g~~~~a~~~~  191 (313)
T PRK05564        151 RLSKEEIEKFISYKYND---IKEEEKKSAIAFSDGIPGKVEKFI  191 (313)
T ss_pred             CcCHHHHHHHHHHHhcC---CCHHHHHHHHHHcCCCHHHHHHHh
Confidence            99999988887765532   123445555655566666655443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.37  E-value=6.6e-12  Score=123.11  Aligned_cols=127  Identities=20%  Similarity=0.269  Sum_probs=89.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChh-------------------hHHHHHHHcccCCeeeeec
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNN-------------------DLRHILIATENKSILVVED   90 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~-------------------~l~~~~~~~~~~~vl~iDe   90 (266)
                      .+||+||||||||++|+++|..+   ...++.++++.+....                   .+...+. ..+.+||+|||
T Consensus       598 ~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~g~~~gyvg~~~~g~L~~~v~-~~p~svvllDE  676 (852)
T TIGR03345       598 VFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVR-RKPYSVVLLDE  676 (852)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhccccCCCCCcccccccchHHHHHH-hCCCcEEEEec
Confidence            38999999999999999999998   3577888877654221                   1222222 25679999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCCC----------
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHK----------  153 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~----------  153 (266)
                      |+.+.+                           ...+.|++.++...-..       -.+.+||+|||..          
T Consensus       677 ieka~~---------------------------~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~~~~  729 (852)
T TIGR03345       677 VEKAHP---------------------------DVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCAD  729 (852)
T ss_pred             hhhcCH---------------------------HHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHhccC
Confidence            996532                           34455666665332111       1357899999842          


Q ss_pred             -------------------CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          154 -------------------ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       154 -------------------~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                                         ..+.|+|+.  |++ .|.|...+.++..+|+...+..
T Consensus       730 ~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv~~~L~~  782 (852)
T TIGR03345       730 PETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIPYLPLDDDVLAAIVRLKLDR  782 (852)
T ss_pred             cccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEEeCCCCHHHHHHHHHHHHHH
Confidence                               114677788  997 7999999999999999888743

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.36  E-value=7.4e-11  Score=104.84  Aligned_cols=153  Identities=18%  Similarity=0.216  Sum_probs=100.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc-------E-----------------------EEEeCC--c-------ccCh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD-------V-----------------------YDLELS--N-------LLGN   70 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~-------~-----------------------~~i~~~--~-------~~~~   70 (266)
                      .++.+||+||+|+|||++++.+|+.+.+.       .                       +.+...  .       ..+-
T Consensus        44 l~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~v  123 (351)
T PRK09112         44 LHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITV  123 (351)
T ss_pred             CCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCCHHHHHHHcCCCCCEEEeecccccccccccccCCH
Confidence            35679999999999999999999988551       1                       111100  0       0001


Q ss_pred             hhHHHH---HHHc---ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCce
Q 024550           71 NDLRHI---LIAT---ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDER  144 (266)
Q Consensus        71 ~~l~~~---~~~~---~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~  144 (266)
                      ..++.+   +...   ....|++|||+|.|.                           ....+.||..++.-    +...
T Consensus       124 d~iR~l~~~l~~~~~~g~~rVviIDeAd~l~---------------------------~~aanaLLk~LEEp----p~~~  172 (351)
T PRK09112        124 DEIRRVGHFLSQTSGDGNWRIVIIDPADDMN---------------------------RNAANAILKTLEEP----PARA  172 (351)
T ss_pred             HHHHHHHHHhhhccccCCceEEEEEchhhcC---------------------------HHHHHHHHHHHhcC----CCCc
Confidence            122222   2221   135699999999773                           22445677777652    3456


Q ss_pred             EEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          145 IIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       145 ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++|..|+.+..+.+.+.+  || ..+.|+.|+.++...++........ .....+..++...+.+|....+++
T Consensus       173 ~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~~~~~L~~~~~~~~-~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        173 LFILISHSSGRLLPTIRS--RC-QPISLKPLDDDELKKALSHLGSSQG-SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             eEEEEECChhhccHHHHh--hc-cEEEecCCCHHHHHHHHHHhhcccC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            777777888888999999  88 6899999999999999987432222 113345556666677777766665

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=99.36  E-value=4.8e-12  Score=110.61  Aligned_cols=86  Identities=16%  Similarity=0.178  Sum_probs=52.8

Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC----------
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH----------  152 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~----------  152 (266)
                      |+||||||++.|.                           -...+.|-+.|+.-.     ..++|.+||+          
T Consensus       279 pGVLFIDEvHmLD---------------------------iEcFsfLnralEs~~-----sPiiIlATNRg~~~irGt~~  326 (398)
T PF06068_consen  279 PGVLFIDEVHMLD---------------------------IECFSFLNRALESEL-----SPIIILATNRGITKIRGTDI  326 (398)
T ss_dssp             E-EEEEESGGGSB---------------------------HHHHHHHHHHHTSTT-------EEEEEES-SEEE-BTTS-
T ss_pred             cceEEecchhhcc---------------------------HHHHHHHHHHhcCCC-----CcEEEEecCceeeeccCccC
Confidence            6899999999773                           122333334444332     2466777773          


Q ss_pred             --CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHh
Q 024550          153 --KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLI  203 (266)
Q Consensus       153 --~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~  203 (266)
                        |..+|..|+.  |+ ..|...+++.++..+|++.....++..+.++.-.++
T Consensus       327 ~sphGiP~DlLD--Rl-lII~t~py~~~ei~~Il~iR~~~E~v~i~~~al~~L  376 (398)
T PF06068_consen  327 ISPHGIPLDLLD--RL-LIIRTKPYSEEEIKQILKIRAKEEDVEISEDALDLL  376 (398)
T ss_dssp             EEETT--HHHHT--TE-EEEEE----HHHHHHHHHHHHHHCT--B-HHHHHHH
T ss_pred             cCCCCCCcchHh--hc-EEEECCCCCHHHHHHHHHhhhhhhcCcCCHHHHHHH
Confidence              5678889999  98 789999999999999999999888888876654433

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.

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

Probab=99.36  E-value=7.9e-12  Score=116.56  Aligned_cols=182  Identities=29%  Similarity=0.371  Sum_probs=137.8

Q ss_pred             HhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHHHHcc--cCCeee
Q 024550           16 FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHILIATE--NKSILV   87 (266)
Q Consensus        16 ~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~~~~~--~~~vl~   87 (266)
                      ++..+..+...+..++++++++||||||||+++++++.. +..+..++......      ...+..+|..+.  .+++++
T Consensus         3 ~~~~~~~~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~   81 (494)
T COG0464           3 PLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIF   81 (494)
T ss_pred             CccCHHHHHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEe
Confidence            456778899999999999999999999999999999998 55555555444332      344556665554  469999


Q ss_pred             eecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcce
Q 024550           88 VEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMD  167 (266)
Q Consensus        88 iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~  167 (266)
                      +|++|.+.+.+.. .               .......+...++..+++..  .+. +++++.||.+..+++++.+||||+
T Consensus        82 ~d~~~~~~~~~~~-~---------------~~~~~~~v~~~l~~~~d~~~--~~~-v~~~~~~~~~~~~~~a~~~~~~~~  142 (494)
T COG0464          82 IDEIDALAPKRSS-D---------------QGEVERRVVAQLLALMDGLK--RGQ-VIVIGATNRPDGLDPAKRRPGRFD  142 (494)
T ss_pred             echhhhcccCccc-c---------------ccchhhHHHHHHHHhccccc--CCc-eEEEeecCCccccChhHhCccccc
Confidence            9999999874443 0               12344567788888888886  345 888899999999999999999999


Q ss_pred             eEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhh-cCCCCHHHHHHHH
Q 024550          168 MHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQL  217 (266)
Q Consensus       168 ~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~-~~~~s~~~i~~~l  217 (266)
                      ..+.+..|+...+.+++.................++. ..+++.+++..++
T Consensus       143 ~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~  193 (494)
T COG0464         143 REIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALA  193 (494)
T ss_pred             eeeecCCCCHHHHHHHHHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHH
Confidence            9999999999999888877775554333334444444 3558888887776

>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=99.36  E-value=5e-13  Score=100.36  Aligned_cols=106  Identities=27%  Similarity=0.284  Sum_probs=60.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHH--HHH-------cc---cCCeeeeecchhhHHHhHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHI--LIA-------TE---NKSILVVEDIDCCIELQDR  100 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~--~~~-------~~---~~~vl~iDeid~l~~~~~~  100 (266)
                      .+||+|+||+|||++++++|+.++..|.++.+..-.-..++...  +..       ..   -..|+++|||+...     
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNrap-----   75 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRAP-----   75 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS------
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccCC-----
Confidence            37999999999999999999999999999987532222222111  000       01   13799999999654     


Q ss_pred             HhhhhhcCCccccccccccccchhhhhhhhhhhhc-------cccCCCCceEEEEecCCCC-----CCcccccCCCcce
Q 024550          101 LSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG-------LWSSCGDERIIIFTTNHKE-----RLDPALLRPGRMD  167 (266)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~-------~~~~~~~~~ivi~ttn~~~-----~ld~al~r~~Rf~  167 (266)
                                            ..+++.+|+.|..       .....+.+.+||||.|+.+     .|+.+++.  ||-
T Consensus        76 ----------------------pktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~D--RF~  130 (131)
T PF07726_consen   76 ----------------------PKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLD--RFM  130 (131)
T ss_dssp             ----------------------HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHT--TSS
T ss_pred             ----------------------HHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhc--ccc
Confidence                                  3456677777752       2223345688999999875     68889998  883

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.36  E-value=8e-11  Score=105.17  Aligned_cols=151  Identities=17%  Similarity=0.202  Sum_probs=99.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc----------------------------------EEEEeCC--cc------
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD----------------------------------VYDLELS--NL------   67 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~----------------------------------~~~i~~~--~~------   67 (266)
                      .++.+||+||+|+||+++|.++|+.+.+.                                  ++.+...  .-      
T Consensus        40 l~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~  119 (365)
T PRK07471         40 LHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRT  119 (365)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHHHHHHccCCCCeEEEecccccccccccc
Confidence            46789999999999999999999988431                                  1112110  00      


Q ss_pred             -cChhhHHHHHHHc------ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC
Q 024550           68 -LGNNDLRHILIAT------ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC  140 (266)
Q Consensus        68 -~~~~~l~~~~~~~------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~  140 (266)
                       ..-..++.+....      ..+.|++|||+|.+.                           ....+.|+..++.-    
T Consensus       120 ~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~---------------------------~~aanaLLK~LEep----  168 (365)
T PRK07471        120 VITVDEVRELISFFGLTAAEGGWRVVIVDTADEMN---------------------------ANAANALLKVLEEP----  168 (365)
T ss_pred             cccHHHHHHHHHHhCcCcccCCCEEEEEechHhcC---------------------------HHHHHHHHHHHhcC----
Confidence             0112233333222      235799999999763                           33556677777743    


Q ss_pred             CCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          141 GDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       141 ~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +...+||.+|+.++.+.+.+.+  || ..|.|+.|+.++...++.......   ....+..++...+.+|.....++
T Consensus       169 p~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~i~~~L~~~~~~~---~~~~~~~l~~~s~Gsp~~Al~ll  239 (365)
T PRK07471        169 PARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPEDVIDALAAAGPDL---PDDPRAALAALAEGSVGRALRLA  239 (365)
T ss_pred             CCCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHHHHHHHHHhcccC---CHHHHHHHHHHcCCCHHHHHHHh
Confidence            3457888899999889999988  88 569999999999999888765321   12222445555566666655554

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.35  E-value=6.2e-12  Score=110.67  Aligned_cols=129  Identities=20%  Similarity=0.269  Sum_probs=85.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-------CCc--EEEEeCC----------------------------cccChhhHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-------KFD--VYDLELS----------------------------NLLGNNDLR   74 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-------~~~--~~~i~~~----------------------------~~~~~~~l~   74 (266)
                      .++||+||||||||+++++++..+       +.+  +..+.+.                            .+.+.-.+.
T Consensus        30 ~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~  109 (334)
T PRK13407         30 GGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIE  109 (334)
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcccCCcccccccCCcccccCCccccCCCCCCcceeecchhhh
Confidence            579999999999999999999988       331  1111100                            011111111


Q ss_pred             HHHHH-----------cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc-------
Q 024550           75 HILIA-----------TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL-------  136 (266)
Q Consensus        75 ~~~~~-----------~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-------  136 (266)
                      ..+..           ...+++||+||++.+..                           .+++.|++.|+.-       
T Consensus       110 ~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~~---------------------------~~q~~Lle~mee~~v~v~r~  162 (334)
T PRK13407        110 RALTRGEKAFEPGLLARANRGYLYIDEVNLLED---------------------------HIVDLLLDVAQSGENVVERE  162 (334)
T ss_pred             hhhhcCCeeecCCceEEcCCCeEEecChHhCCH---------------------------HHHHHHHHHHHcCCeEEEEC
Confidence            11111           12457999999998742                           3455566666432       


Q ss_pred             --ccCCCCceEEEEecCCCC-CCcccccCCCcceeEEEcCCCCH-HHHHHHHHHhhC
Q 024550          137 --WSSCGDERIIIFTTNHKE-RLDPALLRPGRMDMHINMSHCTP-SGFKMLASNYLG  189 (266)
Q Consensus       137 --~~~~~~~~ivi~ttn~~~-~ld~al~r~~Rf~~~i~~~~p~~-~~~~~i~~~~~~  189 (266)
                        ....+.++++++|+|..+ .++++++.  ||.+.|.++.|.. +++.+++.+...
T Consensus       163 G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~~~e~~~il~~~~~  217 (334)
T PRK13407        163 GLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRDVETRVEVIRRRDA  217 (334)
T ss_pred             CeEEecCCCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHhhc
Confidence              112234678888888754 68999999  9999999999988 888999987543

>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=99.34  E-value=2.9e-12  Score=102.66  Aligned_cols=109  Identities=22%  Similarity=0.318  Sum_probs=75.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC----cEEEEeCCcccC----hhhHHHHHHHc------ccCCeeeeecchhhH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF----DVYDLELSNLLG----NNDLRHILIAT------ENKSILVVEDIDCCI   95 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~----~~~~i~~~~~~~----~~~l~~~~~~~------~~~~vl~iDeid~l~   95 (266)
                      |...+||+||+|||||.+++++|..+..    +++.++++.+..    ...+..++...      .+.+||||||||.+.
T Consensus         2 p~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~   81 (171)
T PF07724_consen    2 PKSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAH   81 (171)
T ss_dssp             -SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCS
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhHHHhhcc
Confidence            3456999999999999999999999996    999999999987    44444444433      245799999999886


Q ss_pred             HHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCCCC
Q 024550           96 ELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHKE  154 (266)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~~  154 (266)
                      +..+                ...+.....+++.||+.|++-.-..       -.+.+||+|+|--.
T Consensus        82 ~~~~----------------~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~  131 (171)
T PF07724_consen   82 PSNS----------------GGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGA  131 (171)
T ss_dssp             HTTT----------------TCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSST
T ss_pred             cccc----------------ccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccccc
Confidence            5210                0112233457777888886432211       14578999999643

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 ....

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.34  E-value=5e-11  Score=111.13  Aligned_cols=148  Identities=19%  Similarity=0.198  Sum_probs=95.5

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHc----------ccCCeeeeecchhhHHH
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIAT----------ENKSILVVEDIDCCIEL   97 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~----------~~~~vl~iDeid~l~~~   97 (266)
                      .|+.+.+||+||||-||||||+.+|+..|..++++++++-.+...+...+..+          .+|..|++||||.-.  
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~--  400 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAP--  400 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHhcCceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCc--
Confidence            44456699999999999999999999999999999999887766665554432          468899999999543  


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhh--ccccCCC---------------CceEEEEecCCCCCCcccc
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID--GLWSSCG---------------DERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~--~~~~~~~---------------~~~ivi~ttn~~~~ld~al  160 (266)
                                               ...++.++..+.  +....+.               -..-||+.||..-  -|+|
T Consensus       401 -------------------------~~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLY--aPaL  453 (877)
T KOG1969|consen  401 -------------------------RAAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLY--APAL  453 (877)
T ss_pred             -------------------------HHHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCcc--chhh
Confidence                                     112222222221  0000000               0145899999643  3566


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhh
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIA  204 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~  204 (266)
                      ..---|..+|.|..|......+-++.+-..++... ...+..++.
T Consensus       454 R~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~e  498 (877)
T KOG1969|consen  454 RPLRPFAEIIAFVPPSQSRLVERLNEICHRENMRADSKALNALCE  498 (877)
T ss_pred             hhcccceEEEEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHH
Confidence            42116788999999998876655555544444333 234444544

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.32  E-value=3.6e-11  Score=106.17  Aligned_cols=79  Identities=20%  Similarity=0.273  Sum_probs=57.8

Q ss_pred             cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc---------cccCCCCceEEEEecCC
Q 024550           82 NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG---------LWSSCGDERIIIFTTNH  152 (266)
Q Consensus        82 ~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~~~~~~~~~ivi~ttn~  152 (266)
                      .+++||+||++.+..                           .+++.|++.|+.         .....+.++++|+|.|.
T Consensus       144 ~~GiL~lDEInrL~~---------------------------~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np  196 (350)
T CHL00081        144 NRGILYVDEVNLLDD---------------------------HLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNP  196 (350)
T ss_pred             CCCEEEecChHhCCH---------------------------HHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCc
Confidence            468999999998853                           234445555542         11122346778888886


Q ss_pred             CC-CCcccccCCCcceeEEEcCCCC-HHHHHHHHHHhhC
Q 024550          153 KE-RLDPALLRPGRMDMHINMSHCT-PSGFKMLASNYLG  189 (266)
Q Consensus       153 ~~-~ld~al~r~~Rf~~~i~~~~p~-~~~~~~i~~~~~~  189 (266)
                      .+ .++++|+.  ||.++|.+..|+ .+.+.+|+++...
T Consensus       197 ~eg~l~~~Lld--Rf~l~i~l~~~~~~~~e~~il~~~~~  233 (350)
T CHL00081        197 EEGELRPQLLD--RFGMHAEIRTVKDPELRVKIVEQRTS  233 (350)
T ss_pred             ccCCCCHHHHH--HhCceeecCCCCChHHHHHHHHhhhc
Confidence            65 68999999  999999999998 5899999987643

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

Probab=99.31  E-value=1.4e-11  Score=117.38  Aligned_cols=197  Identities=19%  Similarity=0.192  Sum_probs=120.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccChh--------hHHHHHHHcc--cCCeeeeec
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGNN--------DLRHILIATE--NKSILVVED   90 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~~--------~l~~~~~~~~--~~~vl~iDe   90 (266)
                      ..+.+|+|+||+|||.++..+|...          +..++.++...+....        .+..++....  .+.||||||
T Consensus       191 KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDE  270 (786)
T COG0542         191 KNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDE  270 (786)
T ss_pred             CCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecHHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEec
Confidence            5678999999999999999999876          6778888888877543        3444444432  389999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC------CCCcccccCCC
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK------ERLDPALLRPG  164 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~------~~ld~al~r~~  164 (266)
                      +|.+.+.....+                  ..-..-|-|.-.|.    +  ...-+|++|+.-      +. |+||-|  
T Consensus       271 iHtiVGAG~~~G------------------~a~DAaNiLKPaLA----R--GeL~~IGATT~~EYRk~iEK-D~AL~R--  323 (786)
T COG0542         271 IHTIVGAGATEG------------------GAMDAANLLKPALA----R--GELRCIGATTLDEYRKYIEK-DAALER--  323 (786)
T ss_pred             hhhhcCCCcccc------------------cccchhhhhHHHHh----c--CCeEEEEeccHHHHHHHhhh-chHHHh--
Confidence            999976222111                  00111222222222    2  346677777532      23 899999  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhhCCC----CCCcHHHHHHHhhcCCCCHHHHHHHHHcCCCHHHHHHHHHHHHHhhhhh
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYLGIA----EHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA  240 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~~~~----~~~~~~~~~~l~~~~~~s~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~  240 (266)
                      || ..|.+..|+.++-..|++..-...    +..+.++.-..+.  .+|...|.+.    --|+++++-+.++..+.+-.
T Consensus       324 RF-Q~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv--~LS~RYI~dR----~LPDKAIDLiDeA~a~~~l~  396 (786)
T COG0542         324 RF-QKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAV--TLSDRYIPDR----FLPDKAIDLLDEAGARVRLE  396 (786)
T ss_pred             cC-ceeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHH--HHHHhhcccC----CCCchHHHHHHHHHHHHHhc
Confidence            99 569999999999988887555443    2333333322222  1444444322    34777777777777776665


Q ss_pred             c-cchhhHHHHHHHHHhhhhhh
Q 024550          241 N-DGSEAKEAEERAVQAEKKVL  261 (266)
Q Consensus       241 ~-~~~~~~~~~~~~~~~~~~~~  261 (266)
                      . .+..-++.+++..+.+.+..
T Consensus       397 ~~~p~~l~~~~~~~~~l~~e~~  418 (786)
T COG0542         397 IDKPEELDELERELAQLEIEKE  418 (786)
T ss_pred             ccCCcchhHHHHHHHHHHHHHH
Confidence            3 24444444444444433333

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.31  E-value=2.4e-10  Score=100.96  Aligned_cols=125  Identities=16%  Similarity=0.202  Sum_probs=87.8

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCcE-------------------------EEEeCCc-----------------
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDV-------------------------YDLELSN-----------------   66 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~~-------------------------~~i~~~~-----------------   66 (266)
                      ..++++||+||+|+||+++|+++|..+.+..                         +.+....                 
T Consensus        19 rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~~~   98 (342)
T PRK06964         19 RLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEADA   98 (342)
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccchh
Confidence            5577899999999999999999999885422                         1221110                 


Q ss_pred             ------------ccChhhHHHHHHHcc------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhh
Q 024550           67 ------------LLGNNDLRHILIATE------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG  128 (266)
Q Consensus        67 ------------~~~~~~l~~~~~~~~------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (266)
                                  ...-..++.+.....      ..-|++||++|.|.                           ....|.
T Consensus        99 ~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~---------------------------~~AaNa  151 (342)
T PRK06964         99 DEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALN---------------------------VAAANA  151 (342)
T ss_pred             hcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhcC---------------------------HHHHHH
Confidence                        011123333332221      23477777777653                           335567


Q ss_pred             hhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHh
Q 024550          129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNY  187 (266)
Q Consensus       129 ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~  187 (266)
                      ||+.|+    .++.+++||.+|++++.|.|++++  || ..|.|+.|+.++....+...
T Consensus       152 LLKtLE----EPp~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        152 LLKTLE----EPPPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             HHHHhc----CCCcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            777777    456779999999999999999999  98 67999999999988877654

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=99.28  E-value=2.2e-11  Score=108.78  Aligned_cols=156  Identities=14%  Similarity=0.202  Sum_probs=102.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccCh-------hhHHHHHHHcccCCeeeeecchhhHHHhH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGN-------NDLRHILIATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~-------~~l~~~~~~~~~~~vl~iDeid~l~~~~~   99 (266)
                      .-++||||.|+|||+|++|++++.     +..+++++...+...       ......-... .-.+++|||++.+.+   
T Consensus       114 nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y-~~dlllIDDiq~l~g---  189 (408)
T COG0593         114 NPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY-SLDLLLIDDIQFLAG---  189 (408)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh-ccCeeeechHhHhcC---
Confidence            349999999999999999999988     334566665544311       1111121223 567999999998864   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC---cccccCCCcce--eEEEcCC
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL---DPALLRPGRMD--MHINMSH  174 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l---d~al~r~~Rf~--~~i~~~~  174 (266)
                                         ....+..+..++|.+-..     .+.+++.+...|..+   .+.|.+  ||.  ..+.+..
T Consensus       190 -------------------k~~~qeefFh~FN~l~~~-----~kqIvltsdr~P~~l~~~~~rL~S--R~~~Gl~~~I~~  243 (408)
T COG0593         190 -------------------KERTQEEFFHTFNALLEN-----GKQIVLTSDRPPKELNGLEDRLRS--RLEWGLVVEIEP  243 (408)
T ss_pred             -------------------ChhHHHHHHHHHHHHHhc-----CCEEEEEcCCCchhhccccHHHHH--HHhceeEEeeCC
Confidence                               112233334444444432     335666666677554   588888  665  7899999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCcHHHHHHHhh-cCCCCHHHHHHHH
Q 024550          175 CTPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQL  217 (266)
Q Consensus       175 p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~-~~~~s~~~i~~~l  217 (266)
                      |+.+.|..|+.......+..+.+++..++. ...-+.+++..++
T Consensus       244 Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~~nvReLegaL  287 (408)
T COG0593         244 PDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNVRELEGAL  287 (408)
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccHHHHHHHH
Confidence            999999999999888888887776655444 3344455544444

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.28  E-value=6.6e-11  Score=106.86  Aligned_cols=135  Identities=19%  Similarity=0.230  Sum_probs=71.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc-----EEEEeCC------ccc-----C-------hhhHHHHHHHc----cc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD-----VYDLELS------NLL-----G-------NNDLRHILIAT----EN   82 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~-----~~~i~~~------~~~-----~-------~~~l~~~~~~~----~~   82 (266)
                      ..++++|+||||||||++|+.+|..+...     +..+.++      ++.     .       ...+..++..+    ..
T Consensus       193 ~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~  272 (459)
T PRK11331        193 IKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEK  272 (459)
T ss_pred             cCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccC
Confidence            35689999999999999999999988431     1112221      111     0       01122233333    35


Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchh-hhhhhhhh--hhccccCCCCceEEEEecCCCC----C
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI-TLSGLLNF--IDGLWSSCGDERIIIFTTNHKE----R  155 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ll~~--l~~~~~~~~~~~ivi~ttn~~~----~  155 (266)
                      +.||+||||+.....+--...-.         ....+..... .+.-....  .+.+  ..+.++.||||+|..+    .
T Consensus       273 ~~vliIDEINRani~kiFGel~~---------lLE~~~rg~~~~v~l~y~e~d~e~f--~iP~Nl~IIgTMNt~Drs~~~  341 (459)
T PRK11331        273 KYVFIIDEINRANLSKVFGEVMM---------LMEHDKRGENWSVPLTYSENDEERF--YVPENVYIIGLMNTADRSLAV  341 (459)
T ss_pred             CcEEEEehhhccCHHHhhhhhhh---------hccccccccccceeeeccccccccc--cCCCCeEEEEecCccccchhh
Confidence            79999999996543110000000         0000000000 00000000  0112  2246799999999886    7


Q ss_pred             CcccccCCCcceeEEEcCC-CCHH
Q 024550          156 LDPALLRPGRMDMHINMSH-CTPS  178 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~-p~~~  178 (266)
                      +|.||+|  ||.+ |++.. ++.+
T Consensus       342 lD~AlrR--RF~f-i~i~p~~~~~  362 (459)
T PRK11331        342 VDYALRR--RFSF-IDIEPGFDTP  362 (459)
T ss_pred             ccHHHHh--hhhe-EEecCCCChH
Confidence            8999999  9955 66654 4444

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.26  E-value=4.5e-10  Score=99.36  Aligned_cols=123  Identities=20%  Similarity=0.284  Sum_probs=88.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCcc-cChhhHHHHHHHcc---
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSNL-LGNNDLRHILIATE---   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~~-~~~~~l~~~~~~~~---   81 (266)
                      .++.+|||||+|+||+++|+++|+.+.++                        +..+....- .+...++.+.....   
T Consensus        27 l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~  106 (329)
T PRK08058         27 LSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSG  106 (329)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCC
Confidence            46789999999999999999999987432                        333322211 12234444443322   


Q ss_pred             ---cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           82 ---NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        82 ---~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                         ..-|++|||+|.+.                           ....+.||..|+.    ++...++|.+|+.+..+.+
T Consensus       107 ~~~~~kvviI~~a~~~~---------------------------~~a~NaLLK~LEE----Pp~~~~~Il~t~~~~~ll~  155 (329)
T PRK08058        107 VESNKKVYIIEHADKMT---------------------------ASAANSLLKFLEE----PSGGTTAILLTENKHQILP  155 (329)
T ss_pred             cccCceEEEeehHhhhC---------------------------HHHHHHHHHHhcC----CCCCceEEEEeCChHhCcH
Confidence               35799999999773                           2245667777774    3456888889989999999


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHH
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASN  186 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~  186 (266)
                      ++.+  || ..++|+.|+.++....+..
T Consensus       156 TIrS--Rc-~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        156 TILS--RC-QVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             HHHh--hc-eeeeCCCCCHHHHHHHHHH
Confidence            9999  88 6699999999998777754

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.25  E-value=1.9e-10  Score=101.30  Aligned_cols=120  Identities=22%  Similarity=0.308  Sum_probs=87.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC------------------------CcEEEEeCCcccCh----hhHHHHHHHc--
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK------------------------FDVYDLELSNLLGN----NDLRHILIAT--   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~------------------------~~~~~i~~~~~~~~----~~l~~~~~~~--   80 (266)
                      ++.+||+||||||||++|.++|+.+.                        ..++++++++....    ..++.+....  
T Consensus        24 ~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~  103 (325)
T COG0470          24 PHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSE  103 (325)
T ss_pred             CceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHHhcc
Confidence            44799999999999999999999986                        57788888776552    2334333332  


Q ss_pred             ----ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC
Q 024550           81 ----ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL  156 (266)
Q Consensus        81 ----~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l  156 (266)
                          ...-|++|||+|.+..                           ...+.++..++.    .+....||.+||.+..+
T Consensus       104 ~~~~~~~kviiidead~mt~---------------------------~A~nallk~lEe----p~~~~~~il~~n~~~~i  152 (325)
T COG0470         104 SPLEGGYKVVIIDEADKLTE---------------------------DAANALLKTLEE----PPKNTRFILITNDPSKI  152 (325)
T ss_pred             CCCCCCceEEEeCcHHHHhH---------------------------HHHHHHHHHhcc----CCCCeEEEEEcCChhhc
Confidence                2357999999998853                           234455555553    35678999999999999


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLA  184 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~  184 (266)
                      -+.+.+  || ..+.|+.|+........
T Consensus       153 l~tI~S--Rc-~~i~f~~~~~~~~i~~~  177 (325)
T COG0470         153 LPTIRS--RC-QRIRFKPPSRLEAIAWL  177 (325)
T ss_pred             cchhhh--cc-eeeecCCchHHHHHHHh
Confidence            999999  88 56888876665544333

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.25  E-value=3.2e-10  Score=100.18  Aligned_cols=151  Identities=16%  Similarity=0.174  Sum_probs=102.4

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCc---ccChhhHHHHHHHcc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSN---LLGNNDLRHILIATE   81 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~---~~~~~~l~~~~~~~~   81 (266)
                      ..++++||+||+|+||+++|.++|..+.+                        .++.+.+..   ..+-..++++.....
T Consensus        22 rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~idqiR~l~~~~~  101 (334)
T PRK07993         22 RGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKSSLGVDAVREVTEKLY  101 (334)
T ss_pred             CcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccCCHHHHHHHHHHHh
Confidence            34678999999999999999999998833                        233333221   123344554444332


Q ss_pred             ------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           82 ------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        82 ------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                            ..-|++||++|.|-                           ....|.||+.|+    .++.+.+||.+|+.++.
T Consensus       102 ~~~~~g~~kV~iI~~ae~m~---------------------------~~AaNaLLKtLE----EPp~~t~fiL~t~~~~~  150 (334)
T PRK07993        102 EHARLGGAKVVWLPDAALLT---------------------------DAAANALLKTLE----EPPENTWFFLACREPAR  150 (334)
T ss_pred             hccccCCceEEEEcchHhhC---------------------------HHHHHHHHHHhc----CCCCCeEEEEEECChhh
Confidence                  35699999999874                           234566777776    45678999999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      |.|++++  ||. .+.|+.|+.++....+....+.    ...++..++.-.+.+|....+.+
T Consensus       151 lLpTIrS--RCq-~~~~~~~~~~~~~~~L~~~~~~----~~~~a~~~~~la~G~~~~Al~l~  205 (334)
T PRK07993        151 LLATLRS--RCR-LHYLAPPPEQYALTWLSREVTM----SQDALLAALRLSAGAPGAALALL  205 (334)
T ss_pred             ChHHHHh--ccc-cccCCCCCHHHHHHHHHHccCC----CHHHHHHHHHHcCCCHHHHHHHh
Confidence            9999999  985 5899999999988777543221    12334444455556665544443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.25  E-value=6e-10  Score=97.75  Aligned_cols=125  Identities=15%  Similarity=0.170  Sum_probs=90.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCC--cccChhhHHHHHHHcc--
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELS--NLLGNNDLRHILIATE--   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~--~~~~~~~l~~~~~~~~--   81 (266)
                      .++++||+||+|+||+++|+++|..+.+                        .++.+.+.  ...+-..++++.....  
T Consensus        23 l~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~I~id~iR~l~~~~~~~  102 (325)
T PRK06871         23 GHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKDIGVDQVREINEKVSQH  102 (325)
T ss_pred             cceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCCCCHHHHHHHHHHHhhc
Confidence            4678999999999999999999998843                        13333221  1113344554443321  


Q ss_pred             ----cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc
Q 024550           82 ----NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD  157 (266)
Q Consensus        82 ----~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld  157 (266)
                          ..-|++||++|.|-                           ....|.||+.|+.    ++..++||.+|+.++.+.
T Consensus       103 ~~~g~~KV~iI~~a~~m~---------------------------~~AaNaLLKtLEE----Pp~~~~fiL~t~~~~~ll  151 (325)
T PRK06871        103 AQQGGNKVVYIQGAERLT---------------------------EAAANALLKTLEE----PRPNTYFLLQADLSAALL  151 (325)
T ss_pred             cccCCceEEEEechhhhC---------------------------HHHHHHHHHHhcC----CCCCeEEEEEECChHhCc
Confidence                34689999999874                           2345667777764    456789999999999999


Q ss_pred             ccccCCCcceeEEEcCCCCHHHHHHHHHHhh
Q 024550          158 PALLRPGRMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       158 ~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                      |++++  || ..+.|+.|+.++....+....
T Consensus       152 pTI~S--RC-~~~~~~~~~~~~~~~~L~~~~  179 (325)
T PRK06871        152 PTIYS--RC-QTWLIHPPEEQQALDWLQAQS  179 (325)
T ss_pred             hHHHh--hc-eEEeCCCCCHHHHHHHHHHHh
Confidence            99999  98 569999999999887776543

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.24  E-value=3.6e-11  Score=106.05  Aligned_cols=129  Identities=22%  Similarity=0.315  Sum_probs=84.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-------CCcEE-------------EE------------------eCC------c
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-------KFDVY-------------DL------------------ELS------N   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-------~~~~~-------------~i------------------~~~------~   66 (266)
                      ..+++|.|+||+|||+++++++..+       +.++-             ..                  +..      .
T Consensus        25 ~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~  104 (337)
T TIGR02030        25 IGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPEMMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDR  104 (337)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCccccChHHhhhhhcccccccccCCCCcCCCCCCCcccc
Confidence            3469999999999999999999877       22221             00                  000      1


Q ss_pred             ccChhhHHHHHH-----------HcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc
Q 024550           67 LLGNNDLRHILI-----------ATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG  135 (266)
Q Consensus        67 ~~~~~~l~~~~~-----------~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~  135 (266)
                      +.+.-.+...+.           ....+++||+||++.+..                           .+++.|++.|+.
T Consensus       105 l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~~---------------------------~~Q~~Ll~~l~~  157 (337)
T TIGR02030       105 VCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLED---------------------------HLVDVLLDVAAS  157 (337)
T ss_pred             eecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCCH---------------------------HHHHHHHHHHHh
Confidence            111112222221           123468999999998743                           244455555532


Q ss_pred             c---------ccCCCCceEEEEecCCCC-CCcccccCCCcceeEEEcCCCCH-HHHHHHHHHhh
Q 024550          136 L---------WSSCGDERIIIFTTNHKE-RLDPALLRPGRMDMHINMSHCTP-SGFKMLASNYL  188 (266)
Q Consensus       136 ~---------~~~~~~~~ivi~ttn~~~-~ld~al~r~~Rf~~~i~~~~p~~-~~~~~i~~~~~  188 (266)
                      -         ....+.++++|+|+|..+ .++++|+.  ||.+.+.++.|.. +++.+|+++..
T Consensus       158 g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p~~~eer~eIL~~~~  219 (337)
T TIGR02030       158 GWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTVRDVELRVEIVERRT  219 (337)
T ss_pred             CCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--hcceEEECCCCCCHHHHHHHHHhhh
Confidence            1         112234578888888654 68999999  9999999999987 88889988754

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.24  E-value=2.7e-10  Score=99.95  Aligned_cols=150  Identities=17%  Similarity=0.238  Sum_probs=102.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc------------------EEEEeCCccc-----------------------C
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD------------------VYDLELSNLL-----------------------G   69 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~------------------~~~i~~~~~~-----------------------~   69 (266)
                      ++.+||+||+|+||+++|.++|..+.+.                  ++.+.+....                       .
T Consensus        26 ~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~  105 (314)
T PRK07399         26 APAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIR  105 (314)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccccccccchhhhhhccccccccccCc
Confidence            5689999999999999999999987432                  1222221100                       0


Q ss_pred             hhhHHHHHHHc------ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCc
Q 024550           70 NNDLRHILIAT------ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDE  143 (266)
Q Consensus        70 ~~~l~~~~~~~------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~  143 (266)
                      -..++++....      ....|++||++|.+.                           ....+.||+.|+.-    + .
T Consensus       106 id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~---------------------------~~aaNaLLK~LEEP----p-~  153 (314)
T PRK07399        106 LEQIREIKRFLSRPPLEAPRKVVVIEDAETMN---------------------------EAAANALLKTLEEP----G-N  153 (314)
T ss_pred             HHHHHHHHHHHccCcccCCceEEEEEchhhcC---------------------------HHHHHHHHHHHhCC----C-C
Confidence            11233333222      135799999998773                           23456778887752    3 4


Q ss_pred             eEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          144 RIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       144 ~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+||.+|+.++.|.+++.+  || ..+.|+.|+.++..+++.........  ..+...++...+.+|+...+.+
T Consensus       154 ~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~~~~~~~L~~~~~~~~~--~~~~~~l~~~a~Gs~~~al~~l  222 (314)
T PRK07399        154 GTLILIAPSPESLLPTIVS--RC-QIIPFYRLSDEQLEQVLKRLGDEEIL--NINFPELLALAQGSPGAAIANI  222 (314)
T ss_pred             CeEEEEECChHhCcHHHHh--hc-eEEecCCCCHHHHHHHHHHhhccccc--hhHHHHHHHHcCCCHHHHHHHH
Confidence            5778888899999999999  98 67999999999999988876533221  1223556666778888877765

>PRK04132 replication factor C small subunit; Provisional

Probab=99.24  E-value=1.1e-10  Score=113.26  Aligned_cols=150  Identities=13%  Similarity=0.115  Sum_probs=112.6

Q ss_pred             eEEec--CCCCChHHHHHHHHHHc-----CCcEEEEeCCcccChhhHHHHHHHcc--------cCCeeeeecchhhHHHh
Q 024550           34 YLLYG--PPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGNNDLRHILIATE--------NKSILVVEDIDCCIELQ   98 (266)
Q Consensus        34 iLl~G--ppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~~~l~~~~~~~~--------~~~vl~iDeid~l~~~~   98 (266)
                      -+..|  |++.||||+|+++|+++     +.+++++++++..+...++..+....        +..|++|||+|.|..  
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~--  644 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ--  644 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCCH--
Confidence            45678  99999999999999998     55799999998766666766654321        125999999998842  


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHH
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPS  178 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~  178 (266)
                                               ...+.|+..|+..    +..+.||++||++..+.+++.+  || ..+.|+.|+.+
T Consensus       645 -------------------------~AQnALLk~lEep----~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~  692 (846)
T PRK04132        645 -------------------------DAQQALRRTMEMF----SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDE  692 (846)
T ss_pred             -------------------------HHHHHHHHHhhCC----CCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHH
Confidence                                     2455677777743    3568899999999999999999  98 66999999999


Q ss_pred             HHHHHHHHhhCCCCCCc-HHHHHHHhhcCCCCHHHHHHHH
Q 024550          179 GFKMLASNYLGIAEHPL-FVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       179 ~~~~i~~~~~~~~~~~~-~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +....+......++... .+.+..++.....+++...+.+
T Consensus       693 ~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~GDlR~AIn~L  732 (846)
T PRK04132        693 DIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINIL  732 (846)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99888887776665543 3445555555556666555555

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=99.24  E-value=1.7e-10  Score=91.77  Aligned_cols=112  Identities=20%  Similarity=0.314  Sum_probs=78.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC-----------------------CcEEEEeCCcc---cChhhHHHHHHHcc--
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK-----------------------FDVYDLELSNL---LGNNDLRHILIATE--   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~-----------------------~~~~~i~~~~~---~~~~~l~~~~~~~~--   81 (266)
                      .++.+||+||+|+||+++|+++|..+.                       ..++.+.....   .....++.+.....  
T Consensus        18 l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~   97 (162)
T PF13177_consen   18 LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLS   97 (162)
T ss_dssp             --SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHHHHHHHHHHH
Confidence            367899999999999999999998772                       23455554433   23455665555442  


Q ss_pred             ----cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc
Q 024550           82 ----NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD  157 (266)
Q Consensus        82 ----~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld  157 (266)
                          ..-|++||++|.|-                           ....+.||..|+.-    +..+++|.+|+.++.+.
T Consensus        98 ~~~~~~KviiI~~ad~l~---------------------------~~a~NaLLK~LEep----p~~~~fiL~t~~~~~il  146 (162)
T PF13177_consen   98 PSEGKYKVIIIDEADKLT---------------------------EEAQNALLKTLEEP----PENTYFILITNNPSKIL  146 (162)
T ss_dssp             -TTSSSEEEEEETGGGS----------------------------HHHHHHHHHHHHST----TTTEEEEEEES-GGGS-
T ss_pred             HhcCCceEEEeehHhhhh---------------------------HHHHHHHHHHhcCC----CCCEEEEEEECChHHCh
Confidence                35699999999874                           34567788888753    46799999999999999


Q ss_pred             ccccCCCcceeEEEcCCC
Q 024550          158 PALLRPGRMDMHINMSHC  175 (266)
Q Consensus       158 ~al~r~~Rf~~~i~~~~p  175 (266)
                      +.+++  || ..|.|+..
T Consensus       147 ~TI~S--Rc-~~i~~~~l  161 (162)
T PF13177_consen  147 PTIRS--RC-QVIRFRPL  161 (162)
T ss_dssp             HHHHT--TS-EEEEE---
T ss_pred             HHHHh--hc-eEEecCCC
Confidence            99999  98 56777654

...

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.23  E-value=4.7e-11  Score=91.08  Aligned_cols=66  Identities=27%  Similarity=0.466  Sum_probs=48.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc---EEEEeCCcccC--------------------hhhHHHHHHHcc--cCCe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD---VYDLELSNLLG--------------------NNDLRHILIATE--NKSI   85 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~---~~~i~~~~~~~--------------------~~~l~~~~~~~~--~~~v   85 (266)
                      +..++|+||||||||++++.+|..+...   ++.+++.....                    .......+..+.  .+.+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            4579999999999999999999999775   77787765432                    112233333333  2599


Q ss_pred             eeeecchhhHH
Q 024550           86 LVVEDIDCCIE   96 (266)
Q Consensus        86 l~iDeid~l~~   96 (266)
                      |++||++.+..
T Consensus        82 iiiDei~~~~~   92 (148)
T smart00382       82 LILDEITSLLD   92 (148)
T ss_pred             EEEECCcccCC
Confidence            99999998865

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.21  E-value=1.2e-10  Score=106.12  Aligned_cols=131  Identities=18%  Similarity=0.206  Sum_probs=80.1

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCC--cEEEEeCC-----cccChhhHHH-----HHHHcc-----cCCeeeeec
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKF--DVYDLELS-----NLLGNNDLRH-----ILIATE-----NKSILVVED   90 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~--~~~~i~~~-----~~~~~~~l~~-----~~~~~~-----~~~vl~iDe   90 (266)
                      .-...++||+||||||||++|++++..++.  +|....+.     ++.+...+..     .|....     ...+||+||
T Consensus        36 alag~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDE  115 (498)
T PRK13531         36 ALSGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDE  115 (498)
T ss_pred             HccCCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcCcHHHhhhhhcCchhhhcCCccccccEEeecc
Confidence            334567999999999999999999998753  33333222     2222111111     111111     234899999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC------CceEEEEecCCCC---CCccccc
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG------DERIIIFTTNHKE---RLDPALL  161 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~------~~~ivi~ttn~~~---~ld~al~  161 (266)
                      |..+.                           ..+++.||..|..-.-+.+      ...++++|||...   ...++++
T Consensus       116 I~ras---------------------------p~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~  168 (498)
T PRK13531        116 IWKAG---------------------------PAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALY  168 (498)
T ss_pred             cccCC---------------------------HHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhH
Confidence            98553                           4466778888842221111      1245666667432   2335899


Q ss_pred             CCCcceeEEEcCCCCH-HHHHHHHHHh
Q 024550          162 RPGRMDMHINMSHCTP-SGFKMLASNY  187 (266)
Q Consensus       162 r~~Rf~~~i~~~~p~~-~~~~~i~~~~  187 (266)
                      .  ||.+.|.+|+|+. ++...|+...
T Consensus       169 D--RFliri~vp~l~~~~~e~~lL~~~  193 (498)
T PRK13531        169 D--RMLIRLWLDKVQDKANFRSMLTSQ  193 (498)
T ss_pred             h--hEEEEEECCCCCchHHHHHHHHcc
Confidence            9  9999999999974 5557777654

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.21  E-value=1e-09  Score=96.16  Aligned_cols=150  Identities=15%  Similarity=0.165  Sum_probs=99.6

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCc---------------------EEEE--eCCcc-------cChhhHHHHHH
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFD---------------------VYDL--ELSNL-------LGNNDLRHILI   78 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~---------------------~~~i--~~~~~-------~~~~~l~~~~~   78 (266)
                      ..++++||+||+|+||+++|.++|..+.+.                     ++.+  .+..-       ..-..++++..
T Consensus        24 rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~  103 (319)
T PRK08769         24 RLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQ  103 (319)
T ss_pred             CcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHHH
Confidence            346789999999999999999999877321                     2333  11110       11223343333


Q ss_pred             Hcc------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC
Q 024550           79 ATE------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH  152 (266)
Q Consensus        79 ~~~------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~  152 (266)
                      ...      ..-|++||++|.|.                           ....|.||+.|+.    ++.+.+||.+|+.
T Consensus       104 ~~~~~p~~g~~kV~iI~~ae~m~---------------------------~~AaNaLLKtLEE----Pp~~~~fiL~~~~  152 (319)
T PRK08769        104 KLALTPQYGIAQVVIVDPADAIN---------------------------RAACNALLKTLEE----PSPGRYLWLISAQ  152 (319)
T ss_pred             HHhhCcccCCcEEEEeccHhhhC---------------------------HHHHHHHHHHhhC----CCCCCeEEEEECC
Confidence            221      24689999999773                           3355677777764    4567889999999


Q ss_pred             CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          153 KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       153 ~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++.|.|.+++  || ..|.|+.|+.++....+...    +. ...++..++.-.+.+|......+
T Consensus       153 ~~~lLpTIrS--RC-q~i~~~~~~~~~~~~~L~~~----~~-~~~~a~~~~~l~~G~p~~A~~~~  209 (319)
T PRK08769        153 PARLPATIRS--RC-QRLEFKLPPAHEALAWLLAQ----GV-SERAAQEALDAARGHPGLAAQWL  209 (319)
T ss_pred             hhhCchHHHh--hh-eEeeCCCcCHHHHHHHHHHc----CC-ChHHHHHHHHHcCCCHHHHHHHh
Confidence            9999999999  98 56999999998887777642    11 12334445555667776665544

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

Probab=99.20  E-value=1e-09  Score=94.49  Aligned_cols=136  Identities=16%  Similarity=0.208  Sum_probs=79.2

Q ss_pred             cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC------CceEEEEecC----
Q 024550           82 NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG------DERIIIFTTN----  151 (266)
Q Consensus        82 ~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~------~~~ivi~ttn----  151 (266)
                      +.+|+||||||.++.......               .+...+-++..+|-.++|..-...      ..++||++.-    
T Consensus       250 ~~GIvFIDEIDKIa~~~~~g~---------------~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~s  314 (444)
T COG1220         250 QNGIVFIDEIDKIAKRGGSGG---------------PDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVA  314 (444)
T ss_pred             hcCeEEEehhhHHHhcCCCCC---------------CCcchhhhcccccccccCceeeccccccccceEEEEecCceecC
Confidence            468999999999986332111               012334466667777776533221      2367777653    


Q ss_pred             CCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCC----CCHHHHHHHH---H--cCCC
Q 024550          152 HKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAK----VTPADVAEQL---M--RNEA  222 (266)
Q Consensus       152 ~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~----~s~~~i~~~l---~--~~~~  222 (266)
                      .|.+|-|.|.-  ||...+++...+.+....|+.    .-...+..+...+....+    ||-..|.++.   +  +...
T Consensus       315 KPSDLiPELQG--RfPIRVEL~~Lt~~Df~rILt----ep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA~~vN~~~  388 (444)
T COG1220         315 KPSDLIPELQG--RFPIRVELDALTKEDFERILT----EPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAYQVNEKT  388 (444)
T ss_pred             ChhhcChhhcC--CCceEEEcccCCHHHHHHHHc----CcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHHHHhcccc
Confidence            56777788887  999999999999999776653    222333344444444333    5544443332   1  1223


Q ss_pred             HHHHHHHHHHHHHhhh
Q 024550          223 PEFALSGLIEFLESKK  238 (266)
Q Consensus       223 ~~~~~~~~~~~~~~~~  238 (266)
                      ....++++-..+++..
T Consensus       389 ENIGARRLhTvlErlL  404 (444)
T COG1220         389 ENIGARRLHTVLERLL  404 (444)
T ss_pred             cchhHHHHHHHHHHHH
Confidence            3345555555555443

>PRK08116 hypothetical protein; Validated

Probab=99.20  E-value=5.6e-11  Score=102.08  Aligned_cols=117  Identities=26%  Similarity=0.345  Sum_probs=73.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh----------hhHHHHHHHcccCCeeeeecchhhHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN----------NDLRHILIATENKSILVVEDIDCCIEL   97 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~----------~~l~~~~~~~~~~~vl~iDeid~l~~~   97 (266)
                      +.+++||||||||||+|+.++++.+   +.+++.++...+...          .....++.......+|+|||++.... 
T Consensus       114 ~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~~-  192 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNADLLILDDLGAERD-  192 (268)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCCCEEEEecccCCCC-
Confidence            4579999999999999999999986   678888876654321          11224445556678999999964211 


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-CC----CcccccCCCcc---eeE
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-ER----LDPALLRPGRM---DMH  169 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-~~----ld~al~r~~Rf---~~~  169 (266)
                                           ..+   ....+.+.++....   .+..+|.|||.+ +.    ++.++.+  |+   ...
T Consensus       193 ---------------------t~~---~~~~l~~iin~r~~---~~~~~IiTsN~~~~eL~~~~~~ri~s--Rl~e~~~~  243 (268)
T PRK08116        193 ---------------------TEW---AREKVYNIIDSRYR---KGLPTIVTTNLSLEELKNQYGKRIYD--RILEMCTP  243 (268)
T ss_pred             ---------------------CHH---HHHHHHHHHHHHHH---CCCCEEEECCCCHHHHHHHHhHHHHH--HHHHcCEE
Confidence                                 011   22334444443322   234577777754 33    4667777  63   345


Q ss_pred             EEcCCCCH
Q 024550          170 INMSHCTP  177 (266)
Q Consensus       170 i~~~~p~~  177 (266)
                      |.|+.|+.
T Consensus       244 v~~~g~d~  251 (268)
T PRK08116        244 VENEGKSY  251 (268)
T ss_pred             EEeeCcCh
Confidence            77777765

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

Probab=99.19  E-value=3e-10  Score=97.02  Aligned_cols=94  Identities=24%  Similarity=0.334  Sum_probs=66.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh--------hhHHHHHHHc------ccCCeeeeecchhhHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN--------NDLRHILIAT------ENKSILVVEDIDCCIEL   97 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~--------~~l~~~~~~~------~~~~vl~iDeid~l~~~   97 (266)
                      +++||.||.|||||.||+.+|+.+++||-..++..++..        .-+..++..+      .+.+|++|||||.+...
T Consensus        98 SNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIark  177 (408)
T COG1219          98 SNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARK  177 (408)
T ss_pred             ccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhcc
Confidence            469999999999999999999999999999999888631        2234444443      36899999999999753


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS  138 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~  138 (266)
                      ...-+..             .+...+-.+..||..++|...
T Consensus       178 SeN~SIT-------------RDVSGEGVQQALLKiiEGTva  205 (408)
T COG1219         178 SENPSIT-------------RDVSGEGVQQALLKIIEGTVA  205 (408)
T ss_pred             CCCCCcc-------------cccCchHHHHHHHHHHcCcee
Confidence            2221111             123345566677777775443

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.19  E-value=1.4e-09  Score=95.17  Aligned_cols=148  Identities=14%  Similarity=0.155  Sum_probs=99.8

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCC-----------------------cEEEEeCCc---ccChhhHHHHHHHcc-
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKF-----------------------DVYDLELSN---LLGNNDLRHILIATE-   81 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~-----------------------~~~~i~~~~---~~~~~~l~~~~~~~~-   81 (266)
                      ..++++||+||.|+||+++|+++|..+.+                       .++.+.+..   ..+-..++.+..... 
T Consensus        23 rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~vdqiR~l~~~~~~  102 (319)
T PRK06090         23 RIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGKSITVEQIRQCNRLAQE  102 (319)
T ss_pred             CcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCCcCCHHHHHHHHHHHhh
Confidence            34678999999999999999999987732                       344444321   122334444332221 


Q ss_pred             -----cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC
Q 024550           82 -----NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL  156 (266)
Q Consensus        82 -----~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l  156 (266)
                           ..-|++||++|.|-                           ....|.||+.++.    ++.+++||.+|+.++.+
T Consensus       103 ~~~~~~~kV~iI~~ae~m~---------------------------~~AaNaLLKtLEE----Pp~~t~fiL~t~~~~~l  151 (319)
T PRK06090        103 SSQLNGYRLFVIEPADAMN---------------------------ESASNALLKTLEE----PAPNCLFLLVTHNQKRL  151 (319)
T ss_pred             CcccCCceEEEecchhhhC---------------------------HHHHHHHHHHhcC----CCCCeEEEEEECChhhC
Confidence                 24699999999773                           3355667777764    45679999999999999


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .|++++  || ..+.|+.|+.++....+...    +..   .....+.-.+.+|....+.+
T Consensus       152 LpTI~S--RC-q~~~~~~~~~~~~~~~L~~~----~~~---~~~~~l~l~~G~p~~A~~~~  202 (319)
T PRK06090        152 LPTIVS--RC-QQWVVTPPSTAQAMQWLKGQ----GIT---VPAYALKLNMGSPLKTLAMM  202 (319)
T ss_pred             hHHHHh--cc-eeEeCCCCCHHHHHHHHHHc----CCc---hHHHHHHHcCCCHHHHHHHh
Confidence            999999  98 56999999999988777642    111   11233344446666555544

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.18  E-value=4e-10  Score=99.59  Aligned_cols=157  Identities=16%  Similarity=0.184  Sum_probs=94.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHH-HH-----------------HHcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRH-IL-----------------IATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~-~~-----------------~~~~~~~vl~iD   89 (266)
                      ...|||+|++||||+++|+++....   +.+|+.++|..+.. ..+.. +|                 .....+++||||
T Consensus        22 ~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~-~~l~~~lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ld  100 (329)
T TIGR02974        22 DRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSE-NLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLFLD  100 (329)
T ss_pred             CCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCCh-HHHHHHHhccccccccCcccccCCchhhCCCCEEEeC
Confidence            4569999999999999999998766   47999999998743 23322 22                 122357999999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-------cCCCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-------SSCGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-------~~~~~~~ivi~ttn~~-------~~  155 (266)
                      ||+.|..                           ..+..|+..++...       ......+.+|++||..       ..
T Consensus       101 ei~~L~~---------------------------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~~~~~~g~  153 (329)
T TIGR02974       101 ELATASL---------------------------LVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGR  153 (329)
T ss_pred             ChHhCCH---------------------------HHHHHHHHHHHcCcEEecCCCceeccceEEEEechhhHHHHhhcCc
Confidence            9998853                           23344555554221       0112346778888743       34


Q ss_pred             CcccccCCCcce-eEEEcCCCC--HHHHHHHHHHhhCCC----C----CCcHHHHHHHhhcCC--CCHHHHHHHH
Q 024550          156 LDPALLRPGRMD-MHINMSHCT--PSGFKMLASNYLGIA----E----HPLFVEIEKLIATAK--VTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~-~~i~~~~p~--~~~~~~i~~~~~~~~----~----~~~~~~~~~l~~~~~--~s~~~i~~~l  217 (266)
                      +.+.|..  ||. ..|.+|...  .++...|+.+|+...    +    ..+..+.-..+..+.  .+..++.+++
T Consensus       154 fr~dL~~--rl~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvrEL~n~i  226 (329)
T TIGR02974       154 FRADLLD--RLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLEYHWPGNVRELKNVV  226 (329)
T ss_pred             hHHHHHH--HhcchhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHhCCCCchHHHHHHHH
Confidence            5566777  774 345555444  244456666655321    1    234445444444444  5566666655

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

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

Probab=99.15  E-value=1.6e-10  Score=102.20  Aligned_cols=65  Identities=22%  Similarity=0.393  Sum_probs=53.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh--------hhHHHHHHHc------ccCCeeeeecchhhHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN--------NDLRHILIAT------ENKSILVVEDIDCCIE   96 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~--------~~l~~~~~~~------~~~~vl~iDeid~l~~   96 (266)
                      .+|||.||.|+|||.|++.||+.+++||..++|..++..        .-+..++..+      .+.+|+||||+|.+..
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~  305 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITK  305 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcc
Confidence            469999999999999999999999999999999998732        2244444443      3689999999999964

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=99.14  E-value=9.7e-10  Score=93.02  Aligned_cols=88  Identities=16%  Similarity=0.228  Sum_probs=61.8

Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC----------
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH----------  152 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~----------  152 (266)
                      |+||||||++.|.                           -..+..|...++.-.     ..++|++||+          
T Consensus       297 PGVLFIDEVhMLD---------------------------iEcFTyL~kalES~i-----aPivifAsNrG~~~irGt~d  344 (456)
T KOG1942|consen  297 PGVLFIDEVHMLD---------------------------IECFTYLHKALESPI-----APIVIFASNRGMCTIRGTED  344 (456)
T ss_pred             CcceEeeehhhhh---------------------------hHHHHHHHHHhcCCC-----CceEEEecCCcceeecCCcC
Confidence            6899999999773                           123333445555432     2456666664          


Q ss_pred             ---CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc
Q 024550          153 ---KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT  205 (266)
Q Consensus       153 ---~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~  205 (266)
                         |..+++.|+.  |+ +.|..-.++.++.++|+++....++.+..++.-.++..
T Consensus       345 ~~sPhGip~dllD--Rl-~Iirt~~y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~  397 (456)
T KOG1942|consen  345 ILSPHGIPPDLLD--RL-LIIRTLPYDEEEIRQIIKIRAQVEGLQVEEEALDLLAE  397 (456)
T ss_pred             CCCCCCCCHHHhh--he-eEEeeccCCHHHHHHHHHHHHhhhcceecHHHHHHHHh
Confidence               5678899999  98 66888888888899999999888888877665544443

>smart00350 MCM minichromosome maintenance proteins

Probab=99.13  E-value=1.2e-10  Score=108.63  Aligned_cols=128  Identities=16%  Similarity=0.229  Sum_probs=83.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE----eCCcccChh---------hHHHHHHHcccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL----ELSNLLGNN---------DLRHILIATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i----~~~~~~~~~---------~l~~~~~~~~~~~vl~iDeid~l~~~~~   99 (266)
                      ++||+|+||||||++++++++.+....+..    ++..+....         .+.........+++++|||++.+..   
T Consensus       238 ~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~~---  314 (509)
T smart00350      238 NILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTAAVTRDPETREFTLEGGALVLADNGVCCIDEFDKMDD---  314 (509)
T ss_pred             eEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcCCccccceEccCcceEEecCccEEecCCCEEEEechhhCCH---
Confidence            599999999999999999999876543332    222221100         0000011123578999999998743   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhcc---------ccCCCCceEEEEecCCCC-------------CCc
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL---------WSSCGDERIIIFTTNHKE-------------RLD  157 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~~~~ivi~ttn~~~-------------~ld  157 (266)
                                              .....|+..|+.-         ....+.+..+|+|+|+..             .|+
T Consensus       315 ------------------------~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n~~l~  370 (509)
T smart00350      315 ------------------------SDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEENIDLP  370 (509)
T ss_pred             ------------------------HHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhccCCC
Confidence                                    2233444444321         111224578999999752             589


Q ss_pred             ccccCCCcceeE-EEcCCCCHHHHHHHHHHhhC
Q 024550          158 PALLRPGRMDMH-INMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       158 ~al~r~~Rf~~~-i~~~~p~~~~~~~i~~~~~~  189 (266)
                      +++++  ||++. +....|+.+...+|..+.+.
T Consensus       371 ~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~~  401 (509)
T smart00350      371 APILS--RFDLLFVVLDEVDEERDRELAKHVVD  401 (509)
T ss_pred             hHHhC--ceeeEEEecCCCChHHHHHHHHHHHH
Confidence            99999  99875 55588999998898887653

>PRK08181 transposase; Validated

Probab=99.12  E-value=1.9e-10  Score=98.47  Aligned_cols=65  Identities=28%  Similarity=0.472  Sum_probs=49.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-------hhhHHHHHHHcccCCeeeeecchhhH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-------NNDLRHILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-------~~~l~~~~~~~~~~~vl~iDeid~l~   95 (266)
                      ..+++|+||||||||+|+.+++..+   |..++.++...+..       ...+...+.......+|+|||++.+.
T Consensus       106 ~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~~  180 (269)
T PRK08181        106 GANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYVT  180 (269)
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEecccccc
Confidence            4679999999999999999999765   66777777655442       12344556666778999999998764

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.11  E-value=4.8e-10  Score=107.19  Aligned_cols=128  Identities=23%  Similarity=0.292  Sum_probs=86.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-----------------------------------CCcEEEEeCCcc----cChhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-----------------------------------KFDVYDLELSNL----LGNND   72 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-----------------------------------~~~~~~i~~~~~----~~~~~   72 (266)
                      .++||+||||||||+++++++..+                                   ..+|+.+++...    .+.-.
T Consensus        26 g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d  105 (633)
T TIGR02442        26 GGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPEEWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLD  105 (633)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCccccChhhhhcccccccCCCCeeeCCCCCcHHHcCCccc
Confidence            469999999999999999999987                                   246666655432    12222


Q ss_pred             HHHHHHH-----------cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc-----
Q 024550           73 LRHILIA-----------TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL-----  136 (266)
Q Consensus        73 l~~~~~~-----------~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----  136 (266)
                      +...+..           ...++||||||++.+..                           .+++.|++.|+.-     
T Consensus       106 ~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~~---------------------------~~q~~Ll~~le~g~~~v~  158 (633)
T TIGR02442       106 IERALREGEKAFQPGLLAEAHRGILYIDEVNLLDD---------------------------HLVDVLLDAAAMGVNRVE  158 (633)
T ss_pred             HHHHhhcCCeeecCcceeecCCCeEEeChhhhCCH---------------------------HHHHHHHHHHhcCCEEEE
Confidence            3322211           12468999999998743                           3455566666421     


Q ss_pred             ----ccCCCCceEEEEecCCC-CCCcccccCCCcceeEEEcCCCC-HHHHHHHHHHhh
Q 024550          137 ----WSSCGDERIIIFTTNHK-ERLDPALLRPGRMDMHINMSHCT-PSGFKMLASNYL  188 (266)
Q Consensus       137 ----~~~~~~~~ivi~ttn~~-~~ld~al~r~~Rf~~~i~~~~p~-~~~~~~i~~~~~  188 (266)
                          ......++++|+|+|.. ..+.++|+.  ||++.|.++.+. .+++.+++.+.+
T Consensus       159 r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~~l~i~v~~~~~~~~~~~il~~~~  214 (633)
T TIGR02442       159 REGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RFGLCVDVAAPRDPEERVEIIRRRL  214 (633)
T ss_pred             ECCceeeecCCeEEEEecCCCCCCCCHHHHh--hcceEEEccCCCchHHHHHHHHHHH
Confidence                11112457889999864 468899999  999999998876 466777776544

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.

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.11  E-value=2.5e-10  Score=108.06  Aligned_cols=128  Identities=21%  Similarity=0.223  Sum_probs=87.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCC--cEEEEeCCcc----cChhhHHHHHH-----------HcccCCeeeeecchhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKF--DVYDLELSNL----LGNNDLRHILI-----------ATENKSILVVEDIDCC   94 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~--~~~~i~~~~~----~~~~~l~~~~~-----------~~~~~~vl~iDeid~l   94 (266)
                      .++||.|+||||||+++++++..+..  +|+.+++...    .+.-.+...+.           ....+++||+||++.+
T Consensus        17 g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~lDEi~rl   96 (589)
T TIGR02031        17 GGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYVDMANLL   96 (589)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcEeccchhhC
Confidence            36999999999999999999998754  5887775321    11111111111           1234689999999987


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc---------ccCCCCceEEEEecCCCC---CCcccccC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL---------WSSCGDERIIIFTTNHKE---RLDPALLR  162 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~~~~ivi~ttn~~~---~ld~al~r  162 (266)
                      ..                           .+++.|++.|+.-         ....+..+.+|+|+|..+   .++++|+.
T Consensus        97 ~~---------------------------~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld  149 (589)
T TIGR02031        97 DD---------------------------GLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD  149 (589)
T ss_pred             CH---------------------------HHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH
Confidence            53                           3455566666422         111124578889999765   78999999


Q ss_pred             CCcceeEEEcCC-CCHHHHHHHHHHhh
Q 024550          163 PGRMDMHINMSH-CTPSGFKMLASNYL  188 (266)
Q Consensus       163 ~~Rf~~~i~~~~-p~~~~~~~i~~~~~  188 (266)
                        ||.++|.+.. |+..+|.+|+++++
T Consensus       150 --Rf~l~v~~~~~~~~~er~eil~~~~  174 (589)
T TIGR02031       150 --RLALHVSLEDVASQDLRVEIVRRER  174 (589)
T ss_pred             --hccCeeecCCCCCHHHHHHHHHHHH
Confidence              9999888865 46666889888876

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.

>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=99.10  E-value=4.7e-11  Score=97.34  Aligned_cols=25  Identities=44%  Similarity=0.749  Sum_probs=20.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++|++||||||||++|+.+..-+
T Consensus        22 ~h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen   22 GHHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             C--EEEES-CCCTHHHHHHHHHHCS
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHhC
Confidence            4689999999999999999999866

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.

>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=99.10  E-value=1.4e-10  Score=99.78  Aligned_cols=134  Identities=25%  Similarity=0.351  Sum_probs=82.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc---EEEEeCCcccChhhHHHHHHHc-------------ccCCeeeeecchhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD---VYDLELSNLLGNNDLRHILIAT-------------ENKSILVVEDIDCC   94 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~---~~~i~~~~~~~~~~l~~~~~~~-------------~~~~vl~iDeid~l   94 (266)
                      .+.+||+||+|||||++++.+-..+...   ...++++..++...++..+...             .+..|+||||++..
T Consensus        33 ~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDDlN~p  112 (272)
T PF12775_consen   33 GRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDDLNMP  112 (272)
T ss_dssp             TEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEETTT-S
T ss_pred             CCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecccCCC
Confidence            5679999999999999999877666432   3456676665555555544331             13479999999965


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhh---ccccCCC------CceEEEEecCCCC---CCcccccC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID---GLWSSCG------DERIIIFTTNHKE---RLDPALLR  162 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~---~~~~~~~------~~~ivi~ttn~~~---~ld~al~r  162 (266)
                      ..                      +........++|..+-   ++++...      ..+.+|+++|++.   .++++|+|
T Consensus       113 ~~----------------------d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r  170 (272)
T PF12775_consen  113 QP----------------------DKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR  170 (272)
T ss_dssp             -------------------------TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT
T ss_pred             CC----------------------CCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh
Confidence            32                      1111122234444332   4433221      2467889988653   47899999


Q ss_pred             CCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          163 PGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                        +| ..+.++.|+.++...|+..++.
T Consensus       171 --~f-~i~~~~~p~~~sl~~If~~il~  194 (272)
T PF12775_consen  171 --HF-NILNIPYPSDESLNTIFSSILQ  194 (272)
T ss_dssp             --TE-EEEE----TCCHHHHHHHHHHH
T ss_pred             --he-EEEEecCCChHHHHHHHHHHHh
Confidence              88 5699999999998888766664

>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=99.09  E-value=2.9e-10  Score=90.91  Aligned_cols=65  Identities=22%  Similarity=0.223  Sum_probs=48.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHH-HHHH-----------------HcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLR-HILI-----------------ATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~-~~~~-----------------~~~~~~vl~iD   89 (266)
                      +..|||+|++||||+.+|+++.+..   +.||+.++|+.+.. ..+. .+|.                 ....+++||||
T Consensus        22 ~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~-~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld  100 (168)
T PF00158_consen   22 DLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPE-ELLESELFGHEKGAFTGARSDKKGLLEQANGGTLFLD  100 (168)
T ss_dssp             TS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-H-HHHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEE
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhc-chhhhhhhccccccccccccccCCceeeccceEEeec
Confidence            4679999999999999999999976   47999999998843 3333 3332                 12357999999


Q ss_pred             cchhhHH
Q 024550           90 DIDCCIE   96 (266)
Q Consensus        90 eid~l~~   96 (266)
                      ||+.|..
T Consensus       101 ~I~~L~~  107 (168)
T PF00158_consen  101 EIEDLPP  107 (168)
T ss_dssp             TGGGS-H
T ss_pred             chhhhHH
Confidence            9999863

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 ....

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.09  E-value=1e-09  Score=96.97  Aligned_cols=157  Identities=14%  Similarity=0.155  Sum_probs=93.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHH------------------HHcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHIL------------------IATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~------------------~~~~~~~vl~iD   89 (266)
                      +..|||+|++||||+++|+++....   +.+|+.++|..+.. ..+...+                  .....+++||||
T Consensus        29 ~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~-~~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~  107 (326)
T PRK11608         29 DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-NLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLD  107 (326)
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCH-HHHHHHHccccccccCCcccccCCchhccCCCeEEeC
Confidence            4569999999999999999998765   47999999998743 3333222                  123357899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-cC------CCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-SS------CGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~------~~~~~ivi~ttn~~-------~~  155 (266)
                      |++.|..                           ..+..|++.++... ..      ....+.+|+||+..       ..
T Consensus       108 ~i~~L~~---------------------------~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~l~~l~~~g~  160 (326)
T PRK11608        108 ELATAPM---------------------------LVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGK  160 (326)
T ss_pred             ChhhCCH---------------------------HHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCchhHHHHHHcCC
Confidence            9998853                           23344455554211 11      11246677777653       34


Q ss_pred             CcccccCCCcce-eEEEcCCCCH--HHHHHHHHHhhCCC----C----CCcHHHHHHHhhcCC--CCHHHHHHHH
Q 024550          156 LDPALLRPGRMD-MHINMSHCTP--SGFKMLASNYLGIA----E----HPLFVEIEKLIATAK--VTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~-~~i~~~~p~~--~~~~~i~~~~~~~~----~----~~~~~~~~~l~~~~~--~s~~~i~~~l  217 (266)
                      +.+.|..  ||. ..|.+|....  ++...|+.+|+...    +    ..+..+....+..+.  .+-.++.+++
T Consensus       161 f~~dL~~--~l~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL~~vl  233 (326)
T PRK11608        161 FRADLLD--RLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERARETLLNYRWPGNIRELKNVV  233 (326)
T ss_pred             chHHHHH--hcCCCEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHH
Confidence            5567777  774 4555554443  33445666655321    1    123444444444444  4556666655

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=99.08  E-value=1.1e-10  Score=94.14  Aligned_cols=65  Identities=31%  Similarity=0.546  Sum_probs=48.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCccc-------ChhhHHHHHHHcccCCeeeeecchhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLL-------GNNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~-------~~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      .+.+++|+||||||||++|.++++++   |.++..++..++.       ........+.......+|+|||+...
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~  120 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYE  120 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCccccccEeccccccee
Confidence            35689999999999999999999876   7777888776654       12334455666677899999999854

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.07  E-value=1.3e-09  Score=102.69  Aligned_cols=157  Identities=17%  Similarity=0.164  Sum_probs=94.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHH-H-----------------HcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHIL-I-----------------ATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~-~-----------------~~~~~~vl~iD   89 (266)
                      ...|||+|++||||+++|++++...   +.+|+.++|..+.. ..+...+ .                 ....+++||||
T Consensus       219 ~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ld  297 (534)
T TIGR01817       219 NSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSE-TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLD  297 (534)
T ss_pred             CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCCH-HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEe
Confidence            3469999999999999999999875   57999999998843 2332222 1                 12347899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-cCC------CCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-SSC------GDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~~------~~~~ivi~ttn~~-------~~  155 (266)
                      ||+.+..                           ..+..|+..++... ...      ...+.+|+||+..       ..
T Consensus       298 ei~~L~~---------------------------~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~l~~~~~~~~  350 (534)
T TIGR01817       298 EIGEISP---------------------------AFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGE  350 (534)
T ss_pred             chhhCCH---------------------------HHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCCHHHHHHcCC
Confidence            9998853                           23344555554321 110      1235677777643       23


Q ss_pred             CcccccCCCcce-eEEEcCCCC--HHHHHHHHHHhhCCC----C--CCcHHHHHHHhhcCC--CCHHHHHHHH
Q 024550          156 LDPALLRPGRMD-MHINMSHCT--PSGFKMLASNYLGIA----E--HPLFVEIEKLIATAK--VTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~-~~i~~~~p~--~~~~~~i~~~~~~~~----~--~~~~~~~~~l~~~~~--~s~~~i~~~l  217 (266)
                      +.+.|..  |+. ..|.+|...  .++...|+.+|+...    +  ..+..+.-..+..+.  .+..++.+++
T Consensus       351 f~~~L~~--rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~~~WPGNvrEL~~v~  421 (534)
T TIGR01817       351 FRADLYY--RINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCKWPGNVRELENCL  421 (534)
T ss_pred             CCHHHHH--HhcCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhCCCCChHHHHHHHH
Confidence            4445555  554 456666555  355566666666432    1  233444444444443  5566666655

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.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=99.07  E-value=1.3e-09  Score=96.07  Aligned_cols=124  Identities=12%  Similarity=0.211  Sum_probs=87.6

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCC-------------------------cEEEEeCCc----------ccChhhH
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKF-------------------------DVYDLELSN----------LLGNNDL   73 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~-------------------------~~~~i~~~~----------~~~~~~l   73 (266)
                      ..++++||+||+|+|||++|+.+|+.+.+                         .++.+.+..          ..+-..+
T Consensus        19 r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~i   98 (325)
T PRK08699         19 RRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDAV   98 (325)
T ss_pred             CcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHHH
Confidence            45778999999999999999999998732                         344555421          1123345


Q ss_pred             HHHHHHcc------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEE
Q 024550           74 RHILIATE------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIII  147 (266)
Q Consensus        74 ~~~~~~~~------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi  147 (266)
                      +++.....      ...|+++|+++.+.                           ....+.++..++...    .+..+|
T Consensus        99 R~l~~~~~~~p~~~~~kV~iiEp~~~Ld---------------------------~~a~naLLk~LEep~----~~~~~I  147 (325)
T PRK08699         99 REIIDNVYLTSVRGGLRVILIHPAESMN---------------------------LQAANSLLKVLEEPP----PQVVFL  147 (325)
T ss_pred             HHHHHHHhhCcccCCceEEEEechhhCC---------------------------HHHHHHHHHHHHhCc----CCCEEE
Confidence            55544332      34688899999774                           234455667666541    346677


Q ss_pred             EecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHH
Q 024550          148 FTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASN  186 (266)
Q Consensus       148 ~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~  186 (266)
                      .+|+.++.+.+.+.+  || ..+.|+.|+.++....+..
T Consensus       148 lvth~~~~ll~ti~S--Rc-~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        148 LVSHAADKVLPTIKS--RC-RKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             EEeCChHhChHHHHH--Hh-hhhcCCCCCHHHHHHHHHh
Confidence            799999999999999  88 6699999999987776653

>PRK12377 putative replication protein; Provisional

Probab=99.06  E-value=2.8e-10  Score=96.30  Aligned_cols=64  Identities=25%  Similarity=0.399  Sum_probs=48.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC--------hhhHHHHHHHcccCCeeeeecchhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG--------NNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~--------~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      ..+++|+||||||||+|+.++++.+   |.+++.++..++..        .......+.......+|+|||++..
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~  175 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVMSRLHESYDNGQSGEKFLQELCKVDLLVLDEIGIQ  175 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            3579999999999999999999988   56677777665542        1123345666678899999999754

>PRK06526 transposase; Provisional

Probab=99.05  E-value=1.4e-10  Score=98.69  Aligned_cols=65  Identities=22%  Similarity=0.361  Sum_probs=46.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-------hhhHHHHHHHcccCCeeeeecchhhH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-------NNDLRHILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-------~~~l~~~~~~~~~~~vl~iDeid~l~   95 (266)
                      +.+++|+||||||||+++.+++.++   |..++.+++..+..       ...+...+.......+|+|||++.+.
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~  172 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIP  172 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCC
Confidence            4579999999999999999998876   55555554443321       11233445555667899999999763

>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=99.04  E-value=3.1e-09  Score=89.13  Aligned_cols=140  Identities=19%  Similarity=0.123  Sum_probs=82.4

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcc-cCCeeeeecchhhHHHhHHHhhhhh
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATE-NKSILVVEDIDCCIELQDRLSRARA  106 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~-~~~vl~iDeid~l~~~~~~~~~~~~  106 (266)
                      +....+..++||+|||||.+++.+|..+|.+++.++|+...+...+.+++.... .++.+++||++.+-...=  +.-  
T Consensus        29 l~~~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~~~~l~ril~G~~~~GaW~cfdefnrl~~~vL--S~i--  104 (231)
T PF12774_consen   29 LSLNLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMDYQSLSRILKGLAQSGAWLCFDEFNRLSEEVL--SVI--  104 (231)
T ss_dssp             HCTTTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-HHHHHHHHHHHHHHT-EEEEETCCCSSHHHH--HHH--
T ss_pred             hccCCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccccHHHHHHHHHHHhhcCchhhhhhhhhhhHHHH--HHH--
Confidence            344567789999999999999999999999999999999999999999997765 599999999998843110  000  


Q ss_pred             cCCccccccccccccchhhhhhhhhhhhcc---------ccCCCCceEEEEecCC----CCCCcccccCCCcceeEEEcC
Q 024550          107 ANPDFLIAGYEQQKQYHITLSGLLNFIDGL---------WSSCGDERIIIFTTNH----KERLDPALLRPGRMDMHINMS  173 (266)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~~~~ivi~ttn~----~~~ld~al~r~~Rf~~~i~~~  173 (266)
                                      ...+..+.+.+..-         .-......-++.|.|+    ...||+.|..  -| +.+.+.
T Consensus       105 ----------------~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~--lF-Rpvam~  165 (231)
T PF12774_consen  105 ----------------SQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKA--LF-RPVAMM  165 (231)
T ss_dssp             ----------------HHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCT--TE-EEEE--
T ss_pred             ----------------HHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHH--Hh-heeEEe
Confidence                            00011111111100         0000112224445563    3578888886  55 679999


Q ss_pred             CCCHHHHHHHHHHhhCC
Q 024550          174 HCTPSGFKMLASNYLGI  190 (266)
Q Consensus       174 ~p~~~~~~~i~~~~~~~  190 (266)
                      .||.....+++-...+.
T Consensus       166 ~PD~~~I~ei~L~s~GF  182 (231)
T PF12774_consen  166 VPDLSLIAEILLLSQGF  182 (231)
T ss_dssp             S--HHHHHHHHHHCCCT
T ss_pred             CCCHHHHHHHHHHHcCc
Confidence            99988877765544443

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.02  E-value=6.6e-09  Score=91.66  Aligned_cols=69  Identities=20%  Similarity=0.145  Sum_probs=47.4

Q ss_pred             ccchhhhhhhhhhhhccccCC-------CCceEEEEecCCC-------CCCcccccCCCcceeEEEcCCCCH-HHHHHHH
Q 024550          120 KQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHK-------ERLDPALLRPGRMDMHINMSHCTP-SGFKMLA  184 (266)
Q Consensus       120 ~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~-------~~ld~al~r~~Rf~~~i~~~~p~~-~~~~~i~  184 (266)
                      ......++.||+.++...-..       .-..+||++||..       .....+|++  ||. .|.+|.|.. .+-.+|.
T Consensus       247 K~~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~d--R~~-~i~vpY~l~~~~E~~Iy  323 (361)
T smart00763      247 KADIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLD--RII-KVKVPYCLRVSEEAQIY  323 (361)
T ss_pred             cCCHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhhh--ceE-EEeCCCcCCHHHHHHHH
Confidence            445567777887776322211       1235789999976       355899999  996 799998876 4556788


Q ss_pred             HHhhCCC
Q 024550          185 SNYLGIA  191 (266)
Q Consensus       185 ~~~~~~~  191 (266)
                      ++.+...
T Consensus       324 ~k~~~~s  330 (361)
T smart00763      324 EKLLRNS  330 (361)
T ss_pred             HHHhccC
Confidence            8777654

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=99.01  E-value=3.8e-10  Score=100.52  Aligned_cols=96  Identities=16%  Similarity=0.293  Sum_probs=65.8

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCC-cEEEEeCCcccC------------hhhHHHHHHHcccC-Ceeeeecchh
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKF-DVYDLELSNLLG------------NNDLRHILIATENK-SILVVEDIDC   93 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~-~~~~i~~~~~~~------------~~~l~~~~~~~~~~-~vl~iDeid~   93 (266)
                      .++++|++||||+|+|||+|+-.+...+.. .-..+....++.            ...+..+.....+. .+|++||++.
T Consensus        59 ~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~~~~~lLcfDEF~V  138 (362)
T PF03969_consen   59 PPPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELAKESRLLCFDEFQV  138 (362)
T ss_pred             CCCCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHHhcCCEEEEeeeec
Confidence            457899999999999999999999998855 333444444432            12233333333344 4999999985


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK  153 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~  153 (266)
                      -                        +.....++..|+..+-.      .++++|+|+|.+
T Consensus       139 ~------------------------DiaDAmil~rLf~~l~~------~gvvlVaTSN~~  168 (362)
T PF03969_consen  139 T------------------------DIADAMILKRLFEALFK------RGVVLVATSNRP  168 (362)
T ss_pred             c------------------------chhHHHHHHHHHHHHHH------CCCEEEecCCCC
Confidence            3                        23445677777777654      479999999964

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

>PRK06835 DNA replication protein DnaC; Validated

Probab=99.01  E-value=1.8e-09  Score=95.16  Aligned_cols=63  Identities=25%  Similarity=0.362  Sum_probs=47.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh---------hhHHHHHHHcccCCeeeeecchhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN---------NDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~---------~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      .+++||||+|||||+|+.++|+++   |..++.++...+...         ......+.......+|+|||+...
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e  258 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTE  258 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCC
Confidence            689999999999999999999987   677777777665321         111122445566789999999865

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

Probab=99.00  E-value=1.6e-09  Score=98.03  Aligned_cols=135  Identities=24%  Similarity=0.384  Sum_probs=89.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE-eCCcccC------hhhHHHHHHHcc--cCCeeeeecchhhHHHhHHHh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL-ELSNLLG------NNDLRHILIATE--NKSILVVEDIDCCIELQDRLS  102 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i-~~~~~~~------~~~l~~~~~~~~--~~~vl~iDeid~l~~~~~~~~  102 (266)
                      .++||+||||+|||+||..+|...+.||+.+ ++.++.+      ...+...|..+.  .-+||++|+++.|..-..-  
T Consensus       539 vSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD~vpI--  616 (744)
T KOG0741|consen  539 VSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYVPI--  616 (744)
T ss_pred             eEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhccccc--
Confidence            4599999999999999999999999999975 4444432      244667777663  4689999999998641111  


Q ss_pred             hhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc-ccccCCCcceeEEEcCCCCH-HHH
Q 024550          103 RARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD-PALLRPGRMDMHINMSHCTP-SGF  180 (266)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld-~al~r~~Rf~~~i~~~~p~~-~~~  180 (266)
                           .|          .-.+.++..|+-.+... .+.+.+.+|++||...+-|. -.++.  +|+..|++|..+. ++.
T Consensus       617 -----GP----------RfSN~vlQaL~VllK~~-ppkg~kLli~~TTS~~~vL~~m~i~~--~F~~~i~Vpnl~~~~~~  678 (744)
T KOG0741|consen  617 -----GP----------RFSNLVLQALLVLLKKQ-PPKGRKLLIFGTTSRREVLQEMGILD--CFSSTIHVPNLTTGEQL  678 (744)
T ss_pred             -----Cc----------hhhHHHHHHHHHHhccC-CCCCceEEEEecccHHHHHHHcCHHH--hhhheeecCccCchHHH
Confidence                 11          12233444444444433 23334556667776654442 34566  8999999999887 566


Q ss_pred             HHHHHH
Q 024550          181 KMLASN  186 (266)
Q Consensus       181 ~~i~~~  186 (266)
                      .+++..
T Consensus       679 ~~vl~~  684 (744)
T KOG0741|consen  679 LEVLEE  684 (744)
T ss_pred             HHHHHH
Confidence            666654

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.00  E-value=4.8e-09  Score=99.41  Aligned_cols=133  Identities=22%  Similarity=0.285  Sum_probs=76.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEE-EeCC---c--------------c----cChhhHHHHHHHc-------
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYD-LELS---N--------------L----LGNNDLRHILIAT-------   80 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~-i~~~---~--------------~----~~~~~l~~~~~~~-------   80 (266)
                      +.+.++|+||||||||++++.+|+.++..+++ .+..   .              +    .....+..++..+       
T Consensus       109 ~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~  188 (637)
T TIGR00602       109 PKRILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQML  188 (637)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHhhhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhccc
Confidence            34559999999999999999999999765433 1111   0              0    0112233333322       


Q ss_pred             -----ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhh-hhhccccCCCCceEEEEecCCCC
Q 024550           81 -----ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLN-FIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        81 -----~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~-~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                           ....||+|||++.++..                        ....+..++. ....   . +...+|+.+|..+.
T Consensus       189 g~~~~~~~~IILIDEiPn~~~r------------------------~~~~lq~lLr~~~~e---~-~~~pLI~I~TE~~~  240 (637)
T TIGR00602       189 GDDLMTDKKIILVEDLPNQFYR------------------------DTRALHEILRWKYVS---I-GRCPLVFIITESLE  240 (637)
T ss_pred             ccccCCceeEEEeecchhhchh------------------------hHHHHHHHHHHHhhc---C-CCceEEEEecCCcc
Confidence                 24579999999987531                        1112333433 1111   1 11223333332221


Q ss_pred             --------------CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCC
Q 024550          155 --------------RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA  191 (266)
Q Consensus       155 --------------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~  191 (266)
                                    .|.++++...|+ ..|.|+..+.....+.+...+..+
T Consensus       241 ~~~~~~~~~f~~~~lL~~eLls~~rv-~~I~FnPia~t~l~K~L~rIl~~E  290 (637)
T TIGR00602       241 GDNNQRRLLFPAETIMNKEILEEPRV-SNISFNPIAPTIMKKFLNRIVTIE  290 (637)
T ss_pred             ccccccccccchhcccCHhHhcccce-eEEEeCCCCHHHHHHHHHHHHHhh
Confidence                          123677753344 469999999999888888888654

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK08939 primosomal protein DnaI; Reviewed

Probab=99.00  E-value=1.9e-09  Score=94.15  Aligned_cols=65  Identities=29%  Similarity=0.459  Sum_probs=50.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-------hhhHHHHHHHcccCCeeeeecchhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-------NNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-------~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      ..+|++||||+|||||+|+.++|+++   |.++..+....+..       ...+...+.......+|+|||+...
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e  229 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIRELKNSISDGSVKEKIDAVKEAPVLMLDDIGAE  229 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHhcCCCEEEEecCCCc
Confidence            35789999999999999999999998   67777777665431       1234556666778999999999854

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.99  E-value=3.4e-08  Score=84.75  Aligned_cols=57  Identities=9%  Similarity=-0.013  Sum_probs=40.7

Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCC----CCc-HHHHHHHhhcCCCCHHHHHHHH
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE----HPL-FVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~----~~~-~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+.+  |+...++++..+.++...++...+...+    ..+ .+.+..+....+..|..|..++
T Consensus       178 ~l~~--r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~  239 (269)
T TIGR03015       178 QLRQ--RIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILC  239 (269)
T ss_pred             HHHh--heeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHH
Confidence            3556  8888899999999999999888775432    223 3455666666777777776655

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.

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.98  E-value=4.8e-09  Score=97.93  Aligned_cols=65  Identities=15%  Similarity=0.160  Sum_probs=49.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH-----------cCCcEEEEeCCcccChhhHHHH-H------------------HHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY-----------LKFDVYDLELSNLLGNNDLRHI-L------------------IAT   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~-----------~~~~~~~i~~~~~~~~~~l~~~-~------------------~~~   80 (266)
                      ...|||+|++||||+++|+++...           .+.||+.++|..+.. ..+... |                  ...
T Consensus       242 ~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e-~lleseLFG~~~gaftga~~~~~~Gl~e~  320 (538)
T PRK15424        242 SAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAE-SLLEAELFGYEEGAFTGSRRGGRAGLFEI  320 (538)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCCh-hhHHHHhcCCccccccCccccccCCchhc
Confidence            346999999999999999999987           367999999998853 222222 1                  112


Q ss_pred             ccCCeeeeecchhhHH
Q 024550           81 ENKSILVVEDIDCCIE   96 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~   96 (266)
                      ..++.||||||+.|..
T Consensus       321 A~gGTLfLdeI~~Lp~  336 (538)
T PRK15424        321 AHGGTLFLDEIGEMPL  336 (538)
T ss_pred             cCCCEEEEcChHhCCH
Confidence            3578999999998853

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.98  E-value=7.5e-10  Score=93.51  Aligned_cols=63  Identities=27%  Similarity=0.492  Sum_probs=48.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC---------hhhHHHHHHHcccCCeeeeecchhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG---------NNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~---------~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      .+++|+||||||||+++.++|.++   +.+++.++..++..         ......++.......+|+|||++..
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~~~dlLvIDDig~~  174 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEIGVQ  174 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhccCCEEEEeCCCCC
Confidence            479999999999999999999988   67777777665542         1122345555667889999999865

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.97  E-value=6e-09  Score=100.21  Aligned_cols=158  Identities=15%  Similarity=0.061  Sum_probs=93.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHH--------------cccCCeeeeecchh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIA--------------TENKSILVVEDIDC   93 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~--------------~~~~~vl~iDeid~   93 (266)
                      ...|||+|++||||+++|+++....   +.+|+.++|..+....--..+|..              ...+++||||||+.
T Consensus       348 ~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~~~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~  427 (638)
T PRK11388        348 SFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEY  427 (638)
T ss_pred             CCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCChHHHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhh
Confidence            3459999999999999999999876   479999999988542212233321              23578999999998


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-CCC------CceEEEEecCCC-------CCCccc
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-SCG------DERIIIFTTNHK-------ERLDPA  159 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~------~~~ivi~ttn~~-------~~ld~a  159 (266)
                      |..                           ..+..|+..++.-.. +.+      ..+.+|+||+..       ..+.+.
T Consensus       428 l~~---------------------------~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~l~~~~~~~~f~~d  480 (638)
T PRK11388        428 LSP---------------------------ELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQ  480 (638)
T ss_pred             CCH---------------------------HHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCCHHHHHhcCCChHH
Confidence            853                           233445555543211 111      145688888753       223333


Q ss_pred             ccCCCcceeEEEcCCCCHHHH----HHHHHHhhCCC------CCCcHHHHHHHhhcCC--CCHHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGF----KMLASNYLGIA------EHPLFVEIEKLIATAK--VTPADVAEQLM  218 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~----~~i~~~~~~~~------~~~~~~~~~~l~~~~~--~s~~~i~~~l~  218 (266)
                      |..  |+. .+.+..|.-.+|    ..|+.+|+...      ...+..+....+..+.  .+..++.+++.
T Consensus       481 L~~--~l~-~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvreL~~~l~  548 (638)
T PRK11388        481 LYY--ALH-AFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIE  548 (638)
T ss_pred             Hhh--hhc-eeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHcCCCCChHHHHHHHHH
Confidence            444  442 244555555444    45555555322      1224455545555444  56667776663

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

Probab=98.96  E-value=4.8e-09  Score=95.68  Aligned_cols=160  Identities=17%  Similarity=0.142  Sum_probs=98.5

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHH-HHH------------------HHcccCCe
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLR-HIL------------------IATENKSI   85 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~-~~~------------------~~~~~~~v   85 (266)
                      .+.+..||+.|.+||||..+|+++.+..   +.||+.++|+.+.. .-+. .+|                  ....+++.
T Consensus       265 A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe-~LlESELFGye~GAFTGA~~~GK~GlfE~A~gGT  343 (560)
T COG3829         265 AKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPE-TLLESELFGYEKGAFTGASKGGKPGLFELANGGT  343 (560)
T ss_pred             cCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCCH-HHHHHHHhCcCCccccccccCCCCcceeeccCCe
Confidence            3345679999999999999999999877   68999999999842 2222 122                  12235789


Q ss_pred             eeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc-------cccCCCCceEEEEecCCC-----
Q 024550           86 LVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG-------LWSSCGDERIIIFTTNHK-----  153 (266)
Q Consensus        86 l~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~-------~~~~~~~~~ivi~ttn~~-----  153 (266)
                      ||||||..|.                           ..++..||..|+.       ........+-||+|||..     
T Consensus       344 LFLDEIgemp---------------------------l~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~~~i  396 (560)
T COG3829         344 LFLDEIGEMP---------------------------LPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLEKMI  396 (560)
T ss_pred             EEehhhccCC---------------------------HHHHHHHHHHHhhceEEecCCCCceeeEEEEEeccCcCHHHHH
Confidence            9999999874                           3355667777752       111222357799999964     


Q ss_pred             --CCCcccccCCCcceeEEEcCCCCHHHHH----HHHHHhhCC----C---CCCcHHHHHHHhhcCC--CCHHHHHHHHH
Q 024550          154 --ERLDPALLRPGRMDMHINMSHCTPSGFK----MLASNYLGI----A---EHPLFVEIEKLIATAK--VTPADVAEQLM  218 (266)
Q Consensus       154 --~~ld~al~r~~Rf~~~i~~~~p~~~~~~----~i~~~~~~~----~---~~~~~~~~~~l~~~~~--~s~~~i~~~l~  218 (266)
                        ..+-..|.-  |+. ++.+..|.--+|.    .+...|+.+    .   -..+..+.-.++..+.  .+.+++.|++-
T Consensus       397 ~~G~FReDLYY--RLN-V~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviE  473 (560)
T COG3829         397 AEGTFREDLYY--RLN-VIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIE  473 (560)
T ss_pred             hcCcchhhhee--eec-eeeecCCCcccCcchHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHhCCCCchHHHHHHHHH
Confidence              222333444  553 3666666665543    344444432    1   1223445444444444  56777777763

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.95  E-value=1.9e-09  Score=91.80  Aligned_cols=65  Identities=29%  Similarity=0.507  Sum_probs=50.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh-------hhHHH-HHHHcccCCeeeeecchhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN-------NDLRH-ILIATENKSILVVEDIDCC   94 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~-------~~l~~-~~~~~~~~~vl~iDeid~l   94 (266)
                      .+.+++|+||||||||+|+-|+++++   |.+++.+...++...       ..... +......-.+|+|||+...
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~  179 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYE  179 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhcCchHHHHHHHhhcCCEEEEecccCc
Confidence            36689999999999999999999988   778888888777531       12222 2333677899999999975

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

Probab=98.93  E-value=9.4e-09  Score=93.42  Aligned_cols=157  Identities=17%  Similarity=0.150  Sum_probs=97.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHH-HHHH-----------------HcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLR-HILI-----------------ATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~-~~~~-----------------~~~~~~vl~iD   89 (266)
                      ...|||+|++||||..+||+|....   +.||+.++|..+.. ..+. .+|.                 ....++.||||
T Consensus       164 ~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~-~l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLD  242 (464)
T COG2204         164 DASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPE-NLLESELFGHEKGAFTGAITRRIGRFEQANGGTLFLD  242 (464)
T ss_pred             CCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCH-HHHHHHhhcccccCcCCcccccCcceeEcCCceEEee
Confidence            3459999999999999999999877   56999999999853 2232 2332                 12357999999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc-cccC------CCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG-LWSS------CGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~-~~~~------~~~~~ivi~ttn~~-------~~  155 (266)
                      ||..|..                           .++..||..+.. ...+      ....+-||++||..       ..
T Consensus       243 EI~~mpl---------------------------~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~dL~~~v~~G~  295 (464)
T COG2204         243 EIGEMPL---------------------------ELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDLEEEVAAGR  295 (464)
T ss_pred             ccccCCH---------------------------HHHHHHHHHHHcCeeEecCCCcccceeeEEEeecCcCHHHHHHcCC
Confidence            9998852                           355567776652 1111      12346799999863       23


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHH----HHHHHhhCCC-------CCCcHHHHHHHhhcCC--CCHHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFK----MLASNYLGIA-------EHPLFVEIEKLIATAK--VTPADVAEQLM  218 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~----~i~~~~~~~~-------~~~~~~~~~~l~~~~~--~s~~~i~~~l~  218 (266)
                      +-+.|..  |+. ++.+..|.--+|.    .|+.+|+...       ...+..+.-.....+.  .+.+++.|++.
T Consensus       296 FReDLyy--RLn-V~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNVREL~N~ve  368 (464)
T COG2204         296 FREDLYY--RLN-VVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLAYDWPGNVRELENVVE  368 (464)
T ss_pred             cHHHHHh--hhc-cceecCCcccccchhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCChHHHHHHHHHH
Confidence            3445555  663 4777777776554    5566665432       1223333333333333  45666666653

>TIGR00368 Mg chelatase-related protein

Probab=98.92  E-value=3.8e-09  Score=97.94  Aligned_cols=120  Identities=19%  Similarity=0.249  Sum_probs=73.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC----------------------------CcEEEEeCCcc----cC-hhhHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK----------------------------FDVYDLELSNL----LG-NNDLRHIL   77 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~----------------------------~~~~~i~~~~~----~~-~~~l~~~~   77 (266)
                      ...++|+||||||||++++.++..+.                            .||...+++..    .+ ....+.-.
T Consensus       211 g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~le~~~i~s~~g~~~~~~~~~~~Pf~~p~~s~s~~~~~ggg~~~~pG~  290 (499)
T TIGR00368       211 GHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSLVGKLIDRKQIKQRPFRSPHHSASKPALVGGGPIPLPGE  290 (499)
T ss_pred             CCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEEeccccccchhhhccccccccCCccccccccchhhhhCCccccchhh
Confidence            45699999999999999999987441                            11111111110    00 00011112


Q ss_pred             HHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc---------cCCCCceEEEE
Q 024550           78 IATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW---------SSCGDERIIIF  148 (266)
Q Consensus        78 ~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~~~~ivi~  148 (266)
                      .....+++|||||++.+..                           ..+..|++.|+...         ...+.++.+|+
T Consensus       291 i~lA~~GvLfLDEi~e~~~---------------------------~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIa  343 (499)
T TIGR00368       291 ISLAHNGVLFLDELPEFKR---------------------------SVLDALREPIEDGSISISRASAKIFYPARFQLVA  343 (499)
T ss_pred             hhccCCCeEecCChhhCCH---------------------------HHHHHHHHHHHcCcEEEEecCcceeccCCeEEEE
Confidence            2344679999999997742                           23344444443211         11124578899


Q ss_pred             ecCCC-----C------------------CCcccccCCCcceeEEEcCCCCHHH
Q 024550          149 TTNHK-----E------------------RLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       149 ttn~~-----~------------------~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                      ++|.-     .                  .+...|++  ||+.++.++.++.++
T Consensus       344 a~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllD--R~dl~~~~~~~~~~~  395 (499)
T TIGR00368       344 AMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLD--RIDLSVEVPLLPPEK  395 (499)
T ss_pred             ecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHh--hCCEEEEEcCCCHHH
Confidence            98852     1                  47788899  999999999887664

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.92  E-value=5.9e-08  Score=87.02  Aligned_cols=159  Identities=17%  Similarity=0.155  Sum_probs=106.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccChhh---------------------HHHHHHHc----
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGNND---------------------LRHILIAT----   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~~~---------------------l~~~~~~~----   80 (266)
                      +.++++.|-||||||....-+-..+     ....++++|..+.....                     ....|...    
T Consensus       175 ~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~  254 (529)
T KOG2227|consen  175 SGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQS  254 (529)
T ss_pred             CcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcc
Confidence            5579999999999998877665444     23457888887653211                     11222221    


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCc---
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLD---  157 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld---  157 (266)
                      +.+-++++||+|.|+.                            .-+..|..+..+....+..+++|+..|..+.-|   
T Consensus       255 k~~~llVlDEmD~L~t----------------------------r~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~L  306 (529)
T KOG2227|consen  255 KFMLLLVLDEMDHLIT----------------------------RSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFL  306 (529)
T ss_pred             cceEEEEechhhHHhh----------------------------cccceeeeehhcccCCcceeeeeeehhhhhHHHHHh
Confidence            2357899999999973                            112344455555555567899999999875533   


Q ss_pred             ccccC-CCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH--HHHHHHhhcCCCCHHHHHHHH
Q 024550          158 PALLR-PGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF--VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       158 ~al~r-~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~--~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.|.. .+.-...+.|++++.++..+|+...+........  ..+...+.+.....+|+..+|
T Consensus       307 prL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SGDlRkaL  369 (529)
T KOG2227|consen  307 PRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSGDLRKAL  369 (529)
T ss_pred             hhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCchhHHHHH
Confidence            33332 2334467999999999999999999877654332  356666777777777877766

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=98.91  E-value=4.7e-09  Score=86.26  Aligned_cols=130  Identities=17%  Similarity=0.242  Sum_probs=86.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC-----cEEEEeCCcccChhhHH---HHHHHcc------cCCeeeeecchhhHHHh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF-----DVYDLELSNLLGNNDLR---HILIATE------NKSILVVEDIDCCIELQ   98 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~-----~~~~i~~~~~~~~~~l~---~~~~~~~------~~~vl~iDeid~l~~~~   98 (266)
                      +++|.|||||||||-+.++|.++-.     .++++++++-.+..-++   ..|...+      +.-|+++||+|++..- 
T Consensus        50 ~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~g-  128 (333)
T KOG0991|consen   50 NLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTAG-  128 (333)
T ss_pred             ceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhhH-
Confidence            5999999999999999999998833     35677777665543333   3343322      3469999999988530 


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHH
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPS  178 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~  178 (266)
                                                .+..+-..|+-..    ...-|..++|..+.+-..+.+  ||.. +.|...+..
T Consensus       129 --------------------------AQQAlRRtMEiyS----~ttRFalaCN~s~KIiEPIQS--RCAi-LRysklsd~  175 (333)
T KOG0991|consen  129 --------------------------AQQALRRTMEIYS----NTTRFALACNQSEKIIEPIQS--RCAI-LRYSKLSDQ  175 (333)
T ss_pred             --------------------------HHHHHHHHHHHHc----ccchhhhhhcchhhhhhhHHh--hhHh-hhhcccCHH
Confidence                                      1112223333221    234577889998888888888  8854 777777777


Q ss_pred             HHHHHHHHhhCCCCCCcH
Q 024550          179 GFKMLASNYLGIAEHPLF  196 (266)
Q Consensus       179 ~~~~i~~~~~~~~~~~~~  196 (266)
                      +...-+......++....
T Consensus       176 qiL~Rl~~v~k~Ekv~yt  193 (333)
T KOG0991|consen  176 QILKRLLEVAKAEKVNYT  193 (333)
T ss_pred             HHHHHHHHHHHHhCCCCC
Confidence            766555555555555543

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.91  E-value=2.6e-09  Score=98.78  Aligned_cols=120  Identities=21%  Similarity=0.273  Sum_probs=74.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC----cEEEEeC------C-----ccc-----------------Ch-hhHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF----DVYDLEL------S-----NLL-----------------GN-NDLRHI   76 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~----~~~~i~~------~-----~~~-----------------~~-~~l~~~   76 (266)
                      ....++|+||||||||++++.++..+..    ..+++..      .     .+.                 +. ...+.-
T Consensus       209 ~G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG  288 (506)
T PRK09862        209 GGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPG  288 (506)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhhccccccCCcCCCCccCCCccchHHHHhCCCceehhh
Confidence            3456999999999999999999976521    1111110      0     000                 00 011112


Q ss_pred             HHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc---------cCCCCceEEE
Q 024550           77 LIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW---------SSCGDERIII  147 (266)
Q Consensus        77 ~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~~~~ivi  147 (266)
                      ......+++|||||++.+.                           ..++..|++.|+.-.         ...+.++.+|
T Consensus       289 ~l~~A~gGvLfLDEi~e~~---------------------------~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lI  341 (506)
T PRK09862        289 EISLAHNGVLFLDELPEFE---------------------------RRTLDALREPIESGQIHLSRTRAKITYPARFQLV  341 (506)
T ss_pred             HhhhccCCEEecCCchhCC---------------------------HHHHHHHHHHHHcCcEEEecCCcceeccCCEEEE
Confidence            2334567999999998763                           234455555553211         0113457899


Q ss_pred             EecCCCC---------------------CCcccccCCCcceeEEEcCCCCHH
Q 024550          148 FTTNHKE---------------------RLDPALLRPGRMDMHINMSHCTPS  178 (266)
Q Consensus       148 ~ttn~~~---------------------~ld~al~r~~Rf~~~i~~~~p~~~  178 (266)
                      +|+|...                     .++.++++  ||++++.++.|+.+
T Consensus       342 Aa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~  391 (506)
T PRK09862        342 AAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPG  391 (506)
T ss_pred             EeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHh--hccEEEEeCCCCHH
Confidence            9999642                     36778999  99999999999876

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=98.91  E-value=5.1e-08  Score=91.15  Aligned_cols=142  Identities=17%  Similarity=0.230  Sum_probs=93.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccChhhH----------------------HHHHH-
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGNNDL----------------------RHILI-   78 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~~~l----------------------~~~~~-   78 (266)
                      .++++.|-||||||.+++.+.+++          ...+++++.-.+.+...+                      ...|. 
T Consensus       423 ~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~  502 (767)
T KOG1514|consen  423 SCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFTV  502 (767)
T ss_pred             eeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhcc
Confidence            369999999999999999999876          366778887777653222                      12222 


Q ss_pred             --HcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC-
Q 024550           79 --ATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER-  155 (266)
Q Consensus        79 --~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~-  155 (266)
                        ....++||+|||+|.|..                        ..+.    ++..+..+....+.+.+||+..|..+. 
T Consensus       503 ~k~~~~~~VvLiDElD~Lvt------------------------r~Qd----VlYn~fdWpt~~~sKLvvi~IaNTmdlP  554 (767)
T KOG1514|consen  503 PKPKRSTTVVLIDELDILVT------------------------RSQD----VLYNIFDWPTLKNSKLVVIAIANTMDLP  554 (767)
T ss_pred             CCCCCCCEEEEeccHHHHhc------------------------ccHH----HHHHHhcCCcCCCCceEEEEecccccCH
Confidence              123479999999999974                        1122    223333333344567788887775543 


Q ss_pred             ---CcccccCCCcce-eEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhh
Q 024550          156 ---LDPALLRPGRMD-MHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA  204 (266)
Q Consensus       156 ---ld~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~  204 (266)
                         |....-+  |++ ..|.|..++..|..+|+...+... ..+...+.++++
T Consensus       555 Er~l~nrvsS--Rlg~tRi~F~pYth~qLq~Ii~~RL~~~-~~f~~~aielva  604 (767)
T KOG1514|consen  555 ERLLMNRVSS--RLGLTRICFQPYTHEQLQEIISARLKGL-DAFENKAIELVA  604 (767)
T ss_pred             HHHhccchhh--hccceeeecCCCCHHHHHHHHHHhhcch-hhcchhHHHHHH
Confidence               2233334  555 459999999999999999888766 344445545544

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=98.89  E-value=3.5e-08  Score=87.70  Aligned_cols=81  Identities=19%  Similarity=0.226  Sum_probs=59.6

Q ss_pred             cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc---------cccCCCCceEEEEecCC
Q 024550           82 NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG---------LWSSCGDERIIIFTTNH  152 (266)
Q Consensus        82 ~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~~~~~~~~~ivi~ttn~  152 (266)
                      +.+||++||+..|.                           ..+++.||+.+..         ..-+-+-++++|+|+|+
T Consensus       144 nRGIlYvDEvnlL~---------------------------d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNP  196 (423)
T COG1239         144 NRGILYVDEVNLLD---------------------------DHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNP  196 (423)
T ss_pred             cCCEEEEecccccc---------------------------HHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCc
Confidence            46999999999874                           3455666666653         22122346899999997


Q ss_pred             C-CCCcccccCCCcceeEEEcCCCCH-HHHHHHHHHhhCCC
Q 024550          153 K-ERLDPALLRPGRMDMHINMSHCTP-SGFKMLASNYLGIA  191 (266)
Q Consensus       153 ~-~~ld~al~r~~Rf~~~i~~~~p~~-~~~~~i~~~~~~~~  191 (266)
                      - ..|-+.|+.  ||+..|.+..|.. ++|.+|+.+-....
T Consensus       197 EeGeLrpqLlD--Rfg~~v~~~~~~~~~~rv~Ii~r~~~f~  235 (423)
T COG1239         197 EEGELRPQLLD--RFGLEVDTHYPLDLEERVEIIRRRLAFE  235 (423)
T ss_pred             cccccchhhHh--hhcceeeccCCCCHHHHHHHHHHHHHhh
Confidence            6 567889999  9999999977655 66788888777663

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=98.89  E-value=1.3e-08  Score=95.01  Aligned_cols=65  Identities=17%  Similarity=0.265  Sum_probs=49.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHH-HHH------------------HcccCCeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRH-ILI------------------ATENKSILVV   88 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~-~~~------------------~~~~~~vl~i   88 (266)
                      ...|||+|++||||+++|+++....   +.||+.++|..+.. ..+.. +|.                  ....++.|||
T Consensus       235 ~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~e-~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfL  313 (526)
T TIGR02329       235 DATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAE-SLLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFL  313 (526)
T ss_pred             CCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCCh-hHHHHHhcCCcccccccccccccccchhhcCCceEEe
Confidence            3469999999999999999999765   57999999998853 22222 221                  1235789999


Q ss_pred             ecchhhHH
Q 024550           89 EDIDCCIE   96 (266)
Q Consensus        89 Deid~l~~   96 (266)
                      |||+.|..
T Consensus       314 deI~~Lp~  321 (526)
T TIGR02329       314 DEIGEMPL  321 (526)
T ss_pred             cChHhCCH
Confidence            99998853

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.

>PF13173 AAA_14: AAA domain

Probab=98.89  E-value=1.1e-08  Score=77.99  Aligned_cols=63  Identities=19%  Similarity=0.358  Sum_probs=47.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC--CcEEEEeCCcccChhh----HHHHHHHc--ccCCeeeeecchhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK--FDVYDLELSNLLGNND----LRHILIAT--ENKSILVVEDIDCC   94 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~--~~~~~i~~~~~~~~~~----l~~~~~~~--~~~~vl~iDeid~l   94 (266)
                      +.++|+||+|||||++++.++..+.  .+++++++.+......    +...+...  ..+.+|||||++.+
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEiq~~   73 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLADPDLLEYFLELIKPGKKYIFIDEIQYL   73 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHhhhhhHHHHHHhhccCCcEEEEehhhhh
Confidence            4589999999999999999999886  7788888876543211    22333333  35799999999977

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.88  E-value=2.2e-09  Score=79.33  Aligned_cols=62  Identities=21%  Similarity=0.348  Sum_probs=43.7

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhH
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~   95 (266)
                      |+||||||+|||++++.|+..+...+-......+.....-...+.......++++||+....
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~~q~vvi~DD~~~~~   62 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQGQPVVIIDDFGQDN   62 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccCCCcEEEEeecCccc
Confidence            58999999999999999998885443222222222222344567777788999999999653

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

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.86  E-value=4.7e-08  Score=91.55  Aligned_cols=156  Identities=15%  Similarity=0.115  Sum_probs=92.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHH-HHHH-----------------HcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLR-HILI-----------------ATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~-~~~~-----------------~~~~~~vl~iD   89 (266)
                      +..|||+|++||||+++|+++....   +.+|+.++|..+.. ..+. .+|.                 ....+++||||
T Consensus       210 ~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~-~~~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ld  288 (509)
T PRK05022        210 DLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPE-SLAESELFGHVKGAFTGAISNRSGKFELADGGTLFLD  288 (509)
T ss_pred             CCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCCh-HHHHHHhcCccccccCCCcccCCcchhhcCCCEEEec
Confidence            4469999999999999999999875   57999999998853 2222 1221                 22457889999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-------cCCCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-------SSCGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-------~~~~~~~ivi~ttn~~-------~~  155 (266)
                      ||+.|..                           ..+..|++.++...       ......+-+|++||..       ..
T Consensus       289 eI~~L~~---------------------------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~  341 (509)
T PRK05022        289 EIGELPL---------------------------ALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGR  341 (509)
T ss_pred             ChhhCCH---------------------------HHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCCCHHHHHHcCC
Confidence            9998853                           23344455543211       0111246678877753       23


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHH----HHHHHHhhCCC-------CCCcHHHHHHHhhcCC--CCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGF----KMLASNYLGIA-------EHPLFVEIEKLIATAK--VTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~----~~i~~~~~~~~-------~~~~~~~~~~l~~~~~--~s~~~i~~~l  217 (266)
                      +.+.|..  |+.. +.+..|.-.+|    ..|+.+|+...       ...+..+....+..+.  .+-.++.+.+
T Consensus       342 f~~dL~~--rl~~-~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvrEL~~~i  413 (509)
T PRK05022        342 FRADLYH--RLSV-FPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAYDWPGNVRELEHVI  413 (509)
T ss_pred             ccHHHHh--cccc-cEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCCcHHHHHHHH
Confidence            4555555  6542 44445554443    35555554321       1234455545555544  5666777655

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.86  E-value=1.3e-07  Score=79.90  Aligned_cols=113  Identities=16%  Similarity=0.154  Sum_probs=76.4

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCc----------------------EEEEeCCc-ccChhhHHHHHHHc---c-
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFD----------------------VYDLELSN-LLGNNDLRHILIAT---E-   81 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~----------------------~~~i~~~~-~~~~~~l~~~~~~~---~-   81 (266)
                      .+++.+||+||+|+||..+|.++|..+-+.                      ++.+.... ......++++....   + 
T Consensus         5 ~~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s~   84 (261)
T PRK05818          5 NKTHPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPSV   84 (261)
T ss_pred             CCCcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCch
Confidence            467889999999999999999999877332                      12211110 11222333333221   1 


Q ss_pred             ---cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           82 ---NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        82 ---~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                         ..-|++|+++|.+-                           ....+.||..++    .++.+.++|.+|+.++.+.+
T Consensus        85 e~~~~KV~II~~ae~m~---------------------------~~AaNaLLK~LE----EPp~~t~fiLit~~~~~lLp  133 (261)
T PRK05818         85 ESNGKKIYIIYGIEKLN---------------------------KQSANSLLKLIE----EPPKNTYGIFTTRNENNILN  133 (261)
T ss_pred             hcCCCEEEEeccHhhhC---------------------------HHHHHHHHHhhc----CCCCCeEEEEEECChHhCch
Confidence               24688888888763                           234566677666    45678999999999999999


Q ss_pred             cccCCCcceeEEEcCCC
Q 024550          159 ALLRPGRMDMHINMSHC  175 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p  175 (266)
                      .+++  || ..+.|+.+
T Consensus       134 TI~S--RC-q~~~~~~~  147 (261)
T PRK05818        134 TILS--RC-VQYVVLSK  147 (261)
T ss_pred             Hhhh--he-eeeecCCh
Confidence            9999  98 44778776

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.86  E-value=2.1e-07  Score=80.93  Aligned_cols=165  Identities=15%  Similarity=0.146  Sum_probs=104.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC-------------cEEEEeC-CcccChhhHHHHHHHc-------ccCCeeee
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF-------------DVYDLEL-SNLLGNNDLRHILIAT-------ENKSILVV   88 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~-------------~~~~i~~-~~~~~~~~l~~~~~~~-------~~~~vl~i   88 (266)
                      .++.+||+|+.|.||+.+++.++..+.+             .++.++. ....+...++.+....       ...-|++|
T Consensus        17 l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir~l~~~~~~~~~~~~~~KvvII   96 (299)
T PRK07132         17 ISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFLSAINKLYFSSFVQSQKKILII   96 (299)
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHHHHHHHhccCCcccCCceEEEE
Confidence            3567999999999999999999988722             1223331 1112334555554443       25679999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCccee
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDM  168 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~  168 (266)
                      |++|.+.                           ....+.||..|+.    ++...++|.+|+.++.+.+++.+  || .
T Consensus        97 ~~~e~m~---------------------------~~a~NaLLK~LEE----Pp~~t~~il~~~~~~kll~TI~S--Rc-~  142 (299)
T PRK07132         97 KNIEKTS---------------------------NSLLNALLKTIEE----PPKDTYFLLTTKNINKVLPTIVS--RC-Q  142 (299)
T ss_pred             ecccccC---------------------------HHHHHHHHHHhhC----CCCCeEEEEEeCChHhChHHHHh--Ce-E
Confidence            9998763                           2345567777775    35667888888788999999999  88 5


Q ss_pred             EEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHcCCCHHHHHHHHHHHHHh
Q 024550          169 HINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLES  236 (266)
Q Consensus       169 ~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~~~~~~~~~~~~~~~~~~  236 (266)
                      .++|+.|+.++....+... +     ...+...++....-+++.....+.  .......+.+..|+..
T Consensus       143 ~~~f~~l~~~~l~~~l~~~-~-----~~~~~a~~~a~~~~~~~~a~~~~~--~~~~~~~~~~~~~l~~  202 (299)
T PRK07132        143 VFNVKEPDQQKILAKLLSK-N-----KEKEYNWFYAYIFSNFEQAEKYIN--KESENLLKKFEEALNK  202 (299)
T ss_pred             EEECCCCCHHHHHHHHHHc-C-----CChhHHHHHHHHcCCHHHHHHHHh--cCCHHHHHHHHHHHHH
Confidence            6999999999888766543 1     222333333332235666655542  2233444445455433

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.85  E-value=3.2e-08  Score=92.79  Aligned_cols=65  Identities=18%  Similarity=0.199  Sum_probs=48.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHH-HHHH-----------------HcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLR-HILI-----------------ATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~-~~~~-----------------~~~~~~vl~iD   89 (266)
                      ...+||+|++||||+++|+++....   +.+|+.++|+.+.. ..+. .+|.                 ....++.||||
T Consensus       227 ~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~~-~~~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~Ld  305 (520)
T PRK10820        227 DAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPD-DVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLD  305 (520)
T ss_pred             CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCCH-HHHHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEEe
Confidence            3459999999999999999997765   46899999998753 2222 2221                 12346889999


Q ss_pred             cchhhHH
Q 024550           90 DIDCCIE   96 (266)
Q Consensus        90 eid~l~~   96 (266)
                      ||+.+..
T Consensus       306 eI~~L~~  312 (520)
T PRK10820        306 EIGEMSP  312 (520)
T ss_pred             ChhhCCH
Confidence            9998853

>PRK09183 transposase/IS protein; Provisional

Probab=98.85  E-value=6.3e-09  Score=89.00  Aligned_cols=64  Identities=22%  Similarity=0.340  Sum_probs=45.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-------hhhHHHHHHH-cccCCeeeeecchhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-------NNDLRHILIA-TENKSILVVEDIDCC   94 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-------~~~l~~~~~~-~~~~~vl~iDeid~l   94 (266)
                      ..+++|+||||||||+++.+++..+   |..+..+++..+..       ...+...+.. ...+.+++|||++.+
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~~dlLiiDdlg~~  176 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYL  176 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcCCCEEEEcccccC
Confidence            4579999999999999999998664   66676666554431       1123334433 456789999999865

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.85  E-value=4e-08  Score=82.70  Aligned_cols=142  Identities=16%  Similarity=0.206  Sum_probs=98.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCC-c--E--------------------------EEEeCCcccCh--hhHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKF-D--V--------------------------YDLELSNLLGN--NDLRHILIAT   80 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~-~--~--------------------------~~i~~~~~~~~--~~l~~~~~~~   80 (266)
                      ..+++|||+|+||-|.+.++-+++.. .  -                          +++++++....  --+++++...
T Consensus        35 PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKev  114 (351)
T KOG2035|consen   35 PHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEV  114 (351)
T ss_pred             CeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHH
Confidence            36999999999999999999888721 1  1                          12222222111  1134555443


Q ss_pred             c-----------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEe
Q 024550           81 E-----------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFT  149 (266)
Q Consensus        81 ~-----------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~t  149 (266)
                      .           .--|++|.|+|.|..                           ..+..|-..|+...    ...-+|..
T Consensus       115 AQt~qie~~~qr~fKvvvi~ead~LT~---------------------------dAQ~aLRRTMEkYs----~~~RlIl~  163 (351)
T KOG2035|consen  115 AQTQQIETQGQRPFKVVVINEADELTR---------------------------DAQHALRRTMEKYS----SNCRLILV  163 (351)
T ss_pred             HhhcchhhccccceEEEEEechHhhhH---------------------------HHHHHHHHHHHHHh----cCceEEEE
Confidence            2           236899999998853                           23444556666553    34668888


Q ss_pred             cCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhcCC
Q 024550          150 TNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEI-EKLIATAK  207 (266)
Q Consensus       150 tn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~~~  207 (266)
                      +|....+-+++.+  || ..|.+|.|+.++...++.....+++..+..++ ..++.+.+
T Consensus       164 cns~SriIepIrS--RC-l~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~rIa~kS~  219 (351)
T KOG2035|consen  164 CNSTSRIIEPIRS--RC-LFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLKRIAEKSN  219 (351)
T ss_pred             ecCcccchhHHhh--he-eEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHHHHHHHhc
Confidence            9999999999999  88 66999999999999999999999988877655 34444433

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=98.85  E-value=5.7e-08  Score=94.19  Aligned_cols=156  Identities=13%  Similarity=0.149  Sum_probs=90.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHH-HH-----------------HHHcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLR-HI-----------------LIATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~-~~-----------------~~~~~~~~vl~iD   89 (266)
                      ...+||+|++|||||++|+++....   +.+++.++|..+... .+. .+                 ......+++||||
T Consensus       399 ~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~~-~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ld  477 (686)
T PRK15429        399 DSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAG-LLESDLFGHERGAFTGASAQRIGRFELADKSSLFLD  477 (686)
T ss_pred             CCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCChh-HhhhhhcCcccccccccccchhhHHHhcCCCeEEEe
Confidence            3469999999999999999999865   579999999987421 111 11                 1123457899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-c------CCCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-S------SCGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~------~~~~~~ivi~ttn~~-------~~  155 (266)
                      ||+.+..                           .....|+..++... .      .....+-+|++|+..       ..
T Consensus       478 ei~~L~~---------------------------~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~  530 (686)
T PRK15429        478 EVGDMPL---------------------------ELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADRE  530 (686)
T ss_pred             chhhCCH---------------------------HHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCCHHHHHHcCc
Confidence            9998853                           23344455543211 0      111346688888753       12


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHH----HHHHHhhCCC----CC---CcHHHHHHHhhcCC--CCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFK----MLASNYLGIA----EH---PLFVEIEKLIATAK--VTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~----~i~~~~~~~~----~~---~~~~~~~~l~~~~~--~s~~~i~~~l  217 (266)
                      +.+.|..  |+. .+.+..|.-.+|.    .|+.+|+...    +.   .+..+....+..+.  .+-.++.+.+
T Consensus       531 f~~~L~~--~l~-~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL~~~i  602 (686)
T PRK15429        531 FRSDLYY--RLN-VFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPGNVRELENVI  602 (686)
T ss_pred             ccHHHHh--ccC-eeEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCCcHHHHHHHH
Confidence            3333444  543 3455555555543    4555555322    11   23444444444444  5566666665

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.83  E-value=3.5e-09  Score=81.89  Aligned_cols=60  Identities=27%  Similarity=0.344  Sum_probs=44.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCC---cEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKF---DVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIE   96 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~---~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~   96 (266)
                      ...+||+|++||||+++|++++...+.   +++.++|....     .+++..+ .++.|+|+|+|.+..
T Consensus        21 ~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-----~~~l~~a-~~gtL~l~~i~~L~~   83 (138)
T PF14532_consen   21 SSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-----AELLEQA-KGGTLYLKNIDRLSP   83 (138)
T ss_dssp             SS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-----HHHHHHC-TTSEEEEECGCCS-H
T ss_pred             CCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-----HHHHHHc-CCCEEEECChHHCCH
Confidence            346999999999999999999987753   55666666543     3444444 889999999998853

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.82  E-value=6.4e-07  Score=77.44  Aligned_cols=145  Identities=15%  Similarity=0.228  Sum_probs=90.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc------------------------EEEEeCCc-ccChhhHHHHHHHcc---
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD------------------------VYDLELSN-LLGNNDLRHILIATE---   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~------------------------~~~i~~~~-~~~~~~l~~~~~~~~---   81 (266)
                      .++++||+||  +||+++|+.+|..+.+.                        ++.+.... ..+...++++.....   
T Consensus        23 l~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~~p  100 (290)
T PRK07276         23 LNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSG  100 (290)
T ss_pred             cceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhhCc
Confidence            4678999996  68999999999877332                        22222211 112234444433322   


Q ss_pred             ---cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           82 ---NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        82 ---~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                         ...|++||++|.|.                           ....|.||+.++.    ++.+.++|.+|+.++.+.|
T Consensus       101 ~~~~~kV~II~~ad~m~---------------------------~~AaNaLLKtLEE----Pp~~t~~iL~t~~~~~lLp  149 (290)
T PRK07276        101 YEGKQQVFIIKDADKMH---------------------------VNAANSLLKVIEE----PQSEIYIFLLTNDENKVLP  149 (290)
T ss_pred             ccCCcEEEEeehhhhcC---------------------------HHHHHHHHHHhcC----CCCCeEEEEEECChhhCch
Confidence               34689999999774                           2345667777764    4567899999999999999


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+.+  || ..|.|+. +.+...+++..    .+.  ..+...++.....+++......
T Consensus       150 TI~S--Rc-q~i~f~~-~~~~~~~~L~~----~g~--~~~~a~~la~~~~s~~~A~~l~  198 (290)
T PRK07276        150 TIKS--RT-QIFHFPK-NEAYLIQLLEQ----KGL--LKTQAELLAKLAQSTSEAEKLA  198 (290)
T ss_pred             HHHH--cc-eeeeCCC-cHHHHHHHHHH----cCC--ChHHHHHHHHHCCCHHHHHHHh
Confidence            9999  98 5688876 55555555542    221  1222333443344676666544

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.81  E-value=6e-08  Score=90.29  Aligned_cols=49  Identities=31%  Similarity=0.540  Sum_probs=36.3

Q ss_pred             HHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           10 MDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        10 ~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ++.+..|+....    .+..+.+-+||+||||||||++++.+|+++|..+.+-
T Consensus        28 v~eV~~wl~~~~----~~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~Ew   76 (519)
T PF03215_consen   28 VEEVRSWLEEMF----SGSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQEW   76 (519)
T ss_pred             HHHHHHHHHHHh----ccCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEEe
Confidence            455677775421    2333445688899999999999999999998877763

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.80  E-value=5.3e-08  Score=81.15  Aligned_cols=158  Identities=21%  Similarity=0.276  Sum_probs=82.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE---EEEeCCcccC--------------------------------------
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV---YDLELSNLLG--------------------------------------   69 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~---~~i~~~~~~~--------------------------------------   69 (266)
                      ...++|+||+|+|||++++.+.......-   +.+.......                                      
T Consensus        20 ~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   99 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDLS   99 (234)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-
T ss_pred             CcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcch
Confidence            56799999999999999999999883211   1111111100                                      


Q ss_pred             ---hhhHHHHHHH---cccCCeeeeecchhhH-HHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCC
Q 024550           70 ---NNDLRHILIA---TENKSILVVEDIDCCI-ELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGD  142 (266)
Q Consensus        70 ---~~~l~~~~~~---~~~~~vl~iDeid~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  142 (266)
                         ...+..++..   ...+.||+|||++.+. ..                      ......+..+.+.++..... ..
T Consensus       100 ~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~----------------------~~~~~~~~~l~~~~~~~~~~-~~  156 (234)
T PF01637_consen  100 EDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIAS----------------------EEDKDFLKSLRSLLDSLLSQ-QN  156 (234)
T ss_dssp             GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCT----------------------TTTHHHHHHHHHHHHH-----TT
T ss_pred             hhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcc----------------------cchHHHHHHHHHHHhhcccc-CC
Confidence               0111122222   1234899999999885 20                      11233444555555553222 12


Q ss_pred             ceEEEEecCCC---C--CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCC---cHHHHHHHhhcCCCCHHHHH
Q 024550          143 ERIIIFTTNHK---E--RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHP---LFVEIEKLIATAKVTPADVA  214 (266)
Q Consensus       143 ~~ivi~ttn~~---~--~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~---~~~~~~~l~~~~~~s~~~i~  214 (266)
                      ..+|++++...   .  .-...+..  |+.. +.++..+.++..+++...+... ..   ...++..+..-.+..|+.|.
T Consensus       157 ~~~v~~~S~~~~~~~~~~~~~~~~~--~~~~-~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~gG~P~~l~  232 (234)
T PF01637_consen  157 VSIVITGSSDSLMEEFLDDKSPLFG--RFSH-IELKPLSKEEAREFLKELFKEL-IKLPFSDEDIEEIYSLTGGNPRYLQ  232 (234)
T ss_dssp             EEEEEEESSHHHHHHTT-TTSTTTT-----E-EEE----HHHHHHHHHHHHHCC-------HHHHHHHHHHHTT-HHHHH
T ss_pred             ceEEEECCchHHHHHhhcccCcccc--ccce-EEEeeCCHHHHHHHHHHHHHHh-hcccCCHHHHHHHHHHhCCCHHHHh
Confidence            23334444311   1  12344555  8877 9999999999999999877554 32   34566777777778887775


Q ss_pred             H
Q 024550          215 E  215 (266)
Q Consensus       215 ~  215 (266)
                      .
T Consensus       233 ~  233 (234)
T PF01637_consen  233 E  233 (234)
T ss_dssp             H
T ss_pred             c
Confidence            4

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.79  E-value=1.2e-07  Score=81.44  Aligned_cols=160  Identities=13%  Similarity=0.174  Sum_probs=93.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhHH-HHH-----------------------H
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDLR-HIL-----------------------I   78 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l~-~~~-----------------------~   78 (266)
                      .++||+|++|.|||++++.++...         ..|++.+.+..-.+...+. .++                       .
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~ll  141 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLL  141 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHH
Confidence            479999999999999999998755         2567777655443322221 111                       1


Q ss_pred             HcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC--C
Q 024550           79 ATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER--L  156 (266)
Q Consensus        79 ~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~--l  156 (266)
                      ...+.-+|+|||++.+..-.                        ..-...+++.+..+.....-.++.+||......  -
T Consensus       142 r~~~vrmLIIDE~H~lLaGs------------------------~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~  197 (302)
T PF05621_consen  142 RRLGVRMLIIDEFHNLLAGS------------------------YRKQREFLNALKFLGNELQIPIVGVGTREAYRALRT  197 (302)
T ss_pred             HHcCCcEEEeechHHHhccc------------------------HHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhcc
Confidence            22346799999999975311                        111233444444443333344666665543332  2


Q ss_pred             cccccCCCcceeEEEcCCCCH-HHHHHHHHHhh---CCCC--CCcHHHH-HHHhhcCCCCHHHHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTP-SGFKMLASNYL---GIAE--HPLFVEI-EKLIATAKVTPADVAEQLM  218 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~-~~~~~i~~~~~---~~~~--~~~~~~~-~~l~~~~~~s~~~i~~~l~  218 (266)
                      |+.+-+  ||.. +.+|.... ++...++..+-   +-..  .-...++ ..+....+.+.+++.+++.
T Consensus       198 D~QLa~--RF~~-~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~~ll~  263 (302)
T PF05621_consen  198 DPQLAS--RFEP-FELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELSRLLN  263 (302)
T ss_pred             CHHHHh--ccCC-ccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHHHHHH
Confidence            788888  9954 66666554 34455554443   3221  1122344 4566667788888888873

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.79  E-value=2.2e-08  Score=89.48  Aligned_cols=66  Identities=15%  Similarity=0.144  Sum_probs=51.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcccChhhHHHHHHH-----------------cccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNLLGNNDLRHILIA-----------------TENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~~~~~~l~~~~~~-----------------~~~~~vl~iD   89 (266)
                      ...+|++|++||||+.+|+.+....    ..||+.+||+.+..+-....+|..                 ...+++||+|
T Consensus       101 ~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLD  180 (403)
T COG1221         101 GLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQGGKAGLFEQANGGTLFLD  180 (403)
T ss_pred             CCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHHHHhccccceeecccCCcCchheecCCCEEehh
Confidence            4469999999999999999887543    679999999999765444444431                 2257999999


Q ss_pred             cchhhHH
Q 024550           90 DIDCCIE   96 (266)
Q Consensus        90 eid~l~~   96 (266)
                      ||..+..
T Consensus       181 EI~~LP~  187 (403)
T COG1221         181 EIHRLPP  187 (403)
T ss_pred             hhhhCCH
Confidence            9998864

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.78  E-value=3.9e-08  Score=83.66  Aligned_cols=49  Identities=16%  Similarity=0.138  Sum_probs=39.1

Q ss_pred             CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhh
Q 024550          153 KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA  204 (266)
Q Consensus       153 ~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~  204 (266)
                      |..+|-.|+.  |+ ..|...+++.++.++|++..-..+...+..+.-.++.
T Consensus       339 phGiP~D~lD--R~-lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt  387 (454)
T KOG2680|consen  339 PHGIPIDLLD--RM-LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLT  387 (454)
T ss_pred             CCCCcHHHhh--hh-heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHH
Confidence            6778999999  88 6799999999999999998887777666665544444

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=98.78  E-value=2.1e-08  Score=90.33  Aligned_cols=25  Identities=44%  Similarity=0.784  Sum_probs=22.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++|++||||||||++++.+..-+
T Consensus       198 gHnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         198 GHNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CCcEEEecCCCCchHHhhhhhcccC
Confidence            5789999999999999999887655

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.76  E-value=2.2e-08  Score=97.23  Aligned_cols=125  Identities=18%  Similarity=0.296  Sum_probs=76.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC-------CcEEEEeCCcccC-hh----h--HHHHHHHcccCCeeeeecchhhHHHh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK-------FDVYDLELSNLLG-NN----D--LRHILIATENKSILVVEDIDCCIELQ   98 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~-------~~~~~i~~~~~~~-~~----~--l~~~~~~~~~~~vl~iDeid~l~~~~   98 (266)
                      .|||+|+||||||.+++++++...       .++..+.+..... ..    .  +..-......+++++|||++.+..  
T Consensus       494 hVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~vgLTa~~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkms~--  571 (915)
T PTZ00111        494 NVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSVGLTASIKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCHN--  571 (915)
T ss_pred             eEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccccccchhhhcccccCcccccCCcEEEcCCCeEEecchhhCCH--
Confidence            599999999999999999998653       2333333332211 00    0  000001123578999999998742  


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc---------ccCCCCceEEEEecCCC-------------CCC
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL---------WSSCGDERIIIFTTNHK-------------ERL  156 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~~~~ivi~ttn~~-------------~~l  156 (266)
                                               .....|+..|+.-         ......+.-||||+|+.             -.|
T Consensus       572 -------------------------~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~L  626 (915)
T PTZ00111        572 -------------------------ESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIENINI  626 (915)
T ss_pred             -------------------------HHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCcccccCC
Confidence                                     2234455555422         11223467899999974             246


Q ss_pred             cccccCCCcceeE-EEcCCCCHHHHHHHHHH
Q 024550          157 DPALLRPGRMDMH-INMSHCTPSGFKMLASN  186 (266)
Q Consensus       157 d~al~r~~Rf~~~-i~~~~p~~~~~~~i~~~  186 (266)
                      +++|++  ||+.. +-++.|+.+.=..|..+
T Consensus       627 p~~LLS--RFDLIf~l~D~~d~~~D~~lA~h  655 (915)
T PTZ00111        627 SPSLFT--RFDLIYLVLDHIDQDTDQLISLS  655 (915)
T ss_pred             ChHHhh--hhcEEEEecCCCChHHHHHHHHH
Confidence            799999  99865 55677777654444433

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.74  E-value=2e-07  Score=80.36  Aligned_cols=113  Identities=17%  Similarity=0.212  Sum_probs=78.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc----------------EEEEeCCc---ccChhhHHHHHHHcc------cCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD----------------VYDLELSN---LLGNNDLRHILIATE------NKS   84 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~----------------~~~i~~~~---~~~~~~l~~~~~~~~------~~~   84 (266)
                      .++.+||+||+|+||+.+|.++|..+.+.                ++.+.+..   ..+-..++.+.....      ..-
T Consensus        18 l~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~k   97 (290)
T PRK05917         18 VPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYK   97 (290)
T ss_pred             cCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCce
Confidence            46789999999999999999999887432                23332221   112333444433321      246


Q ss_pred             eeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCC
Q 024550           85 ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPG  164 (266)
Q Consensus        85 vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~  164 (266)
                      |++||++|.+-                           ....|.||+.|+.    ++.++++|..|+.++.+.|.+++  
T Consensus        98 v~ii~~ad~mt---------------------------~~AaNaLLK~LEE----Pp~~~~fiL~~~~~~~ll~TI~S--  144 (290)
T PRK05917         98 IYIIHEADRMT---------------------------LDAISAFLKVLED----PPQHGVIILTSAKPQRLPPTIRS--  144 (290)
T ss_pred             EEEEechhhcC---------------------------HHHHHHHHHHhhc----CCCCeEEEEEeCChhhCcHHHHh--
Confidence            88999999774                           2355677777774    45679999999999999999999  


Q ss_pred             cceeEEEcCCCC
Q 024550          165 RMDMHINMSHCT  176 (266)
Q Consensus       165 Rf~~~i~~~~p~  176 (266)
                      || ..+.|+.+.
T Consensus       145 Rc-q~~~~~~~~  155 (290)
T PRK05917        145 RS-LSIHIPMEE  155 (290)
T ss_pred             cc-eEEEccchh
Confidence            88 557887553

>PRK06921 hypothetical protein; Provisional

Probab=98.73  E-value=3.1e-08  Score=84.98  Aligned_cols=63  Identities=29%  Similarity=0.413  Sum_probs=44.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcccCh-----hhHHHHHHHcccCCeeeeecchh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNLLGN-----NDLRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~~~~-----~~l~~~~~~~~~~~vl~iDeid~   93 (266)
                      ..+++|+||||||||+|+.++|+++    |.++++++...+...     ......+.......+|+|||++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~~~~~~~~~~~~~~~~dlLiIDDl~~  188 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKVEVLFIDDLFK  188 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHHHHHHHHHHHHHhcCCCEEEEecccc
Confidence            4679999999999999999999986    456667765443211     11222334455689999999953

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

Probab=98.73  E-value=3.5e-07  Score=88.83  Aligned_cols=95  Identities=25%  Similarity=0.377  Sum_probs=65.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-------------hhhHHHHHHHc--ccCCeeeeecch
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-------------NNDLRHILIAT--ENKSILVVEDID   92 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-------------~~~l~~~~~~~--~~~~vl~iDeid   92 (266)
                      ...++|.||.|+|||-+|+++|..+   .-.++.++++.++.             ......+....  +..+||+|||||
T Consensus       591 ~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskligsp~gyvG~e~gg~LteavrrrP~sVVLfdeIE  670 (898)
T KOG1051|consen  591 DAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIE  670 (898)
T ss_pred             CeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhccCCCcccccchhHHHHHHHHhcCCceEEEEechh
Confidence            3458999999999999999999988   35678888886331             12222333333  357999999999


Q ss_pred             hhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC-------CceEEEEecCC
Q 024550           93 CCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG-------DERIIIFTTNH  152 (266)
Q Consensus        93 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~-------~~~ivi~ttn~  152 (266)
                      ..                           ....++.|++.++...-+.+       .+.|||+|+|.
T Consensus       671 kA---------------------------h~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~  710 (898)
T KOG1051|consen  671 KA---------------------------HPDVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSNV  710 (898)
T ss_pred             hc---------------------------CHHHHHHHHHHHhcCccccCCCcEeeccceEEEEeccc
Confidence            54                           24466667777764433322       35789999885

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.72  E-value=1.5e-07  Score=86.76  Aligned_cols=156  Identities=17%  Similarity=0.184  Sum_probs=92.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHH------------------cccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIA------------------TENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~------------------~~~~~vl~iD   89 (266)
                      ...++++|++||||+++|+++....   +.+|+.++|..+.. ..+...+..                  ...+++||||
T Consensus       162 ~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~  240 (445)
T TIGR02915       162 DITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPE-NLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLD  240 (445)
T ss_pred             CCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCCh-HHHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEe
Confidence            3469999999999999999998876   46899999998843 333332211                  1347899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-c------CCCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-S------SCGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~------~~~~~~ivi~ttn~~-------~~  155 (266)
                      |++.|..                           ..+..|+..++... .      .....+.+|+||+..       ..
T Consensus       241 ~i~~l~~---------------------------~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~  293 (445)
T TIGR02915       241 EIGDLPL---------------------------NLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGT  293 (445)
T ss_pred             chhhCCH---------------------------HHHHHHHHHHhhCeEEeCCCCceeeeceEEEEecCCCHHHHHHcCC
Confidence            9998853                           23344555554221 1      011245677777654       33


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHH----HHHHHhhCCC----C---CCcHHHHHHHhhcCC--CCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFK----MLASNYLGIA----E---HPLFVEIEKLIATAK--VTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~----~i~~~~~~~~----~---~~~~~~~~~l~~~~~--~s~~~i~~~l  217 (266)
                      +.+.|..  |+. .+.+..|.-.+|.    .++.+|+...    +   ..+..+.-..+..+.  .+..++.+++
T Consensus       294 ~~~~L~~--~l~-~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~i  365 (445)
T TIGR02915       294 FREDLFY--RIA-EISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKV  365 (445)
T ss_pred             ccHHHHH--Hhc-cceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHhCCCCChHHHHHHHH
Confidence            4555555  653 3555566655554    3445444321    1   234444444444444  5566666665

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).

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.71  E-value=4.6e-08  Score=74.48  Aligned_cols=38  Identities=34%  Similarity=0.540  Sum_probs=29.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc--------CCcEEEEeCCccc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL--------KFDVYDLELSNLL   68 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~--------~~~~~~i~~~~~~   68 (266)
                      ++.++++||||+|||++++.++..+        ..+++.+++....
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   49 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSR   49 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHS
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCC
Confidence            3569999999999999999999988        6777877766554

>COG1485 Predicted ATPase [General function prediction only]

Probab=98.71  E-value=2.4e-08  Score=86.85  Aligned_cols=99  Identities=19%  Similarity=0.299  Sum_probs=66.7

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcE-EEEeCCcccCh------------hhHHHHHHH-cccCCeeeeecchh
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV-YDLELSNLLGN------------NDLRHILIA-TENKSILVVEDIDC   93 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~-~~i~~~~~~~~------------~~l~~~~~~-~~~~~vl~iDeid~   93 (266)
                      ..+++|+++|||-|+|||+|.-.....+..+- ..+....++..            ..+..+-.. +.+-.||++||+..
T Consensus        62 ~~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~FM~~vH~~l~~l~g~~dpl~~iA~~~~~~~~vLCfDEF~V  141 (367)
T COG1485          62 HGPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQGQTDPLPPIADELAAETRVLCFDEFEV  141 (367)
T ss_pred             CCCCceEEEECCCCccHHHHHHHHHhhCCccccccccHHHHHHHHHHHHHHHcCCCCccHHHHHHHHhcCCEEEeeeeee
Confidence            45678999999999999999999998885543 44444444310            111111111 23457999999984


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC-CCCC
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH-KERL  156 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~-~~~l  156 (266)
                      -                        +.....++..|++.|-.      .++++|+|+|. |++|
T Consensus       142 t------------------------DI~DAMiL~rL~~~Lf~------~GV~lvaTSN~~P~~L  175 (367)
T COG1485         142 T------------------------DIADAMILGRLLEALFA------RGVVLVATSNTAPDNL  175 (367)
T ss_pred             c------------------------ChHHHHHHHHHHHHHHH------CCcEEEEeCCCChHHh
Confidence            2                        34446688888888764      47999999995 4444

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.66  E-value=2.3e-07  Score=85.70  Aligned_cols=157  Identities=17%  Similarity=0.165  Sum_probs=91.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHH------------------cccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIA------------------TENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~------------------~~~~~vl~iD   89 (266)
                      ...++++|++||||+++++++....   +.+++.++|..+.. ..+...+..                  ...+++||||
T Consensus       166 ~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld  244 (457)
T PRK11361        166 QASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPE-SLLESELFGHEKGAFTGAQTLRQGLFERANEGTLLLD  244 (457)
T ss_pred             CcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCH-HHHHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEe
Confidence            3469999999999999999998765   57999999998843 233322211                  2346899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-------CCCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-------SCGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-------~~~~~~ivi~ttn~~-------~~  155 (266)
                      |++.+..                           ..+..|+..++....       ....++.+|+|||..       ..
T Consensus       245 ~i~~l~~---------------------------~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~l~~~~~~g~  297 (457)
T PRK11361        245 EIGEMPL---------------------------VLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGT  297 (457)
T ss_pred             chhhCCH---------------------------HHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCC
Confidence            9998854                           123445555442210       011236788888753       23


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHH----HHHHHhhCCC----C---CCcHHHHHHHhhcCC--CCHHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFK----MLASNYLGIA----E---HPLFVEIEKLIATAK--VTPADVAEQLM  218 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~----~i~~~~~~~~----~---~~~~~~~~~l~~~~~--~s~~~i~~~l~  218 (266)
                      +.+.+..  |+. .+.+..|.-.+|.    .++..|+...    +   ..+..+.-..+..+.  .+..++.+.+.
T Consensus       298 ~~~~l~~--~l~-~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~~~  370 (457)
T PRK11361        298 FREDLFY--RLN-VIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIE  370 (457)
T ss_pred             chHHHHH--Hhc-cceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHcCCCCCcHHHHHHHHH
Confidence            4444554  553 3556666665543    3444444321    1   223444444444444  45666666653

>PF05729 NACHT: NACHT domain

Probab=98.65  E-value=2.7e-07  Score=72.81  Aligned_cols=132  Identities=18%  Similarity=0.286  Sum_probs=69.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC---------cEEEEeCCcccChh---hHHHHH------------------HHccc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF---------DVYDLELSNLLGNN---DLRHIL------------------IATEN   82 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~---------~~~~i~~~~~~~~~---~l~~~~------------------~~~~~   82 (266)
                      -++|+|+||+|||++++.++..+..         -++.+.+.......   .+...+                  .....
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~   81 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKNK   81 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcCC
Confidence            4789999999999999999987711         12233333332111   122111                  22345


Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC--CCCcccc
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK--ERLDPAL  160 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~--~~ld~al  160 (266)
                      ..+++||.+|.+.......                   ........+...+.... .  .++-++.|++..  ..+...+
T Consensus        82 ~~llilDglDE~~~~~~~~-------------------~~~~~~~~l~~l~~~~~-~--~~~~liit~r~~~~~~~~~~~  139 (166)
T PF05729_consen   82 RVLLILDGLDELEEQDQSQ-------------------ERQRLLDLLSQLLPQAL-P--PGVKLIITSRPRAFPDLRRRL  139 (166)
T ss_pred             ceEEEEechHhcccchhhh-------------------HHHHHHHHHHHHhhhcc-C--CCCeEEEEEcCChHHHHHHhc
Confidence            6899999999885411110                   00111111222222211 1  223333333321  1222222


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      ..   . ..+.++..+.+++.++++.+++.
T Consensus       140 ~~---~-~~~~l~~~~~~~~~~~~~~~f~~  165 (166)
T PF05729_consen  140 KQ---A-QILELEPFSEEDIKQYLRKYFSN  165 (166)
T ss_pred             CC---C-cEEEECCCCHHHHHHHHHHHhhc
Confidence            22   1 56899999999999999998864

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.65  E-value=4.7e-07  Score=83.98  Aligned_cols=157  Identities=17%  Similarity=0.206  Sum_probs=93.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHH------------------cccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIA------------------TENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~------------------~~~~~vl~iD   89 (266)
                      ...++++|++|||||++|+++....   +.+|+.++|..+.. ..+...+..                  ...++.||||
T Consensus       161 ~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~-~~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~  239 (469)
T PRK10923        161 SISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPK-DLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLD  239 (469)
T ss_pred             CCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCH-HHHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEe
Confidence            4459999999999999999999876   47999999998843 333332211                  2346889999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-C------CCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-S------CGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~------~~~~~ivi~ttn~~-------~~  155 (266)
                      |++.+..                           ..+..|+..++...- .      ....+-+|+||+..       ..
T Consensus       240 ~i~~l~~---------------------------~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~  292 (469)
T PRK10923        240 EIGDMPL---------------------------DVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGK  292 (469)
T ss_pred             ccccCCH---------------------------HHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEeCCCCHHHHHHcCC
Confidence            9998853                           123344555442110 0      01234677777643       24


Q ss_pred             CcccccCCCcce-eEEEcCCCCH--HHHHHHHHHhhCCC----C---CCcHHHHHHHhhcCC--CCHHHHHHHH
Q 024550          156 LDPALLRPGRMD-MHINMSHCTP--SGFKMLASNYLGIA----E---HPLFVEIEKLIATAK--VTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~-~~i~~~~p~~--~~~~~i~~~~~~~~----~---~~~~~~~~~l~~~~~--~s~~~i~~~l  217 (266)
                      +.+.|..  ||. ..|++|+...  ++...|+.+|+...    +   ..+..+....+..+.  .+..++.+++
T Consensus       293 ~~~~L~~--~l~~~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~i  364 (469)
T PRK10923        293 FREDLFH--RLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENTC  364 (469)
T ss_pred             chHHHHH--HhcceeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCChHHHHHHHH
Confidence            5566776  773 4455544333  33445666665322    1   123445544555444  5566766665

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.62  E-value=6.7e-07  Score=82.81  Aligned_cols=158  Identities=15%  Similarity=0.174  Sum_probs=94.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHH------------------cccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIA------------------TENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~------------------~~~~~vl~iD   89 (266)
                      ...+++.|.+||||+++++++....   +.+|+.++|..+.. ..+...+..                  ...+++||||
T Consensus       157 ~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~  235 (463)
T TIGR01818       157 DITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPK-DLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLD  235 (463)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCH-HHHHHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEE
Confidence            3459999999999999999998875   57899999998843 333322211                  2347899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-------CCCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-------SCGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-------~~~~~~ivi~ttn~~-------~~  155 (266)
                      |++.+..                           .....|++.++....       .....+-+|+||+..       ..
T Consensus       236 ei~~l~~---------------------------~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~  288 (463)
T TIGR01818       236 EIGDMPL---------------------------DAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGK  288 (463)
T ss_pred             chhhCCH---------------------------HHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCCHHHHHHcCC
Confidence            9998853                           123445555542110       001235677777643       23


Q ss_pred             CcccccCCCcce-eEEEcCCCC--HHHHHHHHHHhhCCC----C---CCcHHHHHHHhhcCC--CCHHHHHHHHH
Q 024550          156 LDPALLRPGRMD-MHINMSHCT--PSGFKMLASNYLGIA----E---HPLFVEIEKLIATAK--VTPADVAEQLM  218 (266)
Q Consensus       156 ld~al~r~~Rf~-~~i~~~~p~--~~~~~~i~~~~~~~~----~---~~~~~~~~~l~~~~~--~s~~~i~~~l~  218 (266)
                      +.+.|..  |+. ..|++|+..  .++...++.+|+...    +   ..+..+....+..+.  .+.+++.+++.
T Consensus       289 f~~~L~~--rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~~~  361 (463)
T TIGR01818       289 FREDLFH--RLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCR  361 (463)
T ss_pred             cHHHHHH--HhCcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHH
Confidence            4445555  554 466666666  456666766665332    1   223444444444444  44567766663

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.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.62  E-value=3.1e-07  Score=87.39  Aligned_cols=28  Identities=54%  Similarity=0.712  Sum_probs=25.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      +++++|+||||||||++++++++.++..
T Consensus        37 ~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        37 KRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            3589999999999999999999999654

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.57  E-value=2.6e-07  Score=87.21  Aligned_cols=119  Identities=22%  Similarity=0.205  Sum_probs=84.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCC--cEEEEeCCc----ccChhhHHHHHHH-----------cccCCeeeeecchhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKF--DVYDLELSN----LLGNNDLRHILIA-----------TENKSILVVEDIDCC   94 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~--~~~~i~~~~----~~~~~~l~~~~~~-----------~~~~~vl~iDeid~l   94 (266)
                      .|++|.|++|||||+++++++.-+..  ||+.+..+.    +.+.-++...+..           ...++|||+||+..+
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            47999999999999999999998754  777665443    3344444444322           234699999999966


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc---------cccCCCCceEEEEecCCC---CCCcccccC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG---------LWSSCGDERIIIFTTNHK---ERLDPALLR  162 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~~~~~~~~~ivi~ttn~~---~~ld~al~r  162 (266)
                      .                           ..+++.|++.|+.         .....+.++++|+|.|..   ..|+++++.
T Consensus       106 ~---------------------------~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLD  158 (584)
T PRK13406        106 E---------------------------PGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALAD  158 (584)
T ss_pred             C---------------------------HHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHh
Confidence            3                           3466777777753         222223457788875432   458899999


Q ss_pred             CCcceeEEEcCCCCHHH
Q 024550          163 PGRMDMHINMSHCTPSG  179 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~~~  179 (266)
                        ||+++|.++.|+..+
T Consensus       159 --Rf~l~v~v~~~~~~~  173 (584)
T PRK13406        159 --RLAFHLDLDGLALRD  173 (584)
T ss_pred             --heEEEEEcCCCChHH
Confidence              999999999988764

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.55  E-value=5.6e-08  Score=86.07  Aligned_cols=129  Identities=24%  Similarity=0.281  Sum_probs=69.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC----ccc---------ChhhHHHHHHHcccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS----NLL---------GNNDLRHILIATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~----~~~---------~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~   99 (266)
                      ++||+|.||||||.+.+.++......++.....    .++         ++..+..-..-...++|.+|||+|.+-.   
T Consensus        59 hiLlvGdpg~gKS~ll~~~~~~~pr~v~~~g~~~s~~gLta~~~~d~~~~~~~leaGalvlad~GiccIDe~dk~~~---  135 (331)
T PF00493_consen   59 HILLVGDPGTGKSQLLKYVAKLAPRSVYTSGKGSSAAGLTASVSRDPVTGEWVLEAGALVLADGGICCIDEFDKMKE---  135 (331)
T ss_dssp             -EEEECSCHHCHHHHHHCCCCT-SSEEEEECCGSTCCCCCEEECCCGGTSSECEEE-HHHHCTTSEEEECTTTT--C---
T ss_pred             ceeeccchhhhHHHHHHHHHhhCCceEEECCCCcccCCccceeccccccceeEEeCCchhcccCceeeecccccccc---
Confidence            599999999999999998877665554433211    111         0111111122234789999999998743   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhc---------cccCCCCceEEEEecCCCC-------------CCc
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG---------LWSSCGDERIIIFTTNHKE-------------RLD  157 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~~~~~~~~~ivi~ttn~~~-------------~ld  157 (266)
                                              .....++..|+.         .....+.+.-|+|++|+..             .++
T Consensus       136 ------------------------~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~ni~l~  191 (331)
T PF00493_consen  136 ------------------------DDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSENINLP  191 (331)
T ss_dssp             ------------------------HHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCCT-S-
T ss_pred             ------------------------hHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHhcccc
Confidence                                    122334444442         1111123467899999654             478


Q ss_pred             ccccCCCcceeEEEc-CCCCHHHHHHHHHHhhCC
Q 024550          158 PALLRPGRMDMHINM-SHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       158 ~al~r~~Rf~~~i~~-~~p~~~~~~~i~~~~~~~  190 (266)
                      +.|++  ||+..+.+ ..|+.+.=..+..+.+..
T Consensus       192 ~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~  223 (331)
T PF00493_consen  192 PPLLS--RFDLIFLLRDKPDEEEDERLAEHILDS  223 (331)
T ss_dssp             CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTT
T ss_pred             hhhHh--hcCEEEEeccccccccccccceEEEec
Confidence            89999  99987665 666655555555555544

; 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.

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

Probab=98.54  E-value=5.6e-07  Score=81.52  Aligned_cols=65  Identities=17%  Similarity=0.178  Sum_probs=49.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHH-------HH----------cccCCeeeeec
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHIL-------IA----------TENKSILVVED   90 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~-------~~----------~~~~~vl~iDe   90 (266)
                      ...|||.|..||||..+|++|....   ..||+.+||+.+...--=.++|       ..          ...++.||+||
T Consensus       246 d~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPesLlESELFGHeKGAFTGA~~~r~GrFElAdGGTLFLDE  325 (550)
T COG3604         246 DSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPESLLESELFGHEKGAFTGAINTRRGRFELADGGTLFLDE  325 (550)
T ss_pred             CCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccchHHHHHHHhcccccccccchhccCcceeecCCCeEechh
Confidence            4569999999999999999999877   5799999999985321111222       21          23679999999


Q ss_pred             chhhH
Q 024550           91 IDCCI   95 (266)
Q Consensus        91 id~l~   95 (266)
                      |..|.
T Consensus       326 IGelP  330 (550)
T COG3604         326 IGELP  330 (550)
T ss_pred             hccCC
Confidence            99885

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.54  E-value=6.1e-07  Score=90.52  Aligned_cols=131  Identities=21%  Similarity=0.301  Sum_probs=94.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh-------------hh----HHHHHHHcccCCeeeeecchh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN-------------ND----LRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~-------------~~----l~~~~~~~~~~~vl~iDeid~   93 (266)
                      .+++||-|.||+|||+++.++|+..|-.+++++.++-+.-             ..    =...+..++.+..+++||+..
T Consensus      1543 ~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVlLDEiNL 1622 (4600)
T COG5271        1543 GKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVLLDEINL 1622 (4600)
T ss_pred             CCceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhhcCCEEEeehhhh
Confidence            5679999999999999999999999999999998865420             00    113445567899999999984


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhh-----------ccccCCCCceEEEEecCCC------CCC
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID-----------GLWSSCGDERIIIFTTNHK------ERL  156 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~-----------~~~~~~~~~~ivi~ttn~~------~~l  156 (266)
                      ..                           +.++.+|-.+++           ... .+..+..|+||-|+.      ..|
T Consensus      1623 aS---------------------------QSVlEGLNacLDhR~eayIPEld~~f-~~HpnfrVFAaqNPq~qggGRKgL 1674 (4600)
T COG5271        1623 AS---------------------------QSVLEGLNACLDHRREAYIPELDKTF-DVHPNFRVFAAQNPQDQGGGRKGL 1674 (4600)
T ss_pred             hH---------------------------HHHHHHHHHHHhhcccccccccccee-eccCCeeeeeecCchhcCCCcccC
Confidence            42                           223333333332           111 123456777777754      468


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCC
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE  192 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~  192 (266)
                      |..|+.  ||. +|.+...+.+....|...+++.-.
T Consensus      1675 PkSF~n--RFs-vV~~d~lt~dDi~~Ia~~~yp~v~ 1707 (4600)
T COG5271        1675 PKSFLN--RFS-VVKMDGLTTDDITHIANKMYPQVN 1707 (4600)
T ss_pred             CHHHhh--hhh-eEEecccccchHHHHHHhhCCccC
Confidence            999999  995 599999999999999998887654

>PRK15115 response regulator GlrR; Provisional

Probab=98.51  E-value=1.7e-06  Score=79.66  Aligned_cols=65  Identities=20%  Similarity=0.190  Sum_probs=48.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHH-HH-----------------HcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHI-LI-----------------ATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~-~~-----------------~~~~~~vl~iD   89 (266)
                      ...++++|++|||||++|+++....   +.+|+.++|..+.. ..+... |.                 ....+++||||
T Consensus       157 ~~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~  235 (444)
T PRK15115        157 DVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPE-QLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLD  235 (444)
T ss_pred             CCeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCH-HHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEE
Confidence            3459999999999999999998875   47999999998743 333322 21                 12346899999


Q ss_pred             cchhhHH
Q 024550           90 DIDCCIE   96 (266)
Q Consensus        90 eid~l~~   96 (266)
                      |++.|..
T Consensus       236 ~i~~l~~  242 (444)
T PRK15115        236 EIGDMPA  242 (444)
T ss_pred             ccccCCH
Confidence            9998854

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.51  E-value=2.7e-06  Score=77.88  Aligned_cols=52  Identities=23%  Similarity=0.468  Sum_probs=36.1

Q ss_pred             HHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           10 MDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        10 ~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +..+..||..-..+.  .--..+-+||+||+||||||+++.+++++|..+++=+
T Consensus        91 I~eVk~WL~~~~~~~--~~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew~  142 (634)
T KOG1970|consen   91 ISEVKQWLKQVAEFT--PKLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIEWS  142 (634)
T ss_pred             HHHHHHHHHHHHHhc--cCCCceEEEEeCCCCCCchhHHHHHHHhhCceeeeec
Confidence            344677776221111  1112345889999999999999999999998887644

>PHA02624 large T antigen; Provisional

Probab=98.51  E-value=3.1e-07  Score=85.64  Aligned_cols=124  Identities=19%  Similarity=0.175  Sum_probs=76.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhh
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARA  106 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~  106 (266)
                      |+|..+.++||||||||||+++.+|++.++...+.++...    ..++-.+.-+...-+.+|||+-.-+-....      
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt----~ks~FwL~pl~D~~~~l~dD~t~~~~~~~~------  496 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQPADNKD------  496 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCc----chhHHHhhhhhhceEEEeeecccccccccc------
Confidence            6677788999999999999999999999977777766332    234444445556778888888643210000      


Q ss_pred             cCCccccccccccccchhhhhhhhhhhhcccc----CCCC------ceEEEEecCCCCCCcccccCCCcceeEEEcC
Q 024550          107 ANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS----SCGD------ERIIIFTTNHKERLDPALLRPGRMDMHINMS  173 (266)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~----~~~~------~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~  173 (266)
                                ...+..-..+..+-+.|||.-.    ....      -.-.|.|||. ..||..+.-  ||...+.|.
T Consensus       497 ----------Lp~G~~~dNl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlliT~Ne-y~iP~T~~~--Rf~~~~~F~  560 (647)
T PHA02624        497 ----------LPSGQGMNNLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIVTMNE-YLIPQTVKA--RFAKVLDFK  560 (647)
T ss_pred             ----------CCcccccchhhHHHhhcCCCCccccchhccCchhccCCCeEEeecC-cccchhHHH--HHHHhcccc
Confidence                      0001222223455566666510    0000      0125567775 356888888  998888886

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.46  E-value=4.9e-07  Score=77.64  Aligned_cols=128  Identities=21%  Similarity=0.266  Sum_probs=82.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCc------EEEEeCCcccChhh---HHHHHHHc---------ccCCeeeeecchhh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFD------VYDLELSNLLGNND---LRHILIAT---------ENKSILVVEDIDCC   94 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~------~~~i~~~~~~~~~~---l~~~~~~~---------~~~~vl~iDeid~l   94 (266)
                      +.|+|||||||||+...+.|..+..+      +...++++-.+..-   -...|...         .....+++||+|.+
T Consensus        64 h~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaSd~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaM  143 (360)
T KOG0990|consen   64 HLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAM  143 (360)
T ss_pred             cccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhccCccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHh
Confidence            79999999999999999999988663      11223332222111   11222222         24578999999988


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSH  174 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~  174 (266)
                      ..                           ..++.|-..+....    .+.-|+..+|++..+.+++.+  ||.. ..|..
T Consensus       144 T~---------------------------~AQnALRRviek~t----~n~rF~ii~n~~~ki~pa~qs--Rctr-frf~p  189 (360)
T KOG0990|consen  144 TR---------------------------DAQNALRRVIEKYT----ANTRFATISNPPQKIHPAQQS--RCTR-FRFAP  189 (360)
T ss_pred             hH---------------------------HHHHHHHHHHHHhc----cceEEEEeccChhhcCchhhc--cccc-CCCCC
Confidence            53                           12233334444432    346677788999999999999  8854 67777


Q ss_pred             CCHHHHHHHHHHhhCCCCCC
Q 024550          175 CTPSGFKMLASNYLGIAEHP  194 (266)
Q Consensus       175 p~~~~~~~i~~~~~~~~~~~  194 (266)
                      .+..+......++...+...
T Consensus       190 l~~~~~~~r~shi~e~e~~~  209 (360)
T KOG0990|consen  190 LTMAQQTERQSHIRESEQKE  209 (360)
T ss_pred             CChhhhhhHHHHHHhcchhh
Confidence            77666666677666555433

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=98.46  E-value=4.7e-06  Score=72.04  Aligned_cols=148  Identities=20%  Similarity=0.165  Sum_probs=76.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHH--cCCc---EEEEeCCcccChh------------------------hHHHHHHH-
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANY--LKFD---VYDLELSNLLGNN------------------------DLRHILIA-   79 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~--~~~~---~~~i~~~~~~~~~------------------------~l~~~~~~-   79 (266)
                      ..+.+.|+|++|+|||++|+.++..  ....   ++.++.....+..                        .+...+.. 
T Consensus        18 ~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~   97 (287)
T PF00931_consen   18 EVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLREL   97 (287)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHH
T ss_pred             CeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhh
Confidence            3556999999999999999999987  3221   2334333222111                        11111111 


Q ss_pred             -cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc
Q 024550           80 -TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP  158 (266)
Q Consensus        80 -~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~  158 (266)
                       ...+++|+||+++...                             .+..+...+...    ..+.-||.||....- -.
T Consensus        98 L~~~~~LlVlDdv~~~~-----------------------------~~~~l~~~~~~~----~~~~kilvTTR~~~v-~~  143 (287)
T PF00931_consen   98 LKDKRCLLVLDDVWDEE-----------------------------DLEELREPLPSF----SSGSKILVTTRDRSV-AG  143 (287)
T ss_dssp             HCCTSEEEEEEEE-SHH-----------------------------HH-------HCH----HSS-EEEEEESCGGG-GT
T ss_pred             hccccceeeeeeecccc-----------------------------cccccccccccc----ccccccccccccccc-cc
Confidence             1247899999998542                             111222222111    123455667665321 11


Q ss_pred             cccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCC----CCcHHHHHHHhhcCCCCHHHHH
Q 024550          159 ALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE----HPLFVEIEKLIATAKVTPADVA  214 (266)
Q Consensus       159 al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~----~~~~~~~~~l~~~~~~s~~~i~  214 (266)
                      ..-   .-...++++..+.++..+++..+.....    .........++...+..|-.|.
T Consensus       144 ~~~---~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~  200 (287)
T PF00931_consen  144 SLG---GTDKVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALK  200 (287)
T ss_dssp             THH---SCEEEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHH
T ss_pred             ccc---cccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            111   1146799999999999999999876543    2222334455555555555543

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.

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=98.41  E-value=6.9e-07  Score=87.28  Aligned_cols=148  Identities=20%  Similarity=0.268  Sum_probs=98.6

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHc--------------------ccCCeeeeecchh
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIAT--------------------ENKSILVVEDIDC   93 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~--------------------~~~~vl~iDeid~   93 (266)
                      ++++||||+|||+.+..+|.++|..+++.+.+...+...+...+..+                    ....||++||+|.
T Consensus       360 ~l~~G~pGigKT~~~h~~~k~~g~~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~  439 (871)
T KOG1968|consen  360 LLLSGPPGIGKTTAAHKAAKELGFKVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDG  439 (871)
T ss_pred             HHhcCCCCCCchhhHhhhhhhcccceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEecccc
Confidence            68999999999999999999999999999999776543333332221                    1235999999998


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcC
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMS  173 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~  173 (266)
                      ++. .++...                    ..+..+..   .      ..+-+|+++|..+..+..-+.  |-...++|+
T Consensus       440 ~~~-~dRg~v--------------------~~l~~l~~---k------s~~Piv~~cndr~~p~sr~~~--~~~~~l~f~  487 (871)
T KOG1968|consen  440 MFG-EDRGGV--------------------SKLSSLCK---K------SSRPLVCTCNDRNLPKSRALS--RACSDLRFS  487 (871)
T ss_pred             ccc-hhhhhH--------------------HHHHHHHH---h------ccCCeEEEecCCCCccccchh--hhcceeeec
Confidence            875 222221                    12222333   1      235578888887776664444  444779999


Q ss_pred             CCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHH
Q 024550          174 HCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQ  216 (266)
Q Consensus       174 ~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~  216 (266)
                      .|+.+++..-+..+.......+. ..+..+..   ++.+||.+.
T Consensus       488 kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~---~~~~DiR~~  528 (871)
T KOG1968|consen  488 KPSSELIRSRIMSICKSEGIKISDDVLEEISK---LSGGDIRQI  528 (871)
T ss_pred             CCcHHHHHhhhhhhhcccceecCcHHHHHHHH---hcccCHHHH
Confidence            99999988777767666554443 45555655   334444444

>PHA00729 NTP-binding motif containing protein

Probab=98.40  E-value=7.3e-07  Score=74.05  Aligned_cols=26  Identities=19%  Similarity=0.434  Sum_probs=23.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      .+++|+|+||||||++|.+++..++.
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~~   43 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVFW   43 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            37999999999999999999998763

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.39  E-value=7.6e-06  Score=75.25  Aligned_cols=65  Identities=20%  Similarity=0.219  Sum_probs=49.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHH------------------cccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIA------------------TENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~------------------~~~~~vl~iD   89 (266)
                      ...++++|.+||||+++++++....   +.+|+.++|..+.. ..+...+..                  ...+++||||
T Consensus       162 ~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld  240 (441)
T PRK10365        162 EATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNE-SLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLD  240 (441)
T ss_pred             CCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCH-HHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEe
Confidence            3469999999999999999998765   47899999998743 333333211                  2347899999


Q ss_pred             cchhhHH
Q 024550           90 DIDCCIE   96 (266)
Q Consensus        90 eid~l~~   96 (266)
                      ||+.|..
T Consensus       241 ei~~l~~  247 (441)
T PRK10365        241 EIGDISP  247 (441)
T ss_pred             ccccCCH
Confidence            9999864

>PHA02774 E1; Provisional

Probab=98.38  E-value=3.6e-06  Score=78.31  Aligned_cols=58  Identities=28%  Similarity=0.454  Sum_probs=42.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEE-EeCCcccChhhHHHHHHHcccCCeeeeecc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYD-LELSNLLGNNDLRHILIATENKSILVVEDI   91 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~-i~~~~~~~~~~l~~~~~~~~~~~vl~iDei   91 (266)
                      ++|..++++||||||||||+++.+|++.++..++. ++....       -.+..+....|+++||+
T Consensus       430 ~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s~-------FwLqpl~d~ki~vlDD~  488 (613)
T PHA02774        430 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKSH-------FWLQPLADAKIALLDDA  488 (613)
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECccc-------cccchhccCCEEEEecC
Confidence            56666789999999999999999999999765544 553211       11334445679999999

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.37  E-value=6.7e-06  Score=64.36  Aligned_cols=63  Identities=16%  Similarity=0.371  Sum_probs=42.7

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC--------------------------hhhH------HHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG--------------------------NNDL------RHILI   78 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~--------------------------~~~l------~~~~~   78 (266)
                      ++|+||||+|||+++..++...   +.+++.++......                          ....      ...+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATADDPAAARLLSKAERLR   81 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcchHHHHHHHhhhhhccccccEEEEEcCCCCCcHHHHHHHHHHHH
Confidence            6899999999999999998877   45666665542211                          0001      11223


Q ss_pred             HcccCCeeeeecchhhHH
Q 024550           79 ATENKSILVVEDIDCCIE   96 (266)
Q Consensus        79 ~~~~~~vl~iDeid~l~~   96 (266)
                      ....+.+++|||+..+..
T Consensus        82 ~~~~~~~lviDe~~~~~~   99 (165)
T cd01120          82 ERGGDDLIILDELTRLVR   99 (165)
T ss_pred             hCCCCEEEEEEcHHHHHH
Confidence            344678999999998865

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.

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=98.36  E-value=1.4e-06  Score=81.31  Aligned_cols=129  Identities=24%  Similarity=0.332  Sum_probs=76.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC----ccc----ChhhHHHHH-H----HcccCCeeeeecchhhHHHh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS----NLL----GNNDLRHIL-I----ATENKSILVVEDIDCCIELQ   98 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~----~~~----~~~~l~~~~-~----~~~~~~vl~iDeid~l~~~~   98 (266)
                      -+|||+|.||||||-+.+.+++-+....|..--.    .++    ....-.++. .    -+..++|=+|||||.|-.. 
T Consensus       463 INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVtrd~dtkqlVLesGALVLSD~GiCCIDEFDKM~dS-  541 (804)
T KOG0478|consen  463 INILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVTKDPDTRQLVLESGALVLSDNGICCIDEFDKMSDS-  541 (804)
T ss_pred             ceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEEecCccceeeeecCcEEEcCCceEEchhhhhhhHH-
Confidence            4699999999999999999999885554433211    111    001111111 1    1356889999999998421 


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhh---------ccccCCCCceEEEEecCCC-----------C--CC
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID---------GLWSSCGDERIIIFTTNHK-----------E--RL  156 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~---------~~~~~~~~~~ivi~ttn~~-----------~--~l  156 (266)
                                                .-+-|+++|+         |...+.+.+.-|+|+.|+.           +  +|
T Consensus       542 --------------------------trSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp~k~i~eNI~L  595 (804)
T KOG0478|consen  542 --------------------------TRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNPNKSIIENINL  595 (804)
T ss_pred             --------------------------HHHHHHHHHHHhhhhHhhcceeeeccccceeeeeeccccccCCCCCchhhccCC
Confidence                                      1122333333         2222223445688999953           2  36


Q ss_pred             cccccCCCcceeE-EEcCCCCHHHHH----HHHHHhhC
Q 024550          157 DPALLRPGRMDMH-INMSHCTPSGFK----MLASNYLG  189 (266)
Q Consensus       157 d~al~r~~Rf~~~-i~~~~p~~~~~~----~i~~~~~~  189 (266)
                      +|.|++  ||+.+ +-+..||...=+    .|...|+.
T Consensus       596 pptLLS--RFDLIylllD~~DE~~Dr~La~HivsLy~e  631 (804)
T KOG0478|consen  596 PPTLLS--RFDLIFLLLDKPDERSDRRLADHIVALYPE  631 (804)
T ss_pred             Chhhhh--hhcEEEEEecCcchhHHHHHHHHHHHhccc
Confidence            899999  99965 455777776333    44454554

>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=98.36  E-value=4.4e-07  Score=68.17  Aligned_cols=30  Identities=40%  Similarity=0.793  Sum_probs=27.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      |+|.|||||||||+++.||..+|.+++.++
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d   31 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMD   31 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEec
Confidence            789999999999999999999998877665

...

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=98.33  E-value=3.6e-06  Score=84.51  Aligned_cols=139  Identities=19%  Similarity=0.205  Sum_probs=90.6

Q ss_pred             CCCCceeEEecCCCCChHHH-HHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcc-----------------cCCeeeee
Q 024550           28 KAWKRGYLLYGPPGTGKSSL-IAAMANYLKFDVYDLELSNLLGNNDLRHILIATE-----------------NKSILVVE   89 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~l-a~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~-----------------~~~vl~iD   89 (266)
                      +...++++++||||+|||++ .-++-++.-..++.++.+.-+.....-..+....                 ...|||.|
T Consensus      1491 lnt~R~~i~cGppGSgK~mlM~~sLrs~~~~ev~~~Nfs~~t~T~s~ls~Ler~t~yy~~tg~~~l~PK~~vK~lVLFcD 1570 (3164)
T COG5245        1491 LNTLRSYIYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMTPSKLSVLERETEYYPNTGVVRLYPKPVVKDLVLFCD 1570 (3164)
T ss_pred             HhccceEEEECCCCCccchhcchhhhhhhheeeeEEeeccccCCHHHHHHHHhhceeeccCCeEEEccCcchhheEEEee
Confidence            34467999999999999985 5578888888999999887765554444444321                 24799999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhh---hhhccccCCC------CceEEEEecCCCCC-----
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLN---FIDGLWSSCG------DERIIIFTTNHKER-----  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~---~l~~~~~~~~------~~~ivi~ttn~~~~-----  155 (266)
                      ||+ |.....                     ......--++.   +-.|+|.+..      .++++.+++|++..     
T Consensus      1571 eIn-Lp~~~~---------------------y~~~~vI~FlR~l~e~QGfw~s~~~~wvTI~~i~l~Gacnp~td~gRv~ 1628 (3164)
T COG5245        1571 EIN-LPYGFE---------------------YYPPTVIVFLRPLVERQGFWSSIAVSWVTICGIILYGACNPGTDEGRVK 1628 (3164)
T ss_pred             ccC-Cccccc---------------------cCCCceEEeeHHHHHhcccccchhhhHhhhcceEEEccCCCCCCcccCc
Confidence            999 432110                     00111111221   1123443322      35788999998754     


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCC
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA  191 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~  191 (266)
                      ++..|+|  | ...+.+..|.-.....|+..++...
T Consensus      1629 ~~eRf~r--~-~v~vf~~ype~~SL~~Iyea~l~~s 1661 (3164)
T COG5245        1629 YYERFIR--K-PVFVFCCYPELASLRNIYEAVLMGS 1661 (3164)
T ss_pred             cHHHHhc--C-ceEEEecCcchhhHHHHHHHHHHHH
Confidence            3466665  4 4668889999999999988777543

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=98.29  E-value=2.6e-06  Score=69.80  Aligned_cols=113  Identities=20%  Similarity=0.291  Sum_probs=65.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhh
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARA  106 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~  106 (266)
                      |......++|.|+-|+|||++.+.|+.+.    +.-+.... ...   +........-++.+||++.+....        
T Consensus        48 g~k~d~~lvl~G~QG~GKStf~~~L~~~~----~~d~~~~~-~~k---d~~~~l~~~~iveldEl~~~~k~~--------  111 (198)
T PF05272_consen   48 GCKNDTVLVLVGKQGIGKSTFFRKLGPEY----FSDSINDF-DDK---DFLEQLQGKWIVELDELDGLSKKD--------  111 (198)
T ss_pred             CCcCceeeeEecCCcccHHHHHHHHhHHh----ccCccccC-CCc---HHHHHHHHhHheeHHHHhhcchhh--------
Confidence            44444558899999999999999996662    21111222 111   233344556888999999874211        


Q ss_pred             cCCccccccccccccchhhhhhhhhh-hhccc-------cCCCCceEEEEecCCCCCC-cccccCCCcceeEEEcCC
Q 024550          107 ANPDFLIAGYEQQKQYHITLSGLLNF-IDGLW-------SSCGDERIIIFTTNHKERL-DPALLRPGRMDMHINMSH  174 (266)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~ll~~-l~~~~-------~~~~~~~ivi~ttn~~~~l-d~al~r~~Rf~~~i~~~~  174 (266)
                                      ...+..++.. .+...       ...+...++|+|||..+-| |+.--|  || ..|++..
T Consensus       112 ----------------~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnR--Rf-~~v~v~~  169 (198)
T PF05272_consen  112 ----------------VEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNR--RF-WPVEVSK  169 (198)
T ss_pred             ----------------HHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCe--EE-EEEEEcC
Confidence                            1111122211 11111       1112346899999998766 466678  88 6677765

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=98.26  E-value=4.6e-05  Score=68.58  Aligned_cols=91  Identities=23%  Similarity=0.259  Sum_probs=61.7

Q ss_pred             eEEEEecC--CCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCC---------------------CCcHHHHH
Q 024550          144 RIIIFTTN--HKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE---------------------HPLFVEIE  200 (266)
Q Consensus       144 ~ivi~ttn--~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~---------------------~~~~~~~~  200 (266)
                      .+|+.|++  ....|..+|-.  |.-..|.+...+.+..++.+...+....                     .....+++
T Consensus       185 HVIFlT~dv~~~k~LskaLPn--~vf~tI~L~Das~~~Ak~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld  262 (431)
T PF10443_consen  185 HVIFLTDDVSYSKPLSKALPN--RVFKTISLSDASPESAKQYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELD  262 (431)
T ss_pred             EEEEECCCCchhhhHHHhCCC--CceeEEeecCCCHHHHHHHHHHHhcccccccccccccccccccccccccccchHHHH
Confidence            34444444  22455666655  6667899999999999988888886541                     12456777


Q ss_pred             HHhhcCCCCHHHHHHHHHc---CCCHHHHHHHHHHHHHh
Q 024550          201 KLIATAKVTPADVAEQLMR---NEAPEFALSGLIEFLES  236 (266)
Q Consensus       201 ~l~~~~~~s~~~i~~~l~~---~~~~~~~~~~~~~~~~~  236 (266)
                      ..+...|.-.-|+..+..+   .+.+..|++.++.--..
T Consensus       263 ~~i~~LGGRltDLe~lvrRiksGe~p~~Av~~iI~qsa~  301 (431)
T PF10443_consen  263 ECIEPLGGRLTDLEFLVRRIKSGESPEEAVEEIISQSAS  301 (431)
T ss_pred             HHHHHcCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence            7778788777777655543   67888888887654433

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PRK00131 aroK shikimate kinase; Reviewed

Probab=98.24  E-value=1.3e-06  Score=69.69  Aligned_cols=35  Identities=29%  Similarity=0.364  Sum_probs=30.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +++..++|+||||||||++++.+|..++.+++..+
T Consensus         2 ~~~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d   36 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD   36 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            35668999999999999999999999999888544

>PF14516 AAA_35: AAA-like domain

Probab=98.22  E-value=4.1e-05  Score=67.93  Aligned_cols=135  Identities=15%  Similarity=0.186  Sum_probs=80.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-----h--------------------------------
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-----N--------------------------------   70 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-----~--------------------------------   70 (266)
                      +.-+.++||..+|||++...+...+   |...+.+++..+..     .                                
T Consensus        31 G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~  110 (331)
T PF14516_consen   31 GSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSK  110 (331)
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCCh
Confidence            4568999999999999998887665   67778888776431     0                                


Q ss_pred             hhHHHHH-----HHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC----
Q 024550           71 NDLRHIL-----IATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG----  141 (266)
Q Consensus        71 ~~l~~~~-----~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~----  141 (266)
                      ......|     .....|-||+|||+|.++..                         ......++..+..++....    
T Consensus       111 ~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~-------------------------~~~~~dF~~~LR~~~~~~~~~~~  165 (331)
T PF14516_consen  111 ISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEY-------------------------PQIADDFFGLLRSWYEQRKNNPI  165 (331)
T ss_pred             hhHHHHHHHHHHhcCCCCEEEEEechhhhccC-------------------------cchHHHHHHHHHHHHHhcccCcc
Confidence            0111111     12246889999999998641                         1122334444433332211    


Q ss_pred             -Cce-EEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          142 -DER-IIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       142 -~~~-ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                       ... ++++.+..+......-.+|..++..|.++..+.++...++..+-..
T Consensus       166 ~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~  216 (331)
T PF14516_consen  166 WQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLE  216 (331)
T ss_pred             cceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhcc
Confidence             122 2222222222211122355566778999999999999998877543

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=98.21  E-value=4.2e-05  Score=69.00  Aligned_cols=61  Identities=16%  Similarity=0.274  Sum_probs=39.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~   95 (266)
                      ..++++.||+|||||+++.+++...    |   ..++++.+...- ....+.......+|+|||+..+.
T Consensus       209 ~~Nli~lGp~GTGKThla~~l~~~~a~~sG---~f~T~a~Lf~~L-~~~~lg~v~~~DlLI~DEvgylp  273 (449)
T TIGR02688       209 NYNLIELGPKGTGKSYIYNNLSPYVILISG---GTITVAKLFYNI-STRQIGLVGRWDVVAFDEVATLK  273 (449)
T ss_pred             CCcEEEECCCCCCHHHHHHHHhHHHHHHcC---CcCcHHHHHHHH-HHHHHhhhccCCEEEEEcCCCCc
Confidence            4579999999999999999988772    3   112222221110 11333445568999999999864

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=98.21  E-value=1.1e-05  Score=66.68  Aligned_cols=40  Identities=25%  Similarity=0.399  Sum_probs=33.5

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      |++...-++++||||||||+++..++...   +.+.++++...
T Consensus         8 Gi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~   50 (209)
T TIGR02237         8 GVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG   50 (209)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            67777789999999999999999888654   66788888865

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.17  E-value=2.3e-05  Score=64.23  Aligned_cols=64  Identities=30%  Similarity=0.433  Sum_probs=38.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC----------hhhHHHHHHH-----------cccCCeee
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG----------NNDLRHILIA-----------TENKSILV   87 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~----------~~~l~~~~~~-----------~~~~~vl~   87 (266)
                      +..++.||||||||++++.+...+   +..++.+.+..-..          ...+..++..           .....+|+
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~~~~~~~~~~~vli   98 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKTGIEAQTIHSFLYRIPNGDDEGRPELPKKDVLI   98 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHTS-EEEHHHHTTEECCEECCSSCC-TSTSEEE
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhhCcchhhHHHHHhcCCcccccccccCCcccEEE
Confidence            458889999999999999887665   55666665543211          1112222211           12347999


Q ss_pred             eecchhhH
Q 024550           88 VEDIDCCI   95 (266)
Q Consensus        88 iDeid~l~   95 (266)
                      +||+..+.
T Consensus        99 VDEasmv~  106 (196)
T PF13604_consen   99 VDEASMVD  106 (196)
T ss_dssp             ESSGGG-B
T ss_pred             EecccccC
Confidence            99999764

>PRK07261 topology modulation protein; Provisional

Probab=98.17  E-value=5.1e-06  Score=66.64  Aligned_cols=32  Identities=25%  Similarity=0.394  Sum_probs=28.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      -++++|+||+||||+++.++..++.+++..+.
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~   33 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDT   33 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCC
Confidence            37899999999999999999999988776653

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.16  E-value=4.5e-06  Score=71.24  Aligned_cols=70  Identities=19%  Similarity=0.272  Sum_probs=56.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHH------HcCCcEEEEeCCcccChhhHHHHHHHc-----------------ccC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMAN------YLKFDVYDLELSNLLGNNDLRHILIAT-----------------ENK   83 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~------~~~~~~~~i~~~~~~~~~~l~~~~~~~-----------------~~~   83 (266)
                      .+.....+||.||.|.|||.+++.+..      .+..+|++++|..+.+...+..+|...                 ..+
T Consensus       204 a~rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadg  283 (531)
T COG4650         204 AIRSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADG  283 (531)
T ss_pred             HhhccCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCC
Confidence            445556699999999999999998863      557899999999998776666666432                 357


Q ss_pred             CeeeeecchhhHH
Q 024550           84 SILVVEDIDCCIE   96 (266)
Q Consensus        84 ~vl~iDeid~l~~   96 (266)
                      ++||+|||..+..
T Consensus       284 gmlfldeigelga  296 (531)
T COG4650         284 GMLFLDEIGELGA  296 (531)
T ss_pred             ceEehHhhhhcCc
Confidence            9999999998865

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=98.15  E-value=4.3e-06  Score=65.79  Aligned_cols=25  Identities=32%  Similarity=0.542  Sum_probs=21.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +-.+++.||+|||||++.+.+|.-.
T Consensus        29 Ge~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          29 GEFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             CceEEEeCCCCccHHHHHHHHHhcc
Confidence            3349999999999999999999855

>PRK08118 topology modulation protein; Reviewed

Probab=98.15  E-value=1.9e-06  Score=68.79  Aligned_cols=32  Identities=31%  Similarity=0.501  Sum_probs=29.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      .|+++||||+||||+++.|++.++.+++.++.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~   34 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDA   34 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecch
Confidence            58999999999999999999999999887773

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=98.14  E-value=3.5e-05  Score=69.99  Aligned_cols=125  Identities=16%  Similarity=0.194  Sum_probs=72.9

Q ss_pred             HHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc-ChhhHHHHH---HHcc--cCCeeeeecchhhHH
Q 024550           23 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL-GNNDLRHIL---IATE--NKSILVVEDIDCCIE   96 (266)
Q Consensus        23 ~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~-~~~~l~~~~---~~~~--~~~vl~iDeid~l~~   96 (266)
                      .......++ .++++||.+|||||+++.+.....-.++.++..+.. ....+.+.+   ....  ....+|||||+.+- 
T Consensus        30 ~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~~~l~d~~~~~~~~~~~~~~yifLDEIq~v~-  107 (398)
T COG1373          30 IKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLDEIQNVP-  107 (398)
T ss_pred             HhhcccCCc-EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcchhhHHHHHHHHHHhhccCCceEEEecccCch-
Confidence            333344444 799999999999999998888886555555554443 222232222   2222  35899999999763 


Q ss_pred             HhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC-cccccCCCcceeEEEcCCC
Q 024550           97 LQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL-DPALLRPGRMDMHINMSHC  175 (266)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l-d~al~r~~Rf~~~i~~~~p  175 (266)
                                              .+...+..+.+.       ... -++|.+++..-.. ..+-.-+||. ..+++.+.
T Consensus       108 ------------------------~W~~~lk~l~d~-------~~~-~v~itgsss~ll~~~~~~~L~GR~-~~~~l~Pl  154 (398)
T COG1373         108 ------------------------DWERALKYLYDR-------GNL-DVLITGSSSSLLSKEISESLAGRG-KDLELYPL  154 (398)
T ss_pred             ------------------------hHHHHHHHHHcc-------ccc-eEEEECCchhhhccchhhhcCCCc-eeEEECCC
Confidence                                    223333333322       111 3455555443222 2233335684 77899999


Q ss_pred             CHHHHHH
Q 024550          176 TPSGFKM  182 (266)
Q Consensus       176 ~~~~~~~  182 (266)
                      +..+...
T Consensus       155 SF~Efl~  161 (398)
T COG1373         155 SFREFLK  161 (398)
T ss_pred             CHHHHHh
Confidence            9988854

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=98.12  E-value=2.1e-05  Score=71.91  Aligned_cols=38  Identities=24%  Similarity=0.351  Sum_probs=29.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      .|..++|+|++|+||||++..+|..+   |..+..+++..+
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~  134 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTY  134 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCC
Confidence            35669999999999999999999877   555666665544

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=98.12  E-value=8.3e-06  Score=66.68  Aligned_cols=115  Identities=17%  Similarity=0.235  Sum_probs=57.9

Q ss_pred             eEEecCCCCChHHHHHHH-HHHc---CCcEEEEeCCccc-----C--hh------------------hHHHHHHHcccCC
Q 024550           34 YLLYGPPGTGKSSLIAAM-ANYL---KFDVYDLELSNLL-----G--NN------------------DLRHILIATENKS   84 (266)
Q Consensus        34 iLl~GppGtGKT~la~al-a~~~---~~~~~~i~~~~~~-----~--~~------------------~l~~~~~~~~~~~   84 (266)
                      .+++|.||+|||+.|-.. ....   |.+++. +...+.     .  ..                  .....+.....++
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t-ni~gL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT-NIPGLNIEKIQPVLGYDIPTRLIDLSDPDFEEDWDDPDDWRKLPKGS   81 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE---TTB-S--EEEE--TTT-S-----S--SSSEEGGGHHHHTTSGTT-
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE-ccCCcchhhhhhhccccccccccccccccchhhhhhhhhhcccCCCc
Confidence            578999999999876554 3322   565554 444222     0  00                  0111122233689


Q ss_pred             eeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCC
Q 024550           85 ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPG  164 (266)
Q Consensus        85 vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~  164 (266)
                      +++|||+...++.+.....                     .....++.+...   ...+.-||.+|-.+..+|+.+++  
T Consensus        82 liviDEa~~~~~~r~~~~~---------------------~~~~~~~~l~~h---Rh~g~diiliTQ~~~~id~~ir~--  135 (193)
T PF05707_consen   82 LIVIDEAQNFFPSRSWKGK---------------------KVPEIIEFLAQH---RHYGWDIILITQSPSQIDKFIRD--  135 (193)
T ss_dssp             EEEETTGGGTSB---T-T-------------------------HHHHGGGGC---CCTT-EEEEEES-GGGB-HHHHC--
T ss_pred             EEEEECChhhcCCCccccc---------------------cchHHHHHHHHh---CcCCcEEEEEeCCHHHHhHHHHH--
Confidence            9999999998763332100                     011222333222   22467899999999999999987  


Q ss_pred             cceeEEEcCCC
Q 024550          165 RMDMHINMSHC  175 (266)
Q Consensus       165 Rf~~~i~~~~p  175 (266)
                      ..+.++.+..+
T Consensus       136 lve~~~~~~k~  146 (193)
T PF05707_consen  136 LVEYHYHCRKL  146 (193)
T ss_dssp             CEEEEEEEEE-
T ss_pred             HHheEEEEEee
Confidence            88887777654

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=98.11  E-value=7.5e-05  Score=62.39  Aligned_cols=128  Identities=10%  Similarity=0.085  Sum_probs=92.3

Q ss_pred             CceeEEecCCC-CChHHHHHHHHHHcC---------CcEEEEeCCc-------ccChhhHHHHHHHcc------cCCeee
Q 024550           31 KRGYLLYGPPG-TGKSSLIAAMANYLK---------FDVYDLELSN-------LLGNNDLRHILIATE------NKSILV   87 (266)
Q Consensus        31 ~~~iLl~GppG-tGKT~la~ala~~~~---------~~~~~i~~~~-------~~~~~~l~~~~~~~~------~~~vl~   87 (266)
                      .+.+||.|..+ +||..++..++..+.         -.++.+....       ..+-..++++.....      ..-|++
T Consensus        15 shAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~~~p~~g~~KViI   94 (263)
T PRK06581         15 YNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLSKTSAISGYKVAI   94 (263)
T ss_pred             hheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHhhCcccCCcEEEE
Confidence            45799999998 999999888887662         3344554331       123344555444321      357999


Q ss_pred             eecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcce
Q 024550           88 VEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMD  167 (266)
Q Consensus        88 iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~  167 (266)
                      |+++|.|.                           ....+.||..++.    ++...++|..|..+..+.+.+++  || 
T Consensus        95 I~~ae~mt---------------------------~~AANALLKtLEE----PP~~t~fILit~~~~~LLpTIrS--RC-  140 (263)
T PRK06581         95 IYSAELMN---------------------------LNAANSCLKILED----APKNSYIFLITSRAASIISTIRS--RC-  140 (263)
T ss_pred             EechHHhC---------------------------HHHHHHHHHhhcC----CCCCeEEEEEeCChhhCchhHhh--ce-
Confidence            99999874                           2345667777664    45678888889899999999999  98 


Q ss_pred             eEEEcCCCCHHHHHHHHHHhhCCCC
Q 024550          168 MHINMSHCTPSGFKMLASNYLGIAE  192 (266)
Q Consensus       168 ~~i~~~~p~~~~~~~i~~~~~~~~~  192 (266)
                      ..+.|+.|....-.+++..++....
T Consensus       141 q~i~~~~p~~~~~~e~~~~~~~p~~  165 (263)
T PRK06581        141 FKINVRSSILHAYNELYSQFIQPIA  165 (263)
T ss_pred             EEEeCCCCCHHHHHHHHHHhccccc
Confidence            6699999999888888877776543

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=98.10  E-value=7.4e-06  Score=71.94  Aligned_cols=58  Identities=26%  Similarity=0.244  Sum_probs=42.4

Q ss_pred             CChHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550            1 MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus         1 l~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      |+++.++.+...+..++.....     +.+...|+|+|+||||||++++.+|..+|.+++.++
T Consensus       108 l~~~~~~~~~~~l~~~~~~~~~-----~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~id~D  165 (309)
T PRK08154        108 ASPAQLARVRDALSGMLGAGRR-----AARRRRIALIGLRGAGKSTLGRMLAARLGVPFVELN  165 (309)
T ss_pred             CCHHHHHHHHHHHHHHHhhhhh-----ccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEeHH
Confidence            3555555555555554444332     445667999999999999999999999999998543

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=98.10  E-value=8.7e-06  Score=77.66  Aligned_cols=26  Identities=50%  Similarity=0.773  Sum_probs=23.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ++.++|+||||||||+++++++..+.
T Consensus        50 ~~~~l~~G~~G~GKttla~~l~~~l~   75 (637)
T PRK13765         50 RRHVMMIGSPGTGKSMLAKAMAELLP   75 (637)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHcC
Confidence            35799999999999999999998875

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.09  E-value=2.1e-05  Score=70.92  Aligned_cols=25  Identities=44%  Similarity=0.773  Sum_probs=21.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..++|+||+|+||||++..+|..+
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~  198 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIY  198 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4569999999999999999998765

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=98.06  E-value=4.6e-05  Score=65.25  Aligned_cols=63  Identities=14%  Similarity=0.207  Sum_probs=39.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCC-----cEEE--EeCCcccChhhH-------HHHHH---HcccCCeeeeecchhhHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKF-----DVYD--LELSNLLGNNDL-------RHILI---ATENKSILVVEDIDCCIE   96 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~-----~~~~--i~~~~~~~~~~l-------~~~~~---~~~~~~vl~iDeid~l~~   96 (266)
                      +=|+|++||||+++++.+|+.+..     +++.  +....+...+.+       ...+.   ...+.+++++||+|.|.+
T Consensus       113 LSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKmp~  192 (344)
T KOG2170|consen  113 LSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKLPP  192 (344)
T ss_pred             EEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHHHHHHHHHHHHHHHHHHhcCCceEEechhhhcCH
Confidence            458999999999999999998832     2221  111222222222       11111   135689999999998853

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.06  E-value=4.9e-05  Score=59.36  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=22.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...++++|+||+||||++.-++..+
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHH
Confidence            4469999999999999999999877

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=98.05  E-value=1.6e-05  Score=71.22  Aligned_cols=64  Identities=25%  Similarity=0.345  Sum_probs=42.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----C-CcEEEEeCCccc----------------------ChhhHHHHHHHcccC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----K-FDVYDLELSNLL----------------------GNNDLRHILIATENK   83 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~-~~~~~i~~~~~~----------------------~~~~l~~~~~~~~~~   83 (266)
                      +..++|+||+|+||||++..||..+    | ..+..+....+.                      +...+...+......
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~~  216 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELRNK  216 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhcCC
Confidence            4469999999999999999999764    3 234444433321                      123344455556677


Q ss_pred             Ceeeeecchhh
Q 024550           84 SILVVEDIDCC   94 (266)
Q Consensus        84 ~vl~iDeid~l   94 (266)
                      .+++||.....
T Consensus       217 DlVLIDTaG~~  227 (374)
T PRK14722        217 HMVLIDTIGMS  227 (374)
T ss_pred             CEEEEcCCCCC
Confidence            88999988743

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=98.05  E-value=5.2e-06  Score=69.01  Aligned_cols=64  Identities=25%  Similarity=0.442  Sum_probs=38.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCc--cc--------------ChhhHHHHHHH----cccCCeeeeec
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSN--LL--------------GNNDLRHILIA----TENKSILVVED   90 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~--~~--------------~~~~l~~~~~~----~~~~~vl~iDe   90 (266)
                      +..+||||+||+|||++|+.++...  -++..+.+.  +.              .-..+.+.+..    .....+|+||.
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~~~~--~~~~~d~~~~~l~g~~~~~v~~~d~~~~~~~~~d~l~~~~~~~~~ydtVVIDs   89 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLPGKT--LVLSFDMSSKVLIGDENVDIADHDDMPPIQAMVEFYVMQNIQAVKYDNIVIDN   89 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcCCCC--EEEeccccchhccCCCCCceeecCCCCCHHHHHHHHHHHHhccccCCEEEEec
Confidence            4569999999999999999987421  122222211  00              11223233322    23468999999


Q ss_pred             chhhHH
Q 024550           91 IDCCIE   96 (266)
Q Consensus        91 id~l~~   96 (266)
                      ++.+..
T Consensus        90 I~~l~~   95 (220)
T TIGR01618        90 ISALQN   95 (220)
T ss_pred             HHHHHH
Confidence            999854

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.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=98.04  E-value=3.1e-05  Score=61.99  Aligned_cols=64  Identities=19%  Similarity=0.263  Sum_probs=45.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChh-----------------------hHHHHHHH-cccCCeeee
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNN-----------------------DLRHILIA-TENKSILVV   88 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~-----------------------~l~~~~~~-~~~~~vl~i   88 (266)
                      .+|+.||||+|||++|..++..++.+.+++.........                       .+...+.. ..++.+++|
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~~~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~~~~VlI   82 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATAQPFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAPGRCVLV   82 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCCCCChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCCCCEEEe
Confidence            489999999999999999999988887777765543221                       23444444 344667888


Q ss_pred             ecchhhHH
Q 024550           89 EDIDCCIE   96 (266)
Q Consensus        89 Deid~l~~   96 (266)
                      |-+..+..
T Consensus        83 D~Lt~~~~   90 (170)
T PRK05800         83 DCLTTWVT   90 (170)
T ss_pred             hhHHHHHH
Confidence            88877653

>PRK13947 shikimate kinase; Provisional

Probab=98.04  E-value=4.9e-06  Score=66.42  Aligned_cols=31  Identities=32%  Similarity=0.460  Sum_probs=28.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +|+|.|+||||||++++.+|+.+|.+++..+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d   33 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTD   33 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            5899999999999999999999999998766

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=98.04  E-value=1.5e-05  Score=70.57  Aligned_cols=27  Identities=33%  Similarity=0.564  Sum_probs=23.4

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+|+|++|||.-|||||+|.-.+...+
T Consensus       112 ~~PkGlYlYG~VGcGKTmLMDlFy~~~  138 (467)
T KOG2383|consen  112 GPPKGLYLYGSVGCGKTMLMDLFYDAL  138 (467)
T ss_pred             CCCceEEEecccCcchhHHHHHHhhcC
Confidence            358999999999999999998877555

>PRK03839 putative kinase; Provisional

Probab=98.03  E-value=4.8e-06  Score=67.19  Aligned_cols=31  Identities=29%  Similarity=0.514  Sum_probs=27.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .|+|.|+||+||||+++.+|+.++.+++.++
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            3889999999999999999999999887654

>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=98.03  E-value=4.7e-06  Score=64.33  Aligned_cols=26  Identities=46%  Similarity=0.724  Sum_probs=23.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      ++++|||||||||+++.++..++..+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~~~   27 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGAVV   27 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCEE
Confidence            68999999999999999999998333

...

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=98.03  E-value=3.6e-05  Score=67.83  Aligned_cols=39  Identities=23%  Similarity=0.307  Sum_probs=34.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL   68 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~   68 (266)
                      .|..+.|||-.|||||++++.+-+.++.+.+.+++-+..
T Consensus        29 ~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecf   67 (438)
T KOG2543|consen   29 IPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECF   67 (438)
T ss_pred             cceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhc
Confidence            466789999999999999999999999999998877654

>PRK00625 shikimate kinase; Provisional

Probab=98.02  E-value=5.6e-06  Score=66.48  Aligned_cols=31  Identities=32%  Similarity=0.596  Sum_probs=28.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .|+|+|.||+|||++++.+|+.++.+++.++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhh
Confidence            4899999999999999999999999998776

>PRK05973 replicative DNA helicase; Provisional

Probab=98.01  E-value=4.4e-05  Score=64.25  Aligned_cols=39  Identities=23%  Similarity=0.016  Sum_probs=30.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |+++...+++.|+||+|||+++-.++...   |.+.+++++.
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSlE  101 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLE  101 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence            67677779999999999999888776644   6666666544

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

Probab=98.00  E-value=2.7e-05  Score=76.08  Aligned_cols=130  Identities=18%  Similarity=0.298  Sum_probs=84.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccC--------hhhHHHHHHH---cccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLG--------NNDLRHILIA---TENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~--------~~~l~~~~~~---~~~~~vl~iD   89 (266)
                      +++.+|+|.||+|||.++.-+|...          +..++.++...+..        +..+..+...   ...+.|||||
T Consensus       208 k~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfig  287 (898)
T KOG1051|consen  208 KNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLG  287 (898)
T ss_pred             CCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEec
Confidence            4689999999999999999999866          45666777665543        2334555544   3367899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-----CCCcccccCCC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-----ERLDPALLRPG  164 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-----~~ld~al~r~~  164 (266)
                      |++.+.+.....                  .     .....+.+......  .+..+|+||..-     ..-+|+|-+  
T Consensus       288 elh~lvg~g~~~------------------~-----~~d~~nlLkp~L~r--g~l~~IGatT~e~Y~k~iekdPalEr--  340 (898)
T KOG1051|consen  288 ELHWLVGSGSNY------------------G-----AIDAANLLKPLLAR--GGLWCIGATTLETYRKCIEKDPALER--  340 (898)
T ss_pred             ceeeeecCCCcc------------------h-----HHHHHHhhHHHHhc--CCeEEEecccHHHHHHHHhhCcchhh--
Confidence            999986522110                  0     11222333322222  337888877632     223899999  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhh
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                      ||.. +.++.|+.+....|+...-
T Consensus       341 rw~l-~~v~~pS~~~~~~iL~~l~  363 (898)
T KOG1051|consen  341 RWQL-VLVPIPSVENLSLILPGLS  363 (898)
T ss_pred             Ccce-eEeccCcccchhhhhhhhh
Confidence            9965 7899999877555554433

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=97.99  E-value=9.2e-05  Score=65.23  Aligned_cols=30  Identities=37%  Similarity=0.334  Sum_probs=25.5

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      ..+..|-|+|+-|+|||++++.+-+.+...
T Consensus        18 ~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen   18 DDPFVIGLYGEWGSGKSSFLNMLKEELKED   47 (325)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            456779999999999999999998887444

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.99  E-value=6e-06  Score=63.47  Aligned_cols=44  Identities=30%  Similarity=0.508  Sum_probs=33.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHI   76 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~   76 (266)
                      ..+||++|-|||||||++..+|..++.+.+.++  ++..+.++..-
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~~i~is--d~vkEn~l~~g   50 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLEYIEIS--DLVKENNLYEG   50 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCceEehh--hHHhhhcchhc
Confidence            347999999999999999999999988766554  44444444333

>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=97.99  E-value=7e-06  Score=64.17  Aligned_cols=31  Identities=29%  Similarity=0.436  Sum_probs=27.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +|+|+||||+|||++++.+|..++.+++..+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d   31 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD   31 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            3789999999999999999999999887655

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.

>PRK13949 shikimate kinase; Provisional

Probab=97.98  E-value=7e-06  Score=65.68  Aligned_cols=31  Identities=35%  Similarity=0.482  Sum_probs=28.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .|+|+||||+|||++++.+|..++.+++..+
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~~id~D   33 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLSFIDLD   33 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCeeccc
Confidence            5899999999999999999999999887765

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.97  E-value=4.5e-05  Score=77.77  Aligned_cols=175  Identities=14%  Similarity=0.164  Sum_probs=106.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhH----------------HHHHHHcccCCeeeeecchhhHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDL----------------RHILIATENKSILVVEDIDCCIE   96 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l----------------~~~~~~~~~~~vl~iDeid~l~~   96 (266)
                      .+|+-||..+|||+.+..+|...|..|++++-...+.-...                ..+.....++-.+++||+...+.
T Consensus       890 P~LiQGpTSSGKTSMI~yla~~tghkfVRINNHEHTdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~GyWIVLDELNLApT  969 (4600)
T COG5271         890 PLLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIVLDELNLAPT  969 (4600)
T ss_pred             cEEEecCCCCCcchHHHHHHHHhCccEEEecCcccchHHHHhhceeecCCCceeeehhHHHHHHhcCcEEEeeccccCcH
Confidence            49999999999999999999999999999997766521111                12223445678999999985432


Q ss_pred             HhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC-------CCCceEEEEecCCCC------CCcccccCC
Q 024550           97 LQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS-------CGDERIIIFTTNHKE------RLDPALLRP  163 (266)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-------~~~~~ivi~ttn~~~------~ld~al~r~  163 (266)
                                              ..-..++.||.--..+.-+       +.....++||-|+|.      .|..||+. 
T Consensus       970 ------------------------DVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRN- 1024 (4600)
T COG5271         970 ------------------------DVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRN- 1024 (4600)
T ss_pred             ------------------------HHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHh-
Confidence                                    2223334444322222111       123456778888874      46788888 


Q ss_pred             CcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHcCCCHHHHHHHHHHHHHhh
Q 024550          164 GRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLESK  237 (266)
Q Consensus       164 ~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~~~~~~~~~~~~~~~~~~~  237 (266)
                       || ..++|..-..++...|+...-... ...+..+.+...  +++.+.-.+.+.-..+.-..++++..|.-+.
T Consensus      1025 -RF-lE~hFddipedEle~ILh~rc~ia-pSyakKiVeVyr--~Ls~rRs~~rifeqknsfaTLRDLFrWa~R~ 1093 (4600)
T COG5271        1025 -RF-LEMHFDDIPEDELEEILHGRCEIA-PSYAKKIVEVYR--GLSSRRSINRIFEQKNSFATLRDLFRWAGRI 1093 (4600)
T ss_pred             -hh-HhhhcccCcHHHHHHHHhccCccC-HHHHHHHHHHHH--HhhhhhhHHHHHHhhhhHHHHHHHHHHhccc
Confidence             99 668888888888888776433221 112222322222  2444444444444445666677777775443

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.97  E-value=6.1e-05  Score=63.41  Aligned_cols=39  Identities=28%  Similarity=0.296  Sum_probs=31.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |++.+..++++||||||||+++..++...   |.+.++++..
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e   62 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE   62 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC
Confidence            78888889999999999999999987543   5566666553

>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=97.96  E-value=1.4e-05  Score=63.88  Aligned_cols=23  Identities=35%  Similarity=0.739  Sum_probs=20.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++|+|+||+||||+++.+...+
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            37999999999999999999887

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.

>PLN03210 Resistant to P

Probab=97.96  E-value=0.00021  Score=73.49  Aligned_cols=28  Identities=25%  Similarity=0.324  Sum_probs=23.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      ..+-+-|+||+|+||||+|+++++.+..
T Consensus       206 ~~~vvgI~G~gGiGKTTLA~~l~~~l~~  233 (1153)
T PLN03210        206 EVRMVGIWGSSGIGKTTIARALFSRLSR  233 (1153)
T ss_pred             ceEEEEEEcCCCCchHHHHHHHHHHHhh
Confidence            3455889999999999999999887743

syringae 6; Provisional

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.96  E-value=6.9e-06  Score=65.22  Aligned_cols=32  Identities=31%  Similarity=0.415  Sum_probs=29.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+++|+|++|+||||+.+++|+.++.+|+.++
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D   34 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTD   34 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccch
Confidence            46999999999999999999999999998776

>PRK14532 adenylate kinase; Provisional

Probab=97.95  E-value=8.5e-06  Score=66.16  Aligned_cols=30  Identities=20%  Similarity=0.420  Sum_probs=26.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .++|.||||+||||+++.+|+.+|..++.+
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            489999999999999999999998766543

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=97.95  E-value=1.2e-05  Score=74.90  Aligned_cols=129  Identities=18%  Similarity=0.310  Sum_probs=80.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC----ccc----ChhhHHHHHH-----HcccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS----NLL----GNNDLRHILI-----ATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~----~~~----~~~~l~~~~~-----~~~~~~vl~iDeid~l~~~~~   99 (266)
                      +|+++|.||||||-+.++.+.-+...+|..--+    .++    ....-.+...     ....++|=+|||||.+...  
T Consensus       380 nv~iVGDPgt~KSQfLk~v~~fsPR~vYtsGkaSSaAGLTaaVvkD~esgdf~iEAGALmLADnGICCIDEFDKMd~~--  457 (764)
T KOG0480|consen  380 NVCIVGDPGTGKSQFLKAVCAFSPRSVYTSGKASSAAGLTAAVVKDEESGDFTIEAGALMLADNGICCIDEFDKMDVK--  457 (764)
T ss_pred             eEEEeCCCCccHHHHHHHHhccCCcceEecCcccccccceEEEEecCCCCceeeecCcEEEccCceEEechhcccChH--
Confidence            499999999999999999999887776654322    121    0011111111     1246899999999988430  


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhh---------ccccCCCCceEEEEecCCCC-------------CCc
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID---------GLWSSCGDERIIIFTTNHKE-------------RLD  157 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~---------~~~~~~~~~~ivi~ttn~~~-------------~ld  157 (266)
                                               -.-.++..|+         |...+.+.+.-|||++|+..             ++.
T Consensus       458 -------------------------dqvAihEAMEQQtISIaKAGv~aTLnARtSIlAAANPv~GhYdR~ktl~eNi~ms  512 (764)
T KOG0480|consen  458 -------------------------DQVAIHEAMEQQTISIAKAGVVATLNARTSILAAANPVGGHYDRKKTLRENINMS  512 (764)
T ss_pred             -------------------------hHHHHHHHHHhheehheecceEEeecchhhhhhhcCCcCCccccccchhhhcCCC
Confidence                                     0112334443         22222223445888888642             367


Q ss_pred             ccccCCCccee-EEEcCCCCHHHHHHHHHHhhCC
Q 024550          158 PALLRPGRMDM-HINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       158 ~al~r~~Rf~~-~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      +++++  ||+. .|-+..|++..=..|-++.+..
T Consensus       513 ApimS--RFDL~FiLlD~~nE~~D~~ia~hIld~  544 (764)
T KOG0480|consen  513 APIMS--RFDLFFILLDDCNEVVDYAIARHILDL  544 (764)
T ss_pred             chhhh--hhcEEEEEecCCchHHHHHHHHHHHHH
Confidence            89999  9994 4777889887766666655544

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.94  E-value=8.8e-06  Score=65.69  Aligned_cols=28  Identities=25%  Similarity=0.511  Sum_probs=24.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ++++||||+||||+++.+|..+|...+.
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is   29 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLS   29 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEE
Confidence            6899999999999999999999865443

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.

>PF13479 AAA_24: AAA domain

Probab=97.94  E-value=2.7e-05  Score=64.66  Aligned_cols=61  Identities=25%  Similarity=0.394  Sum_probs=37.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc---------------cChhhHHHHHHH----cccCCeeeeecc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL---------------LGNNDLRHILIA----TENKSILVVEDI   91 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~---------------~~~~~l~~~~~~----~~~~~vl~iDei   91 (266)
                      +-.++||||||+|||+++..+    +-+ +.+++..-               .+-..+.+.+..    ...--+|+||.+
T Consensus         3 ~~~~lIyG~~G~GKTt~a~~~----~k~-l~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y~tiVIDsi   77 (213)
T PF13479_consen    3 PIKILIYGPPGSGKTTLAASL----PKP-LFIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEEDEADYDTIVIDSI   77 (213)
T ss_pred             ceEEEEECCCCCCHHHHHHhC----CCe-EEEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhccCCCCEEEEECH
Confidence            346999999999999999887    222 22222111               122334444432    235689999998


Q ss_pred             hhhHH
Q 024550           92 DCCIE   96 (266)
Q Consensus        92 d~l~~   96 (266)
                      +.+..
T Consensus        78 s~~~~   82 (213)
T PF13479_consen   78 SWLED   82 (213)
T ss_pred             HHHHH
Confidence            88744

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=97.94  E-value=6.8e-06  Score=78.23  Aligned_cols=63  Identities=22%  Similarity=0.347  Sum_probs=41.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe----CCcccCh---hhH-HHHHHH-----cccCCeeeeecchhhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE----LSNLLGN---NDL-RHILIA-----TENKSILVVEDIDCCI   95 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~----~~~~~~~---~~l-~~~~~~-----~~~~~vl~iDeid~l~   95 (266)
                      ++||.|-||||||.|.+.+++-+...++..-    ...++..   ... .++...     ...++|.+|||+|.+-
T Consensus       321 nILLvGDPgtaKSqlLk~v~~~aPr~vytsgkgss~~GLTAav~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm~  396 (682)
T COG1241         321 HILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSSAAGLTAAVVRDKVTGEWVLEAGALVLADGGVCCIDEFDKMN  396 (682)
T ss_pred             eEEEcCCCchhHHHHHHHHHhhCCceEEEccccccccCceeEEEEccCCCeEEEeCCEEEEecCCEEEEEeccCCC
Confidence            5999999999999999999998876655432    2222210   001 111111     2468999999999773

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.93  E-value=0.00019  Score=64.29  Aligned_cols=23  Identities=35%  Similarity=0.626  Sum_probs=21.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+++||||+|||+|++.+++...
T Consensus       172 ~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        172 GLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             EEEeCCCCCChhHHHHHHHHHHH
Confidence            89999999999999999998763

>PRK13948 shikimate kinase; Provisional

Probab=97.92  E-value=1.3e-05  Score=64.86  Aligned_cols=35  Identities=26%  Similarity=0.159  Sum_probs=31.4

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +++..|+|.|++|||||++++.+|..++.+|+..+
T Consensus         8 ~~~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D   42 (182)
T PRK13948          8 RPVTWVALAGFMGTGKSRIGWELSRALMLHFIDTD   42 (182)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEECC
Confidence            34578999999999999999999999999998666

>PRK14531 adenylate kinase; Provisional

Probab=97.92  E-value=1.2e-05  Score=65.18  Aligned_cols=31  Identities=26%  Similarity=0.467  Sum_probs=27.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..++++||||+||||+++.+|..+|.+.+.+
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            4599999999999999999999998876543

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.91  E-value=6.3e-05  Score=65.20  Aligned_cols=36  Identities=25%  Similarity=0.313  Sum_probs=27.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----C-CcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----K-FDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~-~~~~~i~~~~   66 (266)
                      +..++|+||+|+||||++..+|..+    | ..+..+++..
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~  234 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDT  234 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCc
Confidence            3458899999999999999998766    3 4555666554

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.91  E-value=5.4e-05  Score=68.01  Aligned_cols=69  Identities=23%  Similarity=0.307  Sum_probs=47.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCccc--------------------ChhhHHHHHHH--cc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLL--------------------GNNDLRHILIA--TE   81 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~--------------------~~~~l~~~~~~--~~   81 (266)
                      |+++..-++|+||||+|||+++..+|...   +.++++++.....                    ....+..++..  ..
T Consensus        78 Gi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EEs~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~  157 (372)
T cd01121          78 GLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEESPEQIKLRADRLGISTENLYLLAETNLEDILASIEEL  157 (372)
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCcCHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHHhc
Confidence            57777779999999999999999888765   3567777654321                    01122223222  23


Q ss_pred             cCCeeeeecchhhH
Q 024550           82 NKSILVVEDIDCCI   95 (266)
Q Consensus        82 ~~~vl~iDeid~l~   95 (266)
                      ++.+|+||++..+.
T Consensus       158 ~~~lVVIDSIq~l~  171 (372)
T cd01121         158 KPDLVIIDSIQTVY  171 (372)
T ss_pred             CCcEEEEcchHHhh
Confidence            68899999998875

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=97.91  E-value=4.3e-05  Score=67.05  Aligned_cols=70  Identities=19%  Similarity=0.251  Sum_probs=45.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC------------------hhhHH---HHH---HH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG------------------NNDLR---HIL---IA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~------------------~~~l~---~~~---~~   79 (266)
                      |++..+.++++||||||||+|+..++...   |.+.+.+++.....                  .....   ...   ..
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~  130 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVR  130 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhh
Confidence            57777779999999999999988766544   56666666543221                  01111   111   11


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      .....+++||-+..+.+
T Consensus       131 ~~~~~lIVIDSv~al~~  147 (321)
T TIGR02012       131 SGAVDIIVVDSVAALVP  147 (321)
T ss_pred             ccCCcEEEEcchhhhcc
Confidence            23578899999998864

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.

>PRK06217 hypothetical protein; Validated

Probab=97.91  E-value=1.2e-05  Score=65.22  Aligned_cols=31  Identities=29%  Similarity=0.430  Sum_probs=28.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .|+|.|+||+||||+++.|+..++.+++..+
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcC
Confidence            4899999999999999999999998876655

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=97.90  E-value=0.00017  Score=63.33  Aligned_cols=156  Identities=15%  Similarity=0.218  Sum_probs=93.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHH------------HcccCCeeeeecchhhHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILI------------ATENKSILVVEDIDCCIEL   97 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~------------~~~~~~vl~iDeid~l~~~   97 (266)
                      .+|+.|..||||-.+|+++....   ..||+.++|+.+.....=.++|.            ....++.+|+|||..+.+ 
T Consensus       229 PLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNCA~lPe~~aEsElFG~apg~~gk~GffE~AngGTVlLDeIgEmSp-  307 (511)
T COG3283         229 PLLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLPEDAAESELFGHAPGDEGKKGFFEQANGGTVLLDEIGEMSP-  307 (511)
T ss_pred             CeEEecCCCchHHHHHHHHhhcCcccCCCeeEeecCCCchhHhHHHHhcCCCCCCCccchhhhccCCeEEeehhhhcCH-
Confidence            48999999999999999988766   68999999999875433334443            334578899999998753 


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhh-ccccCCCC------ceEEEEecCCC-------CCCcccccCC
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID-GLWSSCGD------ERIIIFTTNHK-------ERLDPALLRP  163 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~-~~~~~~~~------~~ivi~ttn~~-------~~ld~al~r~  163 (266)
                                                ..+..+|..+. +...+.+.      .+-||+||..+       ..+-..|.- 
T Consensus       308 --------------------------~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~~lv~~g~fReDLfy-  360 (511)
T COG3283         308 --------------------------RLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVELVQKGKFREDLFY-  360 (511)
T ss_pred             --------------------------HHHHHHHHHhcCCceeecCCcceEEEEEEEEecccccHHHHHhcCchHHHHHH-
Confidence                                      23344555553 33222222      36788888653       222333443 


Q ss_pred             CcceeEEEcCCCCHHHH----HHHHHHhhC-------CCCCCcHHHHHHHhhcCC--CCHHHHHHHHH
Q 024550          164 GRMDMHINMSHCTPSGF----KMLASNYLG-------IAEHPLFVEIEKLIATAK--VTPADVAEQLM  218 (266)
Q Consensus       164 ~Rf~~~i~~~~p~~~~~----~~i~~~~~~-------~~~~~~~~~~~~l~~~~~--~s~~~i~~~l~  218 (266)
                       |+. ++.+..|.-.+|    .-+.+.|+.       .....+..++......+.  .+.+++.|.+.
T Consensus       361 -RLN-VLtl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~~y~WpGNVRqL~N~iy  426 (511)
T COG3283         361 -RLN-VLTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLTRYAWPGNVRQLKNAIY  426 (511)
T ss_pred             -Hhh-eeeecCCccccCcccchHHHHHHHHHHHHHhCCCCCccCHHHHHHHHHcCCCccHHHHHHHHH
Confidence             553 355555554433    223333332       223344455555555554  56677777764

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.90  E-value=1.2e-05  Score=62.75  Aligned_cols=28  Identities=32%  Similarity=0.443  Sum_probs=24.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ++|+|+||+||||+++.++..++..++.
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~   29 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFID   29 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEe
Confidence            6899999999999999999998876553

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

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.90  E-value=7.1e-05  Score=65.09  Aligned_cols=132  Identities=20%  Similarity=0.232  Sum_probs=77.7

Q ss_pred             CCceeEEecCCCCChHHHHHH-H--HHHcCCcEEEEeCCcccCh---------------------------hhHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAA-M--ANYLKFDVYDLELSNLLGN---------------------------NDLRHILIA   79 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~a-l--a~~~~~~~~~i~~~~~~~~---------------------------~~l~~~~~~   79 (266)
                      ...++++.||.|+|||++... +  +.+.|-+++.+........                           ..+..++..
T Consensus        48 EsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~al~~I~rql~~e~~~~~k~~gsfte~l~~lL~~  127 (408)
T KOG2228|consen   48 ESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIALKGITRQLALELNRIVKSFGSFTENLSKLLEA  127 (408)
T ss_pred             CCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHHHHHHHHHHHHHHhhhheeecccchhHHHHHHH
Confidence            466799999999999986543 3  3367888888776654421                           111222221


Q ss_pred             c------ccCCeee-eecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC
Q 024550           80 T------ENKSILV-VEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH  152 (266)
Q Consensus        80 ~------~~~~vl~-iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~  152 (266)
                      .      +...|+| +||||..++                        ....  .-+.|.+|- ......++.+|+.|.+
T Consensus       128 L~~~~~~t~~~ViFIldEfDlf~~------------------------h~rQ--tllYnlfDi-sqs~r~Piciig~Ttr  180 (408)
T KOG2228|consen  128 LKKGDETTSGKVIFILDEFDLFAP------------------------HSRQ--TLLYNLFDI-SQSARAPICIIGVTTR  180 (408)
T ss_pred             HhcCCCCCCceEEEEeehhhcccc------------------------chhh--HHHHHHHHH-HhhcCCCeEEEEeecc
Confidence            1      1223555 678997653                        1111  112333332 2222356888887776


Q ss_pred             CC---CCcccccCCCcceeE-EEcCC-CCHHHHHHHHHHhhCC
Q 024550          153 KE---RLDPALLRPGRMDMH-INMSH-CTPSGFKMLASNYLGI  190 (266)
Q Consensus       153 ~~---~ld~al~r~~Rf~~~-i~~~~-p~~~~~~~i~~~~~~~  190 (266)
                      .+   .|.....+  ||... |+|+. ...++...+++..+..
T Consensus       181 ld~lE~LEKRVKS--RFshr~I~m~~~~~l~~yv~l~r~ll~v  221 (408)
T KOG2228|consen  181 LDILELLEKRVKS--RFSHRVIFMLPSLPLGDYVDLYRKLLSV  221 (408)
T ss_pred             ccHHHHHHHHHHh--hcccceeeccCCCChHHHHHHHHHHhcC
Confidence            54   45577788  88854 66644 4457778888877743

>PTZ00202 tuzin; Provisional

Probab=97.88  E-value=0.00066  Score=61.69  Aligned_cols=36  Identities=22%  Similarity=0.191  Sum_probs=30.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      .+.-+.|.||+|||||++++.+...++.+.+.++..
T Consensus       285 ~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNpr  320 (550)
T PTZ00202        285 HPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVR  320 (550)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCC
Confidence            345678999999999999999999998777777766

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.87  E-value=1.2e-05  Score=64.65  Aligned_cols=33  Identities=27%  Similarity=0.320  Sum_probs=28.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      +.++|.||||+||||+++.++..++.+++.++.
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~~~~~~~~~   35 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLAEPWLHFGV   35 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhCCCccccCc
Confidence            468999999999999999999999877665543

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>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=97.86  E-value=1.4e-05  Score=64.96  Aligned_cols=29  Identities=31%  Similarity=0.535  Sum_probs=25.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |+|+||||+|||++++.||..+|..++.+
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~   30 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHIST   30 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            78999999999999999999998766553

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.86  E-value=0.00014  Score=58.19  Aligned_cols=63  Identities=17%  Similarity=0.247  Sum_probs=44.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh-----------------------hhHHHHHHHcccCCeeeeec
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN-----------------------NDLRHILIATENKSILVVED   90 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~-----------------------~~l~~~~~~~~~~~vl~iDe   90 (266)
                      +|++||+|+|||++|..++...+.+.+++....-.+.                       ..+...+...+.+.+++||-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~~~~d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLIDc   81 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATAEAFDDEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLIDC   81 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEccCcCCHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEEc
Confidence            6899999999999999999887777877765543321                       22333343333456788888


Q ss_pred             chhhHH
Q 024550           91 IDCCIE   96 (266)
Q Consensus        91 id~l~~   96 (266)
                      +..+..
T Consensus        82 lt~~~~   87 (169)
T cd00544          82 LTLWVT   87 (169)
T ss_pred             HhHHHH
Confidence            876653

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.86  E-value=6.8e-05  Score=69.12  Aligned_cols=70  Identities=26%  Similarity=0.323  Sum_probs=48.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC--------------------hhhHHHHHHHc--c
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG--------------------NNDLRHILIAT--E   81 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~--------------------~~~l~~~~~~~--~   81 (266)
                      |+++..-++|+||||+|||+++..++...   +.++++++......                    ...+..++...  .
T Consensus        76 Gi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~  155 (446)
T PRK11823         76 GLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEE  155 (446)
T ss_pred             CccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccccHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHHhh
Confidence            67777779999999999999999998765   56777777543211                    11222332222  2


Q ss_pred             cCCeeeeecchhhHH
Q 024550           82 NKSILVVEDIDCCIE   96 (266)
Q Consensus        82 ~~~vl~iDeid~l~~   96 (266)
                      .+.+++||.+..+..
T Consensus       156 ~~~lVVIDSIq~l~~  170 (446)
T PRK11823        156 KPDLVVIDSIQTMYS  170 (446)
T ss_pred             CCCEEEEechhhhcc
Confidence            578899999987753

>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=97.85  E-value=1.6e-05  Score=61.53  Aligned_cols=30  Identities=30%  Similarity=0.481  Sum_probs=27.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      |.+.|+||||||++++.+|..++.+++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            679999999999999999999999987776

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.84  E-value=1.5e-05  Score=63.13  Aligned_cols=27  Identities=33%  Similarity=0.593  Sum_probs=24.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      ++++|||||||||+++.++..++..++
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v   27 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFI   27 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEE
Confidence            578999999999999999999986554

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.

>PRK14530 adenylate kinase; Provisional

Probab=97.84  E-value=1.9e-05  Score=65.69  Aligned_cols=30  Identities=27%  Similarity=0.443  Sum_probs=26.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.||||+||||+++.||..++.+++.+
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            589999999999999999999999876644

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.84  E-value=1.6e-05  Score=62.00  Aligned_cols=29  Identities=24%  Similarity=0.477  Sum_probs=26.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |-+.|||||||||+++.+|..+|.+++..
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vsa   31 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVSA   31 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceeec
Confidence            56789999999999999999999998763

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.83  E-value=0.00039  Score=62.08  Aligned_cols=23  Identities=30%  Similarity=0.535  Sum_probs=21.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..+|+||||||||++++.+++.+
T Consensus       135 R~LIvG~pGtGKTTLl~~la~~i  157 (380)
T PRK12608        135 RGLIVAPPRAGKTVLLQQIAAAV  157 (380)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999999998877

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.83  E-value=0.00047  Score=69.06  Aligned_cols=167  Identities=14%  Similarity=0.135  Sum_probs=89.2

Q ss_pred             hhCHHHHHHhCC-CCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh-------------------------
Q 024550           17 LQRKEFYRRVGK-AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN-------------------------   70 (266)
Q Consensus        17 l~~~~~~~~~~~-~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~-------------------------   70 (266)
                      +.++.+...+.- ...+-++|+||+|.|||+++...+...+ ++..+++..-.+.                         
T Consensus        17 ~~R~rl~~~l~~~~~~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~   95 (903)
T PRK04841         17 VVRERLLAKLSGANNYRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEA   95 (903)
T ss_pred             CcchHHHHHHhcccCCCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhh
Confidence            445555555432 2334599999999999999999887776 5655555322100                         


Q ss_pred             -------hh----HHHHHHH---cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc
Q 024550           71 -------ND----LRHILIA---TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL  136 (266)
Q Consensus        71 -------~~----l~~~~~~---~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~  136 (266)
                             ..    +..++..   ...+.+|+|||++.+..                       ......+..++..+   
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~-----------------------~~~~~~l~~l~~~~---  149 (903)
T PRK04841         96 LAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITN-----------------------PEIHEAMRFFLRHQ---  149 (903)
T ss_pred             hhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCC-----------------------hHHHHHHHHHHHhC---
Confidence                   00    1111221   24578999999997632                       11122333333332   


Q ss_pred             ccCCCCceEEEEecCCCCCCc-ccccCCCcceeEEEcC--CCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHH
Q 024550          137 WSSCGDERIIIFTTNHKERLD-PALLRPGRMDMHINMS--HCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADV  213 (266)
Q Consensus       137 ~~~~~~~~ivi~ttn~~~~ld-~al~r~~Rf~~~i~~~--~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i  213 (266)
                          +....+|.++.....++ ..+...+.+ ..|...  ..+.++...++...++..  ....++..+...++..|.-+
T Consensus       150 ----~~~~~lv~~sR~~~~~~~~~l~~~~~~-~~l~~~~l~f~~~e~~~ll~~~~~~~--~~~~~~~~l~~~t~Gwp~~l  222 (903)
T PRK04841        150 ----PENLTLVVLSRNLPPLGIANLRVRDQL-LEIGSQQLAFDHQEAQQFFDQRLSSP--IEAAESSRLCDDVEGWATAL  222 (903)
T ss_pred             ----CCCeEEEEEeCCCCCCchHhHHhcCcc-eecCHHhCCCCHHHHHHHHHhccCCC--CCHHHHHHHHHHhCChHHHH
Confidence                23344434554321222 122211222 223333  778888888887666543  23456667777777777666


Q ss_pred             HHHH
Q 024550          214 AEQL  217 (266)
Q Consensus       214 ~~~l  217 (266)
                      .-+.
T Consensus       223 ~l~~  226 (903)
T PRK04841        223 QLIA  226 (903)
T ss_pred             HHHH
Confidence            5443

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=97.82  E-value=9.2e-05  Score=69.20  Aligned_cols=155  Identities=15%  Similarity=0.085  Sum_probs=90.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc--CCcEEEEeCCcccChhhHH-HHHHH------------------cccCCeeeeec
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL--KFDVYDLELSNLLGNNDLR-HILIA------------------TENKSILVVED   90 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~--~~~~~~i~~~~~~~~~~l~-~~~~~------------------~~~~~vl~iDe   90 (266)
                      -.+|+.|.+||||-.+++++....  ..+|+.++|..+.. ..+. ++|..                  ...++.+|+||
T Consensus       337 ~pvll~GEtGtGKe~laraiH~~s~~~gpfvAvNCaAip~-~liesELFGy~~GafTga~~kG~~g~~~~A~gGtlFlde  415 (606)
T COG3284         337 LPVLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPE-ALIESELFGYVAGAFTGARRKGYKGKLEQADGGTLFLDE  415 (606)
T ss_pred             CCeEecCCcchhHHHHHHHHHhcccccCCeEEEEeccchH-HhhhHHHhccCccccccchhccccccceecCCCccHHHH
Confidence            359999999999999999998766  57899999998853 2222 22211                  12468999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-C-----CCCceEEEEecCCCCCCcccccCCC
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-S-----CGDERIIIFTTNHKERLDPALLRPG  164 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~-----~~~~~ivi~ttn~~~~ld~al~r~~  164 (266)
                      |..|.                           ...++.||..|..-.- +     ....+-||+||+..   -..|.+-|
T Consensus       416 Igd~p---------------------------~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~d---l~~lv~~g  465 (606)
T COG3284         416 IGDMP---------------------------LALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRD---LAQLVEQG  465 (606)
T ss_pred             hhhch---------------------------HHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcC---HHHHHHcC
Confidence            99875                           3456677777752111 0     11246688888863   12333444


Q ss_pred             ccee-------EEEcCCCCHHHH---HHHHHHhhCCCC---CCcHHHH-HHHhhc-CCCCHHHHHHHH
Q 024550          165 RMDM-------HINMSHCTPSGF---KMLASNYLGIAE---HPLFVEI-EKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       165 Rf~~-------~i~~~~p~~~~~---~~i~~~~~~~~~---~~~~~~~-~~l~~~-~~~s~~~i~~~l  217 (266)
                      ||..       ...+..|.-.+|   ..++.+++..++   ..++.+. ..+... --.+-.++-+++
T Consensus       466 ~fredLyyrL~~~~i~lP~lr~R~d~~~~l~~~~~~~~~~~~~l~~~~~~~l~~~~WPGNirel~~v~  533 (606)
T COG3284         466 RFREDLYYRLNAFVITLPPLRERSDRIPLLDRILKRENDWRLQLDDDALARLLAYRWPGNIRELDNVI  533 (606)
T ss_pred             CchHHHHHHhcCeeeccCchhcccccHHHHHHHHHHccCCCccCCHHHHHHHHhCCCCCcHHHHHHHH
Confidence            4442       233455555444   455555554443   3333333 333332 225555665555

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.82  E-value=0.0005  Score=57.76  Aligned_cols=162  Identities=18%  Similarity=0.151  Sum_probs=88.3

Q ss_pred             CCCCce-eEEecCCCCChHHHHHHHHHHcCCc---EEEEeCCcccC--------------------------hhhHHHHH
Q 024550           28 KAWKRG-YLLYGPPGTGKSSLIAAMANYLKFD---VYDLELSNLLG--------------------------NNDLRHIL   77 (266)
Q Consensus        28 ~~~~~~-iLl~GppGtGKT~la~ala~~~~~~---~~~i~~~~~~~--------------------------~~~l~~~~   77 (266)
                      +...++ +.++|+.|||||++.|++...++..   .+.++...+..                          ...+..++
T Consensus        47 i~d~qg~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~  126 (269)
T COG3267          47 IADGQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALV  126 (269)
T ss_pred             HhcCCceEEEEecCCCchhHHHHHHHHhcCCCceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHH
Confidence            444554 6789999999999999777766422   22333332221                          12233334


Q ss_pred             HHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC-CCCC
Q 024550           78 IATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH-KERL  156 (266)
Q Consensus        78 ~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~-~~~l  156 (266)
                      ....++-++++||++.+....                        -..+..|.+.-.+....  -.++.++=..- +..-
T Consensus       127 ~~g~r~v~l~vdEah~L~~~~------------------------le~Lrll~nl~~~~~~~--l~ivL~Gqp~L~~~lr  180 (269)
T COG3267         127 KKGKRPVVLMVDEAHDLNDSA------------------------LEALRLLTNLEEDSSKL--LSIVLIGQPKLRPRLR  180 (269)
T ss_pred             HhCCCCeEEeehhHhhhChhH------------------------HHHHHHHHhhcccccCc--eeeeecCCcccchhhc
Confidence            445567999999999885311                        11111222222222111  12555553321 1111


Q ss_pred             ---cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCC--c-HHH-HHHHhhcCCCCHHHHHHHH
Q 024550          157 ---DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHP--L-FVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       157 ---d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~--~-~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                         -..+..  |++..|++++.+..+-...+++.++..+.+  + ..+ +..+.....-.|.-|.+.+
T Consensus       181 ~~~l~e~~~--R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~  246 (269)
T COG3267         181 LPVLRELEQ--RIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLA  246 (269)
T ss_pred             hHHHHhhhh--eEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHH
Confidence               123445  888889999999998887788777654322  2 223 3333333444677666654

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=97.81  E-value=0.00026  Score=60.14  Aligned_cols=27  Identities=30%  Similarity=0.530  Sum_probs=23.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      +..++|.||+|+|||++++.+++....
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            445999999999999999999988754

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.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.81  E-value=2.3e-05  Score=62.86  Aligned_cols=34  Identities=38%  Similarity=0.661  Sum_probs=30.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      +..|+|.||+|+|||++++.+|..++.+++..+.
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~~~~vd~D~   37 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQ   37 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcCCcEEECCc
Confidence            4469999999999999999999999998877663

>PRK06696 uridine kinase; Validated

Probab=97.80  E-value=5.6e-05  Score=63.20  Aligned_cols=41  Identities=12%  Similarity=0.178  Sum_probs=34.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNN   71 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~   71 (266)
                      +.-|.+.|++|+||||+|+.|+..+   |.+++.++..++....
T Consensus        22 ~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~~~~   65 (223)
T PRK06696         22 PLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFHNPR   65 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeccccccCCH
Confidence            4468899999999999999999998   6778888877776443

>PRK06762 hypothetical protein; Provisional

Probab=97.79  E-value=3e-05  Score=61.64  Aligned_cols=33  Identities=15%  Similarity=0.269  Sum_probs=27.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +.-++|+|+||+||||+++.++..++..++.++
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~   34 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERLGRGTLLVS   34 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEec
Confidence            346889999999999999999999865555554

>PRK13946 shikimate kinase; Provisional

Probab=97.79  E-value=2.2e-05  Score=63.71  Aligned_cols=33  Identities=33%  Similarity=0.456  Sum_probs=30.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +..|+|.|+||||||++++.+|+.+|.+++..+
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D   42 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDAD   42 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcC
Confidence            457999999999999999999999999988766

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=97.78  E-value=9e-05  Score=63.46  Aligned_cols=39  Identities=21%  Similarity=0.106  Sum_probs=31.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |++....++++||||||||+++..++...   |.+.++++..
T Consensus        32 Gip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~E   73 (259)
T TIGR03878        32 GIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVE   73 (259)
T ss_pred             CeECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec
Confidence            67777889999999999999999876643   6677777765

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PF13245 AAA_19: Part of AAA domain

Probab=97.78  E-value=4.8e-05  Score=52.42  Aligned_cols=33  Identities=39%  Similarity=0.607  Sum_probs=21.7

Q ss_pred             eeEEecCCCCChH-HHHHHHHHHc------CCcEEEEeCC
Q 024550           33 GYLLYGPPGTGKS-SLIAAMANYL------KFDVYDLELS   65 (266)
Q Consensus        33 ~iLl~GppGtGKT-~la~ala~~~------~~~~~~i~~~   65 (266)
                      -+++.|||||||| ++++.++...      +..++.+.+.
T Consensus        12 ~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t   51 (76)
T PF13245_consen   12 LFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPT   51 (76)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCC
Confidence            3666999999999 4555555555      4455555543

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.77  E-value=2.9e-05  Score=62.02  Aligned_cols=32  Identities=28%  Similarity=0.472  Sum_probs=28.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ..++|+|++|||||++++.+|..+|.+++..+
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~~~~d~D   34 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGYRFVDTD   34 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEEcc
Confidence            35899999999999999999999999988654

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.77  E-value=0.00015  Score=59.56  Aligned_cols=67  Identities=19%  Similarity=0.320  Sum_probs=41.7

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHH-----cCCcEE-------------EEeCCc-cc--------ChhhHHHHHH
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANY-----LKFDVY-------------DLELSN-LL--------GNNDLRHILI   78 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~-----~~~~~~-------------~i~~~~-~~--------~~~~l~~~~~   78 (266)
                      +.+...+.++|.||+|+||||+++.++..     .|.++-             .....+ +.        ....+..++.
T Consensus        20 i~l~~g~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~l~~~~s~~~~e~~~~~~iL~   99 (199)
T cd03283          20 IDMEKKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVE   99 (199)
T ss_pred             EEEcCCcEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcccceEEEeccchhccccccChHHHHHHHHHHHHH
Confidence            34444556899999999999999999853     343321             000000 00        0123455666


Q ss_pred             Hcc--cCCeeeeecch
Q 024550           79 ATE--NKSILVVEDID   92 (266)
Q Consensus        79 ~~~--~~~vl~iDeid   92 (266)
                      ...  .+.++++||.-
T Consensus       100 ~~~~~~p~llllDEp~  115 (199)
T cd03283         100 KAKKGEPVLFLLDEIF  115 (199)
T ss_pred             hccCCCCeEEEEeccc
Confidence            666  89999999975

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

>PRK06547 hypothetical protein; Provisional

Probab=97.77  E-value=3.6e-05  Score=61.72  Aligned_cols=34  Identities=29%  Similarity=0.428  Sum_probs=28.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+.-|+++|++|||||++++.++..++.+++..+
T Consensus        14 ~~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         14 GMITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            3456888999999999999999999887766544

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.77  E-value=5.4e-05  Score=56.99  Aligned_cols=22  Identities=32%  Similarity=0.338  Sum_probs=20.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      +-|+||||||||++++.||+.+
T Consensus        56 lSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   56 LSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             EEeecCCCCcHHHHHHHHHHHH
Confidence            5589999999999999999986

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

>PLN02200 adenylate kinase family protein

Probab=97.76  E-value=3.5e-05  Score=64.94  Aligned_cols=35  Identities=23%  Similarity=0.387  Sum_probs=27.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~   67 (266)
                      +..+++.|||||||||+++.+|..+|...  ++..++
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~~g~~h--is~gdl   77 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVETFGFKH--LSAGDL   77 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCeE--EEccHH
Confidence            34588999999999999999999998754  454443

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.75  E-value=9.2e-05  Score=65.08  Aligned_cols=70  Identities=19%  Similarity=0.227  Sum_probs=46.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC---------------------hhhHHHHHH---H
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG---------------------NNDLRHILI---A   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~---------------------~~~l~~~~~---~   79 (266)
                      |+|..+-+.+|||||||||+|+-.++...   +...+.+++.....                     ......+..   .
T Consensus        51 Glp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~  130 (325)
T cd00983          51 GYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSLVR  130 (325)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHHHh
Confidence            57777779999999999999999877544   66677776643221                     011111111   1


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      .....+++||-+-.+.+
T Consensus       131 s~~~~lIVIDSvaal~~  147 (325)
T cd00983         131 SGAVDLIVVDSVAALVP  147 (325)
T ss_pred             ccCCCEEEEcchHhhcc
Confidence            23578899999988864

RecA couples ATP hydrolysis to DNA strand exchange.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=97.75  E-value=1.8e-05  Score=65.87  Aligned_cols=22  Identities=45%  Similarity=0.842  Sum_probs=17.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++||||||||+++..++..+
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            8899999999998766666655

>PRK14528 adenylate kinase; Provisional

Probab=97.75  E-value=3e-05  Score=62.99  Aligned_cols=30  Identities=23%  Similarity=0.503  Sum_probs=26.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .+++.||||+|||++++.++..+|.+.+.+
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~~~~~is~   32 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERLSIPQIST   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCeeeC
Confidence            489999999999999999999998876553

>PTZ00088 adenylate kinase 1; Provisional

Probab=97.74  E-value=2.8e-05  Score=65.22  Aligned_cols=31  Identities=19%  Similarity=0.505  Sum_probs=27.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .++|.||||+||||+++.+|+.+|.+++.+.
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g~~~is~g   38 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKENLKHINMG   38 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEECC
Confidence            4999999999999999999999988766554

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.74  E-value=3.1e-05  Score=62.54  Aligned_cols=30  Identities=20%  Similarity=0.360  Sum_probs=25.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      -+++.||||+||||+++.++..+|...+..
T Consensus         5 ii~i~G~~GsGKsTl~~~l~~~~g~~~~~~   34 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQCEKIVEKYGFTHLST   34 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            488999999999999999999998665443

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.

>TIGR01351 adk adenylate kinases

Probab=97.73  E-value=3e-05  Score=64.23  Aligned_cols=29  Identities=28%  Similarity=0.511  Sum_probs=25.9

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |++.||||+||||+++.||..+|++.+.+
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            78999999999999999999998766553

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.

>PRK02496 adk adenylate kinase; Provisional

Probab=97.72  E-value=3.2e-05  Score=62.62  Aligned_cols=30  Identities=27%  Similarity=0.530  Sum_probs=26.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      -+++.||||+|||++++.++..++.+.+.+
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            388999999999999999999998776554

>TIGR00767 rho transcription termination factor Rho

Probab=97.71  E-value=0.00078  Score=60.66  Aligned_cols=25  Identities=28%  Similarity=0.537  Sum_probs=22.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .-++|.||||+|||++++.+++...
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhc
Confidence            3499999999999999999999753

Members of this family differ in the specificity of RNA binding.

>PRK00279 adk adenylate kinase; Reviewed

Probab=97.69  E-value=3.8e-05  Score=63.82  Aligned_cols=29  Identities=28%  Similarity=0.481  Sum_probs=26.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |+++||||+|||++++.+|..++...+.+
T Consensus         3 I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            89999999999999999999998766653

>PRK14737 gmk guanylate kinase; Provisional

Probab=97.69  E-value=0.00015  Score=58.85  Aligned_cols=25  Identities=24%  Similarity=0.418  Sum_probs=22.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++-++|+||||+|||++++.+....
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcC
Confidence            4568999999999999999998876

>PRK14527 adenylate kinase; Provisional

Probab=97.69  E-value=3.6e-05  Score=62.75  Aligned_cols=32  Identities=25%  Similarity=0.475  Sum_probs=27.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .+.-++++||||+||||+++.++..++...+.
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~~~~~is   36 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQELGLKKLS   36 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhCCCCCC
Confidence            34569999999999999999999999875543

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.69  E-value=0.00019  Score=54.06  Aligned_cols=23  Identities=30%  Similarity=0.306  Sum_probs=19.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +++++||+|+|||+++-.++...
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~   24 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILEL   24 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHH
Confidence            68999999999999887777665

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.68  E-value=0.00013  Score=60.62  Aligned_cols=22  Identities=27%  Similarity=0.413  Sum_probs=20.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      +.++|+||.|+|||++.+.++.
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            5699999999999999999983

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

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.68  E-value=0.00029  Score=64.54  Aligned_cols=36  Identities=31%  Similarity=0.379  Sum_probs=26.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~   66 (266)
                      +..++|.||+|+||||++..+|..+     +..+..+++..
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~  261 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDT  261 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCc
Confidence            3468999999999999888887654     34555566544

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.68  E-value=5e-05  Score=60.99  Aligned_cols=38  Identities=32%  Similarity=0.452  Sum_probs=25.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc---EEEEeCCcc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD---VYDLELSNL   67 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~---~~~i~~~~~   67 (266)
                      .++.++|+|++|+|||++++.+...+..+   ++.+++...
T Consensus        23 ~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen   23 SPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             ----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            35679999999999999999988877443   666666655

>PRK13695 putative NTPase; Provisional

Probab=97.67  E-value=0.00028  Score=56.56  Aligned_cols=23  Identities=39%  Similarity=0.742  Sum_probs=20.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++|.|++|+||||+++.++..+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999987765

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.67  E-value=0.00051  Score=61.74  Aligned_cols=35  Identities=31%  Similarity=0.357  Sum_probs=26.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      ++.++|.||+|+||||++..||..+   |..+..+++.
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aD  278 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTD  278 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecC
Confidence            3568999999999999999999877   3344445544

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=97.66  E-value=3.4e-05  Score=60.96  Aligned_cols=30  Identities=27%  Similarity=0.509  Sum_probs=26.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .++++|.|||||||+++.|+ .+|...+.++
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~lg~~~i~l~   31 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-ELGYKVIELN   31 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-HhCCceeeHH
Confidence            37899999999999999999 8988877655

>PRK04040 adenylate kinase; Provisional

Probab=97.66  E-value=5.4e-05  Score=61.64  Aligned_cols=29  Identities=21%  Similarity=0.511  Sum_probs=24.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc--CCcE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL--KFDV   59 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~--~~~~   59 (266)
                      +.-++++|+|||||||+++.++..+  +..+
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~   32 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLKEDYKI   32 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhccCCeE
Confidence            3468999999999999999999999  4444

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=97.66  E-value=4.7e-05  Score=61.36  Aligned_cols=28  Identities=39%  Similarity=0.668  Sum_probs=24.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      .++|.||||+||||+|+.|++.++.+.+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~hl   29 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLPHL   29 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4789999999999999999999655444

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.66  E-value=0.00016  Score=60.71  Aligned_cols=51  Identities=18%  Similarity=0.185  Sum_probs=36.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDLRHIL   77 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l~~~~   77 (266)
                      |++...-+.|+||||||||+++..++...         +...++++...-.....+..+.
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~~~   74 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQIA   74 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHHHH
Confidence            67777779999999999999999998543         2566777766543444444443

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 .

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=97.65  E-value=8.8e-05  Score=50.04  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=20.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      +.+.|+||+|||++++.++..+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999996

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.

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=97.64  E-value=0.00016  Score=67.96  Aligned_cols=28  Identities=32%  Similarity=0.437  Sum_probs=24.1

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++++..+|+.||+|||||++.|++|.-.
T Consensus       416 v~~G~~llI~G~SG~GKTsLlRaiaGLW  443 (604)
T COG4178         416 VRPGERLLITGESGAGKTSLLRALAGLW  443 (604)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            4455569999999999999999999866

>PLN02674 adenylate kinase

Probab=97.64  E-value=0.00011  Score=62.01  Aligned_cols=31  Identities=23%  Similarity=0.445  Sum_probs=26.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ...++|.||||+||||.++.+|..+|...+.
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~~~~his   61 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEYCLCHLA   61 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHcCCcEEc
Confidence            4569999999999999999999999865543

>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=97.64  E-value=4.1e-05  Score=57.64  Aligned_cols=22  Identities=32%  Similarity=0.579  Sum_probs=21.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      |+|.|+|||||||+++.|+..+
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            6899999999999999999998

...

>PRK04296 thymidine kinase; Provisional

Probab=97.62  E-value=0.00035  Score=56.94  Aligned_cols=30  Identities=23%  Similarity=0.284  Sum_probs=23.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i   62 (266)
                      -.+++||||+|||+++..++..+   +..++.+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            47889999999999888887766   4455544

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.61  E-value=7.3e-05  Score=57.18  Aligned_cols=30  Identities=27%  Similarity=0.419  Sum_probs=26.1

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      ++..-++|.|+.|+|||++++.+++.++..
T Consensus        20 ~~~~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        20 DFGTVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            344568999999999999999999999865

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.

>PRK09354 recA recombinase A; Provisional

Probab=97.61  E-value=0.00027  Score=62.66  Aligned_cols=40  Identities=20%  Similarity=0.216  Sum_probs=30.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      |++..+-+++|||||||||+|+-.++...   |...+++++..
T Consensus        56 Gip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~   98 (349)
T PRK09354         56 GLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEH   98 (349)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCcc
Confidence            56666679999999999999998776544   66666666554

>PRK10867 signal recognition particle protein; Provisional

Probab=97.61  E-value=0.00087  Score=61.38  Aligned_cols=38  Identities=24%  Similarity=0.294  Sum_probs=29.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNL   67 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~   67 (266)
                      +|.-++++||+|+||||++..+|..+    |..+..+++..+
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~  140 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVY  140 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEcccc
Confidence            35568999999999999888777655    566677776654

>PRK01184 hypothetical protein; Provisional

Probab=97.61  E-value=5.9e-05  Score=60.98  Aligned_cols=29  Identities=24%  Similarity=0.322  Sum_probs=24.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      -++|+||||+||||+++ ++..+|.+++..
T Consensus         3 ~i~l~G~~GsGKsT~a~-~~~~~g~~~i~~   31 (184)
T PRK01184          3 IIGVVGMPGSGKGEFSK-IAREMGIPVVVM   31 (184)
T ss_pred             EEEEECCCCCCHHHHHH-HHHHcCCcEEEh
Confidence            47899999999999987 788898877554

>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=97.60  E-value=4.8e-05  Score=59.52  Aligned_cols=26  Identities=27%  Similarity=0.526  Sum_probs=22.6

Q ss_pred             EecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           36 LYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        36 l~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      |.||||+|||++++.||..+|...+.
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            68999999999999999999775443

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 ....

>smart00072 GuKc Guanylate kinase homologues

Probab=97.60  E-value=0.00028  Score=57.17  Aligned_cols=24  Identities=38%  Similarity=0.711  Sum_probs=22.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +-++|+||+|+||++++..+....
T Consensus         3 r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             cEEEEECCCCCCHHHHHHHHHhcC
Confidence            458999999999999999999986

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>PLN02199 shikimate kinase

Probab=97.59  E-value=0.00014  Score=62.76  Aligned_cols=33  Identities=27%  Similarity=0.499  Sum_probs=30.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ..+|+|+|.+|+|||++++.+|+.+|.+++..+
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD  134 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCD  134 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEehH
Confidence            558999999999999999999999999998766

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.58  E-value=0.00023  Score=59.00  Aligned_cols=24  Identities=38%  Similarity=0.710  Sum_probs=21.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.|+.|||||||||+.|-+|..+
T Consensus       138 lntLiigpP~~GKTTlLRdiaR~~  161 (308)
T COG3854         138 LNTLIIGPPQVGKTTLLRDIARLL  161 (308)
T ss_pred             eeeEEecCCCCChHHHHHHHHHHh
Confidence            458899999999999999999876

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.57  E-value=0.0016  Score=57.14  Aligned_cols=46  Identities=15%  Similarity=0.125  Sum_probs=29.3

Q ss_pred             EEEcCCCCHHHHHHHHHHhhCCCCC---CcHH-HHHHHhhcCCCCHHHHH
Q 024550          169 HINMSHCTPSGFKMLASNYLGIAEH---PLFV-EIEKLIATAKVTPADVA  214 (266)
Q Consensus       169 ~i~~~~p~~~~~~~i~~~~~~~~~~---~~~~-~~~~l~~~~~~s~~~i~  214 (266)
                      .|+++..+.++...++..|....-.   .... -.+.+....+.+|+++.
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el~  307 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPRELE  307 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHhc
Confidence            6899999999999999977755321   1222 22333444456776654

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.56  E-value=0.00024  Score=59.39  Aligned_cols=39  Identities=26%  Similarity=0.385  Sum_probs=33.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |++...-++++||||+|||+++..+|...   +.+.+++++.
T Consensus        19 Gi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         19 GFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            67777779999999999999999998754   6778888877

>cd01394 radB RadB

Probab=97.55  E-value=0.00022  Score=59.31  Aligned_cols=39  Identities=28%  Similarity=0.401  Sum_probs=31.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |++...-++++||||||||+++..+|...   +.+.++++..
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~e   56 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTE   56 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            67777779999999999999999998765   5667677654

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK04182 cytidylate kinase; Provisional

Probab=97.55  E-value=8.4e-05  Score=59.55  Aligned_cols=29  Identities=28%  Similarity=0.496  Sum_probs=26.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .|+|.|+||||||++++.+|..+|.+++.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg~~~id   30 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLGLKHVS   30 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEec
Confidence            37899999999999999999999988765

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.54  E-value=0.0005  Score=57.31  Aligned_cols=52  Identities=19%  Similarity=0.207  Sum_probs=37.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---C------CcEEEEeCCcccChhhHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---K------FDVYDLELSNLLGNNDLRHILI   78 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~------~~~~~i~~~~~~~~~~l~~~~~   78 (266)
                      |++...-+.|+||||+|||+++..+|...   +      ...++++.........+..+..
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~~~~~   75 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLVQLAV   75 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHHHHHH
Confidence            67777779999999999999999988764   2      5667777765444445554443

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.54  E-value=0.00027  Score=63.50  Aligned_cols=28  Identities=43%  Similarity=0.693  Sum_probs=24.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      .+..+++.||.|||||++.+++...+..
T Consensus        21 ~~~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   21 EGLNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            3567999999999999999999888743

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.53  E-value=0.00023  Score=55.96  Aligned_cols=29  Identities=41%  Similarity=0.521  Sum_probs=24.4

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +.+...+.|.||+|+|||+++++++....
T Consensus        22 i~~g~~~~i~G~nGsGKStll~~l~g~~~   50 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            44455689999999999999999998763

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.

>PRK14526 adenylate kinase; Provisional

Probab=97.53  E-value=9.2e-05  Score=61.40  Aligned_cols=28  Identities=29%  Similarity=0.668  Sum_probs=24.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ++|+||||+||||+++.+|..++.+.+.
T Consensus         3 i~l~G~pGsGKsT~a~~La~~~~~~~is   30 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNELNYYHIS   30 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            7899999999999999999999876543

>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=97.52  E-value=0.00021  Score=63.45  Aligned_cols=63  Identities=27%  Similarity=0.388  Sum_probs=43.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~   95 (266)
                      |+|...+++|||||.||||+++.+|.+-++..+++.--+.      -+-.+......-|-+|||+-.-+
T Consensus       258 g~PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViSf~Ns~------ShFWLqPL~d~Ki~llDDAT~~c  320 (432)
T PF00519_consen  258 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSK------SHFWLQPLADAKIALLDDATYPC  320 (432)
T ss_dssp             TBTTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-GGGTT------SCGGGGGGCT-SSEEEEEE-HHH
T ss_pred             CCCcccEEEEECCCCCchhHHHHHHHHHhCCEEEEecCCC------CcccccchhcCcEEEEcCCcccH
Confidence            7888889999999999999999999999998876632111      01122233455788899887543

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.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=97.50  E-value=0.00011  Score=64.20  Aligned_cols=30  Identities=30%  Similarity=0.296  Sum_probs=25.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-CCcEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-KFDVYD   61 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-~~~~~~   61 (266)
                      .-+++.|||||||||+++.++..+ +..++.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l~   33 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVN   33 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEEe
Confidence            458899999999999999999998 554444

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=97.50  E-value=0.00013  Score=60.93  Aligned_cols=41  Identities=24%  Similarity=0.295  Sum_probs=30.8

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCc
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSN   66 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~   66 (266)
                      -|+|.+..+|+.||||||||+++..++...    |-+.+.++...
T Consensus        14 GGip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee   58 (226)
T PF06745_consen   14 GGIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEE   58 (226)
T ss_dssp             TSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS
T ss_pred             CCCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecC
Confidence            378888889999999999999988766433    67777777543

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 ....

>TIGR00416 sms DNA repair protein RadA

Probab=97.50  E-value=0.00046  Score=63.76  Aligned_cols=69  Identities=26%  Similarity=0.316  Sum_probs=46.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC--------------------hhhHHHHHHH--cc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG--------------------NNDLRHILIA--TE   81 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~--------------------~~~l~~~~~~--~~   81 (266)
                      |+++..-++++|+||+|||+++..++...   +.++++++......                    ...+..+...  ..
T Consensus        90 Gi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EEs~~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i~~~  169 (454)
T TIGR00416        90 GIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICANIEEE  169 (454)
T ss_pred             CccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcCCHHHHHHHHHHcCCChHHeEEcCCCCHHHHHHHHHhc
Confidence            67777779999999999999999887755   45667776543210                    1112222222  23


Q ss_pred             cCCeeeeecchhhH
Q 024550           82 NKSILVVEDIDCCI   95 (266)
Q Consensus        82 ~~~vl~iDeid~l~   95 (266)
                      .+.+++||.+..+.
T Consensus       170 ~~~~vVIDSIq~l~  183 (454)
T TIGR00416       170 NPQACVIDSIQTLY  183 (454)
T ss_pred             CCcEEEEecchhhc
Confidence            57889999998764

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)).

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.50  E-value=0.00036  Score=61.32  Aligned_cols=53  Identities=15%  Similarity=0.102  Sum_probs=38.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhHHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDLRHILIA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l~~~~~~   79 (266)
                      |++...-+.|+||||||||.++..+|-..         +...++++...-.....+.++...
T Consensus        92 Gi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~  153 (313)
T TIGR02238        92 GIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAER  153 (313)
T ss_pred             CCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHH
Confidence            56666678999999999999998877422         457788887765556666655443

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.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=97.50  E-value=0.00011  Score=59.71  Aligned_cols=29  Identities=34%  Similarity=0.550  Sum_probs=24.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      ..++|.||+|+||||+++.++...+.+++
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~~~~~   31 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQTQLL   31 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCCCeEE
Confidence            35889999999999999999998876543

>TIGR01069 mutS2 MutS2 family protein

Probab=97.50  E-value=0.00063  Score=66.76  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..++|+||.|+|||++.+.++..
T Consensus       323 ~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       323 RVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             eEEEEECCCCCCchHHHHHHHHH
Confidence            45889999999999999999876

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.50  E-value=0.00017  Score=60.91  Aligned_cols=41  Identities=27%  Similarity=0.215  Sum_probs=32.2

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHH---cCCcEEEEeCCc
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANY---LKFDVYDLELSN   66 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~---~~~~~~~i~~~~   66 (266)
                      -|++++..+|++||||||||+++..++.+   -|.+.++++...
T Consensus        16 GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~ee   59 (237)
T TIGR03877        16 GGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALEE   59 (237)
T ss_pred             CCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEeeC
Confidence            37888888999999999999999876554   266777777554

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.

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=97.49  E-value=0.00011  Score=58.39  Aligned_cols=29  Identities=28%  Similarity=0.603  Sum_probs=26.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |.++|++|+|||++++.++..+|.+++..
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~~~   31 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLISA   31 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCceecH
Confidence            78999999999999999999999887553

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.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=97.49  E-value=8.3e-05  Score=58.92  Aligned_cols=26  Identities=38%  Similarity=0.634  Sum_probs=20.9

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      |.|+|+||||||||++.|+.. |.+++
T Consensus         2 I~i~G~~stGKTTL~~~L~~~-g~~~v   27 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR-GYPVV   27 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH-T-EEE
T ss_pred             EEEECCCCCCHHHHHHHHHHc-CCeEE
Confidence            789999999999999999998 77765

>PRK08233 hypothetical protein; Provisional

Probab=97.48  E-value=0.00014  Score=58.42  Aligned_cols=33  Identities=18%  Similarity=0.200  Sum_probs=25.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC-CcEEEEeCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK-FDVYDLELS   65 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~-~~~~~i~~~   65 (266)
                      -+.+.|+||+||||+++.|+..++ .+++..+..
T Consensus         5 iI~I~G~~GsGKtTla~~L~~~l~~~~~~~~d~~   38 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHKLKNSKALYFDRY   38 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCCCCceEEECCE
Confidence            467889999999999999999985 444444433

>TIGR00959 ffh signal recognition particle protein

Probab=97.48  E-value=0.0026  Score=58.22  Aligned_cols=37  Identities=24%  Similarity=0.294  Sum_probs=29.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~   67 (266)
                      |..++++||+|+||||++..+|..+    |..+..+++..+
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~  139 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLY  139 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEecccc
Confidence            4569999999999999988888764    456777776654

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.48  E-value=0.00018  Score=67.38  Aligned_cols=33  Identities=36%  Similarity=0.594  Sum_probs=26.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC-CcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK-FDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~-~~~~~i~   63 (266)
                      .+.++|.||||+|||+|++.|+..+. .++|.+.
T Consensus       103 ~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~k  136 (644)
T PRK15455        103 KQILYLLGPVGGGKSSLAERLKSLMERVPIYVLK  136 (644)
T ss_pred             CceEEEecCCCCCchHHHHHHHHHHHhCcceeec
Confidence            34688999999999999999999883 4666553

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.48  E-value=0.00047  Score=59.27  Aligned_cols=25  Identities=32%  Similarity=0.588  Sum_probs=23.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+++++||+|+||||+.+.++..+.
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccC
Confidence            5799999999999999999998873

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.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.47  E-value=0.00017  Score=57.29  Aligned_cols=28  Identities=25%  Similarity=0.337  Sum_probs=23.8

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +.+...+.|.||+|+|||||++.++...
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~i~G~~   50 (163)
T cd03216          23 VRRGEVHALLGENGAGKSTLMKILSGLY   50 (163)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4455568899999999999999999865

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.

>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=97.47  E-value=0.00017  Score=58.13  Aligned_cols=32  Identities=28%  Similarity=0.262  Sum_probs=25.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      ++++||||||||+++..++...   |.+.+.++..
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~e   36 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLE   36 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEECC
Confidence            7899999999999998877654   5566666543

A related protein is found in archaea.

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=97.47  E-value=0.00016  Score=67.50  Aligned_cols=120  Identities=20%  Similarity=0.302  Sum_probs=68.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc----cC---hhhHHHHH-H-----HcccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL----LG---NNDLRHIL-I-----ATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~----~~---~~~l~~~~-~-----~~~~~~vl~iDeid~l~~~~~   99 (266)
                      ++||+|.||||||-+.+.+++-....++..-...-    +.   ...+..-| .     -...++|-+|||+|.+-. .+
T Consensus       484 nvLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGASavGLTa~v~KdPvtrEWTLEaGALVLADkGvClIDEFDKMnd-qD  562 (854)
T KOG0477|consen  484 NVLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGASAVGLTAYVRKDPVTREWTLEAGALVLADKGVCLIDEFDKMND-QD  562 (854)
T ss_pred             eEEEecCCCccHHHHHHHHHhcCcceeEeccCCccccceeEEEeeCCccceeeeccCeEEEccCceEEeehhhhhcc-cc
Confidence            49999999999999999999988777665432211    10   01111111 1     124678999999998842 11


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-----------C--CCcccccCCCcc
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-----------E--RLDPALLRPGRM  166 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-----------~--~ld~al~r~~Rf  166 (266)
                      +.+.          +-+..+........++...|..       ...+|+|+|+.           +  .+...+++  ||
T Consensus       563 RtSI----------HEAMEQQSISISKAGIVtsLqA-------rctvIAAanPigGRY~~s~tFaqNV~ltePIlS--RF  623 (854)
T KOG0477|consen  563 RTSI----------HEAMEQQSISISKAGIVTSLQA-------RCTVIAAANPIGGRYNPSLTFAQNVDLTEPILS--RF  623 (854)
T ss_pred             cchH----------HHHHHhcchhhhhhhHHHHHHh-------hhhhheecCCCCCccCCccchhhccccccchhh--hc
Confidence            1110          0001112222333334444443       36789999862           2  34567788  99


Q ss_pred             eeEEEc
Q 024550          167 DMHINM  172 (266)
Q Consensus       167 ~~~i~~  172 (266)
                      +.-.-+
T Consensus       624 DiLcVv  629 (854)
T KOG0477|consen  624 DILCVV  629 (854)
T ss_pred             ceeeee
Confidence            865444

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=97.46  E-value=0.0002  Score=61.34  Aligned_cols=42  Identities=24%  Similarity=0.207  Sum_probs=33.9

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      -|++..+.+|++|+||||||+++..++...   |.+.+.++....
T Consensus        18 GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e~   62 (260)
T COG0467          18 GGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEES   62 (260)
T ss_pred             CCCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecCC
Confidence            468888889999999999999988777655   677888776644

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=97.46  E-value=0.0005  Score=55.37  Aligned_cols=67  Identities=18%  Similarity=0.260  Sum_probs=39.7

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCC--cEEEEe-------CCcc-cChhhHHHH---HHHcccCCeeeeecchhh
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKF--DVYDLE-------LSNL-LGNNDLRHI---LIATENKSILVVEDIDCC   94 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~--~~~~i~-------~~~~-~~~~~l~~~---~~~~~~~~vl~iDeid~l   94 (266)
                      +.+...+.|.||.|+|||||++.++.....  --+.++       .... .+....+.+   ..-+.+|.++++||--.-
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~~~p~lllLDEPts~  101 (177)
T cd03222          22 VKEGEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAY  101 (177)
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHhcCCCEEEEECCccc
Confidence            344556889999999999999999986521  011111       1110 122222222   122357999999998743

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=97.45  E-value=0.00039  Score=61.10  Aligned_cols=47  Identities=15%  Similarity=0.189  Sum_probs=34.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDL   73 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l   73 (266)
                      |++...-++++||||||||+++..+|...         +...++++...-.....+
T Consensus        91 Gi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl  146 (310)
T TIGR02236        91 GIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERI  146 (310)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHH
Confidence            46666668999999999999999888663         346788887663333333

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PF06431 Polyoma_lg_T_C: Polyomavirus large T antigen C-terminus; InterPro: IPR010932 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []

Probab=97.44  E-value=0.00036  Score=61.49  Aligned_cols=124  Identities=19%  Similarity=0.192  Sum_probs=69.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhh
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARA  106 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~  106 (266)
                      ++|..+.+||-||-.|||||+|.|+-.-+|...+.+++..    ..+.--+.-+-..-.++++|+-.-....        
T Consensus       151 N~PKkRy~lFkGPvNsGKTTlAAAlLdL~gG~~LNvN~p~----dkl~FELG~AiDQfmVvFEDVKGq~~~~--------  218 (417)
T PF06431_consen  151 NIPKKRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQPSDN--------  218 (417)
T ss_dssp             TBTTB-EEEEE-STTSSHHHHHHHHHHHH-EEEE-TSS-T----TTHHHHHCCCTT-SEEEEEEE--SSTTT--------
T ss_pred             CCCcceeEEEecCcCCchHHHHHHHHHhcCCceeecCCCh----hhcchhhheeeceEEEEEEecCCCcCCC--------
Confidence            6777889999999999999999999999999888888653    2444334444556677777765321100        


Q ss_pred             cCCccccccccccccchhhhhhhhhhhhcccc----CCCCc------eEEEEecCCCCCCcccccCCCcceeEEEcC
Q 024550          107 ANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS----SCGDE------RIIIFTTNHKERLDPALLRPGRMDMHINMS  173 (266)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~----~~~~~------~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~  173 (266)
                              .....+..-..+..|-++|||.-.    ...-+      .--|.|+|.. .+|..+.-  ||...+.|.
T Consensus       219 --------~~Lp~G~G~~NLDNLRD~LDG~V~VNLErKH~NK~sQiFPPgIvTmNeY-~iP~Tv~v--Rf~~~~~F~  284 (417)
T PF06431_consen  219 --------KDLPPGQGMNNLDNLRDYLDGAVKVNLERKHQNKRSQIFPPGIVTMNEY-KIPQTVKV--RFCKVLDFR  284 (417)
T ss_dssp             --------TT----SHHHHHHTTHHHHH-SS-EEEECSSSEEEEE----EEEEESS--B--HHHHT--TEEEEEE--
T ss_pred             --------CCCCCCCCcccchhhhhhccCceeechhhhhcccccccCCCceEeeccc-cCCcceee--eeEeeEecc
Confidence                    001123334556667777776421    00000      1256788864 45888888  999888886

Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA []. ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA []. These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 2H1L_H 1SVO_A 1SVM_E 1SVL_B 1N25_A 4E2I_K.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=97.44  E-value=0.00018  Score=56.29  Aligned_cols=30  Identities=37%  Similarity=0.516  Sum_probs=25.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      ++++|+||+|||++++.++..+   +.+.+.++
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~   34 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLD   34 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEc
Confidence            6899999999999999999988   55555554

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=97.44  E-value=0.00083  Score=66.10  Aligned_cols=22  Identities=18%  Similarity=0.314  Sum_probs=19.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|+||.++|||++.+.++-.
T Consensus       329 ~~iITGpN~gGKTt~lktigl~  350 (782)
T PRK00409        329 VLVITGPNTGGKTVTLKTLGLA  350 (782)
T ss_pred             EEEEECCCCCCcHHHHHHHHHH
Confidence            4889999999999999988743

>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=97.44  E-value=0.00016  Score=59.22  Aligned_cols=35  Identities=37%  Similarity=0.549  Sum_probs=27.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL   68 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~   68 (266)
                      ++|+||+|||||.++-++|+.+|.+++..+--...
T Consensus         4 ~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Driq~y   38 (233)
T PF01745_consen    4 YLIVGPTGTGKTALAIALAQKTGAPVISLDRIQCY   38 (233)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH--EEEEE-SGGG-
T ss_pred             EEEECCCCCChhHHHHHHHHHhCCCEEEecceecc
Confidence            78999999999999999999999999998855443

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.42  E-value=0.003  Score=57.41  Aligned_cols=36  Identities=28%  Similarity=0.393  Sum_probs=26.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~   66 (266)
                      +..++|.||+|+||||++..+|..+    |..+..+++..
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt  262 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDN  262 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccc
Confidence            3458899999999999999999754    34454455443

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.42  E-value=0.00058  Score=61.21  Aligned_cols=62  Identities=23%  Similarity=0.371  Sum_probs=38.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-------CCcEEEEeCCccc--------------------ChhhHHHHHHHcccC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-------KFDVYDLELSNLL--------------------GNNDLRHILIATENK   83 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-------~~~~~~i~~~~~~--------------------~~~~l~~~~~~~~~~   83 (266)
                      ++-+.|.||.|+||||...-||..+       .+.++.++.-.+.                    +...+...+......
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l~~~  282 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEALRDC  282 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHhhcC
Confidence            4558899999999998666666555       2445555544333                    233444444445556


Q ss_pred             Ceeeeecch
Q 024550           84 SILVVEDID   92 (266)
Q Consensus        84 ~vl~iDeid   92 (266)
                      .+|++|=+.
T Consensus       283 d~ILVDTaG  291 (407)
T COG1419         283 DVILVDTAG  291 (407)
T ss_pred             CEEEEeCCC
Confidence            777776655

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=97.41  E-value=0.0006  Score=60.57  Aligned_cols=53  Identities=13%  Similarity=0.069  Sum_probs=38.5

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhHHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDLRHILIA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l~~~~~~   79 (266)
                      |++...-..|+||||||||.++..+|-..         +...++++...-.....+.++...
T Consensus       122 Gi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~  183 (344)
T PLN03187        122 GIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAER  183 (344)
T ss_pred             CCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            46666668899999999999999887432         357788887765556666665543

>PLN02459 probable adenylate kinase

Probab=97.41  E-value=0.00019  Score=61.10  Aligned_cols=29  Identities=21%  Similarity=0.477  Sum_probs=25.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .++|.||||+||||+++.+|+.++...+.
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~~~~is   59 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLGVPHIA   59 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEe
Confidence            48889999999999999999999865544

>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=97.40  E-value=0.00034  Score=54.37  Aligned_cols=66  Identities=21%  Similarity=0.241  Sum_probs=40.3

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCC---cEE-----EEeC-CcccChhhHHHH---HHHcccCCeeeeecchhh
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKF---DVY-----DLEL-SNLLGNNDLRHI---LIATENKSILVVEDIDCC   94 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~---~~~-----~i~~-~~~~~~~~l~~~---~~~~~~~~vl~iDeid~l   94 (266)
                      +.+...+.|.||+|+||||+++.++.....   .++     .+.. ..+ +....+.+   ..-+.+|.++++||-..-
T Consensus        23 ~~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~~i~~~~~l-S~G~~~rv~laral~~~p~illlDEP~~~  100 (144)
T cd03221          23 INPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQL-SGGEKMRLALAKLLLENPNLLLLDEPTNH  100 (144)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCeEEEEEEccC-CHHHHHHHHHHHHHhcCCCEEEEeCCccC
Confidence            344556889999999999999999987621   110     1111 112 22222222   223468999999998743

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.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=97.40  E-value=0.0002  Score=58.69  Aligned_cols=29  Identities=28%  Similarity=0.394  Sum_probs=25.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      +.-++++|+||+||||+++.+|..++..+
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~~~~~   31 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHRAIDI   31 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            34588999999999999999999988754

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=97.39  E-value=0.00097  Score=58.43  Aligned_cols=66  Identities=21%  Similarity=0.264  Sum_probs=40.9

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh-hhHHHHHHHcccCCeeeeecchh
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN-NDLRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~-~~l~~~~~~~~~~~vl~iDeid~   93 (266)
                      .+....++|+|+.|+|||+++..+..-+|.....+..+..... ..-.-.+.......+++.||++.
T Consensus        73 ~~~~~~~~l~G~g~nGKStl~~~l~~l~G~~~~~~~~~~~~~~~~~~~f~~a~l~gk~l~~~~E~~~  139 (304)
T TIGR01613        73 YTEQKLFFLYGNGGNGKSTFQNLLSNLLGDYATTAVASLKMNEFQEHRFGLARLEGKRAVIGDEVQK  139 (304)
T ss_pred             CCceEEEEEECCCCCcHHHHHHHHHHHhChhhccCCcchhhhhccCCCchhhhhcCCEEEEecCCCC
Confidence            3445669999999999999999999888765432221111110 00011223445678888999873

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.38  E-value=0.00081  Score=62.63  Aligned_cols=25  Identities=36%  Similarity=0.543  Sum_probs=21.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..+.|+||+|+||||++..||..+
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4458899999999999999998754

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.38  E-value=0.00018  Score=57.71  Aligned_cols=27  Identities=26%  Similarity=0.324  Sum_probs=23.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+.-++|.|+||+||||+++.++..+.
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            345689999999999999999999885

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=97.38  E-value=0.0004  Score=60.29  Aligned_cols=30  Identities=23%  Similarity=0.244  Sum_probs=26.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      ..|-.+++.|++|||||++|..+|..++.+
T Consensus        90 ~~p~iIlI~G~sgsGKStlA~~La~~l~~~  119 (301)
T PRK04220         90 KEPIIILIGGASGVGTSTIAFELASRLGIR  119 (301)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            345569999999999999999999999887

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.37  E-value=0.0002  Score=60.81  Aligned_cols=31  Identities=39%  Similarity=0.551  Sum_probs=25.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      |+|+|+||+||||+++.++..+   +.+++.++.
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~~   35 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGT   35 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEcc
Confidence            6899999999999999999987   455555543

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.

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=97.37  E-value=0.00073  Score=55.54  Aligned_cols=24  Identities=29%  Similarity=0.366  Sum_probs=20.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~   53 (266)
                      .+.-++|+||.|+|||++.+.++.
T Consensus        28 ~~~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          28 SGRLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             CCeEEEEECCCCCccHHHHHHHHH
Confidence            344599999999999999999993

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

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.37  E-value=0.00098  Score=65.34  Aligned_cols=64  Identities=23%  Similarity=0.321  Sum_probs=40.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC----------hhhHHHHHHH-------cccCCeeeeecc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG----------NNDLRHILIA-------TENKSILVVEDI   91 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~----------~~~l~~~~~~-------~~~~~vl~iDei   91 (266)
                      +-++|.|+||||||++++++...+   |..++.+.+.....          ...+..++..       .....+|++||+
T Consensus       369 ~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg~Aa~~L~~~~g~~a~Ti~~~~~~~~~~~~~~~~~~llIvDEa  448 (744)
T TIGR02768       369 DIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKAAEGLQAESGIESRTLASLEYAWANGRDLLSDKDVLVIDEA  448 (744)
T ss_pred             CEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHhccCCceeeHHHHHhhhccCcccCCCCcEEEEECc
Confidence            357899999999999999987654   55666554433210          1112222211       124689999999


Q ss_pred             hhhH
Q 024550           92 DCCI   95 (266)
Q Consensus        92 d~l~   95 (266)
                      -.+.
T Consensus       449 sMv~  452 (744)
T TIGR02768       449 GMVG  452 (744)
T ss_pred             ccCC
Confidence            8764

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.

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=97.37  E-value=0.001  Score=54.54  Aligned_cols=36  Identities=33%  Similarity=0.367  Sum_probs=27.7

Q ss_pred             HHHHHHh--CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           20 KEFYRRV--GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        20 ~~~~~~~--~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++-.++  |+|.+.-+++-|+.|||||.+.+.++.-+
T Consensus        15 delDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~   52 (235)
T COG2874          15 DELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGF   52 (235)
T ss_pred             HHHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHH
Confidence            3444455  47777779999999999999999988655

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.36  E-value=0.00052  Score=60.51  Aligned_cols=41  Identities=17%  Similarity=0.206  Sum_probs=32.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNL   67 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~   67 (266)
                      |++.+.-++++||||||||+++..+|...         +...++++...-
T Consensus        98 Gi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~  147 (317)
T PRK04301         98 GIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGT  147 (317)
T ss_pred             CccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCC
Confidence            57766679999999999999999998653         346777777653

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.36  E-value=0.0012  Score=64.55  Aligned_cols=24  Identities=33%  Similarity=0.599  Sum_probs=20.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +-+++.|+||||||++++++...+
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~  362 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELA  362 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            358899999999999999887655

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.

>PRK14529 adenylate kinase; Provisional

Probab=97.36  E-value=0.00015  Score=60.45  Aligned_cols=28  Identities=25%  Similarity=0.468  Sum_probs=25.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      .|+|.||||+||||+++.|+..++.+.+
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~~~~~i   29 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKYDLAHI   29 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCCCc
Confidence            3789999999999999999999987765

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=97.34  E-value=0.00082  Score=56.15  Aligned_cols=62  Identities=23%  Similarity=0.301  Sum_probs=39.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHH-Hc----CCcEE--------------EEeCCc-ccC--------hhhHHHHHHHccc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMAN-YL----KFDVY--------------DLELSN-LLG--------NNDLRHILIATEN   82 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~-~~----~~~~~--------------~i~~~~-~~~--------~~~l~~~~~~~~~   82 (266)
                      ...++|.||.|+|||++.+.++. .+    |....              .+...+ +..        -..+..++..+..
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~  110 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTS  110 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCccccccccchHHHHHHHHHHHHHhCCC
Confidence            34589999999999999999987 22    22111              111110 100        1335566777788


Q ss_pred             CCeeeeecch
Q 024550           83 KSILVVEDID   92 (266)
Q Consensus        83 ~~vl~iDeid   92 (266)
                      +.++++||+.
T Consensus       111 ~sLvllDE~~  120 (222)
T cd03287         111 RSLVILDELG  120 (222)
T ss_pred             CeEEEEccCC
Confidence            9999999986

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

>PRK04328 hypothetical protein; Provisional

Probab=97.34  E-value=0.00034  Score=59.50  Aligned_cols=40  Identities=28%  Similarity=0.185  Sum_probs=30.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      |+++...+|++||||||||+++..++.+.   |-+.++++...
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~ee   61 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVALEE   61 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEeeC
Confidence            68888889999999999999988766542   56666666543

>PRK00889 adenylylsulfate kinase; Provisional

Probab=97.33  E-value=0.00034  Score=56.06  Aligned_cols=34  Identities=26%  Similarity=0.335  Sum_probs=26.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      +..+.|.|+||+|||++++.++..+   +..+..++.
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id~   40 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDG   40 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEcC
Confidence            4468899999999999999999987   334455543

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.33  E-value=0.00074  Score=60.24  Aligned_cols=27  Identities=37%  Similarity=0.661  Sum_probs=23.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +...++++||+|+||||+++++...+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~  147 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYIN  147 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhC
Confidence            345689999999999999999988764

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.33  E-value=0.0011  Score=61.99  Aligned_cols=39  Identities=23%  Similarity=0.189  Sum_probs=31.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |+++...+|+.||||+|||+++-.++...   |-+.++++..
T Consensus       259 G~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s~e  300 (484)
T TIGR02655       259 GFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFAYE  300 (484)
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEee
Confidence            68888889999999999999998887755   4556666544

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.

>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=97.32  E-value=0.0011  Score=54.52  Aligned_cols=24  Identities=42%  Similarity=0.472  Sum_probs=19.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .-+.+.||+|||||++|-+.|-++
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            358899999999999999988765

; GO: 0005524 ATP binding; PDB: 3B85_A.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=97.32  E-value=0.0011  Score=55.08  Aligned_cols=22  Identities=32%  Similarity=0.437  Sum_probs=19.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      .-++|+||.|+|||++.+.++.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            4588999999999999999864

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

>PTZ00494 tuzin-like protein; Provisional

Probab=97.31  E-value=0.012  Score=53.62  Aligned_cols=47  Identities=11%  Similarity=0.134  Sum_probs=39.9

Q ss_pred             HHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc
Q 024550           21 EFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL   67 (266)
Q Consensus        21 ~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~   67 (266)
                      ..+.++....|+.+.|.|..|||||++.|.--..-+.+.+.++.-..
T Consensus       385 qvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE~~paV~VDVRg~  431 (664)
T PTZ00494        385 SVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVEGVALVHVDVGGT  431 (664)
T ss_pred             HHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHcCCCeEEEEecCC
Confidence            44667778889999999999999999999999989999888876543

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=97.31  E-value=0.00058  Score=58.68  Aligned_cols=63  Identities=19%  Similarity=0.424  Sum_probs=40.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCC---cEEEEeC-Cccc-------------ChhhHHHHHHHc--ccCCeeeeecc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKF---DVYDLEL-SNLL-------------GNNDLRHILIAT--ENKSILVVEDI   91 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~---~~~~i~~-~~~~-------------~~~~l~~~~~~~--~~~~vl~iDei   91 (266)
                      ..++++.||+|+||||+++++...+..   .++.+.- .++.             ....+..++..+  ..|.++++.|+
T Consensus       127 ~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~~l~~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEi  206 (270)
T PF00437_consen  127 RGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPELRLPGPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIGEI  206 (270)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S--SCSSEEEEEEETTTBSHHHHHHHHTTS--SEEEESCE
T ss_pred             ceEEEEECCCccccchHHHHHhhhccccccceEEeccccceeecccceEEEEeecCcccHHHHHHHHhcCCCCccccccc
Confidence            567999999999999999999988833   3343331 1111             122455555544  46899999999


Q ss_pred             hh
Q 024550           92 DC   93 (266)
Q Consensus        92 d~   93 (266)
                      ..
T Consensus       207 R~  208 (270)
T PF00437_consen  207 RD  208 (270)
T ss_dssp             -S
T ss_pred             CC
Confidence            84

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 ....

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=97.31  E-value=0.00084  Score=57.88  Aligned_cols=37  Identities=30%  Similarity=0.293  Sum_probs=28.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      ++.+.|+||+|+||||++..+|..+   |..+..+++..+
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~  111 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTF  111 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCC
Confidence            4568889999999999999888766   555666665543

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.

>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=97.31  E-value=0.00023  Score=58.37  Aligned_cols=39  Identities=18%  Similarity=0.277  Sum_probs=30.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc-CCcEEEEeCCccc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL-KFDVYDLELSNLL   68 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~-~~~~~~i~~~~~~   68 (266)
                      .|..+++.|+||+|||+++..+...+ +..++.++...+.
T Consensus        14 ~P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~r   53 (199)
T PF06414_consen   14 KPTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEFR   53 (199)
T ss_dssp             S-EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGGG
T ss_pred             CCEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHHH
Confidence            35668999999999999999999988 7778888877664

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.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.30  E-value=0.0014  Score=65.64  Aligned_cols=63  Identities=17%  Similarity=0.298  Sum_probs=39.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCccc----------ChhhHHHHHHH-------cccCCeeeeecch
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLL----------GNNDLRHILIA-------TENKSILVVEDID   92 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~----------~~~~l~~~~~~-------~~~~~vl~iDeid   92 (266)
                      -++|.|++||||||+++++...+   |..++.+.+....          ....+..++..       .....||+|||+-
T Consensus       364 v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTGkAA~~L~e~tGi~a~TI~sll~~~~~~~~~l~~~~vlIVDEAS  443 (988)
T PRK13889        364 LGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIAAENLEGGSGIASRTIASLEHGWGQGRDLLTSRDVLVIDEAG  443 (988)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcHHHHHHHhhccCcchhhHHHHHhhhcccccccccCcEEEEECcc
Confidence            46799999999999988766543   6666655443221          01223333321       1245799999999


Q ss_pred             hhH
Q 024550           93 CCI   95 (266)
Q Consensus        93 ~l~   95 (266)
                      .+.
T Consensus       444 Mv~  446 (988)
T PRK13889        444 MVG  446 (988)
T ss_pred             cCC
Confidence            764

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=97.30  E-value=0.00083  Score=55.14  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=19.4

Q ss_pred             ceeEEecCCCCChHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMA   52 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala   52 (266)
                      +.++|+||.|+|||++.+.++
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            359999999999999999988

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

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=97.29  E-value=0.00044  Score=57.86  Aligned_cols=39  Identities=23%  Similarity=0.112  Sum_probs=30.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |++....++++||||+|||+++..++...   +.+.+.++..
T Consensus        16 Gi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~e   57 (229)
T TIGR03881        16 GIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTTE   57 (229)
T ss_pred             CCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            68888889999999999999998776432   5566666653

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=97.29  E-value=0.00022  Score=57.34  Aligned_cols=25  Identities=28%  Similarity=0.381  Sum_probs=22.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -++|.||||+||||+++.++..++.
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCc
Confidence            4789999999999999999998753

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.

>PRK12338 hypothetical protein; Provisional

Probab=97.28  E-value=0.00028  Score=61.80  Aligned_cols=29  Identities=24%  Similarity=0.323  Sum_probs=25.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      |.-+++.|+|||||||+++.+|..+|...
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l~~~~   32 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTLNIKH   32 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHCCCeE
Confidence            45688999999999999999999998764

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=97.28  E-value=0.00059  Score=60.13  Aligned_cols=35  Identities=23%  Similarity=0.170  Sum_probs=27.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +.-++|.||+|+||||++..+|..+   +..+..+++.
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~D  151 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAGD  151 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            4458899999999999999999877   4455555543

>PRK13808 adenylate kinase; Provisional

Probab=97.28  E-value=0.00024  Score=62.57  Aligned_cols=29  Identities=24%  Similarity=0.471  Sum_probs=25.6

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |+|+||||+|||++++.|+..+|++.+.+
T Consensus         3 Iiv~GpPGSGK~T~a~~LA~~ygl~~is~   31 (333)
T PRK13808          3 LILLGPPGAGKGTQAQRLVQQYGIVQLST   31 (333)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceecc
Confidence            89999999999999999999998755543

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.28  E-value=0.00018  Score=58.51  Aligned_cols=23  Identities=35%  Similarity=0.681  Sum_probs=21.6

Q ss_pred             eEEecCCCCChHHHHHHHHHHcC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ++|.|+||+|||++++.+|+.+.
T Consensus         4 iIlTGyPgsGKTtfakeLak~L~   26 (261)
T COG4088           4 IILTGYPGSGKTTFAKELAKELR   26 (261)
T ss_pred             EEEecCCCCCchHHHHHHHHHHH
Confidence            78999999999999999999984

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=97.28  E-value=0.00029  Score=56.84  Aligned_cols=29  Identities=31%  Similarity=0.413  Sum_probs=24.9

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      |.|+|++|+||||+++.++. +|.+++..+
T Consensus         2 i~itG~~gsGKst~~~~l~~-~g~~~i~~D   30 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE-LGIPVIDAD   30 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH-CCCCEEecC
Confidence            67999999999999999999 787765544

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.28  E-value=0.00052  Score=61.41  Aligned_cols=23  Identities=39%  Similarity=0.502  Sum_probs=21.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -+++.|.||||||.++-.++..+
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh
Confidence            47889999999999999999988

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK05480 uridine/cytidine kinase; Provisional

Probab=97.28  E-value=0.00047  Score=56.90  Aligned_cols=37  Identities=14%  Similarity=0.138  Sum_probs=28.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC-CcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK-FDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~-~~~~~i~~~~~   67 (266)
                      +.-|.|.||+|||||||++.|+..++ ..+..++...+
T Consensus         6 ~~iI~I~G~sGsGKTTl~~~l~~~l~~~~~~~i~~D~~   43 (209)
T PRK05480          6 PIIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQDSY   43 (209)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCceEEEeCCcc
Confidence            34588999999999999999999984 34455555444

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.27  E-value=0.00051  Score=57.74  Aligned_cols=39  Identities=26%  Similarity=0.213  Sum_probs=28.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |++....++++||||||||+++..++...   |...++++..
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e   61 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQ   61 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCC
Confidence            57777789999999999999976554433   5556666543

>cd04177 RSR1 RSR1 subgroup

Probab=97.27  E-value=0.0012  Score=52.19  Aligned_cols=23  Identities=26%  Similarity=0.478  Sum_probs=20.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|+||+|||++++++....
T Consensus         3 ki~liG~~~~GKTsli~~~~~~~   25 (168)
T cd04177           3 KIVVLGAGGVGKSALTVQFVQNV   25 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48999999999999999987544

RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.26  E-value=0.001  Score=53.13  Aligned_cols=24  Identities=29%  Similarity=0.491  Sum_probs=18.2

Q ss_pred             ceeEEecCCCCChHH-HHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSS-LIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~-la~ala~~~   55 (266)
                      +.+++.||+|||||+ ++..+...+
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~   49 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEAL   49 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHh
Confidence            579999999999999 444444443

>PTZ00035 Rad51 protein; Provisional

Probab=97.26  E-value=0.001  Score=59.16  Aligned_cols=52  Identities=17%  Similarity=0.122  Sum_probs=36.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDLRHILI   78 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l~~~~~   78 (266)
                      |++...-+.|+||||||||+++..++...         +...++++.........+..+..
T Consensus       114 Gi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri~~ia~  174 (337)
T PTZ00035        114 GIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERIVQIAE  174 (337)
T ss_pred             CCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHHHHHHH
Confidence            56666668899999999999999887533         34566777665445555555543

>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=97.24  E-value=0.00037  Score=56.23  Aligned_cols=36  Identities=22%  Similarity=0.386  Sum_probs=29.2

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG   69 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~   69 (266)
                      +.+.|+||||||++++.++..+   +.+...++..++..
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~~~~~~~i~~Ddf~~   40 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYYV   40 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEehhhccc
Confidence            6789999999999999999987   35666777666653

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=97.23  E-value=0.00057  Score=57.62  Aligned_cols=40  Identities=18%  Similarity=0.173  Sum_probs=32.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~   66 (266)
                      |+++..-++|.|+||+|||+++..++...    +.+++.+++..
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~   52 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEM   52 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCC
Confidence            77777789999999999999988877654    77888887654

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.22  E-value=0.0032  Score=53.08  Aligned_cols=44  Identities=18%  Similarity=0.194  Sum_probs=32.7

Q ss_pred             ceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          143 ERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       143 ~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      ++.+|..+-..-.+|+.++.  -.+..+-++ .+...+..|++.+..
T Consensus       128 ~is~i~l~Q~~~~lp~~iR~--n~~y~i~~~-~s~~dl~~i~~~~~~  171 (241)
T PF04665_consen  128 NISIIFLSQSYFHLPPNIRS--NIDYFIIFN-NSKRDLENIYRNMNI  171 (241)
T ss_pred             ceEEEEEeeecccCCHHHhh--cceEEEEec-CcHHHHHHHHHhccc
Confidence            46778888888889999876  677777675 577777777776653

This is thought to be an ATPase involved in viral DNA packaging [].

>PLN02165 adenylate isopentenyltransferase

Probab=97.22  E-value=0.00036  Score=61.41  Aligned_cols=33  Identities=21%  Similarity=0.363  Sum_probs=28.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      .++|.||+|+|||+++..||..++..++..+.-
T Consensus        45 iivIiGPTGSGKStLA~~LA~~l~~eIIsaDs~   77 (334)
T PLN02165         45 VVVIMGATGSGKSRLSVDLATRFPSEIINSDKM   77 (334)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHcCCceecCChh
Confidence            488999999999999999999998877665544

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=97.21  E-value=0.0021  Score=53.79  Aligned_cols=29  Identities=21%  Similarity=0.389  Sum_probs=25.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.+...+.++||.|+|||||++.++.+.
T Consensus        53 ~V~~ge~W~I~G~NGsGKTTLL~ll~~~~   81 (257)
T COG1119          53 QVNPGEHWAIVGPNGAGKTTLLSLLTGEH   81 (257)
T ss_pred             eecCCCcEEEECCCCCCHHHHHHHHhccc
Confidence            45566679999999999999999998766

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=97.21  E-value=0.0019  Score=50.62  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=18.9

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      +++.|+||+|||+|++++...
T Consensus         3 i~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        3 LVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999999753

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=97.21  E-value=0.00037  Score=52.52  Aligned_cols=31  Identities=29%  Similarity=0.366  Sum_probs=24.8

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      ++..-++|+|+=|+|||+++|.++..+|..-
T Consensus        13 ~~g~vi~L~GdLGaGKTtf~r~l~~~lg~~~   43 (123)
T PF02367_consen   13 KPGDVILLSGDLGAGKTTFVRGLARALGIDE   43 (123)
T ss_dssp             SS-EEEEEEESTTSSHHHHHHHHHHHTT--S
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcCCCC
Confidence            3345699999999999999999999998754

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.

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=97.21  E-value=0.00036  Score=57.12  Aligned_cols=31  Identities=23%  Similarity=0.209  Sum_probs=26.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      -+.++|++|+|||++++.++..+|.+++..+
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~~g~~~i~~D   33 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQKGIPILDAD   33 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCeEeeCc
Confidence            4789999999999999999998888776443

>PRK12337 2-phosphoglycerate kinase; Provisional

Probab=97.21  E-value=0.0012  Score=60.55  Aligned_cols=29  Identities=34%  Similarity=0.361  Sum_probs=26.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      .|.-++++|+||||||+++..+|..++..
T Consensus       254 ~p~vil~~G~~G~GKSt~a~~LA~~lg~~  282 (475)
T PRK12337        254 RPLHVLIGGVSGVGKSVLASALAYRLGIT  282 (475)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHcCCc
Confidence            36679999999999999999999999885

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=97.20  E-value=0.00046  Score=55.57  Aligned_cols=27  Identities=30%  Similarity=0.523  Sum_probs=24.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      ..+.+.||+|+||||+++.++..++..
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~~~   30 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFSAK   30 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCE
Confidence            358899999999999999999988764

>PRK08356 hypothetical protein; Provisional

Probab=97.20  E-value=0.00039  Score=56.83  Aligned_cols=31  Identities=16%  Similarity=0.114  Sum_probs=24.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSN   66 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~   66 (266)
                      -++|+||||+||||+++.+. ..|.+  .+++.+
T Consensus         7 ~i~~~G~~gsGK~t~a~~l~-~~g~~--~is~~~   37 (195)
T PRK08356          7 IVGVVGKIAAGKTTVAKFFE-EKGFC--RVSCSD   37 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHH-HCCCc--EEeCCC
Confidence            47889999999999999996 46665  444443

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=97.20  E-value=0.00037  Score=56.61  Aligned_cols=32  Identities=19%  Similarity=0.307  Sum_probs=24.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHc-CCcEEEEeCCcc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL-KFDVYDLELSNL   67 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~-~~~~~~i~~~~~   67 (266)
                      |.+.|+|||||||+++.++..+ +..+  ++..++
T Consensus         2 i~i~G~sgsGKTtla~~l~~~~~~~~~--i~~Ddf   34 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRILPNCCV--IHQDDF   34 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeE--Eccccc
Confidence            5688999999999999999998 3444  444444

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=97.20  E-value=0.00068  Score=56.60  Aligned_cols=40  Identities=18%  Similarity=0.127  Sum_probs=32.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      |+++...+++.|+||+|||+++..++...   |.+.++++...
T Consensus        12 Gi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e~   54 (224)
T TIGR03880        12 GFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEE   54 (224)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            67777789999999999999988887543   66777777654

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=97.19  E-value=0.0017  Score=52.26  Aligned_cols=35  Identities=23%  Similarity=0.475  Sum_probs=26.4

Q ss_pred             HHHHHhCCC--CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           21 EFYRRVGKA--WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        21 ~~~~~~~~~--~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..|..+.+.  +...+.+.||.|+|||||.|.+|.-+
T Consensus        16 ~lf~~L~f~l~~Ge~~~i~G~NG~GKTtLLRilaGLl   52 (209)
T COG4133          16 TLFSDLSFTLNAGEALQITGPNGAGKTTLLRILAGLL   52 (209)
T ss_pred             eeecceeEEEcCCCEEEEECCCCCcHHHHHHHHHccc
Confidence            344444433  34458899999999999999999876

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=97.19  E-value=0.00059  Score=53.63  Aligned_cols=36  Identities=36%  Similarity=0.448  Sum_probs=28.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      .-|+|+|.||+||||+|+++...+   |.+.+.++...+
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~l   41 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGDNL   41 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcch
Confidence            348899999999999999999887   677777775433

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 ....

>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=97.19  E-value=0.00066  Score=58.40  Aligned_cols=63  Identities=22%  Similarity=0.323  Sum_probs=34.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCccc----------ChhhHHHHHH-----HcccCCeeeeecchhhH
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLL----------GNNDLRHILI-----ATENKSILVVEDIDCCI   95 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~----------~~~~l~~~~~-----~~~~~~vl~iDeid~l~   95 (266)
                      ++|+|.||+|||++++.|+..+   +..++.++...+.          .+...+..+.     ......|+++|+...+-
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls~~~iVI~Dd~nYiK   83 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALSKDTIVILDDNNYIK   83 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHTT-SEEEE-S---SH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhccCeEEEEeCCchHH
Confidence            7899999999999999999876   4556556533222          1122222222     22456899999988764


Q ss_pred             H
Q 024550           96 E   96 (266)
Q Consensus        96 ~   96 (266)
                      +
T Consensus        84 g   84 (270)
T PF08433_consen   84 G   84 (270)
T ss_dssp             H
T ss_pred             H
Confidence            4

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=97.18  E-value=0.00055  Score=56.00  Aligned_cols=35  Identities=17%  Similarity=0.236  Sum_probs=26.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHcC-CcEEEEeCCccc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLK-FDVYDLELSNLL   68 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~-~~~~~i~~~~~~   68 (266)
                      +.|.||+|+||||+++.++..++ .....++...+.
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l~~~~~~v~~~D~~~   37 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQDSYY   37 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCCeEEEEecccc
Confidence            56899999999999999999873 344555555443

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.17  E-value=0.00056  Score=63.84  Aligned_cols=39  Identities=21%  Similarity=0.208  Sum_probs=31.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHH----cCCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANY----LKFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~----~~~~~~~i~~~   65 (266)
                      |+++.+.+|++||||||||+++..++..    .|-+.+++++.
T Consensus        17 Glp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e   59 (484)
T TIGR02655        17 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE   59 (484)
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe
Confidence            6888889999999999999999987543    25677777764

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.

>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=97.17  E-value=0.00043  Score=65.43  Aligned_cols=32  Identities=19%  Similarity=0.365  Sum_probs=29.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      .++|.|.||+||||+.+.+|+.++.+|+.++.
T Consensus         8 ~i~LiG~~GaGKttvg~~LA~~L~~~fiD~D~   39 (542)
T PRK14021          8 QAVIIGMMGAGKTRVGKEVAQMMRLPFADADV   39 (542)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEEchH
Confidence            49999999999999999999999999998873

>PRK14974 cell division protein FtsY; Provisional

Probab=97.17  E-value=0.0012  Score=58.46  Aligned_cols=35  Identities=34%  Similarity=0.401  Sum_probs=26.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +.-++|+||||+||||++..+|..+   |..+..+.+.
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~D  177 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGD  177 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            4569999999999999988888766   4445445444

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=97.17  E-value=0.00052  Score=60.10  Aligned_cols=34  Identities=21%  Similarity=0.400  Sum_probs=29.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      .-+++.||+|||||+++..+|..++..++..+.-
T Consensus         5 ~~i~i~GptgsGKt~la~~la~~~~~~iis~Ds~   38 (307)
T PRK00091          5 KVIVIVGPTASGKTALAIELAKRLNGEIISADSM   38 (307)
T ss_pred             eEEEEECCCCcCHHHHHHHHHHhCCCcEEecccc
Confidence            4588999999999999999999998877766543

>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=97.17  E-value=0.0023  Score=52.38  Aligned_cols=25  Identities=40%  Similarity=0.604  Sum_probs=21.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      |+-++|+||+|+||||++--+|..+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~   25 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARL   25 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHH
Confidence            4568999999999999888887766

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 ....

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=97.16  E-value=0.00041  Score=53.88  Aligned_cols=40  Identities=23%  Similarity=0.336  Sum_probs=31.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLR   74 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~   74 (266)
                      .+++.|++||||||++++++.+++.+|+.-  .++....++.
T Consensus        14 ~i~vmGvsGsGKSTigk~L~~~l~~~F~dg--Dd~Hp~~Nve   53 (191)
T KOG3354|consen   14 VIVVMGVSGSGKSTIGKALSEELGLKFIDG--DDLHPPANVE   53 (191)
T ss_pred             eEEEEecCCCChhhHHHHHHHHhCCccccc--ccCCCHHHHH
Confidence            478889999999999999999999887643  3444444443

>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]

Probab=97.16  E-value=0.00023  Score=65.04  Aligned_cols=63  Identities=24%  Similarity=0.386  Sum_probs=40.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe----CCcccC----hhhHHHH-HHH----cccCCeeeeecchhhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE----LSNLLG----NNDLRHI-LIA----TENKSILVVEDIDCCI   95 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~----~~~~~~----~~~l~~~-~~~----~~~~~vl~iDeid~l~   95 (266)
                      ++||-|.|||.||-|.+-+-+.....+|..-    ++.++.    ...-+.. ++.    ...++|++|||+|.+-
T Consensus       366 NVLLLGDPgtAKSQlLKFvEkvsPIaVYTSGKGSSAAGLTASV~RD~~tReFylEGGAMVLADgGVvCIDEFDKMr  441 (729)
T KOG0481|consen  366 NVLLLGDPGTAKSQLLKFVEKVSPIAVYTSGKGSSAAGLTASVIRDPSTREFYLEGGAMVLADGGVVCIDEFDKMR  441 (729)
T ss_pred             eEEEecCCchhHHHHHHHHHhcCceEEEecCCCcccccceeeEEecCCcceEEEecceEEEecCCEEEeehhhccC
Confidence            4999999999999999988877765555432    222221    0001111 111    2468999999999884

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=97.16  E-value=0.00031  Score=58.75  Aligned_cols=22  Identities=36%  Similarity=0.596  Sum_probs=19.9

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++++|+||+|||++++.++...
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc
Confidence            4789999999999999999884

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

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=97.16  E-value=0.00034  Score=57.15  Aligned_cols=23  Identities=35%  Similarity=0.626  Sum_probs=21.4

Q ss_pred             eEEecCCCCChHHHHHHHHHHcC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~   56 (266)
                      |-+.||||+||||+|+.|+..++
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            56899999999999999999996

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 ....

>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=97.16  E-value=0.00062  Score=54.38  Aligned_cols=34  Identities=32%  Similarity=0.400  Sum_probs=27.9

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      ++++||||+|||++++.++..+   +..+..+++...
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D~~   39 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTY   39 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcCCC
Confidence            6889999999999999998876   566777776654

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.

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=97.16  E-value=0.0023  Score=50.35  Aligned_cols=23  Identities=17%  Similarity=0.479  Sum_probs=19.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +++|.|++|+|||+|+..+....
T Consensus         1 ~i~~vG~~~~GKstLi~~l~~~~   23 (167)
T cd04160           1 SVLILGLDNAGKTTFLEQLKTLF   23 (167)
T ss_pred             CEEEEecCCCCHHHHHHHHhhhc
Confidence            47899999999999999987643

Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.

>TIGR00235 udk uridine kinase

Probab=97.15  E-value=0.00058  Score=56.38  Aligned_cols=25  Identities=20%  Similarity=0.196  Sum_probs=22.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -+.|.||+|+||||++++++..++.
T Consensus         8 vi~I~G~sGsGKSTl~~~l~~~l~~   32 (207)
T TIGR00235         8 IIGIGGGSGSGKTTVARKIYEQLGK   32 (207)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcc
Confidence            3678999999999999999998763

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=97.15  E-value=0.00044  Score=53.28  Aligned_cols=25  Identities=32%  Similarity=0.592  Sum_probs=22.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      ++|.||+|+|||++++.++..+...
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~~~   26 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFDPN   26 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCCcc
Confidence            6789999999999999999987544

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK00300 gmk guanylate kinase; Provisional

Probab=97.14  E-value=0.00044  Score=56.77  Aligned_cols=27  Identities=33%  Similarity=0.426  Sum_probs=23.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ++.-+.|+||+|+|||++++.++..+.
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            455689999999999999999999875

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=97.14  E-value=0.00098  Score=53.00  Aligned_cols=37  Identities=30%  Similarity=0.449  Sum_probs=30.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      +.-++|+|.+|+||||+|.++...+   |.+.+.++...+
T Consensus        23 ~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDGDnv   62 (197)
T COG0529          23 GAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGDNV   62 (197)
T ss_pred             CeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecChhH
Confidence            4458899999999999999999887   778887775433

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=97.13  E-value=0.00088  Score=51.75  Aligned_cols=23  Identities=35%  Similarity=0.619  Sum_probs=20.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -++|.||.|+|||||+++|-..-
T Consensus         3 rimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    3 RIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             eEEEECCCCCCHHHHHHHHcCCC
Confidence            48999999999999999998754

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=97.13  E-value=0.0017  Score=57.76  Aligned_cols=53  Identities=17%  Similarity=0.107  Sum_probs=38.4

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhHHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDLRHILIA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l~~~~~~   79 (266)
                      |++...-+.++|+||+|||.++..+|...         +...++++...-....++.++...
T Consensus       119 G~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~qia~~  180 (342)
T PLN03186        119 GIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAER  180 (342)
T ss_pred             CCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHHHHHH
Confidence            46666668899999999999998887432         236788887765566666666443

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.13  E-value=0.0014  Score=58.70  Aligned_cols=38  Identities=21%  Similarity=0.210  Sum_probs=28.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      .+..++|+||+|+||||++..+|..+   +..+..+++...
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDty  245 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTF  245 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCcc
Confidence            34568999999999999999998766   445555555444

>PRK06761 hypothetical protein; Provisional

Probab=97.12  E-value=0.0005  Score=59.33  Aligned_cols=32  Identities=25%  Similarity=0.406  Sum_probs=26.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +-++|.||||+||||+++.++..+....+.+.
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~g~~v~   35 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQNGIEVE   35 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcCceEEE
Confidence            35889999999999999999999976555444

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.12  E-value=0.0023  Score=54.89  Aligned_cols=62  Identities=21%  Similarity=0.284  Sum_probs=38.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC---CcEEEEe-CCccc----------C--hhhHHHHHHHc--ccCCeeeeecchh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLE-LSNLL----------G--NNDLRHILIAT--ENKSILVVEDIDC   93 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~-~~~~~----------~--~~~l~~~~~~~--~~~~vl~iDeid~   93 (266)
                      ..++|.||+|+||||+++++...+.   ..++.+. ..++.          .  ...+...+..+  ..|.+++++|+..
T Consensus        81 GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~~~~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR~  160 (264)
T cd01129          81 GIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQIPGINQVQVNEKAGLTFARGLRAILRQDPDIIMVGEIRD  160 (264)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceecCCCceEEEeCCcCCcCHHHHHHHHhccCCCEEEeccCCC
Confidence            3489999999999999999977663   2344432 11110          0  11233333332  4699999999974

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.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=97.11  E-value=0.0016  Score=53.76  Aligned_cols=22  Identities=32%  Similarity=0.454  Sum_probs=19.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      .-++|.||.|+|||++.+.++.
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4589999999999999998873

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

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=97.11  E-value=0.0018  Score=50.72  Aligned_cols=22  Identities=27%  Similarity=0.397  Sum_probs=19.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|+||+|||+++..+...
T Consensus         2 ki~~vG~~~vGKTsli~~l~~~   23 (168)
T cd04119           2 KVISMGNSGVGKSCIIKRYCEG   23 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999998864

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.11  E-value=0.0008  Score=64.03  Aligned_cols=28  Identities=25%  Similarity=0.406  Sum_probs=23.5

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++|...+-|+||+|+||||++.-+-+.+
T Consensus       491 i~pGe~vALVGPSGsGKSTiasLL~rfY  518 (716)
T KOG0058|consen  491 IRPGEVVALVGPSGSGKSTIASLLLRFY  518 (716)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            5556669999999999999999887755

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=97.11  E-value=0.0028  Score=49.24  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|+||+|||+++..+...
T Consensus         3 ki~iiG~~~vGKTsl~~~~~~~   24 (162)
T cd04138           3 KLVVVGAGGVGKSALTIQLIQN   24 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999998863

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=97.11  E-value=0.0011  Score=60.36  Aligned_cols=37  Identities=19%  Similarity=0.331  Sum_probs=29.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      +.-++|+||+|+||||++..+|..+   |..+..+++..+
T Consensus       100 ~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~D~~  139 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADTF  139 (429)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcCccc
Confidence            4558999999999999999999877   666666666544

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.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.10  E-value=0.0011  Score=56.18  Aligned_cols=27  Identities=26%  Similarity=0.203  Sum_probs=22.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ....+-|.|.+||||||++|.+..-..
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~   64 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEE   64 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcC
Confidence            344588999999999999999998663

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=97.10  E-value=0.0019  Score=52.29  Aligned_cols=19  Identities=26%  Similarity=0.508  Sum_probs=18.0

Q ss_pred             eEEecCCCCChHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMA   52 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala   52 (266)
                      ++|+||.|+|||++++.++
T Consensus         2 ~~ltG~N~~GKst~l~~i~   20 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVG   20 (185)
T ss_pred             EEEECCCCCcHHHHHHHHH
Confidence            6899999999999999998

>TIGR03263 guanyl_kin guanylate kinase

Probab=97.10  E-value=0.00042  Score=55.64  Aligned_cols=25  Identities=32%  Similarity=0.448  Sum_probs=22.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -++|.||+|+|||++++.|+.....
T Consensus         3 ii~l~G~~GsGKsTl~~~L~~~~~~   27 (180)
T TIGR03263         3 LIVISGPSGVGKSTLVKALLEEDPN   27 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHccCcc
Confidence            4889999999999999999997644

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.

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=97.10  E-value=0.0024  Score=51.00  Aligned_cols=23  Identities=30%  Similarity=0.380  Sum_probs=20.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      +.++|.|+||+|||+++..+...
T Consensus         2 ~kv~l~G~~g~GKTtl~~~~~~~   24 (180)
T cd04137           2 RKIAVLGSRSVGKSSLTVQFVEG   24 (180)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999988753

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=97.09  E-value=0.0016  Score=63.27  Aligned_cols=28  Identities=21%  Similarity=0.307  Sum_probs=23.4

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +++..-+-+.|++|||||||++.+..-.
T Consensus       496 I~~Ge~vaIvG~SGsGKSTL~KLL~gly  523 (709)
T COG2274         496 IPPGEKVAIVGRSGSGKSTLLKLLLGLY  523 (709)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4444459999999999999999998755

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=97.09  E-value=0.00044  Score=54.90  Aligned_cols=26  Identities=31%  Similarity=0.439  Sum_probs=22.2

Q ss_pred             ecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           37 YGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        37 ~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|||||||||+++.++..++..++.-
T Consensus         1 ~G~sGsGKSTla~~la~~l~~~~~~~   26 (163)
T PRK11545          1 MGVSGSGKSAVASEVAHQLHAAFLDG   26 (163)
T ss_pred             CCCCCCcHHHHHHHHHHHhCCeEEeC
Confidence            49999999999999999998755544

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=97.09  E-value=0.0032  Score=53.84  Aligned_cols=49  Identities=18%  Similarity=0.203  Sum_probs=33.5

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChhhHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNNDLRH   75 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~~l~~   75 (266)
                      |++...-.=|+||||||||.++..+|-..         +...++++...-.....+.+
T Consensus        34 Gi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~   91 (256)
T PF08423_consen   34 GIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQ   91 (256)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHH
T ss_pred             CCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHH
Confidence            45544445599999999999999887554         44588888776544333333

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	266
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		9e-14
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		1e-13
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		3e-12
2ce7_A	476	Edta Treated Length = 476		4e-12
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		7e-12
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-11
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		2e-11
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		5e-11
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		1e-10
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		1e-09
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		1e-08
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		1e-08
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		1e-08
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		2e-08
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		4e-08
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		9e-08
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		4e-07
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		8e-07
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		9e-07
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		9e-07
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		1e-06
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		1e-06
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		1e-06
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		1e-06
3vfd_A	389	Human Spastin Aaa Domain Length = 389		4e-05
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		1e-04
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		2e-04
2qgz_A	308	Crystal Structure Of A Putative Primosome Component		2e-04

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 73.9 bits (180), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 85/163 (52%), Gaps = 21/163 (12%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           FL+  E Y  +G    +G LL GPPGTGK+ L  A+A       + +  S+       LG
Sbjct: 29  FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLG 88
Query: 70  NNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
            + +R +    + +  SI+ +++ID        + ++RAA    +++G ++++Q   TL+
Sbjct: 89  ASRVRDLFETAKKQAPSIIFIDEIDA-------IGKSRAAGG--VVSGNDEREQ---TLN 136
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            LL  +DG  S      I++  TN  E LDPAL+RPGR D  +
Sbjct: 137 QLLAEMDGFGSENA-PVIVLAATNRPEILDPALMRPGRFDRQV 178

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 73.2 bits (178), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 122/251 (48%), Gaps = 38/251 (15%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL----- 67
           L  +L+    ++++G    +G L+ GPPGTGK+ L  A+A   K   + +  S+      
Sbjct: 27  LVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFV 86
Query: 68  -LGNNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
            +G + +R +    +  +  I+ +++ID        + R R A    L  G+++++Q   
Sbjct: 87  GVGASRVRDMFEQAKKAAPCIIFIDEIDA-------VGRQRGAG---LGGGHDEREQ--- 133
Query: 125 TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLA 184
           TL+ +L  +DG   + G   I+I  TN  + LDPALLRPGR D  + +      G + + 
Sbjct: 134 TLNQMLVEMDGFEGNEG--IIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQIL 191
Query: 185 SNYLGIAEHPLFVEIEKLIATAKVTP----ADVAEQLMRNEAPEFALSG------LIEFL 234
             ++     PL  +I+  I  A+ TP    AD+A   + NEA  FA  G      ++EF 
Sbjct: 192 KVHM--RRVPLAPDIDAAI-IARGTPGFSGADLAN--LVNEAALFAARGNKRVVSMVEFE 246
Query: 235 ESKKRANDGSE 245
           ++K +   G E
Sbjct: 247 KAKDKIMMGLE 257

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 53/162 (32%), Positives = 77/162 (47%), Gaps = 23/162 (14%)
Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
           L + + Y ++G    RG LLYGPPGTGK+ L+ A+AN  K     +  S  +      G 
Sbjct: 192 LVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVHKYLGEGP 251
Query: 71  NDLRHIL-IATEN-KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
             +R +  +A EN  SI+ ++++D              A   F  A     ++    L  
Sbjct: 252 RMVRDVFRLARENAPSIIFIDEVDSI------------ATKRF-DAQTGSDREVQRILIE 298
Query: 129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
           LL  +DG   S   +  +I  TN  + LDPALLRPGR+D  I
Sbjct: 299 LLTQMDGFDQSTNVK--VIMATNRADTLDPALLRPGRLDRKI 338

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 81/163 (49%), Gaps = 23/163 (14%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           FL+    + R+G    +G LL GPPGTGK+ L  A+A       + +  S+       +G
Sbjct: 34  FLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVELFVGVG 93
Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +    +  +  I+ +++ID        + R R A    L  G+++++Q   TL+
Sbjct: 94  AARVRDLFAQAKAHAPCIVFIDEIDA-------VGRHRGAG---LGGGHDEREQ---TLN 140
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            LL  +DG  S  G   I++  TN  + LDPALLRPGR D  I
Sbjct: 141 QLLVEMDGFDSKEG--IIVMAATNRPDILDPALLRPGRFDKKI 181

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 67.4 bits (163), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 77/255 (30%), Positives = 123/255 (48%), Gaps = 39/255 (15%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL---- 68
           +E  L   E Y  +G    +G +LYG PGTGK+ L  A+AN        +  S L+    
Sbjct: 198 VELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELIQKYL 257
Query: 69  --GNNDLRHIL-IATEN-KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
             G    R I  +A EN  SI+ +++ID         ++   +N     +G E++ Q   
Sbjct: 258 GDGPRLCRQIFKVAGENAPSIVFIDEIDAI------GTKRYDSN-----SGGEREIQR-- 304
Query: 125 TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI---NMSHCTPSGFK 181
           T+  LLN +DG +   GD ++I+  TN  E LDPAL+RPGR+D  I   N    T     
Sbjct: 305 TMLELLNQLDG-FDDRGDVKVIM-ATNKIETLDPALIRPGRIDRKILFENPDLSTKKKIL 362
Query: 182 MLASNYLGIAEHPLFVEIEKLIATA-KVTPADVAEQLMRNEAPEFALSGLIEFLESKKRA 240
            + ++ + ++E    V +E L+ T   ++ AD+  Q M  EA      GL+   E + + 
Sbjct: 363 GIHTSKMNLSED---VNLETLVTTKDDLSGADI--QAMCTEA------GLLALRERRMQV 411
Query: 241 NDGSEAKEAEERAVQ 255
               + K+A+ER ++
Sbjct: 412 T-AEDFKQAKERVMK 425

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 51/163 (31%), Positives = 80/163 (49%), Gaps = 23/163 (14%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           FL+    + R+G    +G LL GPPGTG + L  A+A       + +  S+       +G
Sbjct: 34  FLKDPSKFNRIGARMPKGILLVGPPGTGATLLARAVAGEANVPFFHISGSDFVELFVGVG 93
Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +    +  +  I+ +++ID        + R R A    L  G+++++Q   TL+
Sbjct: 94  AARVRDLFAQAKAHAPCIVFIDEIDA-------VGRHRGAG---LGGGHDEREQ---TLN 140
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            LL  +DG  S  G   I++  TN  + LDPALLRPGR D  I
Sbjct: 141 QLLVEMDGFDSKEG--IIVMAATNRPDILDPALLRPGRFDKKI 181

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 55/171 (32%), Positives = 80/171 (46%), Gaps = 23/171 (13%)
Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
           L+  E + +VG    +G LLYGPPGTGK+ L  A+A         +  S L+      G 
Sbjct: 37  LKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGA 96
Query: 71  NDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
           + ++ I    + K  SI+ +++ID             A   D L  G    ++   TL  
Sbjct: 97  SLVKDIFKLAKEKAPSIIFIDEIDAIA----------AKRTDALTGG---DREVQRTLMQ 143
Query: 129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
           LL  +DG + + GD + II  TN  + LDPA+LRPGR D  I +      G
Sbjct: 144 LLAEMDG-FDARGDVK-IIGATNRPDILDPAILRPGRFDRIIEVPAPDEKG 192

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 64.7 bits (156), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 78/167 (46%), Gaps = 7/167 (4%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNND 72
           +E  L+  E ++RVG    +G LLYGPPGTGK+ L  A+A  +  +      S ++    
Sbjct: 197 IELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDKYI 256
Query: 73  LRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNF 132
                I  E       ++ + CI   D +    A        G    ++   TL  LL  
Sbjct: 257 GESARIIRE--MFAYAKEHEPCIIFMDEVD---AIGGRRFSEGTSADREIQRTLMELLTQ 311
Query: 133 IDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
           +DG + + G  +II+  TN  + LDPALLRPGR+D  + +     +G
Sbjct: 312 MDG-FDNLGQTKIIM-ATNRPDTLDPALLRPGRLDRKVEIPLPNEAG 356

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/166 (30%), Positives = 81/166 (48%), Gaps = 23/166 (13%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL---- 68
           +E  ++  E +  +G A  +G +LYGPPGTGK+ L  A+A++       +  + L+    
Sbjct: 164 IELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQKYI 223
Query: 69  --GNNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
             G+  +R + +       SI+ +++ID        +   R         G + + Q   
Sbjct: 224 GEGSRMVRELFVMAREHAPSIIFMDEIDS-------IGSTRVEGS----GGGDSEVQR-- 270
Query: 125 TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
           T+  LLN +DG  +S   +  II  TN  + LDPALLRPGR+D  I
Sbjct: 271 TMLELLNQLDGFETSKNIK--IIMATNRLDILDPALLRPGRIDRKI 314

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 83/163 (50%), Gaps = 22/163 (13%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL------ELSNLLG 69
           +L+  E + ++G    +G LL GPPG GK+ L  A+A   +     +      E+   LG
Sbjct: 24  YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGLG 83
Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +      ++  I+ +++ID        + + R+      ++G+   ++   TL+
Sbjct: 84  AARVRSLFKEARARAPCIVYIDEIDA-------VGKKRSTT----MSGFSNTEEEQ-TLN 131
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            LL  +DG+ ++  D  I++ +TN  + LD AL+RPGR+D H+
Sbjct: 132 QLLVEMDGMGTT--DHVIVLASTNRADILDGALMRPGRLDRHV 172

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 76/165 (46%), Gaps = 23/165 (13%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------G 69
           FL+    +  +G    +G LL GPPG GK+ L  A+A   +        S+ +      G
Sbjct: 49  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 108
Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +    +  +  I+ +++ID        + R R +    +  G ++++Q   TL+
Sbjct: 109 AARVRDLFETAKRHAPCIVFIDEIDA-------VGRKRGSG---VGGGNDEREQ---TLN 155
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINM 172
            LL  +DG         +++  TN  + LDPALLRPGR D  I +
Sbjct: 156 QLLVEMDGFEKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAI 198

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 76/165 (46%), Gaps = 23/165 (13%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------G 69
           FL+    +  +G    +G LL GPPG GK+ L  A+A   +        S+ +      G
Sbjct: 58  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 117
Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +    +  +  I+ +++ID        + R R +    +  G ++++Q   TL+
Sbjct: 118 AARVRDLFETAKRHAPCIVFIDEIDA-------VGRKRGSG---VGGGNDEREQ---TLN 164
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINM 172
            LL  +DG         +++  TN  + LDPALLRPGR D  I +
Sbjct: 165 QLLVEMDGFEKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAI 207

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 76/165 (46%), Gaps = 23/165 (13%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------G 69
           FL+    +  +G    +G LL GPPG GK+ L  A+A   +        S+ +      G
Sbjct: 34  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 93
Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +    +  +  I+ +++ID        + R R +    +  G ++++Q   TL+
Sbjct: 94  AARVRDLFETAKRHAPCIVFIDEIDA-------VGRKRGSG---VGGGNDEREQ---TLN 140
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINM 172
            LL  +DG         +++  TN  + LDPALLRPGR D  I +
Sbjct: 141 QLLVEMDGFEKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAI 183

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 76/165 (46%), Gaps = 23/165 (13%)
Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------G 69
           FL+    +  +G    +G LL GPPG GK+ L  A+A   +        S+ +      G
Sbjct: 58  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 117
Query: 70  NNDLRHILIATENKS--ILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +    +  +  I+ +++ID        + R R +    +  G ++++Q   TL+
Sbjct: 118 AARVRDLFETAKRHAPCIVFIDEIDA-------VGRKRGSG---VGGGNDEREQ---TLN 164
Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINM 172
            LL  +DG         +++  TN  + LDPALLRPGR D  I +
Sbjct: 165 QLLVEMDGFEKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAI 207

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 45/163 (27%), Positives = 76/163 (46%), Gaps = 25/163 (15%)
Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
           ++R + ++ +G    +G L+YGPPGTGK+ L  A A         L    L+      G 
Sbjct: 201 MKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQMYIGEGA 260
Query: 71  NDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
             +R      + K  +I+ ++++D       R    ++ +           ++   T+  
Sbjct: 261 KLVRDAFALAKEKAPTIIFIDELDAIG--TKRFDSEKSGD-----------REVQRTMLE 307
Query: 129 LLNFIDGLWSSCGDERI-IIFTTNHKERLDPALLRPGRMDMHI 170
           LLN +DG  S   D+R+ ++  TN  + LDPALLR GR+D  I
Sbjct: 308 LLNQLDGFSS---DDRVKVLAATNRVDVLDPALLRSGRLDRKI 347

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score = 53.9 bits (128), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 68/159 (42%), Gaps = 19/159 (11%)
Query: 21  EFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLR 74
           E +  +G    +G LLYGPPGTGK+    A+AN        +  S L+      G   +R
Sbjct: 233 ERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVR 292
Query: 75  HILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFID 134
            +      K          CI   D +     A  D    G     +   T+  L+  +D
Sbjct: 293 ELFEMARTKK--------ACIIFFDEIDAVGGARFD---DGAGGDNEVQRTMLELITQLD 341
Query: 135 GLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMS 173
           G +   G+ +++ F TN    LDPALLRPGR+D  +  S
Sbjct: 342 G-FDPRGNIKVM-FATNRPNTLDPALLRPGRIDRKVEFS 378

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 41/154 (26%), Positives = 69/154 (44%), Gaps = 19/154 (12%)
Query: 23  YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI 76
           + + G    +G L YGPPG GK+ L  A+AN  + +   ++   LL         ++R I
Sbjct: 41  FLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREI 100
Query: 77  LIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL 136
                  +  V+       +  D +++AR  N        ++       ++ +L  +DG+
Sbjct: 101 FDKARQAAPCVL-----FFDELDSIAKARGGNIGDGGGAADR------VINQILTEMDGM 149
Query: 137 WSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
             S      II  TN  + +DPA+LRPGR+D  I
Sbjct: 150 --STKKNVFIIGATNRPDIIDPAILRPGRLDQLI 181

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 77/178 (43%), Gaps = 32/178 (17%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE----LSNLL 68
           +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      + +     +S L 
Sbjct: 220 VELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLA 279
Query: 69  G--NNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
           G   ++LR      E    +I+ ++++D                    IA   ++    +
Sbjct: 280 GESESNLRKAFEEAEKNAPAIIFIDELDA-------------------IAPKREKTHGEV 320
Query: 125 ---TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
               +S LL  +DGL        I++  TN    +DPAL R GR D  +++     +G
Sbjct: 321 ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 77/178 (43%), Gaps = 32/178 (17%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE----LSNLL 68
           +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      + +     +S L 
Sbjct: 220 VELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLA 279
Query: 69  G--NNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
           G   ++LR      E    +I+ ++++D                    IA   ++    +
Sbjct: 280 GESESNLRKAFEEAEKNAPAIIFIDELDA-------------------IAPKREKTHGEV 320
Query: 125 ---TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
               +S LL  +DGL        I++  TN    +DPAL R GR D  +++     +G
Sbjct: 321 ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 78/165 (47%), Gaps = 28/165 (16%)
Query: 23  YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY--LKF-DVYDLELSNL-LGNND--LRHI 76
           ++ +G     G LL GPPG GK+ L  A+AN   L F  V   EL N+ +G ++  +R +
Sbjct: 36  FKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLNMYVGESERAVRQV 95
Query: 77  LIATENKSILVV--EDIDC-CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFI 133
               +N +  V+  +++D  C    DR + A                     ++ LL  +
Sbjct: 96  FQRAKNSAPCVIFFDEVDALCPRRSDRETGASVR-----------------VVNQLLTEM 138
Query: 134 DGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPS 178
           DGL +    +  I+  TN  + +DPA+LRPGR+D  + +    P+
Sbjct: 139 DGLEAR--QQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPA 181

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/178 (26%), Positives = 78/178 (43%), Gaps = 32/178 (17%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLE-LSNLL 68
           +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      F +   E +S L 
Sbjct: 220 VELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLA 279
Query: 69  G--NNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
           G   ++LR      E    +I+ ++++D                    IA   ++    +
Sbjct: 280 GESESNLRKAFEEAEKNAPAIIFIDELDA-------------------IAPKREKTHGEV 320
Query: 125 ---TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
               +S LL  +DGL        I++  TN    +DPAL R GR D  +++     +G
Sbjct: 321 ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 77/178 (43%), Gaps = 32/178 (17%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE----LSNLL 68
           +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      + +     +S L 
Sbjct: 220 VELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLA 279
Query: 69  G--NNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
           G   ++LR      E    +I+ ++++D                    IA   ++    +
Sbjct: 280 GESESNLRKAFEEAEKNAPAIIFIDELDA-------------------IAPKREKTHGEV 320
Query: 125 ---TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
               +S LL  +DGL        I++  TN    +DPAL R GR D  +++     +G
Sbjct: 321 ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/178 (26%), Positives = 78/178 (43%), Gaps = 32/178 (17%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLE-LSNLL 68
           +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      F +   E +S L 
Sbjct: 220 VELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLA 279
Query: 69  G--NNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
           G   ++LR      E    +I+ ++++D                    IA   ++    +
Sbjct: 280 GESESNLRKAFEEAEKNAPAIIFIDELDA-------------------IAPKREKTHGEV 320
Query: 125 ---TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
               +S LL  +DGL        I++  TN    +DPAL R GR D  +++     +G
Sbjct: 321 ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/178 (26%), Positives = 78/178 (43%), Gaps = 32/178 (17%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLE-LSNLL 68
           +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      F +   E +S L 
Sbjct: 220 VELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLA 279
Query: 69  G--NNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
           G   ++LR      E    +I+ ++++D                    IA   ++    +
Sbjct: 280 GESESNLRKAFEEAEKNAPAIIFIDELDA-------------------IAPKREKTHGEV 320
Query: 125 ---TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
               +S LL  +DGL        I++  TN    +DPAL R GR D  +++     +G
Sbjct: 321 ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 67/146 (45%), Gaps = 30/146 (20%)
Query: 28  KAWKRGYLLYGPPGTGKSSL---IAAMANYLKFDVYDLEL-SNLLGNND-LRHILIATEN 82
           +A  RG LL+GPPG GK+ L   +AA +N   F++    L S  +G  + L   L A   
Sbjct: 145 RAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVAR 204
Query: 83  K---SILVVEDIDC--CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW 137
           +   SI+ ++ +D   C   +     +R    +FLI                    DG+ 
Sbjct: 205 ELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIE------------------FDGVQ 246
Query: 138 SSCGDERIIIF-TTNHKERLDPALLR 162
            S GD+R+++   TN  + LD A+LR
Sbjct: 247 -SAGDDRVLVMGATNRPQELDEAVLR 271

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 53/93 (56%), Gaps = 11/93 (11%)
Query: 32  RGYLLYGPPGTGKSSLIAAMA----NYLKFDVYDLEL-SNLLGNND--LRHIL-IATENK 83
           RG LL+GPPGTGKS L  A+A    N   F +   +L S  LG ++  ++++  +A ENK
Sbjct: 168 RGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENK 227
Query: 84  -SILVVEDID--CCIELQDRLSRARAANPDFLI 113
            SI+ +++ID  C    ++    AR    +FL+
Sbjct: 228 PSIIFIDEIDSLCGSRSENESEAARRIKTEFLV 260

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 53/93 (56%), Gaps = 11/93 (11%)
Query: 32  RGYLLYGPPGTGKSSLIAAMA----NYLKFDVYDLEL-SNLLGNND--LRHIL-IATENK 83
           RG LL+GPPGTGKS L  A+A    N   F +   +L S  LG ++  ++++  +A ENK
Sbjct: 46  RGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENK 105
Query: 84  -SILVVEDID--CCIELQDRLSRARAANPDFLI 113
            SI+ +++ID  C    ++    AR    +FL+
Sbjct: 106 PSIIFIDEIDSLCGSRSENESEAARRIKTEFLV 138

>pdb|2QGZ|A Chain A, Crystal Structure Of A Putative Primosome Component From Streptococcus Pyogenes Serotype M3. Northeast Structural Genomics Target Dr58 Length = 308

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 11/90 (12%)
Query: 13  LERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN-----------YLKFDVYD 61
           +E F    +F  +   A ++G  LYG  G GKS L+AAMA+            L F  + 
Sbjct: 134 MEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFA 193
Query: 62  LELSNLLGNNDLRHILIATENKSILVVEDI 91
           +++ N + N  ++  + A +N  +L+++DI
Sbjct: 194 IDVKNAISNGSVKEEIDAVKNVPVLILDDI 223

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	266
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-17
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-13
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	1e-13
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	4e-12
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	4e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	8e-12
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	8e-12
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	3e-11
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	4e-11
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	5e-11
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	6e-11
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	3e-08
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	1e-07
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	1e-07
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	3e-06
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	5e-06
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	9e-06
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	5e-06
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	9e-06
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	5e-05
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	1e-05
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	2e-05
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	2e-05
2qgz_A	308	Helicase loader, putative primosome component; str	4e-05
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	8e-05
2chg_A	226	Replication factor C small subunit; DNA-binding pr	2e-04
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	2e-04
2fna_A	357	Conserved hypothetical protein; structural genomic	2e-04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	3e-04
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	4e-04
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	4e-04
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	5e-04
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	7e-04

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score = 69.1 bits (169), Expect = 1e-13
 Identities = 44/177 (24%), Positives = 76/177 (42%), Gaps = 26/177 (14%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
                I + +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      + + 
Sbjct: 211 KQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLIN 270

Query: 64  LSNLL------GNNDLRHILIATENK--SILVVEDIDCCIELQDRLSRARAANPDFLIAG 115
              ++        ++LR      E    +I+ ++++D           A A   +     
Sbjct: 271 GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELD-----------AIAPKREKTHGE 319

Query: 116 YEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINM 172
            E++      +S LL  +DGL        I++  TN    +DPAL R GR D  +++
Sbjct: 320 VERR-----IVSQLLTLMDGL--KQRAHVIVMAATNRPNSIDPALRRFGRFDREVDI 369

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Length = 262

 Score = 63.8 bits (156), Expect = 4e-12
 Identities = 59/251 (23%), Positives = 107/251 (42%), Gaps = 37/251 (14%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------G 69
           +L+  E + ++G    +G LL GPPG GK+ L  A+A   +     +  +  +      G
Sbjct: 24  YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGLG 83

Query: 70  NNDLRHILI-ATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +   A      I+ +++ID        + + R+           +++Q   TL+
Sbjct: 84  AARVRSLFKEARARAPCIVYIDEIDA-------VGKKRSTTMSG--FSNTEEEQ---TLN 131

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNY 187
            LL  +DG+ ++     I++ +TN  + LD AL+RPGR+D H+ +   T    + +   +
Sbjct: 132 QLLVEMDGMGTTDH--VIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQH 189

Query: 188 LGIAEHPLFVEIEKLIAT-AKVTP----ADVAEQLMRNEAPEFA------LSGLIEFLES 236
           L      L           A++TP    AD+A   + NEA   A          + F  +
Sbjct: 190 L--KSLKLTQSSTFYSQRLAELTPGFSGADIAN--ICNEAALHAAREGHTSVHTLNFEYA 245

Query: 237 KKRANDGSEAK 247
            +R   G+  K
Sbjct: 246 VERVLAGTAKK 256

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score = 63.8 bits (156), Expect = 4e-12
 Identities = 53/165 (32%), Positives = 74/165 (44%), Gaps = 29/165 (17%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
           L+  E + +VG    +G LLYGPPGTGK+ L  A+A         +  S L+      G 
Sbjct: 37  LKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGA 96

Query: 71  NDLRHIL-IATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
           + ++ I  +A E   SI+ +++ID             A       A     ++   TL  
Sbjct: 97  SLVKDIFKLAKEKAPSIIFIDEID-------------AIAAKRTDALTGGDREVQRTLMQ 143

Query: 129 LLNFIDGLWSSCGDER---IIIFTTNHKERLDPALLRPGRMDMHI 170
           LL  +DG      D R    II  TN  + LDPA+LRPGR D  I
Sbjct: 144 LLAEMDGF-----DARGDVKIIGATNRPDILDPAILRPGRFDRII 183

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 64.5 bits (156), Expect = 7e-12
 Identities = 46/270 (17%), Positives = 83/270 (30%), Gaps = 78/270 (28%)

Query: 15  RFLQRKEFYRRVGKAWKR-----GYLLYGPPGTGKSSLIAAMANYLK------FDVYDLE 63
             + R + Y ++ +A          L+ G  G+GK+ +   +    K      F ++ L 
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188

Query: 64  LSN-------LLGNNDLRHILIATENKSILVVEDIDCCI-----ELQDRLSRARAANPDF 111
           L N       L     L + +    + +     D    I      +Q  L R        
Sbjct: 189 LKNCNSPETVLEMLQKLLYQI----DPNWTSRSDHSSNIKLRIHSIQAELRR-------L 237

Query: 112 LIAGYEQQKQYHITLSGLLNFIDGLWSS---------CGDERIIIFTTNHKERLDPALLR 162
           L     + K Y   L  L+  +  + ++         C   +I++ TT  K+  D   L 
Sbjct: 238 L-----KSKPYENCL--LV--LLNVQNAKAWNAFNLSC---KILL-TTRFKQVTD--FLS 282

Query: 163 PGRMDMHINMSHC----TPSGFKMLASNYLGIAE----------HPLFVEIEKLIATAKV 208
                 HI++ H     TP   K L   YL              +P  +    +IA +  
Sbjct: 283 AATT-THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL---SIIAESIR 338

Query: 209 TPADVAEQLMRNEAPEF--ALSGLIEFLES 236
                 +        +    +   +  LE 
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLNVLEP 368

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 5e-04
 Identities = 24/122 (19%), Positives = 41/122 (33%), Gaps = 26/122 (21%)

Query: 2   DFDMKKMIMDDLERFLQRKEFYRRVGKAWK-RGYLLYGPPGTGKSSLIAAMANYLKF-DV 59
              + +M+  D  RFL++K   R    AW   G +L         + +  +  Y  +   
Sbjct: 489 RMTLFRMVFLDF-RFLEQK--IRHDSTAWNASGSIL---------NTLQQLKFYKPYICD 536

Query: 60  YDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQ 119
            D +   L+  N +   L   E     ++      + L+  L        D  I   E  
Sbjct: 537 NDPKYERLV--NAILDFLPKIEEN---LICSKYTDL-LRIALM-----AEDEAIF-EEAH 584

Query: 120 KQ 121
           KQ
Sbjct: 585 KQ 586

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score = 63.3 bits (154), Expect = 8e-12
 Identities = 29/180 (16%), Positives = 53/180 (29%), Gaps = 25/180 (13%)

Query: 10  MDDLERFLQR------KEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
                 F+ +      K F +           ++G  G GKS     +   +  +   + 
Sbjct: 9   FYIAPAFMDKLVVHITKNFLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMS 68

Query: 64  LSNLLGNN------------DLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDF 111
              L   N                 +I   N   L + D+D         ++    N   
Sbjct: 69  AGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYTVNNQM- 127

Query: 112 LIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERI-IIFTTNHKERLDPALLRPGRMDMHI 170
                      +I  +     + G+++   + R+ II T N    L   L+R GRM+   
Sbjct: 128 -----VNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFY 182

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A* Length = 268

 Score = 62.7 bits (153), Expect = 8e-12
 Identities = 75/269 (27%), Positives = 121/269 (44%), Gaps = 48/269 (17%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           FL+  E Y  +G    +G LL GPPGTGK+ L  A+A       + +  S+       LG
Sbjct: 29  FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLG 88

Query: 70  NNDLRHILI-ATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
            + +R +   A +   SI+ +++ID        + ++RAA    +++G ++++Q   TL+
Sbjct: 89  ASRVRDLFETAKKQAPSIIFIDEIDA-------IGKSRAAGG--VVSGNDEREQ---TLN 136

Query: 128 GLLNFIDGLWSSCGDERIIIF-TTNHKERLDPALLRPGRMDMHINMSHCTPSG----FKM 182
            LL  +DG  S   +  +I+   TN  E LDPAL+RPGR D  + +     +G     K+
Sbjct: 137 QLLAEMDGFGS--ENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKV 194

Query: 183 LASNYLGIAEHPLFVEIEKLIATAKVTP----ADVAEQLMRNEAPEFALSGLIEFLESKK 238
                       L  ++  L   AK+T     AD+A  +  NEA   A         + +
Sbjct: 195 HIKGV------KLANDVN-LQEVAKLTAGLAGADLANII--NEAALLA-------GRNNQ 238

Query: 239 RANDGSEAKEAEERAVQ-AEKKVLEISEE 266
           +       KEA ER +   EKK+      
Sbjct: 239 KEVRQQHLKEAVERGIAGLEKKLEHHHHH 267

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A* Length = 272

 Score = 61.3 bits (149), Expect = 3e-11
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 31/177 (17%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL- 62
           D    ++DD E  +Q+ +   R         LL GPP +GK++L A +A    F    + 
Sbjct: 40  DPVTRVLDDGELLVQQTKNSDRTPL---VSVLLEGPPHSGKTALAAKIAEESNFPFIKIC 96

Query: 63  ---ELSNLLGNNDLRHIL----IATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIA 114
              ++         + +      A +++ S +VV+DI       +RL       P F   
Sbjct: 97  SPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDI-------ERLLDYVPIGPRF--- 146

Query: 115 GYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHIN 171
                      L  LL  +       G + +II TT+ K+ L   +         I+
Sbjct: 147 --SNL-----VLQALLVLLKKA-PPQGRKLLIIGTTSRKDVLQ-EMEMLNAFSTTIH 194

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Length = 254

 Score = 60.4 bits (147), Expect = 4e-11
 Identities = 46/163 (28%), Positives = 75/163 (46%), Gaps = 23/163 (14%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------G 69
           FL+    +  +G    +G LL GPPG GK+ L  A+A   +        S+ +      G
Sbjct: 34  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 93

Query: 70  NNDLRHILI-ATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +   A  +   I+ +++ID        + R R +    +  G ++++Q   TL+
Sbjct: 94  AARVRDLFETAKRHAPCIVFIDEIDA-------VGRKRGSG---VGGGNDEREQ---TLN 140

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            LL  +DG         +++  TN  + LDPALLRPGR D  I
Sbjct: 141 QLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQI 181

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score = 60.4 bits (147), Expect = 5e-11
 Identities = 46/163 (28%), Positives = 75/163 (46%), Gaps = 23/163 (14%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           FL+    +  +G    +G LL GPPG GK+ L  A+A   +        S+       +G
Sbjct: 58  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 117

Query: 70  NNDLRHILI-ATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
              +R +   A  +   I+ +++ID        + R R +    +  G ++++Q   TL+
Sbjct: 118 AARVRDLFETAKRHAPCIVFIDEIDA-------VGRKRGSG---VGGGNDEREQ---TLN 164

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            LL  +DG         +++  TN  + LDPALLRPGR D  I
Sbjct: 165 QLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQI 205

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score = 60.0 bits (146), Expect = 6e-11
 Identities = 49/163 (30%), Positives = 84/163 (51%), Gaps = 23/163 (14%)

Query: 16  FLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL------LG 69
           +L+    ++++G    +G L+ GPPGTGK+ L  A+A   K   + +  S+       +G
Sbjct: 30  YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVG 89

Query: 70  NNDLRHILI-ATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLS 127
            + +R +   A +    I+ +++ID        + R R A    L  G+++++Q   TL+
Sbjct: 90  ASRVRDMFEQAKKAAPCIIFIDEIDA-------VGRQRGAG---LGGGHDEREQ---TLN 136

Query: 128 GLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            +L  +DG   + G   I+I  TN  + LDPALLRPGR D  +
Sbjct: 137 QMLVEMDGFEGNEG--IIVIAATNRPDVLDPALLRPGRFDRQV 177

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Length = 357

 Score = 52.8 bits (127), Expect = 3e-08
 Identities = 35/162 (21%), Positives = 68/162 (41%), Gaps = 27/162 (16%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
           + R + +  +    K G LL+GPPGTGK+ +   +A+      + +  S+L       G 
Sbjct: 104 MLRPDIFTGLRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEGE 162

Query: 71  NDLRHI-LIATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
             +R +  +A   + +++ +++ID        L   R           E +    I  + 
Sbjct: 163 KMVRALFAVARCQQPAVIFIDEIDS-------LLSQRGDG--------EHESSRRI-KTE 206

Query: 129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            L  +DG  +S  D  +++  TN  + +D A  R  R+   +
Sbjct: 207 FLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRL 246

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score = 51.4 bits (123), Expect = 1e-07
 Identities = 38/162 (23%), Positives = 67/162 (41%), Gaps = 27/162 (16%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
             R E +  +    + G LL+GPPG GK+ L  A+A       +++  ++L       G 
Sbjct: 135 SLRPELFTGLRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGE 193

Query: 71  NDLRHI-LIATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
             +R +  +A E + SI+ ++ +D        L   R           E      +  + 
Sbjct: 194 KLVRALFAVARELQPSIIFIDQVDS-------LLCERREG--------EHDASRRLK-TE 237

Query: 129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
            L   DG+ S+  D  +++  TN  + LD A+LR  R    +
Sbjct: 238 FLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRV 277

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score = 50.4 bits (121), Expect = 1e-07
 Identities = 39/163 (23%), Positives = 69/163 (42%), Gaps = 28/163 (17%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN 70
             R E +  +    K G LL+GPPG GK+ L  A+A        ++  ++L       G 
Sbjct: 41  SVRPELFTGLRAPAK-GLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSKYVGDGE 99

Query: 71  NDLRHI-LIATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
             +R +  +A   + SI+ ++++D        L   R+++        E +    +  + 
Sbjct: 100 KLVRALFAVARHMQPSIIFIDEVDS-------LLSERSSS--------EHEASRRL-KTE 143

Query: 129 LLNFIDGLWSSCGDERIIIF-TTNHKERLDPALLRPGRMDMHI 170
            L   DGL  +   +RI++   TN  + LD A LR  R    +
Sbjct: 144 FLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRV 184

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score = 46.8 bits (111), Expect = 3e-06
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 27  GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL 64
           G    R  +LYGPPG GK++    +A  L +D+  LE 
Sbjct: 73  GSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI--LEQ 108

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus} Length = 301

 Score = 46.1 bits (110), Expect = 5e-06
 Identities = 16/50 (32%), Positives = 30/50 (60%)

Query: 4  DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 53
          D+K+ + + ++  ++  + + + G    +G L YGPPG GK+ L  A+AN
Sbjct: 22 DVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN 71

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus} Length = 301

 Score = 44.9 bits (107), Expect = 9e-06
 Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 126 LSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI 170
           ++ +L  +DG+  S      II  TN  + +DPA+LRPGR+D  I
Sbjct: 139 INQILTEMDGM--STKKNVFIIGATNRPDIIDPAILRPGRLDQLI 181

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A Length = 377

 Score = 45.8 bits (108), Expect = 5e-06
 Identities = 29/153 (18%), Positives = 47/153 (30%), Gaps = 32/153 (20%)

Query: 20  KEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIA 79
           K     + K  KR +L  GP  +GK++L AA+            L+  L  + L   L  
Sbjct: 160 KCMVYNIPK--KRYWLFKGPIDSGKTTLAAALLELCGGKA----LNVNLPLDRLNFELGV 213

Query: 80  TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS 139
             ++ ++V ED+         L                   Q    L  L +++DG    
Sbjct: 214 AIDQFLVVFEDVKGTGGESRDL----------------PSGQGINNLDNLRDYLDGSVKV 257

Query: 140 CGDE----------RIIIFTTNHKERLDPALLR 162
             ++             I T N          R
Sbjct: 258 NLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQAR 290

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score = 44.9 bits (107), Expect = 9e-06
 Identities = 15/50 (30%), Positives = 28/50 (56%)

Query: 4  DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 53
          D+++ +   +   ++  + ++ +G     G LL GPPG GK+ L  A+AN
Sbjct: 17 DIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVAN 66

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score = 42.6 bits (101), Expect = 5e-05
 Identities = 39/144 (27%), Positives = 67/144 (46%), Gaps = 19/144 (13%)

Query: 126 LSGLLNFIDGLWSSCGDER---IIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG-FK 181
           ++ LL  +DGL     + R    I+  TN  + +DPA+LRPGR+D  + +    P+    
Sbjct: 131 VNQLLTEMDGL-----EARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLA 185

Query: 182 MLASNYLGIAEHPL-----FVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLES 236
           +L +      + PL        I   +     T AD++  L+R EA   ++  L + +  
Sbjct: 186 ILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSA-LVR-EA---SICALRQEMAR 240

Query: 237 KKRANDGSEAKEAEERAVQAEKKV 260
           +K  N+  E K + +   +A KKV
Sbjct: 241 QKSGNEKGELKVSHKHFEEAFKKV 264

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 45.1 bits (107), Expect = 1e-05
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 17 LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 53
          ++    +      W+ G LL+GPPGTGKS L  A+A 
Sbjct: 32 IKFPHLFTGKRTPWR-GILLFGPPGTGKSYLAKAVAT 67

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Length = 322

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 17 LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 53
          ++    ++   K    G LLYGPPGTGKS L  A+A 
Sbjct: 38 VKFPHLFKGNRKPTS-GILLYGPPGTGKSYLAKAVAT 73

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 15/101 (14%)

Query: 1   MDFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK---- 56
           ++ D +   +   ERF+   E  ++      +G  L+G  G GK+ L+AA+AN L     
Sbjct: 29  LNDDGRIKAIRFAERFVAEYEPGKK-----MKGLYLHGSFGVGKTYLLAAIANELAKRNV 83

Query: 57  ----FDVYDL--ELSNLLGNNDLRHILIATENKSILVVEDI 91
                 V +L  EL + L +  +   L   +   +L+++D+
Sbjct: 84  SSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDL 124

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 43.3 bits (102), Expect = 4e-05
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 11/83 (13%)

Query: 20  KEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK---------FDVYDL--ELSNLL 68
            +F  +   A ++G  LYG  G GKS L+AAMA+ L                  ++ N +
Sbjct: 141 LDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKNAI 200

Query: 69  GNNDLRHILIATENKSILVVEDI 91
            N  ++  + A +N  +L+++DI
Sbjct: 201 SNGSVKEEIDAVKNVPVLILDDI 223

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A* Length = 180

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 20/83 (24%), Positives = 30/83 (36%), Gaps = 11/83 (13%)

Query: 20  KEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK---------FDVYDL--ELSNLL 68
           + F         +G    G PG GK+ L  A    +          FD  DL   L +L+
Sbjct: 27  RVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLIFRLKHLM 86

Query: 69  GNNDLRHILIATENKSILVVEDI 91
                   L    N  +LV++D+
Sbjct: 87  DEGKDTKFLKTVLNSPVLVLDDL 109

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 3/33 (9%)

Query: 35 LLYGPPGTGKSSLIAAMANYLKFDVYD---LEL 64
          L  GPPGTGK++   A+A  L  + +    +E+
Sbjct: 42 LFSGPPGTGKTATAIALARDLFGENWRDNFIEM 74

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A* Length = 456

 Score = 41.1 bits (96), Expect = 2e-04
 Identities = 34/177 (19%), Positives = 54/177 (30%), Gaps = 29/177 (16%)

Query: 25  RVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV----------YDLELS--NLLGNND 72
           +  K   R  LL GPPGTGK++L  A+A  L   V          Y  E+    +L  N 
Sbjct: 57  KSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENF 116

Query: 73  LRHILIATENKSILVVEDIDCCIELQDRLSRARAANP---------DFLIAGYEQQKQYH 123
            R I +  +    +   ++         L+     NP           +I     +    
Sbjct: 117 RRAIGLRIKETKEVYEGEV-------TELTPCETENPMGGYGKTISHVIIGLKTAKGTKQ 169

Query: 124 ITLSG-LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG 179
           + L   +   +       GD   I   +   +R           D+        P G
Sbjct: 170 LKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKG 226

>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 Length = 357

 Score = 40.8 bits (95), Expect = 2e-04
 Identities = 23/140 (16%), Positives = 48/140 (34%), Gaps = 9/140 (6%)

Query: 11  DDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV--YDLELSNLL 68
           D+ + F  R++   ++        L+ G   TGKSS+I    N L       DL      
Sbjct: 10  DNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEER 69

Query: 69  GNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
                +  L+  + +   +V+ +     L   L   +          +   ++  ++ + 
Sbjct: 70  NYISYKDFLLELQKEINKLVKRLP---SLLKALKNIQGIVIMGNEIKFNWNRKDRLSFAN 126

Query: 129 LLNFIDGLWSSCGDERIIIF 148
           LL   +        + +II 
Sbjct: 127 LLESFEQA----SKDNVIIV 142

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 3/33 (9%)

Query: 35 LLYGPPGTGKSSLIAAMANYLKFDVYD---LEL 64
          L  GPPGTGK++   A+A  L  + +    +E+
Sbjct: 42 LFSGPPGTGKTATAIALARDLFGENWRDNFIEM 74

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score = 40.7 bits (96), Expect = 4e-04
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 145 IIIFTTNHKERLDPALLRPGRMDMHI 170
           +++  TN  + LDPALLRPGR D  I
Sbjct: 171 VVMAATNRPDILDPALLRPGRFDRQI 196

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E* Length = 476

 Score = 40.6 bits (96), Expect = 4e-04
 Identities = 15/26 (57%), Positives = 18/26 (69%)

Query: 145 IIIFTTNHKERLDPALLRPGRMDMHI 170
           I++  TN  + LDPALLRPGR D  I
Sbjct: 156 IVMAATNRPDILDPALLRPGRFDKKI 181

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score = 39.7 bits (93), Expect = 5e-04
 Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 3/33 (9%)

Query: 35 LLYGPPGTGKSSLIAAMANYLKFDVYD---LEL 64
          L  GPPG GK++   A+A  L  + +    LEL
Sbjct: 50 LFAGPPGVGKTTAALALARELFGENWRHNFLEL 82

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A Length = 444

 Score = 39.6 bits (92), Expect = 7e-04
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 17  LQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 53
           ++    +      W+ G LL+GPPGTGKS L  A+A 
Sbjct: 154 IKFPHLFTGKRTPWR-GILLFGPPGTGKSYLAKAVAT 189

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	266
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.97
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.96
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.96
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.95
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.95
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.95
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.95
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.95
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.95
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.94
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.94
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.94
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.93
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.93
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.93
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.92
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.92
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.91
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.91
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.91
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.87
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.83
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.82
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.8
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.79
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.78
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.77
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.75
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.74
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.73
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.73
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.73
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.72
3pvs_A	447	Replication-associated recombination protein A; ma	99.71
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.7
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.7
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.69
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.69
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.68
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.68
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.68
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.67
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.67
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.66
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.66
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.66
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.66
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.66
3bos_A	242	Putative DNA replication factor; P-loop containing	99.66
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.64
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.62
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.62
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.61
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.61
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.61
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.61
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.61
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.59
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.58
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.58
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.56
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.56
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.56
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.53
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.53
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.53
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.53
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.52
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.51
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.47
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.46
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.44
3co5_A	143	Putative two-component system transcriptional RES	99.42
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.4
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.26
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.2
1tue_A	212	Replication protein E1; helicase, replication, E1E	99.17
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	99.16
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.1
2fna_A	357	Conserved hypothetical protein; structural genomic	99.07
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.07
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	99.03
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	99.03
2qgz_A	308	Helicase loader, putative primosome component; str	99.01
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	99.01
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.98
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.97
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.93
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.92
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.9
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.87
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.82
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.73
3f8t_A	506	Predicted ATPase involved in replication control,	98.51
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.5
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.42
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.35
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	98.12
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	98.1
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	98.09
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.06
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	98.05
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	98.04
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	98.02
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.0
2z43_A	324	DNA repair and recombination protein RADA; archaea	98.0
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.99
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.98
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.96
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.94
1via_A	175	Shikimate kinase; structural genomics, transferase	97.93
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.92
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.91
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.9
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.88
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.87
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.84
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.84
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.84
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.83
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.83
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.82
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.82
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.82
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.81
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.81
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.79
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.78
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.77
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.76
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.76
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.75
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.75
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.75
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.75
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.75
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.75
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.75
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.74
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.73
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.73
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.73
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.72
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.72
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.72
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.72
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.72
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.7
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.7
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.68
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.68
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.67
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	97.65
3io5_A	333	Recombination and repair protein; storage dimer, i	97.64
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.64
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.64
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	97.62
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	97.62
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	97.61
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	97.57
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	97.57
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.56
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	97.56
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	97.55
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	97.55
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	97.55
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	97.54
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	97.54
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.54
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	97.53
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	97.52
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	97.5
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.49
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	97.48
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	97.48
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	97.47
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	97.47
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	97.46
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.46
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.46
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.44
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	97.42
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	97.42
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.4
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	97.4
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	97.39
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	97.39
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	97.39
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.39
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	97.38
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	97.36
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	97.36
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.35
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	97.35
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	97.34
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	97.34
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.33
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	97.33
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	97.31
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	97.31
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	97.31
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.3
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	97.29
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	97.29
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	97.29
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	97.28
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	97.27
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	97.26
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.26
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	97.24
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	97.23
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	97.22
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.22
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	97.21
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	97.21
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	97.2
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	97.2
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	97.2
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	97.2
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	97.19
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.18
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	97.18
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	97.16
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	97.14
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	97.12
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	97.11
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	97.1
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	97.1
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	97.08
3kw6_A	78	26S protease regulatory subunit 8; structural geno	97.08
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	97.07
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	97.07
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	97.06
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.05
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	97.05
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	97.05
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	97.04
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.03
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	97.03
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	97.01
2og2_A	359	Putative signal recognition particle receptor; nuc	97.0
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	96.99
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	96.99
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	96.98
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	96.98
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.97
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.97
2eyu_A	261	Twitching motility protein PILT; pilus retraction	96.97
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	96.96
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	96.96
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.96
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	96.96
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	96.95
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.94
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	96.93
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.93
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	96.93
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	96.93
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.89
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.88
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	96.87
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.86
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	96.85
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	96.84
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	96.84
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.84
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.82
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.8
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	96.77
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.77
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	96.77
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.77
3b6e_A	216	Interferon-induced helicase C domain-containing P;	96.76
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	96.76
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	96.74
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	96.74
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.74
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	96.73
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	96.73
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.72
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	96.72
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	96.71
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	96.71
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.71
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	96.7
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	96.7
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.7
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	96.69
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	96.69
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	96.69
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	96.66
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	96.62
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	96.61
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.59
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	96.58
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	96.58
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	96.58
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	96.53
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	96.51
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	96.5
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	96.5
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.49
2krk_A	86	26S protease regulatory subunit 8; structural geno	96.49
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	96.48
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.48
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.47
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	96.47
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	96.46
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.45
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	96.45
2ged_A	193	SR-beta, signal recognition particle receptor beta	96.44
3kta_A	182	Chromosome segregation protein SMC; structural mai	96.44
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.44
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	96.44
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	96.43
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	96.43
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	96.42
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	96.41
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	96.41
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	96.41
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	96.4
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	96.4
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	96.39
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	96.38
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	96.38
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	96.37
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	96.36
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	96.35
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	96.33
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.32
1b0u_A	262	Histidine permease; ABC transporter, transport pro	96.32
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	96.32
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	96.31
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	96.3
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	96.29
3ice_A	422	Transcription termination factor RHO; transcriptio	96.29
1g6h_A	257	High-affinity branched-chain amino acid transport	96.29
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	96.28
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.27
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	96.27
2ghi_A	260	Transport protein; multidrug resistance protein, M	96.26
1p9r_A	418	General secretion pathway protein E; bacterial typ	96.25
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	96.25
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.24
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	96.24
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	96.24
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	96.24
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	96.24
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	96.23
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	96.23
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	96.22
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	96.21
1ji0_A	240	ABC transporter; ATP binding protein, structural g	96.19
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	96.19
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	96.19
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	96.18
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	96.18
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	96.18
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.18
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	96.17
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	96.17
2xxa_A	433	Signal recognition particle protein; protein trans	96.17
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	96.16
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	96.16
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	96.16
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	96.15
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	96.15
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	96.14
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	96.14
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	96.14
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	96.14
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	96.13
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	96.13
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	96.13
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	96.1
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	96.09
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	96.09
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	96.08
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	96.08
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	96.08
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	96.07
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.07
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	96.07
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	96.06
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	96.06
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.06
1nrj_B	218	SR-beta, signal recognition particle receptor beta	96.05
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.04
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	96.03
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	96.03
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	96.02
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	96.01
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.01
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	96.0
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	96.0
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.98
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	95.97
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	95.97
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	95.96
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	95.96
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	95.95
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.94
2wji_A	165	Ferrous iron transport protein B homolog; membrane	95.93
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	95.92
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	95.92
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	95.92
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	95.9
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.9
3bor_A	237	Human initiation factor 4A-II; translation initiat	95.9
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	95.89
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	95.89
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	95.89
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.88
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	95.88
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	95.84
3llu_A	196	RAS-related GTP-binding protein C; structural geno	95.83
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	95.81
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	95.8
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	95.79
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	95.77
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	95.77
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	95.77
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.77
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	95.76
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	95.76
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	95.76
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	95.76
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.75
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	95.75
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	95.74
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	95.72
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	95.72
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	95.72
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	95.7
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	95.67
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.67
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	95.62
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	95.62
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	95.62
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	95.61
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	95.6
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	95.6
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.59
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	95.58
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	95.58
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	95.57
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	95.56
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	95.54
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	95.51
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	95.49
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.49
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	95.48
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	95.48
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	95.47
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	95.43
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	95.41
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	95.39
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	95.38
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	95.37
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	95.36
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	95.34
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	95.33
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.33
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	95.32
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	95.32
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	95.32
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	95.31
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	95.29
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	95.28
1dek_A	241	Deoxynucleoside monophosphate kinase; transferase,	95.27
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	95.27
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	95.27
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	95.27
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	95.25
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	95.25
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	95.23
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	95.23
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	95.22
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	95.21
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	95.2
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	95.19
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	95.19
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	95.16
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	95.15
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	95.14
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	95.12
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	95.08
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	95.06
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	95.01
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	95.0
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	94.98
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	94.98

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.7e-41  Score=300.75  Aligned_cols=200  Identities=27%  Similarity=0.353  Sum_probs=171.6

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+.+..++.+++.|..+|+++|+|+|||||||||||++|+++|++++.+|+.++++.+.+      ...++.+
T Consensus       154 ~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l~sk~vGese~~vr~l  233 (405)
T 4b4t_J          154 TKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVREL  233 (405)
T ss_dssp             HHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGGSCSSTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHhhccccchHHHHHHHH
Confidence            4689999999999999999999999999999999999999999999999999999999999998763      4568888


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||+|.+++.+......             .+.....+++.+|+.|+++...  .+++||+|||+|+
T Consensus       234 F~~Ar~~aP~IIFiDEiDai~~~R~~~~~~-------------~~~~~~~~l~~lL~~lDg~~~~--~~V~vIaATNrpd  298 (405)
T 4b4t_J          234 FVMAREHAPSIIFMDEIDSIGSTRVEGSGG-------------GDSEVQRTMLELLNQLDGFETS--KNIKIIMATNRLD  298 (405)
T ss_dssp             HHHHHHTCSEEEEEESSSCCTTSCSCSSSG-------------GGGHHHHHHHHHHHHHHTTTCC--CCEEEEEEESCSS
T ss_pred             HHHHHHhCCceEeeecchhhccCCCCCCCC-------------CcHHHHHHHHHHHHhhhccCCC--CCeEEEeccCChh
Confidence            87764  69999999999998744332211             1234467889999999998654  6799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||+||+|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+||++||.+++
T Consensus       299 ~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~  362 (405)
T 4b4t_J          299 ILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVC  362 (405)
T ss_dssp             SSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHH
T ss_pred             hCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999987654444556677765 469999999987

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1e-39  Score=291.52  Aligned_cols=200  Identities=28%  Similarity=0.357  Sum_probs=170.3

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+.+..++.++++|..+|+++++|+|||||||||||++|+++|++++.+|+.++++.+.+      ...++.+
T Consensus       188 d~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s~l~sk~vGesek~ir~l  267 (437)
T 4b4t_I          188 ESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELIQKYLGDGPRLCRQI  267 (437)
T ss_dssp             HHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESGGGCCSSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHHHhhhccCchHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999999988863      3567788


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||+|.++..+.....             ..+.....+++.+|+.+++....  .+++||+|||+|+
T Consensus       268 F~~Ar~~aP~IIfiDEiDai~~~R~~~~~-------------~~~~~~~~~l~~LL~~lDg~~~~--~~ViVIaATNrpd  332 (437)
T 4b4t_I          268 FKVAGENAPSIVFIDEIDAIGTKRYDSNS-------------GGEREIQRTMLELLNQLDGFDDR--GDVKVIMATNKIE  332 (437)
T ss_dssp             HHHHHHTCSEEEEEEEESSSSCCCSCSSC-------------SSCCHHHHHHHHHHHHHHHCCCS--SSEEEEEEESCST
T ss_pred             HHHHHhcCCcEEEEehhhhhcccCCCCCC-------------CccHHHHHHHHHHHHHhhCcCCC--CCEEEEEeCCChh
Confidence            87664  6999999999999864432211             11234567888999999987554  5799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||+||+|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+||++||.+++
T Consensus       333 ~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~  396 (437)
T 4b4t_I          333 TLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMC  396 (437)
T ss_dssp             TCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHH
T ss_pred             hcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999987654444456666665 569999999987

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.3e-40  Score=297.62  Aligned_cols=200  Identities=22%  Similarity=0.308  Sum_probs=170.0

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+.+..|+.++++|..+|+++|+|+|||||||||||++|+++|++++.+|+.++++.+.+      ...++.+
T Consensus       187 ~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s~l~~~~vGese~~ir~l  266 (434)
T 4b4t_M          187 DKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQMYIGEGAKLVRDA  266 (434)
T ss_dssp             HHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGGCSSCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehhhhhhcccchHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999999998863      3567788


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||+|.++..+.......             ......+++.+|+.|+++...  .+++||+|||+|+
T Consensus       267 F~~A~~~aP~IifiDEiDal~~~R~~~~~~~-------------~~~~~~~~~~lL~~ldg~~~~--~~ViVIaaTNrp~  331 (434)
T 4b4t_M          267 FALAKEKAPTIIFIDELDAIGTKRFDSEKSG-------------DREVQRTMLELLNQLDGFSSD--DRVKVLAATNRVD  331 (434)
T ss_dssp             HHHHHHHCSEEEEEECTHHHHCCCSSGGGGT-------------THHHHHHHHHHHHHHTTSCSS--CSSEEEEECSSCC
T ss_pred             HHHHHhcCCeEEeecchhhhhhccCCCCCCC-------------chHHHHHHHHHHHHhhccCCC--CCEEEEEeCCCch
Confidence            87654  699999999999987553322211             134456788999999998654  5799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||+||+|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+||++||.+++
T Consensus       332 ~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~  395 (434)
T 4b4t_M          332 VLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVT  395 (434)
T ss_dssp             CCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHH
T ss_pred             hcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999876644433456666665 469999999987

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=5.9e-40  Score=296.18  Aligned_cols=200  Identities=25%  Similarity=0.347  Sum_probs=169.9

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+.+..++.+++.|..+|+++|+|+|||||||||||++|+++|++++.+|+.++++.+.+      ...++.+
T Consensus       187 ~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s~l~sk~~Gese~~ir~~  266 (437)
T 4b4t_L          187 TEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREM  266 (437)
T ss_dssp             HHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGTCCSSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehhhhccccchHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999999998864      3557778


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..||||||||+|.++..+.....             ..+.....+++.||+.|+++...  .+++||+|||+|+
T Consensus       267 F~~A~~~~P~IifiDEiDai~~~R~~~~~-------------~~~~~~~~~l~~lL~~lDg~~~~--~~vivI~ATNrp~  331 (437)
T 4b4t_L          267 FAYAKEHEPCIIFMDEVDAIGGRRFSEGT-------------SADREIQRTLMELLTQMDGFDNL--GQTKIIMATNRPD  331 (437)
T ss_dssp             HHHHHHSCSEEEEEECCCSSSCCCSSSCC-------------SSTTHHHHHHHHHHHHHHSSSCT--TSSEEEEEESSTT
T ss_pred             HHHHHhcCCceeeeecccccccccccCCC-------------CcchHHHHHHHHHHHHhhcccCC--CCeEEEEecCCch
Confidence            8766  46999999999999864422111             11234466889999999998654  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||+||+|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+||++||.+++
T Consensus       332 ~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~  395 (437)
T 4b4t_L          332 TLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCA  395 (437)
T ss_dssp             SSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHH
T ss_pred             hhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999977654444456667665 469999999987

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=8.1e-39  Score=288.17  Aligned_cols=200  Identities=24%  Similarity=0.283  Sum_probs=169.6

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+.+..++.++++|..+|+++|+|+|||||||||||++|+++|++++.+|+.++++.+.+      ...++.+
T Consensus       215 ~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s~L~sk~vGesek~ir~l  294 (467)
T 4b4t_H          215 KDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVREL  294 (467)
T ss_dssp             HHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGGGGCCCSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhHHhhcccCCHHHHHHHHH
Confidence            4689999999999999999999999999999999999999999999999999999999999998864      4567888


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..||||||||+|.++..+......             .......+++.+|+.|++....  .+++||+|||+|+
T Consensus       295 F~~Ar~~aP~IIfiDEiDai~~~R~~~~~~-------------~~~~~~~~l~~lL~~lDg~~~~--~~ViVIaATNrpd  359 (467)
T 4b4t_H          295 FEMARTKKACIIFFDEIDAVGGARFDDGAG-------------GDNEVQRTMLELITQLDGFDPR--GNIKVMFATNRPN  359 (467)
T ss_dssp             HHHHHHTCSEEEEEECCTTTSBCCSSSSCG-------------GGGHHHHHHHHHHHHHHSSCCT--TTEEEEEECSCTT
T ss_pred             HHHHHhcCCceEeecccccccccccCcCCC-------------ccHHHHHHHHHHHHHhhccCCC--CcEEEEeCCCCcc
Confidence            8766  469999999999998644322111             1234456788899999987554  6799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||+||+|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+||++||.+++
T Consensus       360 ~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~  423 (467)
T 4b4t_H          360 TLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVC  423 (467)
T ss_dssp             SBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHH
T ss_pred             cCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999987654444456666664 469999999987

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.5e-39  Score=288.55  Aligned_cols=200  Identities=27%  Similarity=0.390  Sum_probs=170.3

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+.+..|+.++++|..+|+++|+|+|||||||||||++|+++|++++.+|+.++++.+.+      ...++.+
T Consensus       178 ~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l~~~~~Ge~e~~ir~l  257 (428)
T 4b4t_K          178 DMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDV  257 (428)
T ss_dssp             HHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGTCCSSCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchhhccccchhHHHHHHH
Confidence            4689999999999999999999999999999999999999999999999999999999999998763      3567888


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|||+||||+|.++..+.....             ..+.....+++.||+.|+++...  .+++||+|||+|+
T Consensus       258 F~~A~~~aP~IifiDEiD~i~~~R~~~~~-------------~~~~~~~r~l~~lL~~ldg~~~~--~~v~vI~aTN~~~  322 (428)
T 4b4t_K          258 FRLARENAPSIIFIDEVDSIATKRFDAQT-------------GSDREVQRILIELLTQMDGFDQS--TNVKVIMATNRAD  322 (428)
T ss_dssp             HHHHHHTCSEEEEEECTHHHHCSCSSSCS-------------CCCCHHHHHHHHHHHHHHHSCSS--CSEEEEEEESCSS
T ss_pred             HHHHHHcCCCeeechhhhhhhccccCCCC-------------CCChHHHHHHHHHHHHhhCCCCC--CCEEEEEecCChh
Confidence            87764  6999999999999864422111             11234567899999999998665  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcC-CCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMS-HCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~-~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||+||+|||||+..|+|| .|+.++|..||+.++.........++..++.. .+||++||.+++
T Consensus       323 ~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~  387 (428)
T 4b4t_K          323 TLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIM  387 (428)
T ss_dssp             SCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHH
T ss_pred             hcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHH
Confidence            9999999999999999997 89999999999999977654444456666665 569999999987

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=2.4e-35  Score=282.94  Aligned_cols=200  Identities=23%  Similarity=0.339  Sum_probs=148.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++|+++.+.+..++.++..|..+|+.+++|+|||||||||||++|+++|.+++.+|+.++.+++.      ++..++.+
T Consensus       483 ~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~l~s~~vGese~~vr~l  562 (806)
T 3cf2_A          483 EDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREI  562 (806)
T ss_dssp             HHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHHHHTTTCSSCHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccchhhccccchHHHHHHHH
Confidence            578899999999999999999999999999999999999999999999999999999999987765      45678999


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||||.+++.+......             .......++++||..|+++...  .+++||+|||+|+
T Consensus       563 F~~Ar~~~P~IifiDEiDsl~~~R~~~~~~-------------~~~~~~rv~~~lL~~mdg~~~~--~~V~vi~aTN~p~  627 (806)
T 3cf2_A          563 FDKARQAAPCVLFFDELDSIAKARGGNIGD-------------GGGAADRVINQILTEMDGMSTK--KNVFIIGATNRPD  627 (806)
T ss_dssp             HHHHHTTCSEEEECSCGGGCC---------------------------CHHHHHHHHHHHSSCSS--SSEEEECC-CCSS
T ss_pred             HHHHHHcCCceeechhhhHHhhccCCCCCC-------------CchHHHHHHHHHHHHHhCCCCC--CCEEEEEeCCCch
Confidence            98875  59999999999998765432211             1234567899999999998654  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||+|++|||||+..|+|+.|+.++|.+||+.++.+.......++..++.. .+||++||.+++
T Consensus       628 ~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~  691 (806)
T 3cf2_A          628 IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEIC  691 (806)
T ss_dssp             SSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHH
T ss_pred             hCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999987655555567777765 459999999998

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=1.6e-33  Score=270.26  Aligned_cols=197  Identities=24%  Similarity=0.340  Sum_probs=168.8

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++++.+.+..++.+++.|..+|+.+|+|+|||||||||||++|+++|++++.+++.+++.++.+      ...++.+
T Consensus       210 ~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l~sk~~gese~~lr~l  289 (806)
T 3cf2_A          210 RKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKA  289 (806)
T ss_dssp             CTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHHHSSCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHhhcccchHHHHHHHHH
Confidence            3578899999999999999999999999999999999999999999999999999999999887653      4568888


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||+|.+++.++...                ......++++|+..|+++...  .+++||+|||+++
T Consensus       290 F~~A~~~~PsIIfIDEiDal~~~r~~~~----------------~~~~~riv~~LL~~mdg~~~~--~~V~VIaaTN~~d  351 (806)
T 3cf2_A          290 FEEAEKNAPAIIFIDELDAIAPKREKTH----------------GEVERRIVSQLLTLMDGLKQR--AHVIVMAATNRPN  351 (806)
T ss_dssp             HHHHTTSCSEEEEEESGGGTCCTTTTCC----------------CTTHHHHHHHHHTHHHHCCGG--GCEEEEEECSSTT
T ss_pred             HHHHHHcCCeEEEEehhcccccccCCCC----------------ChHHHHHHHHHHHHHhccccc--CCEEEEEecCChh
Confidence            88775  599999999999987443211                233456888999999998665  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||++|+|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+|+++||..++
T Consensus       352 ~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv  415 (806)
T 3cf2_A          352 SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALC  415 (806)
T ss_dssp             TSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHH
T ss_pred             hcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHH
Confidence            999999999999999999999999999999999987654444556667665 569999999987

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=99.97  E-value=3.5e-29  Score=217.57  Aligned_cols=200  Identities=24%  Similarity=0.349  Sum_probs=160.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------ChhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GNNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~~~l~~~   76 (266)
                      +++++.+.+.+..++..++.|..+|+.+++++|||||||||||++|+++|..++.+++.+++..+.      ....+..+
T Consensus        21 ~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~~~~~g~~~~~~~~~  100 (301)
T 3cf0_A           21 EDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREI  100 (301)
T ss_dssp             HHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHHHHHHTTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHHhhhcCchHHHHHHH
Confidence            467889999999999999999999999999999999999999999999999999999999987653      23456677


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .++||||||+|.+...+.....             .........++.++..+++....  .+++||+|||.++
T Consensus       101 f~~a~~~~p~il~iDEid~l~~~~~~~~~-------------~~~~~~~~~~~~lL~~l~~~~~~--~~v~vi~atn~~~  165 (301)
T 3cf0_A          101 FDKARQAAPCVLFFDELDSIAKARGGNIG-------------DGGGAADRVINQILTEMDGMSTK--KNVFIIGATNRPD  165 (301)
T ss_dssp             HHHHHHTCSEEEEECSTTHHHHHHTTTTC-------------CSSCSCCHHHHHHHHHHHSSCTT--SSEEEEEEESCGG
T ss_pred             HHHHHhcCCeEEEEEChHHHhhccCCCcC-------------CcchHHHHHHHHHHHHhhcccCC--CCEEEEEecCCcc
Confidence            76653  5899999999999764322110             00123345678888988876433  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhh-cCCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~-~~~~s~~~i~~~l  217 (266)
                      .+|++++|+|||+..|+++.|+.++|.+|++.++.........++..++. ..+|+++||.+++
T Consensus       166 ~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~  229 (301)
T 3cf0_A          166 IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEIC  229 (301)
T ss_dssp             GSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHH
T ss_pred             ccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHH
Confidence            99999999999999999999999999999999997764332333444444 3569999999987

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.96  E-value=7e-29  Score=212.83  Aligned_cols=197  Identities=22%  Similarity=0.342  Sum_probs=156.8

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+.+.+.+..++..+..|..+++.+++|++|+||||||||++++++|..++.+++.++...+..      ...+..+
T Consensus        16 ~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~~~~~~~~~~~i~~v   95 (274)
T 2x8a_A           16 EDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLNMYVGESERAVRQV   95 (274)
T ss_dssp             HHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTCSSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHHhhhhhHHHHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999999999999887753      2345666


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..++++|+||+|.++..+....                ........+.++..|++....  ..++++++||+|+
T Consensus        96 f~~a~~~~p~i~~~Deid~~~~~r~~~~----------------~~~~~~~~~~~l~~Lsgg~~~--~~~i~ia~tn~p~  157 (274)
T 2x8a_A           96 FQRAKNSAPCVIFFDEVDALCPRRSDRE----------------TGASVRVVNQLLTEMDGLEAR--QQVFIMAATNRPD  157 (274)
T ss_dssp             HHHHHHTCSEEEEEETCTTTCC-------------------------CTTHHHHHHHHHHTCCST--TCEEEEEEESCGG
T ss_pred             HHHHHhcCCCeEeeehhhhhhcccCCCc----------------chHHHHHHHHHHHhhhccccc--CCEEEEeecCChh
Confidence            7664  3589999999998865322110                012245677888889877443  5688999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCC-CC--cHHHHHHHhhc---CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAE-HP--LFVEIEKLIAT---AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~-~~--~~~~~~~l~~~---~~~s~~~i~~~l  217 (266)
                      .||++++|||||+..|+++.|+.++|.+||+.++.... ..  ...++..++..   .+||++||..++
T Consensus       158 ~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~  226 (274)
T 2x8a_A          158 IIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALV  226 (274)
T ss_dssp             GSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHH
T ss_pred             hCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHH
Confidence            99999999999999999999999999999999885421 11  22345556654   489999999987

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.96  E-value=6.3e-28  Score=207.47  Aligned_cols=201  Identities=26%  Similarity=0.321  Sum_probs=158.0

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+.+..++..+..+..+|..+++++|||||||||||++++++|+.++.+++.+++..+..      ...+..+
T Consensus        23 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~  102 (285)
T 3h4m_A           23 EKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDI  102 (285)
T ss_dssp             HHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGGCCCSTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHHHHhccchHHHHHHHH
Confidence            4678889999999999999999999999999999999999999999999999999999999887753      2334555


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..++||||||+|.+...+.....             .........+..+++.+++....  .+++||+|||.++
T Consensus       103 ~~~~~~~~~~vl~iDEid~l~~~~~~~~~-------------~~~~~~~~~l~~ll~~~~~~~~~--~~~~vI~ttn~~~  167 (285)
T 3h4m_A          103 FKLAKEKAPSIIFIDEIDAIAAKRTDALT-------------GGDREVQRTLMQLLAEMDGFDAR--GDVKIIGATNRPD  167 (285)
T ss_dssp             HHHHHHTCSEEEEEETTHHHHBCCSSSCC-------------GGGGHHHHHHHHHHHHHHTTCSS--SSEEEEEECSCGG
T ss_pred             HHHHHHcCCeEEEEECHHHhcccCccccC-------------CccHHHHHHHHHHHHHhhCCCCC--CCEEEEEeCCCch
Confidence            5544  35789999999998752211100             01123345666777777765333  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .+++++++++||+..+.++.|+.++|.+|++.++.........++..++.. .++++++|..++.
T Consensus       168 ~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~  232 (285)
T 3h4m_A          168 ILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICT  232 (285)
T ss_dssp             GBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             hcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999877654444445555554 4589999998763

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.95  E-value=1.6e-27  Score=209.02  Aligned_cols=195  Identities=21%  Similarity=0.287  Sum_probs=156.9

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHc-CCcEEEEeCCcccC------hhhHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-KFDVYDLELSNLLG------NNDLRH   75 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~-~~~~~~i~~~~~~~------~~~l~~   75 (266)
                      +++|+.+.+.+..++..+..|.. +..+++++|||||||||||++|+++|+++ +.+++.+++..+..      ...+..
T Consensus        18 ~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~~~~~g~~~~~~~~   96 (322)
T 1xwi_A           18 EGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKN   96 (322)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGSCT-TCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSCCSSCCSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHhC-CCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHHhhhhhHHHHHHHH
Confidence            46788999999999998888763 35677899999999999999999999999 89999999987753      345667


Q ss_pred             HHHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC
Q 024550           76 ILIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK  153 (266)
Q Consensus        76 ~~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~  153 (266)
                      +|..+  ..++||||||+|.++..+...                .......+++.++..+++.... ..+++||+|||.+
T Consensus        97 lf~~a~~~~~~vl~iDEid~l~~~~~~~----------------~~~~~~~~~~~ll~~ld~~~~~-~~~v~vI~atn~~  159 (322)
T 1xwi_A           97 LFQLARENKPSIIFIDEIDSLCGSRSEN----------------ESEAARRIKTEFLVQMQGVGVD-NDGILVLGATNIP  159 (322)
T ss_dssp             HHHHHHHTSSEEEEEETTTGGGCCSSSC----------------CTTHHHHHHHHHHHHHHCSSSC-CTTEEEEEEESCT
T ss_pred             HHHHHHhcCCcEEEeecHHHhccccccc----------------cchHHHHHHHHHHHHHhccccc-CCCEEEEEecCCc
Confidence            77655  468999999999997532211                0123346778889998876432 3579999999999


Q ss_pred             CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhhc-CCCCHHHHHHHH
Q 024550          154 ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       154 ~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      +.+|++++|  ||+..++++.|+.++|..|++.++......+ ..++..++.. .+|+++||..++
T Consensus       160 ~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~  223 (322)
T 1xwi_A          160 WVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIV  223 (322)
T ss_dssp             TTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             ccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            999999999  9999999999999999999999998765443 4566777765 469999999987

>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=99.95  E-value=8e-28  Score=219.91  Aligned_cols=200  Identities=25%  Similarity=0.347  Sum_probs=155.2

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      ++.++++.+ +..++..+..|..+|...++++||+||||||||++++++|.+++.+|+.++++++..      ...++.+
T Consensus        22 ~~~~~~l~e-~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~~~~g~~~~~~r~l  100 (476)
T 2ce7_A           22 EEAIEELKE-VVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVELFVGVGAARVRDL  100 (476)
T ss_dssp             HHHHHHHHH-HHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTTCCTTHHHHHHHHH
T ss_pred             HHHHHHHHH-HHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHHHHhcccHHHHHHH
Confidence            355666665 456788889999999999999999999999999999999999999999999987753      2446677


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .|+||||||+|.+...+.....             ..+.....+++.++..|+++...  .+++||+|||.++
T Consensus       101 f~~A~~~~p~ILfIDEid~l~~~r~~~~~-------------g~~~~~~~~l~~LL~~ld~~~~~--~~viVIaaTn~~~  165 (476)
T 2ce7_A          101 FAQAKAHAPCIVFIDEIDAVGRHRGAGLG-------------GGHDEREQTLNQLLVEMDGFDSK--EGIIVMAATNRPD  165 (476)
T ss_dssp             HHHHHHTCSEEEEEETGGGTCCC----------------------CHHHHHHHHHHHHHHHSCGG--GTEEEEEEESCGG
T ss_pred             HHHHHhcCCCEEEEechhhhhhhcccccC-------------cCcHHHHHHHHHHHHHHhccCCC--CCEEEEEecCChh
Confidence            76654  6899999999999753321100             01233356788999999876443  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .+|++++|||||+..|.++.|+.++|.+|++.++.........++..++.. .++++++|.+++.
T Consensus       166 ~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~  230 (476)
T 2ce7_A          166 ILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVN  230 (476)
T ss_dssp             GSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             hhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHH
Confidence            999999999999999999999999999999999876543322234445544 5699999998873

>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=99.95  E-value=3.1e-27  Score=207.12  Aligned_cols=195  Identities=19%  Similarity=0.264  Sum_probs=154.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+.+..++..+.++.. +..+++++|||||||||||++|+++|++++.+++.+++..+.+      ...+..+
T Consensus        24 ~~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~  102 (322)
T 3eie_A           24 EGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQL  102 (322)
T ss_dssp             HHHHHHHHHHTHHHHHCGGGCCT-TCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHHHTTTGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHhc-CCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHHhhcccchHHHHHHHH
Confidence            46788888888888888877765 4556789999999999999999999999999999999877643      2345666


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..++||||||+|.+...+....                ......+.+.++..+++.... ..+++||+|||.++
T Consensus       103 f~~a~~~~~~vl~iDEid~l~~~~~~~~----------------~~~~~~~~~~ll~~l~~~~~~-~~~v~vi~atn~~~  165 (322)
T 3eie_A          103 FAMARENKPSIIFIDQVDALTGTRGEGE----------------SEASRRIKTELLVQMNGVGND-SQGVLVLGATNIPW  165 (322)
T ss_dssp             HHHHHHTSSEEEEEECGGGGSCC----------------------CCTHHHHHHHHHHHGGGGTS-CCCEEEEEEESCGG
T ss_pred             HHHHHhcCCeEEEechhhhhhccCCCCc----------------chHHHHHHHHHHHHhcccccc-CCceEEEEecCChh
Confidence            6554  3579999999999975332211                133456778888888876432 35799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhhcC-CCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIATA-KVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~~~-~~s~~~i~~~l  217 (266)
                      .+|++++|  ||+..|+++.|+.++|.+|++.++......+ ...+..++... +|++++|..++
T Consensus       166 ~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          166 QLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             GSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHH
T ss_pred             hCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            99999999  9999999999999999999999998776543 45667776654 59999999887

>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=99.95  E-value=7e-27  Score=198.23  Aligned_cols=201  Identities=23%  Similarity=0.323  Sum_probs=141.7

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+. ..++..+..|..+|...++++|||||||||||++|+++|+.++.+++.+++..+..      ...+..+
T Consensus        12 ~~~~~~l~~~-~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (262)
T 2qz4_A           12 HEAKLEVREF-VDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGLGAARVRSL   90 (262)
T ss_dssp             HHHHHHHHHH-HHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSSTTHHHHHHHHH
T ss_pred             HHHHHHHHHH-HHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhccChhHHHHHHH
Confidence            3466666554 55688888899999999999999999999999999999999999999999987753      2345566


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .++||||||+|.+...+.......            ........++.+++.+++...  ..++++|+|||.++
T Consensus        91 ~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~------------~~~~~~~~l~~ll~~~~~~~~--~~~~~vi~~tn~~~  156 (262)
T 2qz4_A           91 FKEARARAPCIVYIDEIDAVGKKRSTTMSGF------------SNTEEEQTLNQLLVEMDGMGT--TDHVIVLASTNRAD  156 (262)
T ss_dssp             HHHHHHTCSEEEEEECC-------------------------------CHHHHHHHHHHHTCCT--TCCEEEEEEESCGG
T ss_pred             HHHHHhcCCeEEEEeCcchhhccccccccCc------------cchhHHHHHHHHHHHhhCcCC--CCCEEEEecCCChh
Confidence            65543  489999999999976332211000            012334567778888876533  35789999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH--HHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEI--EKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~--~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .+|++++|+|||+..++|+.|+.++|.+|++.++...+.....+.  ..++.. .++++++|.+++.
T Consensus       157 ~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~  223 (262)
T 2qz4_A          157 ILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICN  223 (262)
T ss_dssp             GGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             hcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999977655544332  445544 4699999988873

>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=99.95  E-value=5.5e-27  Score=215.74  Aligned_cols=197  Identities=24%  Similarity=0.342  Sum_probs=160.1

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      ...++.+.+.+..++..+.+|..+|.+++.++|||||||||||++|+++|+.++.+|+.++|..+.+      ...+..+
T Consensus       210 ~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~~~~~g~~~~~~~~~  289 (489)
T 3hu3_A          210 RKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKA  289 (489)
T ss_dssp             HHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHHTSCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhhhhhcchhHHHHHHH
Confidence            3567888888888899999999999999999999999999999999999999999999999877653      2345667


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .+++|||||||.+...++..                .......+++.|+..|++....  ..++||+|||+++
T Consensus       290 f~~A~~~~p~iLfLDEId~l~~~~~~~----------------~~~~~~~~~~~LL~~ld~~~~~--~~v~vIaaTn~~~  351 (489)
T 3hu3_A          290 FEEAEKNAPAIIFIDELDAIAPKREKT----------------HGEVERRIVSQLLTLMDGLKQR--AHVIVMAATNRPN  351 (489)
T ss_dssp             HHHHHHTCSEEEEEESHHHHCBCTTSC----------------CCHHHHHHHHHHHHHHHHSCTT--SCEEEEEEESCGG
T ss_pred             HHHHHhcCCcEEEecchhhhccccccc----------------cchHHHHHHHHHHHHhhccccC--CceEEEEecCCcc
Confidence            76654  47899999999997532111                0122345778888888876443  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+++++.++|||+..|+|+.|+.++|.+|++.++.........++..++.. .++++++|..++
T Consensus       352 ~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~  415 (489)
T 3hu3_A          352 SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALC  415 (489)
T ss_dssp             GBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             ccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHH
Confidence            999999999999999999999999999999999877654444445555554 569999999887

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.95  E-value=8.3e-27  Score=197.82  Aligned_cols=199  Identities=23%  Similarity=0.360  Sum_probs=147.2

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+ +..++..+..|..+|...+++++||||||||||++++++|+.++.+++.+++..+..      ...+..+
T Consensus        18 ~~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   96 (257)
T 1lv7_A           18 DEAKEEVAE-LVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDM   96 (257)
T ss_dssp             HHHHHHTHH-HHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTSCCCCCHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHHHHHhhhhhHHHHHHH
Confidence            345666655 456688888888889888999999999999999999999999999999999887652      3456677


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .++++||||+|.+...+....             ..........++.++..+++...  ..++++|+|||.++
T Consensus        97 ~~~a~~~~~~il~iDeid~l~~~~~~~~-------------~~~~~~~~~~~~~ll~~l~~~~~--~~~~~vI~~tn~~~  161 (257)
T 1lv7_A           97 FEQAKKAAPCIIFIDEIDAVGRQRGAGL-------------GGGHDEREQTLNQMLVEMDGFEG--NEGIIVIAATNRPD  161 (257)
T ss_dssp             HHHHHTTCSEEEEETTHHHHTCCCSTTS-------------CCTTCHHHHHHHHHHHHHHTCCS--SSCEEEEEEESCTT
T ss_pred             HHHHHHcCCeeehhhhhhhhccCCCCCc-------------CCCchHHHHHHHHHHHHhhCccc--CCCEEEEEeeCCch
Confidence            76654  478999999999865221100             00112223567788888887643  35699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .++++++|++||+..++++.|+.++|.+|++.++..........+..++.. .+|++++|.+++
T Consensus       162 ~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~  225 (257)
T 1lv7_A          162 VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLV  225 (257)
T ss_dssp             TSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             hCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999999999999999999999876543222233444444 457999999887

>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=99.94  E-value=1e-26  Score=206.39  Aligned_cols=195  Identities=19%  Similarity=0.265  Sum_probs=152.4

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+.+..++..+..|.. +..+++++|||||||||||++|+++|++++.+++.+++..+..      ...+..+
T Consensus        57 ~~~~~~l~~~v~~~~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~  135 (355)
T 2qp9_X           57 EGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQL  135 (355)
T ss_dssp             GGHHHHHHHHTHHHHHCGGGGCS-SCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEHHHHHSCC---CHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHhc-CCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeHHHHhhhhcchHHHHHHHH
Confidence            35778888888888888887765 5667789999999999999999999999999999999876542      3445666


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .++||||||+|.+...+....                ......+.+.++..|++.... ..+++||+|||.++
T Consensus       136 f~~a~~~~~~vl~iDEid~l~~~r~~~~----------------~~~~~~~~~~ll~~l~~~~~~-~~~v~vI~atn~~~  198 (355)
T 2qp9_X          136 FAMARENKPSIIFIDQVDALTGTRGEGE----------------SEASRRIKTELLVQMNGVGND-SQGVLVLGATNIPW  198 (355)
T ss_dssp             HHHHHHTSSEEEEEECGGGGTC----------------------CTHHHHHHHHHHHHHHHCC----CCEEEEEEESCGG
T ss_pred             HHHHHHcCCeEEEEechHhhcccCCCCc----------------chHHHHHHHHHHHHhhccccc-CCCeEEEeecCCcc
Confidence            66553  689999999999975332211                123345677888888876432 35699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhhcC-CCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIATA-KVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~~~-~~s~~~i~~~l  217 (266)
                      .++++++|  ||+..++++.|+.++|..|++.++......+ ..++..++... +|++++|..++
T Consensus       199 ~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          199 QLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             GSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             cCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            99999999  9999999999999999999999998765443 45666666654 59999999987

>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=99.94  E-value=5.3e-26  Score=207.42  Aligned_cols=195  Identities=20%  Similarity=0.267  Sum_probs=151.4

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHc-CCcEEEEeCCcccC------hhhHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-KFDVYDLELSNLLG------NNDLRH   75 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~-~~~~~~i~~~~~~~------~~~l~~   75 (266)
                      +++++.+.+.+..++..+..|.. +..+++++|||||||||||++|+++|.++ +.+++.+++..+.+      ...+..
T Consensus       140 ~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~l~~~~~g~~~~~~~~  218 (444)
T 2zan_A          140 EGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKN  218 (444)
T ss_dssp             HHHHHHHHHHHTHHHHCTTTTSG-GGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC---------CCCTHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHhhc-cCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHHHHhhhcchHHHHHHH
Confidence            45778888888888888877653 34567899999999999999999999999 89999999987753      345666


Q ss_pred             HHHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC
Q 024550           76 ILIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK  153 (266)
Q Consensus        76 ~~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~  153 (266)
                      +|..+  ..++||||||+|.+++.+...                .......+.+.++..+++... ...+++||+|||.+
T Consensus       219 ~f~~a~~~~~~vl~iDEid~l~~~~~~~----------------~~~~~~~~~~~lL~~l~~~~~-~~~~v~vI~atn~~  281 (444)
T 2zan_A          219 LFQLARENKPSIIFIDEIDSLCGSRSEN----------------ESEAARRIKTEFLVQMQGVGV-DNDGILVLGATNIP  281 (444)
T ss_dssp             HHHHHHHSCSEEEEESCTTTTCCCSSCC----------------CCGGGHHHHHHHHTTTTCSSC-CCSSCEEEEEESCG
T ss_pred             HHHHHHHcCCeEEEEechHhhccCCCCc----------------cccHHHHHHHHHHHHHhCccc-CCCCEEEEecCCCc
Confidence            77654  468999999999986522111                112345677888888887642 23579999999999


Q ss_pred             CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhhc-CCCCHHHHHHHH
Q 024550          154 ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       154 ~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      +.+|++++|  ||+..++++.|+.++|..|++.++......+ ..++..++.. .+|++++|..++
T Consensus       282 ~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~  345 (444)
T 2zan_A          282 WVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIV  345 (444)
T ss_dssp             GGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             cccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            999999999  9999999999999999999999997765433 4566666665 469999999987

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=99.94  E-value=7.5e-27  Score=199.11  Aligned_cols=202  Identities=26%  Similarity=0.369  Sum_probs=148.8

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+ +..++..+..|..++...++++|||||||||||++|+++|+.++.+++.+++..+..      ...+..+
T Consensus        17 ~~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~   95 (268)
T 2r62_A           17 EEAKEEVVE-IVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDL   95 (268)
T ss_dssp             TTTHHHHHH-HHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTTTTSCSSSCSSSSSTT
T ss_pred             HHHHHHHHH-HHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHHHHhhcchHHHHHHHH
Confidence            345666666 455788999999999999999999999999999999999999999999999877642      2233344


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..++||||||+|.+...+.......            .+......++.++..+++... ...+++||+|||.++
T Consensus        96 ~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~------------~~~~~~~~~~~ll~~l~~~~~-~~~~v~vi~ttn~~~  162 (268)
T 2r62_A           96 FETAKKQAPSIIFIDEIDAIGKSRAAGGVVS------------GNDEREQTLNQLLAEMDGFGS-ENAPVIVLAATNRPE  162 (268)
T ss_dssp             HHHHHHSCSCEEEESCGGGTTC----------------------CCCSCSSTTTTTTTTTCSSC-SCSCCEEEECBSCCT
T ss_pred             HHHHHhcCCeEEEEeChhhhcccccccccCC------------CchhHHHHHHHHHHHhhCccc-CCCCEEEEEecCCch
Confidence            4443  3579999999999975332211110            112334567788888876533 234589999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .++++++|+|||+..++|+.|+.++|.++++.++.........++..++.. .++++++|.+++.
T Consensus       163 ~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~  227 (268)
T 2r62_A          163 ILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIIN  227 (268)
T ss_dssp             TSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHH
T ss_pred             hcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999876543322233444443 4589999988763

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.93  E-value=4e-25  Score=198.43  Aligned_cols=197  Identities=22%  Similarity=0.276  Sum_probs=148.4

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+.+..++..+.+|...+. +++++|||||||||||++|+++|..++.+++.+++..+..      ...+..+
T Consensus       121 ~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~  199 (389)
T 3vfd_A          121 DLAKQALQEIVILPSLRPELFTGLRA-PARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRAL  199 (389)
T ss_dssp             HHHHHHHHHHTHHHHHCTTTSCGGGC-CCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC-------CHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHhcccCC-CCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHhhccccchHHHHHHHH
Confidence            45677777777777777777766663 4679999999999999999999999999999999988753      2345556


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..++||||||||.++..+....                ......+++.++..+++........++||+|||.++
T Consensus       200 ~~~a~~~~~~il~iDEid~l~~~~~~~~----------------~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~  263 (389)
T 3vfd_A          200 FAVARELQPSIIFIDQVDSLLCERREGE----------------HDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQ  263 (389)
T ss_dssp             HHHHHHSSSEEEEEETGGGGC------------------------CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGG
T ss_pred             HHHHHhcCCeEEEEECchhhcccCCCcc----------------chHHHHHHHHHHHHhhcccccCCCCEEEEEecCCch
Confidence            6554  3579999999999975332211                123456777888888887665556799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .+++++++  ||...|+|+.|+.++|..|+..++...+..+. ..+..++.. .++++++|..++.
T Consensus       264 ~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          264 ELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             GCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             hcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            99999999  99999999999999999999999988766554 445555554 4689999988763

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.93  E-value=1.4e-25  Score=206.16  Aligned_cols=218  Identities=22%  Similarity=0.318  Sum_probs=160.1

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~   77 (266)
                      +.+.++.+ +..++..+..|..++...++|+||+||||||||++++++|..++.+++.+++..+..      ...+..+|
T Consensus        38 ~~k~~l~~-lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~~g~~~~~v~~lf  116 (499)
T 2dhr_A           38 EAKEELKE-IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLF  116 (499)
T ss_dssp             HHHHHHHH-HHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSCTTHHHHHHHHHT
T ss_pred             HHHHHHHH-HHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhhhhhHHHHHHHHH
Confidence            45566555 456677888888899999999999999999999999999999999999999987653      23455666


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..+.  .++++||||+|.+...+....             ..........++.++..|++....  ..++++++||+|+.
T Consensus       117 q~a~~~~p~il~IDEId~l~~~r~~~~-------------~~~~~e~~~~l~~LL~~Ldg~~~~--~~viviAatn~p~~  181 (499)
T 2dhr_A          117 ETAKRHAPCIVFIDEIDAVGRKRGSGV-------------GGGNDEREQTLNQLLVEMDGFEKD--TAIVVMAATNRPDI  181 (499)
T ss_dssp             TTSSSSSSCEEEEECGGGTCCCSSSST-------------TTSSHHHHHHHHHHHHHGGGCCSS--CCCEEEECCSCGGG
T ss_pred             HHHHhcCCCEEEEehHHHHHHhhccCc-------------CCCcHHHHHHHHHHHHHhcccccC--ccEEEEEecCChhh
Confidence            6654  479999999998864221100             001123346778889988876432  56899999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHHHc-------CCCHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQLMR-------NEAPEFAL  227 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l~~-------~~~~~~~~  227 (266)
                      +|++++|||||+..|.|+.|+.++|.+|++.++.........++..++.. .+++++||.+++..       ........
T Consensus       182 LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~Aa~~A~~~~~~~It~  261 (499)
T 2dhr_A          182 LDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITM  261 (499)
T ss_dssp             SCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHHHHHHTTTCCSSCCS
T ss_pred             cCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhCCCccCH
Confidence            99999999999999999999999999999988865433322334445554 46899999988732       11122344


Q ss_pred             HHHHHHHHhh
Q 024550          228 SGLIEFLESK  237 (266)
Q Consensus       228 ~~~~~~~~~~  237 (266)
                      +++..+++..
T Consensus       262 ~dl~~al~~v  271 (499)
T 2dhr_A          262 KDLEEAADRV  271 (499)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555555554

>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=99.93  E-value=1.7e-24  Score=183.15  Aligned_cols=198  Identities=24%  Similarity=0.346  Sum_probs=146.9

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHH
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHIL   77 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~   77 (266)
                      +.+.++.+ +..++..+..+...+...++|++|+||||||||+++++++..++.+++.+++..+..      ...+..+|
T Consensus        23 ~~~~~l~~-l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~~~  101 (254)
T 1ixz_A           23 EAKEELKE-IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLF  101 (254)
T ss_dssp             HHHHHHHH-HHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHSCTTHHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHHHHHHhhHHHHHHHHHH
Confidence            45555554 555677888899999999999999999999999999999999999999998765421      23355666


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ....  .++++++||+|.+...+.....             .........++.++..+++...  ...++++++||.|+.
T Consensus       102 ~~~~~~~~~i~~~Deid~l~~~~~~~~~-------------~~~~~~~~~~~~ll~~l~g~~~--~~~~i~~a~t~~p~~  166 (254)
T 1ixz_A          102 ETAKRHAPCIVFIDEIDAVGRKRGSGVG-------------GGNDEREQTLNQLLVEMDGFEK--DTAIVVMAATNRPDI  166 (254)
T ss_dssp             HHHTTSSSEEEEEETHHHHHC----------------------CHHHHHHHHHHHHHHHTCCT--TCCEEEEEEESCGGG
T ss_pred             HHHHhcCCeEEEehhhhhhhcccCcccc-------------ccchHHHHHHHHHHHHHhCCCC--CCCEEEEEccCCchh
Confidence            6653  4799999999988653221000             0012334567788888887643  245788999999999


Q ss_pred             CcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      +|++++|++||+..|+++.|+.++|.+|++.+..........++..++.. .+++++||.+++
T Consensus       167 ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~  229 (254)
T 1ixz_A          167 LDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLL  229 (254)
T ss_dssp             SCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHH
Confidence            99999999999999999999999999999988765432222334455554 468999999887

>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=99.92  E-value=5.8e-25  Score=195.27  Aligned_cols=197  Identities=20%  Similarity=0.288  Sum_probs=149.0

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+.+..++..+..|...+ .+++++|||||||||||++|+++|..++.+++.++++.+..      ...+..+
T Consensus        90 ~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~~~g~~~~~~~~~  168 (357)
T 3d8b_A           90 EFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEGEKMVRAL  168 (357)
T ss_dssp             HHHHHHHHHHTHHHHHCTTTSCGGG-SCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGCCSSTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhChHhHhhcc-CCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhhccccchHHHHHHHH
Confidence            4567777777777777777665554 45779999999999999999999999999999999988753      2334555


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..++||||||+|.+...+....                .......++.++..+++.......+++||+|||.++
T Consensus       169 ~~~a~~~~~~vl~iDEid~l~~~~~~~~----------------~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~  232 (357)
T 3d8b_A          169 FAVARCQQPAVIFIDEIDSLLSQRGDGE----------------HESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQ  232 (357)
T ss_dssp             HHHHHHTCSEEEEEETHHHHTBC----------------------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGG
T ss_pred             HHHHHhcCCeEEEEeCchhhhccCCCCc----------------chHHHHHHHHHHHHHhcccccCCCCEEEEEecCChh
Confidence            5544  3589999999999965322111                123356778888888877654456799999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhhc-CCCCHHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      .+++++++  ||...++++.|+.++|..++..++...+..+ ...+..++.. .++++++|..++.
T Consensus       233 ~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          233 EIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             GBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             hCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            99999999  9999999999999999999999987665444 3455566554 4589999998873

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.92  E-value=1.4e-24  Score=187.86  Aligned_cols=170  Identities=16%  Similarity=0.136  Sum_probs=118.1

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHHHHHc------ccCCeeeeecchh
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHILIAT------ENKSILVVEDIDC   93 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~~~~~------~~~~vl~iDeid~   93 (266)
                      .+..+|+++|||||||||||++|+++|+.++.+++.++++.+.+      ...+...|..+      ..++||||||||.
T Consensus        31 ~~~~~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~  110 (293)
T 3t15_A           31 PNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDA  110 (293)
T ss_dssp             TTCCCCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC-
T ss_pred             CCCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechhh
Confidence            46778899999999999999999999999999999999887653      23456666555      2689999999999


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc---------cCCCCceEEEEecCCCCCCcccccCCC
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW---------SSCGDERIIIFTTNHKERLDPALLRPG  164 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~~~~ivi~ttn~~~~ld~al~r~~  164 (266)
                      +++.......              .......+.+.|++.|++..         .....+++||+|||.++.+|++++|||
T Consensus       111 ~~~~~~~~~~--------------~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~  176 (293)
T 3t15_A          111 GAGRMGGTTQ--------------YTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDG  176 (293)
T ss_dssp             ---------------------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHH
T ss_pred             hcCCCCCCcc--------------ccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCC
Confidence            8762221110              01122345677788876332         112356999999999999999999999


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHH
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVA  214 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~  214 (266)
                      ||+..|+  .|+.++|.+|++.++...... ...+..+...  |++++|.
T Consensus       177 R~d~~i~--~P~~~~r~~Il~~~~~~~~~~-~~~l~~~~~~--~~~~~l~  221 (293)
T 3t15_A          177 RMEKFYW--APTREDRIGVCTGIFRTDNVP-AEDVVKIVDN--FPGQSID  221 (293)
T ss_dssp             HEEEEEE--CCCHHHHHHHHHHHHGGGCCC-HHHHHHHHHH--SCSCCHH
T ss_pred             CCceeEe--CcCHHHHHHHHHHhccCCCCC-HHHHHHHhCC--CCcccHH
Confidence            9998887  479999999999988765332 4555555554  5555553

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.91  E-value=2.6e-24  Score=186.01  Aligned_cols=197  Identities=21%  Similarity=0.295  Sum_probs=145.4

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++++.+.+.+..++..+..|...+ .+++++||+||||||||++|+++|+.++.+++.+++..+..      ...+..+
T Consensus        27 ~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~  105 (297)
T 3b9p_A           27 DVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSKYVGDGEKLVRAL  105 (297)
T ss_dssp             HHHHHHHHHHTHHHHHCGGGSCGGG-CCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTTSSSSCSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhCHHHHhcCC-CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHHhhcccchHHHHHHHH
Confidence            4567777777777777777666554 35679999999999999999999999999999999987653      2334455


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC-CCCceEEEEecCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS-CGDERIIIFTTNHK  153 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-~~~~~ivi~ttn~~  153 (266)
                      |..+  ..++||||||+|.+...+....                ........+.++..+++.... .+.+++||++||.+
T Consensus       106 ~~~~~~~~~~vl~iDEid~l~~~~~~~~----------------~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~  169 (297)
T 3b9p_A          106 FAVARHMQPSIIFIDEVDSLLSERSSSE----------------HEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRP  169 (297)
T ss_dssp             HHHHHHTCSEEEEEETGGGTSBCC---------------------CCSHHHHHHHHHHHHHCC------CEEEEEEESCG
T ss_pred             HHHHHHcCCcEEEeccHHHhccccccCc----------------chHHHHHHHHHHHHHhcccccCCCCcEEEEeecCCh
Confidence            5443  4689999999999865322111                122344566788888765432 12468999999999


Q ss_pred             CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhc-CCCCHHHHHHHHH
Q 024550          154 ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIAT-AKVTPADVAEQLM  218 (266)
Q Consensus       154 ~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~-~~~s~~~i~~~l~  218 (266)
                      +.+++++++  ||+..++++.|+.++|..|+..++...+..+. ..+..++.. .+++++++..++.
T Consensus       170 ~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          170 QELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAK  234 (297)
T ss_dssp             GGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             hhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999  99999999999999999999999877655443 445555544 5689999988763

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.91  E-value=1.8e-23  Score=179.44  Aligned_cols=199  Identities=24%  Similarity=0.338  Sum_probs=146.1

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      ++++.++.+ +..++..+..+...++..++|++|+||||||||+++++++..++.+++.+++..+..      ...+..+
T Consensus        46 ~~~~~~l~~-l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~~  124 (278)
T 1iy2_A           46 EEAKEELKE-IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDL  124 (278)
T ss_dssp             HHHHHHHHH-HHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHSTTTHHHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHHHHHHhhHHHHHHHHH
Confidence            345555544 556677888899999999999999999999999999999999999999998765421      2234556


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |....  .++++++||+|.+...+.....             .........++.++..+++...  ...++++++||.|+
T Consensus       125 ~~~~~~~~~~i~~iDeid~l~~~~~~~~~-------------~~~~~~~~~~~~ll~~lsgg~~--~~~~i~~a~t~~p~  189 (278)
T 1iy2_A          125 FETAKRHAPCIVFIDEIDAVGRKRGSGVG-------------GGNDEREQTLNQLLVEMDGFEK--DTAIVVMAATNRPD  189 (278)
T ss_dssp             HHHHHTSCSEEEEEETHHHHHCC---------------------CHHHHHHHHHHHHHHTTCCT--TCCEEEEEEESCTT
T ss_pred             HHHHHhcCCcEEehhhhHhhhcccccccC-------------CcchHHHHHHHHHHHHHhCCCC--CCCEEEEEecCCch
Confidence            66543  4799999999988642211000             0012234566777888876533  24578899999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|++++|++||+..|+|+.|+.++|.+|++.+..........++..++.. .++++++|.+++
T Consensus       190 ~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~  253 (278)
T 1iy2_A          190 ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLL  253 (278)
T ss_dssp             SSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             hCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999999999999999999988865432222334445544 468899998887

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.83  E-value=3.7e-19  Score=156.33  Aligned_cols=160  Identities=16%  Similarity=0.140  Sum_probs=125.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANP  109 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~  109 (266)
                      +..++||+||||||||++|+++|+.++.+++.+++..+.....+...+.....+++|||||++.+..             
T Consensus        54 ~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~-------------  120 (338)
T 3pfi_A           54 CLDHILFSGPAGLGKTTLANIISYEMSANIKTTAAPMIEKSGDLAAILTNLSEGDILFIDEIHRLSP-------------  120 (338)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEEGGGCCSHHHHHHHHHTCCTTCEEEEETGGGCCH-------------
T ss_pred             CCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEecchhccchhHHHHHHHhccCCCEEEEechhhcCH-------------
Confidence            4557999999999999999999999999999999998877777888888888899999999998743             


Q ss_pred             ccccccccccccchhhhhhhhhhhhcccc--------------CCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCC
Q 024550          110 DFLIAGYEQQKQYHITLSGLLNFIDGLWS--------------SCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHC  175 (266)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~ll~~l~~~~~--------------~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p  175 (266)
                                    .....|+..++....              ....++++|++||....++++|++  ||+..+.|+.|
T Consensus       121 --------------~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~  184 (338)
T 3pfi_A          121 --------------AIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFY  184 (338)
T ss_dssp             --------------HHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCC
T ss_pred             --------------HHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCc
Confidence                          123334444443210              000147899999999999999999  99999999999


Q ss_pred             CHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHHH
Q 024550          176 TPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQLM  218 (266)
Q Consensus       176 ~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l~  218 (266)
                      +.+++..++..+....+..+.. .+..++.....+++++.+.+.
T Consensus       185 ~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~  228 (338)
T 3pfi_A          185 KDSELALILQKAALKLNKTCEEKAALEIAKRSRSTPRIALRLLK  228 (338)
T ss_dssp             CHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHH
Confidence            9999999999988776655544 345556656678887777663

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.82  E-value=2.5e-19  Score=155.34  Aligned_cols=188  Identities=17%  Similarity=0.264  Sum_probs=130.5

Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHhCCCCC---ceeEEecCCCCChHHHHHHHHHHc-------CCcEEEEeCCcccC----
Q 024550            4 DMKKMIMDDLERFLQRKEFYRRVGKAWK---RGYLLYGPPGTGKSSLIAAMANYL-------KFDVYDLELSNLLG----   69 (266)
Q Consensus         4 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~---~~iLl~GppGtGKT~la~ala~~~-------~~~~~~i~~~~~~~----   69 (266)
                      ++++.+.+.+..+. .+..+..+|+..+   .++|||||||||||++|+++|+.+       ..+++.+++..+..    
T Consensus        38 ~~~~~l~~~~~~~~-~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~g  116 (309)
T 3syl_A           38 PVKDRIRETAALLL-VERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIG  116 (309)
T ss_dssp             HHHHHHHHHHHHHH-HHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGTCCSSTT
T ss_pred             HHHHHHHHHHHHHH-hHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHhhhhccc
Confidence            45556655544433 4666777776543   359999999999999999999988       34899999887753    


Q ss_pred             --hhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEE
Q 024550           70 --NNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIII  147 (266)
Q Consensus        70 --~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi  147 (266)
                        ...+...|..+ .++||||||+|.++..++.                  .......++.|++.++..    ..++++|
T Consensus       117 ~~~~~~~~~~~~~-~~~vl~iDEid~l~~~~~~------------------~~~~~~~~~~Ll~~l~~~----~~~~~~i  173 (309)
T 3syl_A          117 HTAPKTKEVLKRA-MGGVLFIDEAYYLYRPDNE------------------RDYGQEAIEILLQVMENN----RDDLVVI  173 (309)
T ss_dssp             CHHHHHHHHHHHH-TTSEEEEETGGGSCCCC---------------------CCTHHHHHHHHHHHHHC----TTTCEEE
T ss_pred             ccHHHHHHHHHhc-CCCEEEEEChhhhccCCCc------------------ccccHHHHHHHHHHHhcC----CCCEEEE
Confidence              22345555544 5789999999988642111                  122345667777777753    2467888


Q ss_pred             EecCCCC-----CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc---------CCCCHHHH
Q 024550          148 FTTNHKE-----RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT---------AKVTPADV  213 (266)
Q Consensus       148 ~ttn~~~-----~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~---------~~~s~~~i  213 (266)
                      ++||.+.     .++++|.+  ||+..|+|+.|+.+++..|+..++...+..+..+....+..         ...+.+++
T Consensus       174 ~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l  251 (309)
T 3syl_A          174 LAGYADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSI  251 (309)
T ss_dssp             EEECHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHH
T ss_pred             EeCChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHH
Confidence            8888653     35799999  99999999999999999999999987665555444332221         12346666


Q ss_pred             HHHH
Q 024550          214 AEQL  217 (266)
Q Consensus       214 ~~~l  217 (266)
                      .+++
T Consensus       252 ~~~l  255 (309)
T 3syl_A          252 RNAL  255 (309)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6665

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=99.80  E-value=5.3e-20  Score=168.38  Aligned_cols=152  Identities=15%  Similarity=0.101  Sum_probs=99.4

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHcC--CcEEEEeCCcccC-----hhhHHHHHHHc-----ccCCeeeeecchh
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLK--FDVYDLELSNLLG-----NNDLRHILIAT-----ENKSILVVEDIDC   93 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~~--~~~~~i~~~~~~~-----~~~l~~~~~~~-----~~~~vl~iDeid~   93 (266)
                      .|..+++++|||||||||||++|+++|+.++  .+++.++++.+..     ...+...|..+     ..|+||||||+|.
T Consensus        58 ~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~il~iDEid~  137 (456)
T 2c9o_A           58 SKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTE  137 (456)
T ss_dssp             TTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGCCSSSCHHHHHHHHHHHTEEEEEEEEEEEEEEEEEE
T ss_pred             hCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHHHHhhhhhHHHHHHHHHHHhhhhcCCcEEEEechhh
Confidence            3666778999999999999999999999999  9999999987763     23377777776     4689999999999


Q ss_pred             hHHHhHHHhhhhhc--CCcccc-ccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCccee--
Q 024550           94 CIELQDRLSRARAA--NPDFLI-AGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDM--  168 (266)
Q Consensus        94 l~~~~~~~~~~~~~--~~~~~~-~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~--  168 (266)
                      ++..+.........  ...... ....+......+.+.++..++......+..++|++|||+++.+|+++.|||||+.  
T Consensus       138 l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~  217 (456)
T 2c9o_A          138 LTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEA  217 (456)
T ss_dssp             EEEC--------------CEEEEEEETTEEEEEEECHHHHHHHHHTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSS
T ss_pred             cccccCCCCCCCcchHHHHHHHHHhccccchhHhhhHHHHHHHhhccCCCCCEEEEEcCCCCcccCChhhcCCcccCcce
Confidence            98755433211100  000000 0000111222333445555543222223445666899999999999999999988  


Q ss_pred             EEEcCCCCH
Q 024550          169 HINMSHCTP  177 (266)
Q Consensus       169 ~i~~~~p~~  177 (266)
                      .+.++.|+.
T Consensus       218 ~~~v~~p~~  226 (456)
T 2c9o_A          218 EEYVPLPKG  226 (456)
T ss_dssp             SSEECCCCS
T ss_pred             eEecCCCch
Confidence            566677754

>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=99.79  E-value=1.3e-18  Score=151.71  Aligned_cols=160  Identities=18%  Similarity=0.149  Sum_probs=124.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHH-cccCCeeeeecchhhHHHhHHHhhhhhcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIA-TENKSILVVEDIDCCIELQDRLSRARAAN  108 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~-~~~~~vl~iDeid~l~~~~~~~~~~~~~~  108 (266)
                      .+.++||+||||||||++|+++++.++.+++.+++..+.....+...+.. ...+++|||||++.+...           
T Consensus        37 ~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~lDEi~~l~~~-----------  105 (324)
T 1hqc_A           37 PLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQ-----------  105 (324)
T ss_dssp             CCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCCSHHHHHHHHTTTCCTTCEEEETTTTSCCHH-----------
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccCChHHHHHHHHHhccCCCEEEEECCcccccc-----------
Confidence            35689999999999999999999999999999999988776677777666 567899999999987531           


Q ss_pred             Cccccccccccccchhhhhhhhhhhhcccc--------------CCCCceEEEEecCCCCCCcccccCCCcceeEEEcCC
Q 024550          109 PDFLIAGYEQQKQYHITLSGLLNFIDGLWS--------------SCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSH  174 (266)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~--------------~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~  174 (266)
                                      ....++..++....              ....++++|++||.+..++++|.+  ||+..+.++.
T Consensus       106 ----------------~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~  167 (324)
T 1hqc_A          106 ----------------AEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLS--RFGIVEHLEY  167 (324)
T ss_dssp             ----------------HHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTT--TCSCEEECCC
T ss_pred             ----------------hHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHh--cccEEEecCC
Confidence                            12233333332210              001247899999999999999999  9988999999


Q ss_pred             CCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHHH
Q 024550          175 CTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQLM  218 (266)
Q Consensus       175 p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l~  218 (266)
                      |+.+++..++..+....+..+. ..+..++.....+++++.+++.
T Consensus       168 ~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~  212 (324)
T 1hqc_A          168 YTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFR  212 (324)
T ss_dssp             CCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHHH
Confidence            9999999999998876655554 4455666666788888888764

>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=99.78  E-value=3.4e-18  Score=145.85  Aligned_cols=144  Identities=20%  Similarity=0.250  Sum_probs=99.4

Q ss_pred             HHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC-------hhhHHHHHHHc--ccCCeeeeecchh
Q 024550           23 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG-------NNDLRHILIAT--ENKSILVVEDIDC   93 (266)
Q Consensus        23 ~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~-------~~~l~~~~~~~--~~~~vl~iDeid~   93 (266)
                      +...+..++.++|||||||||||++|+++|..++.+++.+++.+...       ...+..+|..+  ..+++|||||+|.
T Consensus        56 l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~  135 (272)
T 1d2n_A           56 TKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIER  135 (272)
T ss_dssp             HHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHH
T ss_pred             HhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHHhcCCchHHHHHHHHHHHHHHHhcCCcEEEEEChhh
Confidence            33445667788999999999999999999999999999998765321       13345566554  3589999999999


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcc-cccCCCcceeEEEc
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDP-ALLRPGRMDMHINM  172 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~-al~r~~Rf~~~i~~  172 (266)
                      +++.....                 .......+..|...+++.. ..+..+++|+|||.++.+++ .+.+  ||...|++
T Consensus       136 l~~~~~~~-----------------~~~~~~~l~~L~~~~~~~~-~~~~~~~ii~ttn~~~~l~~~~l~~--rf~~~i~~  195 (272)
T 1d2n_A          136 LLDYVPIG-----------------PRFSNLVLQALLVLLKKAP-PQGRKLLIIGTTSRKDVLQEMEMLN--AFSTTIHV  195 (272)
T ss_dssp             HTTCBTTT-----------------TBCCHHHHHHHHHHTTCCC-STTCEEEEEEEESCHHHHHHTTCTT--TSSEEEEC
T ss_pred             hhccCCCC-----------------hhHHHHHHHHHHHHhcCcc-CCCCCEEEEEecCChhhcchhhhhc--ccceEEcC
Confidence            86421100                 0112333444444444332 22456889999999988887 6677  99999999


Q ss_pred             CCCCH-HHHHHHHHH
Q 024550          173 SHCTP-SGFKMLASN  186 (266)
Q Consensus       173 ~~p~~-~~~~~i~~~  186 (266)
                      |.++. ++...++..
T Consensus       196 p~l~~r~~i~~i~~~  210 (272)
T 1d2n_A          196 PNIATGEQLLEALEL  210 (272)
T ss_dssp             CCEEEHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHh
Confidence            87776 566666554

>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=99.77  E-value=1.4e-18  Score=150.32  Aligned_cols=141  Identities=16%  Similarity=0.283  Sum_probs=100.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC--------hhhHHHHHHHc-------ccCCeeeeecchhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG--------NNDLRHILIAT-------ENKSILVVEDIDCC   94 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~--------~~~l~~~~~~~-------~~~~vl~iDeid~l   94 (266)
                      .+.++||+||||||||++++++|+.++.+++.+++..+..        ...+..++...       ..++||||||+|.+
T Consensus        49 ~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l  128 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKI  128 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGG
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccCCccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhc
Confidence            3568999999999999999999999999999999987653        12345554432       34799999999998


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc------CCCCceEEEEe----cCCCCCCcccccCCC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS------SCGDERIIIFT----TNHKERLDPALLRPG  164 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~------~~~~~~ivi~t----tn~~~~ld~al~r~~  164 (266)
                      .......               ..+.....+.+.|+..+++...      .....++||++    ++.+..++++|++  
T Consensus       129 ~~~~~~~---------------~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--  191 (310)
T 1ofh_A          129 CKKGEYS---------------GADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--  191 (310)
T ss_dssp             SCCSSCC---------------SSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--
T ss_pred             Ccccccc---------------ccchhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--
Confidence            6411000               0001112235566666664310      01235788887    4577889999999  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHh
Q 024550          165 RMDMHINMSHCTPSGFKMLASNY  187 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~  187 (266)
                      ||+..|+|+.|+.+++..|+...
T Consensus       192 R~~~~i~~~~~~~~~~~~il~~~  214 (310)
T 1ofh_A          192 RLPIRVELTALSAADFERILTEP  214 (310)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             hCCceEEcCCcCHHHHHHHHHhh
Confidence            99989999999999999999853

>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=99.75  E-value=1.1e-18  Score=155.04  Aligned_cols=142  Identities=20%  Similarity=0.280  Sum_probs=98.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh--------hhHHHHHHHc------ccCCeeeeecchhhH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN--------NDLRHILIAT------ENKSILVVEDIDCCI   95 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~--------~~l~~~~~~~------~~~~vl~iDeid~l~   95 (266)
                      ++.++||+||||||||++|+++|..++.+++.++++.+...        ..+..++...      ..++||||||+|.+.
T Consensus        50 ~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~  129 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKIS  129 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHC
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHhcccccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhc
Confidence            46689999999999999999999999999999999876532        2344455443      357999999999986


Q ss_pred             HHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC-----------------CCCceEEEEecCCC-----
Q 024550           96 ELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS-----------------CGDERIIIFTTNHK-----  153 (266)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-----------------~~~~~ivi~ttn~~-----  153 (266)
                      ..+......             .......+++.|+..|++....                 ...+++||+++|..     
T Consensus       130 ~~~~~~~~~-------------~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~  196 (363)
T 3hws_A          130 RKSDNPSIT-------------RDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKV  196 (363)
T ss_dssp             CCSSCC----------------CHHHHHHHHHHHHHHHHCC----------------CCCCCTTSSEEEEEECCTTHHHH
T ss_pred             ccccccccc-------------cccchHHHHHHHHHHhcCceeeccCccccccCCCceEEEECCCceEEecCCcHHHHHH
Confidence            522111000             0111123678888888843110                 11345566665532     


Q ss_pred             -----CC-----------------------------------CcccccCCCcceeEEEcCCCCHHHHHHHHHH
Q 024550          154 -----ER-----------------------------------LDPALLRPGRMDMHINMSHCTPSGFKMLASN  186 (266)
Q Consensus       154 -----~~-----------------------------------ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~  186 (266)
                           ..                                   +.++|++  ||+..+.|+.|+.+.+..|+..
T Consensus       197 i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~--R~~~~~~~~pl~~~~~~~I~~~  267 (363)
T 3hws_A          197 ISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG--RLPVVATLNELSEEALIQILKE  267 (363)
T ss_dssp             HHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             HHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc--ccCeeeecCCCCHHHHHHHHHH
Confidence                 11                                   6788888  9999999999999999999886

>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=99.74  E-value=8.9e-19  Score=158.27  Aligned_cols=157  Identities=14%  Similarity=0.158  Sum_probs=61.5

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCC-CCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC--------hhhH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGK-AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG--------NNDL   73 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~-~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~--------~~~l   73 (266)
                      ++.|+.+...+.+++.+...+..... .+++++||+||||||||++++++|..++.+++.++++.+..        ...+
T Consensus        21 e~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~~~~~g~vG~d~e~~l  100 (444)
T 1g41_A           21 ADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSII  100 (444)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC----CCCCTHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchhhcccceeeccHHHHH
Confidence            34566666666565554443333322 24678999999999999999999999999999999876542        2345


Q ss_pred             HHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEe-cCC
Q 024550           74 RHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFT-TNH  152 (266)
Q Consensus        74 ~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~t-tn~  152 (266)
                      ..+|..+..  ++++||++.+....                   .......+++.|+..|+++...  .. + +++ ||+
T Consensus       101 r~lf~~a~~--~~~~De~d~~~~~~-------------------~~~~e~rvl~~LL~~~dg~~~~--~~-v-~a~~TN~  155 (444)
T 1g41_A          101 RDLTDSAMK--LVRQQEIAKNRARA-------------------EDVAEERILDALLPPAKNQWGE--VE-N-HDSHSST  155 (444)
T ss_dssp             HHHHHHHHH--HHHHHHHHSCC----------------------------------------------------------
T ss_pred             HHHHHHHHh--cchhhhhhhhhccc-------------------hhhHHHHHHHHHHHHhhccccc--cc-c-ccccccC
Confidence            555554432  34578877653211                   1233467889999999988543  22 2 454 999


Q ss_pred             CCCCcccccCCCcceeEEEcCCCCHH-HHHHHH
Q 024550          153 KERLDPALLRPGRMDMHINMSHCTPS-GFKMLA  184 (266)
Q Consensus       153 ~~~ld~al~r~~Rf~~~i~~~~p~~~-~~~~i~  184 (266)
                      ++.||++|+|||||+..|+++.|+.. .+.+|+
T Consensus       156 ~~~ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          156 RQAFRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             ---------------------------------
T ss_pred             HHHHHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            99999999999999999999999997 566654

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.73  E-value=4e-17  Score=144.75  Aligned_cols=158  Identities=16%  Similarity=0.177  Sum_probs=108.4

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCC--cEEEEeCCcccC-----------------------------------
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKF--DVYDLELSNLLG-----------------------------------   69 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~--~~~~i~~~~~~~-----------------------------------   69 (266)
                      +..+++++|||||||||||++|+++|+.++.  +++.+++..+..                                   
T Consensus        66 ~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld  145 (368)
T 3uk6_A           66 GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEID  145 (368)
T ss_dssp             TCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGGGSCSSSCHHHHHHHHHHHSBEECC------CEEHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchhhhhcccchhHHHHHHHHHHHHHHhhhhccccccHhhhh
Confidence            4555679999999999999999999999974  777777644211                                   


Q ss_pred             --------------------hhhHHHHHHHcc-----------cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccc
Q 024550           70 --------------------NNDLRHILIATE-----------NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQ  118 (266)
Q Consensus        70 --------------------~~~l~~~~~~~~-----------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~  118 (266)
                                          ...+...+....           .++||||||+|.+..                      
T Consensus       146 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~~l~~----------------------  203 (368)
T 3uk6_A          146 VINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDI----------------------  203 (368)
T ss_dssp             HHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGGGSBH----------------------
T ss_pred             hhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhccccCh----------------------
Confidence                                112333332211           157999999998742                      


Q ss_pred             cccchhhhhhhhhhhhccccCCCCceEEEEec-----------CCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHh
Q 024550          119 QKQYHITLSGLLNFIDGLWSSCGDERIIIFTT-----------NHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNY  187 (266)
Q Consensus       119 ~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~tt-----------n~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~  187 (266)
                           ...+.|+..++..    ...++++++.           |.+..++++|++  ||.. +.|+.|+.+++..++..+
T Consensus       204 -----~~~~~L~~~le~~----~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~~~-i~~~~~~~~e~~~il~~~  271 (368)
T 3uk6_A          204 -----ESFSFLNRALESD----MAPVLIMATNRGITRIRGTSYQSPHGIPIDLLD--RLLI-VSTTPYSEKDTKQILRIR  271 (368)
T ss_dssp             -----HHHHHHHHHTTCT----TCCEEEEEESCSEEECBTSSCEEETTCCHHHHT--TEEE-EEECCCCHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHhhCc----CCCeeeeecccceeeeeccCCCCcccCCHHHHh--hccE-EEecCCCHHHHHHHHHHH
Confidence                 2334445554432    2335555544           357789999999  9976 899999999999999998


Q ss_pred             hCCCCCCcHHH-HHHHhhcCC-CCHHHHHHHHH
Q 024550          188 LGIAEHPLFVE-IEKLIATAK-VTPADVAEQLM  218 (266)
Q Consensus       188 ~~~~~~~~~~~-~~~l~~~~~-~s~~~i~~~l~  218 (266)
                      +...+..+..+ +..++.... .+++++.+++.
T Consensus       272 ~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~  304 (368)
T 3uk6_A          272 CEEEDVEMSEDAYTVLTRIGLETSLRYAIQLIT  304 (368)
T ss_dssp             HHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             HHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHH
Confidence            87766555544 444555454 78888877763

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=99.73  E-value=1.3e-16  Score=130.43  Aligned_cols=151  Identities=18%  Similarity=0.197  Sum_probs=108.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccChhhHHHHHHH--------cccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGNNDLRHILIA--------TENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~~~l~~~~~~--------~~~~~vl~iDeid~l~~~~~   99 (266)
                      +++|+||||||||++++++++.+     ...++.+++........+...+..        ...+.+|+|||+|.+..   
T Consensus        40 ~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~---  116 (226)
T 2chg_A           40 HLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA---  116 (226)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCH---
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCH---
Confidence            49999999999999999999876     466888888776654444433322        14578999999998743   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                              ...+.++..++..    ..++.+|++||.+..+++++.+  ||. .+.++.|+.++
T Consensus       117 ------------------------~~~~~l~~~l~~~----~~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~  165 (226)
T 2chg_A          117 ------------------------DAQAALRRTMEMY----SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEA  165 (226)
T ss_dssp             ------------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHH
T ss_pred             ------------------------HHHHHHHHHHHhc----CCCCeEEEEeCChhhcCHHHHH--hCc-eeecCCCCHHH
Confidence                                    1223344555432    2457888999999999999999  987 89999999999


Q ss_pred             HHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          180 FKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       180 ~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ...++..++...+..+. ..+..++...+.++..+.+.+
T Consensus       166 ~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l  204 (226)
T 2chg_A          166 MKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINAL  204 (226)
T ss_dssp             HHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999988765444443 334444444455666555544

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.73  E-value=3.1e-17  Score=142.08  Aligned_cols=130  Identities=18%  Similarity=0.353  Sum_probs=96.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHH---------------H---HcccCCeeeeec
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHIL---------------I---ATENKSILVVED   90 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~---------------~---~~~~~~vl~iDe   90 (266)
                      ..+||+||||||||++|+++|..+   +.+++.++++.+........++               .   ....++||||||
T Consensus        48 ~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDE  127 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDA  127 (311)
T ss_dssp             EEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHHHHHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEET
T ss_pred             eEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccHHHhcCCCCccccccccchHHHHHHhCCCeEEEEeC
Confidence            469999999999999999999988   5679999998775432222221               1   123468999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC-------CceEEEEecCC-----------
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG-------DERIIIFTTNH-----------  152 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~-------~~~ivi~ttn~-----------  152 (266)
                      +|.+..                           ..++.|+..|+.......       .++++|+|||.           
T Consensus       128 i~~l~~---------------------------~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~  180 (311)
T 4fcw_A          128 IEKAHP---------------------------DVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQK  180 (311)
T ss_dssp             GGGSCH---------------------------HHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTS
T ss_pred             hhhcCH---------------------------HHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcc
Confidence            998742                           244556666653321111       25779999998           


Q ss_pred             ---------------CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          153 ---------------KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       153 ---------------~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                                     ...++++|++  ||+..+.|+.|+.+++..|+..++..
T Consensus       181 ~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p~~~~~~~~i~~~~l~~  231 (311)
T 4fcw_A          181 GWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQMSY  231 (311)
T ss_dssp             CCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHTHH
T ss_pred             cccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCCCCHHHHHHHHHHHHHH
Confidence                           4568889998  99999999999999999999988754

>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=99.72  E-value=2.2e-17  Score=153.92  Aligned_cols=133  Identities=21%  Similarity=0.208  Sum_probs=95.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh---------------hhHHHHHHHcc-cCCeeeeecchh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN---------------NDLRHILIATE-NKSILVVEDIDC   93 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~---------------~~l~~~~~~~~-~~~vl~iDeid~   93 (266)
                      ++..++|+||||||||++++++|..++.++..+++......               ..+...|..+. .++|+||||+|.
T Consensus       107 ~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~g~~~~~ig~~~~~~~~~~~~a~~~~~vl~lDEid~  186 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRGHRRTYVGAMPGRIIQGMKKAGKLNPVFLLDEIDK  186 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC--------------------CHHHHHHTTCSSSEEEEEEESSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhhhHHHHHhccCchHHHHHHHHhhccCCEEEEhhhhh
Confidence            34579999999999999999999999999999998775421               12233444442 456999999999


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC-----------CCCceEEEEecCCCCCCcccccC
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS-----------CGDERIIIFTTNHKERLDPALLR  162 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-----------~~~~~ivi~ttn~~~~ld~al~r  162 (266)
                      +....                       .....+.|+..|+.....           ....++||+|||.++.++++|++
T Consensus       187 l~~~~-----------------------~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~  243 (543)
T 3m6a_A          187 MSSDF-----------------------RGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRD  243 (543)
T ss_dssp             CC--------------------------------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHH
T ss_pred             hhhhh-----------------------ccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHh
Confidence            86411                       111334555555432110           01457999999999999999999


Q ss_pred             CCcceeEEEcCCCCHHHHHHHHHHhh
Q 024550          163 PGRMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                        ||. .|+|+.|+.+++..|+..++
T Consensus       244 --R~~-vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          244 --RME-IINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             --HEE-EEECCCCCHHHHHHHHHHTH
T ss_pred             --hcc-eeeeCCCCHHHHHHHHHHHH
Confidence              995 69999999999999999887

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.71  E-value=7.4e-17  Score=146.86  Aligned_cols=149  Identities=20%  Similarity=0.293  Sum_probs=104.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHc------ccCCeeeeecchhhHHHhHHHhhhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIAT------ENKSILVVEDIDCCIELQDRLSRAR  105 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~------~~~~vl~iDeid~l~~~~~~~~~~~  105 (266)
                      .++|||||||||||++++++++.++.+++.+++... +...+...+..+      ..++||||||+|.+..         
T Consensus        51 ~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~~~-~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~---------  120 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAEVIARYANADVERISAVTS-GVKEIREAIERARQNRNAGRRTILFVDEVHRFNK---------  120 (447)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETTTC-CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC-----------
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEeccC-CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCH---------
Confidence            579999999999999999999999999999998664 444555555443      3579999999998742         


Q ss_pred             hcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEec--CCCCCCcccccCCCcceeEEEcCCCCHHHHHHH
Q 024550          106 AANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTT--NHKERLDPALLRPGRMDMHINMSHCTPSGFKML  183 (266)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~tt--n~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i  183 (266)
                                        ..++.|+..++.      ..+++|++|  |....++++|++  ||. .+.|+.|+.+++..+
T Consensus       121 ------------------~~q~~LL~~le~------~~v~lI~att~n~~~~l~~aL~s--R~~-v~~l~~l~~edi~~i  173 (447)
T 3pvs_A          121 ------------------SQQDAFLPHIED------GTITFIGATTENPSFELNSALLS--RAR-VYLLKSLSTEDIEQV  173 (447)
T ss_dssp             ----------------------CCHHHHHT------TSCEEEEEESSCGGGSSCHHHHT--TEE-EEECCCCCHHHHHHH
T ss_pred             ------------------HHHHHHHHHHhc------CceEEEecCCCCcccccCHHHhC--cee-EEeeCCcCHHHHHHH
Confidence                              134557777764      235666655  444688999999  985 688999999999999


Q ss_pred             HHHhhCC-------CCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          184 ASNYLGI-------AEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       184 ~~~~~~~-------~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+++..       ....+. ..+..++.....+.+++.+.+
T Consensus       174 l~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~L  215 (447)
T 3pvs_A          174 LTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTL  215 (447)
T ss_dssp             HHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHH
T ss_pred             HHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHH
Confidence            9998865       222233 233444444445555555444

>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=99.70  E-value=1.1e-16  Score=142.71  Aligned_cols=142  Identities=21%  Similarity=0.289  Sum_probs=93.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC--------hhhHHHHHHHc------ccCCeeeeecchhhH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG--------NNDLRHILIAT------ENKSILVVEDIDCCI   95 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~--------~~~l~~~~~~~------~~~~vl~iDeid~l~   95 (266)
                      ++.++||+||||||||++|+++|+.++.+++.+++..+..        ...+..++...      ..++||||||+|.+.
T Consensus        71 ~~~~ill~Gp~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~  150 (376)
T 1um8_A           71 SKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKIS  150 (376)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC-
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHhCCCEEEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHh
Confidence            4567999999999999999999999999999999887642        12234444332      258999999999987


Q ss_pred             HHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-----------------CCCCceEEEEecCC------
Q 024550           96 ELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-----------------SCGDERIIIFTTNH------  152 (266)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-----------------~~~~~~ivi~ttn~------  152 (266)
                      ..+.......             +......++.|+..|++...                 -...++++|+|+|.      
T Consensus       151 ~~~~~~~~~~-------------~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~  217 (376)
T 1um8_A          151 RLSENRSITR-------------DVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEI  217 (376)
T ss_dssp             --------------------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHH
T ss_pred             hhcCCCceec-------------ccchHHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHH
Confidence            5321111000             11122356777777774310                 00134577777762      


Q ss_pred             -----------------------------------CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHH
Q 024550          153 -----------------------------------KERLDPALLRPGRMDMHINMSHCTPSGFKMLASN  186 (266)
Q Consensus       153 -----------------------------------~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~  186 (266)
                                                         ...+.++|++  ||+..+.|+.++.++...|+..
T Consensus       218 l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~~p~l~~--R~~~~i~~~~l~~~~l~~i~~~  284 (376)
T 1um8_A          218 IKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIG--RLPVLSTLDSISLEAMVDILQK  284 (376)
T ss_dssp             TTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             HHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhcCCChHHhc--CCCceeeccCCCHHHHHHHHhh
Confidence                                               0125677788  9989999999999999998874

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=99.70  E-value=5.3e-17  Score=141.85  Aligned_cols=156  Identities=15%  Similarity=0.257  Sum_probs=108.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh-------hhHHHHHHHcccCCeeeeecchhhHHHhHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN-------NDLRHILIATENKSILVVEDIDCCIELQDR  100 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~-------~~l~~~~~~~~~~~vl~iDeid~l~~~~~~  100 (266)
                      ..+++||||||||||++++++++.+   +.+++.+++..+...       ............+++|||||++.+....  
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~iDEi~~l~~~~--  114 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKE--  114 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTTCH--
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHcCcHHHHHHHhcCCCEEEEcCcccccCCh--
Confidence            4679999999999999999999998   899999998765321       0111222223458999999999875310  


Q ss_pred             HhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC---CCcccccCCCcce--eEEEcCCC
Q 024550          101 LSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE---RLDPALLRPGRMD--MHINMSHC  175 (266)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~---~ld~al~r~~Rf~--~~i~~~~p  175 (266)
                                             .....++..++.....  ...+|+++++.+.   .++++|.+  ||.  ..++++. 
T Consensus       115 -----------------------~~~~~l~~~l~~~~~~--~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-  166 (324)
T 1l8q_A          115 -----------------------RTQIEFFHIFNTLYLL--EKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-  166 (324)
T ss_dssp             -----------------------HHHHHHHHHHHHHHHT--TCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECCC-
T ss_pred             -----------------------HHHHHHHHHHHHHHHC--CCeEEEEecCChHHHHHhhhHhhh--cccCceEEEeCC-
Confidence                                   1222333333332222  3467777777765   68899999  886  7799999 


Q ss_pred             CHHHHHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          176 TPSGFKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       176 ~~~~~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+++..|+..++...+..+..+ +..++... .+.+++.+.+
T Consensus       167 ~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g~~r~l~~~l  208 (324)
T 1l8q_A          167 DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKI  208 (324)
T ss_dssp             CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-CCHHHHHHHH
Confidence            99999999999987665555444 45555556 6777766655

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.69  E-value=8.3e-17  Score=139.83  Aligned_cols=131  Identities=13%  Similarity=0.209  Sum_probs=95.5

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh----------------------hhHHH
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN----------------------NDLRH   75 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~----------------------~~l~~   75 (266)
                      -..+.++|||||||||||++++.+++++          ...+++++|..+.+.                      ..+..
T Consensus        42 ~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~  121 (318)
T 3te6_A           42 SSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNF  121 (318)
T ss_dssp             TTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHH
T ss_pred             CCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHH
Confidence            3457789999999999999999999998          356888998775432                      23455


Q ss_pred             HHHHc----ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecC
Q 024550           76 ILIAT----ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTN  151 (266)
Q Consensus        76 ~~~~~----~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn  151 (266)
                      .|...    ..++|++|||+|.+.                          ....+..+++...    ....++++|+++|
T Consensus       122 ~f~~~~~~~~~~~ii~lDE~d~l~--------------------------~q~~L~~l~~~~~----~~~s~~~vI~i~n  171 (318)
T 3te6_A          122 YITNVPKAKKRKTLILIQNPENLL--------------------------SEKILQYFEKWIS----SKNSKLSIICVGG  171 (318)
T ss_dssp             HHHHSCGGGSCEEEEEEECCSSSC--------------------------CTHHHHHHHHHHH----CSSCCEEEEEECC
T ss_pred             HHHHhhhccCCceEEEEecHHHhh--------------------------cchHHHHHHhccc----ccCCcEEEEEEec
Confidence            56543    346899999999873                          1234444444322    2235689999999


Q ss_pred             CCCC----CcccccCCCcce-eEEEcCCCCHHHHHHHHHHhhCC
Q 024550          152 HKER----LDPALLRPGRMD-MHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       152 ~~~~----ld~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      ..+.    +++++.+  ||. ..|.|+.++.++...|+++.+..
T Consensus       172 ~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          172 HNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             SSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             Ccccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHHh
Confidence            8764    4566677  886 57999999999999999888854

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=99.69  E-value=1.9e-16  Score=138.17  Aligned_cols=125  Identities=18%  Similarity=0.188  Sum_probs=94.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHc----c---cCCeeeeecchhhHHHhHHHh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIAT----E---NKSILVVEDIDCCIELQDRLS  102 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~----~---~~~vl~iDeid~l~~~~~~~~  102 (266)
                      .++.+|++||||||||++++++|+.++.++++++++... ...+...+...    .   .+.||+|||+|.+.+      
T Consensus        47 ~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~~~~~~-~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~------  119 (324)
T 3u61_B           47 IPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDCK-IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGL------  119 (324)
T ss_dssp             CCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEETTTCC-HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGG------
T ss_pred             CCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEcccccC-HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCc------
Confidence            345788999999999999999999999999999988764 44444433321    1   578999999998851      


Q ss_pred             hhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHH
Q 024550          103 RARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKM  182 (266)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~  182 (266)
                                          ....+.|+..++...    ..+.+|+|||.+..+++++.+  ||. .+.|+.|+.+++.+
T Consensus       120 --------------------~~~~~~L~~~le~~~----~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e~~~  172 (324)
T 3u61_B          120 --------------------AESQRHLRSFMEAYS----SNCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDEDKIE  172 (324)
T ss_dssp             --------------------HHHHHHHHHHHHHHG----GGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHHHHH
T ss_pred             --------------------HHHHHHHHHHHHhCC----CCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHHHHH
Confidence                                112344555555432    357889999999999999999  995 69999999999776


Q ss_pred             HHHHhh
Q 024550          183 LASNYL  188 (266)
Q Consensus       183 i~~~~~  188 (266)
                      |+..++
T Consensus       173 il~~~~  178 (324)
T 3u61_B          173 MMKQMI  178 (324)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            665544

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.68  E-value=2.6e-17  Score=131.68  Aligned_cols=128  Identities=20%  Similarity=0.258  Sum_probs=87.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHH---cccCCeee
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIA---TENKSILV   87 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~---~~~~~vl~   87 (266)
                      ..+.+++|+||||||||+++++++..+          +.+++.+++..+...        ..+..++..   ...++||+
T Consensus        41 ~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~  120 (195)
T 1jbk_A           41 RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILF  120 (195)
T ss_dssp             SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEE
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEE
Confidence            345679999999999999999999986          688888887665421        123344432   34577999


Q ss_pred             eecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccC
Q 024550           88 VEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLR  162 (266)
Q Consensus        88 iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r  162 (266)
                      |||+|.+......                   .......+.+...++.      .++.+|++||.+.     .+++++.+
T Consensus       121 iDe~~~l~~~~~~-------------------~~~~~~~~~l~~~~~~------~~~~~i~~~~~~~~~~~~~~~~~l~~  175 (195)
T 1jbk_A          121 IDELHTMVGAGKA-------------------DGAMDAGNMLKPALAR------GELHCVGATTLDEYRQYIEKDAALER  175 (195)
T ss_dssp             EETGGGGTT-------------------------CCCCHHHHHHHHHT------TSCCEEEEECHHHHHHHTTTCHHHHT
T ss_pred             EeCHHHHhccCcc-------------------cchHHHHHHHHHhhcc------CCeEEEEeCCHHHHHHHHhcCHHHHH
Confidence            9999998642110                   0001122222222221      3577888888775     78999999


Q ss_pred             CCcceeEEEcCCCCHHHHHHHH
Q 024550          163 PGRMDMHINMSHCTPSGFKMLA  184 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~~~~~~i~  184 (266)
                        ||. .|+++.|+.+++.+|+
T Consensus       176 --r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          176 --RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             --TEE-EEECCCCCHHHHHTTC
T ss_pred             --Hhc-eeecCCCCHHHHHHHh
Confidence              997 6999999999998765

>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=99.68  E-value=8.2e-16  Score=142.64  Aligned_cols=156  Identities=19%  Similarity=0.241  Sum_probs=103.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHH-------------Hc-------ccCCeeeee
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILI-------------AT-------ENKSILVVE   89 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~-------------~~-------~~~~vl~iD   89 (266)
                      +++++||+||||||||++|+++|++++.+++.++++.......+...+.             ..       ..++|||||
T Consensus        76 ~~~~lLL~GppGtGKTtla~~la~~l~~~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliID  155 (516)
T 1sxj_A           76 VFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMD  155 (516)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEEC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHcCCCEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEE
Confidence            4578999999999999999999999999999999988765433222221             11       357899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeE
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMH  169 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~  169 (266)
                      |+|.+..                        .....+..+++.++..    ...+++++++.....++ .+.+  |+ ..
T Consensus       156 Eid~l~~------------------------~~~~~l~~L~~~l~~~----~~~iIli~~~~~~~~l~-~l~~--r~-~~  203 (516)
T 1sxj_A          156 EVDGMSG------------------------GDRGGVGQLAQFCRKT----STPLILICNERNLPKMR-PFDR--VC-LD  203 (516)
T ss_dssp             SGGGCCT------------------------TSTTHHHHHHHHHHHC----SSCEEEEESCTTSSTTG-GGTT--TS-EE
T ss_pred             CCCccch------------------------hhHHHHHHHHHHHHhc----CCCEEEEEcCCCCccch-hhHh--ce-EE
Confidence            9998853                        1111234445554432    23344444444434444 4554  44 68


Q ss_pred             EEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          170 INMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       170 i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      |.|+.|+.+++.+++.......+..+. +.+..++.....+.+.+.+.+
T Consensus       204 i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~GdiR~~i~~L  252 (516)
T 1sxj_A          204 IQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLL  252 (516)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHH
Confidence            999999999999999887755444333 345556665556666666655

>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=99.68  E-value=1.3e-15  Score=125.88  Aligned_cols=153  Identities=15%  Similarity=0.253  Sum_probs=107.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc-----
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE-----   81 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~-----   81 (266)
                      ++.++|+||||||||++++.+++.++.                        .++.++.........+..++....     
T Consensus        45 ~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (250)
T 1njg_A           45 HHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPAR  124 (250)
T ss_dssp             CSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhc
Confidence            347999999999999999999988743                        234444333222334555555432     


Q ss_pred             -cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           82 -NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        82 -~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                       .+.+|+|||+|.+..                           ..++.++..++..    +.++++|++||.+..+++++
T Consensus       125 ~~~~vlviDe~~~l~~---------------------------~~~~~l~~~l~~~----~~~~~~i~~t~~~~~~~~~l  173 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSR---------------------------HSFNALLKTLEEP----PEHVKFLLATTDPQKLPVTI  173 (250)
T ss_dssp             SSSEEEEEETGGGSCH---------------------------HHHHHHHHHHHSC----CTTEEEEEEESCGGGSCHHH
T ss_pred             CCceEEEEECcccccH---------------------------HHHHHHHHHHhcC----CCceEEEEEeCChHhCCHHH
Confidence             468999999997632                           2334455555532    34688899999988899999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+  |+ ..++++.|+.++..+++..++...+.... ..+..++...+.+|..+.+.+
T Consensus       174 ~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~~~~~~~~  228 (250)
T 1njg_A          174 LS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLT  228 (250)
T ss_dssp             HT--TS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HH--Hh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            98  76 67999999999999999988866554443 334455555556777766654

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.67  E-value=2.4e-16  Score=138.03  Aligned_cols=131  Identities=17%  Similarity=0.205  Sum_probs=92.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHH---------HHHccc---CCeeeeecchhhHHHh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHI---------LIATEN---KSILVVEDIDCCIELQ   98 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~---------~~~~~~---~~vl~iDeid~l~~~~   98 (266)
                      +.++|||||||||||++++++|+.++.+++.+++........+...         +.....   .+||||||++.+..  
T Consensus        46 ~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~~~l~g~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~~--  123 (331)
T 2r44_A           46 GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLPSDLIGTMIYNQHKGNFEVKKGPVFSNFILADEVNRSPA--  123 (331)
T ss_dssp             TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCHHHHHEEEEEETTTTEEEEEECTTCSSEEEEETGGGSCH--
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCChhhcCCceeecCCCCceEeccCcccccEEEEEccccCCH--
Confidence            4579999999999999999999999999999987533222211100         000011   37999999998743  


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc-------ccCCCCceEEEEecCCCC-----CCcccccCCCcc
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL-------WSSCGDERIIIFTTNHKE-----RLDPALLRPGRM  166 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-------~~~~~~~~ivi~ttn~~~-----~ld~al~r~~Rf  166 (266)
                                               ...+.|+..++..       ....+.++++|+|+|+.+     .++++|++  ||
T Consensus       124 -------------------------~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~--Rf  176 (331)
T 2r44_A          124 -------------------------KVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVD--RF  176 (331)
T ss_dssp             -------------------------HHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHT--TS
T ss_pred             -------------------------HHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHh--he
Confidence                                     1223344444321       111234578888888553     38999999  99


Q ss_pred             eeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          167 DMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       167 ~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      ...+.++.|+.+++.+|++.+...
T Consensus       177 ~~~i~i~~p~~~~~~~il~~~~~~  200 (331)
T 2r44_A          177 MMKIHLTYLDKESELEVMRRVSNM  200 (331)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHCT
T ss_pred             eEEEEcCCCCHHHHHHHHHhcccc
Confidence            989999999999999999988765

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=99.67  E-value=1.9e-15  Score=132.68  Aligned_cols=158  Identities=19%  Similarity=0.235  Sum_probs=115.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPD  110 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~  110 (266)
                      +..++|+|||||||||+++++|+.++.++...+...+.....+...+.....+.|+||||++.+.....+.         
T Consensus        51 ~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~~~~~~l~~~~~~~~~~~v~~iDE~~~l~~~~~e~---------  121 (334)
T 1in4_A           51 LDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEEL---------  121 (334)
T ss_dssp             CCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSHHHHHHHHHHCCTTCEEEEETGGGCCHHHHHH---------
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHhcCHHHHHHHHHHccCCCEEEEcchhhcCHHHHHH---------
Confidence            35699999999999999999999999998877776665556666666666678899999999886421111         


Q ss_pred             cccccccccccchhhhhhhhhhhhccc--------------cCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCC
Q 024550          111 FLIAGYEQQKQYHITLSGLLNFIDGLW--------------SSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCT  176 (266)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~ll~~l~~~~--------------~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~  176 (266)
                                        ++..+....              ...-..+.++++|+.+..|++++++  ||...+.++.|+
T Consensus       122 ------------------L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~  181 (334)
T 1in4_A          122 ------------------LYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRS--RFGIILELDFYT  181 (334)
T ss_dssp             ------------------HHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCC
T ss_pred             ------------------HHHHHHhcccceeeccCcccccccccCCCeEEEEecCCcccCCHHHHH--hcCceeeCCCCC
Confidence                              111111000              0001235677899999999999999  999899999999


Q ss_pred             HHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          177 PSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       177 ~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+++.+++++.....+.... +.+..++.....+++.+.+++
T Consensus       182 ~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll  223 (334)
T 1in4_A          182 VKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLT  223 (334)
T ss_dssp             HHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            99999999988765555554 445566666778888776665

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.66  E-value=2.7e-16  Score=152.23  Aligned_cols=128  Identities=18%  Similarity=0.299  Sum_probs=96.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChh-----hHHHHHHHcccCCeeeeecchhhHHHhHHHhhh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNN-----DLRHILIATENKSILVVEDIDCCIELQDRLSRA  104 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~-----~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~  104 (266)
                      ++||+||||||||++|+++|..+   +.+++.++++.+....     .+...+. ...++|||||||+.+.         
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~~~~~l~~~~~-~~~~~vl~lDEi~~~~---------  592 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHSTSGGQLTEKVR-RKPYSVVLLDAIEKAH---------  592 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCCC---CHHHHH-HCSSSEEEEECGGGSC---------
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhcccccccccchhhHHHH-hCCCeEEEEeCccccC---------
Confidence            59999999999999999999998   6889999999886421     2233322 3457899999999763         


Q ss_pred             hhcCCccccccccccccchhhhhhhhhhhhccccC-------CCCceEEEEecCCCCC------------CcccccCCCc
Q 024550          105 RAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS-------CGDERIIIFTTNHKER------------LDPALLRPGR  165 (266)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-------~~~~~ivi~ttn~~~~------------ld~al~r~~R  165 (266)
                                        ...++.|++.|+...-.       ...+++||+|||.+..            +.++|++  |
T Consensus       593 ------------------~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~--R  652 (758)
T 3pxi_A          593 ------------------PDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFIN--R  652 (758)
T ss_dssp             ------------------HHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHT--T
T ss_pred             ------------------HHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHh--h
Confidence                              23556677777642211       1235789999996543            7889998  9


Q ss_pred             ceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          166 MDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       166 f~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      |+..|.|+.|+.+++..|+..++..
T Consensus       653 l~~~i~~~~l~~~~~~~i~~~~l~~  677 (758)
T 3pxi_A          653 IDEIIVFHSLEKKHLTEIVSLMSDQ  677 (758)
T ss_dssp             SSEEEECC--CHHHHHHHHHHHHHH
T ss_pred             CCeEEecCCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999888743

>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=99.66  E-value=1.2e-15  Score=132.18  Aligned_cols=151  Identities=18%  Similarity=0.202  Sum_probs=109.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccChhhHHHHHHH----c----ccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGNNDLRHILIA----T----ENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~~~l~~~~~~----~----~~~~vl~iDeid~l~~~~~   99 (266)
                      ++|||||||||||++++++++.+     +.+++.++++...+...+...+..    .    ..+.|++|||+|.+..   
T Consensus        40 ~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~---  116 (319)
T 2chq_A           40 HLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA---  116 (319)
T ss_dssp             CEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTSTTCTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCH---
T ss_pred             eEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccccChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCH---
Confidence            49999999999999999999986     456788888765443333222221    1    3478999999998742   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                              ...+.|+..++.    .+..+++|++||.+..+++++.+  ||. .+.|+.|+.++
T Consensus       117 ------------------------~~~~~L~~~le~----~~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~  165 (319)
T 2chq_A          117 ------------------------DAQAALRRTMEM----YSKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEA  165 (319)
T ss_dssp             ------------------------HHHHTTGGGTSS----SSSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHH
T ss_pred             ------------------------HHHHHHHHHHHh----cCCCCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHH
Confidence                                    123445555543    23568889999999999999999  885 79999999999


Q ss_pred             HHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          180 FKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       180 ~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +..++..++...+..+.. .+..++...+.+++.+.+.+
T Consensus       166 ~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l  204 (319)
T 2chq_A          166 MKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINAL  204 (319)
T ss_dssp             HHHHHHHHHHTTCCCBCHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999999888776665544 44555555566666665554

>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=99.66  E-value=4.6e-16  Score=150.53  Aligned_cols=128  Identities=18%  Similarity=0.336  Sum_probs=98.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh-------------------hhHHHHHHHcccCCeeeeecch
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN-------------------NDLRHILIATENKSILVVEDID   92 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~-------------------~~l~~~~~~~~~~~vl~iDeid   92 (266)
                      .++||+||||||||++|+++|..++.+++.++++.+...                   ..+...+. ...++||||||++
T Consensus       489 ~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~~~l~g~~~g~~g~~~~~~l~~~~~-~~~~~vl~lDEi~  567 (758)
T 1r6b_X          489 GSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVI-KHPHAVLLLDEIE  567 (758)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHHH-HCSSEEEEEETGG
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhHhhhcCCCCCCcCccccchHHHHHH-hCCCcEEEEeCcc
Confidence            369999999999999999999999999999999877531                   11223332 2457999999999


Q ss_pred             hhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC--C-----CCceEEEEecCCCC-----------
Q 024550           93 CCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS--C-----GDERIIIFTTNHKE-----------  154 (266)
Q Consensus        93 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~--~-----~~~~ivi~ttn~~~-----------  154 (266)
                      .+.                           ..+++.|+..|+...-.  .     -.+++||+|||...           
T Consensus       568 ~~~---------------------------~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~  620 (758)
T 1r6b_X          568 KAH---------------------------PDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLI  620 (758)
T ss_dssp             GSC---------------------------HHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC----------
T ss_pred             ccC---------------------------HHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcccCcc
Confidence            763                           23556677777632111  0     13578999999753           


Q ss_pred             --------------CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          155 --------------RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       155 --------------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                                    .++++|++  ||+..|.|+.|+.+++..|+..++.
T Consensus       621 ~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l~~~~~~~i~~~~l~  667 (758)
T 1r6b_X          621 HQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_dssp             -------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCCCHHHHHHHHHHHHH
Confidence                          57889999  9999999999999999999998885

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.66  E-value=1.4e-15  Score=135.33  Aligned_cols=127  Identities=18%  Similarity=0.260  Sum_probs=91.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc-----------CCcEEEEeCCccc-Ch-----------------------hh-H
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL-----------KFDVYDLELSNLL-GN-----------------------ND-L   73 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~-----------~~~~~~i~~~~~~-~~-----------------------~~-l   73 (266)
                      .+++++|+||||||||++++++++.+           +.+++.+++.... +.                       .. +
T Consensus        44 ~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~  123 (384)
T 2qby_B           44 VKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYI  123 (384)
T ss_dssp             CCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHH
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHH
Confidence            35689999999999999999999987           8899999976543 21                       11 2


Q ss_pred             HHHHHHccc-CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhh-hhhhhhhhhccccCCCCceEEEEecC
Q 024550           74 RHILIATEN-KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHIT-LSGLLNFIDGLWSSCGDERIIIFTTN  151 (266)
Q Consensus        74 ~~~~~~~~~-~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ll~~l~~~~~~~~~~~ivi~ttn  151 (266)
                      ..++..... +.||+|||+|.+..                       ...... +..++...        .++.+|+|||
T Consensus       124 ~~l~~~l~~~~~vlilDEi~~l~~-----------------------~~~~~~~l~~l~~~~--------~~~~iI~~t~  172 (384)
T 2qby_B          124 DKIKNGTRNIRAIIYLDEVDTLVK-----------------------RRGGDIVLYQLLRSD--------ANISVIMISN  172 (384)
T ss_dssp             HHHHHHHSSSCEEEEEETTHHHHH-----------------------STTSHHHHHHHHTSS--------SCEEEEEECS
T ss_pred             HHHHHHhccCCCEEEEECHHHhcc-----------------------CCCCceeHHHHhcCC--------cceEEEEEEC
Confidence            222222222 33999999998853                       111122 33333322        3588889998


Q ss_pred             CC---CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          152 HK---ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       152 ~~---~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      .+   ..+++++.+  ||...|+|+.|+.++...++..++.
T Consensus       173 ~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~  211 (384)
T 2qby_B          173 DINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAE  211 (384)
T ss_dssp             STTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHH
T ss_pred             CCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHH
Confidence            76   678999998  8877999999999999999998774

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=99.66  E-value=1.7e-16  Score=144.39  Aligned_cols=158  Identities=17%  Similarity=0.284  Sum_probs=109.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccCh-------hhHHHHHHHcc-cCCeeeeecchhhHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGN-------NDLRHILIATE-NKSILVVEDIDCCIEL   97 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~-------~~l~~~~~~~~-~~~vl~iDeid~l~~~   97 (266)
                      ..+++||||||||||++++++++.+     +.+++.+++..+...       .....+..... .+.||||||++.+...
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~~  209 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGK  209 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSSC
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccCC
Confidence            4679999999999999999999988     888999988765321       01112222334 6899999999987531


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC---CcccccCCCcce--eEEEc
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER---LDPALLRPGRMD--MHINM  172 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~---ld~al~r~~Rf~--~~i~~  172 (266)
                                               ......++..++.....  ...+||+|.+.+..   ++++|++  ||.  ..+.+
T Consensus       210 -------------------------~~~q~~l~~~l~~l~~~--~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l  260 (440)
T 2z4s_A          210 -------------------------TGVQTELFHTFNELHDS--GKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKL  260 (440)
T ss_dssp             -------------------------HHHHHHHHHHHHHHHTT--TCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCBC
T ss_pred             -------------------------hHHHHHHHHHHHHHHHC--CCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEEe
Confidence                                     01223344444433322  34566655565654   7899999  885  78999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          173 SHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       173 ~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.|+.+++..|+..++...+..+. +.+..++.....+++++.+++
T Consensus       261 ~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~~L  306 (440)
T 2z4s_A          261 EPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAI  306 (440)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            999999999999988865444443 334555666677888877766

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=99.66  E-value=3e-16  Score=130.36  Aligned_cols=157  Identities=13%  Similarity=0.140  Sum_probs=104.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC---CcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARA  106 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~  106 (266)
                      .+.+++|+||||||||+++++++..+.   .+++.+++..+...  +...+.....+.+|+|||++.+....        
T Consensus        51 ~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~vliiDe~~~~~~~~--------  120 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASI--STALLEGLEQFDLICIDDVDAVAGHP--------  120 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGGGS--CGGGGTTGGGSSEEEEETGGGGTTCH--------
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHH--HHHHHHhccCCCEEEEeccccccCCH--------
Confidence            456899999999999999999999874   77888888765421  12223334568999999999874310        


Q ss_pred             cCCccccccccccccchhhhhhhhhhhhccccCCCCce-EEEEecCCCC---CCcccccCCCcce--eEEEcCCCCHHHH
Q 024550          107 ANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDER-IIIFTTNHKE---RLDPALLRPGRMD--MHINMSHCTPSGF  180 (266)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~-ivi~ttn~~~---~ld~al~r~~Rf~--~~i~~~~p~~~~~  180 (266)
                                       .....++..++.....  ... +|++++..+.   .+++++.+  ||.  ..++++.|+.+++
T Consensus       121 -----------------~~~~~l~~~l~~~~~~--~~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~  179 (242)
T 3bos_A          121 -----------------LWEEAIFDLYNRVAEQ--KRGSLIVSASASPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEK  179 (242)
T ss_dssp             -----------------HHHHHHHHHHHHHHHH--CSCEEEEEESSCTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGH
T ss_pred             -----------------HHHHHHHHHHHHHHHc--CCCeEEEEcCCCHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHH
Confidence                             0122333443333221  223 4444544444   45688888  875  8899999999999


Q ss_pred             HHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          181 KMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       181 ~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+++..++...+..+.. .+..++.....+.+++.+.+
T Consensus       180 ~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l  217 (242)
T 3bos_A          180 LAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVL  217 (242)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence            99999988765554443 34455555556666666654

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.64  E-value=2.3e-15  Score=133.57  Aligned_cols=162  Identities=15%  Similarity=0.091  Sum_probs=105.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChh----------------------h-HHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNN----------------------D-LRHIL   77 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~----------------------~-l~~~~   77 (266)
                      .+.+++|+||||||||++++++++.+         +.+++.+++....+..                      . +..++
T Consensus        43 ~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~  122 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLV  122 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHH
Confidence            45679999999999999999999988         7889999987654321                      1 12222


Q ss_pred             HHc---ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-
Q 024550           78 IAT---ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-  153 (266)
Q Consensus        78 ~~~---~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-  153 (266)
                      ...   ..+++|+|||+|.+....                      .....+..+++.+.....  +.++.+|++||.+ 
T Consensus       123 ~~l~~~~~~~vlilDEi~~l~~~~----------------------~~~~~l~~l~~~~~~~~~--~~~~~~I~~t~~~~  178 (387)
T 2v1u_A          123 KRLSRLRGIYIIVLDEIDFLPKRP----------------------GGQDLLYRITRINQELGD--RVWVSLVGITNSLG  178 (387)
T ss_dssp             HHHTTSCSEEEEEEETTTHHHHST----------------------THHHHHHHHHHGGGCC-------CEEEEECSCST
T ss_pred             HHHhccCCeEEEEEccHhhhcccC----------------------CCChHHHhHhhchhhcCC--CceEEEEEEECCCc
Confidence            222   236799999999985410                      012344444444432210  2468899999877 


Q ss_pred             --CCCcccccCCCccee-EEEcCCCCHHHHHHHHHHhhCC--CCCCcH-HHHHHHhhcC---CCCHHHHHHHH
Q 024550          154 --ERLDPALLRPGRMDM-HINMSHCTPSGFKMLASNYLGI--AEHPLF-VEIEKLIATA---KVTPADVAEQL  217 (266)
Q Consensus       154 --~~ld~al~r~~Rf~~-~i~~~~p~~~~~~~i~~~~~~~--~~~~~~-~~~~~l~~~~---~~s~~~i~~~l  217 (266)
                        ..+++++.+  ||.. .+.|+.|+.+++..++..++..  .+.... ..+..++...   ..++..+.+++
T Consensus       179 ~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l  249 (387)
T 2v1u_A          179 FVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLL  249 (387)
T ss_dssp             TSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHH
T ss_pred             hHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHH
Confidence              778899999  8875 8999999999999999988753  222222 2223333332   26666655554

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.62  E-value=1.2e-14  Score=133.21  Aligned_cols=121  Identities=20%  Similarity=0.228  Sum_probs=86.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccC---hhhHHHHHHHcc--cCCeeeeecchhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLG---NNDLRHILIATE--NKSILVVEDIDCC   94 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~---~~~l~~~~~~~~--~~~vl~iDeid~l   94 (266)
                      ...++||+||||||||++++++|..+          +.+++.+++.....   ...+..+|....  .++|||||     
T Consensus       200 ~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~~~~g~~e~~~~~~~~~~~~~~~~iLfiD-----  274 (468)
T 3pxg_A          200 TKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID-----  274 (468)
T ss_dssp             SSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------CTTHHHHHHHHHTCCCCEEEEC-----
T ss_pred             CCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCccccchHHHHHHHHHHHHHhcCCeEEEEe-----
Confidence            45679999999999999999999997          78888888762211   234566665543  57899999     


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccCCCcceeE
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLRPGRMDMH  169 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r~~Rf~~~  169 (266)
                      ..                          ....+.|+..|+.      ..+.+|++||.+.     .++++|.+  ||. .
T Consensus       275 ~~--------------------------~~a~~~L~~~L~~------g~v~vI~at~~~e~~~~~~~~~al~~--Rf~-~  319 (468)
T 3pxg_A          275 AA--------------------------IDASNILKPSLAR------GELQCIGATTLDEYRKYIEKDAALER--RFQ-P  319 (468)
T ss_dssp             C----------------------------------CCCTTS------SSCEEEEECCTTTTHHHHTTCSHHHH--SEE-E
T ss_pred             Cc--------------------------hhHHHHHHHhhcC------CCEEEEecCCHHHHHHHhhcCHHHHH--hCc-c
Confidence            10                          0122334444432      4588999999887     68999999  997 4


Q ss_pred             EEcCCCCHHHHHHHHHHhhCC
Q 024550          170 INMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       170 i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      |.|+.|+.+++..|++.+...
T Consensus       320 i~v~~p~~e~~~~iL~~~~~~  340 (468)
T 3pxg_A          320 IQVDQPSVDESIQILQGLRDR  340 (468)
T ss_dssp             EECCCCCHHHHHHHHHHTTTT
T ss_pred             ceeCCCCHHHHHHHHHHHHHH
Confidence            999999999999999988866

>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=99.62  E-value=6.7e-15  Score=127.66  Aligned_cols=150  Identities=16%  Similarity=0.211  Sum_probs=107.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccChhhHHHHHHHc--------c-cCCeeeeecchhhHHHhH
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLGNNDLRHILIAT--------E-NKSILVVEDIDCCIELQD   99 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~~~~l~~~~~~~--------~-~~~vl~iDeid~l~~~~~   99 (266)
                      +|||||||||||++++++++.+     +.+++.+++....+...+...+...        . .+.|++|||+|.+..   
T Consensus        45 ~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~---  121 (323)
T 1sxj_B           45 MIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA---  121 (323)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH---
T ss_pred             EEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCH---
Confidence            9999999999999999999986     4568888887654444454444321        2 368999999998742   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                              ...+.|+..++..    +...++|.+||.+..+++++.+  ||. .+.|+.|+.++
T Consensus       122 ------------------------~~~~~L~~~le~~----~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~  170 (323)
T 1sxj_B          122 ------------------------GAQQALRRTMELY----SNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDED  170 (323)
T ss_dssp             ------------------------HHHHTTHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHH
T ss_pred             ------------------------HHHHHHHHHHhcc----CCCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHH
Confidence                                    1234455555542    2457788888999999999999  875 79999999999


Q ss_pred             HHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCHHHHHHHH
Q 024550          180 FKMLASNYLGIAEHPLF-VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       180 ~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ...++..++...+..+. ..+..++...+.+++.+.+.+
T Consensus       171 ~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~a~~~l  209 (323)
T 1sxj_B          171 VLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNL  209 (323)
T ss_dssp             HHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999988765544443 334455555556666655554

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=99.61  E-value=1.5e-14  Score=126.92  Aligned_cols=150  Identities=19%  Similarity=0.205  Sum_probs=109.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCC---cccChhhHHHHHHHcc-
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELS---NLLGNNDLRHILIATE-   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~---~~~~~~~l~~~~~~~~-   81 (266)
                      .++.+|||||||+|||++++++|+.+.+                        .++.++..   ...+...++.++.... 
T Consensus        23 ~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~~~i~~ir~l~~~~~~  102 (334)
T 1a5t_A           23 GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNE  102 (334)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTS
T ss_pred             cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccccCCCCCHHHHHHHHHHHhh
Confidence            4668999999999999999999998753                        35556553   2223445666665542 


Q ss_pred             -----cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC
Q 024550           82 -----NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL  156 (266)
Q Consensus        82 -----~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l  156 (266)
                           ...|++|||+|.+..                           ...+.|+..++.    ++..+++|.+||.++.+
T Consensus       103 ~~~~~~~kvviIdead~l~~---------------------------~a~naLLk~lEe----p~~~~~~Il~t~~~~~l  151 (334)
T 1a5t_A          103 HARLGGAKVVWVTDAALLTD---------------------------AAANALLKTLEE----PPAETWFFLATREPERL  151 (334)
T ss_dssp             CCTTSSCEEEEESCGGGBCH---------------------------HHHHHHHHHHTS----CCTTEEEEEEESCGGGS
T ss_pred             ccccCCcEEEEECchhhcCH---------------------------HHHHHHHHHhcC----CCCCeEEEEEeCChHhC
Confidence                 357999999998742                           234567777664    34568889999999999


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ++++.+  || ..+.|+.|+.++...++.....    .....+..++...+.+++.+.+.+
T Consensus       152 ~~ti~S--Rc-~~~~~~~~~~~~~~~~L~~~~~----~~~~~~~~l~~~s~G~~r~a~~~l  205 (334)
T 1a5t_A          152 LATLRS--RC-RLHYLAPPPEQYAVTWLSREVT----MSQDALLAALRLSAGSPGAALALF  205 (334)
T ss_dssp             CHHHHT--TS-EEEECCCCCHHHHHHHHHHHCC----CCHHHHHHHHHHTTTCHHHHHHTT
T ss_pred             cHHHhh--cc-eeeeCCCCCHHHHHHHHHHhcC----CCHHHHHHHHHHcCCCHHHHHHHh
Confidence            999999  88 4699999999999998887761    123445556666667777766654

>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=99.61  E-value=5.3e-15  Score=144.78  Aligned_cols=132  Identities=20%  Similarity=0.258  Sum_probs=85.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHHcc---cCCeeee
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIATE---NKSILVV   88 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~~~---~~~vl~i   88 (266)
                      .+.+++|+||||||||++++++|..+          +.+++.+++..+...        ..+..++....   .++||||
T Consensus       190 ~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~I  269 (854)
T 1qvr_A          190 TKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFI  269 (854)
T ss_dssp             SCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEE
T ss_pred             CCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEE
Confidence            45679999999999999999999987          889999998877532        23555555543   5789999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC----CCcccccCCC
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE----RLDPALLRPG  164 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~----~ld~al~r~~  164 (266)
                      ||+|.+.+.....+                   .....+.+...+..      ..+.+|++||.++    .++++|.+  
T Consensus       270 DEi~~l~~~~~~~g-------------------~~~~~~~L~~~l~~------~~i~~I~at~~~~~~~~~~d~aL~r--  322 (854)
T 1qvr_A          270 DELHTVVGAGKAEG-------------------AVDAGNMLKPALAR------GELRLIGATTLDEYREIEKDPALER--  322 (854)
T ss_dssp             CCC--------------------------------------HHHHHT------TCCCEEEEECHHHHHHHTTCTTTCS--
T ss_pred             ecHHHHhccCCccc-------------------hHHHHHHHHHHHhC------CCeEEEEecCchHHhhhccCHHHHh--
Confidence            99999875322110                   01122223333332      3577888888764    47999999  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      ||.. |.|+.|+.+++..|++.++.
T Consensus       323 Rf~~-i~l~~p~~~e~~~iL~~~~~  346 (854)
T 1qvr_A          323 RFQP-VYVDEPTVEETISILRGLKE  346 (854)
T ss_dssp             CCCC-EEECCCCHHHHHHHHHHHHH
T ss_pred             CCce-EEeCCCCHHHHHHHHHhhhh
Confidence            9986 99999999999999986654

>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=99.61  E-value=4.4e-15  Score=129.02  Aligned_cols=151  Identities=16%  Similarity=0.180  Sum_probs=106.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCcccChhhHHHHHH---H-c----ccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNLLGNNDLRHILI---A-T----ENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~~~~~~l~~~~~---~-~----~~~~vl~iDeid~l~~~~~   99 (266)
                      ++|||||||||||++++++++.+.     ..++.+++++..+...+...+.   . .    ..+.|++|||+|.+..   
T Consensus        48 ~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~---  124 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ---  124 (327)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH---
T ss_pred             eEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCchHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCH---
Confidence            499999999999999999999863     3477888765432222222221   1 1    3478999999998742   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                              ...+.|+..++..    +..+.+|++||.+..+++++.+  ||. .+.|+.|+.++
T Consensus       125 ------------------------~~~~~L~~~le~~----~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l~~~~  173 (327)
T 1iqp_A          125 ------------------------DAQQALRRTMEMF----SSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDED  173 (327)
T ss_dssp             ------------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHH
T ss_pred             ------------------------HHHHHHHHHHHhc----CCCCeEEEEeCCccccCHHHHh--hCc-EEEecCCCHHH
Confidence                                    1234455665542    2457888899999999999998  886 79999999999


Q ss_pred             HHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          180 FKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       180 ~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ...++..++...+..... .+..++...+.+++.+.+.+
T Consensus       174 ~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~~~~~l  212 (327)
T 1iqp_A          174 IAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINIL  212 (327)
T ss_dssp             HHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHCCCCHHHHHHHH
Confidence            999999888766655543 34445555556676666554

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=99.61  E-value=1.2e-14  Score=128.74  Aligned_cols=153  Identities=15%  Similarity=0.253  Sum_probs=111.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc-----
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE-----   81 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~-----   81 (266)
                      ++.+||+||||||||++++++++.++.                        .++.++.........+..++....     
T Consensus        38 ~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (373)
T 1jr3_A           38 HHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPAR  117 (373)
T ss_dssp             CSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCCCceEEecccccCCHHHHHHHHHHHhhcccc
Confidence            457999999999999999999998854                        245555443233345666665543     


Q ss_pred             -cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           82 -NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        82 -~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                       .+.|++|||+|.+..                           ...+.|+..++..    +..+++|++|+.+..+.+++
T Consensus       118 ~~~~vliiDe~~~l~~---------------------------~~~~~Ll~~le~~----~~~~~~Il~~~~~~~l~~~l  166 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSR---------------------------HSFNALLKTLEEP----PEHVKFLLATTDPQKLPVTI  166 (373)
T ss_dssp             SSSEEEEEECGGGSCH---------------------------HHHHHHHHHHHSC----CSSEEEEEEESCGGGSCHHH
T ss_pred             CCeEEEEEECcchhcH---------------------------HHHHHHHHHHhcC----CCceEEEEEeCChHhCcHHH
Confidence             357999999998732                           2345566666542    35688888899888899999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+  |+ ..+.|+.|+.++...++..++...+..... .+..++...+.++..+.+.+
T Consensus       167 ~s--r~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G~~r~~~~~l  221 (373)
T 1jr3_A          167 LS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLT  221 (373)
T ss_dssp             HT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSSCHHHHHHHH
T ss_pred             Hh--he-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCCCHHHHHHHH
Confidence            98  87 679999999999999999888665555443 34556666677777776665

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.61  E-value=7.7e-15  Score=129.03  Aligned_cols=151  Identities=18%  Similarity=0.166  Sum_probs=107.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC------CcEEEEeCCcccChhhHHHHH---HHc---------------ccCCeeee
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK------FDVYDLELSNLLGNNDLRHIL---IAT---------------ENKSILVV   88 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~------~~~~~i~~~~~~~~~~l~~~~---~~~---------------~~~~vl~i   88 (266)
                      ++|||||||||||++++++++.++      ..++.+++++..+...+...+   ...               ..+.||+|
T Consensus        60 ~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlii  139 (353)
T 1sxj_D           60 HMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIIL  139 (353)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEE
Confidence            499999999999999999999864      458888887754433332222   211               23469999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCccee
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDM  168 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~  168 (266)
                      ||+|.+..                           ...+.|+..++..    .....+|.+||.+..+++++.+  ||. 
T Consensus       140 DE~~~l~~---------------------------~~~~~Ll~~le~~----~~~~~~il~~~~~~~l~~~l~s--R~~-  185 (353)
T 1sxj_D          140 DEADSMTA---------------------------DAQSALRRTMETY----SGVTRFCLICNYVTRIIDPLAS--QCS-  185 (353)
T ss_dssp             TTGGGSCH---------------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--HSE-
T ss_pred             ECCCccCH---------------------------HHHHHHHHHHHhc----CCCceEEEEeCchhhCcchhhc--cCc-
Confidence            99998743                           1234456666543    2346677788999999999999  985 


Q ss_pred             EEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          169 HINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       169 ~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+.|+.|+.++...++...+...+..+.. .+..++.....+++.+.+.+
T Consensus       186 ~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l  235 (353)
T 1sxj_D          186 KFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLL  235 (353)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHH
T ss_pred             eEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            79999999999999999888666555443 34555555556666665555

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.59  E-value=1.3e-15  Score=121.42  Aligned_cols=121  Identities=23%  Similarity=0.302  Sum_probs=80.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHH---cccCCeee
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIA---TENKSILV   87 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~---~~~~~vl~   87 (266)
                      ..+.+++|+||||||||+++++++..+          +.+++.+++..+...        ..+..++..   ...+.+|+
T Consensus        41 ~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~  120 (187)
T 2p65_A           41 RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMF  120 (187)
T ss_dssp             SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEE
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEE
Confidence            345679999999999999999999987          778888877654311        123333333   23568999


Q ss_pred             eecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccC
Q 024550           88 VEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLR  162 (266)
Q Consensus        88 iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r  162 (266)
                      |||+|.+......                  ........+.+...++.      ..+++|++||.+.     .+++++.+
T Consensus       121 iDe~~~l~~~~~~------------------~~~~~~~~~~l~~~~~~------~~~~ii~~~~~~~~~~~~~~~~~l~~  176 (187)
T 2p65_A          121 IDEIHTVVGAGAV------------------AEGALDAGNILKPMLAR------GELRCIGATTVSEYRQFIEKDKALER  176 (187)
T ss_dssp             ETTGGGGSSSSSS------------------CTTSCCTHHHHHHHHHT------TCSCEEEEECHHHHHHHTTTCHHHHH
T ss_pred             EeCHHHhcccccc------------------cccchHHHHHHHHHHhc------CCeeEEEecCHHHHHHHHhccHHHHH
Confidence            9999988531100                  00011222333333332      4578888888764     68999999


Q ss_pred             CCcceeEEEcCCCC
Q 024550          163 PGRMDMHINMSHCT  176 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~  176 (266)
                        ||.. |+++.|+
T Consensus       177 --R~~~-i~i~~p~  187 (187)
T 2p65_A          177 --RFQQ-ILVEQPS  187 (187)
T ss_dssp             --HEEE-EECCSCC
T ss_pred             --hcCc-ccCCCCC
Confidence              9985 9999886

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.58  E-value=3e-14  Score=126.69  Aligned_cols=156  Identities=15%  Similarity=0.060  Sum_probs=104.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcccChhh--------------------------HHHHHHHccc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNLLGNND--------------------------LRHILIATEN   82 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~~~~~~--------------------------l~~~~~~~~~   82 (266)
                      .++|+||||||||+++++++..+    +..++.+++....+...                          +...+.....
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~  125 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDL  125 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCC
Confidence            79999999999999999999998    67888999776543211                          1111222234


Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC---CCCccc
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK---ERLDPA  159 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~---~~ld~a  159 (266)
                      +.||+|||++.+.                           ...+..|+..++........++.+|++||.+   ..+++.
T Consensus       126 ~~vlilDE~~~l~---------------------------~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~  178 (389)
T 1fnn_A          126 YMFLVLDDAFNLA---------------------------PDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPS  178 (389)
T ss_dssp             CEEEEEETGGGSC---------------------------HHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHH
T ss_pred             eEEEEEECccccc---------------------------hHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHH
Confidence            7799999999772                           1234444455443221001357888888887   677888


Q ss_pred             ccCCCccee-EEEcCCCCHHHHHHHHHHhhCC--CCCCc-HHHHHHHhhcC---------CCCHHHHHHHH
Q 024550          160 LLRPGRMDM-HINMSHCTPSGFKMLASNYLGI--AEHPL-FVEIEKLIATA---------KVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~-~i~~~~p~~~~~~~i~~~~~~~--~~~~~-~~~~~~l~~~~---------~~s~~~i~~~l  217 (266)
                      +.+  ||.. .+.|+.++.++...++...+..  ....+ ...+..++...         ...+..+.+.+
T Consensus       179 ~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l  247 (389)
T 1fnn_A          179 TRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDIL  247 (389)
T ss_dssp             HHH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHH
T ss_pred             hhh--cCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHH
Confidence            888  8875 7999999999999999887753  11122 23344444443         46666666655

>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=99.58  E-value=1.5e-14  Score=127.10  Aligned_cols=128  Identities=22%  Similarity=0.285  Sum_probs=82.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCC---------------------------------cEEEEeCCcc----cChhhH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKF---------------------------------DVYDLELSNL----LGNNDL   73 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~---------------------------------~~~~i~~~~~----~~~~~l   73 (266)
                      ..++|||||||||||++|+++++.++.                                 +++.+.....    .+...+
T Consensus        45 ~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~  124 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDI  124 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECH
T ss_pred             CceEEEECCCCccHHHHHHHHHHhCccccccccccccccccccccchhhhhccccccCCCcccccCCCcchhhheeechh
Confidence            346999999999999999999998863                                 1222211110    011011


Q ss_pred             HHHHHHc-----------ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc---ccC
Q 024550           74 RHILIAT-----------ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL---WSS  139 (266)
Q Consensus        74 ~~~~~~~-----------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---~~~  139 (266)
                      ...+...           ..++||||||+|.+..                           ..++.|+..++..   ...
T Consensus       125 ~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~~---------------------------~~~~~Ll~~le~~~~~~~~  177 (350)
T 1g8p_A          125 ERAISKGEKAFEPGLLARANRGYLYIDECNLLED---------------------------HIVDLLLDVAQSGENVVER  177 (350)
T ss_dssp             HHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCH---------------------------HHHHHHHHHHHHSEEEECC
T ss_pred             hhhhcCCceeecCceeeecCCCEEEEeChhhCCH---------------------------HHHHHHHHHHhcCceEEEe
Confidence            2222221           1378999999998753                           1233444444421   000


Q ss_pred             ------CCCceEEEEecCCCC-CCcccccCCCcceeEEEcCCC-CHHHHHHHHHHh
Q 024550          140 ------CGDERIIIFTTNHKE-RLDPALLRPGRMDMHINMSHC-TPSGFKMLASNY  187 (266)
Q Consensus       140 ------~~~~~ivi~ttn~~~-~ld~al~r~~Rf~~~i~~~~p-~~~~~~~i~~~~  187 (266)
                            .+..+++|+|||..+ .++++|++  ||+..++++.| +.+.+..|+.+.
T Consensus       178 ~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~~~~~~il~~~  231 (350)
T 1g8p_A          178 DGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRRR  231 (350)
T ss_dssp             TTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHHH
T ss_pred             cceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHH
Confidence                  012588999999744 89999999  99999999999 677777888764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.56  E-value=5.6e-14  Score=135.96  Aligned_cols=122  Identities=20%  Similarity=0.209  Sum_probs=87.3

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCccc---ChhhHHHHHHHcc--cCCeeeeecchh
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLL---GNNDLRHILIATE--NKSILVVEDIDC   93 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~---~~~~l~~~~~~~~--~~~vl~iDeid~   93 (266)
                      ..+.++|||||||||||++|+++|..+          +.+++.+++..-.   ....+..+|..+.  .++|||||  . 
T Consensus       199 ~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD--~-  275 (758)
T 3pxi_A          199 RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID--A-  275 (758)
T ss_dssp             SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------CTTHHHHHHHHHTCCCCEEEEC--C-
T ss_pred             CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecccccccchHHHHHHHHHHHHHhcCCEEEEEc--C-
Confidence            345689999999999999999999997          7888888772111   1235666666543  58999999  1 


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccCCCccee
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLRPGRMDM  168 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r~~Rf~~  168 (266)
                        .                          ....+.++..++.      ..+.+|++||...     .++++|.|  || .
T Consensus       276 --~--------------------------~~~~~~L~~~l~~------~~v~~I~at~~~~~~~~~~~d~al~r--Rf-~  318 (758)
T 3pxi_A          276 --A--------------------------IDASNILKPSLAR------GELQCIGATTLDEYRKYIEKDAALER--RF-Q  318 (758)
T ss_dssp             ------------------------------------CCCTTS------SSCEEEEECCTTTTHHHHTTCSHHHH--SE-E
T ss_pred             --c--------------------------hhHHHHHHHHHhc------CCEEEEeCCChHHHHHHhhccHHHHh--hC-c
Confidence              0                          0122334444442      4688999999887     78999999  99 5


Q ss_pred             EEEcCCCCHHHHHHHHHHhhCC
Q 024550          169 HINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       169 ~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      .|.|+.|+.+++..|++.+...
T Consensus       319 ~i~v~~p~~~~~~~il~~~~~~  340 (758)
T 3pxi_A          319 PIQVDQPSVDESIQILQGLRDR  340 (758)
T ss_dssp             EEECCCCCHHHHHHHHHHTTTT
T ss_pred             EEEeCCCCHHHHHHHHHHHHHH
Confidence            6999999999999999987765

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.56  E-value=2.1e-14  Score=127.17  Aligned_cols=132  Identities=17%  Similarity=0.246  Sum_probs=92.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc------CCcEEEEeCCcccC----------------------hhh-HHHH---H
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL------KFDVYDLELSNLLG----------------------NND-LRHI---L   77 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~------~~~~~~i~~~~~~~----------------------~~~-l~~~---~   77 (266)
                      .+..++|+||||||||++++.+++.+      +.+++.+++.....                      ... +..+   +
T Consensus        44 ~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l  123 (386)
T 2qby_A           44 KPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAV  123 (386)
T ss_dssp             CCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHH
Confidence            35679999999999999999999988      88899988653221                      111 1122   2


Q ss_pred             HHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC---C
Q 024550           78 IATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK---E  154 (266)
Q Consensus        78 ~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~---~  154 (266)
                      .....+.||+|||++.+..                       ......+..++..++..   ...++.+|++||.+   .
T Consensus       124 ~~~~~~~vlilDE~~~l~~-----------------------~~~~~~l~~l~~~~~~~---~~~~~~~I~~~~~~~~~~  177 (386)
T 2qby_A          124 RDYGSQVVIVLDEIDAFVK-----------------------KYNDDILYKLSRINSEV---NKSKISFIGITNDVKFVD  177 (386)
T ss_dssp             HTCCSCEEEEEETHHHHHH-----------------------SSCSTHHHHHHHHHHSC---CC--EEEEEEESCGGGGG
T ss_pred             hccCCeEEEEEcChhhhhc-----------------------cCcCHHHHHHhhchhhc---CCCeEEEEEEECCCChHh
Confidence            2223478999999998853                       11123455555555433   12468888888876   4


Q ss_pred             CCcccccCCCcce-eEEEcCCCCHHHHHHHHHHhhC
Q 024550          155 RLDPALLRPGRMD-MHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       155 ~ld~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      .+++.+.+  ||. ..|.|+.++.++..+++..++.
T Consensus       178 ~~~~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~  211 (386)
T 2qby_A          178 LLDPRVKS--SLSEEEIIFPPYNAEELEDILTKRAQ  211 (386)
T ss_dssp             GCTTHHHH--TTTTEEEEECCCCHHHHHHHHHHHHH
T ss_pred             hhCHHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHH
Confidence            67788888  775 4899999999999999988764

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.56  E-value=7.4e-15  Score=113.54  Aligned_cols=110  Identities=13%  Similarity=0.083  Sum_probs=76.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARA  106 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~  106 (266)
                      .+..+||+||||||||++|++++...   +.+++ ++|..+.........+..+ .+++|||||+|.+..          
T Consensus        23 ~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~~~~~~~~~~a-~~g~l~ldei~~l~~----------   90 (145)
T 3n70_A           23 TDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNAPQLNDFIALA-QGGTLVLSHPEHLTR----------   90 (145)
T ss_dssp             CCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTSSCHHHHHHHH-TTSCEEEECGGGSCH----------
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcchhhhcHHHHc-CCcEEEEcChHHCCH----------
Confidence            34579999999999999999999987   77899 9999887665555555544 568999999998843          


Q ss_pred             cCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-------CCCcccccCCCcce-eEEEcCC
Q 024550          107 ANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-------ERLDPALLRPGRMD-MHINMSH  174 (266)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-------~~ld~al~r~~Rf~-~~i~~~~  174 (266)
                                       .....++..|...    ...+.+|+|||.+       ..+.+.|..  |+. ..|++|.
T Consensus        91 -----------------~~q~~Ll~~l~~~----~~~~~~I~~t~~~~~~~~~~~~~~~~L~~--rl~~~~i~lPp  143 (145)
T 3n70_A           91 -----------------EQQYHLVQLQSQE----HRPFRLIGIGDTSLVELAASNHIIAELYY--CFAMTQIACLP  143 (145)
T ss_dssp             -----------------HHHHHHHHHHHSS----SCSSCEEEEESSCHHHHHHHSCCCHHHHH--HHHHHEEECCC
T ss_pred             -----------------HHHHHHHHHHhhc----CCCEEEEEECCcCHHHHHHcCCCCHHHHH--HhcCCEEeCCC
Confidence                             1234455555332    2346788888864       234555555  543 3466654

>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=99.53  E-value=5.4e-14  Score=119.23  Aligned_cols=128  Identities=16%  Similarity=0.182  Sum_probs=84.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC---CcEEEEeCCcccChhhHHH-HHH-----------------HcccCCeeeee
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLELSNLLGNNDLRH-ILI-----------------ATENKSILVVE   89 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~~~~~~~~~~l~~-~~~-----------------~~~~~~vl~iD   89 (266)
                      +.++||+||||||||++|++++..+.   .+++.++|+.+.. ..+.. +|.                 ....+++||||
T Consensus        29 ~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~-~~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lD  107 (265)
T 2bjv_A           29 DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-NLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLD  107 (265)
T ss_dssp             CSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCH-HHHHHHHHCCC---------CCCCHHHHTTTSEEEEE
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCCh-hHHHHHhcCCcccccccccccccchhhhcCCcEEEEe
Confidence            46799999999999999999999874   6899999998742 22211 111                 11246899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-c------CCCCceEEEEecCCC-------CC
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-S------SCGDERIIIFTTNHK-------ER  155 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~------~~~~~~ivi~ttn~~-------~~  155 (266)
                      |++.+..                           ..+..|+..++... .      .....+.+|+|||.+       ..
T Consensus       108 Ei~~l~~---------------------------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~  160 (265)
T 2bjv_A          108 ELATAPM---------------------------MVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGT  160 (265)
T ss_dssp             SGGGSCH---------------------------HHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTS
T ss_pred             chHhcCH---------------------------HHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCC
Confidence            9998753                           12334455554211 0      011346788899874       34


Q ss_pred             CcccccCCCcce-eEEEcCCCCH--HHHHHHHHHhh
Q 024550          156 LDPALLRPGRMD-MHINMSHCTP--SGFKMLASNYL  188 (266)
Q Consensus       156 ld~al~r~~Rf~-~~i~~~~p~~--~~~~~i~~~~~  188 (266)
                      +.++|.+  ||. ..|.+|....  ++...++.+++
T Consensus       161 ~~~~L~~--Rl~~~~i~lp~L~~R~~di~~l~~~~l  194 (265)
T 2bjv_A          161 FRADLLD--ALAFDVVQLPPLRERESDIMLMAEYFA  194 (265)
T ss_dssp             SCHHHHH--HHCSEEEECCCGGGCHHHHHHHHHHHH
T ss_pred             ccHHHHH--hhcCcEEeCCChhhhhHHHHHHHHHHH
Confidence            6788998  985 4566666654  45566666554

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.53  E-value=1e-13  Score=121.79  Aligned_cols=130  Identities=24%  Similarity=0.328  Sum_probs=93.6

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCC-----cEEEEeCCcccChhhHHHHHHH---c-----ccCCeeeeecchhhHHHhHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKF-----DVYDLELSNLLGNNDLRHILIA---T-----ENKSILVVEDIDCCIELQDR  100 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~-----~~~~i~~~~~~~~~~l~~~~~~---~-----~~~~vl~iDeid~l~~~~~~  100 (266)
                      ++||||||||||++++++|+.+..     .+..+++++..+...++..+..   .     ....|++|||+|.+..    
T Consensus        49 ~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~~~~~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~----  124 (340)
T 1sxj_C           49 LLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN----  124 (340)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH----
T ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCcccccHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCH----
Confidence            999999999999999999998732     4677777654443333333221   1     1368999999998742    


Q ss_pred             HhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHH
Q 024550          101 LSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGF  180 (266)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~  180 (266)
                                             ...+.|+..++..    +....+|.+||.+..+.+++.+  ||. .+.|+.++.++.
T Consensus       125 -----------------------~~~~~L~~~le~~----~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~~~~  174 (340)
T 1sxj_C          125 -----------------------AAQNALRRVIERY----TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQEAI  174 (340)
T ss_dssp             -----------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHH
T ss_pred             -----------------------HHHHHHHHHHhcC----CCCeEEEEEecCccccchhHHh--hce-eEeccCCCHHHH
Confidence                                   1234456666543    2456778889999999999999  885 689999999999


Q ss_pred             HHHHHHhhCCCCCCcHH
Q 024550          181 KMLASNYLGIAEHPLFV  197 (266)
Q Consensus       181 ~~i~~~~~~~~~~~~~~  197 (266)
                      ..++...+...+..+..
T Consensus       175 ~~~l~~~~~~~~~~i~~  191 (340)
T 1sxj_C          175 ERRIANVLVHEKLKLSP  191 (340)
T ss_dssp             HHHHHHHHHTTTCCBCH
T ss_pred             HHHHHHHHHHcCCCCCH
Confidence            98888877555544443

>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=99.53  E-value=2e-14  Score=140.71  Aligned_cols=128  Identities=20%  Similarity=0.341  Sum_probs=95.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChh-------------------hHHHHHHHcccCCeeeee
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNN-------------------DLRHILIATENKSILVVE   89 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~-------------------~l~~~~~~~~~~~vl~iD   89 (266)
                      .++||+||||||||++|++++..+   +.+++.++|+.+....                   .+...+. ...++|||||
T Consensus       589 ~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~s~l~g~~~~~~G~~~~g~l~~~~~-~~~~~vl~lD  667 (854)
T 1qvr_A          589 GSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVR-RRPYSVILFD  667 (854)
T ss_dssp             EEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC--------------CHHHHHH-HCSSEEEEES
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHHHHHcCCCCCCcCccccchHHHHHH-hCCCeEEEEe
Confidence            469999999999999999999998   7899999998775421                   1122221 1346899999


Q ss_pred             cchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCCC---------
Q 024550           90 DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNHK---------  153 (266)
Q Consensus        90 eid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~~---------  153 (266)
                      |++.+.                           ..+++.|+..|+...-..       -.+++||+|||..         
T Consensus       668 Ei~~l~---------------------------~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~  720 (854)
T 1qvr_A          668 EIEKAH---------------------------PDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQ  720 (854)
T ss_dssp             SGGGSC---------------------------HHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHH
T ss_pred             cccccC---------------------------HHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhcc
Confidence            999763                           235566777776332111       1357899999972         


Q ss_pred             -----------------CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          154 -----------------ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       154 -----------------~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                                       ..+.++|+.  ||+..+.|+.|+.+++..|+..++.
T Consensus       721 ~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~pl~~edi~~i~~~~l~  771 (854)
T 1qvr_A          721 KGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLS  771 (854)
T ss_dssp             TTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCCCCCHHHHHHHHHHHHH
Confidence                             346678888  9998999999999999999988875

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.53  E-value=8.7e-14  Score=122.54  Aligned_cols=150  Identities=13%  Similarity=0.164  Sum_probs=102.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCC-----------------------------cEEEEeCCcccChh--hHHHHHHH---
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKF-----------------------------DVYDLELSNLLGNN--DLRHILIA---   79 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~-----------------------------~~~~i~~~~~~~~~--~l~~~~~~---   79 (266)
                      ++|+||+|||||++++++++.+..                             .++.++........  .+...+..   
T Consensus        39 ~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  118 (354)
T 1sxj_E           39 LLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQ  118 (354)
T ss_dssp             EEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECSSEEEECCC----CCHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceeeeecccceEEecHhhcCCcchHHHHHHHHHHHH
Confidence            999999999999999999996421                             13334333221111  23343332   


Q ss_pred             -------------cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEE
Q 024550           80 -------------TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERII  146 (266)
Q Consensus        80 -------------~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~iv  146 (266)
                                   ..++.|++|||++.+..                           ...+.++..++..    ..+..+
T Consensus       119 ~~~~~~~~~ls~l~~~~~vlilDE~~~L~~---------------------------~~~~~L~~~le~~----~~~~~~  167 (354)
T 1sxj_E          119 MEQVDFQDSKDGLAHRYKCVIINEANSLTK---------------------------DAQAALRRTMEKY----SKNIRL  167 (354)
T ss_dssp             TTC------------CCEEEEEECTTSSCH---------------------------HHHHHHHHHHHHS----TTTEEE
T ss_pred             hccccccccccccCCCCeEEEEeCccccCH---------------------------HHHHHHHHHHHhh----cCCCEE
Confidence                         12456999999998632                           2334556666543    235788


Q ss_pred             EEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH--HHHHHHhhcCCCCHHHHHHHH
Q 024550          147 IFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF--VEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       147 i~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~--~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      |.+||.+..+.+++.+  || ..+.|+.|+.+++..++.......+..+.  ..+..++...+.+++++.+.+
T Consensus       168 Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          168 IMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             EEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             EEEeCCHHHHHHHHHh--hc-eEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence            8899999999999999  88 77999999999999999988866554443  344555565667777777766

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.52  E-value=6.1e-14  Score=135.70  Aligned_cols=135  Identities=24%  Similarity=0.322  Sum_probs=92.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccC--------hhhHHHHHHHcc--cCCeeee
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLG--------NNDLRHILIATE--NKSILVV   88 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~--------~~~l~~~~~~~~--~~~vl~i   88 (266)
                      ..+.++||+||||||||++++++|..+          +..++.+++..+..        ...+..++....  .++||||
T Consensus       205 ~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~I  284 (758)
T 1r6b_X          205 RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFI  284 (758)
T ss_dssp             SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEE
T ss_pred             cCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEE
Confidence            346789999999999999999999987          66788877766542        234566666554  3799999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC-----CCcccccCC
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE-----RLDPALLRP  163 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~-----~ld~al~r~  163 (266)
                      ||+|.+.+.....                  .......    +.+..+...  ..+.+|++||.++     .+|++|.+ 
T Consensus       285 DEi~~l~~~~~~~------------------~~~~~~~----~~L~~~l~~--~~~~~I~at~~~~~~~~~~~d~aL~~-  339 (758)
T 1r6b_X          285 DEIHTIIGAGAAS------------------GGQVDAA----NLIKPLLSS--GKIRVIGSTTYQEFSNIFEKDRALAR-  339 (758)
T ss_dssp             TTTTTTTTSCCSS------------------SCHHHHH----HHHSSCSSS--CCCEEEEEECHHHHHCCCCCTTSSGG-
T ss_pred             echHHHhhcCCCC------------------cchHHHH----HHHHHHHhC--CCeEEEEEeCchHHhhhhhcCHHHHh-
Confidence            9999986411100                  0011112    222222222  4578888888643     46899999 


Q ss_pred             CcceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          164 GRMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       164 ~Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                       ||. .+.|+.|+.+++..|++.+...
T Consensus       340 -Rf~-~i~v~~p~~~e~~~il~~l~~~  364 (758)
T 1r6b_X          340 -RFQ-KIDITEPSIEETVQIINGLKPK  364 (758)
T ss_dssp             -GEE-EEECCCCCHHHHHHHHHHHHHH
T ss_pred             -Cce-EEEcCCCCHHHHHHHHHHHHHH
Confidence             997 6999999999999999876643

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.51  E-value=7.2e-14  Score=121.11  Aligned_cols=158  Identities=16%  Similarity=0.187  Sum_probs=96.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHH-HHHH-----------------HcccCCeeee
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLR-HILI-----------------ATENKSILVV   88 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~-~~~~-----------------~~~~~~vl~i   88 (266)
                      .+.++||+||||||||++|++++...   +.+++.++|..+... .+. .+|.                 ....+++|||
T Consensus        24 ~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~-l~~~~lfg~~~g~~tg~~~~~~g~~~~a~~g~L~L  102 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNES-LLESELFGHEKGAFTGADKRREGRFVEADGGTLFL  102 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHH-HHHHHHTCCCSSCCC---CCCCCHHHHHTTSEEEE
T ss_pred             CCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChH-HHHHHhcCccccccCchhhhhcCHHHhcCCCEEEE
Confidence            35679999999999999999999976   678999999887421 111 1111                 1124689999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-------cCCCCceEEEEecCCC-------C
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-------SSCGDERIIIFTTNHK-------E  154 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-------~~~~~~~ivi~ttn~~-------~  154 (266)
                      |||+.+..                           ..+..|+..++...       ......+.||+|||.+       .
T Consensus       103 DEi~~l~~---------------------------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g  155 (304)
T 1ojl_A          103 DEIGDISP---------------------------LMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAG  155 (304)
T ss_dssp             ESCTTCCH---------------------------HHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHT
T ss_pred             eccccCCH---------------------------HHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhC
Confidence            99998853                           12344555555321       0112347888999875       3


Q ss_pred             CCcccccCCCcce-eEEEcCCCC--HHHHHHHHHHhhCC-------CCCCcHHHHHHHhhcC--CCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMD-MHINMSHCT--PSGFKMLASNYLGI-------AEHPLFVEIEKLIATA--KVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~-~~i~~~~p~--~~~~~~i~~~~~~~-------~~~~~~~~~~~l~~~~--~~s~~~i~~~l  217 (266)
                      .+.+.|..  ||. ..|.+|...  .++...++.+++..       ....+..+....+...  ..+.+++.+.+
T Consensus       156 ~fr~~L~~--Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~~~wpGnvReL~~~l  228 (304)
T 1ojl_A          156 RFRQDLYY--RLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAI  228 (304)
T ss_dssp             SSCHHHHH--HHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHHCCCSSHHHHHHHHH
T ss_pred             CcHHHHHh--hcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHcCCCCCCHHHHHHHH
Confidence            46677887  874 446666655  35555666665532       1223444443333333  34556666655

>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=99.47  E-value=2.1e-13  Score=118.18  Aligned_cols=122  Identities=16%  Similarity=0.261  Sum_probs=95.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc------CCcEEEEeCCc-ccChhhHHHHHHHcc------cCCeeeeecchhhHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL------KFDVYDLELSN-LLGNNDLRHILIATE------NKSILVVEDIDCCIEL   97 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~------~~~~~~i~~~~-~~~~~~l~~~~~~~~------~~~vl~iDeid~l~~~   97 (266)
                      .+.+|||||||+|||++++++|+.+      +..++.+++.. -.+...++.++..+.      ...|++|||+|.+.. 
T Consensus        18 ~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~-   96 (305)
T 2gno_A           18 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ-   96 (305)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH-
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccccCCceEEEeccHHHhCH-
Confidence            4579999999999999999999863      45788888764 334445666665543      246999999998742 


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCH
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTP  177 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~  177 (266)
                                                ...+.|+..|+.    ++...++|.+||.+..+.+++.+  |   .+.|+.|+.
T Consensus        97 --------------------------~a~naLLk~LEe----p~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~  141 (305)
T 2gno_A           97 --------------------------QAANAFLKALEE----PPEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVP  141 (305)
T ss_dssp             --------------------------HHHHHTHHHHHS----CCTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCC
T ss_pred             --------------------------HHHHHHHHHHhC----CCCCeEEEEEECChHhChHHHHc--e---eEeCCCCCH
Confidence                                      234667777774    34568888888999999999999  8   799999999


Q ss_pred             HHHHHHHHHhh
Q 024550          178 SGFKMLASNYL  188 (266)
Q Consensus       178 ~~~~~i~~~~~  188 (266)
                      ++...++....
T Consensus       142 ~~i~~~L~~~~  152 (305)
T 2gno_A          142 KEFRDLVKEKI  152 (305)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99998888776

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.46  E-value=1.3e-13  Score=146.22  Aligned_cols=138  Identities=20%  Similarity=0.327  Sum_probs=96.1

Q ss_pred             CCceeEEecCCCCChHHHH-HHHHHHcCCcEEEEeCCcccChhhHHHHHHHc-----------------ccCCeeeeecc
Q 024550           30 WKRGYLLYGPPGTGKSSLI-AAMANYLKFDVYDLELSNLLGNNDLRHILIAT-----------------ENKSILVVEDI   91 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la-~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~-----------------~~~~vl~iDei   91 (266)
                      .++++||+||||||||++| +.++...+..++.++++..++...++..+...                 ..++|+||||+
T Consensus      1266 ~~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEi 1345 (2695)
T 4akg_A         1266 SKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEI 1345 (2695)
T ss_dssp             HTCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETT
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEeccc
Confidence            3578999999999999999 55555557889999999988877777776542                 12369999999


Q ss_pred             hhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC------CceEEEEecCCCC-----CCcccc
Q 024550           92 DCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG------DERIIIFTTNHKE-----RLDPAL  160 (266)
Q Consensus        92 d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~------~~~ivi~ttn~~~-----~ld~al  160 (266)
                      +....  ++.+                .......+.++++. .+++....      .++.+|||||+|.     .++++|
T Consensus      1346 nmp~~--d~yg----------------~q~~lelLRq~le~-gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rl 1406 (2695)
T 4akg_A         1346 NLPKL--DKYG----------------SQNVVLFLRQLMEK-QGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERF 1406 (2695)
T ss_dssp             TCSCC--CSSS----------------CCHHHHHHHHHHHT-SSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHH
T ss_pred             ccccc--cccC----------------chhHHHHHHHHHhc-CCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhh
Confidence            85321  0000                01112222222211 12222111      2478999999994     799999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                      +|  || ..+.++.|+.+++..|+..++.
T Consensus      1407 lR--rf-~vi~i~~P~~~~l~~I~~~il~ 1432 (2695)
T 4akg_A         1407 TR--HA-AILYLGYPSGKSLSQIYEIYYK 1432 (2695)
T ss_dssp             HT--TE-EEEECCCCTTTHHHHHHHHHHH
T ss_pred             hh--ee-eEEEeCCCCHHHHHHHHHHHHH
Confidence            99  99 6799999999999999887774

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.44  E-value=1.9e-14  Score=135.36  Aligned_cols=129  Identities=20%  Similarity=0.245  Sum_probs=86.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe----CCcccCh---hhH------HHHHHHcccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE----LSNLLGN---NDL------RHILIATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~----~~~~~~~---~~l------~~~~~~~~~~~vl~iDeid~l~~~~~   99 (266)
                      ++||+||||||||++|+++|+.++..++...    +..+...   ...      .........++|+||||||.+..   
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A~~gil~IDEid~l~~---  405 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGEYYLEAGALVLADGGIAVIDEIDKMRD---  405 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECSSGGGTSSCSEEECHHHHHSSSEECCTTTTCCCS---
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceeeeccccccccccCCeeEecCCCcEEeehhhhCCH---
Confidence            7999999999999999999999987665532    2222110   000      00001122579999999998742   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccc---------cCCCCceEEEEecCCCC-------------CCc
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW---------SSCGDERIIIFTTNHKE-------------RLD  157 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~~~~ivi~ttn~~~-------------~ld  157 (266)
                                              ...+.|+..|+...         ...+.++.||+|||++.             .++
T Consensus       406 ------------------------~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~  461 (595)
T 3f9v_A          406 ------------------------EDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLP  461 (595)
T ss_dssp             ------------------------HHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSC
T ss_pred             ------------------------hHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCC
Confidence                                    23344555554221         11134678999999886             889


Q ss_pred             ccccCCCcce-eEEEcCCCCHHHHHHHHHHhhCCC
Q 024550          158 PALLRPGRMD-MHINMSHCTPSGFKMLASNYLGIA  191 (266)
Q Consensus       158 ~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~~~  191 (266)
                      ++|++  ||+ ..+..+.|+.+ ...|.++.+...
T Consensus       462 ~aLl~--RFDl~~~~~~~~~~e-~~~i~~~il~~~  493 (595)
T 3f9v_A          462 PTILS--RFDLIFILKDQPGEQ-DRELANYILDVH  493 (595)
T ss_dssp             SSSGG--GCSCCEEECCTTHHH-HHHHHHHHHTTT
T ss_pred             HHHHh--hCeEEEEeCCCCCHH-HHHHHHHHHHHh
Confidence            99999  997 55666777777 888888777653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.42  E-value=6.2e-14  Score=108.09  Aligned_cols=109  Identities=12%  Similarity=0.031  Sum_probs=73.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPD  110 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~  110 (266)
                      +.++||+||||||||++|++++...+ +++.++|..+.. ......+.. ..+++|||||+|.+..              
T Consensus        27 ~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~-~~~~~~~~~-a~~~~l~lDei~~l~~--------------   89 (143)
T 3co5_A           27 TSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLI-DMPMELLQK-AEGGVLYVGDIAQYSR--------------   89 (143)
T ss_dssp             SSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHH-HCHHHHHHH-TTTSEEEEEECTTCCH--------------
T ss_pred             CCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCCh-HhhhhHHHh-CCCCeEEEeChHHCCH--------------
Confidence            45799999999999999999999888 899999887643 223444444 3478999999998843              


Q ss_pred             cccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-CC----CcccccCCCcce-eEEEcCC
Q 024550          111 FLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-ER----LDPALLRPGRMD-MHINMSH  174 (266)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-~~----ld~al~r~~Rf~-~~i~~~~  174 (266)
                                   ..+..++..++...   ...+.+|+|||.+ ..    +++.|..  |+. ..|++|.
T Consensus        90 -------------~~q~~Ll~~l~~~~---~~~~~iI~~tn~~~~~~~~~~~~~L~~--rl~~~~i~lPp  141 (143)
T 3co5_A           90 -------------NIQTGITFIIGKAE---RCRVRVIASCSYAAGSDGISCEEKLAG--LFSESVVRIPP  141 (143)
T ss_dssp             -------------HHHHHHHHHHHHHT---TTTCEEEEEEEECTTTC--CHHHHHHH--HSSSEEEEECC
T ss_pred             -------------HHHHHHHHHHHhCC---CCCEEEEEecCCCHHHHHhCccHHHHH--HhcCcEEeCCC
Confidence                         12333455555431   2356788888753 33    3344555  543 4566664

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.40  E-value=5.2e-13  Score=122.81  Aligned_cols=128  Identities=17%  Similarity=0.179  Sum_probs=81.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC--CcEEEEeCCcccChhhH-----------HHHHHHcc-----cCCeeeeecch
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK--FDVYDLELSNLLGNNDL-----------RHILIATE-----NKSILVVEDID   92 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~--~~~~~i~~~~~~~~~~l-----------~~~~~~~~-----~~~vl~iDeid   92 (266)
                      +.++||+||||||||++|+++|..++  .++..+.+... +...+           ...+....     .++|||||||+
T Consensus        41 ~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~~-t~~dL~G~~~~~~~~~~g~~~~~~~g~l~~~~IL~IDEI~  119 (500)
T 3nbx_X           41 GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFS-TPEEVFGPLSIQALKDEGRYERLTSGYLPEAEIVFLDEIW  119 (500)
T ss_dssp             TCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTTC-CHHHHHCCBC----------CBCCTTSGGGCSEEEEESGG
T ss_pred             CCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhcC-CHHHhcCcccHHHHhhchhHHhhhccCCCcceeeeHHhHh
Confidence            45799999999999999999999884  35555555421 11111           11121111     35689999998


Q ss_pred             hhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcc-------ccCCCCceEEEEecCCC-C--CCcccccC
Q 024550           93 CCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGL-------WSSCGDERIIIFTTNHK-E--RLDPALLR  162 (266)
Q Consensus        93 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-------~~~~~~~~ivi~ttn~~-~--~ld~al~r  162 (266)
                      .+.                           ..+.+.|+..|+..       ....+ ..++|+|||++ +  .+.+++++
T Consensus       120 r~~---------------------------~~~q~~LL~~lee~~v~i~G~~~~~~-~~~iI~ATN~lpe~~~~~~aLld  171 (500)
T 3nbx_X          120 KAG---------------------------PAILNTLLTAINERQFRNGAHVEKIP-MRLLVAASNELPEADSSLEALYD  171 (500)
T ss_dssp             GCC---------------------------HHHHHHHHHHHHSSEEECSSSEEECC-CCEEEEEESSCCCTTCTTHHHHT
T ss_pred             hhc---------------------------HHHHHHHHHHHHHHhccCCCCcCCcc-hhhhhhccccCCCccccHHHHHH
Confidence            653                           22445566666421       11112 23567777753 2  23459999


Q ss_pred             CCcceeEEEcCCCCH-HHHHHHHHHhhC
Q 024550          163 PGRMDMHINMSHCTP-SGFKMLASNYLG  189 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~-~~~~~i~~~~~~  189 (266)
                        ||...|.++.|+. +++..|+.....
T Consensus       172 --RF~~~i~v~~p~~~ee~~~IL~~~~~  197 (500)
T 3nbx_X          172 --RMLIRLWLDKVQDKANFRSMLTSQQD  197 (500)
T ss_dssp             --TCCEEEECCSCCCHHHHHHHHTCCCC
T ss_pred             --HHHHHHHHHHhhhhhhHHHHHhcccc
Confidence              9999999999997 678888886653

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.26  E-value=3.4e-11  Score=107.73  Aligned_cols=163  Identities=10%  Similarity=0.094  Sum_probs=100.0

Q ss_pred             CceeEE--ecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcccChh----------------------h----H
Q 024550           31 KRGYLL--YGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLLGNN----------------------D----L   73 (266)
Q Consensus        31 ~~~iLl--~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~~~~----------------------~----l   73 (266)
                      +..++|  +||||+|||++++.+++.+         +..++.+++....+..                      .    +
T Consensus        50 ~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l  129 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKAL  129 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHH
Confidence            457999  9999999999999999876         4567778764322111                      1    1


Q ss_pred             HHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC--CceEEEEecC
Q 024550           74 RHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG--DERIIIFTTN  151 (266)
Q Consensus        74 ~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~--~~~ivi~ttn  151 (266)
                      ...+.....+.+|+|||++.+....                     ......+..++..+.... ..+  .++.+|++|+
T Consensus       130 ~~~l~~~~~~~llvlDe~~~l~~~~---------------------~~~~~~l~~l~~~~~~~~-~~~~~~~v~lI~~~~  187 (412)
T 1w5s_A          130 VDNLYVENHYLLVILDEFQSMLSSP---------------------RIAAEDLYTLLRVHEEIP-SRDGVNRIGFLLVAS  187 (412)
T ss_dssp             HHHHHHHTCEEEEEEESTHHHHSCT---------------------TSCHHHHHHHHTHHHHSC-CTTSCCBEEEEEEEE
T ss_pred             HHHHHhcCCeEEEEEeCHHHHhhcc---------------------CcchHHHHHHHHHHHhcc-cCCCCceEEEEEEec
Confidence            1122222357899999999884200                     011234444445444321 012  4678888887


Q ss_pred             CCC---CCc---ccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCC---CCCcHHHHHHHhhcCC------CCHHHHHHH
Q 024550          152 HKE---RLD---PALLRPGRMDMHINMSHCTPSGFKMLASNYLGIA---EHPLFVEIEKLIATAK------VTPADVAEQ  216 (266)
Q Consensus       152 ~~~---~ld---~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~---~~~~~~~~~~l~~~~~------~s~~~i~~~  216 (266)
                      .++   .++   +.+.+  +|...+.++.++.++..+++...+...   .......+..+....+      ..|..+..+
T Consensus       188 ~~~~~~~l~~~~~~~~~--~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G~p~~~~~l  265 (412)
T 1w5s_A          188 DVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVA  265 (412)
T ss_dssp             ETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHH
T ss_pred             cccHHHHHhhhcchhhh--hcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCCcHHHHHHH
Confidence            654   334   56667  665569999999999999997665321   1112334455555555      677766655


Q ss_pred             H
Q 024550          217 L  217 (266)
Q Consensus       217 l  217 (266)
                      +
T Consensus       266 ~  266 (412)
T 1w5s_A          266 L  266 (412)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=99.20  E-value=5.8e-12  Score=100.44  Aligned_cols=70  Identities=21%  Similarity=0.337  Sum_probs=48.2

Q ss_pred             HhCCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcccCh-------hhHHHHHHHcccCCeeeeecchh
Q 024550           25 RVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNLLGN-------NDLRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        25 ~~~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~~~~-------~~l~~~~~~~~~~~vl~iDeid~   93 (266)
                      .+..+.+.+++|+||||||||+++++++..+    |..++.+++..+...       ......+....++.+|+|||++.
T Consensus        32 ~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~  111 (180)
T 3ec2_A           32 NFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLIFRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGS  111 (180)
T ss_dssp             SCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHHHHHHHHHHHHTCCSHHHHHHHTCSEEEEETCSS
T ss_pred             hccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHhcCchHHHHHHHhcCCCEEEEeCCCC
Confidence            3445556789999999999999999999877    556666665443210       00112334445789999999984


Q ss_pred             h
Q 024550           94 C   94 (266)
Q Consensus        94 l   94 (266)
                      .
T Consensus       112 ~  112 (180)
T 3ec2_A          112 E  112 (180)
T ss_dssp             S
T ss_pred             C
Confidence            3

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=99.17  E-value=9.9e-11  Score=94.70  Aligned_cols=62  Identities=19%  Similarity=0.297  Sum_probs=42.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhh
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      ++|..+++|||||||||||+++.++|+.++..++.+.-+.  .  .  -.+.......+++|||+|.-
T Consensus        54 ~iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~fans~--s--~--f~l~~l~~~kIiiLDEad~~  115 (212)
T 1tue_A           54 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNST--S--H--FWLEPLTDTKVAMLDDATTT  115 (212)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCSS--S--C--GGGGGGTTCSSEEEEEECHH
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeEEecc--c--h--hhhcccCCCCEEEEECCCch
Confidence            5666678999999999999999999999976554321111  0  0  01122234569999999843

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=99.16  E-value=7e-11  Score=91.56  Aligned_cols=59  Identities=17%  Similarity=0.162  Sum_probs=47.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~   95 (266)
                      +...++|+||+|+|||+++++++..+   |...+.++...+...       ....++.+|+|||++.+.
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~-------~~~~~~~lLilDE~~~~~   96 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLT-------DAAFEAEYLAVDQVEKLG   96 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCC-------GGGGGCSEEEEESTTCCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHH-------HHHhCCCEEEEeCccccC
Confidence            45679999999999999999999988   667888888776543       113468999999999753

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.10  E-value=7.5e-11  Score=95.54  Aligned_cols=63  Identities=25%  Similarity=0.405  Sum_probs=45.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-------hhhHHHHHHHcccCCeeeeecchhh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-------NNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-------~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      .+++|+||||||||+++++++..+   +.+++.+++..+..       ...+...+.......+|+|||++..
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDei~~~  127 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAE  127 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHHHHHHHHC---CCCHHHHHHHHHSSEEEEEEECCC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            789999999999999999999988   67777777654321       1112233344445679999999764

>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=99.07  E-value=3e-09  Score=92.82  Aligned_cols=155  Identities=17%  Similarity=0.131  Sum_probs=90.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc-----cC-------------------------------------
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL-----LG-------------------------------------   69 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~-----~~-------------------------------------   69 (266)
                      +.++|+||+|+|||++++.+++..+...+.+++...     .+                                     
T Consensus        31 ~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~  110 (357)
T 2fna_A           31 PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGN  110 (357)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSS
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchhhccccCCCHHHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecce
Confidence            479999999999999999999998777777776532     11                                     


Q ss_pred             ----------hhhHHHHHH---Hcc-cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhc
Q 024550           70 ----------NNDLRHILI---ATE-NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDG  135 (266)
Q Consensus        70 ----------~~~l~~~~~---~~~-~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~  135 (266)
                                ...+..++.   ... .+.+|+|||++.+..                       ......+..+-..++.
T Consensus       111 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~-----------------------~~~~~~~~~l~~~~~~  167 (357)
T 2fna_A          111 EIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVK-----------------------LRGVNLLPALAYAYDN  167 (357)
T ss_dssp             SEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGG-----------------------CTTCCCHHHHHHHHHH
T ss_pred             EEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhc-----------------------cCchhHHHHHHHHHHc
Confidence                      011222222   222 378999999998742                       0001111111111221


Q ss_pred             cccCCCCceEEEEecCCCC---------CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcC
Q 024550          136 LWSSCGDERIIIFTTNHKE---------RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATA  206 (266)
Q Consensus       136 ~~~~~~~~~ivi~ttn~~~---------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~  206 (266)
                      .     .++.+|.|+....         .....+.  ||+...+.++.++.++..+++...+...+...... ..+....
T Consensus       168 ~-----~~~~~i~~g~~~~~l~~~l~~~~~~~~l~--~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~-~~i~~~t  239 (357)
T 2fna_A          168 L-----KRIKFIMSGSEMGLLYDYLRVEDPESPLF--GRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY-EVVYEKI  239 (357)
T ss_dssp             C-----TTEEEEEEESSHHHHHHHTTTTCTTSTTT--TCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH-HHHHHHH
T ss_pred             C-----CCeEEEEEcCchHHHHHHHhccCCCCccc--cCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcH-HHHHHHh
Confidence            1     2355555554321         1112233  36667899999999999999987764322222121 5566666


Q ss_pred             CCCHHHHHHHH
Q 024550          207 KVTPADVAEQL  217 (266)
Q Consensus       207 ~~s~~~i~~~l  217 (266)
                      +..|..+..++
T Consensus       240 ~G~P~~l~~~~  250 (357)
T 2fna_A          240 GGIPGWLTYFG  250 (357)
T ss_dssp             CSCHHHHHHHH
T ss_pred             CCCHHHHHHHH
Confidence            77777765544

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.07  E-value=3.7e-10  Score=120.17  Aligned_cols=136  Identities=15%  Similarity=0.161  Sum_probs=97.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcc-cCCeeeeecchhhHHHhHHHhhhhhcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATE-NKSILVVEDIDCCIELQDRLSRARAAN  108 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~-~~~vl~iDeid~l~~~~~~~~~~~~~~  108 (266)
                      ...+.++.||+|||||++++++|+.+|.+++.++|+.-.+...+..+|..+. .++++++|||+.+....-.        
T Consensus       644 ~~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~~~lg~~~~g~~~~Gaw~~~DE~nr~~~evLs--------  715 (2695)
T 4akg_A          644 QKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDEKVLS--------  715 (2695)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCHHHHHHHHHHHHHHTCEEEEETTTSSCHHHHH--------
T ss_pred             hCCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCChhHhhHHHHHHHhcCCEeeehhhhhcChHHHH--------
Confidence            3467899999999999999999999999999999999988888988887765 4899999999987431100        


Q ss_pred             Cccccccccccccchhhhhhhhhhhh---------ccccCCCCceEEEEecCC----CCCCcccccCCCcceeEEEcCCC
Q 024550          109 PDFLIAGYEQQKQYHITLSGLLNFID---------GLWSSCGDERIIIFTTNH----KERLDPALLRPGRMDMHINMSHC  175 (266)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~ll~~l~---------~~~~~~~~~~ivi~ttn~----~~~ld~al~r~~Rf~~~i~~~~p  175 (266)
                                  .....+..+.+.+.         +..-.......+++|.|+    ...||++|.+  || ..|.|..|
T Consensus       716 ------------~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~--~F-r~v~m~~P  780 (2695)
T 4akg_A          716 ------------AVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKK--SF-REFSMKSP  780 (2695)
T ss_dssp             ------------HHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHT--TE-EEEECCCC
T ss_pred             ------------HHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHh--he-EEEEeeCC
Confidence                        00001111112221         110111234567888883    4678999999  88 57999999


Q ss_pred             CHHHHHHHHHHhh
Q 024550          176 TPSGFKMLASNYL  188 (266)
Q Consensus       176 ~~~~~~~i~~~~~  188 (266)
                      +.+...+|+-...
T Consensus       781 d~~~i~ei~l~s~  793 (2695)
T 4akg_A          781 QSGTIAEMILQIM  793 (2695)
T ss_dssp             CHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc
Confidence            9999888854333

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=99.03  E-value=2.7e-10  Score=101.22  Aligned_cols=121  Identities=21%  Similarity=0.264  Sum_probs=80.8

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhh
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRAR  105 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~  105 (266)
                      ++++++..++|+||||+||||++++++...+..++.+....    ......+....+..++++||++.+.....+..   
T Consensus       164 ~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~~~~----~~~~~~lg~~~q~~~~l~dd~~~~~~~~r~l~---  236 (377)
T 1svm_A          164 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPL----DRLNFELGVAIDQFLVVFEDVKGTGGESRDLP---  236 (377)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCT----TTHHHHHGGGTTCSCEEETTCCCSTTTTTTCC---
T ss_pred             cccCCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEeccc----hhHHHHHHHhcchhHHHHHHHHHHHHHHhhcc---
Confidence            47888888999999999999999999999887765533221    12222334445678889999997753100000   


Q ss_pred             hcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCC
Q 024550          106 AANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSH  174 (266)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~  174 (266)
                                   ..........+.+.+++.       +.++.+||+++.+ +++++|||++..+....
T Consensus       237 -------------~~~~~~~~~~l~~~ldG~-------v~v~~~tn~~~~l-~alf~pg~ld~~~~~l~  284 (377)
T 1svm_A          237 -------------SGQGINNLDNLRDYLDGS-------VKVNLEKKHLNKR-TQIFPPGIVTMNEYSVP  284 (377)
T ss_dssp             -------------CCSHHHHHHTTHHHHHCS-------SCEEECCSSSCCE-EECCCCEEEEECSCCCC
T ss_pred             -------------ccCcchHHHHHHHHhcCC-------CeEeeccCchhhH-HHhhcCcccChhHHhhc
Confidence                         000001234556666653       5678889999999 79999999987666644

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=99.03  E-value=7.1e-10  Score=118.76  Aligned_cols=136  Identities=17%  Similarity=0.323  Sum_probs=90.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHH-HcCCcEEEEeCCcccChhhHHHHHHHc-----c-------------cCCeeeeecc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMAN-YLKFDVYDLELSNLLGNNDLRHILIAT-----E-------------NKSILVVEDI   91 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~-~~~~~~~~i~~~~~~~~~~l~~~~~~~-----~-------------~~~vl~iDei   91 (266)
                      .+.+||+||||||||+++..+.. ..+.+++.++++..++...+...+...     .             +..|+||||+
T Consensus      1304 ~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiDDi 1383 (3245)
T 3vkg_A         1304 HRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEI 1383 (3245)
T ss_dssp             TCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEETTT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEeccc
Confidence            56799999999999987765444 446678899999988888887777531     0             1259999999


Q ss_pred             hhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCC------CceEEEEecCCC-----CCCcccc
Q 024550           92 DCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCG------DERIIIFTTNHK-----ERLDPAL  160 (266)
Q Consensus        92 d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~------~~~ivi~ttn~~-----~~ld~al  160 (266)
                      +....  +..+                ....-..+.++++. .+++....      .++.+|+|+|+|     ..++++|
T Consensus      1384 Nmp~~--D~yG----------------tQ~~ielLrqlld~-~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf 1444 (3245)
T 3vkg_A         1384 NLPST--DKYG----------------TQRVITFIRQMVEK-GGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRF 1444 (3245)
T ss_dssp             TCCCC--CTTS----------------CCHHHHHHHHHHHH-SEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHH
T ss_pred             CCCCc--cccc----------------cccHHHHHHHHHHc-CCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHH
Confidence            95321  0000                00111222222221 12222211      356799999988     3589999


Q ss_pred             cCCCcceeEEEcCCCCHHHHHHHHHHhh
Q 024550          161 LRPGRMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       161 ~r~~Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                      +|  ||.. +.++.|+.++...|+..++
T Consensus      1445 ~r--~F~v-i~i~~ps~esL~~If~til 1469 (3245)
T 3vkg_A         1445 LR--HAPI-LLVDFPSTSSLTQIYGTFN 1469 (3245)
T ss_dssp             HT--TCCE-EECCCCCHHHHHHHHHHHH
T ss_pred             Hh--hceE-EEeCCCCHHHHHHHHHHHH
Confidence            99  9955 9999999999999976654

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=99.01  E-value=1.9e-10  Score=99.72  Aligned_cols=64  Identities=33%  Similarity=0.495  Sum_probs=43.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC----CcEEEEeCCcccC-------hhhHHHHHHHcccCCeeeeecchhh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK----FDVYDLELSNLLG-------NNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~----~~~~~i~~~~~~~-------~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      ..+++||||||||||+++.++|..+.    .+++.+++..+..       ...+...+.......+|+|||++..
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~  226 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAE  226 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHHHHHHHCCCC----CCTTHHHHTSSEEEEETCCC-
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            57899999999999999999998664    6777777654321       1111122233345679999999754

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=99.01  E-value=6.7e-10  Score=90.14  Aligned_cols=119  Identities=15%  Similarity=0.140  Sum_probs=75.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHH--------cC-CcEEEEeCCcccC---------------------hhhHHHHHH-Hcc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY--------LK-FDVYDLELSNLLG---------------------NNDLRHILI-ATE   81 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~--------~~-~~~~~i~~~~~~~---------------------~~~l~~~~~-~~~   81 (266)
                      .+|++|+||||||+++..++..        .| .+++..++..+..                     ...+..++. ...
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~   86 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIKKPEN   86 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTTSGGG
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhhcccc
Confidence            4789999999999998886543        34 6676676654421                     012222211 123


Q ss_pred             cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccccc
Q 024550           82 NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALL  161 (266)
Q Consensus        82 ~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~  161 (266)
                      .++||+|||++.+.+.+..                     ... ...++..+..   ....+.-+|.+|+++..|+.++.
T Consensus        87 ~~~vliIDEAq~l~~~~~~---------------------~~e-~~rll~~l~~---~r~~~~~iil~tq~~~~l~~~lr  141 (199)
T 2r2a_A           87 IGSIVIVDEAQDVWPARSA---------------------GSK-IPENVQWLNT---HRHQGIDIFVLTQGPKLLDQNLR  141 (199)
T ss_dssp             TTCEEEETTGGGTSBCCCT---------------------TCC-CCHHHHGGGG---TTTTTCEEEEEESCGGGBCHHHH
T ss_pred             CceEEEEEChhhhccCccc---------------------cch-hHHHHHHHHh---cCcCCeEEEEECCCHHHHhHHHH
Confidence            4899999999988531100                     000 0123333332   22345677888888999999999


Q ss_pred             CCCcceeEEEcCCCCHH
Q 024550          162 RPGRMDMHINMSHCTPS  178 (266)
Q Consensus       162 r~~Rf~~~i~~~~p~~~  178 (266)
                      +  |+...++++.|...
T Consensus       142 ~--ri~~~~~l~~~~~~  156 (199)
T 2r2a_A          142 T--LVRKHYHIASNKMG  156 (199)
T ss_dssp             T--TEEEEEEEEECSSC
T ss_pred             H--HhheEEEEcCcccC
Confidence            9  99999999876544

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=98.98  E-value=7e-09  Score=92.00  Aligned_cols=129  Identities=17%  Similarity=0.217  Sum_probs=83.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCc--EEEEeCCcccChhhHHHHHH-----------------HcccCCeeeeecch
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFD--VYDLELSNLLGNNDLRHILI-----------------ATENKSILVVEDID   92 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~--~~~i~~~~~~~~~~l~~~~~-----------------~~~~~~vl~iDeid   92 (266)
                      ..++++|++||||+++++++....+..  |+.++|..+.....-..+|.                 ....+++||||||+
T Consensus       153 ~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~~lfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~  232 (368)
T 3dzd_A          153 APVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVG  232 (368)
T ss_dssp             SCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHHHHHEECSCSSSSCCCCEECHHHHTTTSEEEEETGG
T ss_pred             hhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHHHhcCccccccCCcccccCChHhhcCCCeEEecChh
Confidence            459999999999999999999887543  99999998854322233331                 12356899999999


Q ss_pred             hhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-CCC------CceEEEEecCCC-------CCCcc
Q 024550           93 CCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-SCG------DERIIIFTTNHK-------ERLDP  158 (266)
Q Consensus        93 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~------~~~ivi~ttn~~-------~~ld~  158 (266)
                      .+..                           ..+..|+..++.-.- ..+      ..+-+|+|||..       ..+.+
T Consensus       233 ~l~~---------------------------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~v~~g~fr~  285 (368)
T 3dzd_A          233 ELDQ---------------------------RVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNFRE  285 (368)
T ss_dssp             GSCH---------------------------HHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESSCHHHHHHTTSSCH
T ss_pred             hCCH---------------------------HHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCccH
Confidence            8843                           244556666653211 111      135688888753       23444


Q ss_pred             cccCCCcce-eEEEcCCCCH--HHHHHHHHHhhC
Q 024550          159 ALLRPGRMD-MHINMSHCTP--SGFKMLASNYLG  189 (266)
Q Consensus       159 al~r~~Rf~-~~i~~~~p~~--~~~~~i~~~~~~  189 (266)
                      .|..  |+. ..|++|....  ++...++.+++.
T Consensus       286 dL~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~  317 (368)
T 3dzd_A          286 DLYY--RLSVFQIYLPPLRERGKDVILLAEYFLK  317 (368)
T ss_dssp             HHHH--HHTSEEEECCCGGGSTTHHHHHHHHHHH
T ss_pred             HHHH--HhCCeEEeCCChhhchhhHHHHHHHHHH
Confidence            5555  554 3466776655  566677776663

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.97  E-value=4.3e-09  Score=99.26  Aligned_cols=26  Identities=62%  Similarity=0.754  Sum_probs=23.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ...++|+||||||||+++++++..+.
T Consensus        60 g~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           60 KRHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHhccCC
Confidence            45799999999999999999999874

>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=98.93  E-value=6.5e-10  Score=96.02  Aligned_cols=116  Identities=16%  Similarity=0.133  Sum_probs=62.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCc--EEEEeCCc----cc-Chh-hHHHHHHHcccCCeeeeecchhhHHHh
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFD--VYDLELSN----LL-GNN-DLRHILIATENKSILVVEDIDCCIELQ   98 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~--~~~i~~~~----~~-~~~-~l~~~~~~~~~~~vl~iDeid~l~~~~   98 (266)
                      |+++++.++|+||||||||+++..+|...|.+  ++.+....    +. ... .+..+........+|+||+++.+....
T Consensus       119 Gi~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~LLVIDsI~aL~~~~  198 (331)
T 2vhj_A          119 HRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAA  198 (331)
T ss_dssp             EEEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEECCTTTC---
T ss_pred             CCCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCCEEEEeccccccccc
Confidence            55566668999999999999999999875544  44441111    11 111 122222323222299999999985422


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccc
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPAL  160 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al  160 (266)
                      .....               .......+..++..|.+....  .++.+|+++|. ...++++
T Consensus       199 ~~~s~---------------~G~v~~~lrqlL~~L~~~~k~--~gvtVIlttnp-~s~deal  242 (331)
T 2vhj_A          199 GGNTT---------------SGGISRGAFDLLSDIGAMAAS--RGCVVIASLNP-TSNDDKI  242 (331)
T ss_dssp             -----------------------CCHHHHHHHHHHHHHHHH--HTCEEEEECCC-SSCSSSH
T ss_pred             ccccc---------------cchHHHHHHHHHHHHHHHHhh--CCCEEEEEeCC-cccchhH
Confidence            11000               011133455666666554433  34678888884 4445443

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=98.92  E-value=9.3e-09  Score=91.81  Aligned_cols=129  Identities=16%  Similarity=0.170  Sum_probs=80.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC---CcEEEEeCCcccChhhHHHHHH-----------------HcccCCeeeeec
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLELSNLLGNNDLRHILI-----------------ATENKSILVVED   90 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~~~~~~~~~~l~~~~~-----------------~~~~~~vl~iDe   90 (266)
                      ...+|++|++|||||+++++++....   .+|+.++|+.+...---..+|.                 ....+++|||||
T Consensus       160 ~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~~~elfg~~~g~~tga~~~~~g~~~~a~~gtlflde  239 (387)
T 1ny5_A          160 ECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDE  239 (387)
T ss_dssp             CSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEES
T ss_pred             CCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHHHHHHhcCCCCCCCCCcccccCCceeeCCCcEEEEcC
Confidence            34589999999999999999998774   7899999998743211122221                 123468999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccc-c------CCCCceEEEEecCCC-------CCC
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLW-S------SCGDERIIIFTTNHK-------ERL  156 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~------~~~~~~ivi~ttn~~-------~~l  156 (266)
                      |+.+..                           ..+..|+..++... .      .....+.+|+|||..       ..+
T Consensus       240 i~~l~~---------------------------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~~~~g~f  292 (387)
T 1ny5_A          240 IGELSL---------------------------EAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKF  292 (387)
T ss_dssp             GGGCCH---------------------------HHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSS
T ss_pred             hhhCCH---------------------------HHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCCHHHHHHcCCc
Confidence            998843                           24445556555311 0      001246788998863       334


Q ss_pred             cccccCCCcce-eEEEcCCCCH--HHHHHHHHHhh
Q 024550          157 DPALLRPGRMD-MHINMSHCTP--SGFKMLASNYL  188 (266)
Q Consensus       157 d~al~r~~Rf~-~~i~~~~p~~--~~~~~i~~~~~  188 (266)
                      .+.|..  |+. ..|++|....  ++...|+.+++
T Consensus       293 r~dl~~--rl~~~~i~lPpLreR~~Di~~l~~~~l  325 (387)
T 1ny5_A          293 REDLYY--RLGVIEIEIPPLRERKEDIIPLANHFL  325 (387)
T ss_dssp             CHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHH
T ss_pred             cHHHHH--hhcCCeecCCcchhccccHHHHHHHHH
Confidence            455554  553 4455555433  55556666665

>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=98.90  E-value=1.2e-09  Score=111.97  Aligned_cols=113  Identities=14%  Similarity=0.151  Sum_probs=71.9

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCccc----------------------ChhhHHHHHHHc--
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLL----------------------GNNDLRHILIAT--   80 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~----------------------~~~~l~~~~~~~--   80 (266)
                      +|..+.+|+|||||||||++|.+++.+.   |.+-+.+++....                      ++..+..++..+  
T Consensus      1079 ~p~g~~~l~~G~~g~GKT~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~ 1158 (1706)
T 3cmw_A         1079 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS 1158 (1706)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEEcCCCCChHHHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHh
Confidence            3344459999999999999999999877   4555566655432                      133444444333  


Q ss_pred             ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC
Q 024550           81 ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK  153 (266)
Q Consensus        81 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~  153 (266)
                      ..++++|+|+++.|++.+........          .+..-..+.++++|..|++....  .+++|| +||+.
T Consensus      1159 ~~~~~i~~d~~~al~~~~~~~g~~~~----------~~~~~~~r~~~q~l~~~~~~~~~--~~v~v~-~~n~~ 1218 (1706)
T 3cmw_A         1159 GAVDVIVVDSVAALTPKAEIEGEIGD----------SHMGLAARMMSQAMRKLAGNLKQ--SNTLLI-FINQI 1218 (1706)
T ss_dssp             TCCSEEEESCGGGCCCHHHHHSCTTC----------CCTTHHHHHHHHHHHHHHHHHHH--TTCEEE-EEECE
T ss_pred             cCCeEEEeCchHhcCccccccccccc----------ccccHHHHHHHHHHHHHHhhhcc--CCeEEE-Eeccc
Confidence            35899999999999875431100000          01123345688899999886554  446666 67754

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.87  E-value=4.9e-08  Score=84.89  Aligned_cols=157  Identities=17%  Similarity=0.076  Sum_probs=91.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc------Ch-----------------------------------
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL------GN-----------------------------------   70 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~------~~-----------------------------------   70 (266)
                      +.++|+||+|+|||++++.+++..+  .+.+++....      +.                                   
T Consensus        32 ~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~  109 (350)
T 2qen_A           32 PLTLLLGIRRVGKSSLLRAFLNERP--GILIDCRELYAERGHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPR  109 (350)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHHHHHHTTTCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGG
T ss_pred             CeEEEECCCcCCHHHHHHHHHHHcC--cEEEEeecccccccCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccc
Confidence            5799999999999999999999875  5555543221      00                                   


Q ss_pred             -hhHHHHHHHc------ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCc
Q 024550           71 -NDLRHILIAT------ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDE  143 (266)
Q Consensus        71 -~~l~~~~~~~------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~  143 (266)
                       ..+..++...      ..+.+|+|||++.+....                    .......+..+...++..     .+
T Consensus       110 ~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~--------------------~~~~~~~~~~L~~~~~~~-----~~  164 (350)
T 2qen_A          110 KLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYG--------------------SRGGKELLALFAYAYDSL-----PN  164 (350)
T ss_dssp             GCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBT--------------------TTTTHHHHHHHHHHHHHC-----TT
T ss_pred             cchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccC--------------------ccchhhHHHHHHHHHHhc-----CC
Confidence             1122222111      138899999999874200                    000011122222222221     23


Q ss_pred             eEEEEecCCC---C------CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHHHHHHhhcCCCCHHHH
Q 024550          144 RIIIFTTNHK---E------RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPL-FVEIEKLIATAKVTPADV  213 (266)
Q Consensus       144 ~ivi~ttn~~---~------~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~~~~l~~~~~~s~~~i  213 (266)
                      +.+|.|+...   .      .....+..  |+...+.++..+.++..+++...+...+... ...+..+....+..|..+
T Consensus       165 ~~~il~g~~~~~l~~~l~~~~~~~~l~~--~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~tgG~P~~l  242 (350)
T 2qen_A          165 LKIILTGSEVGLLHDFLKITDYESPLYG--RIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELLDGIPGWL  242 (350)
T ss_dssp             EEEEEEESSHHHHHHHHCTTCTTSTTTT--CCCEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHTTCHHHH
T ss_pred             eEEEEECCcHHHHHHHHhhcCCCCcccc--CccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHH
Confidence            4555554332   1      11223333  6667899999999999999988775544333 345566667777788776


Q ss_pred             HHHH
Q 024550          214 AEQL  217 (266)
Q Consensus       214 ~~~l  217 (266)
                      ..+.
T Consensus       243 ~~~~  246 (350)
T 2qen_A          243 VVFG  246 (350)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6544

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.82  E-value=2e-08  Score=107.93  Aligned_cols=141  Identities=16%  Similarity=0.103  Sum_probs=97.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcc-cCCeeeeecchhhHHHhHHHhhhhhcCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATE-NKSILVVEDIDCCIELQDRLSRARAANP  109 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~-~~~vl~iDeid~l~~~~~~~~~~~~~~~  109 (266)
                      ..|..+.||+|||||.+++.+|+.+|.+++.++|+.-.+...+..+|..+. .++..++|||+.+-...-..-.      
T Consensus       604 ~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~~~~g~i~~G~~~~GaW~cfDEfNrl~~~vLSvv~------  677 (3245)
T 3vkg_A          604 RMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLEERILSAVS------  677 (3245)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCHHHHHHHHHHHHHHTCEEEEETTTSSCHHHHHHHH------
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCHHHHHHHHhhHhhcCcEEEehhhhcCCHHHHHHHH------
Confidence            456789999999999999999999999999999999888888888887765 5899999999987431100000      


Q ss_pred             ccccccccccccchhhhhhhhhh-----hh-ccccCCCCceEEEEecCC----CCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          110 DFLIAGYEQQKQYHITLSGLLNF-----ID-GLWSSCGDERIIIFTTNH----KERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~ll~~-----l~-~~~~~~~~~~ivi~ttn~----~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                .+...+...+...     +. |..-......-++.|.|+    ...||++|..  || +.|.|..||.+.
T Consensus       678 ----------~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~--lF-r~v~m~~Pd~~~  744 (3245)
T 3vkg_A          678 ----------QQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKK--LF-RSMAMIKPDREM  744 (3245)
T ss_dssp             ----------HHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHT--TE-EEEECCSCCHHH
T ss_pred             ----------HHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHh--hc-EEEEEeCCCHHH
Confidence                      0000111111110     00 111111234667888884    4688999999  98 569999999999


Q ss_pred             HHHHHHHhhCC
Q 024550          180 FKMLASNYLGI  190 (266)
Q Consensus       180 ~~~i~~~~~~~  190 (266)
                      ..+|+-.-.+.
T Consensus       745 i~ei~L~s~Gf  755 (3245)
T 3vkg_A          745 IAQVMLYSQGF  755 (3245)
T ss_dssp             HHHHHHHTTTC
T ss_pred             HHHHHHHHccc
Confidence            88886544333

>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=98.73  E-value=9.6e-08  Score=80.46  Aligned_cols=59  Identities=20%  Similarity=0.269  Sum_probs=38.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhh
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCC   94 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l   94 (266)
                      ++.++++||||||||||+++.++|+.++. .-.++.+..      ...+.....+.+++.||....
T Consensus       102 ~~~n~~~l~GppgtGKt~~a~ala~~~~l-~G~vn~~~~------~f~l~~~~~k~i~l~Ee~~~~  160 (267)
T 1u0j_A          102 GKRNTIWLFGPATTGKTNIAEAIAHTVPF-YGCVNWTNE------NFPFNDCVDKMVIWWEEGKMT  160 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHSSC-EEECCTTCS------SCTTGGGSSCSEEEECSCCEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHhhhcc-cceeecccc------ccccccccccEEEEeccccch
Confidence            44568999999999999999999998654 223333211      112334455667777776543

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=98.51  E-value=3.6e-08  Score=89.09  Aligned_cols=115  Identities=19%  Similarity=0.140  Sum_probs=67.5

Q ss_pred             eeEEecCCCCChHHHHHHH-HHHcCCcEEEEeCCcccChhhHH------------HHHHHcccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAM-ANYLKFDVYDLELSNLLGNNDLR------------HILIATENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~al-a~~~~~~~~~i~~~~~~~~~~l~------------~~~~~~~~~~vl~iDeid~l~~~~~   99 (266)
                      ++||.|+||| ||++++++ ++.+....+.....  .+...+.            .-......++|+|+|||+.+..   
T Consensus       241 hVLL~G~PGt-KS~Lar~i~~~i~pR~~ft~g~~--ss~~gLt~s~r~~tG~~~~~G~l~LAdgGvl~lDEIn~~~~---  314 (506)
T 3f8t_A          241 HVLLAGYPVV-CSEILHHVLDHLAPRGVYVDLRR--TELTDLTAVLKEDRGWALRAGAAVLADGGILAVDHLEGAPE---  314 (506)
T ss_dssp             CEEEESCHHH-HHHHHHHHHHHTCSSEEEEEGGG--CCHHHHSEEEEESSSEEEEECHHHHTTTSEEEEECCTTCCH---
T ss_pred             eEEEECCCCh-HHHHHHHHHHHhCCCeEEecCCC--CCccCceEEEEcCCCcccCCCeeEEcCCCeeehHhhhhCCH---
Confidence            6999999999 99999999 77665444332111  0100010            0011123579999999997743   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-----CCCCceEEEEecCCCC-----------CCcccccCC
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-----SCGDERIIIFTTNHKE-----------RLDPALLRP  163 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-----~~~~~~ivi~ttn~~~-----------~ld~al~r~  163 (266)
                                              ..+..|+..|+.-.-     ..+.++.||||+|+..           .|++++++ 
T Consensus       315 ------------------------~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~alLD-  369 (506)
T 3f8t_A          315 ------------------------PHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQDFLS-  369 (506)
T ss_dssp             ------------------------HHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHHHHT-
T ss_pred             ------------------------HHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChHHhh-
Confidence                                    233444444442100     1235688999999864           78899999 


Q ss_pred             CcceeE-EEcCCCCHHH
Q 024550          164 GRMDMH-INMSHCTPSG  179 (266)
Q Consensus       164 ~Rf~~~-i~~~~p~~~~  179 (266)
                       ||++. +.+..|+.+.
T Consensus       370 -RFDLi~i~~d~pd~e~  385 (506)
T 3f8t_A          370 -HFDLIAFLGVDPRPGE  385 (506)
T ss_dssp             -TCSEEEETTC------
T ss_pred             -heeeEEEecCCCChhH
Confidence             99764 4456666543

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=98.50  E-value=7.1e-07  Score=78.02  Aligned_cols=150  Identities=15%  Similarity=0.077  Sum_probs=95.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CC-cEEEEeCCcccChhhHHHHHHHc------ccCCeeeeecchh-hHHHh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KF-DVYDLELSNLLGNNDLRHILIAT------ENKSILVVEDIDC-CIELQ   98 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~-~~~~i~~~~~~~~~~l~~~~~~~------~~~~vl~iDeid~-l~~~~   98 (266)
                      .++.+|||||+|+||++.++.+++.+   +. +...+....   ...+..++..+      ...-|++|||++. +.   
T Consensus        17 ~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~plf~~~kvvii~~~~~kl~---   90 (343)
T 1jr3_D           17 LRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP---NTDWNAIFSLCQAMSLFASRQTLLLLLPENGPN---   90 (343)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT---TCCHHHHHHHHHHHHHCCSCEEEEEECCSSCCC---
T ss_pred             CCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC---CCCHHHHHHHhcCcCCccCCeEEEEECCCCCCC---
Confidence            35689999999999999999998865   32 222222222   23445554433      2467999999986 52   


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC------CCCcccccCCCcceeEEEc
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK------ERLDPALLRPGRMDMHINM  172 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~------~~ld~al~r~~Rf~~~i~~  172 (266)
                                              ....+.|+..++.-    +...++|.+++.+      ..+.+++.+  |+ ..+.|
T Consensus        91 ------------------------~~~~~aLl~~le~p----~~~~~~il~~~~~~~~~~~~k~~~~i~s--r~-~~~~~  139 (343)
T 1jr3_D           91 ------------------------AAINEQLLTLTGLL----HDDLLLIVRGNKLSKAQENAAWFTALAN--RS-VQVTC  139 (343)
T ss_dssp             ------------------------TTHHHHHHHHHTTC----BTTEEEEEEESCCCTTTTTSHHHHHHTT--TC-EEEEE
T ss_pred             ------------------------hHHHHHHHHHHhcC----CCCeEEEEEcCCCChhhHhhHHHHHHHh--Cc-eEEEe
Confidence                                    22345566666542    2345555444432      356778888  77 56999


Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHH
Q 024550          173 SHCTPSGFKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQ  216 (266)
Q Consensus       173 ~~p~~~~~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~  216 (266)
                      ..++..+....+...+...+..+..+ +..++...+.+..++.+.
T Consensus       140 ~~l~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~gdl~~~~~e  184 (343)
T 1jr3_D          140 QTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQA  184 (343)
T ss_dssp             CCCCTTHHHHHHHHHHHHTTCEECHHHHHHHHHSSTTCHHHHHHH
T ss_pred             eCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhchHHHHHHHH
Confidence            99999999988888887776555443 334444445555555443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.42  E-value=4.7e-07  Score=94.19  Aligned_cols=111  Identities=15%  Similarity=0.188  Sum_probs=67.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC---------------------hhhHHHHHHH---
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG---------------------NNDLRHILIA---   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~---------------------~~~l~~~~~~---   79 (266)
                      |++++++++||||||||||+||.+++.+.   |.....+++.....                     .......+..   
T Consensus      1423 Gi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr 1502 (2050)
T 3cmu_A         1423 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1502 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHHHh
Confidence            38888899999999999999999998776   55666777664321                     1122222222   


Q ss_pred             cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEe
Q 024550           80 TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFT  149 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~t  149 (266)
                      ...+++|+||+++.+.+.........+          .......+.++.+|..|.+....  .++++|+|
T Consensus      1503 ~~~~~lVVIDsi~al~p~~~~~g~~~~----------~~~~~~~R~lsqlL~~L~~~~~~--~~v~VI~t 1560 (2050)
T 3cmu_A         1503 SGAVDVIVVDSVAALTPKAEIEGEIGD----------SHMGLAARMMSQAMRKLAGNLKQ--SNTLLIFI 1560 (2050)
T ss_dssp             HTCCSEEEESCGGGCCCHHHHHSCTTC----------CCTTHHHHHHHHHHHHHHHHHHT--TTCEEEEE
T ss_pred             cCCCCEEEEcChhHhcccccccccccc----------cccchHHHHHHHHHHHHHHHHHh--CCcEEEEE
Confidence            256899999999988753321100000          00011244567777777776654  33444443

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=98.35  E-value=1.7e-06  Score=68.66  Aligned_cols=27  Identities=26%  Similarity=0.524  Sum_probs=23.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      .+.|.||+|+||||+++.++..++..+
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            478999999999999999999876444

>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=98.12  E-value=2.5e-06  Score=67.09  Aligned_cols=34  Identities=21%  Similarity=0.314  Sum_probs=29.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      +..|+|+||||+||||+++.++..++.+++.++.
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~~   36 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCCeEEecc
Confidence            3468999999999999999999999988877653

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=98.10  E-value=1.8e-06  Score=69.52  Aligned_cols=35  Identities=31%  Similarity=0.334  Sum_probs=29.5

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+...++|.|||||||||+++.++..++.+++..+
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~d   57 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGKAFARKLNVPFIDLD   57 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHcCCCEEcch
Confidence            34456999999999999999999999998876543

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=98.09  E-value=1.9e-06  Score=68.25  Aligned_cols=33  Identities=30%  Similarity=0.378  Sum_probs=29.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +..|+|+|||||||||+++.+|..++.+++..+
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~~~~i~~d   37 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTKRILYDSD   37 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            457999999999999999999999999887543

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.06  E-value=1.9e-06  Score=68.77  Aligned_cols=31  Identities=19%  Similarity=0.256  Sum_probs=22.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i   62 (266)
                      .-++++||+|+|||+++..++..+   +..++.+
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~   37 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVF   37 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            357899999999999986666543   4444443

>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=98.05  E-value=3.8e-06  Score=66.72  Aligned_cols=34  Identities=26%  Similarity=0.360  Sum_probs=29.1

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .+.+..|+|.|+||+||||+++.++..++.+++.
T Consensus         2 ~~~~~~I~l~G~~GsGKST~~~~L~~~l~~~~i~   35 (193)
T 2rhm_A            2 MQTPALIIVTGHPATGKTTLSQALATGLRLPLLS   35 (193)
T ss_dssp             CSCCEEEEEEESTTSSHHHHHHHHHHHHTCCEEE
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEec
Confidence            3445678999999999999999999999887665

>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=98.04  E-value=4.8e-06  Score=64.79  Aligned_cols=31  Identities=26%  Similarity=0.292  Sum_probs=27.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .|+|.||||+||||+++.++..++.+++..+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~~~~i~~d   33 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELKYPIIKGS   33 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHCCCEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeeecCc
Confidence            4789999999999999999999998876655

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=98.02  E-value=7e-06  Score=70.11  Aligned_cols=34  Identities=32%  Similarity=0.466  Sum_probs=28.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      +..++|.||||+||||+++.++..++...+.++.
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~   66 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN   66 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEec
Confidence            4568999999999999999999988545566664

>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=98.00  E-value=1.3e-05  Score=75.02  Aligned_cols=34  Identities=35%  Similarity=0.386  Sum_probs=26.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      ...+++.||||||||+++.+++..+   +.+++.+.+
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~Ap  240 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAP  240 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecC
Confidence            3468899999999999999998765   566665544

>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=98.00  E-value=1.2e-05  Score=69.70  Aligned_cols=41  Identities=15%  Similarity=0.192  Sum_probs=33.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNL   67 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~   67 (266)
                      |+++...++|+||||+|||+++..++...         +...++++....
T Consensus       103 Gl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~  152 (324)
T 2z43_A          103 GIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGT  152 (324)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSC
T ss_pred             CCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            56666679999999999999999999865         557778877653

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.99  E-value=1.9e-05  Score=69.32  Aligned_cols=70  Identities=13%  Similarity=0.135  Sum_probs=47.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC------------------hhhHHHH---HH---H
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG------------------NNDLRHI---LI---A   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~------------------~~~l~~~---~~---~   79 (266)
                      |+++...++|+||||+|||+|+..++..+   +..+++++......                  ...+.++   +.   .
T Consensus        57 Gi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~  136 (356)
T 3hr8_A           57 GYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDELVR  136 (356)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHHHhh
Confidence            45566669999999999999999998775   56677777654321                  1111111   11   1


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      ...+.+++||.+..+.+
T Consensus       137 ~~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          137 SGVVDLIVVDSVAALVP  153 (356)
T ss_dssp             TSCCSEEEEECTTTCCC
T ss_pred             hcCCCeEEehHhhhhcC
Confidence            24578999999988764

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.98  E-value=2.3e-05  Score=63.83  Aligned_cols=38  Identities=21%  Similarity=0.072  Sum_probs=29.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      |++++..++|+||||+|||++++.++...   +.+++.++.
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~~   59 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVTT   59 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEES
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEEc
Confidence            46666679999999999999999998654   445555543

>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=97.96  E-value=5e-06  Score=66.05  Aligned_cols=33  Identities=30%  Similarity=0.463  Sum_probs=27.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH-cCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY-LKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~-~~~~~~~i~   63 (266)
                      +..++|+|+|||||||+++.++.. +|.+++.++
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~l~g~~~id~d   43 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAELDGFQHLEVG   43 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTTEEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCCEEeeHH
Confidence            446999999999999999999999 687766543

>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=97.94  E-value=5.7e-06  Score=65.23  Aligned_cols=32  Identities=28%  Similarity=0.429  Sum_probs=28.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +..|+|+|+||+||||+++.++..++.+++..
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~   42 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSGLKYINV   42 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhCCeEEEH
Confidence            45699999999999999999999998877654

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.93  E-value=4.9e-06  Score=65.37  Aligned_cols=30  Identities=33%  Similarity=0.438  Sum_probs=27.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .++|.|||||||||+++.||..++.+++..
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d~   35 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLDS   35 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEcc
Confidence            589999999999999999999999887653

>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=97.92  E-value=5.8e-06  Score=65.37  Aligned_cols=31  Identities=32%  Similarity=0.504  Sum_probs=27.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .|+|.|+||+||||+++.|+..+|.+++..+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg~~~id~D   34 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKALGVGLLDTD   34 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcCCCEEeCc
Confidence            4899999999999999999999998876544

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.91  E-value=6.2e-06  Score=64.24  Aligned_cols=32  Identities=38%  Similarity=0.526  Sum_probs=28.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ..++|.|+|||||||+++.||..+|.+++..+
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~id~D   39 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVLDTD   39 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            36999999999999999999999999887643

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.90  E-value=0.00016  Score=67.42  Aligned_cols=44  Identities=16%  Similarity=0.076  Sum_probs=28.0

Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHH
Q 024550          173 SHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQ  216 (266)
Q Consensus       173 ~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~  216 (266)
                      ...+.++..+++..+..............++...+..|-.|..+
T Consensus       284 ~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  327 (591)
T 1z6t_A          284 SSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLI  327 (591)
T ss_dssp             SSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTTCHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCCCcHHHHHH
Confidence            46888999999988876532222344556666666666665543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.88  E-value=1e-05  Score=63.15  Aligned_cols=30  Identities=40%  Similarity=0.724  Sum_probs=26.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ..+.|+|||||||||+++.++..++.+++.
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id   34 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYD   34 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEe
Confidence            458999999999999999999999876553

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=97.87  E-value=8.6e-06  Score=64.66  Aligned_cols=37  Identities=30%  Similarity=0.345  Sum_probs=30.1

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      +..+..+.|.||||+||||+++.++..++...+.++.
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~   42 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   42 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHhccCCCeEEEcc
Confidence            4455668999999999999999999987766666654

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.84  E-value=5.9e-05  Score=68.54  Aligned_cols=23  Identities=30%  Similarity=0.515  Sum_probs=21.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++|.||||||||+++.+++..+
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            79999999999999999998877

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.84  E-value=1.6e-05  Score=66.50  Aligned_cols=38  Identities=16%  Similarity=0.211  Sum_probs=30.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL   67 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~   67 (266)
                      .+..++|.||||+||||+++.++..++...+.++...+
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            34568999999999999999999999865566665443

>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=97.84  E-value=1.1e-05  Score=64.79  Aligned_cols=31  Identities=32%  Similarity=0.500  Sum_probs=27.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..|+|.|+||+||||+++.|+..++.+++.+
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l~~~~i~~   51 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKLGIPQIST   51 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCcEEeh
Confidence            3588999999999999999999999887655

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.83  E-value=1.1e-05  Score=67.53  Aligned_cols=32  Identities=28%  Similarity=0.464  Sum_probs=28.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      .++|.|||||||||+++.||..++.+++..+.
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            47899999999999999999999988877654

>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=97.83  E-value=9e-06  Score=63.16  Aligned_cols=29  Identities=28%  Similarity=0.358  Sum_probs=25.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      -|+|+||||+||||+++.+ ..+|.+++.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~g~~~i~~   31 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KERGAKVIVM   31 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHTTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCcEEEH
Confidence            4789999999999999999 8888887654

>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=97.82  E-value=9.7e-06  Score=63.23  Aligned_cols=30  Identities=20%  Similarity=0.388  Sum_probs=26.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.|+||+||||+++.++..++.+++..
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg~~~id~   33 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARALGYEFVDT   33 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEcc
Confidence            589999999999999999999999877653

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.82  E-value=1.2e-05  Score=64.06  Aligned_cols=33  Identities=15%  Similarity=0.292  Sum_probs=28.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +..|+|.|+|||||||+++.++..++.+++..+
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            446899999999999999999999998766543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.82  E-value=5e-05  Score=79.38  Aligned_cols=70  Identities=17%  Similarity=0.249  Sum_probs=52.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh------------------------hhHHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN------------------------NDLRHILIA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~------------------------~~l~~~~~~   79 (266)
                      |++.+..++|+||||||||+++.+++.+.   |.+.+.+++......                        ..+...+..
T Consensus      1077 gi~~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~ 1156 (2050)
T 3cmu_A         1077 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1156 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCcEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHH
Confidence            57788889999999999999999988655   677788877765321                        112223334


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      ...+.+|+||++..+.+
T Consensus      1157 ~~~~dlvVIDsl~~L~~ 1173 (2050)
T 3cmu_A         1157 SGAVDVIVVDSVAALTP 1173 (2050)
T ss_dssp             HTCCSEEEESCGGGCCC
T ss_pred             hCCCCEEEECCcccccc
Confidence            45699999999999854

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.81  E-value=1.1e-05  Score=63.98  Aligned_cols=32  Identities=19%  Similarity=0.313  Sum_probs=27.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +..|+|.|+|||||||+++.++..++.+++..
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   34 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKYGYTHLSA   34 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            34689999999999999999999998876543

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=97.81  E-value=7.3e-05  Score=65.96  Aligned_cols=69  Identities=19%  Similarity=0.239  Sum_probs=47.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh---------------------hhHHHHHHH---
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN---------------------NDLRHILIA---   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~---------------------~~l~~~~~~---   79 (266)
                      |+++...++|+||||+|||+++..++...   +.+++.++.......                     ..+...+..   
T Consensus        70 Gl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~  149 (366)
T 1xp8_A           70 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  149 (366)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHh
Confidence            46666679999999999999999888765   567777776542211                     112222222   


Q ss_pred             cccCCeeeeecchhhH
Q 024550           80 TENKSILVVEDIDCCI   95 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~   95 (266)
                      .....+|+||.+..+.
T Consensus       150 ~~~~~lVVIDsl~~l~  165 (366)
T 1xp8_A          150 SGAIDVVVVDSVAALT  165 (366)
T ss_dssp             TTCCSEEEEECTTTCC
T ss_pred             cCCCCEEEEeChHHhc
Confidence            1347899999999885

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=97.79  E-value=5.1e-05  Score=66.54  Aligned_cols=70  Identities=16%  Similarity=0.210  Sum_probs=46.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC---------------------hhhHHHHHH---H
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG---------------------NNDLRHILI---A   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~---------------------~~~l~~~~~---~   79 (266)
                      |+++...++|+||||+|||+++..++...   +...++++......                     ...+..+..   .
T Consensus        57 Gl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~  136 (349)
T 2zr9_A           57 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVR  136 (349)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            45566669999999999999999988654   55667776553221                     011111221   1


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      ...+.+|+||++..+..
T Consensus       137 ~~~~~lIVIDsl~~l~~  153 (349)
T 2zr9_A          137 SGALDIIVIDSVAALVP  153 (349)
T ss_dssp             TTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEcChHhhcc
Confidence            23488999999998863

>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=97.78  E-value=1.3e-05  Score=65.02  Aligned_cols=30  Identities=20%  Similarity=0.304  Sum_probs=26.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.||||+||||+++.|+..++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKYGIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            378999999999999999999998877655

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.77  E-value=1.4e-05  Score=65.60  Aligned_cols=32  Identities=16%  Similarity=0.368  Sum_probs=27.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +..|+|.|||||||||+++.|+..++.+++.+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   38 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHFELKHLSS   38 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHSSSEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCeEEec
Confidence            45699999999999999999999998876654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.76  E-value=1.7e-05  Score=63.78  Aligned_cols=32  Identities=25%  Similarity=0.333  Sum_probs=27.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +.-|+|.||||+||||+++.|+..+|..++..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~   49 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEACGYPFIEG   49 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHHTCCEEEG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCEEEeC
Confidence            34699999999999999999999998766553

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.76  E-value=1.8e-05  Score=62.55  Aligned_cols=31  Identities=29%  Similarity=0.598  Sum_probs=26.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..++|.|||||||||+++.++..++.+++..
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l~~~~i~~   35 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQELGFKKLST   35 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTCEEECH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEecH
Confidence            3588999999999999999999998766543

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.75  E-value=1.4e-05  Score=64.74  Aligned_cols=29  Identities=21%  Similarity=0.364  Sum_probs=26.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |+|.||||+||||+++.++..++.+++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIEKYEIPHIST   31 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEeeH
Confidence            78999999999999999999998877655

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.75  E-value=1.5e-05  Score=63.48  Aligned_cols=32  Identities=19%  Similarity=0.344  Sum_probs=27.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +.-|+|.|+||+||||+++.++..++.+++..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   43 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYGFTHLST   43 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            44699999999999999999999998766544

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.75  E-value=1.5e-05  Score=61.82  Aligned_cols=30  Identities=27%  Similarity=0.379  Sum_probs=26.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.|+||+||||+++.++..++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   31 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDV   31 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            378999999999999999999999887654

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.75  E-value=1.4e-05  Score=62.51  Aligned_cols=28  Identities=32%  Similarity=0.396  Sum_probs=23.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHH-HcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMAN-YLKFD   58 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~-~~~~~   58 (266)
                      +.-|+|.||||+||||+++.++. .++..
T Consensus         2 ~~~I~i~G~~GsGKST~a~~L~~~~~~~~   30 (181)
T 1ly1_A            2 KKIILTIGCPGSGKSTWAREFIAKNPGFY   30 (181)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHSTTEE
T ss_pred             CeEEEEecCCCCCHHHHHHHHHhhcCCcE
Confidence            34689999999999999999998 45543

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=97.75  E-value=7.2e-05  Score=65.77  Aligned_cols=70  Identities=19%  Similarity=0.243  Sum_probs=48.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC---------------------hhhHHHHHHH---
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG---------------------NNDLRHILIA---   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~---------------------~~~l~~~~~~---   79 (266)
                      |+++...++|+||||+|||+++..++...   +.+++.++......                     ...+...+..   
T Consensus        59 Gl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~  138 (356)
T 1u94_A           59 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  138 (356)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHHHHh
Confidence            46667779999999999999999988765   56777777643221                     1112222222   


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      .....+|+||.+..+..
T Consensus       139 ~~~~~lVVIDsl~~l~~  155 (356)
T 1u94_A          139 SGAVDVIVVDSVAALTP  155 (356)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             ccCCCEEEEcCHHHhcc
Confidence            24578999999998863

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=97.75  E-value=1.9e-05  Score=62.54  Aligned_cols=32  Identities=19%  Similarity=0.313  Sum_probs=27.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +..|+|.|+|||||||+++.++..++.+++..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~   37 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEeeH
Confidence            34689999999999999999999998776654

>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=97.75  E-value=2.4e-05  Score=63.77  Aligned_cols=31  Identities=23%  Similarity=0.409  Sum_probs=27.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..|+|.|+||+||||+++.||..++.+++..
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            4589999999999999999999999876654

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=97.74  E-value=0.00036  Score=70.21  Aligned_cols=140  Identities=19%  Similarity=0.192  Sum_probs=79.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH-------cCCcEEEEeCCcccCh---------------------------hhHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY-------LKFDVYDLELSNLLGN---------------------------NDLRHI   76 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~-------~~~~~~~i~~~~~~~~---------------------------~~l~~~   76 (266)
                      .+-+.|+|+.|+|||+||+.++..       +...++.++.+.....                           ..+...
T Consensus       147 ~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  226 (1249)
T 3sfz_A          147 PGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDR  226 (1249)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHH
Confidence            445889999999999999988765       2233445555442110                           111111


Q ss_pred             HHHc----ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC
Q 024550           77 LIAT----ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH  152 (266)
Q Consensus        77 ~~~~----~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~  152 (266)
                      +...    .++.+|+||+++...                             .    +..+       +.+..||.||..
T Consensus       227 l~~~l~~~~~~~LlvlDd~~~~~-----------------------------~----~~~~-------~~~~~ilvTtR~  266 (1249)
T 3sfz_A          227 LRVLMLRKHPRSLLILDDVWDPW-----------------------------V----LKAF-------DNQCQILLTTRD  266 (1249)
T ss_dssp             HHHHTSSSSCSCEEEEESCCCHH-----------------------------H----HTTT-------CSSCEEEEEESS
T ss_pred             HHHHHhccCCCEEEEEecCCCHH-----------------------------H----HHhh-------cCCCEEEEEcCC
Confidence            1111    237888999988431                             0    1111       133456777765


Q ss_pred             CCCCcccccCCCcceeEEEcCC-CCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHH
Q 024550          153 KERLDPALLRPGRMDMHINMSH-CTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVA  214 (266)
Q Consensus       153 ~~~ld~al~r~~Rf~~~i~~~~-p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~  214 (266)
                      +.-.. ...   .....+.++. ++.++..++|..+..............++...+.-|-.|.
T Consensus       267 ~~~~~-~~~---~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~glPLal~  325 (1249)
T 3sfz_A          267 KSVTD-SVM---GPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVS  325 (1249)
T ss_dssp             TTTTT-TCC---SCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTCHHHHH
T ss_pred             HHHHH-hhc---CCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCCHHHHH
Confidence            43221 111   2234577775 8889989999887755443334445556666665555544

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.73  E-value=1.6e-05  Score=64.82  Aligned_cols=31  Identities=19%  Similarity=0.371  Sum_probs=27.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..|+|.|+|||||||+++.|+..++.+++.+
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            3588999999999999999999999877655

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=97.73  E-value=6.4e-05  Score=64.99  Aligned_cols=28  Identities=18%  Similarity=0.177  Sum_probs=24.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      |+++..-++|+||||+|||+++..+|..
T Consensus        94 Gl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           94 GLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4666666999999999999999999875

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.73  E-value=1.6e-05  Score=62.64  Aligned_cols=29  Identities=21%  Similarity=0.222  Sum_probs=22.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      ..|+|.|+||+||||+++.++..++.+++
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            45889999999999999999999998876

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.72  E-value=2.3e-05  Score=64.07  Aligned_cols=33  Identities=21%  Similarity=0.400  Sum_probs=27.5

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      ...++-|+|.||||+||+|.++.|++.+|.+.+
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~~~~g~~hI   58 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLVQKFHFNHL   58 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHHHHHCCEEE
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            334556888999999999999999999987654

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=97.72  E-value=2.9e-05  Score=60.74  Aligned_cols=30  Identities=33%  Similarity=0.537  Sum_probs=25.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ..++|.||||+||||+++.++..+|..++.
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~   38 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQLHAAFLD   38 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhhCcEEEe
Confidence            458899999999999999999988765543

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=97.72  E-value=9.3e-05  Score=62.56  Aligned_cols=29  Identities=28%  Similarity=0.239  Sum_probs=24.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      |++...-++|+||||+|||+|+..++..+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            55556669999999999999999988644

>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=97.72  E-value=2.2e-05  Score=62.08  Aligned_cols=25  Identities=20%  Similarity=0.395  Sum_probs=23.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .-|+|.||||+||||+++.|+..++
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4588999999999999999999887

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.72  E-value=2.2e-05  Score=63.01  Aligned_cols=31  Identities=19%  Similarity=0.322  Sum_probs=27.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .|+|.|+|||||||+++.++..+|.+++..+
T Consensus        17 ~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~d   47 (203)
T 1ukz_A           17 VIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG   47 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCceEEeHH
Confidence            4889999999999999999999988766543

>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=97.70  E-value=2.2e-05  Score=65.27  Aligned_cols=33  Identities=18%  Similarity=0.317  Sum_probs=28.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .+..|+|.||||+||||+++.|+..++.+++.+
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~   60 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLST   60 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            455699999999999999999999998876654

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.70  E-value=3.1e-05  Score=62.14  Aligned_cols=30  Identities=20%  Similarity=0.414  Sum_probs=25.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      +..+.|.||+|+||||+++.++..+|..++
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~~g~~~i   58 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADETGLEFA   58 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHCCEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCCeEE
Confidence            446889999999999999999999976443

>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=97.68  E-value=3.5e-05  Score=63.42  Aligned_cols=31  Identities=26%  Similarity=0.387  Sum_probs=27.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..|+|.|+|||||||+++.||..++.+++..
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   47 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   47 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            3589999999999999999999999876654

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.68  E-value=8.8e-05  Score=59.90  Aligned_cols=40  Identities=23%  Similarity=0.169  Sum_probs=33.4

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~   66 (266)
                      |+++...++|+||||+|||+++..++...+.+++.++...
T Consensus        16 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~~   55 (220)
T 2cvh_A           16 GFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEG   55 (220)
T ss_dssp             SBCTTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESSC
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECCC
Confidence            5777777999999999999999999986677777777654

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.67  E-value=2.5e-05  Score=63.68  Aligned_cols=31  Identities=13%  Similarity=0.265  Sum_probs=26.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      +..|+|.||||+||||+++.||..++..++.
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~   35 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQLAHIS   35 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceec
Confidence            4568999999999999999999999875543

>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=97.65  E-value=3.4e-05  Score=62.56  Aligned_cols=28  Identities=29%  Similarity=0.514  Sum_probs=25.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ++|.||||+||+|.++.|++.+|.+.+.
T Consensus         3 Iil~GpPGsGKgTqa~~La~~~g~~~is   30 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKEKGFVHIS   30 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            7888999999999999999999886554

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=97.64  E-value=0.00011  Score=63.33  Aligned_cols=69  Identities=13%  Similarity=0.109  Sum_probs=45.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCcccC------------------hhhHHHH-H---HH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLLG------------------NNDLRHI-L---IA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~~------------------~~~l~~~-~---~~   79 (266)
                      |+++. -++++||||+|||+|+-.++...     +...++++...-..                  +....++ +   ..
T Consensus        25 Gl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~  103 (333)
T 3io5_A           25 GMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQ  103 (333)
T ss_dssp             CBCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHH
T ss_pred             CCcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHH
Confidence            46666 68999999999999977766544     56677787654321                  1122222 2   11


Q ss_pred             ---c--ccCCeeeeecchhhHH
Q 024550           80 ---T--ENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ---~--~~~~vl~iDeid~l~~   96 (266)
                         .  ..+.+|+||-+..+.+
T Consensus       104 l~~i~~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          104 LDAIERGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             HHTCCTTCCEEEEEECSTTCBC
T ss_pred             HHHhhccCceEEEEeccccccc
Confidence               1  2578999999998863

>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=97.64  E-value=5.1e-05  Score=59.65  Aligned_cols=33  Identities=30%  Similarity=0.521  Sum_probs=28.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      +..+.|.|++|+||||+++.++..+   |.+++.++
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d   40 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   40 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEEC
Confidence            3458899999999999999999988   88888776

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.64  E-value=0.00029  Score=57.70  Aligned_cols=34  Identities=21%  Similarity=0.181  Sum_probs=26.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      ..+++.|+||+||||++-.+|..+   |..++.++..
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D   43 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVE   43 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeC
Confidence            359999999999999988888766   6666655543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=97.62  E-value=4e-05  Score=66.31  Aligned_cols=35  Identities=26%  Similarity=0.494  Sum_probs=30.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      +..++|+||+|||||++++.+|..++..++.++..
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds~   39 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADALPCELISVDSA   39 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEEECTT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCcEEeccch
Confidence            34689999999999999999999999888887643

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=97.62  E-value=5e-05  Score=60.11  Aligned_cols=30  Identities=23%  Similarity=0.325  Sum_probs=27.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      +.|.|+|||||||+++.++..+   |.+++..+
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d   35 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYR   35 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            7899999999999999999988   88888765

>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=97.61  E-value=4e-05  Score=62.13  Aligned_cols=30  Identities=17%  Similarity=0.230  Sum_probs=26.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.||||+||||+++.|+..++.+++.+
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            378999999999999999999998877655

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=97.57  E-value=5.1e-05  Score=62.06  Aligned_cols=29  Identities=21%  Similarity=0.434  Sum_probs=25.7

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |+|.||||+||||+++.++..++.+++..
T Consensus         3 I~l~G~~GsGKsT~a~~La~~lg~~~i~~   31 (223)
T 2xb4_A            3 ILIFGPNGSGKGTQGNLVKDKYSLAHIES   31 (223)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCeEEch
Confidence            78999999999999999999998766554

>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=97.57  E-value=3.6e-05  Score=61.78  Aligned_cols=30  Identities=30%  Similarity=0.314  Sum_probs=26.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+.|.||+||||||+++.++. +|.+++..+
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~i~~d   32 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYVLDAD   32 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEEEEHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEEEEcc
Confidence            478999999999999999999 887776654

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=97.56  E-value=0.00035  Score=55.97  Aligned_cols=34  Identities=15%  Similarity=0.121  Sum_probs=27.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      ..+++|+++|.||||+|-++|-..   |..+..+.+.
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~   65 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFI   65 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEee
Confidence            359999999999999999888765   6777777544

>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=97.56  E-value=5.5e-05  Score=61.64  Aligned_cols=30  Identities=37%  Similarity=0.596  Sum_probs=26.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ..+.|.||+||||||+++.++..+|.+++.
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            358899999999999999999999876654

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=97.55  E-value=5e-05  Score=63.47  Aligned_cols=33  Identities=30%  Similarity=0.503  Sum_probs=29.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ...+.|.||+|+||||+++.+|..+|.+++..+
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg~~~~d~d   80 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLGYTFFDCD   80 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCcEEeCc
Confidence            456999999999999999999999998877643

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=97.55  E-value=3.2e-05  Score=61.11  Aligned_cols=24  Identities=33%  Similarity=0.534  Sum_probs=22.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      -|+|.||||+||||+++.|+..++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999999886

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=97.55  E-value=5.3e-05  Score=60.48  Aligned_cols=29  Identities=24%  Similarity=0.639  Sum_probs=25.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .|.|.|+|||||||+++.|++.++..++.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~~~   30 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEIFK   30 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEEEC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcEEc
Confidence            37899999999999999999999986653

>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=97.54  E-value=8.7e-05  Score=59.51  Aligned_cols=35  Identities=29%  Similarity=0.286  Sum_probs=27.1

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      .++..+.|.||+|+||||+++.++..+   |...+.++
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d   60 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILD   60 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEec
Confidence            345568899999999999999999988   44433444

>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=97.54  E-value=0.00014  Score=59.70  Aligned_cols=40  Identities=18%  Similarity=0.158  Sum_probs=32.1

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHH--c-------CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANY--L-------KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~--~-------~~~~~~i~~~~   66 (266)
                      |+++...++|+||||+|||++++.++..  .       +...++++...
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            5667777999999999999999999985  2       45677777654

>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=97.53  E-value=6.2e-05  Score=62.42  Aligned_cols=30  Identities=23%  Similarity=0.496  Sum_probs=26.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      +..+.|.||+|+||||+++.++..+|...+
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            456999999999999999999999887544

>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=97.52  E-value=8.1e-05  Score=59.49  Aligned_cols=34  Identities=12%  Similarity=0.126  Sum_probs=28.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-CCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-KFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-~~~~~~i~~   64 (266)
                      +.-|.|.|+||+||||+++.++..+ |.+++.+..
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~~   38 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNF   38 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTSCGGGEEEEES
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHCCCceEEEec
Confidence            3458899999999999999999998 577776654

>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=97.50  E-value=9.5e-05  Score=61.98  Aligned_cols=33  Identities=33%  Similarity=0.398  Sum_probs=27.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH---cCCcEEEEeC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY---LKFDVYDLEL   64 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~---~~~~~~~i~~   64 (266)
                      .-|+|+|+||+||||+++.++..   .|.+++.++.
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~   40 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGS   40 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECc
Confidence            45889999999999999999998   6777775543

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=97.49  E-value=0.0034  Score=58.14  Aligned_cols=49  Identities=12%  Similarity=-0.052  Sum_probs=30.7

Q ss_pred             eEEEcCCCCHHHHHHHHHHhhCCCCC-Cc-HHHHHHHhhcCCCCHHHHHHH
Q 024550          168 MHINMSHCTPSGFKMLASNYLGIAEH-PL-FVEIEKLIATAKVTPADVAEQ  216 (266)
Q Consensus       168 ~~i~~~~p~~~~~~~i~~~~~~~~~~-~~-~~~~~~l~~~~~~s~~~i~~~  216 (266)
                      ..+.++..+.++-.++|..+...... .. ......++...+..|-.|.-+
T Consensus       286 ~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~  336 (549)
T 2a5y_B          286 EFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMF  336 (549)
T ss_dssp             EEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             eEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHH
Confidence            56899999999999999988533321 11 122345555555666655543

>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=97.48  E-value=7.3e-05  Score=60.07  Aligned_cols=29  Identities=24%  Similarity=0.310  Sum_probs=25.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .+.|.||+||||||+++.++. +|.+++..
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~id~   32 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPLVDA   32 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcccch
Confidence            478999999999999999998 88877654

>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=97.48  E-value=6.2e-05  Score=60.34  Aligned_cols=31  Identities=26%  Similarity=0.297  Sum_probs=27.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+.|+|++||||||+++.++..+|.+++..+
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vid~D   44 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVVNVD   44 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEEECc
Confidence            3779999999999999999999898776644

>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=97.47  E-value=9.5e-05  Score=61.06  Aligned_cols=32  Identities=34%  Similarity=0.365  Sum_probs=27.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +..+.|.||||+||||+++.++..++.+++..
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            34588999999999999999999998776543

>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=97.47  E-value=8.9e-05  Score=59.38  Aligned_cols=31  Identities=26%  Similarity=0.260  Sum_probs=27.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+.|.|++|+||||+++.++..+|.+++..+
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            5889999999999999999999998777544

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=97.46  E-value=0.0011  Score=61.48  Aligned_cols=41  Identities=7%  Similarity=0.092  Sum_probs=34.0

Q ss_pred             CceEEEEecCCCC--CCcccccCCCcceeEEEcCCCCHHHHHHHH
Q 024550          142 DERIIIFTTNHKE--RLDPALLRPGRMDMHINMSHCTPSGFKMLA  184 (266)
Q Consensus       142 ~~~ivi~ttn~~~--~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~  184 (266)
                      .++-+|.+|.+|.  .++..++.  -|...|.|...+..+...++
T Consensus       377 ~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI~lrv~s~~Dsr~IL  419 (574)
T 2iut_A          377 AGIHLILATQRPSVDVITGLIKA--NIPTRIAFQVSSKIDSRTIL  419 (574)
T ss_dssp             TTEEEEEEESCCCTTTSCHHHHH--TCCEEEEECCSCHHHHHHHH
T ss_pred             CCeEEEEEecCcccccccHHHHh--hhccEEEEEcCCHHHHHHhc
Confidence            4688888888886  78888887  88889999999998877776

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.46  E-value=0.00024  Score=62.01  Aligned_cols=41  Identities=17%  Similarity=0.069  Sum_probs=32.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCcc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNL   67 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~   67 (266)
                      |+++..-++|+||||+|||+++..+|...         +...++++....
T Consensus       118 Gl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~  167 (343)
T 1v5w_A          118 GIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENT  167 (343)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSC
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            56666669999999999999999999862         556777777653

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=97.46  E-value=0.00016  Score=59.28  Aligned_cols=30  Identities=17%  Similarity=0.152  Sum_probs=23.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i   62 (266)
                      -++++||+|+||||++..++..+   |..++.+
T Consensus        14 i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~   46 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELIRRLHRLEYADVKYLVF   46 (223)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            37788999999999888877766   4455555

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.44  E-value=0.00015  Score=65.72  Aligned_cols=101  Identities=16%  Similarity=0.086  Sum_probs=65.8

Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEe---------cC--
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFT---------TN--  151 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~t---------tn--  151 (266)
                      +.|+||||+|.|.                           ....+.|+..|+.-    +..++|++|         ++  
T Consensus       296 ~~VliIDEa~~l~---------------------------~~a~~aLlk~lEe~----~~~~~il~tn~~~~~i~~~~~~  344 (456)
T 2c9o_A          296 PGVLFVDEVHMLD---------------------------IECFTYLHRALESS----IAPIVIFASNRGNCVIRGTEDI  344 (456)
T ss_dssp             ECEEEEESGGGCB---------------------------HHHHHHHHHHTTST----TCCEEEEEECCSEEECBTTSSC
T ss_pred             ceEEEEechhhcC---------------------------HHHHHHHHHHhhcc----CCCEEEEecCCccccccccccc
Confidence            4799999999873                           23556667766642    234444455         32  


Q ss_pred             -CCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHH-hhcC-CCCHHHHHHHH
Q 024550          152 -HKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKL-IATA-KVTPADVAEQL  217 (266)
Q Consensus       152 -~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l-~~~~-~~s~~~i~~~l  217 (266)
                       .+..+++++++  ||.. +.|+.|+.++..++++......+..+..+...+ +... ..+++....++
T Consensus       345 ~~~~~l~~~i~s--R~~~-~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll  410 (456)
T 2c9o_A          345 TSPHGIPLDLLD--RVMI-IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLL  410 (456)
T ss_dssp             EEETTCCHHHHT--TEEE-EECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTH
T ss_pred             cccccCChhHHh--hcce-eeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHH
Confidence             26788999999  9976 699999999999999988765544444433222 2222 24555554443

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=97.42  E-value=0.00031  Score=61.73  Aligned_cols=64  Identities=27%  Similarity=0.453  Sum_probs=40.2

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCC-ccc---------------ChhhHHHHHHH--cccCCee
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELS-NLL---------------GNNDLRHILIA--TENKSIL   86 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~-~~~---------------~~~~l~~~~~~--~~~~~vl   86 (266)
                      .+...+++.||+|+||||++++++..+    +..++.+.-. .+.               ....+...+..  ..+|.+|
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~~~~~~~~La~aL~~~Pdvi  200 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDII  200 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHHHHHHHTTSCCSEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeeeeccccCCHHHHHHHHhhhCcCEE
Confidence            334458999999999999999998876    3344433211 110               01123333333  2579999


Q ss_pred             eeecch
Q 024550           87 VVEDID   92 (266)
Q Consensus        87 ~iDeid   92 (266)
                      ++||+-
T Consensus       201 llDEp~  206 (356)
T 3jvv_A          201 LVGEMR  206 (356)
T ss_dssp             EESCCC
T ss_pred             ecCCCC
Confidence            999996

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=97.42  E-value=0.0001  Score=58.18  Aligned_cols=26  Identities=15%  Similarity=0.390  Sum_probs=22.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +.-+.|.||+|+||||+++.++....
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            44588999999999999999998764

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=97.40  E-value=0.00028  Score=57.32  Aligned_cols=29  Identities=24%  Similarity=0.336  Sum_probs=25.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      |+++..-+.|+||+|+||||+++.++...
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            56666679999999999999999999854

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=97.40  E-value=0.0001  Score=59.22  Aligned_cols=29  Identities=28%  Similarity=0.438  Sum_probs=24.9

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ...+.-++|.||||+||||+++.|+..++
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             cccCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            34456699999999999999999999884

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=97.39  E-value=5e-05  Score=61.14  Aligned_cols=28  Identities=25%  Similarity=0.326  Sum_probs=23.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      +.-|+|.|+|||||||+++.|+..++.+
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~   37 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNN   37 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            3458899999999999999999987543

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=97.39  E-value=0.00035  Score=56.05  Aligned_cols=38  Identities=16%  Similarity=0.200  Sum_probs=29.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      .+.-+.|.||+|+||||+++.++..+   +.+++..+...+
T Consensus        21 ~~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d~~   61 (201)
T 1rz3_A           21 GRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMDDH   61 (201)
T ss_dssp             SSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGG
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccCcc
Confidence            34458899999999999999999876   666666654433

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=97.39  E-value=0.0001  Score=59.08  Aligned_cols=27  Identities=22%  Similarity=0.357  Sum_probs=24.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      .-|+|.|+||+||||+++.|+..++..
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            458899999999999999999998763

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.39  E-value=0.00024  Score=73.48  Aligned_cols=70  Identities=17%  Similarity=0.224  Sum_probs=50.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC------------------hhhHHHHHHHc-----
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG------------------NNDLRHILIAT-----   80 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~------------------~~~l~~~~~~~-----   80 (266)
                      |++++..++|+||||+|||+|+..+|..+   +.++.+++......                  ...+.+++..+     
T Consensus       728 Gl~~G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS~Ees~~ql~A~~lGvd~~~L~i~~~~~leei~~~l~~lv~  807 (1706)
T 3cmw_A          728 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  807 (1706)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEeccchHHHHHHHHcCCChhheEEecCCcHHHHHHHHHHHHH
Confidence            47778889999999999999999998765   45677777654321                  11233333322     


Q ss_pred             -ccCCeeeeecchhhHH
Q 024550           81 -ENKSILVVEDIDCCIE   96 (266)
Q Consensus        81 -~~~~vl~iDeid~l~~   96 (266)
                       ..+.+|+||.+..+.+
T Consensus       808 ~~~~~lVVIDsLq~l~~  824 (1706)
T 3cmw_A          808 SGAVDVIVVDSVAALTP  824 (1706)
T ss_dssp             HTCCSEEEESCSTTCCC
T ss_pred             ccCCCEEEEechhhhcc
Confidence             4689999999998863

>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=97.38  E-value=9.4e-05  Score=59.00  Aligned_cols=31  Identities=29%  Similarity=0.443  Sum_probs=26.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ..|.|.|++||||||+++.|+.. |.+++..+
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~-g~~~id~d   39 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW-GYPVLDLD   39 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT-TCCEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC-CCEEEccc
Confidence            45889999999999999999998 87776544

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=97.36  E-value=0.00017  Score=60.07  Aligned_cols=30  Identities=33%  Similarity=0.556  Sum_probs=26.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ..+.|.||+|+||||+++.++..+|..++.
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~Lg~~~~d   57 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESLNWRLLD   57 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCCcCC
Confidence            458899999999999999999999887654

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=97.36  E-value=0.00012  Score=63.53  Aligned_cols=36  Identities=28%  Similarity=0.429  Sum_probs=30.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL   67 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~   67 (266)
                      .-++|.||+|||||+|+..||+.++..++..+.-.+
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~qv   76 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKMQV   76 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSSTT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCcEEccccccc
Confidence            358899999999999999999999988877765543

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.35  E-value=0.00045  Score=55.22  Aligned_cols=63  Identities=13%  Similarity=0.238  Sum_probs=40.2

Q ss_pred             ceeEEecCCCCChH-HHHHHHHHHc--CCcEEEEeCC---cccC--------------hhhHHHHHHHcccCCeeeeecc
Q 024550           32 RGYLLYGPPGTGKS-SLIAAMANYL--KFDVYDLELS---NLLG--------------NNDLRHILIATENKSILVVEDI   91 (266)
Q Consensus        32 ~~iLl~GppGtGKT-~la~ala~~~--~~~~~~i~~~---~~~~--------------~~~l~~~~~~~~~~~vl~iDei   91 (266)
                      .-.++|||.|+||| .|.+++.+..  +..++.+.+.   ....              .....+++.....-.+|+|||+
T Consensus        21 ~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlIDEa  100 (195)
T 1w4r_A           21 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEG  100 (195)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEESSG
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccccCccchhhhhhccCCcccceecCCHHHHHHhccCCCEEEEEch
Confidence            34788999999999 7888887755  5566666543   1110              0111122223344579999999


Q ss_pred             hhh
Q 024550           92 DCC   94 (266)
Q Consensus        92 d~l   94 (266)
                      ..+
T Consensus       101 QFf  103 (195)
T 1w4r_A          101 QFF  103 (195)
T ss_dssp             GGC
T ss_pred             hhh
Confidence            977

>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=97.35  E-value=0.00015  Score=62.22  Aligned_cols=35  Identities=20%  Similarity=0.500  Sum_probs=29.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      +.-++|.||+|+|||+|+..+|..++..++..+..
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds~   44 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKILPVELISVDSA   44 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEECCTT
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhCCCcEEecccc
Confidence            44688999999999999999999998877766543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=97.34  E-value=0.00019  Score=58.98  Aligned_cols=39  Identities=26%  Similarity=0.179  Sum_probs=30.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |++++..++|+||||+|||+++..++...   +.+.+.++..
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e   60 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALE   60 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            57777779999999999999988877643   5566666654

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=97.34  E-value=0.00021  Score=57.65  Aligned_cols=27  Identities=37%  Similarity=0.503  Sum_probs=23.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+.-+.|.||+|+|||||++.|+..+.
T Consensus        21 ~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            344588999999999999999999875

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.33  E-value=0.0004  Score=65.78  Aligned_cols=33  Identities=27%  Similarity=0.387  Sum_probs=22.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      -.|++||||||||+++-.+...+   +..++.+..+
T Consensus       207 ~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~T  242 (646)
T 4b3f_X          207 LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPS  242 (646)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCc
Confidence            47899999999997555444433   5556555544

>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=97.33  E-value=0.0001  Score=59.31  Aligned_cols=32  Identities=19%  Similarity=0.185  Sum_probs=25.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc-CCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL-KFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~-~~~~~~i   62 (266)
                      +.-+.|.||+|+||||+++.++..+ +..++..
T Consensus        21 ~~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~~   53 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTTLAKNLQKHLPNCSVISQ   53 (207)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTTSTTEEEEEG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcCCcEEEeC
Confidence            3347899999999999999999987 5544443

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=97.31  E-value=0.0014  Score=60.09  Aligned_cols=41  Identities=5%  Similarity=0.101  Sum_probs=32.6

Q ss_pred             ceEEEEecCCCC--CCcccccCCCcceeEEEcCCCCHHHHHHHHH
Q 024550          143 ERIIIFTTNHKE--RLDPALLRPGRMDMHINMSHCTPSGFKMLAS  185 (266)
Q Consensus       143 ~~ivi~ttn~~~--~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~  185 (266)
                      ++-+|.+|.+|.  .++..+..  -|...|.|...+..+...++.
T Consensus       332 GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lrv~s~~dsr~ilg  374 (512)
T 2ius_A          332 GIHLVLATQRPSVDVITGLIKA--NIPTRIAFTVSSKIDSRTILD  374 (512)
T ss_dssp             TEEEEEEESCCCTTTSCHHHHH--HCCEEEEECCSSHHHHHHHHS
T ss_pred             CcEEEEEecCCccccccHHHHh--hcCCeEEEEcCCHHHHHHhcC
Confidence            577778887775  57777777  888889999999998887764

>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=97.31  E-value=7.1e-05  Score=60.29  Aligned_cols=26  Identities=23%  Similarity=0.155  Sum_probs=22.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +.-|+|.|+|||||||+++.|+..++
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            44588999999999999999999764

>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=97.31  E-value=0.00017  Score=57.07  Aligned_cols=25  Identities=36%  Similarity=0.573  Sum_probs=21.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      .+.|.||+|+||||+++.++...+.
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~~g   28 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQLDN   28 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSS
T ss_pred             EEEEECCCCCcHHHHHHHHhcccCC
Confidence            4789999999999999999986654

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.30  E-value=9.2e-05  Score=64.76  Aligned_cols=30  Identities=23%  Similarity=0.434  Sum_probs=26.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .+++|+||||+||||+++++|..++.+++.
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            359999999999999999999999887744

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=97.29  E-value=0.00022  Score=58.64  Aligned_cols=32  Identities=25%  Similarity=0.393  Sum_probs=27.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +..+.|.|++|+||||+++.++..+|.+++..
T Consensus        16 ~~~i~i~G~~gsGKst~~~~l~~~lg~~~~d~   47 (236)
T 1q3t_A           16 TIQIAIDGPASSGKSTVAKIIAKDFGFTYLDT   47 (236)
T ss_dssp             CCEEEEECSSCSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCceecC
Confidence            34588999999999999999999999876643

>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=97.29  E-value=0.00018  Score=64.62  Aligned_cols=30  Identities=23%  Similarity=0.277  Sum_probs=25.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .-|+|+|+||+||||+++.++..++..++.
T Consensus       259 ~lIil~G~pGSGKSTla~~L~~~~~~~~i~  288 (416)
T 3zvl_A          259 EVVVAVGFPGAGKSTFIQEHLVSAGYVHVN  288 (416)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTGGGTCEECC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhcCcEEEc
Confidence            348899999999999999999998765543

>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=97.29  E-value=0.00023  Score=59.16  Aligned_cols=38  Identities=24%  Similarity=0.185  Sum_probs=30.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc--------EEEEeCCccc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD--------VYDLELSNLL   68 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~--------~~~i~~~~~~   68 (266)
                      +..|.|.|++||||||+++.|+..++.+        +..++..++.
T Consensus        22 ~~iI~I~G~~GSGKST~a~~L~~~lg~~~~d~~~~~~~~i~~D~~~   67 (252)
T 1uj2_A           22 PFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFY   67 (252)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGGGGB
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHhhhhcccccCCceEEEecCccc
Confidence            3458899999999999999999999876        3356665554

>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=97.28  E-value=0.00023  Score=57.72  Aligned_cols=31  Identities=35%  Similarity=0.450  Sum_probs=26.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .-|.|.|++|+||||+++.++. +|.+++..+
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 887766543

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=97.27  E-value=0.00015  Score=58.04  Aligned_cols=27  Identities=22%  Similarity=0.240  Sum_probs=23.3

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++.-+.|.||+|+||||+++.++..+
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            344568899999999999999999876

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=97.26  E-value=0.00023  Score=57.59  Aligned_cols=32  Identities=28%  Similarity=0.334  Sum_probs=27.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ..+.|.|++|||||++++.++..+|.+++..+
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~d   35 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDTG   35 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecCC
Confidence            35889999999999999999999998776543

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=97.26  E-value=0.00042  Score=60.67  Aligned_cols=40  Identities=23%  Similarity=0.259  Sum_probs=31.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~   66 (266)
                      |+++..-+.|+||||+|||+|++.++...         +...++++...
T Consensus       127 gi~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~  175 (349)
T 1pzn_A          127 GIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN  175 (349)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSS
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCC
Confidence            56666669999999999999999999876         24556666544

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=97.24  E-value=0.00029  Score=57.84  Aligned_cols=39  Identities=26%  Similarity=0.181  Sum_probs=30.4

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHH----cCCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANY----LKFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~----~~~~~~~i~~~   65 (266)
                      |+++..-++|+|+||+|||+++..+|..    .+.+++.++..
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E   68 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLE   68 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeeccc
Confidence            5777777999999999999999877643    25677777654

>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=97.23  E-value=0.0011  Score=50.34  Aligned_cols=23  Identities=26%  Similarity=0.381  Sum_probs=20.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|+..+...
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            35899999999999999998854

>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=97.22  E-value=0.00018  Score=58.06  Aligned_cols=28  Identities=25%  Similarity=0.271  Sum_probs=23.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      ++.-+.|.||+|+||||+++.|+..+..
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            3445889999999999999999988753

>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=97.22  E-value=0.00059  Score=56.31  Aligned_cols=33  Identities=21%  Similarity=0.169  Sum_probs=27.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      .++++||+|+|||.++..++...+.+.+.+.+.
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~  142 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEESS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCC
Confidence            499999999999999999988887766666544

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=97.21  E-value=0.00019  Score=62.48  Aligned_cols=32  Identities=19%  Similarity=0.299  Sum_probs=27.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .-++|.||+|+|||+++..||..++..++..+
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~~~iis~D   39 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFNGEIISGD   39 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTEEEEECC
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcCCceeccc
Confidence            46889999999999999999999987665554

>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=97.21  E-value=0.00019  Score=60.92  Aligned_cols=29  Identities=31%  Similarity=0.290  Sum_probs=24.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      -|.|.|++||||||+++.++ .+|.+++..
T Consensus        77 iI~I~G~~GSGKSTva~~La-~lg~~~id~  105 (281)
T 2f6r_A           77 VLGLTGISGSGKSSVAQRLK-NLGAYIIDS  105 (281)
T ss_dssp             EEEEEECTTSCHHHHHHHHH-HHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHH-HCCCcEEeh
Confidence            48899999999999999999 578776554

>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=97.20  E-value=0.0004  Score=56.06  Aligned_cols=36  Identities=25%  Similarity=0.355  Sum_probs=28.3

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcC----CcEEEEe
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLK----FDVYDLE   63 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~----~~~~~i~   63 (266)
                      ...+..++|.|+||+||||+++.++..++    .+++.++
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            44455688999999999999999998774    4466555

>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=97.20  E-value=0.00029  Score=56.09  Aligned_cols=28  Identities=32%  Similarity=0.492  Sum_probs=23.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      +-|+|+||+|+|||||++.|.......+
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~~~~   29 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYPDSF   29 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCCCCe
Confidence            3489999999999999999988874433

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=97.20  E-value=0.00024  Score=56.77  Aligned_cols=27  Identities=30%  Similarity=0.544  Sum_probs=22.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ++.-+.|.||+|+||||+++.++....
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L~~~~~   32 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRALVKALA   32 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHSS
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            344588999999999999999999863

>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=97.20  E-value=0.00021  Score=57.39  Aligned_cols=32  Identities=22%  Similarity=0.274  Sum_probs=26.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .++++|.||+|+|||+++..++...+ .++..+
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~-~iIsdD   65 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH-RLIADD   65 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC-EEEESS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC-eEEecc
Confidence            45699999999999999999999876 555443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=97.19  E-value=0.00025  Score=55.94  Aligned_cols=26  Identities=31%  Similarity=0.529  Sum_probs=22.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +..++|.|+||+||||+++.++..++
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~   38 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQ   38 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            44588999999999999999999874

>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=97.18  E-value=0.00023  Score=60.65  Aligned_cols=29  Identities=28%  Similarity=0.297  Sum_probs=24.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-CCcEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-KFDVY   60 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-~~~~~   60 (266)
                      .-|+|.|+||+||||+++.++..+ +..++
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i   32 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEe
Confidence            458999999999999999999974 55444

>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=97.16  E-value=0.00036  Score=54.01  Aligned_cols=29  Identities=24%  Similarity=0.231  Sum_probs=24.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++...+.|.||.|+|||||++.++..+
T Consensus        29 ~i~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           29 HTEKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CCSSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            44555568899999999999999999987

>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=97.14  E-value=0.00025  Score=61.02  Aligned_cols=33  Identities=21%  Similarity=0.265  Sum_probs=27.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      .-++|.||+|+|||+++..+|..++..++..+.
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            357889999999999999999999876665543

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=97.12  E-value=0.00031  Score=60.25  Aligned_cols=25  Identities=24%  Similarity=0.413  Sum_probs=22.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +.-+.|.||+|+||||+++.+|..+
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            4458899999999999999999876

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=97.11  E-value=0.00026  Score=56.70  Aligned_cols=27  Identities=33%  Similarity=0.486  Sum_probs=22.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +++.+.|.||+|+||||+++.++....
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            345689999999999999999998763

>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=97.10  E-value=0.00036  Score=59.87  Aligned_cols=34  Identities=35%  Similarity=0.492  Sum_probs=28.4

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      +.++++..+.|+||+|+|||||++.|+..+...+
T Consensus       121 l~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~~G~I  154 (305)
T 2v9p_A          121 KGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSV  154 (305)
T ss_dssp             HTCTTCSEEEEECSSSSSHHHHHHHHHHHHTCEE
T ss_pred             EEecCCCEEEEECCCCCcHHHHHHHHhhhcCceE
Confidence            3566667799999999999999999999885444

>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=97.10  E-value=0.0015  Score=49.41  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=20.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|++|+|||+++..+....
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            58999999999999999998643

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=97.08  E-value=0.00038  Score=56.01  Aligned_cols=29  Identities=14%  Similarity=0.159  Sum_probs=26.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .|.|.||+|||||++++.+|..+|.+++.
T Consensus         8 iI~i~g~~GsGk~ti~~~la~~lg~~~~D   36 (201)
T 3fdi_A            8 IIAIGREFGSGGHLVAKKLAEHYNIPLYS   36 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTCCEEC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHhCcCEEC
Confidence            58889999999999999999999999874

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=97.08  E-value=0.00043  Score=46.78  Aligned_cols=45  Identities=7%  Similarity=-0.103  Sum_probs=36.0

Q ss_pred             CCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          173 SHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       173 ~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      |.|+.++|.+||+.++.........++..++.. .+||++||.+++
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~   46 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVC   46 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHH
Confidence            689999999999999988654334456666665 469999999988

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=97.07  E-value=0.00034  Score=56.97  Aligned_cols=27  Identities=30%  Similarity=0.489  Sum_probs=22.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +++.-+.|.||+|+||||+++.++...
T Consensus        21 ~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           21 NNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             -CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            334458899999999999999999976

>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=97.07  E-value=0.00037  Score=61.94  Aligned_cols=34  Identities=26%  Similarity=0.380  Sum_probs=28.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      +.-++|.||+|+|||+++..+|..++..++..+.
T Consensus         2 ~~~i~i~GptgsGKttla~~La~~~~~~iis~Ds   35 (409)
T 3eph_A            2 KKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDS   35 (409)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHHHHTEEEEECCT
T ss_pred             CcEEEEECcchhhHHHHHHHHHHHCCCeEeecCc
Confidence            3457899999999999999999999877665543

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=97.05  E-value=0.00096  Score=59.46  Aligned_cols=40  Identities=23%  Similarity=0.142  Sum_probs=30.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~   66 (266)
                      |+++..-+.|+||||+|||+|++.++...         +...++++...
T Consensus       174 GI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~  222 (400)
T 3lda_A          174 GVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEG  222 (400)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCC
Confidence            56666679999999999999999776432         34477777654

>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=97.05  E-value=0.0017  Score=49.32  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|+..+...
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            46899999999999999999864

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=97.05  E-value=0.00038  Score=55.97  Aligned_cols=26  Identities=27%  Similarity=0.261  Sum_probs=23.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +.-+.|.||+|+||||+++.++..++
T Consensus         6 ~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            6 PFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34578999999999999999999887

>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=97.04  E-value=0.0017  Score=49.32  Aligned_cols=22  Identities=27%  Similarity=0.445  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|++.+...
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>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=97.03  E-value=0.0021  Score=54.85  Aligned_cols=36  Identities=19%  Similarity=0.356  Sum_probs=27.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~   66 (266)
                      +..+.|.||+|+||||++..+|..+    |..+..+++..
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~  144 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDT  144 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCc
Confidence            4458899999999999999998765    44666665543

>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=97.03  E-value=0.0015  Score=50.88  Aligned_cols=23  Identities=26%  Similarity=0.423  Sum_probs=20.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|++|+|||+|+..+....
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58999999999999999998643

>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=97.01  E-value=0.0005  Score=54.33  Aligned_cols=33  Identities=24%  Similarity=0.250  Sum_probs=28.9

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL   67 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~   67 (266)
                      +|++|++|+|||++|+.++.. +.+.+++.....
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~~~   34 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATSQI   34 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECCCC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecCCC
Confidence            789999999999999999988 888888877554

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=97.00  E-value=0.00038  Score=61.17  Aligned_cols=26  Identities=23%  Similarity=0.353  Sum_probs=22.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++..+.|.||+|+||||+++.+|..+
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            34458899999999999999999876

>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=96.99  E-value=0.0022  Score=49.66  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..++|.|++|+|||+|+..+...
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhhC
Confidence            35999999999999999999864

>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=96.99  E-value=0.00075  Score=51.50  Aligned_cols=21  Identities=43%  Similarity=0.703  Sum_probs=18.9

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .+++.|++|+|||+|++.+..
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            589999999999999999864

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=96.98  E-value=0.001  Score=60.01  Aligned_cols=94  Identities=17%  Similarity=0.256  Sum_probs=62.7

Q ss_pred             HHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC------CCCceEEEE
Q 024550           75 HILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS------CGDERIIIF  148 (266)
Q Consensus        75 ~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~------~~~~~ivi~  148 (266)
                      ..+..+...+++++||||.+.......               ..+.....++..||..|++....      ....++||+
T Consensus       243 ~ai~~ae~~~il~~DEidki~~~~~~~---------------~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~  307 (444)
T 1g41_A          243 KAIDAVEQNGIVFIDEIDKICKKGEYS---------------GADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIA  307 (444)
T ss_dssp             HHHHHHHHHCEEEEETGGGGSCCSSCS---------------SSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEE
T ss_pred             HHHHHhccCCeeeHHHHHHHhhccCCC---------------CCCchHHHHHHHHHHHhcccccccccceecCCcEEEEe
Confidence            444455578899999999996421100               00112233566788888863211      125688998


Q ss_pred             ec----CCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHH
Q 024550          149 TT----NHKERLDPALLRPGRMDMHINMSHCTPSGFKMLAS  185 (266)
Q Consensus       149 tt----n~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~  185 (266)
                      |.    +.|..+.|.|+.  ||...|.|+.++.++..+|+.
T Consensus       308 ~gaf~~~~~~dlipel~~--R~~i~i~l~~lt~~e~~~Il~  346 (444)
T 1g41_A          308 SGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILT  346 (444)
T ss_dssp             EECCSSCCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             ccccccCChhhcchHHhc--ccceeeeCCCCCHHHHHHHHH
Confidence            87    234445578999  999999999999999999884

>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=96.98  E-value=0.0044  Score=46.96  Aligned_cols=23  Identities=17%  Similarity=0.249  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|++|+|||+|+..+...-
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999997643

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.97  E-value=0.00024  Score=55.51  Aligned_cols=23  Identities=26%  Similarity=0.312  Sum_probs=18.8

Q ss_pred             CCCceeEEecCCCCChHHHHHHH
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAM   51 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~al   51 (266)
                      +.+.-+.|.||+|+||||+++.+
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~~~   29 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAKKH   29 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHH
Confidence            34455889999999999999953

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=96.97  E-value=0.00058  Score=58.67  Aligned_cols=35  Identities=20%  Similarity=0.180  Sum_probs=26.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +.-+++.||+|+||||++..+|..+   +..+..+++.
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~D  141 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAAD  141 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEccc
Confidence            4458899999999999999999876   4455555443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=96.97  E-value=0.00059  Score=57.25  Aligned_cols=34  Identities=32%  Similarity=0.441  Sum_probs=26.5

Q ss_pred             HHHHhCCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           22 FYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        22 ~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+....+.+...++|.||+|+||||++++++..+
T Consensus        16 vl~~i~i~~g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           16 KVLELCHRKMGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             HHHHGGGCSSEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             HHHHHhhCCCCEEEEECCCCccHHHHHHHHHHhC
Confidence            3444445555568999999999999999999865

>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=96.96  E-value=0.00051  Score=56.09  Aligned_cols=29  Identities=38%  Similarity=0.478  Sum_probs=23.6

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+.+.-+.|.||+|+|||||++.++....
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            34455688999999999999999999774

>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=96.96  E-value=0.0025  Score=50.37  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..|+|.|++|+|||+|+..+...
T Consensus        15 ~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           15 HKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35999999999999999999754

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.96  E-value=0.0009  Score=57.65  Aligned_cols=39  Identities=21%  Similarity=0.173  Sum_probs=31.7

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |+++..-++|.|+||+|||+++..+|...   +.+++.+++.
T Consensus        64 Gl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~slE  105 (315)
T 3bh0_A           64 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  105 (315)
T ss_dssp             SBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEECC
Confidence            67777779999999999999999988654   4567777755

>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=96.96  E-value=0.00053  Score=55.16  Aligned_cols=29  Identities=28%  Similarity=0.454  Sum_probs=23.4

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +.++..+.|.||+|+||||+++.++..+.
T Consensus        17 i~~Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           17 AAVGRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             --CCCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            44445588999999999999999999874

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=96.95  E-value=0.00056  Score=54.93  Aligned_cols=26  Identities=23%  Similarity=0.445  Sum_probs=22.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ++-+.|.||+|+|||||++.|+....
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            34588999999999999999998764

>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=96.94  E-value=0.00049  Score=58.52  Aligned_cols=39  Identities=21%  Similarity=0.111  Sum_probs=30.5

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeC
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLEL   64 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~   64 (266)
                      .|+++..-++|.||||+|||++++.++..+    |.+++.++.
T Consensus        30 ~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~   72 (296)
T 1cr0_A           30 LGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (296)
T ss_dssp             CSBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             cCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            467667779999999999999999998765    435655554

>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=96.93  E-value=0.00041  Score=63.30  Aligned_cols=25  Identities=28%  Similarity=0.398  Sum_probs=22.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..+.|.||+|+||||+++.|+..+
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHh
Confidence            4458899999999999999999876

>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=96.93  E-value=0.00071  Score=57.68  Aligned_cols=39  Identities=21%  Similarity=0.231  Sum_probs=28.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC-----cEEEE-eCCccc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF-----DVYDL-ELSNLL   68 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~-----~~~~i-~~~~~~   68 (266)
                      .+.-+.|.||+|+||||+++.++..++.     +.+.+ +...+.
T Consensus        30 ~~~ii~I~G~sGsGKSTla~~L~~~l~~~g~~~~~~~iv~~D~f~   74 (290)
T 1odf_A           30 CPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFY   74 (290)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGB
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhhhcCCCCceEEEecccccc
Confidence            3445889999999999999999988853     23334 555544

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=96.93  E-value=0.0061  Score=60.44  Aligned_cols=36  Identities=25%  Similarity=0.441  Sum_probs=26.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH------cCCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY------LKFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~------~~~~~~~i~~~~   66 (266)
                      .+-+.|+||.|+|||+||+.+++.      +....+.++.+.
T Consensus       150 ~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~  191 (1221)
T 1vt4_I          150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN  191 (1221)
T ss_dssp             SCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCC
T ss_pred             CeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCC
Confidence            456889999999999999998853      344455555443

>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=96.93  E-value=0.003  Score=49.82  Aligned_cols=25  Identities=24%  Similarity=0.432  Sum_probs=21.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ....+++.|++|+|||+|+..+...
T Consensus        27 ~~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           27 AEVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3456999999999999999999864

>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=96.89  E-value=0.00068  Score=60.98  Aligned_cols=35  Identities=20%  Similarity=0.288  Sum_probs=27.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +.-+++.||+|+||||++..+|..+   |..+..+++.
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D  134 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAAD  134 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecC
Confidence            4458899999999999999998766   5555555544

>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=96.88  E-value=0.011  Score=53.48  Aligned_cols=24  Identities=29%  Similarity=0.508  Sum_probs=20.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..++|+||+|+|||+|+..++...
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            458999999999999999887654

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=96.87  E-value=0.00069  Score=56.04  Aligned_cols=27  Identities=19%  Similarity=0.166  Sum_probs=23.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      .-+-|.||+|+||||+++.++..+|..
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            347789999999999999999988643

>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=96.86  E-value=0.0014  Score=56.74  Aligned_cols=26  Identities=35%  Similarity=0.493  Sum_probs=22.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++.-+.|.||+|+||||+++.+|..+
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            34558899999999999999999876

>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=96.85  E-value=0.0022  Score=49.76  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=20.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        20 ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           20 KLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999864

>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=96.84  E-value=0.0015  Score=50.23  Aligned_cols=23  Identities=39%  Similarity=0.593  Sum_probs=20.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|++.+...
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCccHHHHHHHHhcC
Confidence            35899999999999999998753

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=96.84  E-value=0.0007  Score=55.65  Aligned_cols=29  Identities=21%  Similarity=0.395  Sum_probs=25.6

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +-|.||||+||||+++.|+..++.+.+..
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~~~g~~~is~   39 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKEKFGIPQIST   39 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTCCEECH
T ss_pred             eeeECCCCCCHHHHHHHHHHHhCCCeeec
Confidence            66899999999999999999998877644

>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=96.84  E-value=0.00094  Score=60.16  Aligned_cols=36  Identities=25%  Similarity=0.398  Sum_probs=28.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      +.-++++||+|+||||++..+|..+   |..+..+++..
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~  138 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDT  138 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCC
Confidence            4568999999999999999998766   55666665543

>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=96.82  E-value=0.00093  Score=62.77  Aligned_cols=32  Identities=31%  Similarity=0.549  Sum_probs=28.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      ..|+|.|+||+||||+++.|+..+   |.+++.++
T Consensus        53 ~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lD   87 (630)
T 1x6v_B           53 CTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   87 (630)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEES
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEec
Confidence            348899999999999999999999   88888875

>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=96.80  E-value=0.001  Score=58.77  Aligned_cols=33  Identities=33%  Similarity=0.488  Sum_probs=26.3

Q ss_pred             HHHhCCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           23 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        23 ~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..+.+.++..++|.||+|+||||++++++..+
T Consensus       128 l~~l~~~~g~~i~ivG~~GsGKTTll~~l~~~~  160 (372)
T 2ewv_A          128 VLELCHRKMGLILVTGPTGSGKSTTIASMIDYI  160 (372)
T ss_dssp             HHHHTTSSSEEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             HHHHhhcCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            344445555669999999999999999999865

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=96.77  E-value=0.0011  Score=57.19  Aligned_cols=37  Identities=32%  Similarity=0.473  Sum_probs=28.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      ++..+.++||+|+||||++..+|..+   +..+..+++..
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D~  143 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAADT  143 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCC
Confidence            34458899999999999999998766   55666665543

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=96.77  E-value=0.0017  Score=58.50  Aligned_cols=65  Identities=15%  Similarity=0.242  Sum_probs=42.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc------------------------c--Ch-hhHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL------------------------L--GN-NDLRHILIAT   80 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~------------------------~--~~-~~l~~~~~~~   80 (266)
                      +..++++|++|+||||++..+|..+   |..+..+++...                        .  +. .-+...+...
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D~~r~~a~~qL~~~~~~~gv~v~~~~~~~~dp~~i~~~~l~~~  178 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKF  178 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCSCCCTTGGGSSHHHHHHSSCCEECCSSSCCSSSTTHHHHHHTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeccccCchHHHHHHHhhhccCcceEecCCCCCCHHHHHHHHHHHh
Confidence            3468999999999999999999876   355555554321                        0  00 1123444445


Q ss_pred             ccCCeeeeecchhhH
Q 024550           81 ENKSILVVEDIDCCI   95 (266)
Q Consensus        81 ~~~~vl~iDeid~l~   95 (266)
                      ....+++||....+.
T Consensus       179 ~~~D~vIIDT~G~~~  193 (432)
T 2v3c_C          179 KKADVLIIDTAGRHK  193 (432)
T ss_dssp             SSCSEEEEECCCSCS
T ss_pred             hCCCEEEEcCCCCcc
Confidence            567889999877553

>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=96.77  E-value=0.0069  Score=47.16  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=20.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ...+++.|++|+|||+|+..+...
T Consensus        16 ~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           16 EVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            345999999999999999998864

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=96.77  E-value=0.0034  Score=49.88  Aligned_cols=18  Identities=22%  Similarity=0.302  Sum_probs=15.2

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      .+.+++.+|+|+|||..+
T Consensus        38 ~~~~li~~~TGsGKT~~~   55 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAF   55 (207)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEECCCCChHHHHH
Confidence            356999999999999863

>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=96.76  E-value=0.0014  Score=52.39  Aligned_cols=23  Identities=22%  Similarity=0.462  Sum_probs=19.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      +.+++++|+|+|||.++-..+..
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~   71 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKD   71 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHH
Confidence            57999999999999987776654

>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=96.76  E-value=0.00032  Score=56.37  Aligned_cols=24  Identities=21%  Similarity=0.414  Sum_probs=21.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      -|.|.||+|+||||+++.|+..++
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            367899999999999999999885

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=96.74  E-value=0.0065  Score=48.96  Aligned_cols=17  Identities=29%  Similarity=0.390  Sum_probs=14.9

Q ss_pred             CceeEEecCCCCChHHH
Q 024550           31 KRGYLLYGPPGTGKSSL   47 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~l   47 (266)
                      .+.+++++|+|+|||..
T Consensus        51 ~~~~lv~~pTGsGKT~~   67 (224)
T 1qde_A           51 GHDVLAQAQSGTGKTGT   67 (224)
T ss_dssp             TCCEEEECCTTSSHHHH
T ss_pred             CCCEEEECCCCCcHHHH
Confidence            35699999999999976

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=96.74  E-value=0.00043  Score=56.63  Aligned_cols=26  Identities=19%  Similarity=0.257  Sum_probs=16.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHH-HHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMA-NYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala-~~~   55 (266)
                      ++.-+.|.||+|+||||+++.++ ..+
T Consensus        26 ~G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           26 VGVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCCEEEEECSCC----CHHHHHHC---
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            34458899999999999999999 765

>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=96.74  E-value=0.002  Score=51.38  Aligned_cols=63  Identities=16%  Similarity=0.178  Sum_probs=38.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc--------cC----------hhhHHHHHHHccc-CCeeeee
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL--------LG----------NNDLRHILIATEN-KSILVVE   89 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~--------~~----------~~~l~~~~~~~~~-~~vl~iD   89 (266)
                      .-.+++||+|+|||+.+..++..+   |..++.+.+..-        .+          .....+++..... ..+|+||
T Consensus         9 ~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~~~~~dvViID   88 (191)
T 1xx6_A            9 WVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAID   88 (191)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEEEC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHHhccCCEEEEE
Confidence            347789999999999888777765   555544431100        00          0111244544443 5799999


Q ss_pred             cchhh
Q 024550           90 DIDCC   94 (266)
Q Consensus        90 eid~l   94 (266)
                      |+..+
T Consensus        89 Eaqfl   93 (191)
T 1xx6_A           89 EVQFF   93 (191)
T ss_dssp             SGGGS
T ss_pred             CCCCC
Confidence            99876

>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=96.73  E-value=0.0024  Score=48.75  Aligned_cols=21  Identities=33%  Similarity=0.586  Sum_probs=18.9

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .+++.|++|+|||+|+..+..
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            488999999999999999864

>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=96.73  E-value=0.0029  Score=49.51  Aligned_cols=23  Identities=35%  Similarity=0.522  Sum_probs=20.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..++|.|++|+|||+|+..+...
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            35999999999999999999864

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.72  E-value=0.0017  Score=58.57  Aligned_cols=39  Identities=15%  Similarity=0.095  Sum_probs=31.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~   65 (266)
                      |++++.-++|+|+||+|||+++..+|...    |.+++.++..
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE  238 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLE  238 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            57666679999999999999999887654    5577777764

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=96.72  E-value=0.0011  Score=54.37  Aligned_cols=29  Identities=21%  Similarity=0.202  Sum_probs=26.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .|.+.|++|||||++++.||..+|.+++.
T Consensus        16 iI~i~g~~gsGk~~i~~~la~~lg~~~~d   44 (223)
T 3hdt_A           16 IITIEREYGSGGRIVGKKLAEELGIHFYD   44 (223)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHcCCcEEc
Confidence            47789999999999999999999998865

>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=96.71  E-value=0.0011  Score=54.34  Aligned_cols=31  Identities=29%  Similarity=0.441  Sum_probs=25.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC--CcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK--FDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~--~~~~~i   62 (266)
                      .-+.|.||||+||||+++.++..++  .+++..
T Consensus        27 ~~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~~   59 (229)
T 4eaq_A           27 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIMT   59 (229)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCEEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhcCCCceee
Confidence            3477889999999999999999986  455443

>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=96.71  E-value=0.0022  Score=50.21  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=20.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|++|+|||+|+..+....
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998643

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.71  E-value=0.0018  Score=58.70  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=31.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~   65 (266)
                      |++++.-++|.|+||+|||+++..+|...    |.+++.++..
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E  241 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLE  241 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESS
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECC
Confidence            56666679999999999999999888754    5577777754

>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=96.70  E-value=0.0035  Score=49.41  Aligned_cols=23  Identities=17%  Similarity=0.345  Sum_probs=20.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~   53 (266)
                      ...+++.|++|+|||+|+..+..
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            44699999999999999999864

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=96.70  E-value=0.0036  Score=53.37  Aligned_cols=33  Identities=15%  Similarity=0.172  Sum_probs=23.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+.+++.+|+|+|||..+-..+-..+...+.+.
T Consensus        31 ~~~~lv~~~TGsGKT~~~~~~~~~~~~~~liv~   63 (337)
T 2z0m_A           31 GKNVVVRAKTGSGKTAAYAIPILELGMKSLVVT   63 (337)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEC
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHhhcCCEEEEe
Confidence            357999999999999876655555555544443

>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=96.70  E-value=0.0015  Score=61.51  Aligned_cols=23  Identities=43%  Similarity=0.622  Sum_probs=18.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..+++||||||||+++..++..+
T Consensus       197 ~~li~GppGTGKT~~~~~~i~~l  219 (624)
T 2gk6_A          197 LSLIQGPPGTGKTVTSATIVYHL  219 (624)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEECCCCCCHHHHHHHHHHHH
Confidence            57899999999999877766554

>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=96.69  E-value=0.0034  Score=48.35  Aligned_cols=23  Identities=26%  Similarity=0.394  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|+.++...
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            35999999999999999999865

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=96.69  E-value=0.0013  Score=51.46  Aligned_cols=28  Identities=32%  Similarity=0.449  Sum_probs=23.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      ..++||.|++|+|||+++.++... |..+
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r-G~~l   43 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR-GHQL   43 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT-TCEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCeE
Confidence            568999999999999999999874 4433

>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=96.69  E-value=0.003  Score=49.20  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..++|.|++|+|||+|+..+...
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999999863

>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=96.66  E-value=0.003  Score=48.11  Aligned_cols=24  Identities=29%  Similarity=0.331  Sum_probs=20.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -.+++.|++|+|||++++.+...-
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            358999999999999999998654

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=96.62  E-value=0.00071  Score=57.63  Aligned_cols=36  Identities=14%  Similarity=0.238  Sum_probs=26.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC---CcEEEEeCCccc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK---FDVYDLELSNLL   68 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~---~~~~~i~~~~~~   68 (266)
                      -|.|.||+|+||||+++.++..++   ..+..++...+.
T Consensus         7 iIgItG~sGSGKSTva~~L~~~lg~~~~~~~vI~~D~~~   45 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFH   45 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGGB
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCCCeeEeecchhh
Confidence            478999999999999999999776   445667766665

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=96.61  E-value=0.0012  Score=52.65  Aligned_cols=23  Identities=43%  Similarity=0.780  Sum_probs=20.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.|.||+|+||||+++.++..+
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            47899999999999999999876

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.59  E-value=0.0024  Score=55.57  Aligned_cols=39  Identities=23%  Similarity=0.179  Sum_probs=31.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |+.+..-++|.|+||+|||+++..+|...   +.++..++..
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSlE   83 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSLE   83 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence            56666669999999999999999988764   6777777765

>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=96.58  E-value=0.0033  Score=49.91  Aligned_cols=31  Identities=16%  Similarity=0.303  Sum_probs=23.0

Q ss_pred             HHHhCCCC-CceeEEecCCCCChHHHHHHHHH
Q 024550           23 YRRVGKAW-KRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        23 ~~~~~~~~-~~~iLl~GppGtGKT~la~ala~   53 (266)
                      +..+.... +..+++.|++|+|||+|++.+..
T Consensus        16 l~~~~~~~~~~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           16 LQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             HHHHTCTTCCEEEEEEEETTSSHHHHHHHHSC
T ss_pred             HHHhhccCCCcEEEEECCCCCCHHHHHHHHhc
Confidence            34444333 23599999999999999999874

>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=96.58  E-value=0.0057  Score=47.86  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=19.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4999999999999999999853

>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=96.58  E-value=0.0037  Score=47.53  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=20.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -.+++.|++|+|||+|+.++...-
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            4 IKLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            358999999999999999987543

>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=96.53  E-value=0.0043  Score=48.53  Aligned_cols=22  Identities=18%  Similarity=0.283  Sum_probs=19.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        22 ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5999999999999999999753

>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=96.51  E-value=0.0012  Score=54.54  Aligned_cols=28  Identities=25%  Similarity=0.357  Sum_probs=23.2

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+...+.|.||+|+|||||++.++....
T Consensus        29 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl~~   56 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKSTMLNIIGCLDK   56 (235)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            3444588999999999999999998663

>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=96.50  E-value=0.0018  Score=50.80  Aligned_cols=25  Identities=24%  Similarity=0.240  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+|+||||+++.+...+
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            3468899999999999999998865

>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=96.50  E-value=0.0086  Score=46.66  Aligned_cols=23  Identities=13%  Similarity=0.367  Sum_probs=20.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~   53 (266)
                      ...+++.|++|+|||+|+..+..
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            45699999999999999999984

>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=96.49  E-value=0.0018  Score=55.75  Aligned_cols=27  Identities=19%  Similarity=0.078  Sum_probs=22.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+.-+-|.||+|+|||||++.|+..+.
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            344477999999999999999999773

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=96.49  E-value=0.0044  Score=42.67  Aligned_cols=47  Identities=11%  Similarity=-0.043  Sum_probs=36.7

Q ss_pred             EcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcC-CCCHHHHHHHH
Q 024550          171 NMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATA-KVTPADVAEQL  217 (266)
Q Consensus       171 ~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~-~~s~~~i~~~l  217 (266)
                      +-..|+.++|.+||+.++.........++..++..+ +||++||.+++
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~   54 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVC   54 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHH
Confidence            347899999999999999876543344556666654 79999999987

>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=96.48  E-value=0.0058  Score=47.86  Aligned_cols=22  Identities=27%  Similarity=0.555  Sum_probs=20.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           27 KVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5999999999999999999864

>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=96.48  E-value=0.0019  Score=55.42  Aligned_cols=25  Identities=36%  Similarity=0.578  Sum_probs=21.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..+.|.||+|+||||+++.+|..+
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            3458899999999999999999876

>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=96.47  E-value=0.0013  Score=54.39  Aligned_cols=27  Identities=30%  Similarity=0.309  Sum_probs=22.8

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++...+.|.||+|+|||||++.++...
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            344458899999999999999999865

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=96.47  E-value=0.0028  Score=57.29  Aligned_cols=40  Identities=20%  Similarity=0.150  Sum_probs=32.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      |+.++.-++|.|+||+|||+++..+|...   |.++..+++..
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlEm  235 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLEM  235 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSSS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECCC
Confidence            56666679999999999999998887665   66777777653

>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=96.46  E-value=0.005  Score=46.75  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.45  E-value=0.01  Score=51.22  Aligned_cols=36  Identities=19%  Similarity=0.162  Sum_probs=27.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCccc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNLL   68 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~~   68 (266)
                      -+-|.||+||||||+++.++..++     ..+..++...+.
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll~~~~~~~~v~~i~~D~f~  134 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALLSRWPDHPNVEVITTDGFL  134 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGB
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcccCCCCeEEEEeecccc
Confidence            477899999999999999998875     235555555443

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=96.45  E-value=0.0023  Score=50.77  Aligned_cols=24  Identities=25%  Similarity=0.268  Sum_probs=20.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..++|.|++|+|||+|+..+...-
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCcCHHHHHHHHHhCC
Confidence            359999999999999999998643

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=96.44  E-value=0.0038  Score=48.91  Aligned_cols=26  Identities=23%  Similarity=0.544  Sum_probs=22.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ....+++.|++|+|||+++..+....
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34469999999999999999998754

>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=96.44  E-value=0.002  Score=50.30  Aligned_cols=25  Identities=28%  Similarity=0.210  Sum_probs=22.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -.+|+||.|+|||+++++++..++.
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~~   52 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLGG   52 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTC
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHcC
Confidence            4779999999999999999988763

>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=96.44  E-value=0.0028  Score=61.37  Aligned_cols=23  Identities=43%  Similarity=0.622  Sum_probs=18.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -.++.||||||||+++..++..+
T Consensus       373 ~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          373 LSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHH
Confidence            57899999999999877766554

>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=96.44  E-value=0.0029  Score=58.37  Aligned_cols=25  Identities=24%  Similarity=0.499  Sum_probs=22.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ..|+++|.||+||||+++.++..++
T Consensus        36 ~lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           36 TVIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3488999999999999999999884

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=96.43  E-value=0.0011  Score=54.26  Aligned_cols=27  Identities=22%  Similarity=0.225  Sum_probs=22.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ++..+.|.||+|+|||||++.++....
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~~   55 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLYILGLLDA   55 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            344578999999999999999998663

>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=96.43  E-value=0.0034  Score=61.57  Aligned_cols=23  Identities=39%  Similarity=0.485  Sum_probs=19.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~   53 (266)
                      +..+.|.||.|+||||+.+.++.
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            34588999999999999998874

>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=96.42  E-value=0.0088  Score=45.82  Aligned_cols=24  Identities=29%  Similarity=0.491  Sum_probs=20.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..+++.|++|+|||+|+..+...-
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            359999999999999999998643

>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=96.41  E-value=0.0063  Score=46.90  Aligned_cols=22  Identities=36%  Similarity=0.534  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5999999999999999999864

>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=96.41  E-value=0.0052  Score=48.57  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=20.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ...++|.|++|+|||+|+..+...
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhC
Confidence            346999999999999999999754

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=96.41  E-value=0.0046  Score=47.03  Aligned_cols=22  Identities=32%  Similarity=0.508  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>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=96.40  E-value=0.007  Score=58.62  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=20.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+.|.||.|+||||+.+.++..
T Consensus       608 ~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          608 RMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCChHHHHHHHHHH
Confidence            34889999999999999999864

>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=96.40  E-value=0.014  Score=45.37  Aligned_cols=23  Identities=22%  Similarity=0.392  Sum_probs=20.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++|.|++|+|||+|++.+....
T Consensus        16 ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc
Confidence            49999999999999999887654

>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=96.39  E-value=0.0044  Score=48.72  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=20.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      ..+++.|++|+|||++++.+..
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            3599999999999999999986

>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=96.38  E-value=0.0026  Score=59.37  Aligned_cols=31  Identities=26%  Similarity=0.215  Sum_probs=27.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC----CcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK----FDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~----~~~~~i~   63 (266)
                      .|+|.|+||+||||+++.|+..++    .+++.++
T Consensus       398 ~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD  432 (573)
T 1m8p_A          398 TIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLL  432 (573)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEE
T ss_pred             EEEeecCCCCCHHHHHHHHHHHhcccCCceEEEEC
Confidence            488999999999999999999986    6677776

>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=96.38  E-value=0.0035  Score=53.69  Aligned_cols=36  Identities=17%  Similarity=0.113  Sum_probs=27.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNL   67 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~   67 (266)
                      .-+-|.||+|+||||+++.++..++     ..+..++....
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~~~~~~G~i~vi~~d~~  121 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHhhCCCCCeEEEEecCCc
Confidence            3477999999999999999999765     23545554444

>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=96.37  E-value=0.0036  Score=48.99  Aligned_cols=23  Identities=22%  Similarity=0.306  Sum_probs=20.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|++|+|||+|+..+....
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           23 HVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEECTTSSHHHHHHHTSCGG
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999987654

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=96.36  E-value=0.0067  Score=47.46  Aligned_cols=24  Identities=38%  Similarity=0.488  Sum_probs=20.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..++|.|++|+|||+|+..+...-
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            359999999999999999998643

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=96.35  E-value=0.0023  Score=51.83  Aligned_cols=31  Identities=26%  Similarity=0.321  Sum_probs=27.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      .+-|+|..||||||+++.++. +|.+++..+.
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            477999999999999999998 9998887664

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=96.33  E-value=0.002  Score=53.33  Aligned_cols=27  Identities=30%  Similarity=0.507  Sum_probs=23.1

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +++ ..+.|.||+|+|||||++.++...
T Consensus        22 i~~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           22 MGR-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             ECS-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             ECC-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            445 567899999999999999999866

>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=96.32  E-value=0.0023  Score=50.02  Aligned_cols=32  Identities=16%  Similarity=0.232  Sum_probs=24.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      ..+.|.|++|+||||++..++..+   |..+..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik   39 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   39 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEEE
Confidence            358899999999999999999876   44444444

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=96.32  E-value=0.0017  Score=54.48  Aligned_cols=27  Identities=22%  Similarity=0.300  Sum_probs=22.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +...+.|.||+|+|||||++.++....
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~Gl~~   57 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINFLEK   57 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            344478999999999999999998764

>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=96.32  E-value=0.0016  Score=53.89  Aligned_cols=27  Identities=22%  Similarity=0.424  Sum_probs=22.7

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++...+.|.||+|+|||||++.++...
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            344458899999999999999999865

>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=96.31  E-value=0.0026  Score=49.23  Aligned_cols=22  Identities=32%  Similarity=0.406  Sum_probs=19.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      ..++|.|++|+|||+|+..+..
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            3599999999999999999984

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=96.30  E-value=0.003  Score=51.87  Aligned_cols=25  Identities=20%  Similarity=0.321  Sum_probs=22.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .-|.|.|++|+||||+++.++..++
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3588999999999999999999984

>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=96.29  E-value=0.0015  Score=57.30  Aligned_cols=25  Identities=24%  Similarity=0.530  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+|||||||++.++...
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcCC
Confidence            3447799999999999999999865

>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=96.29  E-value=0.022  Score=50.40  Aligned_cols=25  Identities=28%  Similarity=0.521  Sum_probs=21.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...++|.||+|+|||++++.++...
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            4459999999999999999988764

>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=96.29  E-value=0.0012  Score=55.07  Aligned_cols=25  Identities=40%  Similarity=0.731  Sum_probs=21.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...+.|.||+|+|||||++.++...
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3447899999999999999999866

>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=96.28  E-value=0.0055  Score=54.96  Aligned_cols=35  Identities=23%  Similarity=0.318  Sum_probs=27.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +..+.+.||+|+||||++..+|..+   +..+..+++.
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~D  135 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAAD  135 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeecc
Confidence            4558888999999999999999876   4555555553

>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=96.27  E-value=0.0016  Score=52.98  Aligned_cols=27  Identities=33%  Similarity=0.572  Sum_probs=22.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +..-+.|.||.|+|||||++.++....
T Consensus        34 ~Ge~~~iiG~NGsGKSTLlk~l~Gl~~   60 (214)
T 1sgw_A           34 KGNVVNFHGPNGIGKTTLLKTISTYLK   60 (214)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            344588999999999999999998663

>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=96.27  E-value=0.0022  Score=53.84  Aligned_cols=25  Identities=36%  Similarity=0.456  Sum_probs=21.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      +...+.|.||+|+|||||++.++..
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3445889999999999999999986

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=96.26  E-value=0.0019  Score=54.07  Aligned_cols=26  Identities=23%  Similarity=0.374  Sum_probs=22.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++..+.|.||+|+|||||++.++...
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccC
Confidence            44458899999999999999999865

>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=96.25  E-value=0.0039  Score=55.86  Aligned_cols=25  Identities=36%  Similarity=0.446  Sum_probs=22.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ..++|.||+|+||||++++++..+.
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            3488999999999999999998874

>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=96.25  E-value=0.002  Score=54.13  Aligned_cols=27  Identities=22%  Similarity=0.391  Sum_probs=22.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +...+.|.||+|+|||||++.++....
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~Gl~~   75 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNLLED   75 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHcCCC
Confidence            344578999999999999999998763

>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=96.24  E-value=0.0017  Score=53.23  Aligned_cols=26  Identities=27%  Similarity=0.380  Sum_probs=22.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +...+.|.||.|+|||||++.++...
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34458899999999999999999876

>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=96.24  E-value=0.0017  Score=53.87  Aligned_cols=26  Identities=23%  Similarity=0.349  Sum_probs=22.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +...+.|.||+|+|||||++.++...
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34458899999999999999999876

>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=96.24  E-value=0.0068  Score=59.61  Aligned_cols=21  Identities=29%  Similarity=0.317  Sum_probs=18.6

Q ss_pred             ceeEEecCCCCChHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMA   52 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala   52 (266)
                      ..++|.||.|+||||+++.++
T Consensus       663 ~i~~ItGpNGsGKSTlLr~ia  683 (934)
T 3thx_A          663 MFHIITGPNMGGKSTYIRQTG  683 (934)
T ss_dssp             CEEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            348899999999999999984

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=96.24  E-value=0.0019  Score=52.19  Aligned_cols=24  Identities=33%  Similarity=0.371  Sum_probs=21.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ...+.|.||+|+|||||++.++..
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            445889999999999999999975

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=96.24  E-value=0.002  Score=54.30  Aligned_cols=27  Identities=33%  Similarity=0.471  Sum_probs=22.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +...+.|.||+|+|||||++.++....
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~Gl~~   70 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQNLYQ   70 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            344588999999999999999998763

>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=96.23  E-value=0.0022  Score=53.37  Aligned_cols=25  Identities=36%  Similarity=0.375  Sum_probs=21.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      +..-+.|.||+|+|||||++.++..
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            3445889999999999999999985

>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=96.23  E-value=0.0013  Score=54.96  Aligned_cols=25  Identities=16%  Similarity=0.313  Sum_probs=22.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .-|.|.|++|+||||+++.|+..+.
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            3478899999999999999999983

>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=96.22  E-value=0.0035  Score=57.43  Aligned_cols=40  Identities=15%  Similarity=-0.018  Sum_probs=32.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~   66 (266)
                      |+++..-++|.|+||+|||+++..+|...    |.++..++...
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E~  281 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLEE  281 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESSS
T ss_pred             ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEeccC
Confidence            56666679999999999999999888765    45777777653

>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=96.21  E-value=0.0014  Score=55.48  Aligned_cols=25  Identities=28%  Similarity=0.393  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+|+|||||++.++...
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCC
Confidence            3448899999999999999999865

>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=96.19  E-value=0.0019  Score=53.36  Aligned_cols=27  Identities=26%  Similarity=0.446  Sum_probs=22.6

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +..-+.|.||+|+|||||++.++....
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   57 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            344578999999999999999998763

>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=96.19  E-value=0.0019  Score=56.62  Aligned_cols=26  Identities=27%  Similarity=0.368  Sum_probs=22.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...-+.|.||+|||||||++.++...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           28 DGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            33447799999999999999999865

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=96.19  E-value=0.0019  Score=56.70  Aligned_cols=25  Identities=36%  Similarity=0.570  Sum_probs=21.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+|||||||++.++...
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcCC
Confidence            3447799999999999999999865

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=96.18  E-value=0.0031  Score=57.78  Aligned_cols=34  Identities=18%  Similarity=0.330  Sum_probs=26.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      +..|.|+|+||+||||++..+|..+   |..+..+++
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            4468899999999999999999766   555655555

>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=96.18  E-value=0.0022  Score=53.56  Aligned_cols=26  Identities=23%  Similarity=0.447  Sum_probs=22.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +...+.|.||.|+|||||++.++...
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            34458899999999999999999865

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=96.18  E-value=0.0015  Score=57.34  Aligned_cols=29  Identities=24%  Similarity=0.445  Sum_probs=24.8

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +.++..++|.||+|+||||++++++....
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             HhcCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            44556799999999999999999998763

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.18  E-value=0.0041  Score=60.30  Aligned_cols=33  Identities=36%  Similarity=0.404  Sum_probs=22.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELS   65 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~   65 (266)
                      -+++.||||||||+++..+...+    +..++.+..+
T Consensus       377 ~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~t  413 (802)
T 2xzl_A          377 LSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPS  413 (802)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCc
Confidence            47899999999998776655433    4455555443

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=96.17  E-value=0.015  Score=50.04  Aligned_cols=22  Identities=18%  Similarity=0.170  Sum_probs=17.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      +.+++.+|+|+|||..+-..+.
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~   66 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLI   66 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHH
Confidence            5799999999999987654443

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=96.17  E-value=0.0023  Score=53.76  Aligned_cols=26  Identities=31%  Similarity=0.475  Sum_probs=22.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++..+.|.||.|+|||||++.++...
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            44458899999999999999999865

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.17  E-value=0.0036  Score=56.32  Aligned_cols=36  Identities=22%  Similarity=0.348  Sum_probs=28.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~   66 (266)
                      ++.++++|++|+||||++..+|..+    |..+..+++..
T Consensus       100 ~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A          100 PAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            4568889999999999999888665    66677776664

>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=96.16  E-value=0.002  Score=53.61  Aligned_cols=27  Identities=41%  Similarity=0.501  Sum_probs=22.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ++..+.|.||+|+|||||++.++....
T Consensus        25 ~Ge~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            344588999999999999999998764

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=96.16  E-value=0.024  Score=45.77  Aligned_cols=18  Identities=22%  Similarity=0.298  Sum_probs=15.2

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      .+.+++.+|.|+|||...
T Consensus        57 ~~~~l~~apTGsGKT~~~   74 (228)
T 3iuy_A           57 GIDLIVVAQTGTGKTLSY   74 (228)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEECCCCChHHHHH
Confidence            457999999999999753

>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=96.16  E-value=0.0082  Score=47.45  Aligned_cols=21  Identities=33%  Similarity=0.586  Sum_probs=18.9

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .++|.|++|+|||+|+..+..
T Consensus        25 ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           25 KVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999853

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=96.15  E-value=0.0018  Score=56.72  Aligned_cols=25  Identities=28%  Similarity=0.482  Sum_probs=21.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+|||||||++.++...
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3347799999999999999999865

>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=96.15  E-value=0.0021  Score=56.74  Aligned_cols=25  Identities=28%  Similarity=0.482  Sum_probs=21.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+|||||||++.+|...
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC
Confidence            3447799999999999999999865

>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=96.14  E-value=0.0031  Score=51.15  Aligned_cols=31  Identities=32%  Similarity=0.301  Sum_probs=24.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      -|.|.||+|+||||+++.++..+   |.+++.+.
T Consensus         8 ~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~~   41 (213)
T 4edh_A            8 FVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTR   41 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCCccccc
Confidence            47788999999999999999887   45555443

>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=96.14  E-value=0.0021  Score=56.82  Aligned_cols=25  Identities=32%  Similarity=0.506  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+-|.||+|||||||++.++...
T Consensus        29 Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           29 GEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEEcCCCchHHHHHHHHHcCC
Confidence            3447799999999999999999866

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=96.14  E-value=0.024  Score=45.99  Aligned_cols=18  Identities=22%  Similarity=0.281  Sum_probs=15.1

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      .+.+++.+|+|+|||...
T Consensus        62 ~~~~li~a~TGsGKT~~~   79 (236)
T 2pl3_A           62 GKDVLGAAKTGSGKTLAF   79 (236)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEEeCCCCcHHHHH
Confidence            356999999999999853

>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=96.14  E-value=0.0031  Score=49.98  Aligned_cols=22  Identities=32%  Similarity=0.563  Sum_probs=20.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+.|.||+|+|||+|++.++..
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5889999999999999999875

>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=96.13  E-value=0.0029  Score=49.95  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=20.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.|.||+|+|||+|++.++...
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            37899999999999999998754

>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=96.13  E-value=0.0065  Score=48.60  Aligned_cols=22  Identities=23%  Similarity=0.465  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999999853

>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=96.13  E-value=0.0017  Score=59.08  Aligned_cols=26  Identities=23%  Similarity=0.459  Sum_probs=22.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +..|+++|.||+||||+++.++..++
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34589999999999999999999874

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=96.10  E-value=0.003  Score=53.14  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=21.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.|.||+|+|||||++.++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            57899999999999999999876

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=96.09  E-value=0.034  Score=45.43  Aligned_cols=18  Identities=17%  Similarity=0.146  Sum_probs=15.2

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      .+.+++.+|.|+|||...
T Consensus        66 g~~~l~~apTGsGKT~~~   83 (242)
T 3fe2_A           66 GLDMVGVAQTGSGKTLSY   83 (242)
T ss_dssp             TCCEEEEECTTSCHHHHH
T ss_pred             CCCEEEECCCcCHHHHHH
Confidence            357999999999999753

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=96.09  E-value=0.0042  Score=50.92  Aligned_cols=23  Identities=22%  Similarity=0.277  Sum_probs=17.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -|.|.||+|+||||+++.++..+
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37788999999999999999887

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=96.08  E-value=0.0023  Score=53.40  Aligned_cols=26  Identities=23%  Similarity=0.271  Sum_probs=22.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++..+.|.||+|+|||||++.++...
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           30 KGDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34458899999999999999999865

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=96.08  E-value=0.0023  Score=54.18  Aligned_cols=25  Identities=32%  Similarity=0.700  Sum_probs=21.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...+.|.||.|+|||||++.++...
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3447899999999999999999866

>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=96.08  E-value=0.0023  Score=53.71  Aligned_cols=26  Identities=35%  Similarity=0.602  Sum_probs=22.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..-+-|.||+|+|||||++.++...
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            34457899999999999999999865

>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=96.07  E-value=0.0021  Score=56.73  Aligned_cols=25  Identities=28%  Similarity=0.493  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+|||||||++.++...
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           29 GEFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCcHHHHHHHHHHcCC
Confidence            3447899999999999999999865

>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=96.07  E-value=0.0043  Score=52.99  Aligned_cols=37  Identities=24%  Similarity=0.295  Sum_probs=28.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      +..+.+.|++|+||||++..+|..+   +..+..+++...
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D~~  137 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGADVY  137 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECCCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecCCC
Confidence            3457889999999999999999776   666666665533

>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=96.07  E-value=0.0065  Score=47.14  Aligned_cols=22  Identities=14%  Similarity=0.335  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus        23 ~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           23 KVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEETTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4999999999999999999864

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=96.06  E-value=0.02  Score=45.28  Aligned_cols=19  Identities=37%  Similarity=0.377  Sum_probs=15.5

Q ss_pred             CceeEEecCCCCChHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~   49 (266)
                      .+.+++.+|+|+|||..+-
T Consensus        40 ~~~~lv~apTGsGKT~~~~   58 (206)
T 1vec_A           40 GRDILARAKNGTGKSGAYL   58 (206)
T ss_dssp             TCCEEEECCSSSTTHHHHH
T ss_pred             CCCEEEECCCCCchHHHHH
Confidence            3579999999999996443

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=96.06  E-value=0.0027  Score=58.34  Aligned_cols=27  Identities=19%  Similarity=0.401  Sum_probs=23.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+.+++|.||+|+||||++++++..+.
T Consensus       259 ~g~~i~I~GptGSGKTTlL~aL~~~i~  285 (511)
T 2oap_1          259 HKFSAIVVGETASGKTTTLNAIMMFIP  285 (511)
T ss_dssp             TTCCEEEEESTTSSHHHHHHHHGGGSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            455799999999999999999998773

>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=96.06  E-value=0.013  Score=56.48  Aligned_cols=23  Identities=22%  Similarity=0.478  Sum_probs=18.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.||+|+|||+++..+...
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            45999999999999977666543

>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=96.05  E-value=0.0044  Score=49.64  Aligned_cols=25  Identities=24%  Similarity=0.511  Sum_probs=21.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...++|.|++|+|||+++..+....
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            3469999999999999999998754

>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=96.04  E-value=0.013  Score=59.90  Aligned_cols=26  Identities=31%  Similarity=0.562  Sum_probs=22.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +..+.|+||+|+||||+++.+...+.
T Consensus       444 G~~vaivG~sGsGKSTll~ll~~~~~  469 (1321)
T 4f4c_A          444 GQTVALVGSSGCGKSTIISLLLRYYD  469 (1321)
T ss_dssp             TCEEEEEECSSSCHHHHHHHHTTSSC
T ss_pred             CcEEEEEecCCCcHHHHHHHhccccc
Confidence            34478999999999999999998773

>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=96.03  E-value=0.0035  Score=54.95  Aligned_cols=28  Identities=21%  Similarity=0.357  Sum_probs=24.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      ...+.|.||+|+|||||++.|+..+...
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            4458899999999999999999987654

>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=96.03  E-value=0.0032  Score=57.80  Aligned_cols=26  Identities=12%  Similarity=0.014  Sum_probs=23.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      ..|+|.|.+||||||++++||..++.
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            35889999999999999999999984

>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=96.02  E-value=0.0038  Score=47.38  Aligned_cols=23  Identities=26%  Similarity=0.301  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|+..+...
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            35899999999999999999864

>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=96.01  E-value=0.0076  Score=47.18  Aligned_cols=23  Identities=26%  Similarity=0.395  Sum_probs=20.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++|.|++|+|||+|+..+...-
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            49999999999999999998755

>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=96.01  E-value=0.0062  Score=49.33  Aligned_cols=31  Identities=16%  Similarity=0.079  Sum_probs=23.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      .+++||.|+|||+.+-.++..+   |..++.+.+
T Consensus        31 ~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~   64 (214)
T 2j9r_A           31 EVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKP   64 (214)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEe
Confidence            5588999999999877776655   556665543

>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=96.00  E-value=0.0017  Score=56.75  Aligned_cols=26  Identities=23%  Similarity=0.571  Sum_probs=22.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...-+.|.||+|||||||++.+|...
T Consensus        25 ~Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHcCC
Confidence            34457899999999999999999865

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=96.00  E-value=0.004  Score=46.95  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+++..+...
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

>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=95.98  E-value=0.01  Score=50.53  Aligned_cols=35  Identities=23%  Similarity=0.318  Sum_probs=26.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +..+.++|++|+||||++..+|..+   +..+..+++.
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~d  135 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAAD  135 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            3457788999999999999999766   4555555543

>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=95.97  E-value=0.011  Score=46.25  Aligned_cols=23  Identities=30%  Similarity=0.504  Sum_probs=20.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|+.++...
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCcHHHHHHHHHcC
Confidence            45999999999999999999863

>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=95.97  E-value=0.0026  Score=56.40  Aligned_cols=25  Identities=36%  Similarity=0.538  Sum_probs=21.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+.|.||+||||||+++.++...
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCC
Confidence            3448899999999999999999754

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=95.96  E-value=0.013  Score=47.55  Aligned_cols=22  Identities=27%  Similarity=0.413  Sum_probs=19.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -|+|.|.+|+|||+|+..+...
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4999999999999999988753

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=95.96  E-value=0.0039  Score=58.55  Aligned_cols=25  Identities=36%  Similarity=0.602  Sum_probs=20.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.++++||||||||+++..+...+
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            3458999999999999888776554

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=95.95  E-value=0.0062  Score=49.49  Aligned_cols=29  Identities=21%  Similarity=0.196  Sum_probs=24.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      .-|.|.|++|+||||+++.++..++.+..
T Consensus         6 ~~i~~eG~~g~GKst~~~~l~~~l~~~~~   34 (216)
T 3tmk_A            6 KLILIEGLDRTGKTTQCNILYKKLQPNCK   34 (216)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHCSSEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcccce
Confidence            34788899999999999999999986433

>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=95.94  E-value=0.0016  Score=56.51  Aligned_cols=64  Identities=14%  Similarity=0.322  Sum_probs=40.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC--CcEEEEeCCcc------------c--ChhhHHHHHHH--cccCCeeeeecc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK--FDVYDLELSNL------------L--GNNDLRHILIA--TENKSILVVEDI   91 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~--~~~~~i~~~~~------------~--~~~~l~~~~~~--~~~~~vl~iDei   91 (266)
                      ++..++|.||+|+||||++++++....  ...+.+.....            .  +....+..+..  ..+|.+|++||.
T Consensus       170 ~g~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~~~e~~~~~~~~~i~~~~ggg~~~r~~la~aL~~~p~ilildE~  249 (330)
T 2pt7_A          170 IGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGEL  249 (330)
T ss_dssp             HTCCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEECCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECCeeccccccchhEEEEEeCCChhHHHHHHHHhhhCCCEEEEcCC
Confidence            355799999999999999999998773  22333332110            0  11222223322  346889999997


Q ss_pred             hh
Q 024550           92 DC   93 (266)
Q Consensus        92 d~   93 (266)
                      ..
T Consensus       250 ~~  251 (330)
T 2pt7_A          250 RS  251 (330)
T ss_dssp             CS
T ss_pred             Ch
Confidence            63

>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=95.93  E-value=0.0038  Score=47.82  Aligned_cols=22  Identities=32%  Similarity=0.528  Sum_probs=19.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+.|.|++|+|||+|++.++..
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999999863

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=95.92  E-value=0.0025  Score=59.17  Aligned_cols=26  Identities=35%  Similarity=0.407  Sum_probs=23.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +..+.|.|++|+||||++++|+..++
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHHhhc
Confidence            44588999999999999999999885

>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=95.92  E-value=0.017  Score=45.70  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=19.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        31 ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhhC
Confidence            4999999999999999998753

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=95.92  E-value=0.0093  Score=53.73  Aligned_cols=36  Identities=33%  Similarity=0.475  Sum_probs=27.5

Q ss_pred             HHHHhCCCCCce--eEEecCCCCChHHHHHHHHHHcCCc
Q 024550           22 FYRRVGKAWKRG--YLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        22 ~~~~~~~~~~~~--iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      .+... ++..+|  +.|.||+|||||||++.++......
T Consensus       147 vld~v-l~i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~~~  184 (438)
T 2dpy_A          147 AINAL-LTVGRGQRMGLFAGSGVGKSVLLGMMARYTRAD  184 (438)
T ss_dssp             HHHHH-SCCBTTCEEEEEECTTSSHHHHHHHHHHHSCCS
T ss_pred             EEeee-EEecCCCEEEEECCCCCCHHHHHHHHhcccCCC
Confidence            34444 444444  8899999999999999999988544

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=95.90  E-value=0.0077  Score=52.31  Aligned_cols=26  Identities=35%  Similarity=0.456  Sum_probs=21.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...-+.|.||||+||||+++.++..+
T Consensus        54 ~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           54 RAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             CSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            34448899999999999999999765

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=95.90  E-value=0.0038  Score=57.54  Aligned_cols=38  Identities=24%  Similarity=0.202  Sum_probs=28.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      ++++...++|.||+|+|||+|++.++...   |.+.+.+..
T Consensus       277 ~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~~  317 (525)
T 1tf7_A          277 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAY  317 (525)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            56666679999999999999999998755   344444443

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=95.90  E-value=0.012  Score=48.01  Aligned_cols=18  Identities=22%  Similarity=0.333  Sum_probs=15.1

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      .+.+++++|+|+|||...
T Consensus        67 ~~~~li~apTGsGKT~~~   84 (237)
T 3bor_A           67 GYDVIAQAQSGTGKTATF   84 (237)
T ss_dssp             TCCEEECCCSSHHHHHHH
T ss_pred             CCCEEEECCCCCcHHHHH
Confidence            356999999999999753

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=95.89  E-value=0.027  Score=46.79  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=15.2

Q ss_pred             ceeEEecCCCCChHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~   49 (266)
                      +.+++.+|.|+|||..+-
T Consensus        92 ~~~lv~a~TGsGKT~~~~  109 (262)
T 3ly5_A           92 RDLLAAAKTGSGKTLAFL  109 (262)
T ss_dssp             CCCEECCCTTSCHHHHHH
T ss_pred             CcEEEEccCCCCchHHHH
Confidence            569999999999997543

>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=95.89  E-value=0.0033  Score=49.15  Aligned_cols=21  Identities=24%  Similarity=0.626  Sum_probs=19.4

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .+.|.|++|+|||+|++.++.
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            488999999999999999986

>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=95.89  E-value=0.0034  Score=53.42  Aligned_cols=24  Identities=29%  Similarity=0.448  Sum_probs=21.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..+.|.||.|+|||||++.++...
T Consensus        65 e~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           65 QLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCC
Confidence            347899999999999999999865

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.88  E-value=0.0022  Score=50.24  Aligned_cols=24  Identities=29%  Similarity=0.463  Sum_probs=21.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .+.|.||+|+||||+++.++..+.
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            578999999999999999998763

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=95.88  E-value=0.052  Score=44.43  Aligned_cols=62  Identities=11%  Similarity=0.166  Sum_probs=34.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCccc--Ch---------------hhHHHHHHHcccCCeeeeecch
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLL--GN---------------NDLRHILIATENKSILVVEDID   92 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~--~~---------------~~l~~~~~~~~~~~vl~iDeid   92 (266)
                      -.++|||.|+|||+.+-..+...   |..++.+.+..-.  +.               ....+++.......+|+|||+.
T Consensus        21 l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D~Ryg~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvViIDEaQ  100 (234)
T 2orv_A           21 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQ  100 (234)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCCC-----------CEEEEESSGGGGHHHHTTCSEEEESSGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCCccchHHHHhhcCCeeEEEecCCHHHHHHHhccCCEEEEEchh
Confidence            37778999999997555444433   4444444422110  00               0011223333456799999998


Q ss_pred             hh
Q 024550           93 CC   94 (266)
Q Consensus        93 ~l   94 (266)
                      .+
T Consensus       101 F~  102 (234)
T 2orv_A          101 FF  102 (234)
T ss_dssp             GC
T ss_pred             hh
Confidence            76

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=95.84  E-value=0.0038  Score=52.34  Aligned_cols=25  Identities=32%  Similarity=0.713  Sum_probs=21.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...+.|.||+|+|||||++.++...
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            4458899999999999999999865

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=95.83  E-value=0.019  Score=45.10  Aligned_cols=23  Identities=30%  Similarity=0.378  Sum_probs=20.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|++|+|||+|++.+.+.+
T Consensus        22 ki~~vG~~~vGKTsLi~~l~~~~   44 (196)
T 3llu_A           22 RILLMGLRRSGKSSIQKVVFHKM   44 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHHhcC
Confidence            49999999999999999877643

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=95.81  E-value=0.041  Score=45.27  Aligned_cols=18  Identities=22%  Similarity=0.392  Sum_probs=15.2

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      .+.+++.+|.|+|||...
T Consensus        80 ~~~~lv~a~TGsGKT~~~   97 (249)
T 3ber_A           80 GRDIIGLAETGSGKTGAF   97 (249)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEEcCCCCCchhHh
Confidence            357999999999999753

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=95.80  E-value=0.0049  Score=55.87  Aligned_cols=29  Identities=24%  Similarity=0.316  Sum_probs=24.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+....-+.|.||+|+|||||++.++...
T Consensus       134 ~i~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          134 SNFEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             HSSSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             EeCCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            34455569999999999999999999865

>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=95.79  E-value=0.0055  Score=47.03  Aligned_cols=22  Identities=36%  Similarity=0.520  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999754

>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=95.77  E-value=0.0075  Score=45.91  Aligned_cols=24  Identities=21%  Similarity=0.382  Sum_probs=20.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ...+++.|++|+|||+|+..+...
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            346999999999999999999753

>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=95.77  E-value=0.0054  Score=46.62  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+++..+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35899999999999999999753

>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=95.77  E-value=0.0025  Score=55.77  Aligned_cols=26  Identities=23%  Similarity=0.478  Sum_probs=22.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...-+.|.||+|||||||++.+|...
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            33447899999999999999999865

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=95.77  E-value=0.0045  Score=57.05  Aligned_cols=39  Identities=21%  Similarity=0.244  Sum_probs=27.2

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHH--HHHc--CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAM--ANYL--KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~al--a~~~--~~~~~~i~~~   65 (266)
                      ++++...++|.||+|+|||||++.+  +...  +...+.++..
T Consensus        35 ~i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~g~   77 (525)
T 1tf7_A           35 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   77 (525)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe
Confidence            3556667999999999999999994  4433  3344555543

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=95.76  E-value=0.0091  Score=46.88  Aligned_cols=22  Identities=27%  Similarity=0.554  Sum_probs=19.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3999999999999999998743

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=95.76  E-value=0.021  Score=49.73  Aligned_cols=24  Identities=42%  Similarity=0.631  Sum_probs=21.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .-+.|.|+||+|||||..++...+
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            348899999999999999999754

>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=95.76  E-value=0.0058  Score=46.52  Aligned_cols=23  Identities=26%  Similarity=0.313  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|+..+...
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            35999999999999999999864

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=95.76  E-value=0.0099  Score=51.86  Aligned_cols=28  Identities=25%  Similarity=0.436  Sum_probs=24.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      .-+.|.||+|+|||||++.++.......
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~~~~~~   99 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNGASADI   99 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCSE
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCE
Confidence            3488999999999999999999886543

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=95.75  E-value=0.004  Score=54.70  Aligned_cols=25  Identities=32%  Similarity=0.425  Sum_probs=21.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+-|.||+|+|||||++.++...
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEEcCCCchHHHHHHHHhcCC
Confidence            3347799999999999999999865

>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=95.75  E-value=0.0058  Score=46.99  Aligned_cols=24  Identities=29%  Similarity=0.439  Sum_probs=20.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..+++.|++|+|||+|+..+....
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            459999999999999999987643

>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=95.74  E-value=0.0061  Score=54.60  Aligned_cols=28  Identities=29%  Similarity=0.307  Sum_probs=22.1

Q ss_pred             CCCCCce--eEEecCCCCChHHHHHHHHHH
Q 024550           27 GKAWKRG--YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        27 ~~~~~~~--iLl~GppGtGKT~la~ala~~   54 (266)
                      .+..+..  +.|.||+|+|||||+++|+..
T Consensus        36 ~i~~Gei~~vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           36 SVSQGFCFNILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             SCC-CCEEEEEEECSTTSSSHHHHHHHHTS
T ss_pred             EecCCCeeEEEEECCCCCCHHHHHHHHhCc
Confidence            3444444  789999999999999999875

>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=95.72  E-value=0.0065  Score=46.23  Aligned_cols=23  Identities=43%  Similarity=0.522  Sum_probs=20.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -.+|+||.|+|||+++.++.-.+
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999998766

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=95.72  E-value=0.0056  Score=47.63  Aligned_cols=23  Identities=30%  Similarity=0.479  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+.|.|++|+|||+|++.++..
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999999873

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=95.72  E-value=0.0075  Score=46.30  Aligned_cols=24  Identities=21%  Similarity=0.304  Sum_probs=20.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ...+++.|++|+|||+|+..+...
T Consensus         8 ~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            8 PPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            346999999999999999999753

>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=95.70  E-value=0.0068  Score=49.94  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=21.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .-|.|.|++|+||||+++.++..+
T Consensus        28 ~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           28 KFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            347889999999999999999877

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=95.67  E-value=0.0064  Score=46.71  Aligned_cols=23  Identities=26%  Similarity=0.377  Sum_probs=20.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|+..+...
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEEEECcCCCCHHHHHHHHHhC
Confidence            35999999999999999998753

>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=95.67  E-value=0.012  Score=51.48  Aligned_cols=33  Identities=33%  Similarity=0.365  Sum_probs=25.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      ...+.|.|+||+||||++..++..+   |..+..++
T Consensus        79 ~~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~  114 (355)
T 3p32_A           79 AHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLA  114 (355)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEe
Confidence            3458899999999999999998876   44444443

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=95.62  E-value=0.0083  Score=48.98  Aligned_cols=25  Identities=28%  Similarity=0.335  Sum_probs=21.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -|.|.|++|+||||+++.++..++.
T Consensus        23 ~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           23 FITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3778899999999999999987654

>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=95.62  E-value=0.0066  Score=46.95  Aligned_cols=23  Identities=39%  Similarity=0.576  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+.|.|+||+|||+|+..++..
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            35899999999999999999864

>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=95.62  E-value=0.015  Score=51.39  Aligned_cols=35  Identities=17%  Similarity=0.187  Sum_probs=27.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      ..++++.||+|+|||++++.++..+   +..++.++..
T Consensus        35 ~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~~   72 (392)
T 4ag6_A           35 NSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDPE   72 (392)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             cCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence            4569999999999999999888754   5666666643

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=95.61  E-value=0.044  Score=47.53  Aligned_cols=19  Identities=26%  Similarity=0.478  Sum_probs=16.1

Q ss_pred             CceeEEecCCCCChHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~   49 (266)
                      ++.+++.+|.|+|||..+-
T Consensus        44 ~~~~lv~a~TGsGKT~~~~   62 (395)
T 3pey_A           44 PRNMIAQSQSGTGKTAAFS   62 (395)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHH
Confidence            3679999999999998544

>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=95.60  E-value=0.0042  Score=49.42  Aligned_cols=28  Identities=21%  Similarity=0.200  Sum_probs=22.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+.....+.|.|++|+|||||++.++..
T Consensus        22 ~~~~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           22 PSDTGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             SCSCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3444445899999999999999988753

>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=95.60  E-value=0.0068  Score=46.47  Aligned_cols=23  Identities=26%  Similarity=0.349  Sum_probs=20.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|+..+...
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35999999999999999999853

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=95.59  E-value=0.059  Score=45.73  Aligned_cols=17  Identities=24%  Similarity=0.434  Sum_probs=15.0

Q ss_pred             CceeEEecCCCCChHHH
Q 024550           31 KRGYLLYGPPGTGKSSL   47 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~l   47 (266)
                      ++.+++++|.|||||..
T Consensus       131 ~~~~l~~a~TGsGKT~a  147 (300)
T 3fmo_B          131 PQNLIAQSQSGTGKTAA  147 (300)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             CCeEEEECCCCCCccHH
Confidence            46899999999999975

>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=95.58  E-value=0.0035  Score=53.74  Aligned_cols=25  Identities=28%  Similarity=0.614  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...+.|.||+|+|||||++.++..+
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCchHHHHHHHHHcCC
Confidence            3447899999999999999999866

>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=95.58  E-value=0.0082  Score=48.97  Aligned_cols=29  Identities=31%  Similarity=0.520  Sum_probs=23.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      -+.|.||.|+||||+++.++.. +..++..
T Consensus        22 ~i~i~G~~GsGKSTl~~~L~~~-~g~v~~~   50 (230)
T 2vp4_A           22 TVLIEGNIGSGKTTYLNHFEKY-KNDICLL   50 (230)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGG-TTTEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhc-cCCeEEE
Confidence            3778899999999999999987 4444433

>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=95.57  E-value=0.007  Score=47.11  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|++.+...
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            35899999999999999999864

>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=95.56  E-value=0.01  Score=51.00  Aligned_cols=28  Identities=25%  Similarity=0.356  Sum_probs=23.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      ..+++|.|++|+|||+++.++... |..+
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~-g~~l  171 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR-GHRL  171 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc-CCce
Confidence            468999999999999999999875 4443

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=95.54  E-value=0.0072  Score=48.96  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -|.|.|++|+||||.++.++..+
T Consensus         5 ~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            5 YIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47788999999999999999887

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=95.51  E-value=0.0096  Score=46.55  Aligned_cols=24  Identities=25%  Similarity=0.386  Sum_probs=21.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      .-.+++.|++|+|||+|+.++...
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            345999999999999999999875

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=95.49  E-value=0.039  Score=44.19  Aligned_cols=17  Identities=24%  Similarity=0.294  Sum_probs=14.8

Q ss_pred             ceeEEecCCCCChHHHH
Q 024550           32 RGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la   48 (266)
                      +.+++.+|.|+|||...
T Consensus        42 ~~~lv~a~TGsGKT~~~   58 (219)
T 1q0u_A           42 ESMVGQSQTGTGKTHAY   58 (219)
T ss_dssp             CCEEEECCSSHHHHHHH
T ss_pred             CCEEEECCCCChHHHHH
Confidence            56999999999999853

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.49  E-value=0.0076  Score=48.37  Aligned_cols=26  Identities=23%  Similarity=0.328  Sum_probs=22.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ...+.|.|++|+||||++..++..+.
T Consensus        30 ~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           30 TVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            34689999999999999999998763

>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=95.48  E-value=0.0078  Score=46.63  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=20.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|+..+...
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            35999999999999999999754

>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=95.48  E-value=0.0087  Score=46.80  Aligned_cols=24  Identities=33%  Similarity=0.385  Sum_probs=20.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ...+++.|++|+|||+|+..+...
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            345999999999999999999754

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=95.47  E-value=0.0075  Score=46.32  Aligned_cols=22  Identities=41%  Similarity=0.608  Sum_probs=19.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      ..+++.|++|+|||+|+..+..
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            3599999999999999999864

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} SCOP: c.37.1.8 PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 4gmx_A* 4gpt_A* 4hat_A* 4hau_A* 4hav_A* 4haw_A* ...

Probab=95.43  E-value=0.012  Score=47.18  Aligned_cols=22  Identities=27%  Similarity=0.531  Sum_probs=18.8

Q ss_pred             eeEEecCCCCChHHHHHH-HHHH
Q 024550           33 GYLLYGPPGTGKSSLIAA-MANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~a-la~~   54 (266)
                      .+++.|++|+|||+|+.. +...
T Consensus        17 ki~v~G~~~~GKSsli~~~~~~~   39 (221)
T 3gj0_A           17 KLVLVGDGGTGKTTFVKRHLTGE   39 (221)
T ss_dssp             EEEEEECTTSSHHHHHTTBHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            599999999999999998 4443

>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=95.41  E-value=0.0071  Score=46.98  Aligned_cols=22  Identities=27%  Similarity=0.421  Sum_probs=19.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
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            4889999999999999998864

>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=95.39  E-value=0.0094  Score=46.51  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=20.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++|.|++|+|||+|+..+...-
T Consensus        24 ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           24 KLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            49999999999999999998643

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=95.38  E-value=0.014  Score=54.04  Aligned_cols=32  Identities=31%  Similarity=0.343  Sum_probs=25.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC---CcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~   63 (266)
                      ..++|+|++|+||||+++.++..++   .++..++
T Consensus       373 ~~I~l~G~~GsGKSTia~~La~~L~~~G~~~~~ld  407 (546)
T 2gks_A          373 FCVWLTGLPCAGKSTIAEILATMLQARGRKVTLLD  407 (546)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             eEEEccCCCCCCHHHHHHHHHHHhhhcCCeEEEEC
Confidence            3488999999999999999999874   3455554

>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=95.37  E-value=0.0097  Score=45.74  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=20.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|+..+...
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35999999999999999998764

>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=95.36  E-value=0.0096  Score=45.97  Aligned_cols=23  Identities=17%  Similarity=0.310  Sum_probs=20.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|+..+...
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999998753

>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=95.34  E-value=0.0097  Score=45.94  Aligned_cols=24  Identities=21%  Similarity=0.374  Sum_probs=20.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~   53 (266)
                      ....+++.|++|+|||+|+..+..
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            345699999999999999998763

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=95.33  E-value=0.01  Score=46.14  Aligned_cols=23  Identities=35%  Similarity=0.420  Sum_probs=20.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+|+..+...
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            35999999999999999999765

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.33  E-value=0.011  Score=47.53  Aligned_cols=25  Identities=28%  Similarity=0.477  Sum_probs=21.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...++|.|++|+|||+++..++...
T Consensus        38 ~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           38 VVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3468889999999999999999875

>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=95.32  E-value=0.01  Score=46.45  Aligned_cols=22  Identities=27%  Similarity=0.440  Sum_probs=19.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHhC
Confidence            4999999999999999988764

>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=95.32  E-value=0.0091  Score=51.19  Aligned_cols=29  Identities=31%  Similarity=0.328  Sum_probs=23.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      ..|+||.|++|+|||++|-.+.. -|..++
T Consensus       147 g~gvli~G~sG~GKStlal~l~~-~G~~lv  175 (312)
T 1knx_A          147 GVGVLLTGRSGIGKSECALDLIN-KNHLFV  175 (312)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHT-TTCEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH-cCCEEE
Confidence            46799999999999999988866 344443

>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=95.32  E-value=0.01  Score=46.41  Aligned_cols=22  Identities=23%  Similarity=0.218  Sum_probs=19.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4999999999999999887764

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=95.31  E-value=0.01  Score=47.57  Aligned_cols=26  Identities=38%  Similarity=0.473  Sum_probs=22.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      -.+|+||.|+|||+++.++...++.+
T Consensus        25 ~~~I~G~NgsGKStil~ai~~~l~g~   50 (203)
T 3qks_A           25 INLIIGQNGSGKSSLLDAILVGLYWP   50 (203)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhcCC
Confidence            47899999999999999999888653

>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=95.29  E-value=0.019  Score=47.38  Aligned_cols=33  Identities=27%  Similarity=0.557  Sum_probs=25.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc--CCcEEEEeCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL--KFDVYDLELS   65 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~--~~~~~~i~~~   65 (266)
                      .+++.|.+|+||||++..++..+  |..+..++..
T Consensus        16 i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd~D   50 (262)
T 1yrb_A           16 IVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLD   50 (262)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEECC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            37788999999999999999765  5555555543

>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=95.28  E-value=0.0095  Score=49.82  Aligned_cols=23  Identities=26%  Similarity=0.557  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+.|.|+||+|||+|+.++...
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999764

>1dek_A Deoxynucleoside monophosphate kinase; transferase, phosphotransferase; HET: DGP; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1 PDB: 1del_A*

Probab=95.27  E-value=0.0096  Score=49.21  Aligned_cols=26  Identities=15%  Similarity=0.126  Sum_probs=23.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      +.|+|++|||||++++.+...+|.++
T Consensus         4 i~ltG~~~sGK~tv~~~l~~~~g~~~   29 (241)
T 1dek_A            4 IFLSGVKRSGKDTTADFIMSNYSAVK   29 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            67899999999999999999888664

>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=95.27  E-value=0.01  Score=46.59  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5999999999999999999764

>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=95.27  E-value=0.013  Score=45.06  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=20.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      .-.+++.|++|+|||+|+..+...
T Consensus         8 ~~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            8 FIKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            346999999999999999998864

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=95.27  E-value=0.051  Score=47.63  Aligned_cols=19  Identities=26%  Similarity=0.357  Sum_probs=15.6

Q ss_pred             CceeEEecCCCCChHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~   49 (266)
                      .+.+++.+|.|+|||..+-
T Consensus        77 ~~~~lv~a~TGsGKT~~~~   95 (414)
T 3eiq_A           77 GYDVIAQAQSGTGKTATFA   95 (414)
T ss_dssp             TCCEEECCCSCSSSHHHHH
T ss_pred             CCCEEEECCCCCcccHHHH
Confidence            3569999999999998643

>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=95.25  E-value=0.01  Score=46.86  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=20.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..++|.|++|+|||+|+..+...
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999998764

>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=95.25  E-value=0.011  Score=46.71  Aligned_cols=24  Identities=29%  Similarity=0.461  Sum_probs=20.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..++|.|++|+|||+|+..+...-
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            9 LKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            459999999999999999998643

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum}

Probab=95.23  E-value=0.11  Score=47.89  Aligned_cols=22  Identities=27%  Similarity=0.305  Sum_probs=19.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+.|.|.||+|||+|+..+...
T Consensus        43 kV~lvG~~~vGKSSLl~~l~~~   64 (535)
T 3dpu_A           43 KVHLIGDGMAGKTSLLKQLIGE   64 (535)
T ss_dssp             EEEEESSSCSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4999999999999999998764

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=95.23  E-value=0.045  Score=48.05  Aligned_cols=20  Identities=25%  Similarity=0.411  Sum_probs=16.0

Q ss_pred             CceeEEecCCCCChHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAA   50 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~a   50 (266)
                      .+.+++.+|.|+|||...-.
T Consensus        74 ~~~~lv~a~TGsGKT~~~~~   93 (410)
T 2j0s_A           74 GRDVIAQSQSGTGKTATFSI   93 (410)
T ss_dssp             TCCEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEECCCCCCchHHHHH
Confidence            35699999999999975543

>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=95.22  E-value=0.011  Score=46.16  Aligned_cols=22  Identities=32%  Similarity=0.667  Sum_probs=19.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            3999999999999999999864

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=95.21  E-value=0.012  Score=51.57  Aligned_cols=25  Identities=36%  Similarity=0.515  Sum_probs=21.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ..+.|.||+|+|||||+++|+....
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CEEEEECCCCccHHHHHHHHhcccc
Confidence            3488999999999999999997654

>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=95.20  E-value=0.0082  Score=46.21  Aligned_cols=23  Identities=30%  Similarity=0.271  Sum_probs=20.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|+..+...
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            35899999999999999999864

>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=95.19  E-value=0.011  Score=46.84  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..++|.|++|+|||+|+..+...
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999999763

>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=95.19  E-value=0.012  Score=46.14  Aligned_cols=23  Identities=22%  Similarity=0.314  Sum_probs=20.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|++|+|||+|+..+...-
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            59999999999999999998643

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=95.16  E-value=0.02  Score=38.84  Aligned_cols=65  Identities=11%  Similarity=0.080  Sum_probs=43.8

Q ss_pred             CHHHHHHHHHHhhCCCCCCcHHHHHHHhhcC-CCCHHHHHHHHHc-------CCCHHHHHHHHHHHHHhhhhh
Q 024550          176 TPSGFKMLASNYLGIAEHPLFVEIEKLIATA-KVTPADVAEQLMR-------NEAPEFALSGLIEFLESKKRA  240 (266)
Q Consensus       176 ~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~-~~s~~~i~~~l~~-------~~~~~~~~~~~~~~~~~~~~~  240 (266)
                      +.++|.+||+.++.........++..++..+ +||++||.+++..       ........+++..+++..+..
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~df~~Al~~~~ps   74 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKK   74 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHHHHHGGGTSCCSSBCHHHHHHHHHHHCC-
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCCcCHHHHHHHHHHHccC
Confidence            6789999999999876544445566677654 7999999998842       122334455666666655443

>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=95.15  E-value=0.011  Score=47.08  Aligned_cols=22  Identities=23%  Similarity=0.395  Sum_probs=20.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+|+..+...
T Consensus        30 ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           30 KIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5999999999999999999874

>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=95.14  E-value=0.013  Score=45.52  Aligned_cols=25  Identities=16%  Similarity=0.327  Sum_probs=21.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ....+++.|++|+|||+|+..+...
T Consensus        17 ~~~~i~v~G~~~~GKssl~~~l~~~   41 (186)
T 1ksh_A           17 RELRLLMLGLDNAGKTTILKKFNGE   41 (186)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcC
Confidence            3456999999999999999998753

>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=95.12  E-value=0.013  Score=46.57  Aligned_cols=24  Identities=33%  Similarity=0.457  Sum_probs=20.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ...++|.|++|+|||+|+.++...
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346999999999999999999853

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=95.08  E-value=0.021  Score=45.76  Aligned_cols=37  Identities=30%  Similarity=0.252  Sum_probs=27.9

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCc-EEEEeCC
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFD-VYDLELS   65 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~-~~~i~~~   65 (266)
                      .|..-|+|+|.||+||++++..+.+.+|.. +..++++
T Consensus         9 ~~~~II~itGk~~SGKd~va~~l~~~~g~~~~~vv~ms   46 (202)
T 3ch4_B            9 APRLVLLFSGKRKSGKDFVTEALQSRLGADVCAVLRLS   46 (202)
T ss_dssp             CCSEEEEEEECTTSSHHHHHHHHHHHHCTTTEEEECTH
T ss_pred             CCCEEEEEECCCCCChHHHHHHHHHHcCCCCceEEEcc
Confidence            355679999999999999999999877642 3334443

>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=95.06  E-value=0.012  Score=46.72  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5899999999999999998754

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=95.01  E-value=0.0095  Score=50.82  Aligned_cols=25  Identities=40%  Similarity=0.461  Sum_probs=21.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .-+.|.||+|+|||||+++++....
T Consensus       170 eiv~l~G~sG~GKSTll~~l~g~~~  194 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAINPGLK  194 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCC
T ss_pred             CeEEEECCCCCcHHHHHHHhccccc
Confidence            3477999999999999999987654

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=95.00  E-value=0.013  Score=47.94  Aligned_cols=24  Identities=25%  Similarity=0.279  Sum_probs=20.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..|+|.|++|+|||+|+.++....
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHcCCC
Confidence            359999999999999999998643

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=94.98  E-value=0.013  Score=45.71  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=20.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~   53 (266)
                      ....+++.|++|+|||+++..+..
T Consensus        21 ~~~~i~v~G~~~~GKssli~~l~~   44 (189)
T 2x77_A           21 RKIRVLMLGLDNAGKTSILYRLHL   44 (189)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHc
Confidence            455699999999999999999853

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=94.98  E-value=0.016  Score=45.67  Aligned_cols=22  Identities=36%  Similarity=0.522  Sum_probs=19.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|+||+|||+|+..+...
T Consensus         8 kv~lvG~~~vGKSsL~~~~~~~   29 (192)
T 2cjw_A            8 RVVLIGEQGVGKSTLANIFAGV   29 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999853

---

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	266
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	4e-27
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	6e-27
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	2e-25
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	2e-18
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	7e-18
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	2e-13
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	4e-10
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	3e-09
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	6e-07
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	5e-05
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	3e-04
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	4e-04
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	5e-04
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	6e-04
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	0.001
d1tuea_	205	c.37.1.20 (A:) Replication protein E1 helicase dom	0.003
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	0.003

>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 =  103 bits (258), Expect = 4e-27
 Identities = 58/267 (21%), Positives = 113/267 (42%), Gaps = 28/267 (10%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
           D+K+ + + ++  ++  + + + G    +G L YGPPG GK+ L  A+AN  + +   ++
Sbjct: 14  DVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIK 73

Query: 64  LSNLL------GNNDLRHILIATEN--KSILVVEDIDCCIELQDRLSRARAANPDFLIAG 115
              LL         ++R I          +L  +++D         ++AR  N       
Sbjct: 74  GPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSI-------AKARGGNIGDGGGA 126

Query: 116 YEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHC 175
            ++       ++ +L  +DG+ +       II  TN  + +DPA+LRPGR+D  I +   
Sbjct: 127 ADR------VINQILTEMDGMSTKKN--VFIIGATNRPDIIDPAILRPGRLDQLIYIPLP 178

Query: 176 TPSGFKMLASNYLGIAEHPLFVEIEKL-IATAKVTPADVAEQLMRNEAPEFALSGLIE-- 232
                  +    L  +     V++E L   T   + AD+ E  +   A + A+   IE  
Sbjct: 179 DEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTE--ICQRACKLAIRESIESE 236

Query: 233 FLESKKRANDGSEAKEAEERAVQAEKK 259
               ++R  + S  +  E+  V   ++
Sbjct: 237 IRRERERQTNPSAMEVEEDDPVPEIRR 263

>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 =  102 bits (256), Expect = 6e-27
 Identities = 58/233 (24%), Positives = 99/233 (42%), Gaps = 27/233 (11%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
           + K+ + + +E FL+    +  +G    +G LL GPPG GK+ L  A+A   +       
Sbjct: 16  EAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITAS 74

Query: 64  LSNLL------GNNDLRHIL-IATENK-SILVVEDIDCCIELQDRLSRARAANPDFLIAG 115
            S+ +      G   +R +   A  +   I+ +++ID        + R R +       G
Sbjct: 75  GSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDA-------VGRKRGSGVG---GG 124

Query: 116 YEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHC 175
            ++++Q   TL+ LL  +DG         +++  TN  + LDPALLRPGR D  I +   
Sbjct: 125 NDEREQ---TLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQIAIDAP 179

Query: 176 TPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQLMRNEAPEFAL 227
              G + +   +         V++  L   T     AD+    + NEA   A 
Sbjct: 180 DVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLEN--LLNEAALLAA 230

>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 = 98.7 bits (246), Expect = 2e-25
 Identities = 59/243 (24%), Positives = 111/243 (45%), Gaps = 27/243 (11%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
           + K+ + + +E +L+    ++++G    +G L+ GPPGTGK+ L  A+A   K   + + 
Sbjct: 19  EAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTIS 77

Query: 64  LSNLL------GNNDLRHI--LIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAG 115
            S+ +      G + +R +          I+ +++I       D + R R A       G
Sbjct: 78  GSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEI-------DAVGRQRGAGLG---GG 127

Query: 116 YEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHC 175
           +++++Q   TL+ +L  +DG   +  +  I+I  TN  + LDPALLRPGR D  + +   
Sbjct: 128 HDEREQ---TLNQMLVEMDGFEGN--EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLP 182

Query: 176 TPSGFKMLASNYLGIAEHPLFVEIEKLIA-TAKVTPADVAEQLMRNEAPEFALSGLIEFL 234
              G + +   ++        ++   +   T   + AD+A   + NEA  FA  G    +
Sbjct: 183 DVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLAN--LVNEAALFAARGNKRVV 240

Query: 235 ESK 237
              
Sbjct: 241 SMV 243

>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 = 80.5 bits (197), Expect = 2e-18
 Identities = 48/252 (19%), Positives = 89/252 (35%), Gaps = 25/252 (9%)

Query: 4   DMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE 63
                I + +E  L+    ++ +G    RG LLYGPPGTGK+ +  A+AN      + + 
Sbjct: 11  KQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLIN 70

Query: 64  LSNL------LGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYE 117
              +         ++LR      E  +  ++   +       R                 
Sbjct: 71  GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKR--------------EKT 116

Query: 118 QQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTP 177
             +     +S LL  +D          I++  TN    +DPAL R GR D  +++     
Sbjct: 117 HGEVERRIVSQLLTLMD--GLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDA 174

Query: 178 SGFK-MLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFLES 236
           +G   +L  +   +         +    T     AD+A   + +EA   A+   ++ ++ 
Sbjct: 175 TGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAA--LCSEAALQAIRKKMDLIDL 232

Query: 237 KKRANDGSEAKE 248
           +    D      
Sbjct: 233 EDETIDAEVMNS 244

>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 = 79.7 bits (196), Expect = 7e-18
 Identities = 38/267 (14%), Positives = 71/267 (26%), Gaps = 50/267 (18%)

Query: 1   MDFDMKKMIMDDLERFLQRKEF-------YRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 53
            D +     +  L   L + +                KR +L  GP  +GK++L AA+  
Sbjct: 117 ADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE 176

Query: 54  YLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLI 113
                  ++ L     N +L        ++ ++V ED+                     I
Sbjct: 177 LCGGKALNVNLPLDRLNFELG----VAIDQFLVVFEDVKGTGGESRD------LPSGQGI 226

Query: 114 AGYEQQKQYHITLSGLLNFIDGLWSSCGDE----------RIIIFTTNHKERLDPALLRP 163
                       L  L +++DG      ++             I T N            
Sbjct: 227 ----------NNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMN---EYSVPKTLQ 273

Query: 164 GRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKL-IATAKVTPADVAEQLMRNEA 222
            R    I+          +  S +L + +  +   I  L +       A+ A+       
Sbjct: 274 ARFVKQIDFRPKDYLKHCLERSEFL-LEKRIIQSGIALLLMLIWYRPVAEFAQ--SIQSR 330

Query: 223 PEFALS------GLIEFLESKKRANDG 243
                        L  + + K     G
Sbjct: 331 IVEWKERLDKEFSLSVYQKMKFNVAMG 357

>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 = 66.1 bits (160), Expect = 2e-13
 Identities = 39/269 (14%), Positives = 82/269 (30%), Gaps = 13/269 (4%)

Query: 2   DFDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVY- 60
           D   +  + D+LE  +Q K+            +LL G PG+GK+SL +A+    + +V  
Sbjct: 8   DKQFENRLNDNLEELIQGKK-----AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIV 62

Query: 61  ---DLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYE 117
              D         ++L  +      K +    +      +     +      +      +
Sbjct: 63  IDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTD 122

Query: 118 QQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI---NMSH 174
              Q    L            +       + T    E +        R         +  
Sbjct: 123 VPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVK 182

Query: 175 CTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNEAPEFALSGLIEFL 234
             P+  + L    L         E  KL ++ +       E L +    + +   +   L
Sbjct: 183 NLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTL 242

Query: 235 ES-KKRANDGSEAKEAEERAVQAEKKVLE 262
           E  +++       +  E +A+Q + + L+
Sbjct: 243 ERIEQKMVLNKHQETPEFKAIQQKLESLQ 271

>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 = 56.1 bits (134), Expect = 4e-10
 Identities = 28/166 (16%), Positives = 56/166 (33%), Gaps = 13/166 (7%)

Query: 7   KMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSN 66
             ++DD E  +   +  +   +      LL GPP +GK++L A +A    F    +   +
Sbjct: 19  TRVLDDGELLV---QQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPD 75

Query: 67  LLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITL 126
            +          A +       +    C+ + D            L       +  ++ L
Sbjct: 76  KMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDD--------IERLLDYVPIGPRFSNLVL 127

Query: 127 SGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINM 172
             LL  +         + +II TT+ K+ L    +        I++
Sbjct: 128 QALLVLLKKAPPQG-RKLLIIGTTSRKDVLQEMEML-NAFSTTIHV 171

>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 = 54.7 bits (131), Expect = 3e-09
 Identities = 23/171 (13%), Positives = 51/171 (29%), Gaps = 29/171 (16%)

Query: 14  ERFLQRKEFYRRV-GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDV--YDLELSNLL-- 68
           E              +      ++ G   +GK+ L+ A+   L        +     L  
Sbjct: 105 ELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSG 164

Query: 69  ----GNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
                N  +  I  A     ++V++ +         +  A   N     +G   +     
Sbjct: 165 YNTDFNVFVDDIARAMLQHRVIVIDSL-------KNVIGAAGGNTT---SGGISR----- 209

Query: 125 TLSGLLNFIDGLWSSCGDERIIIFTTNHKE---RLDPALLRPGRMDMHINM 172
               LL+ I  + +S G   ++I + N      ++   +    R +    +
Sbjct: 210 GAFDLLSDIGAMAASRG--CVVIASLNPTSNDDKIVELVKEASRSNSTSLV 258

>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 = 47.4 bits (111), Expect = 6e-07
 Identities = 30/211 (14%), Positives = 58/211 (27%), Gaps = 2/211 (0%)

Query: 11  DDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK--FDVYDLELSNLL 68
           D+ + F  R++   ++        L+ G   TGKSS+I    N L   +   DL      
Sbjct: 9   DNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEER 68

Query: 69  GNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSG 128
                +  L+  + +   +V+ +   ++    +        +       + +     L  
Sbjct: 69  NYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLE 128

Query: 129 LLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYL 188
                         +            L PAL         I           +     +
Sbjct: 129 SFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRV 188

Query: 189 GIAEHPLFVEIEKLIATAKVTPADVAEQLMR 219
              E PLF      +     +  +  E L R
Sbjct: 189 EDPESPLFGRAFSTVELKPFSREEAIEFLRR 219

>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 = 41.5 bits (96), Expect = 5e-05
 Identities = 27/186 (14%), Positives = 61/186 (32%), Gaps = 14/186 (7%)

Query: 34  YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDC 93
            LL GPPG GK++L   +A+ L+ +++      L+   D+  IL + E   +L +++I  
Sbjct: 38  VLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHR 97

Query: 94  CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK 153
             +  +                Y   + + I +                   ++  T   
Sbjct: 98  LNKAVEE-------------LLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRS 144

Query: 154 ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADV 213
             L   L     + + ++  +      +++      +         E +   ++ TP   
Sbjct: 145 GLLSSPLRSRFGIILELDF-YTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIA 203

Query: 214 AEQLMR 219
                R
Sbjct: 204 IRLTKR 209

>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 = 39.0 bits (89), Expect = 3e-04
 Identities = 22/173 (12%), Positives = 48/173 (27%), Gaps = 9/173 (5%)

Query: 5   MKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL 64
           +K  + +         +   + G    R  +LYGPPG GK++    +A  L +D+ +   
Sbjct: 26  LKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNA 85

Query: 65  SNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHI 124
           S++     L   +          ++++      +            F+I   E       
Sbjct: 86  SDVRSKTLLNAGVKN-------ALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGG 138

Query: 125 TLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTP 177
              G+       +       +I+              R             + 
Sbjct: 139 DRGGVGQLAQ--FCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSI 189

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 38.6 bits (88), Expect = 4e-04
 Identities = 24/186 (12%), Positives = 46/186 (24%), Gaps = 5/186 (2%)

Query: 32  RGYLLYGPPGTGKSSLIAAMANYLK--FDVYDLELSNLLGNNDLRHILIATENKSILVVE 89
               L G PGTGK+  +  +    K       + ++  +  N    I     + +I    
Sbjct: 44  PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPR 103

Query: 90  DIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIF- 148
                 E    L         ++    +        +      +       G  RI +  
Sbjct: 104 RGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVI 163

Query: 149 TTNHKERLDPALLRPG--RMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATA 206
             ++   L+              I  S  T      +  +             + L   A
Sbjct: 164 VGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIA 223

Query: 207 KVTPAD 212
            +T A 
Sbjct: 224 DITGAQ 229

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 38.7 bits (89), Expect = 5e-04
 Identities = 30/196 (15%), Positives = 67/196 (34%), Gaps = 28/196 (14%)

Query: 31  KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL--------LGNNDLRHILIATEN 82
            +  L+ GP G GK+ +   +A         +E +            ++ +R +  +   
Sbjct: 49  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGG 108

Query: 83  KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGD 142
               V ++    I+  D++ +    +                    LL  ++G   S   
Sbjct: 109 AIDAVEQNGIVFIDEIDKICKKGEYSG--------ADVSREGVQRDLLPLVEGSTVSTKH 160

Query: 143 ERI----IIF-TTNHKERLDPALLRP---GRMDMHINMSHCTPSGFKMLASNYLGIAEHP 194
             +    I+F  +   +   P+ L P   GR+ + + ++  + + F+      L      
Sbjct: 161 GMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFE----RILTEPHAS 216

Query: 195 LFVEIEKLIATAKVTP 210
           L  + + L+AT  V  
Sbjct: 217 LTEQYKALMATEGVNI 232

>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 = 38.0 bits (87), Expect = 6e-04
 Identities = 26/159 (16%), Positives = 48/159 (30%), Gaps = 14/159 (8%)

Query: 25  RVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIA-TENK 83
           +  K      LL+GPPG GK++L   +A+ L  ++       +    DL  IL    E  
Sbjct: 29  KARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEG 88

Query: 84  SILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDE 143
            IL +++I       +                Y   + + + +                 
Sbjct: 89  DILFIDEIHRLSRQAEE-------------HLYPAMEDFVMDIVIGQGPAARTIRLELPR 135

Query: 144 RIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKM 182
             +I  T     +   LL    +  H+           +
Sbjct: 136 FTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGV 174

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.0 bits (84), Expect = 0.001
 Identities = 23/246 (9%), Positives = 58/246 (23%), Gaps = 28/246 (11%)

Query: 10  MDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG 69
            + L R    +             Y   G  G GK++L       +        L+    
Sbjct: 25  AEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQA 84

Query: 70  NNDLRHILIATENKSILVVEDI-------DCCIELQDRLSRARAANP----------DFL 112
             +  +        S++V +            +++   L                    +
Sbjct: 85  YVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSM 144

Query: 113 IAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRP--GRMDMHI 170
           ++      +   TL  +   I           +++ +           +     ++   +
Sbjct: 145 LSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKL 204

Query: 171 NMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTP--------ADVAEQLMRNEA 222
           ++          +      +       E   L   + V          A  A   ++  A
Sbjct: 205 HLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALK-MA 263

Query: 223 PEFALS 228
            E A +
Sbjct: 264 CEMAEA 269

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]} Length = 205

class: Alpha and 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]

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 12 DLERFLQR-KEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLK 56
          +   FL   K F +   K  K   +  GP  TGKS    +  ++++
Sbjct: 35 EFITFLGALKSFLKGTPK--KNCLVFCGPANTGKSYFGMSFIHFIQ 78

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 35.7 bits (81), Expect = 0.003
 Identities = 20/157 (12%), Positives = 47/157 (29%), Gaps = 18/157 (11%)

Query: 34  YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDC 93
            L  GPPG GK++   A+A  L  + +                L A++ + I    ++  
Sbjct: 48  LLFAGPPGVGKTTAALALARELFGENWRHN----------FLELNASDERGI----NVIR 93

Query: 94  CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK 153
               +   ++        +I   E           L   ++   S+       I + N+ 
Sbjct: 94  EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNV----RFILSCNYS 149

Query: 154 ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGI 190
            ++   +     +     +     +      +   G+
Sbjct: 150 SKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL 186

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	266
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.9
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.9
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.88
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.85
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.81
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.77
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.74
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.73
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.7
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.69
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.68
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.65
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.63
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.62
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.62
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.59
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.59
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.56
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.56
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.55
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.52
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.49
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.48
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.37
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.3
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.2
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.09
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.09
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	99.07
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.54
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.51
d1tuea_	205	Replication protein E1 helicase domain {Human papi	98.46
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.43
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	98.39
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	98.35
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	98.34
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	98.29
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	98.28
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	98.25
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	98.23
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.21
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	98.2
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	98.19
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	98.13
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	98.12
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	98.11
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	98.09
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	98.08
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	98.06
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	98.03
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	98.03
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	98.01
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.99
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.98
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.98
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.98
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.96
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.91
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.91
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.9
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.9
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.87
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.84
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.83
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.73
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.65
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	97.63
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.61
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.61
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.61
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.6
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	97.57
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.54
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	97.52
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.5
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	97.47
d1okkd2	207	GTPase domain of the signal recognition particle r	97.47
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	97.46
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	97.46
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.46
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.42
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	97.42
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.41
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	97.39
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.39
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.38
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	97.38
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.38
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	97.36
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	97.34
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	97.33
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	97.33
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	97.29
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.27
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	97.27
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	97.26
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	97.23
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	97.19
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	97.18
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	97.12
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	97.1
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.1
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	97.08
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	97.07
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	97.06
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	97.04
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	97.03
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	97.02
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.94
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	96.92
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.91
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.9
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	96.88
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	96.88
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.86
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	96.86
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	96.83
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.82
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.8
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	96.8
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	96.79
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.76
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	96.75
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	96.72
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.71
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	96.71
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	96.7
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	96.69
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	96.68
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.65
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	96.63
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	96.62
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.58
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.56
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	96.56
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	96.53
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.52
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	96.46
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.44
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	96.41
d2fh5b1	207	Signal recognition particle receptor beta-subunit	96.4
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	96.4
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.39
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	96.38
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.36
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.36
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	96.35
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.28
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	96.26
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.25
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	96.2
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	96.19
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	96.18
d1nrjb_	209	Signal recognition particle receptor beta-subunit	96.15
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.15
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	96.12
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.11
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.09
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	96.08
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	96.08
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	96.01
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.01
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.99
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	95.97
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	95.96
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	95.96
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.94
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.94
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	95.92
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	95.88
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	95.86
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	95.85
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	95.81
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	95.81
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	95.8
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	95.78
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.78
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	95.74
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	95.73
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.72
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	95.71
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	95.7
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	95.67
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	95.64
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	95.62
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	95.61
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.61
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	95.53
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.51
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.5
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	95.49
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	95.49
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	95.49
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	95.49
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.45
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	95.43
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	95.36
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	95.31
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.26
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	95.26
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	95.25
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	95.23
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	95.15
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.13
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.13
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	95.11
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	95.07
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	95.06
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	95.06
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.04
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	95.03
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	95.03
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	94.97
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	94.93
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	94.92
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	94.91
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	94.89
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	94.88
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	94.79
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	94.75
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.71
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	94.66
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	94.59
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	94.49
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	94.35
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	94.34
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	94.3
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	94.29
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	94.27
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.26
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	94.21
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	94.09
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	94.06
d1xpua3	289	Transcription termination factor Rho, ATPase domai	94.05
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	93.97
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	93.83
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	93.8
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	93.7
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.58
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	93.39
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.34
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	93.24
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	93.04
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	92.79
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	92.68
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	92.22
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	92.2
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	91.13
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	91.12
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	90.98
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	90.76
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	90.74
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	90.37
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	90.24
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	90.14
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	90.04
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	89.99
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	89.87
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	89.53
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	89.52
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	89.44
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	89.36
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	89.19
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	89.18
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	89.03
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	88.96
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	88.96
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	88.62
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	88.36
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	88.21
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	87.99
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	87.97
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	87.85
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	87.74
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	87.74
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	87.67
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	86.69
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	86.43
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	85.94
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	85.47
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	85.01
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	84.57
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	84.13
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	84.05
d2axpa1	164	Hypothetical protein YorR {Bacillus subtilis [TaxI	84.01
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	83.98
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	83.18
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	80.65

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.2e-36  Score=255.98  Aligned_cols=199  Identities=23%  Similarity=0.366  Sum_probs=160.1

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+ ++.|+.++..|+++|.++++++|||||||||||++|+++|++++.+++.++++.+.+      ...++.+
T Consensus        18 ~~~k~~l~e-~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~l~~~~~g~~~~~l~~~   96 (256)
T d1lv7a_          18 DEAKEEVAE-LVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDM   96 (256)
T ss_dssp             HHHHHHTHH-HHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTSCCCCCHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHHhhhcchhHHHHHHHHH
Confidence            467888866 457899999999999999999999999999999999999999999999999998863      4668888


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||+|.++..++....             ........+++.|+..+++....  .+++||+|||+|+
T Consensus        97 f~~A~~~~P~il~iDeiD~l~~~r~~~~~-------------~~~~~~~~~~~~ll~~~d~~~~~--~~v~vIatTn~~~  161 (256)
T d1lv7a_          97 FEQAKKAAPCIIFIDEIDAVGRQRGAGLG-------------GGHDEREQTLNQMLVEMDGFEGN--EGIIVIAATNRPD  161 (256)
T ss_dssp             HHHHHTTCSEEEEETTHHHHTCCCSTTSC-------------CTTCHHHHHHHHHHHHHHTCCSS--SCEEEEEEESCTT
T ss_pred             HHHHHHcCCEEEEEEChhhhCccCCCCCC-------------CCcHHHHHHHHHHHHHhhCCCCC--CCEEEEEeCCCcc
Confidence            87764  6899999999999763322111             11133356788899999987543  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|++++|||||+..|+|+.|+.++|.+||+.++.+.......++..++.. .+||++||.+++
T Consensus       162 ~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~  225 (256)
T d1lv7a_         162 VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLV  225 (256)
T ss_dssp             TSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             cCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999988765545566666664 569999999987

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=3e-36  Score=252.50  Aligned_cols=199  Identities=24%  Similarity=0.340  Sum_probs=162.3

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+ +..++..+..|..+|.++++|+|||||||||||++|+++|++++.+++.++++.+.+      ...++.+
T Consensus        15 ~~~k~~l~~-~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~~~g~~~~~l~~~   93 (247)
T d1ixza_          15 EEAKEELKE-IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDL   93 (247)
T ss_dssp             HHHHHHHHH-HHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHSCTTHHHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhhccccHHHHHHHHH
Confidence            467777755 677899999999999999999999999999999999999999999999999887652      3567888


Q ss_pred             HHHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+.  .||||||||+|.++..+......             .+.....+++.|+..|+++...  .+++||+|||+|+
T Consensus        94 f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~-------------~~~~~~~~~~~ll~~~d~~~~~--~~vivi~tTn~~~  158 (247)
T d1ixza_          94 FETAKRHAPCIVFIDEIDAVGRKRGSGVGG-------------GNDEREQTLNQLLVEMDGFEKD--TAIVVMAATNRPD  158 (247)
T ss_dssp             HHHHTTSSSEEEEEETHHHHHC----------------------CHHHHHHHHHHHHHHHTCCTT--CCEEEEEEESCGG
T ss_pred             HHHHHHcCCEEEEEEChhhhCccCCCCCCC-------------CcHHHHHHHHHHHHHhhCCCCC--CCEEEEEeCCCcc
Confidence            87764  68999999999998754332211             1234456788899999987443  5689999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|++++|||||+..|+|+.|+.++|.+||+.++.........++..++.. .+||++||.+++
T Consensus       159 ~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv  222 (247)
T d1ixza_         159 ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLL  222 (247)
T ss_dssp             GSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             ccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999987655555566667775 479999999987

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=4.7e-36  Score=253.31  Aligned_cols=197  Identities=23%  Similarity=0.335  Sum_probs=165.0

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|+++.+.+..++..++.|...|+++++|+|||||||||||++++++|++++.+++.++++.+.+      ...++.+
T Consensus        10 ~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~~l~~~~~g~~~~~l~~~   89 (258)
T d1e32a2          10 RKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKA   89 (258)
T ss_dssp             SHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHHHHTTSCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEEEEEchhhcccccccHHHHHHHH
Confidence            4688999999999999999999999999999999999999999999999999999999999887653      3556777


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..||||||||+|.++..++...                ......+++.++..++.....  .+++||+|||+++
T Consensus        90 f~~A~~~~p~il~iDeid~l~~~r~~~~----------------~~~~~~~~~~~~~~~~~~~~~--~~vlvi~tTn~~~  151 (258)
T d1e32a2          90 FEEAEKNAPAIIFIDELDAIAPKREKTH----------------GEVERRIVSQLLTLMDGLKQR--AHVIVMAATNRPN  151 (258)
T ss_dssp             HHHHHHTCSEEEEESSGGGTCCHHHHCC----------------CTTHHHHHHHHHHHHHTCCCS--SCEEEEEEESCGG
T ss_pred             HHHHHhcCCeEEEehhhhhhccCCCCCC----------------CchHHHHHHHhcccccccccc--CCccEEEeCCCcc
Confidence            7665  4699999999999987554321                123345677777777766443  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .+|++++|||||+..|+|+.|+.++|..||+.+++........++..++.. .+||++||.+++
T Consensus       152 ~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv  215 (258)
T d1e32a2         152 SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALC  215 (258)
T ss_dssp             GSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHH
T ss_pred             ccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHH
Confidence            999999999999999999999999999999999987654444456667665 569999999887

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=1.1e-35  Score=251.96  Aligned_cols=200  Identities=23%  Similarity=0.336  Sum_probs=158.4

Q ss_pred             hHHHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC------hhhHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG------NNDLRHI   76 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~------~~~l~~~   76 (266)
                      +++|++|.+.+..++.++++|..+|+++++|+|||||||||||++++++|++++.+++.++++.+.+      ...++.+
T Consensus        13 ~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~   92 (265)
T d1r7ra3          13 EDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREI   92 (265)
T ss_dssp             SCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHHHTSCTTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHhhhccccchHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999999999999877642      3556777


Q ss_pred             HHHc--ccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC
Q 024550           77 LIAT--ENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE  154 (266)
Q Consensus        77 ~~~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~  154 (266)
                      |..+  ..||||||||+|.++..++......             ......+++.+++.+++....  .+++||+|||.++
T Consensus        93 f~~A~~~~p~il~ideid~l~~~~~~~~~~~-------------~~~~~~~~~~ll~~l~~~~~~--~~v~vi~ttn~~~  157 (265)
T d1r7ra3          93 FDKARQAAPCVLFFDELDSIAKARGGNIGDG-------------GGAADRVINQILTEMDGMSTK--KNVFIIGATNRPD  157 (265)
T ss_dssp             HHHHHHTCSEEEEESSGGGTCCHHHHCCCTT-------------HHHHHHHHHHHHHTCC--------CCEEEECCBSCT
T ss_pred             HHHHHhcCCcceeHHhhhhccccCCCcCCCC-------------cHHHHHHHHHHHHHhhCcCCC--CCEEEEEeCCCch
Confidence            7655  4689999999999987544322111             123345778899999887554  5699999999999


Q ss_pred             CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhc-CCCCHHHHHHHH
Q 024550          155 RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIAT-AKVTPADVAEQL  217 (266)
Q Consensus       155 ~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~-~~~s~~~i~~~l  217 (266)
                      .||++++|||||+..|+|+.|+.++|.+||+.+++........++..++.. .+||++||..++
T Consensus       158 ~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv  221 (265)
T d1r7ra3         158 IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEIC  221 (265)
T ss_dssp             TTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHH
T ss_pred             hCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999876433222344455444 579999999887

>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=99.90  E-value=7.9e-27  Score=200.16  Aligned_cols=154  Identities=14%  Similarity=0.118  Sum_probs=119.4

Q ss_pred             HHHHHhCCCCCceeE-EecCCCCChHHHHHHHHHHcC--CcEEEEeCCcccC------hhhHHHHHHHcccCCeeeeecc
Q 024550           21 EFYRRVGKAWKRGYL-LYGPPGTGKSSLIAAMANYLK--FDVYDLELSNLLG------NNDLRHILIATENKSILVVEDI   91 (266)
Q Consensus        21 ~~~~~~~~~~~~~iL-l~GppGtGKT~la~ala~~~~--~~~~~i~~~~~~~------~~~l~~~~~~~~~~~vl~iDei   91 (266)
                      ..++.+|...++|++ ||||||||||.+|+++|.+++  .+|+.++.+++.+      +..++.+|..+..+||||||||
T Consensus       112 ~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~~~ilf~DEi  191 (321)
T d1w44a_         112 VVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSL  191 (321)
T ss_dssp             EEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEECC
T ss_pred             HHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhhccEEEeehh
Confidence            344555666667755 589999999999999999986  7899999998873      5678999999989999999999


Q ss_pred             hhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC---CCCcccccCCCccee
Q 024550           92 DCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK---ERLDPALLRPGRMDM  168 (266)
Q Consensus        92 d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~---~~ld~al~r~~Rf~~  168 (266)
                      |.+.+.+.....               .....++++++|..|+++...  .+++||+|||+.   +.++++++|||||+.
T Consensus       192 d~~~~~r~~~~~---------------~~~~~r~v~~lL~e~dg~~~~--~~v~viaatN~~~~~~~i~~~~~r~~Rf~~  254 (321)
T d1w44a_         192 KNVIGAAGGNTT---------------SGGISRGAFDLLSDIGAMAAS--RGCVVIASLNPTSNDDKIVELVKEASRSNS  254 (321)
T ss_dssp             TTTC--------------------------CCHHHHHHHHHHHHHHHH--HTCEEEEECCCCCCCHHHHHHHHHHHHHSC
T ss_pred             hhhccccccCCC---------------CCcchhhhhhhhhhccccccC--CCeEEEEeCCCcccccchhhhhhccCcccc
Confidence            999875543221               133456899999999988665  569999999952   345667789999999


Q ss_pred             EEEcCCCCHHHHHHHHHHhhCCC
Q 024550          169 HINMSHCTPSGFKMLASNYLGIA  191 (266)
Q Consensus       169 ~i~~~~p~~~~~~~i~~~~~~~~  191 (266)
                      .|.++.|+.+.|.+|+..+....
T Consensus       255 ~v~v~~pd~~~r~~il~~~~~~~  277 (321)
T d1w44a_         255 TSLVISTDVDGEWQVLTRTGEGL  277 (321)
T ss_dssp             SEEEEECSSTTEEEEEEECBTTC
T ss_pred             eeecCCCChHHHHHHHHHhccCc
Confidence            99999999999999988776443

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.90  E-value=6.8e-24  Score=176.89  Aligned_cols=159  Identities=20%  Similarity=0.238  Sum_probs=110.1

Q ss_pred             HHHHHHHHHHHHhhCHHHHHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC-------hhhHHHHH
Q 024550            5 MKKMIMDDLERFLQRKEFYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG-------NNDLRHIL   77 (266)
Q Consensus         5 ~~~~i~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~-------~~~l~~~~   77 (266)
                      ..+.+++.+..+....   ......+++++|||||||||||++|+++|++++.+++.+++++...       ...++.+|
T Consensus        17 ~i~~i~~~~~~~~~~~---~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~~~~~~~i~~if   93 (246)
T d1d2na_          17 PVTRVLDDGELLVQQT---KNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIF   93 (246)
T ss_dssp             HHHHHHHHHHHHHHHH---HHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH---hccCCCCCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccccchhhhhhhhh
Confidence            3445555555554432   2333456789999999999999999999999999999999876432       23467777


Q ss_pred             HHcc--cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCC
Q 024550           78 IATE--NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKER  155 (266)
Q Consensus        78 ~~~~--~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~  155 (266)
                      ..+.  +||||||||||.++..+...                 ......+++.++..+++... .+.+++||+|||+++.
T Consensus        94 ~~A~~~~p~il~iDEid~l~~~~~~~-----------------~~~~~~~~~~ll~~l~~~~~-~~~~v~vi~tTn~~~~  155 (246)
T d1d2na_          94 DDAYKSQLSCVVVDDIERLLDYVPIG-----------------PRFSNLVLQALLVLLKKAPP-QGRKLLIIGTTSRKDV  155 (246)
T ss_dssp             HHHHTSSEEEEEECCHHHHTTCBTTT-----------------TBCCHHHHHHHHHHTTCCCS-TTCEEEEEEEESCHHH
T ss_pred             hhhhhcccceeehhhhhhHhhhcccc-----------------cchhHHHHHHHHHHhcCCCc-cccceeeeeccCChhh
Confidence            7664  58999999999986522111                 12234566777788776643 2456899999999999


Q ss_pred             CcccccCCCcceeEEEcCCCC-HHHHHHHHH
Q 024550          156 LDPALLRPGRMDMHINMSHCT-PSGFKMLAS  185 (266)
Q Consensus       156 ld~al~r~~Rf~~~i~~~~p~-~~~~~~i~~  185 (266)
                      +|++.++ +||+..|++|.+. .+++.+++.
T Consensus       156 ld~~~~~-~rF~~~i~~P~~~~r~~il~~l~  185 (246)
T d1d2na_         156 LQEMEML-NAFSTTIHVPNIATGEQLLEALE  185 (246)
T ss_dssp             HHHTTCT-TTSSEEEECCCEEEHHHHHHHHH
T ss_pred             ccchhhc-CccceEEecCCchhHHHHHHHHH
Confidence            9865332 3999999986554 333444443

>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=99.88  E-value=5.3e-22  Score=164.21  Aligned_cols=172  Identities=17%  Similarity=0.167  Sum_probs=125.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhHHHhHHHhhhhhcCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCIELQDRLSRARAANPD  110 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~  110 (266)
                      ..++|||||||||||++|+++|++++.+++.++.........+...+.....++++++||++.+................
T Consensus        35 ~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~  114 (238)
T d1in4a2          35 LDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQ  114 (238)
T ss_dssp             CCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSHHHHHHHHHHCCTTCEEEEETGGGCCHHHHHHHHHHHHTSC
T ss_pred             CCeEEEECCCCCcHHHHHHHHHhccCCCcccccCcccccHHHHHHHHHhhccCCchHHHHHHHhhhHHHhhcccceeeee
Confidence            45799999999999999999999999999999998888777888888888889999999999986543332211110000


Q ss_pred             cccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCC
Q 024550          111 FLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      +         ..........    ........++++|++||++..+++++++  ||...+.|+.|+.+++..++..+...
T Consensus       115 ~---------~~~~~~~~~~----~~~~~~~~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~  179 (238)
T d1in4a2         115 I---------DIMIGKGPSA----KSIRIDIQPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASL  179 (238)
T ss_dssp             C---------CC-------------------CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             e---------eeeecCcccc----cccccCCCCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhh
Confidence            0         0000000000    0111112468999999999999999999  99999999999999999999999988


Q ss_pred             CCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          191 AEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       191 ~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+.....+ +..++.....+.+.+.+.+
T Consensus       180 ~~~~~~~~~l~~i~~~s~gd~R~ai~~l  207 (238)
T d1in4a2         180 MDVEIEDAAAEMIAKRSRGTPRIAIRLT  207 (238)
T ss_dssp             TTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             ccchhhHHHHHHHHHhCCCCHHHHHHHH
Confidence            87776554 5566666677777777665

>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=99.85  E-value=8.3e-22  Score=169.48  Aligned_cols=142  Identities=16%  Similarity=0.282  Sum_probs=105.9

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC--------hhhHHHHHHHcc-------cCCeeeeecchhh
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG--------NNDLRHILIATE-------NKSILVVEDIDCC   94 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~--------~~~l~~~~~~~~-------~~~vl~iDeid~l   94 (266)
                      +++|+|||||||||||++|+++|+.++.+++.++++.+..        ...+..+|..+.       ++|||||||||.+
T Consensus        48 ~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki  127 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKI  127 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGG
T ss_pred             CCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhh
Confidence            5689999999999999999999999999999999988752        245666666653       4799999999998


Q ss_pred             HHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC------CCceEEEEe----cCCCCCCcccccCCC
Q 024550           95 IELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC------GDERIIIFT----TNHKERLDPALLRPG  164 (266)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~------~~~~ivi~t----tn~~~~ld~al~r~~  164 (266)
                      .+.+....               .+.....+++.||..+++.....      ..++++|++    ++.+..++|++..  
T Consensus       128 ~~~~~~~~---------------~~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~--  190 (309)
T d1ofha_         128 CKKGEYSG---------------ADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--  190 (309)
T ss_dssp             SCCSSCCS---------------SHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--
T ss_pred             hhhccCcc---------------cchhhhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhhh--
Confidence            65221100               00112336677888888642211      124566765    5677888888887  


Q ss_pred             cceeEEEcCCCCHHHHHHHHHHhh
Q 024550          165 RMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       165 Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                      ||+..+.|+.|+..++.+|+..+.
T Consensus       191 R~~~~i~~~~~~~~~~~~Il~~~~  214 (309)
T d1ofha_         191 RLPIRVELTALSAADFERILTEPH  214 (309)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHSST
T ss_pred             hhheeeeccCCCHHHHHHHHHHHH
Confidence            999999999999999999987554

>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=99.81  E-value=4.5e-19  Score=146.48  Aligned_cols=173  Identities=16%  Similarity=0.110  Sum_probs=115.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHc-ccCCeeeeecchhhHHHhHHHhhhhhcC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIAT-ENKSILVVEDIDCCIELQDRLSRARAAN  108 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~-~~~~vl~iDeid~l~~~~~~~~~~~~~~  108 (266)
                      ++.++|||||||||||++|+++|++++.++..++.............+... ..++|+++||+|.+..............
T Consensus        34 ~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iDe~~~~~~~~~~~l~~~~e~  113 (239)
T d1ixsb2          34 PLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMED  113 (239)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSHHHHHHHHHTTCCTTCEEEEETGGGCCHHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccchhhHHHHHhhccCCCeeeeecccccchhHHHhhhhhhhh
Confidence            456899999999999999999999999999999988876554444444433 3578999999998865332221111000


Q ss_pred             CccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhh
Q 024550          109 PDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                                 .................  ....++++|++||++...+++.++  |+...+.+..|+.+++..++....
T Consensus       114 -----------~~~~~~~~~~~~~~~~~--~~~~~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~  178 (239)
T d1ixsb2         114 -----------FVMDIVIGQGPAARTIR--LELPRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDA  178 (239)
T ss_dssp             -----------SEEEEECSCTTCCCEEE--EECCCCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHH
T ss_pred             -----------hhhhhhhccchhhhhcc--cCCCCEEEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHH
Confidence                       00000000000000011  112457888899988888878888  777899999999999999999888


Q ss_pred             CCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          189 GIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       189 ~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      ...+..... .+..++.....+++...+.+
T Consensus       179 ~~~~i~~~~~~l~~ia~~s~gd~R~a~~~l  208 (239)
T d1ixsb2         179 RLLGVRITEEAALEIGRRSRGTMRVAKRLF  208 (239)
T ss_dssp             GGGCCCBCHHHHHHHHHHTTSSHHHHHHHH
T ss_pred             HHhCCccchHHHHHHHHHcCCCHHHHHHHH
Confidence            877766654 44555555556666665554

>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=99.77  E-value=2.6e-18  Score=142.70  Aligned_cols=176  Identities=17%  Similarity=0.198  Sum_probs=109.0

Q ss_pred             hHHHHHHHHHHHHHhhCHHH----HHHhCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHH
Q 024550            3 FDMKKMIMDDLERFLQRKEF----YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILI   78 (266)
Q Consensus         3 ~~~~~~i~~~~~~~l~~~~~----~~~~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~   78 (266)
                      ++.++++...+..|......    ....+..+.+++|||||||||||++|+++|++++.+++.++++...+...+...+.
T Consensus        20 ~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (253)
T d1sxja2          20 KGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVK   99 (253)
T ss_dssp             HHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECTTSCCCHHHHHHTGG
T ss_pred             HHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhhhccccccchhhHHHHHHHH
Confidence            44455555544444322211    11223445568999999999999999999999999999999988765544433221


Q ss_pred             H--------------------cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc
Q 024550           79 A--------------------TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS  138 (266)
Q Consensus        79 ~--------------------~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~  138 (266)
                      .                    .....++++||+|.+..                        ........++......  
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~------------------------~~~~~~~~~~~~~~~~--  153 (253)
T d1sxja2         100 NALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSG------------------------GDRGGVGQLAQFCRKT--  153 (253)
T ss_dssp             GGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCT------------------------TSTTHHHHHHHHHHHC--
T ss_pred             HHhhcchhhhhhhhhhhcccccccceEEEeeecccccc------------------------chhhhhHHHhhhhccc--
Confidence            1                    01356899999998742                        1122233333333222  


Q ss_pred             CCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcH-HHHHHHhhcCCCCH
Q 024550          139 SCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLF-VEIEKLIATAKVTP  210 (266)
Q Consensus       139 ~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~-~~~~~l~~~~~~s~  210 (266)
                        ...++++++++....++ .+.+  | ...|+|+.|+.+++..+++.+...++..+. ..+..++...+.+.
T Consensus       154 --~~~ii~i~~~~~~~~~~-~l~~--~-~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~GDi  220 (253)
T d1sxja2         154 --STPLILICNERNLPKMR-PFDR--V-CLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDI  220 (253)
T ss_dssp             --SSCEEEEESCTTSSTTG-GGTT--T-SEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCH
T ss_pred             --ccccccccccccccccc-cccc--e-eeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCCcH
Confidence              23455555555555555 4554  4 478999999999999999988866554443 33455555433333

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.74  E-value=2.9e-17  Score=135.68  Aligned_cols=154  Identities=15%  Similarity=0.248  Sum_probs=113.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC------------------------cEEEEeCCcccChhhHHHHHHHcc----
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF------------------------DVYDLELSNLLGNNDLRHILIATE----   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~------------------------~~~~i~~~~~~~~~~l~~~~~~~~----   81 (266)
                      .++++|||||||||||++|+++++.++.                        .+++++.........++.++....    
T Consensus        33 ~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~  112 (239)
T d1njfa_          33 IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPA  112 (239)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCS
T ss_pred             CCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccc
Confidence            3667999999999999999999988743                        356777665555555666665542    


Q ss_pred             --cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCccc
Q 024550           82 --NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPA  159 (266)
Q Consensus        82 --~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~a  159 (266)
                        ...|++|||+|.|..                           ...+.|+..|+..    +....||++||.+..+.++
T Consensus       113 ~~~~kviiIde~d~l~~---------------------------~~q~~Llk~lE~~----~~~~~~il~tn~~~~i~~~  161 (239)
T d1njfa_         113 RGRFKVYLIDEVHMLSR---------------------------HSFNALLKTLEEP----PEHVKFLLATTDPQKLPVT  161 (239)
T ss_dssp             SSSSEEEEEETGGGSCH---------------------------HHHHHHHHHHHSC----CTTEEEEEEESCGGGSCHH
T ss_pred             cCCCEEEEEECcccCCH---------------------------HHHHHHHHHHhcC----CCCeEEEEEcCCccccChh
Confidence              235999999998732                           2345677777643    3568899999999999999


Q ss_pred             ccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHHHHHH
Q 024550          160 LLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       160 l~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +.+  || ..+.|+.|+.++..+++......++....+ .+..++.....+++...+.+
T Consensus       162 i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         162 ILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             HHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             Hhh--hh-cccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            999  88 579999999999999888888766655543 34445554555666555544

>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=99.73  E-value=8.7e-18  Score=137.89  Aligned_cols=148  Identities=16%  Similarity=0.174  Sum_probs=106.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCcccChhhHHHHHHH--------cccCCeeeeecchhhHHHh
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNLLGNNDLRHILIA--------TENKSILVVEDIDCCIELQ   98 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~~~~~~l~~~~~~--------~~~~~vl~iDeid~l~~~~   98 (266)
                      .++|||||||||||++|+++|++++     .++++++++...+...+...+..        ...+.|+++||+|.+..  
T Consensus        46 ~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~~~~~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~--  123 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ--  123 (231)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH--
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCcccchhHHHHHHHHHHhhhhccCCCceEEeehhhhhcch--
Confidence            3699999999999999999999874     47888888765432222222221        12478999999997753  


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHH
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPS  178 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~  178 (266)
                                               .....|+..++..    ...+++|++||.+..+++++.+  || ..+.|+.|+..
T Consensus       124 -------------------------~~~~~ll~~l~~~----~~~~~~i~~~n~~~~i~~~l~s--R~-~~i~~~~~~~~  171 (231)
T d1iqpa2         124 -------------------------DAQQALRRTMEMF----SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDE  171 (231)
T ss_dssp             -------------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--TE-EEEECCCCCHH
T ss_pred             -------------------------hHHHHHhhhcccC----CcceEEEeccCChhhchHhHhC--cc-ccccccccchh
Confidence                                     1223455555543    2458899999999999999999  88 56999999999


Q ss_pred             HHHHHHHHhhCCCCCCcHH-HHHHHhhcCCCCHHHH
Q 024550          179 GFKMLASNYLGIAEHPLFV-EIEKLIATAKVTPADV  213 (266)
Q Consensus       179 ~~~~i~~~~~~~~~~~~~~-~~~~l~~~~~~s~~~i  213 (266)
                      +...+++..+..++..+.. .+..++.....+.+++
T Consensus       172 ~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~gdiR~a  207 (231)
T d1iqpa2         172 DIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRA  207 (231)
T ss_dssp             HHHHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHH
T ss_pred             hHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHH
Confidence            9999999999887766543 3444444434444443

>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=99.70  E-value=5.9e-17  Score=132.32  Aligned_cols=131  Identities=15%  Similarity=0.199  Sum_probs=99.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC-----cEEEEeCCcccChhhHHHHHHH---c------ccCCeeeeecchhhHHHh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF-----DVYDLELSNLLGNNDLRHILIA---T------ENKSILVVEDIDCCIELQ   98 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~-----~~~~i~~~~~~~~~~l~~~~~~---~------~~~~vl~iDeid~l~~~~   98 (266)
                      ++|||||||||||++|+.+|++++.     .++++++++..+...+...+..   .      ....++++||+|.+..  
T Consensus        38 ~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~--  115 (224)
T d1sxjb2          38 HMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA--  115 (224)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH--
T ss_pred             eEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHHHHHHhhccCCCcceEEEEEecccccch--
Confidence            5999999999999999999998863     4788888877654444433322   1      1346999999998753  


Q ss_pred             HHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHH
Q 024550           99 DRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPS  178 (266)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~  178 (266)
                                               ...+.++..++..    ....+++.+|+....+.+++++  || ..|.|+.|+.+
T Consensus       116 -------------------------~~~~~ll~~~e~~----~~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~  163 (224)
T d1sxjb2         116 -------------------------GAQQALRRTMELY----SNSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDE  163 (224)
T ss_dssp             -------------------------HHHHTTHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHH
T ss_pred             -------------------------hHHHHHhhhcccc----ccceeeeeccCchhhhhhHHHH--HH-HHhhhcccchh
Confidence                                     1234455555543    3457888999999999999999  88 56999999999


Q ss_pred             HHHHHHHHhhCCCCCCcHH
Q 024550          179 GFKMLASNYLGIAEHPLFV  197 (266)
Q Consensus       179 ~~~~i~~~~~~~~~~~~~~  197 (266)
                      +...++...+..++..+..
T Consensus       164 ~i~~~l~~i~~~e~~~i~~  182 (224)
T d1sxjb2         164 DVLKRLLQIIKLEDVKYTN  182 (224)
T ss_dssp             HHHHHHHHHHHHHTCCBCH
T ss_pred             hhHHHHHHHHHhcccCCCH
Confidence            9999999888776655543

>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=99.69  E-value=1.8e-16  Score=129.43  Aligned_cols=151  Identities=23%  Similarity=0.296  Sum_probs=106.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC-----cEEEEeCCcccChhhHHHHHH---Hc-----ccCCeeeeecchhhHHHhH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF-----DVYDLELSNLLGNNDLRHILI---AT-----ENKSILVVEDIDCCIELQD   99 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~-----~~~~i~~~~~~~~~~l~~~~~---~~-----~~~~vl~iDeid~l~~~~~   99 (266)
                      ++|||||||||||++++++|++++.     .++..+.+...+.........   ..     ....+++|||+|.+..   
T Consensus        37 ~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~---  113 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN---  113 (227)
T ss_dssp             CEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH---
T ss_pred             eEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhccccccccCCCeEEEEEeccccchh---
Confidence            5999999999999999999998743     356777666554333222221   11     1245999999998743   


Q ss_pred             HHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCHHH
Q 024550          100 RLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTPSG  179 (266)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~~~  179 (266)
                                              ...+.++..++..    +...+++.+||.+..+++++.+  || ..+.|+.|+.++
T Consensus       114 ------------------------~~~~~Ll~~le~~----~~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~  162 (227)
T d1sxjc2         114 ------------------------AAQNALRRVIERY----TKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEA  162 (227)
T ss_dssp             ------------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHH
T ss_pred             ------------------------hHHHHHHHHhhhc----ccceeeccccCcHHHhHHHHHH--HH-hhhccccccccc
Confidence                                    2345566777654    2468889999999999999999  88 569999999999


Q ss_pred             HHHHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          180 FKMLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       180 ~~~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      ..+++.+.+..++..+..+ ++.++.....+.+...+.|
T Consensus       163 i~~~l~~I~~~e~i~i~~~~l~~i~~~s~Gd~R~ain~L  201 (227)
T d1sxjc2         163 IERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVL  201 (227)
T ss_dssp             HHHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHT
T ss_pred             cccccccccccccccCCHHHHHHHHHHcCCcHHHHHHHH
Confidence            9999999888877666544 3445554444444444433

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=99.68  E-value=1.5e-17  Score=145.02  Aligned_cols=162  Identities=17%  Similarity=0.027  Sum_probs=95.5

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHH-------HHHHc--------ccCCeeeeec
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRH-------ILIAT--------ENKSILVVED   90 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~-------~~~~~--------~~~~vl~iDe   90 (266)
                      .|.|.++++|||||||||||++|+++|+.++.+++++++++..+...+..       +|..+        ..++++++||
T Consensus       149 ~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~~l~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~De  228 (362)
T d1svma_         149 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINN  228 (362)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHHHHGGGTTCSCEEETTCCCSTTTTTTCCCCSHHHH
T ss_pred             hCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHHHHHhHHHHHHHHHHHHHHhhhhccCCCCeEEEeh
Confidence            48888899999999999999999999999999999999886642211111       11111        1256777777


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEE
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHI  170 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i  170 (266)
                      +|.+....+...                    ...+..-.......     ....+|+|||.   ++.++++|+||+..|
T Consensus       229 iD~l~~~~dg~~--------------------~~~~~~~~~~~~~~-----~~~p~i~ttN~---~~~~~~r~~Rf~~~i  280 (362)
T d1svma_         229 LDNLRDYLDGSV--------------------KVNLEKKHLNKRTQ-----IFPPGIVTMNE---YSVPKTLQARFVKQI  280 (362)
T ss_dssp             HHTTHHHHHCSS--------------------CEEECCSSSCCEEE-----CCCCEEEEECS---CCCCHHHHTTEEEEE
T ss_pred             HhhcccccCCcc--------------------hhhhhhhhhchhhh-----ccCCceeeccc---ccccccccccCceEE
Confidence            776643111000                    00000000000000     11247789995   467778899999999


Q ss_pred             EcCCCCHHHHH-HHHHHhhCCCCCCcHHH-HHHHhhcCCCCHHHHHHHH
Q 024550          171 NMSHCTPSGFK-MLASNYLGIAEHPLFVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       171 ~~~~p~~~~~~-~i~~~~~~~~~~~~~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+..|+...+. .++..+..........+ +..++.  +++++|+.+.+
T Consensus       281 ~~~~~~~~~~~~~~l~~i~~~~~l~~~~~~L~~li~--~~s~~D~~~~i  327 (362)
T d1svma_         281 DFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIW--YRPVAEFAQSI  327 (362)
T ss_dssp             ECCCCHHHHHHHHTCTHHHHTTCTTCHHHHHHHHHH--HSCGGGSCGGG
T ss_pred             eecCCCcHHHHHHHHHHHhcccCCCCCHHHHHHHcc--CCCHHHHHHHH
Confidence            99998877664 34444444444443322 223332  35666655443

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.65  E-value=2.7e-16  Score=127.58  Aligned_cols=155  Identities=15%  Similarity=0.263  Sum_probs=107.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccC-------hhhHHHHHHHcccCCeeeeecchhhHHHhHHHh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLG-------NNDLRHILIATENKSILVVEDIDCCIELQDRLS  102 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~-------~~~l~~~~~~~~~~~vl~iDeid~l~~~~~~~~  102 (266)
                      .++||||||||||+|++++++++   +..+++++...+..       ......++.......+|+|||+|.+.+      
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~~------  111 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSG------  111 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTT------
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHHHHHHHHHHHccchhhHHHHHhhccchhhhhhhhhcC------
Confidence            49999999999999999999988   56677777665531       122334444556789999999998854      


Q ss_pred             hhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC---cccccCCCcce--eEEEcCCCCH
Q 024550          103 RARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL---DPALLRPGRMD--MHINMSHCTP  177 (266)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l---d~al~r~~Rf~--~~i~~~~p~~  177 (266)
                                      ....+..+..+++.+...     ...+++++...|..+   .+.|.+  |+.  .++.++ |+.
T Consensus       112 ----------------~~~~~~~lf~lin~~~~~-----~~~iiits~~~p~~l~~~~~dL~S--RL~~g~~~~i~-p~d  167 (213)
T d1l8qa2         112 ----------------KERTQIEFFHIFNTLYLL-----EKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIE-LDN  167 (213)
T ss_dssp             ----------------CHHHHHHHHHHHHHHHHT-----TCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECC-CCH
T ss_pred             ----------------chHHHHHHHHHHHHHhhc-----cceEEEecCCcchhccccchHHHH--HhhCceEEEEC-CCc
Confidence                            233344455555554432     456777777777554   477777  554  678886 778


Q ss_pred             HHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          178 SGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       178 ~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      +++.++++.+....+..+.++...++.+..-+++++..++
T Consensus       168 ~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~~~~R~L~~~l  207 (213)
T d1l8qa2         168 KTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKI  207 (213)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHHHCSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCcHHHHHHHH
Confidence            8999999999988888877766555544334566665554

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.63  E-value=3.4e-15  Score=120.47  Aligned_cols=150  Identities=18%  Similarity=0.179  Sum_probs=107.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC------------------------CcEEEEeCCccc---ChhhHHHHHHHcc-
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK------------------------FDVYDLELSNLL---GNNDLRHILIATE-   81 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~------------------------~~~~~i~~~~~~---~~~~l~~~~~~~~-   81 (266)
                      .++++||+||||+|||++|+.+|+.+.                        ..++.+....-.   ....++.+..... 
T Consensus        23 l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~l~~~~~~  102 (207)
T d1a5ta2          23 GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNE  102 (207)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTS
T ss_pred             cCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccchhhHHhhhhhh
Confidence            467899999999999999999999762                        233444322211   2234555554432 


Q ss_pred             -----cCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCC
Q 024550           82 -----NKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERL  156 (266)
Q Consensus        82 -----~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~l  156 (266)
                           ...|++|||+|.+-                           ....+.|+..|+.-    +..++||.+||++..+
T Consensus       103 ~~~~~~~kviIide~d~l~---------------------------~~a~n~Llk~lEep----~~~~~fIl~t~~~~~l  151 (207)
T d1a5ta2         103 HARLGGAKVVWVTDAALLT---------------------------DAAANALLKTLEEP----PAETWFFLATREPERL  151 (207)
T ss_dssp             CCTTSSCEEEEESCGGGBC---------------------------HHHHHHHHHHHTSC----CTTEEEEEEESCGGGS
T ss_pred             ccccCccceEEechhhhhh---------------------------hhhhHHHHHHHHhh----cccceeeeeecChhhh
Confidence                 34599999999874                           23556777777753    4678999999999999


Q ss_pred             cccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHH
Q 024550          157 DPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       157 d~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l  217 (266)
                      .+++.+  || ..|.|+.|+.++...++......    ....+..++.....++++..+++
T Consensus       152 l~tI~S--Rc-~~i~~~~~~~~~~~~~L~~~~~~----~~~~~~~i~~~s~Gs~r~al~~l  205 (207)
T d1a5ta2         152 LATLRS--RC-RLHYLAPPPEQYAVTWLSREVTM----SQDALLAALRLSAGSPGAALALF  205 (207)
T ss_dssp             CHHHHT--TS-EEEECCCCCHHHHHHHHHHHCCC----CHHHHHHHHHHTTTCHHHHHHTT
T ss_pred             hhhhcc--ee-EEEecCCCCHHHHHHHHHHcCCC----CHHHHHHHHHHcCCCHHHHHHHh
Confidence            999999  98 77999999999988888754432    23555566666667777766544

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.62  E-value=4.8e-16  Score=128.59  Aligned_cols=77  Identities=6%  Similarity=0.088  Sum_probs=58.9

Q ss_pred             CCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccC
Q 024550           83 KSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLR  162 (266)
Q Consensus        83 ~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r  162 (266)
                      ..+++|||+|.+..                           ...+.++..++..    +..+.||++||+++.+++++.+
T Consensus       132 ~~iiiide~d~l~~---------------------------~~~~~l~~~~e~~----~~~~~~Il~tn~~~~i~~~l~s  180 (252)
T d1sxje2         132 YKCVIINEANSLTK---------------------------DAQAALRRTMEKY----SKNIRLIMVCDSMSPIIAPIKS  180 (252)
T ss_dssp             CEEEEEECTTSSCH---------------------------HHHHHHHHHHHHS----TTTEEEEEEESCSCSSCHHHHT
T ss_pred             ceEEEecccccccc---------------------------ccchhhhcccccc----cccccceeeeccccchhhhhhc
Confidence            35899999998743                           1233445555532    3457889999999999999999


Q ss_pred             CCcceeEEEcCCCCHHHHHHHHHHhhCCCCC
Q 024550          163 PGRMDMHINMSHCTPSGFKMLASNYLGIAEH  193 (266)
Q Consensus       163 ~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~  193 (266)
                        || ..|+|+.|+.++..+++...+..++.
T Consensus       181 --R~-~~i~~~~~~~~~~~~~l~~i~~~e~~  208 (252)
T d1sxje2         181 --QC-LLIRCPAPSDSEISTILSDVVTNERI  208 (252)
T ss_dssp             --TS-EEEECCCCCHHHHHHHHHHHHHHHTC
T ss_pred             --ch-heeeecccchhhHHHHHHHHHHHcCC
Confidence              98 57999999999999999887765543

>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=99.62  E-value=2.2e-15  Score=123.35  Aligned_cols=146  Identities=18%  Similarity=0.183  Sum_probs=99.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc------CCcEEEEeCCcccChhhHHHHHHH----------------c--ccCCeeee
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL------KFDVYDLELSNLLGNNDLRHILIA----------------T--ENKSILVV   88 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~------~~~~~~i~~~~~~~~~~l~~~~~~----------------~--~~~~vl~i   88 (266)
                      ++|||||||||||++++++|+++      ....+.++.+...........+..                .  ....|++|
T Consensus        35 ~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viii  114 (237)
T d1sxjd2          35 HMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIIL  114 (237)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEE
T ss_pred             eEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEE
Confidence            59999999999999999999986      566777777665433221111111                1  12348999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCccee
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDM  168 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~  168 (266)
                      ||+|.+..                           ...+.++..++..    ....++|.+++....+.+++.+  || .
T Consensus       115 De~d~l~~---------------------------~~~~~l~~~~~~~----~~~~~~i~~~~~~~~~~~~l~s--r~-~  160 (237)
T d1sxjd2         115 DEADSMTA---------------------------DAQSALRRTMETY----SGVTRFCLICNYVTRIIDPLAS--QC-S  160 (237)
T ss_dssp             TTGGGSCH---------------------------HHHHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--HS-E
T ss_pred             ecccccCH---------------------------HHHHHHhhccccc----cccccccccccccccccccccc--hh-h
Confidence            99998853                           1222333333322    2456788888998899999999  98 6


Q ss_pred             EEEcCCCCHHHHHHHHHHhhCCCCCCcHHHH-HHHhhcCCCCHHH
Q 024550          169 HINMSHCTPSGFKMLASNYLGIAEHPLFVEI-EKLIATAKVTPAD  212 (266)
Q Consensus       169 ~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~-~~l~~~~~~s~~~  212 (266)
                      .|.|+.|+.++...++...+..++..+..+. ..++.....+.+.
T Consensus       161 ~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~gd~R~  205 (237)
T d1sxjd2         161 KFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRR  205 (237)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHH
T ss_pred             hhccccccccccchhhhhhhhhhcCcCCHHHHHHHHHHcCCCHHH
Confidence            7999999999999999998887766555443 3344433333333

>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=99.59  E-value=8.7e-15  Score=125.36  Aligned_cols=169  Identities=14%  Similarity=0.252  Sum_probs=110.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh-------------------hhHHHHHHHcccCCeeeeecchh
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN-------------------NDLRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~-------------------~~l~~~~~~~~~~~vl~iDeid~   93 (266)
                      .+||+||||||||.+|+++|..++.+++.++++.+...                   ..+... ....+.+|+++||+|.
T Consensus        54 ~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~~l~g~~~gy~g~~~~~~l~~~-~~~~~~~vvl~DeieK  132 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDA-VIKHPHAVLLLDEIEK  132 (315)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHH-HHHCSSEEEEEETGGG
T ss_pred             EEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhhhhcccCCCccccccCChhhHH-HHhCccchhhhccccc
Confidence            58999999999999999999999999999999887531                   112222 2345679999999997


Q ss_pred             hHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC-------CCCceEEEEecCCC-------------
Q 024550           94 CIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS-------CGDERIIIFTTNHK-------------  153 (266)
Q Consensus        94 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-------~~~~~ivi~ttn~~-------------  153 (266)
                      +.+                           .+++.|++.++.-.-+       ...+.++|+|||--             
T Consensus       133 a~~---------------------------~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~i~~~~~~~~~  185 (315)
T d1r6bx3         133 AHP---------------------------DVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIH  185 (315)
T ss_dssp             SCH---------------------------HHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------
T ss_pred             ccc---------------------------hHhhhhHHhhccceecCCCCCccCccceEEEeccchhhHHHHhhhccchh
Confidence            643                           3456666666531111       12457899999932             


Q ss_pred             ------------CCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHHHHHHcCC
Q 024550          154 ------------ERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVAEQLMRNE  221 (266)
Q Consensus       154 ------------~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~~~l~~~~  221 (266)
                                  ..+.|.|+.  |++..+.|...+.++..+|+..++...    ...+...-....++...+..++..+.
T Consensus       186 ~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~~~~~I~~~~l~~~----~~~l~~~~i~l~~~~~a~~~l~~~~y  259 (315)
T d1r6bx3         186 QDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIVEL----QVQLDQKGVSLEVSQEARNWLAEKGY  259 (315)
T ss_dssp             ------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHH----HHHHHHTTEEEEECHHHHHHHHHHHC
T ss_pred             hhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhhHHHHHHHHHHHHH----HHHHHhcCcchhhHHHHHHHHHHhCC
Confidence                        136778888  999999999999999999988776322    11121111122355555544443334


Q ss_pred             CHHHHHHHHHHHHH
Q 024550          222 APEFALSGLIEFLE  235 (266)
Q Consensus       222 ~~~~~~~~~~~~~~  235 (266)
                      ++...++.+...++
T Consensus       260 d~~~GaR~L~r~Ie  273 (315)
T d1r6bx3         260 DRAMGARPMARVIQ  273 (315)
T ss_dssp             BTTTBTTTHHHHHH
T ss_pred             CCCCChhhHHHHHH
Confidence            44444444444443

>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=99.59  E-value=1.4e-14  Score=126.27  Aligned_cols=142  Identities=22%  Similarity=0.279  Sum_probs=94.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccC--------hhhHHHHHHHc------ccCCeeeeecchhhH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLG--------NNDLRHILIAT------ENKSILVVEDIDCCI   95 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~--------~~~l~~~~~~~------~~~~vl~iDeid~l~   95 (266)
                      ++.++||.||+|||||.+|++||..++.+++.++++.++.        ...+..++...      .+.+|+++||+|...
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~~~~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~  146 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKIS  146 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC-
T ss_pred             CCcceeeeCCCCccHHHHHHHHHhhcccceeehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhc
Confidence            5678999999999999999999999999999999998874        34455555443      357999999999876


Q ss_pred             HHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccC---------CCCceEEEEecCC--------------
Q 024550           96 ELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSS---------CGDERIIIFTTNH--------------  152 (266)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~---------~~~~~ivi~ttn~--------------  152 (266)
                      +.......             ..+.....+.+.||+.+++..-.         ...+.+++.|+|-              
T Consensus       147 ~~s~~~~~-------------~~d~a~~~V~~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~  213 (364)
T d1um8a_         147 RLSENRSI-------------TRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEI  213 (364)
T ss_dssp             --------------------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHH
T ss_pred             cccccccc-------------cccccchHHHHhhhhhhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhh
Confidence            52211111             11123455777788888742211         1123455555553              


Q ss_pred             -----------------------------------CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHH
Q 024550          153 -----------------------------------KERLDPALLRPGRMDMHINMSHCTPSGFKMLASN  186 (266)
Q Consensus       153 -----------------------------------~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~  186 (266)
                                                         ...+.|.|+.  |++..+.|...+.++..+|+..
T Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEf~g--Ri~~iv~f~~L~~~~l~~Il~~  280 (364)
T d1um8a_         214 IKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIG--RLPVLSTLDSISLEAMVDILQK  280 (364)
T ss_dssp             TTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             hhhhcccccccccccccchhhhhhhhccccHHHHhhhhhHHHHHH--HhcchhhHhhhhHHHHHHHHHH
Confidence                                               1125567777  9999999999999999998864

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.56  E-value=8.7e-14  Score=115.77  Aligned_cols=178  Identities=21%  Similarity=0.258  Sum_probs=112.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHHcc--cCCee
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIATE--NKSIL   86 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~~~--~~~vl   86 (266)
                      .....++++|+||||+|||++++.+|..+          +..++.++...+...        ..+..++....  .+.|+
T Consensus        35 ~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~~~~iIl  114 (268)
T d1r6bx2          35 CRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSIL  114 (268)
T ss_dssp             TSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEE
T ss_pred             hcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhHHHHHHHHHHHhhccCCceE
Confidence            33346789999999999999999999865          678999998888742        34555665543  46899


Q ss_pred             eeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-----CCCccccc
Q 024550           87 VVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-----ERLDPALL  161 (266)
Q Consensus        87 ~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-----~~ld~al~  161 (266)
                      ||||++.+++....                   ....   ..+-+.|......  ..+.+|++|+..     -.-|++|.
T Consensus       115 fiDeih~l~~~g~~-------------------~g~~---~d~a~~Lkp~L~r--g~i~vIgatT~eey~~~~e~d~al~  170 (268)
T d1r6bx2         115 FIDEIHTIIGAGAA-------------------SGGQ---VDAANLIKPLLSS--GKIRVIGSTTYQEFSNIFEKDRALA  170 (268)
T ss_dssp             EETTTTTTTTSCCS-------------------SSCH---HHHHHHHSSCSSS--CCCEEEEEECHHHHHCCCCCTTSSG
T ss_pred             EecchHHHhcCCCC-------------------CCcc---ccHHHHhhHHHhC--CCCeEEEeCCHHHHHHHHhhcHHHH
Confidence            99999999751110                   0001   1122333333333  457888877632     34489999


Q ss_pred             CCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhhcCCCCHHHHH------HHHHc-CCCHHHHHHHHHHHH
Q 024550          162 RPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIATAKVTPADVA------EQLMR-NEAPEFALSGLIEFL  234 (266)
Q Consensus       162 r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~~~s~~~i~------~~l~~-~~~~~~~~~~~~~~~  234 (266)
                      |  || ..|.++.|+.++-.+|+..+.....        . -....++...+.      ..... ..-|+++++-+..++
T Consensus       171 r--rF-~~I~V~Eps~e~t~~IL~~~~~~~e--------~-~h~v~~~~~al~~~v~ls~ryi~~~~~PdKAIdllDea~  238 (268)
T d1r6bx2         171 R--RF-QKIDITEPSIEETVQIINGLKPKYE--------A-HHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAG  238 (268)
T ss_dssp             G--GE-EEEECCCCCHHHHHHHHHHHHHHHH--------H-HHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHH
T ss_pred             h--hh-cccccCCCCHHHHHHHHHHhhHHHh--------c-cCCEEeChHHHHHHHHHHHhhccCCCCCcHHHHHHHHHH
Confidence            9  99 5699999999999998876542210        0 011123333232      22222 346888888888887


Q ss_pred             Hhhhhh
Q 024550          235 ESKKRA  240 (266)
Q Consensus       235 ~~~~~~  240 (266)
                      ...+..
T Consensus       239 a~~~~~  244 (268)
T d1r6bx2         239 ARARLM  244 (268)
T ss_dssp             HHHHHS
T ss_pred             HHHHhh
Confidence            766654

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.56  E-value=2.2e-14  Score=125.68  Aligned_cols=197  Identities=18%  Similarity=0.193  Sum_probs=108.5

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccChh--------hHHHHHHHc---ccCCeeee
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGNN--------DLRHILIAT---ENKSILVV   88 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~~--------~l~~~~~~~---~~~~vl~i   88 (266)
                      ...+++|.||||+|||++++.+|...          +..++.++...+....        .+..++...   ..+.||||
T Consensus        42 ~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfi  121 (387)
T d1qvra2          42 TKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFI  121 (387)
T ss_dssp             SCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEE
T ss_pred             CCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEe
Confidence            35679999999999999999999865          5679999999887532        344444443   23578999


Q ss_pred             ecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCC-----CCCCcccccCC
Q 024550           89 EDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNH-----KERLDPALLRP  163 (266)
Q Consensus        89 Deid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~-----~~~ld~al~r~  163 (266)
                      ||++.+++.....+                   .....+-|.-.|..      +.+-+|++|+.     .+. |++|.| 
T Consensus       122 de~h~l~~~g~~~g-------------------~~d~a~~Lkp~L~r------g~~~~I~~tT~~ey~~~e~-d~al~r-  174 (387)
T d1qvra2         122 DELHTVVGAGKAEG-------------------AVDAGNMLKPALAR------GELRLIGATTLDEYREIEK-DPALER-  174 (387)
T ss_dssp             CCC--------------------------------------HHHHHT------TCCCEEEEECHHHHHHHTT-CTTTCS-
T ss_pred             ccHHHHhcCCCCCC-------------------cccHHHHHHHHHhC------CCcceeeecCHHHHHHhcc-cHHHHH-
Confidence            99999976332111                   01122223333332      34667776653     234 899999 


Q ss_pred             CcceeEEEcCCCCHHHHHHHHHHhhCCC----CCCcHHHHHHHhhcCCCCHHHHHHHHHc-CCCHHHHHHHHHHHHHhhh
Q 024550          164 GRMDMHINMSHCTPSGFKMLASNYLGIA----EHPLFVEIEKLIATAKVTPADVAEQLMR-NEAPEFALSGLIEFLESKK  238 (266)
Q Consensus       164 ~Rf~~~i~~~~p~~~~~~~i~~~~~~~~----~~~~~~~~~~l~~~~~~s~~~i~~~l~~-~~~~~~~~~~~~~~~~~~~  238 (266)
                       || ..|.++.|+.++-..|++......    +..+..+....+.       ++...+.. ..-|+++++-+..++...+
T Consensus       175 -rF-~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v-------~ls~ryi~~r~~PdKAidlld~a~a~~~  245 (387)
T d1qvra2         175 -RF-QPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAA-------TLSHRYITERRLPDKAIDLIDEAAARLR  245 (387)
T ss_dssp             -CC-CCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHH-------HHHHHHCCSSCTHHHHHHHHHHHHHHHH
T ss_pred             -hc-ccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHH-------HhcccccccccChhhHHHHHHHHHHHHH
Confidence             99 559999999999998887655332    2222222211111       12222222 3467888888887777766


Q ss_pred             hh--ccchhhHHHHHHHHHhhhhhhc
Q 024550          239 RA--NDGSEAKEAEERAVQAEKKVLE  262 (266)
Q Consensus       239 ~~--~~~~~~~~~~~~~~~~~~~~~~  262 (266)
                      -.  +.++.-...+++..+.+.+...
T Consensus       246 i~~~s~P~el~~ler~I~qLe~E~~a  271 (387)
T d1qvra2         246 MALESAPEEIDALERKKLQLEIEREA  271 (387)
T ss_dssp             HTTTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhccCCcHHHHHHHHHHHHHHHHHHH
Confidence            54  3344444455544444444333

>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=99.55  E-value=1.2e-14  Score=124.34  Aligned_cols=126  Identities=20%  Similarity=0.357  Sum_probs=93.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChh-------------------hHHHHHHHcccCCeeeeec
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNN-------------------DLRHILIATENKSILVVED   90 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~-------------------~l~~~~~~~~~~~vl~iDe   90 (266)
                      .+||+||+|||||.+|+.+|..+   +.+++.++++.+....                   .+...+. ....+|+++||
T Consensus        55 ~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~~~~L~g~~~gyvG~~~~~~l~~~~~-~~p~~Vvl~DE  133 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVR-RRPYSVILFDE  133 (315)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC--------------CHHHHHH-HCSSEEEEESS
T ss_pred             EEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchhhhhhcCCCCCCcCcccCChHHHHHH-hCCCcEEEEeh
Confidence            48899999999999999999998   6789999998776421                   1222222 23479999999


Q ss_pred             chhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCC-------CCceEEEEecCC-----------
Q 024550           91 IDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSC-------GDERIIIFTTNH-----------  152 (266)
Q Consensus        91 id~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-------~~~~ivi~ttn~-----------  152 (266)
                      ||.+.+                           ..++.|+..++.-.-+.       ..+.++|+|||-           
T Consensus       134 ieK~~~---------------------------~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~i~~~~~~  186 (315)
T d1qvra3         134 IEKAHP---------------------------DVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQK  186 (315)
T ss_dssp             GGGSCH---------------------------HHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHT
T ss_pred             HhhcCH---------------------------HHHHHHHHHhccCceeCCCCcEecCcceEEEEecccChHHHhhhccc
Confidence            997643                           24455555554321111       145789999994           


Q ss_pred             ---------------CCCCcccccCCCcceeEEEcCCCCHHHHHHHHHHhh
Q 024550          153 ---------------KERLDPALLRPGRMDMHINMSHCTPSGFKMLASNYL  188 (266)
Q Consensus       153 ---------------~~~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~  188 (266)
                                     ...+.|.|+.  ||+..+.|...+.++..+|+...+
T Consensus       187 ~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l  235 (315)
T d1qvra3         187 GWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQL  235 (315)
T ss_dssp             TCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHH
T ss_pred             ccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeeccchhhhhhHHHHHHHH
Confidence                           2457889999  999999999999999999987666

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.52  E-value=1.8e-13  Score=113.35  Aligned_cols=132  Identities=17%  Similarity=0.052  Sum_probs=84.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCCcccChhh--------------------------HHHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELSNLLGNND--------------------------LRHILIA   79 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~~~~~~~~--------------------------l~~~~~~   79 (266)
                      .+.++||+||||||||++++++++.+    +..++.+++........                          +...+..
T Consensus        42 ~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (276)
T d1fnna2          42 HYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRE  121 (276)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHH
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhh
Confidence            45689999999999999999999987    45667777655432111                          1111222


Q ss_pred             cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC---CCC
Q 024550           80 TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK---ERL  156 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~---~~l  156 (266)
                      .....++++|++|.+....                        ......++..+..   .....+++|++++..   +.+
T Consensus       122 ~~~~~~~~~~~~d~~~~~~------------------------~~~~~~~~~~~~~---~~~~~~~~i~~~~~~~~~~~~  174 (276)
T d1fnna2         122 RDLYMFLVLDDAFNLAPDI------------------------LSTFIRLGQEADK---LGAFRIALVIVGHNDAVLNNL  174 (276)
T ss_dssp             TTCCEEEEEETGGGSCHHH------------------------HHHHHHHTTCHHH---HSSCCEEEEEEESSTHHHHTS
T ss_pred             cccccccchhHHHHhhhhh------------------------hhhHHHHHhcccc---ccccceEEeecCCchhhhhhc
Confidence            3345677788888764311                        1111222222211   112457778888764   567


Q ss_pred             cccccCCCcce-eEEEcCCCCHHHHHHHHHHhhCC
Q 024550          157 DPALLRPGRMD-MHINMSHCTPSGFKMLASNYLGI  190 (266)
Q Consensus       157 d~al~r~~Rf~-~~i~~~~p~~~~~~~i~~~~~~~  190 (266)
                      ++++.+  |+. ..|.|+.|+.+++.+|+.+++..
T Consensus       175 ~~~~~~--r~~~~~i~~~~~~~~e~~~il~~r~~~  207 (276)
T d1fnna2         175 DPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKA  207 (276)
T ss_dssp             CHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             chhhhh--hhcchhccccchhHHHHHHHHHHHHHH
Confidence            788877  654 56899999999999999877643

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.49  E-value=5.1e-14  Score=117.45  Aligned_cols=135  Identities=10%  Similarity=0.078  Sum_probs=81.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC---------CcEEEEeCCcccCh----------------------hhHHHHH----
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK---------FDVYDLELSNLLGN----------------------NDLRHIL----   77 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~---------~~~~~i~~~~~~~~----------------------~~l~~~~----   77 (266)
                      .++||||||||||++++++++.+.         ..+..+++....+.                      ..+...+    
T Consensus        48 ~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  127 (287)
T d1w5sa2          48 IYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNL  127 (287)
T ss_dssp             EEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHH
T ss_pred             EEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHH
Confidence            367899999999999999999872         34445555544321                      1111112    


Q ss_pred             HHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCC---
Q 024550           78 IATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKE---  154 (266)
Q Consensus        78 ~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~---  154 (266)
                      .....+.++++|++|.+.......                  ......+..+.+.+......  ....+|+.+|.++   
T Consensus       128 ~~~~~~~~~iide~d~l~~~~~~~------------------~~~~~~l~~l~~~l~~~~~~--~~~~~i~i~~~~~~~~  187 (287)
T d1w5sa2         128 YVENHYLLVILDEFQSMLSSPRIA------------------AEDLYTLLRVHEEIPSRDGV--NRIGFLLVASDVRALS  187 (287)
T ss_dssp             HHHTCEEEEEEESTHHHHSCTTSC------------------HHHHHHHHTHHHHSCCTTSC--CBEEEEEEEEETHHHH
T ss_pred             HhccCccccceeEEEEeccccccc------------------hhHHHHHHHHHHhcchhhcc--cceeEEeecccHHHHH
Confidence            223356788999999885411100                  01111222233333222222  3455566555443   


Q ss_pred             ---CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhC
Q 024550          155 ---RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLG  189 (266)
Q Consensus       155 ---~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~  189 (266)
                         ..++++.+  ||...++|+.|+.++...|+...+.
T Consensus       188 ~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~  223 (287)
T d1w5sa2         188 YMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAE  223 (287)
T ss_dssp             HHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             HHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHH
Confidence               23467777  8889999999999999999987764

>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=99.48  E-value=3.2e-14  Score=112.54  Aligned_cols=129  Identities=19%  Similarity=0.231  Sum_probs=87.2

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc----------CCcEEEEeCCcccCh--------hhHHHHHHHc---ccCCee
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL----------KFDVYDLELSNLLGN--------NDLRHILIAT---ENKSIL   86 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~----------~~~~~~i~~~~~~~~--------~~l~~~~~~~---~~~~vl   86 (266)
                      .....+++|+||||+|||++++.+|..+          +.+++.++.+.+...        ..+..++...   ..+.||
T Consensus        40 r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iIL  119 (195)
T d1jbka_          40 RRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVIL  119 (195)
T ss_dssp             SSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEE
T ss_pred             ccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEE
Confidence            3346689999999999999999999865          688999998887643        2344555443   235699


Q ss_pred             eeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCC-----CCCccccc
Q 024550           87 VVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHK-----ERLDPALL  161 (266)
Q Consensus        87 ~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~-----~~ld~al~  161 (266)
                      ||||++.+.+..+..+                   .....+-|...|..      ..+.+|++|...     -.-|++|.
T Consensus       120 fIDeih~l~~~g~~~g-------------------~~d~~~~Lkp~L~r------g~l~~IgatT~eey~~~~e~d~aL~  174 (195)
T d1jbka_         120 FIDELHTMVGAGKADG-------------------AMDAGNMLKPALAR------GELHCVGATTLDEYRQYIEKDAALE  174 (195)
T ss_dssp             EEETGGGGTT-------------------------CCCCHHHHHHHHHT------TSCCEEEEECHHHHHHHTTTCHHHH
T ss_pred             EcchHHHHhcCCCCCC-------------------cccHHHHHHHHHhC------CCceEEecCCHHHHHHHHHcCHHHH
Confidence            9999999975222110                   01122233333332      457777777632     23389999


Q ss_pred             CCCcceeEEEcCCCCHHHHHHHH
Q 024550          162 RPGRMDMHINMSHCTPSGFKMLA  184 (266)
Q Consensus       162 r~~Rf~~~i~~~~p~~~~~~~i~  184 (266)
                      |  || ..|.+..|+.++-..|+
T Consensus       175 r--rF-~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         175 R--RF-QKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             T--TE-EEEECCCCCHHHHHTTC
T ss_pred             h--cC-CEeecCCCCHHHHHHHh
Confidence            9  99 56999999999876654

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.37  E-value=1.5e-12  Score=103.84  Aligned_cols=113  Identities=15%  Similarity=0.245  Sum_probs=86.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC------CcEEEEeCCcc-cChhhHHHHHHHcc------cCCeeeeecchhhHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK------FDVYDLELSNL-LGNNDLRHILIATE------NKSILVVEDIDCCIEL   97 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~------~~~~~i~~~~~-~~~~~l~~~~~~~~------~~~vl~iDeid~l~~~   97 (266)
                      +.++|||||||||||++|..++....      ..++.+.+..- .+-..++.+.....      ..-|++|||+|.|-  
T Consensus        15 ~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~--   92 (198)
T d2gnoa2          15 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMT--   92 (198)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBC--
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCccccc--
Confidence            56899999999999999999998773      35888876532 24456666655432      24599999999874  


Q ss_pred             hHHHhhhhhcCCccccccccccccchhhhhhhhhhhhccccCCCCceEEEEecCCCCCCcccccCCCcceeEEEcCCCCH
Q 024550           98 QDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWSSCGDERIIIFTTNHKERLDPALLRPGRMDMHINMSHCTP  177 (266)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~ivi~ttn~~~~ld~al~r~~Rf~~~i~~~~p~~  177 (266)
                                               ....+.||..|+.    ++...+||.+|++++.+.+++.+  || ..+.|+.|..
T Consensus        93 -------------------------~~aqNaLLK~LEE----Pp~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2          93 -------------------------QQAANAFLKALEE----PPEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             -------------------------HHHHHHTHHHHHS----CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCHH
T ss_pred             -------------------------hhhhhHHHHHHhC----CCCCceeeeccCChhhCHHHHhc--ce-EEEeCCCchH
Confidence                                     3456778888874    34678999999999999999999  98 5688987754

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=99.30  E-value=4.7e-12  Score=108.80  Aligned_cols=124  Identities=22%  Similarity=0.286  Sum_probs=78.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCC---------------------------------cEEEEeCCcc----cChhhHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKF---------------------------------DVYDLELSNL----LGNNDLR   74 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~---------------------------------~~~~i~~~~~----~~~~~l~   74 (266)
                      +++||+||||||||++|++++.-+..                                 +++.......    .+.-...
T Consensus        29 h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~d~~  108 (333)
T d1g8pa_          29 GGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIE  108 (333)
T ss_dssp             CCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECHH
T ss_pred             CeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCccccccchhhccccCcccccCceeeccCCCCcccccCcchhh
Confidence            57999999999999999999986611                                 1111111100    0111111


Q ss_pred             HHHHH-----------cccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhhhcccc-----
Q 024550           75 HILIA-----------TENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFIDGLWS-----  138 (266)
Q Consensus        75 ~~~~~-----------~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-----  138 (266)
                      ..+..           ...++|+|+||++.+.                           ..+++.|+..|+.-.-     
T Consensus       109 ~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~~---------------------------~~~~~aLl~~me~~~v~i~r~  161 (333)
T d1g8pa_         109 RAISKGEKAFEPGLLARANRGYLYIDECNLLE---------------------------DHIVDLLLDVAQSGENVVERD  161 (333)
T ss_dssp             HHHHHCGGGEECCHHHHHTTEEEEETTGGGSC---------------------------HHHHHHHHHHHHHSEEEECCT
T ss_pred             hccccCcceeeccccccccccEeecccHHHHH---------------------------HHHHHHHhhhhcCCeEEeccc
Confidence            22211           1246899999999763                           3466777887763211     


Q ss_pred             ----CCCCceEEEEecCCC-CCCcccccCCCcceeEEEcCCCC-HHHHHHHH
Q 024550          139 ----SCGDERIIIFTTNHK-ERLDPALLRPGRMDMHINMSHCT-PSGFKMLA  184 (266)
Q Consensus       139 ----~~~~~~ivi~ttn~~-~~ld~al~r~~Rf~~~i~~~~p~-~~~~~~i~  184 (266)
                          ..+...++++|+|.. ..+++++++  ||+..+.++.|. ...+..+.
T Consensus       162 g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~~~~~  211 (333)
T d1g8pa_         162 GLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVI  211 (333)
T ss_dssp             TCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHH
T ss_pred             CceecCCCCEEEEEecCccccccccchhh--hhcceeeccCcchhhHHHHHH
Confidence                112356888898864 568999999  999999998875 34444443

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.20  E-value=2.3e-10  Score=94.27  Aligned_cols=157  Identities=16%  Similarity=0.140  Sum_probs=92.2

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccCh---------------------------------------
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGN---------------------------------------   70 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~---------------------------------------   70 (266)
                      .++.++|+||+|+|||++++.++...+.....+++......                                       
T Consensus        28 ~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIM  107 (283)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEEC
T ss_pred             cCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccccccccccHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhccccc
Confidence            45689999999999999999999999988888876544311                                       


Q ss_pred             -------------hhHHHHH----HHcccCCeeeeecchhhHHHhHHHhhhhhcCCccccccccccccchhhhhhhhhhh
Q 024550           71 -------------NDLRHIL----IATENKSILVVEDIDCCIELQDRLSRARAANPDFLIAGYEQQKQYHITLSGLLNFI  133 (266)
Q Consensus        71 -------------~~l~~~~----~~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l  133 (266)
                                   ..+..++    .....+.++++||++.+..                       ....    .++..+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~-----------------------~~~~----~~~~~l  160 (283)
T d2fnaa2         108 GNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVK-----------------------LRGV----NLLPAL  160 (283)
T ss_dssp             SSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGG-----------------------CTTC----CCHHHH
T ss_pred             ccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcc-----------------------cchH----HHHHHH
Confidence                         0011111    1123567888999987642                       1111    122222


Q ss_pred             hccccCCCCceEEEEecCCC-------C--CCcccccCCCcceeEEEcCCCCHHHHHHHHHHhhCCCCCCcHHHHHHHhh
Q 024550          134 DGLWSSCGDERIIIFTTNHK-------E--RLDPALLRPGRMDMHINMSHCTPSGFKMLASNYLGIAEHPLFVEIEKLIA  204 (266)
Q Consensus       134 ~~~~~~~~~~~ivi~ttn~~-------~--~ld~al~r~~Rf~~~i~~~~p~~~~~~~i~~~~~~~~~~~~~~~~~~l~~  204 (266)
                      ....... ..+..+.+....       .  .....+.  +|+...+.++..+.++..+++...+...+... ++++.+..
T Consensus       161 ~~~~~~~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~-~~~~~i~~  236 (283)
T d2fnaa2         161 AYAYDNL-KRIKFIMSGSEMGLLYDYLRVEDPESPLF--GRAFSTVELKPFSREEAIEFLRRGFQEADIDF-KDYEVVYE  236 (283)
T ss_dssp             HHHHHHC-TTEEEEEEESSHHHHHHHTTTTCTTSTTT--TCCCEEEEECCCCHHHHHHHHHHHHHHHTCCC-CCHHHHHH
T ss_pred             HHHHHhh-hhhhhhhccccchHHHHHHHhhhhcchhc--ccceeEEeeCCCCHHHHHHHHHhhhhhcCCCH-HHHHHHHH
Confidence            2111111 223333332211       1  1122222  36667899999999999999988775543322 23455666


Q ss_pred             cCCCCHHHHHHHH
Q 024550          205 TAKVTPADVAEQL  217 (266)
Q Consensus       205 ~~~~s~~~i~~~l  217 (266)
                      ..+..|..+..+.
T Consensus       237 ~~~G~P~~L~~~~  249 (283)
T d2fnaa2         237 KIGGIPGWLTYFG  249 (283)
T ss_dssp             HHCSCHHHHHHHH
T ss_pred             HhCCCHHHHHHHH
Confidence            6677887776553

>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=99.09  E-value=1e-09  Score=90.09  Aligned_cols=65  Identities=14%  Similarity=0.132  Sum_probs=48.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccChhhHHHHHH-----------------HcccCCeeeeecc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGNNDLRHILI-----------------ATENKSILVVEDI   91 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~~~l~~~~~-----------------~~~~~~vl~iDei   91 (266)
                      ..+||+||+|||||++|++++...   ..+++.++|..+........+|.                 ...++++||||||
T Consensus        24 ~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i  103 (247)
T d1ny5a2          24 CPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEI  103 (247)
T ss_dssp             SCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESG
T ss_pred             CCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHHhcCcccCCcCCcccccCCHHHccCCCEEEEeCh
Confidence            359999999999999999999776   46788999988754333333331                 1234679999999


Q ss_pred             hhhHH
Q 024550           92 DCCIE   96 (266)
Q Consensus        92 d~l~~   96 (266)
                      |.+..
T Consensus       104 ~~L~~  108 (247)
T d1ny5a2         104 GELSL  108 (247)
T ss_dssp             GGCCH
T ss_pred             HhCCH
Confidence            98853

>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=99.09  E-value=2.1e-10  Score=101.81  Aligned_cols=39  Identities=21%  Similarity=0.405  Sum_probs=36.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL   68 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~   68 (266)
                      .+++||+.||+|||||.+|++||+.+++||+.+++..++
T Consensus        48 ~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fT   86 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFT   86 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC
T ss_pred             ccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceee
Confidence            367899999999999999999999999999999999887

>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=99.07  E-value=3.4e-11  Score=99.65  Aligned_cols=42  Identities=26%  Similarity=0.349  Sum_probs=38.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL   68 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~   68 (266)
                      +...|+++|||||||||||++|+++|.+++.+++.++++.+.
T Consensus        28 ~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~~   69 (273)
T d1gvnb_          28 AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFK   69 (273)
T ss_dssp             CCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHHH
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHHH
Confidence            566788999999999999999999999999999999986654

>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=98.54  E-value=2.7e-08  Score=74.89  Aligned_cols=33  Identities=39%  Similarity=0.697  Sum_probs=29.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+.|+|.|||||||||+++.||..++.+++...
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L~~~~id~~   34 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD   34 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCEEEEHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            357999999999999999999999999987543

>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=98.51  E-value=1.6e-07  Score=72.05  Aligned_cols=25  Identities=28%  Similarity=0.579  Sum_probs=22.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      ++|.||||||||||++.++..+..+
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~~   27 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGKR   27 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCCC
Confidence            8999999999999999999988543

>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=98.46  E-value=1.5e-07  Score=73.59  Aligned_cols=64  Identities=19%  Similarity=0.272  Sum_probs=45.7

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchhhH
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDCCI   95 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~l~   95 (266)
                      .|.|..++++|||||+||||+++.++++.++..++...  ..    ..+=.+..+....++++||+...+
T Consensus        48 ~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vis~~--N~----~s~F~Lq~l~~~kv~l~dD~t~~~  111 (205)
T d1tuea_          48 KGTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFV--NS----TSHFWLEPLTDTKVAMLDDATTTC  111 (205)
T ss_dssp             HTCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCC--CS----SSCGGGGGGTTCSSEEEEEECHHH
T ss_pred             cCCCCceEEEEECCCCccHHHHHHHHHHHhCCEEEecc--CC----CCCcccccccCCeEEEEeccccch
Confidence            37788888999999999999999999999976543322  11    111223344567888999986554

>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=98.43  E-value=5.5e-08  Score=74.74  Aligned_cols=34  Identities=18%  Similarity=0.116  Sum_probs=30.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      ++.|+|.|||||||||+|++||+.+|.+++....
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~~   40 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFNTTSAWEYG   40 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCEEECCTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCCeEeeeh
Confidence            5679999999999999999999999998875543

>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=98.39  E-value=7.2e-08  Score=73.37  Aligned_cols=30  Identities=30%  Similarity=0.491  Sum_probs=27.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.|||||||||+++.||..+|.+++.+
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~i~~   35 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKYINV   35 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEec
Confidence            488999999999999999999999998753

>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=98.35  E-value=1e-07  Score=72.59  Aligned_cols=32  Identities=31%  Similarity=0.466  Sum_probs=28.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ++|+|.|+||+||||+++.+|+.+|.+|+.++
T Consensus         1 k~I~liG~~GsGKsTi~k~La~~l~~~~~d~d   32 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARALAKDLDLVFLDSD   32 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHhCCCEEecC
Confidence            35889999999999999999999999998654

>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=98.34  E-value=1.1e-07  Score=72.68  Aligned_cols=34  Identities=32%  Similarity=0.436  Sum_probs=30.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      +-|+|.|||||||||+++.+++.+|.+++.++..
T Consensus         5 ~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~d   38 (176)
T d1zp6a1           5 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHSD   38 (176)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEecHH
Confidence            4588999999999999999999999999988754

>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=98.29  E-value=1.7e-07  Score=71.71  Aligned_cols=31  Identities=19%  Similarity=0.380  Sum_probs=28.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      +.|+|.|||||||||+++.+|..+|.+++..
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~   33 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDT   33 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEeh
Confidence            4588999999999999999999999998864

>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=98.28  E-value=3.4e-07  Score=69.59  Aligned_cols=34  Identities=21%  Similarity=0.314  Sum_probs=29.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      ++-|+|+||||+||||+|+.|+..++.+++.++.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~~   36 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCCeEEeec
Confidence            3468999999999999999999999988887763

>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=98.25  E-value=3.1e-07  Score=69.72  Aligned_cols=33  Identities=30%  Similarity=0.478  Sum_probs=28.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ++-++|+|||||||||+++.|++.++.+++..+
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d   38 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   38 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeechh
Confidence            445888999999999999999999988776544

>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=98.23  E-value=2.7e-07  Score=70.23  Aligned_cols=30  Identities=33%  Similarity=0.533  Sum_probs=27.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      ++|.|+|||||||+++.+|..+|.+|+..+
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~fiD~D   33 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVGLLDTD   33 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            667799999999999999999999998654

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=98.21  E-value=0.00012  Score=60.06  Aligned_cols=50  Identities=12%  Similarity=-0.012  Sum_probs=31.0

Q ss_pred             eEEEcCCCCHHHHHHHHHHhhCCCCCCc-HHH-HHHHhhcCCCCHHHHHHHH
Q 024550          168 MHINMSHCTPSGFKMLASNYLGIAEHPL-FVE-IEKLIATAKVTPADVAEQL  217 (266)
Q Consensus       168 ~~i~~~~p~~~~~~~i~~~~~~~~~~~~-~~~-~~~l~~~~~~s~~~i~~~l  217 (266)
                      ..++++..+.++..++|..+........ ..+ ...++...+..|-.|.-+.
T Consensus       178 ~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig  229 (277)
T d2a5yb3         178 EFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFF  229 (277)
T ss_dssp             EEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHH
Confidence            4588999999999999987653332221 222 2455666667776665443

>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=98.20  E-value=6.3e-07  Score=68.11  Aligned_cols=29  Identities=34%  Similarity=0.430  Sum_probs=25.3

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      |.+..|+|.||||+||||+++.||..++.
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            34456999999999999999999999875

>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=98.19  E-value=5e-07  Score=68.33  Aligned_cols=29  Identities=34%  Similarity=0.621  Sum_probs=25.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      +-|+|.|||||||||+|+.|+..++..++
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~~~~~   31 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLDNSAY   31 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSSEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            45899999999999999999999987654

>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=98.13  E-value=8.5e-07  Score=69.06  Aligned_cols=32  Identities=19%  Similarity=0.289  Sum_probs=27.7

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      .|.-|+|.||||+||||+++.||..+|...+.
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~~~g~~~i~   36 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVRDFGWVHLS   36 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHCCceEc
Confidence            45568999999999999999999999876554

>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=98.12  E-value=1.6e-06  Score=66.48  Aligned_cols=65  Identities=15%  Similarity=0.103  Sum_probs=42.6

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHH-cccCCeeeeecchhhH
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIA-TENKSILVVEDIDCCI   95 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~-~~~~~vl~iDeid~l~   95 (266)
                      +.|.-++++|+|||||||+++.++...+...  ++...+.+...+...+.. ...+..+++|......
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~~~~~~--i~~D~~~~~~~~~~~~~~~l~~g~~vIiD~t~~~~   77 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVSAGYVH--VNRDTLGSWQRCVSSCQAALRQGKRVVIDNTNPDV   77 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGGGTCEE--EEHHHHCSHHHHHHHHHHHHHTTCCEEEESCCCSH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhcCCEE--EchHHHHHHHHHHHHHHHHHHCCCCceeeCcCCCH
Confidence            3455699999999999999999998887544  444445444333333332 3455667777666443

>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=98.11  E-value=6.6e-07  Score=68.31  Aligned_cols=24  Identities=46%  Similarity=0.812  Sum_probs=22.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++|+|+||||||||++++.++..+
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            579999999999999999999887

>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=98.09  E-value=1.3e-06  Score=67.78  Aligned_cols=31  Identities=26%  Similarity=0.387  Sum_probs=26.5

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..++|.|||||||||+++.||..+|..++.+
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            3477889999999999999999998776553

>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=98.08  E-value=1.2e-06  Score=67.23  Aligned_cols=29  Identities=21%  Similarity=0.339  Sum_probs=26.4

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |+|.|||||||||+++.||+.+|.+++..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~~~~i~~   31 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYGIPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceech
Confidence            78999999999999999999998877654

>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=98.06  E-value=9.5e-07  Score=68.56  Aligned_cols=31  Identities=13%  Similarity=0.265  Sum_probs=27.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      |-.|+|.|||||||||+++.||..+|.+.+.
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~~~~~is   33 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKYQLAHIS   33 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHCCcEEe
Confidence            4458999999999999999999999887653

>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=98.03  E-value=6.7e-06  Score=65.85  Aligned_cols=39  Identities=23%  Similarity=0.198  Sum_probs=31.9

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |+++...++|+||||+|||+++..+|...   +...+.++..
T Consensus        22 Gi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~e   63 (242)
T d1tf7a2          22 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYE   63 (242)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeecc
Confidence            58788889999999999999999998876   5556666544

>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=98.03  E-value=2.2e-06  Score=66.80  Aligned_cols=31  Identities=19%  Similarity=0.328  Sum_probs=26.7

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ..|+|.||||+||||+|+.||+.+|...+.+
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            3488899999999999999999998866553

>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=98.01  E-value=1.4e-06  Score=67.07  Aligned_cols=30  Identities=33%  Similarity=0.535  Sum_probs=26.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.|||||||||+++.||..+|...+.+
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            478999999999999999999999877654

>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=97.99  E-value=2.4e-06  Score=66.51  Aligned_cols=32  Identities=16%  Similarity=0.335  Sum_probs=27.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      ++-|+|.|||||||||+++.||..+|.+.+..
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~is~   39 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   39 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeeEec
Confidence            45689999999999999999999998766543

>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=97.98  E-value=2.3e-06  Score=65.93  Aligned_cols=29  Identities=21%  Similarity=0.304  Sum_probs=26.2

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |+|.|||||||||+++.||..+|.+.+.+
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~g~~~is~   31 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKYGTPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceeeH
Confidence            78999999999999999999998877653

>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=97.98  E-value=1.8e-06  Score=65.52  Aligned_cols=25  Identities=24%  Similarity=0.284  Sum_probs=22.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      .|+|+|+||+||||++++||..++.
T Consensus         8 ~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           8 TIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3889999999999999999999854

>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=97.98  E-value=1.9e-06  Score=67.03  Aligned_cols=30  Identities=17%  Similarity=0.410  Sum_probs=26.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.||||+||||+++.||..+|..++.+
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~g~~~is~   37 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHFELKHLSS   37 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHBCCEEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHCCeEEcH
Confidence            388889999999999999999998776543

>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=97.96  E-value=2.6e-06  Score=65.57  Aligned_cols=30  Identities=23%  Similarity=0.449  Sum_probs=26.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      -|+|.||||+||||+++.||..+|.+.+..
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~g~~~i~~   33 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERFHAAHLAT   33 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceEec
Confidence            378889999999999999999998876654

>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=97.91  E-value=6.1e-07  Score=69.51  Aligned_cols=27  Identities=30%  Similarity=0.442  Sum_probs=23.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      .|+|+|+||+||||+|+.||..++.++
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~~~   47 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVCHG   47 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            477999999999999999999885443

>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=97.91  E-value=3.5e-06  Score=66.49  Aligned_cols=29  Identities=38%  Similarity=0.627  Sum_probs=25.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      -|.+.|||||||||+++.||+.+|.++++
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            57788999999999999999999887643

>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=97.90  E-value=4.1e-06  Score=64.97  Aligned_cols=29  Identities=21%  Similarity=0.360  Sum_probs=25.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      .-|+|.||||+||||.|+.||+.+|...+
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~g~~~i   30 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKYGYTHL   30 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCceE
Confidence            35889999999999999999999987654

>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=97.90  E-value=3.8e-06  Score=64.37  Aligned_cols=30  Identities=17%  Similarity=0.230  Sum_probs=26.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      .|+|.||||+||||.++.||+.+|...+..
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            378899999999999999999998876653

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=97.87  E-value=3e-05  Score=63.40  Aligned_cols=60  Identities=22%  Similarity=0.264  Sum_probs=41.5

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcccChhhHHHHHHHcccCCeeeeecchh
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLLGNNDLRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~vl~iDeid~   93 (266)
                      +.+....++|||||+||||+++.+++..+|.- ..++-+.  +.    -.+..+....++++||...
T Consensus       100 ~~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~~-~~~~~~~--~~----f~l~~l~~k~~~~~~e~~~  159 (267)
T d1u0ja_         100 KFGKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWTN--EN----FPFNDCVDKMVIWWEEGKM  159 (267)
T ss_dssp             CSTTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTTC--SS----CTTGGGSSCSEEEECSCCE
T ss_pred             CCCccEEEEEEcCCCCCHHHHHHHHHHHhcch-hhccccC--CC----ccccccCCCEEEEEeCCCc
Confidence            34556679999999999999999999999653 2222111  11    1134556788999999863

>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=97.84  E-value=5.4e-06  Score=61.38  Aligned_cols=31  Identities=26%  Similarity=0.418  Sum_probs=23.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      +-|+|+||||+||||+|+.++.... ....++
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~~-~~~~~~   33 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKNP-GFYNIN   33 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHST-TEEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhCC-CCEEec
Confidence            3588999999999999999877653 244444

>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=97.83  E-value=5.8e-06  Score=65.38  Aligned_cols=28  Identities=29%  Similarity=0.503  Sum_probs=24.6

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      |.+.||||+||||+|+.||..+|.+++.
T Consensus         6 IaIdGp~GsGKgT~ak~La~~lg~~~is   33 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDFGFTYLD   33 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            4466999999999999999999987655

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=97.73  E-value=3.6e-05  Score=62.76  Aligned_cols=70  Identities=19%  Similarity=0.263  Sum_probs=47.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh---------------------hhHHHH---HHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN---------------------NDLRHI---LIA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~---------------------~~l~~~---~~~   79 (266)
                      |++..+-..|+||||+|||+++-.++...   |...++++...-...                     ...-++   +..
T Consensus        50 Gi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~  129 (263)
T d1u94a1          50 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  129 (263)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHHHh
Confidence            46666679999999999999998887766   566777776643321                     111111   122


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      .....++++|-+..+.+
T Consensus       130 ~~~~~liViDSi~al~~  146 (263)
T d1u94a1         130 SGAVDVIVVDSVAALTP  146 (263)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEECcccccc
Confidence            24568889999988764

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.65  E-value=6.3e-05  Score=61.44  Aligned_cols=70  Identities=19%  Similarity=0.233  Sum_probs=47.5

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh---------------------hhHHHHHHH---
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN---------------------NDLRHILIA---   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~---------------------~~l~~~~~~---   79 (266)
                      |++..+-..++||||||||+++..++...   |...++++...-.+.                     ....+++..   
T Consensus        53 Gip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~  132 (268)
T d1xp8a1          53 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  132 (268)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHh
Confidence            45566668899999999999998887665   667788887644321                     111112222   


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      .....++++|-+..+.+
T Consensus       133 ~~~~~liIiDSi~al~~  149 (268)
T d1xp8a1         133 SGAIDVVVVDSVAALTP  149 (268)
T ss_dssp             TTCCSEEEEECTTTCCC
T ss_pred             cCCCcEEEEeccccccc
Confidence            23578899999988864

>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=97.63  E-value=2.8e-05  Score=61.79  Aligned_cols=42  Identities=21%  Similarity=0.141  Sum_probs=32.5

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCccc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSNLL   68 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~~~   68 (266)
                      |+++.+-++|+||||||||+++..++...         +.+.+.++...-.
T Consensus        30 Gi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~   80 (251)
T d1szpa2          30 GVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTF   80 (251)
T ss_dssp             SEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCC
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchH
Confidence            68888889999999999999999887543         4556666655443

>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=97.61  E-value=1.4e-05  Score=60.75  Aligned_cols=25  Identities=20%  Similarity=0.395  Sum_probs=22.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +-|+|.|||||||||+++.|+..++
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            4588999999999999999999874

>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=97.61  E-value=1.4e-05  Score=59.92  Aligned_cols=23  Identities=26%  Similarity=0.304  Sum_probs=21.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -+.|+|+||||||||++.+++.+
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            47899999999999999999876

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.61  E-value=0.00018  Score=56.37  Aligned_cols=37  Identities=22%  Similarity=0.204  Sum_probs=27.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      |.-++|+||+|+||||.+--+|..+   |..+.-+.+..+
T Consensus         9 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~   48 (211)
T d2qy9a2           9 PFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTF   48 (211)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccc
Confidence            4568899999999999877778655   555555555544

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.60  E-value=8.9e-05  Score=60.51  Aligned_cols=70  Identities=17%  Similarity=0.245  Sum_probs=47.7

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcccCh------------------hhHHHH------HHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLLGN------------------NDLRHI------LIA   79 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~~~------------------~~l~~~------~~~   79 (266)
                      |++.++-..|+||||||||+++..++...   |...++++...-.+.                  ....+.      +..
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~  135 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            56677779999999999999987776554   677778877653321                  111111      122


Q ss_pred             cccCCeeeeecchhhHH
Q 024550           80 TENKSILVVEDIDCCIE   96 (266)
Q Consensus        80 ~~~~~vl~iDeid~l~~   96 (266)
                      .....++++|-+..+.+
T Consensus       136 ~~~~~liIiDSi~al~~  152 (269)
T d1mo6a1         136 SGALDIVVIDSVAALVP  152 (269)
T ss_dssp             TTCEEEEEEECSTTCCC
T ss_pred             cCCCCEEEEeccccccc
Confidence            33567889999998875

>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=97.57  E-value=8.4e-05  Score=60.32  Aligned_cols=29  Identities=28%  Similarity=0.239  Sum_probs=22.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      |+.+..-.+|+|+||+|||+++..+|..+
T Consensus        25 G~~pg~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          25 NMVAGTVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            44445558899999999999998888653

>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=97.54  E-value=2.2e-05  Score=61.06  Aligned_cols=26  Identities=23%  Similarity=0.459  Sum_probs=22.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      |--|+++|.||+||||+|+.||..++
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            44588999999999999999998874

>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=97.52  E-value=6.9e-05  Score=59.81  Aligned_cols=40  Identities=23%  Similarity=0.259  Sum_probs=31.0

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc---------CCcEEEEeCCc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------KFDVYDLELSN   66 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~---------~~~~~~i~~~~   66 (266)
                      |++..+-++|+||||||||+++-.++...         +...+.+....
T Consensus        32 Glp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~   80 (254)
T d1pzna2          32 GIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN   80 (254)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSS
T ss_pred             CccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccc
Confidence            58778889999999999999999888654         34555565543

>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=97.50  E-value=0.00011  Score=53.29  Aligned_cols=34  Identities=29%  Similarity=0.317  Sum_probs=26.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELS   65 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~   65 (266)
                      +..+|.+|.|+|||+++-.++...+..++.+...
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcCh
Confidence            4589999999999998877777777777666554

>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=97.47  E-value=0.0003  Score=51.65  Aligned_cols=22  Identities=18%  Similarity=0.276  Sum_probs=19.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++|.|+||+|||+|+..+...-
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            7899999999999999987543

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.47  E-value=0.00024  Score=55.61  Aligned_cols=37  Identities=27%  Similarity=0.318  Sum_probs=26.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      ++-++|+||+|+||||++--||..+   |..+.-+.+..+
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt~   45 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTF   45 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCCS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeccc
Confidence            4568899999999999777777665   455555554443

>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=97.46  E-value=2.9e-05  Score=60.17  Aligned_cols=29  Identities=21%  Similarity=0.172  Sum_probs=25.8

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      |+++..-++|+||||+|||+++..+|...
T Consensus        19 Gi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          19 GIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            67788889999999999999999988764

>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=97.46  E-value=0.00013  Score=58.04  Aligned_cols=29  Identities=21%  Similarity=0.108  Sum_probs=25.6

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      |+++..-++|+||||||||+++..++...
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            68888889999999999999999998643

>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=97.46  E-value=0.00028  Score=55.43  Aligned_cols=36  Identities=19%  Similarity=0.129  Sum_probs=25.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      .|.-++|+||+|+||||.+--+|..+   +..+.-+.+.
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~D   48 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAAD   48 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeec
Confidence            34558999999999999877777655   4444444444

>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=97.42  E-value=0.00021  Score=55.97  Aligned_cols=35  Identities=23%  Similarity=0.279  Sum_probs=26.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCcc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNL   67 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~   67 (266)
                      -++|.||+|+||||++--||..+   |..+..+++..+
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt~   49 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQ   49 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccc
Confidence            37889999999999887777666   556665655544

>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=97.42  E-value=0.00042  Score=51.63  Aligned_cols=28  Identities=25%  Similarity=0.240  Sum_probs=24.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      ++.-++|+|+=|+|||+++|.+++.+|.
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhccc
Confidence            3445889999999999999999999964

>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=97.41  E-value=0.00018  Score=61.20  Aligned_cols=21  Identities=38%  Similarity=0.649  Sum_probs=16.8

Q ss_pred             ceeEEecCCCCChHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMA   52 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala   52 (266)
                      +-.+|+||||||||+++..+.
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l  184 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLL  184 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHH
T ss_pred             CeEEEEcCCCCCceehHHHHH
Confidence            348899999999999875543

>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=97.39  E-value=2.3e-05  Score=59.81  Aligned_cols=25  Identities=32%  Similarity=0.472  Sum_probs=22.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -++|.|+||+||||+++.|+..++.
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3678999999999999999998853

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.39  E-value=0.00024  Score=57.36  Aligned_cols=27  Identities=22%  Similarity=0.444  Sum_probs=22.8

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++...+-|.||+|+|||||++.++...
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhccc
Confidence            344458899999999999999998766

>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=97.38  E-value=8.1e-05  Score=58.44  Aligned_cols=35  Identities=26%  Similarity=0.379  Sum_probs=28.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELS   65 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~   65 (266)
                      +..|+|+|.||+||||+++.|+..+    +.+.+.++..
T Consensus        24 g~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD   62 (208)
T d1m7ga_          24 GLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGD   62 (208)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcch
Confidence            3458999999999999999999765    5677766644

>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=97.38  E-value=6.3e-05  Score=57.86  Aligned_cols=28  Identities=32%  Similarity=0.492  Sum_probs=24.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      +.|+|+||+|+|||++++.|+......+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~~   29 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDSF   29 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCcce
Confidence            3489999999999999999999875444

>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=97.38  E-value=0.00022  Score=55.99  Aligned_cols=36  Identities=25%  Similarity=0.300  Sum_probs=21.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      |.-++|+||+|+||||++--+|..+   |..+-.+.+..
T Consensus        12 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt   50 (211)
T d1j8yf2          12 PYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADV   50 (211)
T ss_dssp             SEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEECCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEeec
Confidence            4458899999999999877777655   44554455443

>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=97.36  E-value=0.0002  Score=54.08  Aligned_cols=22  Identities=27%  Similarity=0.403  Sum_probs=19.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|.+|+|||+|++.+...
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3999999999999999988753

>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=97.34  E-value=0.00027  Score=57.36  Aligned_cols=40  Identities=20%  Similarity=0.110  Sum_probs=31.2

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCC
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELS   65 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~   65 (266)
                      .|+.+..-++|.|+||+|||+++..+|..+    |.++..+++.
T Consensus        30 ~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E   73 (277)
T d1cr2a_          30 LGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (277)
T ss_dssp             CSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             cCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeec
Confidence            367666679999999999999888887542    6777777755

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.33  E-value=0.00029  Score=56.46  Aligned_cols=27  Identities=22%  Similarity=0.331  Sum_probs=23.0

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++...+-|.||+|+|||||++.++..+
T Consensus        27 ~~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            344458899999999999999999866

>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=97.33  E-value=7.5e-05  Score=57.66  Aligned_cols=28  Identities=29%  Similarity=0.343  Sum_probs=24.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      .|+|+||+|+|||++++.|+...+..+.
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~~~~   29 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSSIFG   29 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTTTEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCcee
Confidence            3889999999999999999998865543

>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=97.29  E-value=0.0003  Score=52.80  Aligned_cols=23  Identities=13%  Similarity=0.329  Sum_probs=20.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..++|.|.||+|||+|+..+...
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999998764

>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=97.27  E-value=0.00012  Score=55.98  Aligned_cols=32  Identities=19%  Similarity=0.344  Sum_probs=24.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHcC---CcEEEEeCC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLK---FDVYDLELS   65 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~---~~~~~i~~~   65 (266)
                      |-|.||+|+||||+|+.|+..++   .....++..
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~~~   59 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMD   59 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhccccccceecccc
Confidence            55899999999999999998774   344444433

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=97.27  E-value=0.00012  Score=57.51  Aligned_cols=39  Identities=21%  Similarity=0.153  Sum_probs=29.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc----CCcEEEEeCC
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----KFDVYDLELS   65 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~----~~~~~~i~~~   65 (266)
                      |++++.-++|+|+||+|||+++..++...    +..++.++..
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            68888889999999999999987665322    4556666554

>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=97.26  E-value=0.00021  Score=57.71  Aligned_cols=27  Identities=26%  Similarity=0.391  Sum_probs=22.5

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++..-+.|.||+|+|||||++.++...
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl~ll~gl~   68 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLINLIPRFY   68 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHHTTTTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHHhcC
Confidence            344458899999999999999998755

>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=97.23  E-value=0.00074  Score=53.72  Aligned_cols=62  Identities=19%  Similarity=0.259  Sum_probs=40.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc-----CCc----EEE----------EeCCc-ccC--------hhhHHHHHHHcccC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL-----KFD----VYD----------LELSN-LLG--------NNDLRHILIATENK   83 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~-----~~~----~~~----------i~~~~-~~~--------~~~l~~~~~~~~~~   83 (266)
                      +.++|+||..+|||+++|+++-..     |..    ...          +...+ +..        -..+..++..+..+
T Consensus        42 ~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~  121 (234)
T d1wb9a2          42 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEY  121 (234)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCTT
T ss_pred             eEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHhcccc
Confidence            458999999999999999988544     211    111          11111 110        13456677778889


Q ss_pred             Ceeeeecchh
Q 024550           84 SILVVEDIDC   93 (266)
Q Consensus        84 ~vl~iDeid~   93 (266)
                      +++++||+-.
T Consensus       122 sLvliDE~~~  131 (234)
T d1wb9a2         122 SLVLMDEIGR  131 (234)
T ss_dssp             EEEEEESCCC
T ss_pred             cEEeeccccc
Confidence            9999999984

>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=97.19  E-value=0.00059  Score=50.88  Aligned_cols=22  Identities=27%  Similarity=0.425  Sum_probs=19.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|++|+|||+|+..+...
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3899999999999999998764

>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=97.18  E-value=0.00012  Score=54.75  Aligned_cols=22  Identities=18%  Similarity=0.410  Sum_probs=19.6

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|+||+|||+|++.+...
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            4899999999999999998764

>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=97.12  E-value=0.00061  Score=50.99  Aligned_cols=21  Identities=29%  Similarity=0.460  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      -++|.|.+|+|||+|+..+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999875

>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=97.10  E-value=0.00015  Score=55.23  Aligned_cols=25  Identities=28%  Similarity=0.549  Sum_probs=22.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      +-++|.||+|+||||+++.+...+.
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4588999999999999999998874

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=97.10  E-value=0.00026  Score=50.73  Aligned_cols=19  Identities=26%  Similarity=0.214  Sum_probs=15.6

Q ss_pred             CCceeEEecCCCCChHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la   48 (266)
                      .....+|++|+|+|||..+
T Consensus         6 ~~~~~il~~~tGsGKT~~~   24 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRF   24 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTH
T ss_pred             cCCcEEEEcCCCCChhHHH
Confidence            3567999999999999654

>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=97.08  E-value=0.0012  Score=49.34  Aligned_cols=21  Identities=33%  Similarity=0.572  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .+++.|+||+|||+|+..+..
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            499999999999999998855

>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=97.07  E-value=0.00042  Score=57.95  Aligned_cols=62  Identities=15%  Similarity=0.377  Sum_probs=40.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC--CcEEEEe-CCccc-------------ChhhHHHHHHHc--ccCCeeeeecch
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK--FDVYDLE-LSNLL-------------GNNDLRHILIAT--ENKSILVVEDID   92 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~--~~~~~i~-~~~~~-------------~~~~l~~~~~~~--~~~~vl~iDeid   92 (266)
                      ++++|++||+|+||||++++++....  ..++.+. ...+.             ..-.+.+++..+  ..|..+++.|+-
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~l~~~~~~~~~~~~~~~~~~~ll~~~lR~~pd~iivgEiR  245 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELR  245 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEESCCC
T ss_pred             CCCEEEEeeccccchHHHHHHhhhcccccceeeccchhhhhcccccccceeccccchhHHHHHHHHhccCCCcccCCccC
Confidence            56799999999999999999998873  3334332 11111             111234444333  368899999886

>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=97.06  E-value=0.00074  Score=50.34  Aligned_cols=22  Identities=27%  Similarity=0.445  Sum_probs=19.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|.+|+|||+|++.+...
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3899999999999999998754

>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=97.04  E-value=0.00067  Score=50.53  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=19.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|++|+|||+|+..+...
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3899999999999999998764

>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=97.03  E-value=0.00073  Score=50.59  Aligned_cols=22  Identities=27%  Similarity=0.404  Sum_probs=19.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|.||+|||+|++.+...
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999988763

>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=97.02  E-value=0.00015  Score=57.33  Aligned_cols=29  Identities=21%  Similarity=0.217  Sum_probs=25.5

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      |+++..-++|+||||+|||+++..+|..+
T Consensus        30 Gl~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          30 GLESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            47777779999999999999999998755

>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=96.94  E-value=0.00062  Score=56.39  Aligned_cols=40  Identities=18%  Similarity=0.111  Sum_probs=31.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC-----CcEEEEeCCcccCh
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK-----FDVYDLELSNLLGN   70 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~-----~~~~~i~~~~~~~~   70 (266)
                      |--|-+.|++|+||||+++.|+..+.     ..+..++..++.-.
T Consensus        80 P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F~~~  124 (308)
T d1sq5a_          80 PYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHP  124 (308)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGBCC
T ss_pred             CEEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeeeECC
Confidence            34477899999999999999999873     45667777777543

>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=96.92  E-value=0.00097  Score=48.68  Aligned_cols=21  Identities=29%  Similarity=0.510  Sum_probs=19.4

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      ++|.|+||+|||+|+..+...
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            889999999999999998874

>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=96.91  E-value=0.0017  Score=53.10  Aligned_cols=37  Identities=22%  Similarity=0.237  Sum_probs=28.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc------CCcEEEEeCCcccC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL------KFDVYDLELSNLLG   69 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~------~~~~~~i~~~~~~~   69 (266)
                      -|-|.|++||||||++..+...+      +..+..++..++.-
T Consensus        29 iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~   71 (286)
T d1odfa_          29 FIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYL   71 (286)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBC
T ss_pred             EEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCC
Confidence            35578999999999999887665      34567777777753

>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=96.90  E-value=0.00028  Score=52.80  Aligned_cols=30  Identities=17%  Similarity=0.280  Sum_probs=23.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      +-+.|++|||||||+..++.++   |..+-.+.
T Consensus         4 i~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            5689999999999999999877   44554443

>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=96.88  E-value=0.00039  Score=52.83  Aligned_cols=30  Identities=23%  Similarity=0.335  Sum_probs=24.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      ..++||.|++|+|||+++-.+... |..++.
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~-g~~lv~   43 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQR-GHRLIA   43 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHT-TCEEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEEe
Confidence            468999999999999999988875 665553

>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=96.88  E-value=0.00037  Score=53.06  Aligned_cols=29  Identities=14%  Similarity=0.296  Sum_probs=24.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      ++.++|.||+|+|||++++.|.......+
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~~~~~   31 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKHPDRF   31 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCTTTE
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCCcCe
Confidence            45689999999999999999998764433

>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=96.86  E-value=0.0013  Score=48.69  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|++|+|||+|+..+...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999988753

>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=96.86  E-value=0.00082  Score=50.20  Aligned_cols=21  Identities=43%  Similarity=0.703  Sum_probs=18.7

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      ++|.|++|+|||+|++.+...
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            789999999999999988753

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.83  E-value=0.00033  Score=55.67  Aligned_cols=34  Identities=29%  Similarity=0.394  Sum_probs=22.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      ++++++.+|.|+|||.++-..+...   +...+.+.+
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~P   94 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFP   94 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEES
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEec
Confidence            4679999999999998655444322   444454443

>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=96.82  E-value=0.00036  Score=54.36  Aligned_cols=25  Identities=28%  Similarity=0.242  Sum_probs=22.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -|-+.||+|+||||+++.|+..++.
T Consensus         4 iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           4 LIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhch
Confidence            3568999999999999999999864

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=96.80  E-value=0.0017  Score=55.69  Aligned_cols=66  Identities=21%  Similarity=0.199  Sum_probs=43.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHcC---CcEEEEeC-Cccc------------ChhhHHHHHHHc--ccCCeeeeecc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYLK---FDVYDLEL-SNLL------------GNNDLRHILIAT--ENKSILVVEDI   91 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~~---~~~~~i~~-~~~~------------~~~~l~~~~~~~--~~~~vl~iDei   91 (266)
                      +...+||.||.|+||||++.++...++   .+++.+.- ....            ........+..+  ..|.||++.|+
T Consensus       157 ~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~~~~~q~~v~~~~~~~~~~~l~~~lR~dPDvi~igEi  236 (401)
T d1p9ra_         157 PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDIDGIGQTQVNPRVDMTFARGLRAILRQDPDVVMVGEI  236 (401)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCCSSSEEEECBGGGTBCHHHHHHHHGGGCCSEEEESCC
T ss_pred             hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccccCCCCeeeecCCcCCCHHHHHHHHHhhcCCEEEecCc
Confidence            344488999999999999999988773   44554431 1111            112344444433  46999999999


Q ss_pred             hhhH
Q 024550           92 DCCI   95 (266)
Q Consensus        92 d~l~   95 (266)
                      ...-
T Consensus       237 Rd~~  240 (401)
T d1p9ra_         237 RDLE  240 (401)
T ss_dssp             CSHH
T ss_pred             CChH
Confidence            8653

>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=96.80  E-value=0.00061  Score=55.66  Aligned_cols=17  Identities=29%  Similarity=0.528  Sum_probs=14.2

Q ss_pred             ceeEEecCCCCChHHHH
Q 024550           32 RGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la   48 (266)
                      ..+|+.||||||||+++
T Consensus        15 ~~~lI~g~aGTGKTt~l   31 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVI   31 (306)
T ss_dssp             SEEEECCCTTSCHHHHH
T ss_pred             CCEEEEeeCCccHHHHH
Confidence            34889999999999854

>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=96.79  E-value=0.0012  Score=49.31  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=19.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|.+|+|||+|+..+...
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999998863

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.76  E-value=0.0013  Score=50.71  Aligned_cols=19  Identities=32%  Similarity=0.448  Sum_probs=16.0

Q ss_pred             CceeEEecCCCCChHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~   49 (266)
                      .+++++.+|+|+|||+++-
T Consensus        40 ~~~~il~apTGsGKT~~a~   58 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAE   58 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHHH
Confidence            4569999999999998753

>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=96.75  E-value=0.00076  Score=50.11  Aligned_cols=21  Identities=29%  Similarity=0.431  Sum_probs=18.9

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .++|.|+||+|||+|+..+..
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999998875

>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=96.72  E-value=0.00075  Score=50.66  Aligned_cols=22  Identities=32%  Similarity=0.667  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|+||||||+|+..+...
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3789999999999999998754

>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=96.71  E-value=0.00056  Score=52.23  Aligned_cols=28  Identities=32%  Similarity=0.460  Sum_probs=23.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |-++|++|+||||+|+.+ .+.|.+++..
T Consensus         6 IgitG~~gSGKstva~~l-~~~g~~~~~~   33 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALL-RSWGYPVLDL   33 (191)
T ss_dssp             EEEEECTTSCHHHHHHHH-HHTTCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHH-HHCCCeEEEc
Confidence            458899999999999998 5688877643

>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=96.71  E-value=0.00053  Score=52.05  Aligned_cols=29  Identities=31%  Similarity=0.328  Sum_probs=24.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      ..|+||.||+|+|||+++-.+... |..++
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~-G~~lv   43 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK-NHLFV   43 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT-TCEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCcee
Confidence            568999999999999999988764 55554

>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=96.70  E-value=0.0022  Score=47.58  Aligned_cols=22  Identities=32%  Similarity=0.616  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|.+|+|||+|++.+...
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999998753

>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=96.69  E-value=0.0013  Score=48.99  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=19.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|.+|+|||+|+..+...
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3899999999999999998853

>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=96.68  E-value=0.0007  Score=52.72  Aligned_cols=25  Identities=40%  Similarity=0.591  Sum_probs=21.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      .-++|+||+|+|||+|.+.+.....
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            3488999999999999999998864

>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=96.65  E-value=0.00082  Score=50.40  Aligned_cols=23  Identities=17%  Similarity=0.283  Sum_probs=20.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|+||+|||+|++.+...-
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999987533

>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=96.63  E-value=0.00074  Score=50.90  Aligned_cols=29  Identities=24%  Similarity=0.331  Sum_probs=23.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      ..|+||.|++|+|||+++-.+... |..++
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~-g~~li   43 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR-GHRLV   43 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            468999999999999999887776 55443

>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=96.62  E-value=0.00074  Score=50.59  Aligned_cols=21  Identities=19%  Similarity=0.477  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      -++|.|+||+|||+|...+..
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            499999999999999999854

>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=96.58  E-value=0.00093  Score=52.11  Aligned_cols=30  Identities=23%  Similarity=0.192  Sum_probs=24.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~   63 (266)
                      |.|.|+.|+||||+++.|++.+   |.+++.+.
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            4556999999999999999877   56666554

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=96.56  E-value=0.0033  Score=49.43  Aligned_cols=61  Identities=25%  Similarity=0.363  Sum_probs=39.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc-----CC----cEEEEeC----------Cc-ccC--------hhhHHHHHHHcccCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL-----KF----DVYDLEL----------SN-LLG--------NNDLRHILIATENKS   84 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~-----~~----~~~~i~~----------~~-~~~--------~~~l~~~~~~~~~~~   84 (266)
                      .++|+||...|||+++|+++-..     |.    ....+..          .+ +..        -..+..++..+..++
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~~~~s  116 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATENS  116 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHCCTTE
T ss_pred             EEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhccCCCCc
Confidence            48899999999999999887544     21    1111111          11 111        134566777778899


Q ss_pred             eeeeecchh
Q 024550           85 ILVVEDIDC   93 (266)
Q Consensus        85 vl~iDeid~   93 (266)
                      +++|||+-.
T Consensus       117 LvliDE~~~  125 (224)
T d1ewqa2         117 LVLLDEVGR  125 (224)
T ss_dssp             EEEEESTTT
T ss_pred             EEeeccccc
Confidence            999999974

>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=96.56  E-value=0.0014  Score=48.82  Aligned_cols=22  Identities=27%  Similarity=0.422  Sum_probs=19.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|++|+|||+|+..+...
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3889999999999999998754

>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=96.53  E-value=0.0023  Score=48.06  Aligned_cols=21  Identities=38%  Similarity=0.651  Sum_probs=19.2

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      -+++.|++|+|||+|+..+..
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999875

>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=96.52  E-value=0.0028  Score=47.09  Aligned_cols=20  Identities=35%  Similarity=0.642  Sum_probs=18.4

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      +++.|.+|+|||+|+..+..
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999998875

>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=96.46  E-value=0.00073  Score=51.07  Aligned_cols=27  Identities=22%  Similarity=0.411  Sum_probs=21.3

Q ss_pred             CCCCCceeEEecCCCCChHHHHHHHHH
Q 024550           27 GKAWKRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        27 ~~~~~~~iLl~GppGtGKT~la~ala~   53 (266)
                      +....-.+++.|+||+|||+|++.+..
T Consensus        13 ~~~k~~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          13 GSNKELRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             TCSSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCCceEEEEEECCCCCCHHHHHHHHhc
Confidence            333444699999999999999998753

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.44  E-value=0.00047  Score=54.69  Aligned_cols=26  Identities=23%  Similarity=0.349  Sum_probs=22.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ....+-|.||+|||||||++.++.-.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCcchhhHhccCCC
Confidence            34458899999999999999998865

>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=96.41  E-value=0.00042  Score=53.86  Aligned_cols=26  Identities=31%  Similarity=0.553  Sum_probs=22.1

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++.-+-|.||.|+|||||.+.++..+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            34447799999999999999999866

>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=96.40  E-value=0.00093  Score=51.57  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=20.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ++|+|.|+||+|||+|+..+...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            47999999999999999999763

>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=96.40  E-value=0.00091  Score=51.99  Aligned_cols=28  Identities=39%  Similarity=0.482  Sum_probs=23.2

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEE
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDL   62 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i   62 (266)
                      |-|+|++|+||||+++.+. .+|.+++..
T Consensus         6 IgitG~igSGKStv~~~l~-~~G~~vida   33 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFA-DLGINVIDA   33 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HTTCEEEEH
T ss_pred             EEEECCCcCCHHHHHHHHH-HCCCcEEEc
Confidence            5589999999999999886 688876653

>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=96.39  E-value=0.0083  Score=48.23  Aligned_cols=26  Identities=23%  Similarity=0.217  Sum_probs=19.9

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHH
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~   53 (266)
                      .+.+..-||+|..|||||.++-..+.
T Consensus       101 ~~~~m~rLL~GdvGSGKT~Va~~a~~  126 (264)
T d1gm5a3         101 SEKPMNRLLQGDVGSGKTVVAQLAIL  126 (264)
T ss_dssp             SSSCCCCEEECCSSSSHHHHHHHHHH
T ss_pred             ccCcceeeeeccccccccHHHHHHHH
Confidence            34456789999999999987765543

>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=96.38  E-value=0.00093  Score=52.60  Aligned_cols=30  Identities=27%  Similarity=0.613  Sum_probs=23.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHc--CCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL--KFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~--~~~~~~i~   63 (266)
                      ++|.||+|+|||||+..+...+  +.....++
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~~~~~~~ivn   34 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   34 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhCCeEEEEe
Confidence            6789999999999999998765  33444443

>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=96.36  E-value=0.00096  Score=49.08  Aligned_cols=22  Identities=23%  Similarity=0.424  Sum_probs=19.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .++|.|+||+|||+|++.+...
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998764

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.36  E-value=0.00091  Score=53.04  Aligned_cols=27  Identities=30%  Similarity=0.406  Sum_probs=22.6

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++..-+-|.||+|||||||++.++...
T Consensus        24 ~~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhcCC
Confidence            344458899999999999999999866

>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=96.35  E-value=0.00091  Score=51.84  Aligned_cols=29  Identities=24%  Similarity=0.335  Sum_probs=24.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      |-|+|++||||||+++.+. ..|.+++..+
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            4479999999999999886 5888877644

>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=96.28  E-value=0.00081  Score=51.42  Aligned_cols=29  Identities=21%  Similarity=0.280  Sum_probs=24.4

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEE
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYD   61 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~   61 (266)
                      -|.|.|+.|+||||+++.|++.++...+.
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~~~~~~   39 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKNDICLL   39 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTTTEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEE
Confidence            37788999999999999999999765443

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.26  E-value=0.00082  Score=53.53  Aligned_cols=26  Identities=27%  Similarity=0.397  Sum_probs=22.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +...+-|.||+|+||||+++.++...
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            34457899999999999999999866

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.25  E-value=0.00074  Score=53.86  Aligned_cols=26  Identities=27%  Similarity=0.408  Sum_probs=22.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..-+-|.||+|+||||+++.++...
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            33457899999999999999999765

>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=96.20  E-value=0.0039  Score=46.17  Aligned_cols=21  Identities=33%  Similarity=0.490  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .++|.|.+|+|||+|++.+..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999999875

>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=96.19  E-value=0.0035  Score=46.17  Aligned_cols=20  Identities=30%  Similarity=0.519  Sum_probs=18.4

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      +++.|.+|+|||+|++.+..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999875

>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=96.18  E-value=0.00076  Score=53.79  Aligned_cols=25  Identities=32%  Similarity=0.425  Sum_probs=21.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+-|.||+||||||+++.++...
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCc
Confidence            3447899999999999999998866

>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=96.15  E-value=0.0017  Score=49.76  Aligned_cols=23  Identities=26%  Similarity=0.564  Sum_probs=20.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..|+|.|+||+|||+|..++.+.
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            46999999999999999999865

>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=96.15  E-value=0.0013  Score=52.39  Aligned_cols=22  Identities=36%  Similarity=0.724  Sum_probs=19.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      +-|.||+|+||||+++.++...
T Consensus        27 ~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEECCCCChHHHHHHHHHcCC
Confidence            4578999999999999999876

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=96.12  E-value=0.0011  Score=52.89  Aligned_cols=28  Identities=21%  Similarity=0.405  Sum_probs=23.1

Q ss_pred             CCCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           28 KAWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +++..-+-|.||+|+|||||++.++..+
T Consensus        25 i~~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          25 AQPNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3344458899999999999999998765

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.11  E-value=0.0012  Score=53.91  Aligned_cols=26  Identities=27%  Similarity=0.368  Sum_probs=22.3

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +..-+-|.||+|+|||||++.++..+
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCC
Confidence            33448899999999999999999877

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.09  E-value=0.0012  Score=52.92  Aligned_cols=27  Identities=33%  Similarity=0.417  Sum_probs=22.8

Q ss_pred             CCCceeEEecCCCCChHHHHHHHHHHc
Q 024550           29 AWKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        29 ~~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++...+-|.||+|+|||||++.+...+
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhccc
Confidence            344458899999999999999998866

>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=96.08  E-value=0.0028  Score=48.60  Aligned_cols=31  Identities=23%  Similarity=0.375  Sum_probs=25.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      |.|.|+.|+||||+++.|++.+   |.+++.+..
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~~   36 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAF   36 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEec
Confidence            5678999999999999999876   566666543

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=96.08  E-value=0.00072  Score=53.53  Aligned_cols=25  Identities=24%  Similarity=0.638  Sum_probs=21.9

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+-|.||+|+||||+++.++.-.
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCc
Confidence            3348899999999999999999866

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.01  E-value=0.013  Score=45.50  Aligned_cols=16  Identities=25%  Similarity=0.380  Sum_probs=14.3

Q ss_pred             CceeEEecCCCCChHH
Q 024550           31 KRGYLLYGPPGTGKSS   46 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~   46 (266)
                      .+.+++..|+|||||.
T Consensus        49 g~dvl~~a~TGsGKTl   64 (218)
T d2g9na1          49 GYDVIAQAQSGTGKTA   64 (218)
T ss_dssp             TCCEEEECCTTSSHHH
T ss_pred             CCCEEEEcccchhhhh
Confidence            4679999999999996

>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=96.01  E-value=0.0018  Score=53.20  Aligned_cols=22  Identities=23%  Similarity=0.442  Sum_probs=16.4

Q ss_pred             ceeEEecCCCCChHHHH-HHHHH
Q 024550           32 RGYLLYGPPGTGKSSLI-AAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la-~ala~   53 (266)
                      ..+++.|+||||||+++ ..++.
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~   47 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAY   47 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCEEEEecCCccHHHHHHHHHHH
Confidence            35899999999999744 44443

>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=95.99  E-value=0.0019  Score=53.77  Aligned_cols=35  Identities=34%  Similarity=0.466  Sum_probs=27.2

Q ss_pred             eEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCccc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLL   68 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~   68 (266)
                      +=+.||||+|||||+..++..+     .+.++.++++.-.
T Consensus        54 igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~   93 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTR   93 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGS
T ss_pred             EeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccHH
Confidence            6689999999999999999765     3456677765543

>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=95.97  E-value=0.0017  Score=48.44  Aligned_cols=22  Identities=32%  Similarity=0.555  Sum_probs=19.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .|.|.|+||+|||||++++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999753

>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=95.96  E-value=0.0064  Score=44.99  Aligned_cols=22  Identities=27%  Similarity=0.472  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|.+|+|||+|+..+...
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999987753

>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=95.96  E-value=0.002  Score=47.96  Aligned_cols=22  Identities=27%  Similarity=0.557  Sum_probs=19.5

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|++|+|||+|++.+...
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999998864

>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=95.94  E-value=0.0019  Score=48.14  Aligned_cols=21  Identities=29%  Similarity=0.574  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      -++|.|++|+|||+|++.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999999886

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.94  E-value=0.0091  Score=45.92  Aligned_cols=16  Identities=38%  Similarity=0.511  Sum_probs=14.1

Q ss_pred             CceeEEecCCCCChHH
Q 024550           31 KRGYLLYGPPGTGKSS   46 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~   46 (266)
                      ++.+++.+|+|+|||.
T Consensus        38 g~dvi~~a~tGsGKTl   53 (206)
T d1s2ma1          38 GRDILARAKNGTGKTA   53 (206)
T ss_dssp             TCCEEEECCTTSCHHH
T ss_pred             CCCEEEecCCcchhhh
Confidence            4579999999999995

>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=95.92  E-value=0.00072  Score=53.97  Aligned_cols=25  Identities=24%  Similarity=0.545  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ...+-|.||+||||||+++.++.-.
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            3458899999999999999999855

>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=95.88  E-value=0.002  Score=50.89  Aligned_cols=25  Identities=16%  Similarity=0.154  Sum_probs=22.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFD   58 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~   58 (266)
                      |-|+|+.||||||+|+.++..+|..
T Consensus         4 IgiTG~igSGKsTva~~l~e~~g~~   28 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNYSAV   28 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEE
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCe
Confidence            6689999999999999999988654

>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=95.86  E-value=0.002  Score=48.76  Aligned_cols=20  Identities=25%  Similarity=0.552  Sum_probs=18.6

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      ++|.|++|+|||+|++.+.+
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            88999999999999999875

>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=95.85  E-value=0.0042  Score=48.29  Aligned_cols=31  Identities=23%  Similarity=0.236  Sum_probs=26.1

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      |.|.|+-|+||||+++.|++.+....+.+..
T Consensus         6 I~iEG~DGsGKST~~~~L~~~L~~~~~~~~~   36 (214)
T d1tmka_           6 ILIEGLDRTGKTTQCNILYKKLQPNCKLLKF   36 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTTSEEEEES
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCEEEEE
Confidence            6678999999999999999999766665543

>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=95.81  E-value=0.0023  Score=49.47  Aligned_cols=22  Identities=23%  Similarity=0.394  Sum_probs=20.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      |.|.|+.|+||||+++.|++.+
T Consensus         5 IviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           5 IVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6677999999999999999877

>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=95.81  E-value=0.0025  Score=47.67  Aligned_cols=21  Identities=33%  Similarity=0.612  Sum_probs=18.8

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .+++.|++|+|||+|+..+..
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999998865

>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=95.80  E-value=0.002  Score=48.40  Aligned_cols=21  Identities=29%  Similarity=0.474  Sum_probs=19.2

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .|.|.|+||+|||||+.++.+
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            488999999999999999975

>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=95.78  E-value=0.035  Score=43.57  Aligned_cols=39  Identities=21%  Similarity=0.135  Sum_probs=25.8

Q ss_pred             hCCCCCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           26 VGKAWKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        26 ~~~~~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      ...+.+...||+|..|+|||.++-..+...   |.....+-+
T Consensus        71 ~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~P  112 (233)
T d2eyqa3          71 MCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVP  112 (233)
T ss_dssp             HHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECS
T ss_pred             HhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEcc
Confidence            344456679999999999998766554433   445444433

>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=95.78  E-value=0.0032  Score=52.44  Aligned_cols=35  Identities=31%  Similarity=0.494  Sum_probs=25.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHc-----CCcEEEEeCCccc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL-----KFDVYDLELSNLL   68 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~-----~~~~~~i~~~~~~   68 (266)
                      |=+.||||+|||||+.+++..+     .+.++.++++.-.
T Consensus        57 IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~   96 (327)
T d2p67a1          57 LGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPV   96 (327)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC---
T ss_pred             EEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceee
Confidence            7789999999999999998765     2455667666543

>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=95.74  E-value=0.0028  Score=47.02  Aligned_cols=21  Identities=29%  Similarity=0.415  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      -++|.|.+|+|||+|++.+..
T Consensus         5 KivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999998875

>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=95.73  E-value=0.0028  Score=47.22  Aligned_cols=20  Identities=35%  Similarity=0.662  Sum_probs=18.4

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      +++.|++|+|||+|+..+..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999999875

>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=95.72  E-value=0.0022  Score=51.61  Aligned_cols=25  Identities=20%  Similarity=0.329  Sum_probs=21.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+-|.||+|+||||++++++...
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            3347799999999999999998755

>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=95.71  E-value=0.0029  Score=47.72  Aligned_cols=24  Identities=17%  Similarity=0.292  Sum_probs=20.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      .--+++.|.+|+|||+|++.+...
T Consensus         5 ~iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           5 AIKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            335999999999999999988764

>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=95.70  E-value=0.0028  Score=46.91  Aligned_cols=21  Identities=38%  Similarity=0.599  Sum_probs=18.9

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      +++.|+||+|||+|++.+...
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998763

>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=95.67  E-value=0.0031  Score=46.49  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=19.0

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      +++.|++|+|||+|+..+...
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998753

>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=95.64  E-value=0.0032  Score=47.48  Aligned_cols=20  Identities=35%  Similarity=0.677  Sum_probs=18.5

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      +++.|.+|||||+|+..+..
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998875

>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=95.62  E-value=0.0029  Score=46.37  Aligned_cols=21  Identities=43%  Similarity=0.686  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .|.|.|+||+|||+|+.++..
T Consensus         3 kI~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            488999999999999999974

>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=95.61  E-value=0.0032  Score=46.64  Aligned_cols=23  Identities=30%  Similarity=0.330  Sum_probs=19.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      .-|+|.|++|+|||+|+..+...
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            34899999999999999998753

>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=95.61  E-value=0.005  Score=48.34  Aligned_cols=30  Identities=17%  Similarity=0.127  Sum_probs=25.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVY   60 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~   60 (266)
                      |+=|.|-|+-||||||+++.|+..++...+
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~~~~i   31 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYPEWHV   31 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCTTSEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhhcCC
Confidence            455888999999999999999999865443

>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=95.53  E-value=0.0038  Score=46.39  Aligned_cols=22  Identities=27%  Similarity=0.508  Sum_probs=19.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|++|+|||+|++.+...
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3899999999999999988663

>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=95.51  E-value=0.0031  Score=47.96  Aligned_cols=21  Identities=38%  Similarity=0.515  Sum_probs=19.2

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .|.|.|+||+|||||+.++.+
T Consensus        25 ~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHhcC
Confidence            389999999999999999974

>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=95.50  E-value=0.003  Score=51.50  Aligned_cols=36  Identities=14%  Similarity=0.203  Sum_probs=26.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCccc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSNLL   68 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~~~   68 (266)
                      -|-++|++|+||||+++++.+.+   +.+...++..++.
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsfy   44 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFH   44 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGGB
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCCC
Confidence            47799999999999999998877   5566667766664

>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=95.49  E-value=0.0036  Score=46.61  Aligned_cols=21  Identities=38%  Similarity=0.695  Sum_probs=18.8

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      -++|.|.+|+|||+|+..+..
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998874

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.49  E-value=0.011  Score=45.71  Aligned_cols=16  Identities=31%  Similarity=0.441  Sum_probs=14.4

Q ss_pred             CceeEEecCCCCChHH
Q 024550           31 KRGYLLYGPPGTGKSS   46 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~   46 (266)
                      ++.+++..|+|||||.
T Consensus        47 g~dvl~~a~TGsGKT~   62 (212)
T d1qdea_          47 GHDVLAQAQSGTGKTG   62 (212)
T ss_dssp             TCCEEEECCTTSSHHH
T ss_pred             CCCEEeecccccchhh
Confidence            4679999999999997

>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=95.49  E-value=0.0039  Score=46.48  Aligned_cols=22  Identities=36%  Similarity=0.520  Sum_probs=19.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|+||+|||+|+..+...
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3889999999999999888753

>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=95.49  E-value=0.0037  Score=46.78  Aligned_cols=23  Identities=17%  Similarity=0.346  Sum_probs=19.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      .-+++.|++|+|||+|+..+...
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34889999999999999988764

>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=95.43  E-value=0.0038  Score=49.04  Aligned_cols=29  Identities=38%  Similarity=0.444  Sum_probs=23.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      .+...|.|++|+|||||+.+|........
T Consensus        95 ~kt~~~~G~SGVGKSTLiN~L~~~~~~~T  123 (225)
T d1u0la2          95 GKISTMAGLSGVGKSSLLNAINPGLKLRV  123 (225)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHSTTCCCC-
T ss_pred             CCeEEEECCCCCCHHHHHHhhcchhhhhc
Confidence            34588999999999999999977665443

>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=95.36  E-value=0.0023  Score=50.89  Aligned_cols=26  Identities=27%  Similarity=0.483  Sum_probs=22.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      ..-+-|.||.|+||||+.++++....
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl~~   57 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34477999999999999999998763

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=95.31  E-value=0.0045  Score=46.31  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=19.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -|.|.|.||+|||+|++++...
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999864

>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=95.26  E-value=0.003  Score=50.17  Aligned_cols=26  Identities=23%  Similarity=0.447  Sum_probs=22.0

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ++.-+-|.||.|+|||||.+.++...
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            33446699999999999999999876

>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=95.26  E-value=0.0069  Score=51.84  Aligned_cols=34  Identities=29%  Similarity=0.319  Sum_probs=26.2

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +++++.|++|+|||+++..+...+   |.+++.+++.
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~k   87 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN   87 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEET
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            569999999999999887666544   6667766654

>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=95.25  E-value=0.0048  Score=46.95  Aligned_cols=21  Identities=38%  Similarity=0.623  Sum_probs=18.8

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      ++|.|++|+|||+|+..+...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            889999999999999988753

>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=95.23  E-value=0.0051  Score=45.85  Aligned_cols=20  Identities=40%  Similarity=0.609  Sum_probs=18.5

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      ++|.|++|+|||+|+..+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999998875

>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=95.15  E-value=0.0054  Score=46.07  Aligned_cols=22  Identities=23%  Similarity=0.395  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|.+|+|||+|+..+...
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3799999999999999988763

>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=95.13  E-value=0.0035  Score=49.06  Aligned_cols=25  Identities=16%  Similarity=0.218  Sum_probs=22.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -|.|-||.|+||||+++.|++.+..
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            4788999999999999999998854

>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=95.13  E-value=0.071  Score=38.16  Aligned_cols=61  Identities=11%  Similarity=0.289  Sum_probs=37.2

Q ss_pred             eEEecCCCCChHH-HHHHHHH--HcCCcEEEEeCCccc--------------------ChhhHHHHHHHc---ccCCeee
Q 024550           34 YLLYGPPGTGKSS-LIAAMAN--YLKFDVYDLELSNLL--------------------GNNDLRHILIAT---ENKSILV   87 (266)
Q Consensus        34 iLl~GppGtGKT~-la~ala~--~~~~~~~~i~~~~~~--------------------~~~~l~~~~~~~---~~~~vl~   87 (266)
                      -+++||-.+|||+ |++.+-+  ..|.+++.+.+..-.                    ....+...+...   ....+++
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dvI~   84 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIG   84 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEE
T ss_pred             EEEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccceEEcccCceeeeEEeccchhhHHHHHhhccccCcCEEE
Confidence            4689999999998 7777643  346676666544110                    012222222222   2467999


Q ss_pred             eecchhh
Q 024550           88 VEDIDCC   94 (266)
Q Consensus        88 iDeid~l   94 (266)
                      |||+..+
T Consensus        85 IDE~QFf   91 (139)
T d2b8ta1          85 IDEVQFF   91 (139)
T ss_dssp             ECSGGGS
T ss_pred             echhhhc
Confidence            9999976

>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=95.11  E-value=0.0056  Score=46.18  Aligned_cols=21  Identities=29%  Similarity=0.455  Sum_probs=19.0

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      ++|.|.+|+|||+|++.+...
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            889999999999999988753

>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=95.06  E-value=0.0034  Score=50.34  Aligned_cols=25  Identities=40%  Similarity=0.731  Sum_probs=21.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+-|.||.|+|||||++.++...
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHCCC
Confidence            3347799999999999999999876

>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=95.06  E-value=0.006  Score=46.24  Aligned_cols=22  Identities=18%  Similarity=0.360  Sum_probs=19.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|++|+|||+|+..+...
T Consensus         5 KvvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999888753

>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=95.04  E-value=0.014  Score=46.87  Aligned_cols=36  Identities=25%  Similarity=0.190  Sum_probs=30.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      .|+-++++|.=|+||||++-++|..+   |..+.-+++.
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            46778899999999999998888777   7778878766

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.03  E-value=0.055  Score=41.36  Aligned_cols=21  Identities=19%  Similarity=0.222  Sum_probs=16.6

Q ss_pred             ceeEEecCCCCChHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMA   52 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala   52 (266)
                      ..+++..|.|+|||...-...
T Consensus        43 ~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1          43 YNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             SEEEEECCSSSSHHHHHHHHH
T ss_pred             CCeeeechhcccccceeeccc
Confidence            479999999999998654433

>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=95.03  E-value=0.0034  Score=46.81  Aligned_cols=20  Identities=30%  Similarity=0.615  Sum_probs=8.5

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      +++.|.+|||||+|++.+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999988775

>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=94.97  E-value=0.0039  Score=46.45  Aligned_cols=22  Identities=27%  Similarity=0.424  Sum_probs=17.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -+++.|++|+|||+|+..+...
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999987653

>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=94.93  E-value=0.0092  Score=47.70  Aligned_cols=24  Identities=29%  Similarity=0.403  Sum_probs=21.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~   54 (266)
                      +-.|+|.|.||+|||+++.++...
T Consensus        32 ~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          32 SLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCcHHHHHHHHhCC
Confidence            346999999999999999999764

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.92  E-value=0.16  Score=40.66  Aligned_cols=23  Identities=35%  Similarity=0.560  Sum_probs=20.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -+++.|++|+|||+|+..++...
T Consensus        70 r~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          70 KIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHH
Confidence            49999999999999999888663

>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=94.91  E-value=0.0037  Score=49.38  Aligned_cols=25  Identities=44%  Similarity=0.587  Sum_probs=20.8

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..-+-|.||.|+||||+.+.++...
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            3347789999999999999998743

>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=94.89  E-value=0.0022  Score=48.42  Aligned_cols=24  Identities=38%  Similarity=0.387  Sum_probs=21.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      .+|+||.|+|||+++.||.-.++.
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~g   50 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALIP   50 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcC
Confidence            678999999999999999987743

>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=94.88  E-value=0.0069  Score=44.97  Aligned_cols=21  Identities=29%  Similarity=0.475  Sum_probs=19.1

Q ss_pred             eeEEecCCCCChHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~   53 (266)
                      .|.|.|.||+|||||+.++.+
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            388999999999999999975

>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=94.79  E-value=0.014  Score=44.51  Aligned_cols=33  Identities=15%  Similarity=0.274  Sum_probs=26.7

Q ss_pred             ceeEEecC-CCCChHHHHHHHHHHc---CCcEEEEeC
Q 024550           32 RGYLLYGP-PGTGKSSLIAAMANYL---KFDVYDLEL   64 (266)
Q Consensus        32 ~~iLl~Gp-pGtGKT~la~ala~~~---~~~~~~i~~   64 (266)
                      +.++++|- +|+|||+++-.||..+   |..+..+++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id~   38 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKP   38 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEECc
Confidence            46899999 5999999888888766   777777764

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.75  E-value=0.061  Score=41.08  Aligned_cols=16  Identities=44%  Similarity=0.511  Sum_probs=14.3

Q ss_pred             CceeEEecCCCCChHH
Q 024550           31 KRGYLLYGPPGTGKSS   46 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~   46 (266)
                      ++.+++..|+|||||.
T Consensus        40 g~dvl~~a~TGsGKTl   55 (206)
T d1veca_          40 GRDILARAKNGTGKSG   55 (206)
T ss_dssp             TCCEEEECCSSSTTHH
T ss_pred             CCCEEeeccCcccccc
Confidence            4679999999999996

>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=94.66  E-value=0.0086  Score=44.83  Aligned_cols=23  Identities=35%  Similarity=0.482  Sum_probs=20.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.|.|.|.+|+|||||+.++...
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            34889999999999999999753

>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=94.59  E-value=0.0067  Score=45.50  Aligned_cols=20  Identities=35%  Similarity=0.556  Sum_probs=17.9

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      |-|.|+||+|||||+.++.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            77999999999999999854

>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=94.49  E-value=0.0048  Score=45.95  Aligned_cols=22  Identities=27%  Similarity=0.376  Sum_probs=19.1

Q ss_pred             ceeEEecCCCCChHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~   53 (266)
                      .-|.|.|+|++|||+|.+++..
T Consensus        17 ~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          17 IEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             EEEEEEECTTSSHHHHHTTTCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3499999999999999998854

>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=94.35  E-value=0.011  Score=44.69  Aligned_cols=19  Identities=37%  Similarity=0.600  Sum_probs=17.6

Q ss_pred             eeEEecCCCCChHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAM   51 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~al   51 (266)
                      -++|.|.+|+|||+|+..+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3899999999999999988

>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=94.34  E-value=0.0031  Score=46.12  Aligned_cols=21  Identities=33%  Similarity=0.626  Sum_probs=19.3

Q ss_pred             eEEecCCCCChHHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~   54 (266)
                      |.|.|.||+|||+|+.++...
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            789999999999999999765

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.30  E-value=0.026  Score=43.22  Aligned_cols=32  Identities=22%  Similarity=0.158  Sum_probs=26.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCCcEEEEeC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKFDVYDLEL   64 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~~~~~i~~   64 (266)
                      ..++.+|+|+|||.++-.++..++.+.+.+-+
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p  118 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVP  118 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             CcEEEeCCCCCceehHHhHHHHhcCceeEEEc
Confidence            45788999999999999999888877666554

>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=94.29  E-value=0.0078  Score=44.95  Aligned_cols=20  Identities=55%  Similarity=0.675  Sum_probs=18.2

Q ss_pred             eEEecCCCCChHHHHHHHHH
Q 024550           34 YLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~   53 (266)
                      |.|.|.||+|||||+.+|.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999864

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=94.27  E-value=0.0031  Score=49.77  Aligned_cols=28  Identities=32%  Similarity=0.506  Sum_probs=19.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcE
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDV   59 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~   59 (266)
                      +..+|.|++|+|||||+.+|........
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~~~~~t  125 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPELGLRT  125 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC------
T ss_pred             ceEEEECCCCccHHHHHHhhccHhHhhh
Confidence            4577889999999999999987665443

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.26  E-value=0.1  Score=40.39  Aligned_cols=16  Identities=31%  Similarity=0.513  Sum_probs=14.3

Q ss_pred             CceeEEecCCCCChHH
Q 024550           31 KRGYLLYGPPGTGKSS   46 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~   46 (266)
                      .+.+++..|+|||||.
T Consensus        54 g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          54 GRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             TCCEEEECCTTSSHHH
T ss_pred             CCCeEEEcCcchhhhh
Confidence            4679999999999996

>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=94.21  E-value=0.083  Score=37.92  Aligned_cols=61  Identities=20%  Similarity=0.269  Sum_probs=36.0

Q ss_pred             eEEecCCCCChHH-HHHHHH--HHcCCcEEEEeCCccc--------C----------hhhHHHHHHHc-ccCCeeeeecc
Q 024550           34 YLLYGPPGTGKSS-LIAAMA--NYLKFDVYDLELSNLL--------G----------NNDLRHILIAT-ENKSILVVEDI   91 (266)
Q Consensus        34 iLl~GppGtGKT~-la~ala--~~~~~~~~~i~~~~~~--------~----------~~~l~~~~~~~-~~~~vl~iDei   91 (266)
                      =+++||-.+|||+ |.+.+-  ...|.+++.+....-.        +          ......++... ....+|+|||+
T Consensus        10 ~lI~GpMfSGKTteLi~~~~~~~~~g~~vl~i~~~~D~Ry~~~~i~sh~g~~~~a~~~~~~~~~~~~~~~~~dvI~IDE~   89 (141)
T d1xx6a1          10 EVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEV   89 (141)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEEECSG
T ss_pred             EEEEeccccHHHHHHHHHHHHhhhcCCcEEEEEeccccccccceeeecccceEEEEEecchhhhhhhhcccccEEEEeeh
Confidence            4578999999998 666553  3346666655543111        0          01122233222 35689999999


Q ss_pred             hhh
Q 024550           92 DCC   94 (266)
Q Consensus        92 d~l   94 (266)
                      ..+
T Consensus        90 QFf   92 (141)
T d1xx6a1          90 QFF   92 (141)
T ss_dssp             GGS
T ss_pred             hhc
Confidence            876

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.09  E-value=0.0092  Score=48.42  Aligned_cols=25  Identities=32%  Similarity=0.440  Sum_probs=21.2

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcCC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      --+|+||.|+|||++..|++-.++.
T Consensus        26 lnvlvG~NgsGKS~iL~Ai~~~lg~   50 (308)
T d1e69a_          26 VTAIVGPNGSGKSNIIDAIKWVFGE   50 (308)
T ss_dssp             EEEEECCTTTCSTHHHHHHHHTSCC
T ss_pred             eEEEECCCCCcHHHHHHHHHHHhCC
Confidence            3579999999999999999876653

>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=94.06  E-value=0.015  Score=43.38  Aligned_cols=23  Identities=30%  Similarity=0.271  Sum_probs=19.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+++.|++|+|||+|+..+...
T Consensus         6 ~ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           6 LRLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999988764

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=94.05  E-value=0.015  Score=47.16  Aligned_cols=24  Identities=29%  Similarity=0.558  Sum_probs=21.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .-+++.||+|||||+++..+++..
T Consensus        44 Qr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          44 QRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CeeeEeCCCCCCHHHHHHHHHHHH
Confidence            349999999999999999888755

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=93.97  E-value=0.081  Score=40.13  Aligned_cols=16  Identities=25%  Similarity=0.329  Sum_probs=14.3

Q ss_pred             CceeEEecCCCCChHH
Q 024550           31 KRGYLLYGPPGTGKSS   46 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~   46 (266)
                      ++.+++..|.|||||.
T Consensus        38 G~dvii~a~TGSGKTl   53 (209)
T d1q0ua_          38 GESMVGQSQTGTGKTH   53 (209)
T ss_dssp             TCCEEEECCSSHHHHH
T ss_pred             CCCeEeecccccccce
Confidence            4579999999999997

>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=93.83  E-value=0.015  Score=48.37  Aligned_cols=24  Identities=33%  Similarity=0.261  Sum_probs=21.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHcC
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      -|.|-|+-|+||||+++.+++.++
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l~   31 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAAS   31 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGGG
T ss_pred             EEEEECCccCCHHHHHHHHHHHhc
Confidence            377889999999999999999884

>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=93.80  E-value=0.016  Score=45.05  Aligned_cols=22  Identities=32%  Similarity=0.496  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|++|+|||++++.+...
T Consensus         8 KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999988643

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.70  E-value=0.025  Score=47.65  Aligned_cols=24  Identities=33%  Similarity=0.587  Sum_probs=21.4

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      -+|+||.|+|||+++.|++-.+|.
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~lg~   51 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVLGV   51 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            578999999999999999887764

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.58  E-value=0.026  Score=43.94  Aligned_cols=23  Identities=35%  Similarity=0.401  Sum_probs=20.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      -++|.|.-|+||||+++.+.+..
T Consensus         5 v~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHSC
T ss_pred             EEEEeeCCCCCHHHHHHHHHhcC
Confidence            47899999999999999988765

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.39  E-value=0.41  Score=38.34  Aligned_cols=23  Identities=26%  Similarity=0.280  Sum_probs=19.0

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      ..+++.|++|+|||+++..++..
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEeecCCCCChHHHHHHHHHh
Confidence            34899999999999998877643

>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=93.34  E-value=0.024  Score=42.46  Aligned_cols=23  Identities=35%  Similarity=0.434  Sum_probs=20.1

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+++.|..|+|||++++.+...-
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48999999999999999987654

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.24  E-value=0.047  Score=41.03  Aligned_cols=33  Identities=27%  Similarity=0.342  Sum_probs=22.3

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH----cCCcEEEEeC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY----LKFDVYDLEL   64 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~----~~~~~~~i~~   64 (266)
                      ++.|+++|.|+|||.++-.++..    .+..++.+.+
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P   60 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAP   60 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECS
T ss_pred             CCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcC
Confidence            45889999999999865555532    3445555544

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.04  E-value=0.084  Score=41.83  Aligned_cols=36  Identities=33%  Similarity=0.376  Sum_probs=28.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      .+-++++|.=|+||||++-.||..+   |..++.+++.-
T Consensus        20 ~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~Dp   58 (279)
T d1ihua2          20 HGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDP   58 (279)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCC
Confidence            3447788999999999877777666   77888888773

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=92.79  E-value=0.27  Score=39.21  Aligned_cols=22  Identities=23%  Similarity=0.256  Sum_probs=18.0

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      .+++.|++|+|||+++..++..
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~   90 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILN   90 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHT
T ss_pred             eEeeccCCCCChHHHHHHHHhh
Confidence            3889999999999998765443

>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=92.68  E-value=0.024  Score=46.98  Aligned_cols=24  Identities=21%  Similarity=0.322  Sum_probs=21.6

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      |.|-|+-|+||||+++.+++.+..
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            678899999999999999998854

>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=92.22  E-value=0.038  Score=41.08  Aligned_cols=22  Identities=32%  Similarity=0.487  Sum_probs=18.9

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      -++|.|..|+|||++++.+...
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3899999999999999987643

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

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: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=92.20  E-value=0.032  Score=46.14  Aligned_cols=24  Identities=21%  Similarity=0.315  Sum_probs=18.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKF   57 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~   57 (266)
                      |.|-|+-|+||||+++.+++.++.
T Consensus         7 I~IEG~iGsGKTTl~~~La~~l~~   30 (329)
T d1e2ka_           7 VYIDGPHGMGKTTTTQLLVALGSR   30 (329)
T ss_dssp             EEECSCTTSSHHHHHHHHTC----
T ss_pred             EEEECCcCCCHHHHHHHHHHHhCC
Confidence            677899999999999999988754

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=91.13  E-value=0.071  Score=42.62  Aligned_cols=25  Identities=32%  Similarity=0.433  Sum_probs=21.6

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcC
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      |++-+.|..|+|||||+.++....|
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~~g   27 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYKTG   27 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHcC
Confidence            5788999999999999999976553

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=91.12  E-value=0.037  Score=45.34  Aligned_cols=18  Identities=33%  Similarity=0.602  Sum_probs=15.4

Q ss_pred             eeEEecCCCCChHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAA   50 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~a   50 (266)
                      ..||.|.+|||||||...
T Consensus        16 valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             EEEEEECTTSCHHHHTCB
T ss_pred             EEEEEccCCCCccccccC
Confidence            489999999999997653

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=90.98  E-value=0.11  Score=41.04  Aligned_cols=34  Identities=21%  Similarity=0.274  Sum_probs=26.8

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      .|-++|.=|+||||++-.+|..+   |..+.-+++.-
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID~D~   39 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVGCDP   39 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEEECT
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEecCC
Confidence            35678989999999888877766   77788787653

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal 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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.76  E-value=0.14  Score=36.17  Aligned_cols=61  Identities=13%  Similarity=0.263  Sum_probs=35.1

Q ss_pred             eEEecCCCCChHH-HHHHHHHH--cCCcEEEEeCCccc--Ch---------------hhHHHHHHHcccCCeeeeecchh
Q 024550           34 YLLYGPPGTGKSS-LIAAMANY--LKFDVYDLELSNLL--GN---------------NDLRHILIATENKSILVVEDIDC   93 (266)
Q Consensus        34 iLl~GppGtGKT~-la~ala~~--~~~~~~~i~~~~~~--~~---------------~~l~~~~~~~~~~~vl~iDeid~   93 (266)
                      -+++||-.+|||+ |.+.+...  .|..++.+.+..-.  +.               ..............+++|||+..
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~g~~v~~ikp~~D~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~I~IDEaQF   84 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQF   84 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCC--------------CEEESSGGGGHHHHHTCSEEEESSGGG
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHcCCcEEEEecccccCCcceeeecCCCcceeeeeechhhhhhhhcccceEEeehhHH
Confidence            4678999999998 55555433  35566655544221  00               00111122234567999999986


Q ss_pred             h
Q 024550           94 C   94 (266)
Q Consensus        94 l   94 (266)
                      +
T Consensus        85 f   85 (133)
T d1xbta1          85 F   85 (133)
T ss_dssp             C
T ss_pred             H
Confidence            6

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=90.74  E-value=0.076  Score=42.63  Aligned_cols=26  Identities=15%  Similarity=0.151  Sum_probs=22.7

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      -+++-+.|..|+|||||+.++....|
T Consensus         6 iRni~i~gh~~~GKTtL~e~ll~~~g   31 (276)
T d2bv3a2           6 LRNIGIAAHIDAGKTTTTERILYYTG   31 (276)
T ss_dssp             EEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhcC
Confidence            36899999999999999999987664

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=90.37  E-value=0.077  Score=39.32  Aligned_cols=22  Identities=18%  Similarity=0.379  Sum_probs=19.3

Q ss_pred             eeEEecCCCCChHHHHHHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~   54 (266)
                      +|=+.|.|++|||||+.++.+.
T Consensus         7 nIaiiG~~naGKSTL~n~L~~~   28 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTEI   28 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTT
T ss_pred             EEEEEeCCCCcHHHHHHHHHHh
Confidence            4779999999999999999753

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=90.24  E-value=0.096  Score=47.54  Aligned_cols=26  Identities=19%  Similarity=0.406  Sum_probs=22.4

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.+|++.|.+|+|||..++.+-+.+
T Consensus        85 ~~QsIiisGeSGsGKTe~~k~il~yL  110 (684)
T d1lkxa_          85 ENQCVIISGESGAGKTEASKKIMQFL  110 (684)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            35689999999999999988887766

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.14  E-value=0.073  Score=45.09  Aligned_cols=23  Identities=30%  Similarity=0.457  Sum_probs=20.6

Q ss_pred             CceeEEecCCCCChHHHHHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMAN   53 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~   53 (266)
                      +-.|.+.|.||+|||||+.++..
T Consensus        56 ~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          56 VLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            45799999999999999999974

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=90.04  E-value=0.061  Score=43.83  Aligned_cols=17  Identities=35%  Similarity=0.643  Sum_probs=14.8

Q ss_pred             eeEEecCCCCChHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~   49 (266)
                      -.||.|.+|||||||..
T Consensus        16 ~alfFGLSGTGKTTLs~   32 (313)
T d2olra1          16 VAVFFGLSGTGKTTLST   32 (313)
T ss_dssp             EEEEECSTTSSHHHHHC
T ss_pred             EEEEEccCCCCccccee
Confidence            47899999999999774

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {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: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=89.99  E-value=0.11  Score=47.27  Aligned_cols=25  Identities=28%  Similarity=0.557  Sum_probs=21.3

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      ..+|++.|.+|+|||..++.+-+.+
T Consensus       125 nQsIiisGeSGaGKTe~~k~il~yL  149 (712)
T d1d0xa2         125 NQSLLITGESGAGKTENTKKVIQYL  149 (712)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CceEEEeCCCCCCHHHHHHHHHHHH
Confidence            5689999999999999888776655

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=89.53  E-value=0.12  Score=47.74  Aligned_cols=25  Identities=24%  Similarity=0.502  Sum_probs=20.5

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +.+|++.|.+|+|||..++.+-+.+
T Consensus       123 ~QsIiisGeSGaGKTe~~K~il~yL  147 (794)
T d2mysa2         123 NQSILITGESGAGKTVNTKRVIQYF  147 (794)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            5689999999999998777666555

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.52  E-value=0.12  Score=42.27  Aligned_cols=20  Identities=20%  Similarity=0.524  Sum_probs=16.7

Q ss_pred             CCceeEEecCCCCChHHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~   49 (266)
                      ....++-||+.|+|||+.+.
T Consensus        75 ~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          75 YNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             CCEEEEEECSTTSSHHHHHT
T ss_pred             CCcceeeecccCCCCceecc
Confidence            35579999999999999763

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=89.44  E-value=0.13  Score=46.82  Aligned_cols=26  Identities=27%  Similarity=0.413  Sum_probs=21.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.+|++.|.+|+|||..++.+-+.+
T Consensus        90 ~~Q~IiisGeSGaGKTe~~k~il~yL  115 (710)
T d1br2a2          90 EDQSILCTGESGAGKTENTKKVIQYL  115 (710)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            35689999999999999888776665

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=89.36  E-value=0.13  Score=46.94  Aligned_cols=26  Identities=19%  Similarity=0.390  Sum_probs=21.8

Q ss_pred             CCceeEEecCCCCChHHHHHHHHHHc
Q 024550           30 WKRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .+.+|++.|.+|+|||..++.+-+.+
T Consensus        93 ~~Q~IiisGeSGsGKTe~~k~il~~l  118 (730)
T d1w7ja2          93 RNQSIIVSGESGAGKTVSAKYAMRYF  118 (730)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            36689999999999999888776655

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.19  E-value=0.22  Score=37.88  Aligned_cols=32  Identities=28%  Similarity=0.360  Sum_probs=24.9

Q ss_pred             EEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           35 LLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        35 Ll~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      +..|-.|+||||++..+|..+   |..+..+++..
T Consensus         6 v~s~KGGvGKTtia~nlA~~la~~g~~VlliD~D~   40 (232)
T d1hyqa_           6 VASGKGGTGKTTITANLGVALAQLGHDVTIVDADI   40 (232)
T ss_dssp             EEESSSCSCHHHHHHHHHHHHHHTTCCEEEEECCC
T ss_pred             EECCCCCChHHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence            344888999999998888766   67777887653

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=89.18  E-value=0.13  Score=47.52  Aligned_cols=25  Identities=28%  Similarity=0.512  Sum_probs=21.0

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      +.+|++.|.+|+|||..++.+-+.+
T Consensus       121 nQ~IiisGESGaGKTe~~K~il~yL  145 (789)
T d1kk8a2         121 NQSCLITGESGAGKTENTKKVIMYL  145 (789)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            5689999999999999877776655

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=89.03  E-value=0.26  Score=40.74  Aligned_cols=19  Identities=32%  Similarity=0.620  Sum_probs=15.9

Q ss_pred             CCceeEEecCCCCChHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la   48 (266)
                      ....++-||+.|+|||+++
T Consensus        79 ~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          79 YNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             CCEEEEEECSTTSSHHHHH
T ss_pred             CceeEEecccCCCCcceee
Confidence            3456999999999999875

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.96  E-value=0.13  Score=35.66  Aligned_cols=23  Identities=13%  Similarity=0.130  Sum_probs=20.7

Q ss_pred             eeEEecCCCCChHHHHHHHHHHc
Q 024550           33 GYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .++|.|-+|+||+++|+++...+
T Consensus         8 ~i~~tg~~~~gk~~ia~al~~~l   30 (122)
T d1g8fa3           8 SIVLGNSLTVSREQLSIALLSTF   30 (122)
T ss_dssp             EEEECTTCCSCHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHH
Confidence            48999999999999999997766

>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=88.96  E-value=0.16  Score=40.40  Aligned_cols=17  Identities=35%  Similarity=0.425  Sum_probs=14.8

Q ss_pred             CCceeEEecCCCCChHH
Q 024550           30 WKRGYLLYGPPGTGKSS   46 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~   46 (266)
                      .++.+++.+|+|+|||+
T Consensus         8 ~~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           8 KKRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TTCEEEECCCTTSSTTT
T ss_pred             cCCcEEEEECCCCCHHH
Confidence            45679999999999995

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=88.62  E-value=0.088  Score=43.03  Aligned_cols=17  Identities=41%  Similarity=0.685  Sum_probs=15.0

Q ss_pred             eeEEecCCCCChHHHHH
Q 024550           33 GYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        33 ~iLl~GppGtGKT~la~   49 (266)
                      ..||.|-+|||||||..
T Consensus        16 ~alfFGLSGTGKTTLs~   32 (323)
T d1ii2a1          16 VTVFFGLSGTGKTTLSA   32 (323)
T ss_dssp             EEEEECCTTSSHHHHHC
T ss_pred             EEEEEccCCCCccccee
Confidence            37899999999999884

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {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: RecA protein-like (ATPase-domain)
domain: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.36  E-value=0.18  Score=37.67  Aligned_cols=34  Identities=26%  Similarity=0.274  Sum_probs=26.0

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL   68 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~   68 (266)
                      +|+.|+..+|||..|..++... .+.+++..+...
T Consensus         2 iLVtGGarSGKS~~AE~l~~~~-~~~~YiAT~~~~   35 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEALIGDA-PQVLYIATSQIL   35 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCSC-SSEEEEECCCC-
T ss_pred             EEEECCCCccHHHHHHHHHhcC-CCcEEEEccCCC
Confidence            6899999999999999998764 455666555443

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {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: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=88.21  E-value=2.5  Score=30.29  Aligned_cols=32  Identities=16%  Similarity=0.185  Sum_probs=21.8

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      +.+|=.+|=||||.|-.+|-..   |..++.+.+-
T Consensus         5 i~vytG~GKGKTTAAlG~alRA~G~G~rV~ivQFl   39 (157)
T d1g5ta_           5 IIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFI   39 (157)
T ss_dssp             EEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHhcCCCEEEEEEEe
Confidence            6677778999999877666444   5555555443

>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=87.99  E-value=0.36  Score=40.83  Aligned_cols=36  Identities=19%  Similarity=0.244  Sum_probs=31.8

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL   67 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~   67 (266)
                      +..+|.|-+|||||.++.+++...+.|++.+..+..
T Consensus        32 ~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~~   67 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKT   67 (413)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSHH
T ss_pred             CcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCHH
Confidence            458899999999999999999999999988886654

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=87.97  E-value=0.24  Score=39.33  Aligned_cols=33  Identities=24%  Similarity=0.298  Sum_probs=25.3

Q ss_pred             eEEecCCCCChHHHHHHHHHHc---CCcEEEEeCCc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL---KFDVYDLELSN   66 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~---~~~~~~i~~~~   66 (266)
                      |-++|-=|+||||++-.+|..+   |..+.-+++.-
T Consensus         5 IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID~Dp   40 (289)
T d2afhe1           5 CAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDP   40 (289)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEECS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEecCC
Confidence            4568988999999777766554   77888887753

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=87.85  E-value=0.15  Score=38.83  Aligned_cols=25  Identities=24%  Similarity=0.211  Sum_probs=21.1

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHc
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~   55 (266)
                      .-++-+.|-+++|||||+.+|...+
T Consensus         3 ~ini~iiGhvd~GKSTL~~~Ll~~~   27 (204)
T d2c78a3           3 HVNVGTIGHVDHGKTTLTAALTYVA   27 (204)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCcHHHHHHHHHHHh
Confidence            3468899999999999999996554

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=87.74  E-value=0.34  Score=36.77  Aligned_cols=32  Identities=25%  Similarity=0.334  Sum_probs=25.1

Q ss_pred             eEEe-cCCCCChHHHHHHHHHHc---CCcEEEEeCC
Q 024550           34 YLLY-GPPGTGKSSLIAAMANYL---KFDVYDLELS   65 (266)
Q Consensus        34 iLl~-GppGtGKT~la~ala~~~---~~~~~~i~~~   65 (266)
                      |-++ +--|+||||++..+|..+   |.++..+++.
T Consensus         5 Iav~~~kGGvGKTtia~nLA~~la~~g~~VlliD~D   40 (237)
T d1g3qa_           5 ISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            4455 678999999998888766   7788888864

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=87.74  E-value=0.18  Score=41.54  Aligned_cols=18  Identities=33%  Similarity=0.569  Sum_probs=15.6

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      ...++-||+.|+|||+.+
T Consensus        81 n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          81 NCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             EEEEEEEECTTSSHHHHH
T ss_pred             CceEEeeeeccccceEEe
Confidence            456999999999999876

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=87.67  E-value=0.18  Score=41.38  Aligned_cols=19  Identities=26%  Similarity=0.503  Sum_probs=16.0

Q ss_pred             CceeEEecCCCCChHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~   49 (266)
                      ...++-||..|+|||+...
T Consensus        85 n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          85 VCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             EEEEEEECCTTSSHHHHHH
T ss_pred             CeEEEeeeccccccceeee
Confidence            4469999999999998864

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=86.69  E-value=0.23  Score=40.97  Aligned_cols=18  Identities=33%  Similarity=0.551  Sum_probs=15.8

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      ...++-||+.|+|||+.+
T Consensus        87 n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          87 NVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             CEEEEEECSTTSSHHHHH
T ss_pred             CceeeeeccCCCCCceee
Confidence            457999999999999886

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), 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: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=86.43  E-value=0.24  Score=41.87  Aligned_cols=28  Identities=25%  Similarity=0.243  Sum_probs=19.7

Q ss_pred             CCCCceeEEecCCCCChHHH-HHHHHHHc
Q 024550           28 KAWKRGYLLYGPPGTGKSSL-IAAMANYL   55 (266)
Q Consensus        28 ~~~~~~iLl~GppGtGKT~l-a~ala~~~   55 (266)
                      .|....+|+.+.+|||||++ +..++.-+
T Consensus        13 ~p~~g~~lv~A~AGsGKT~~l~~r~~~ll   41 (485)
T d1w36b1          13 LPLQGERLIEASAGTGKTFTIAALYLRLL   41 (485)
T ss_dssp             CCCSSCEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCeEEEEcCchHHHHHHHHHHHHHH
Confidence            45556689999999999974 44444443

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=85.94  E-value=0.26  Score=40.56  Aligned_cols=18  Identities=28%  Similarity=0.538  Sum_probs=15.5

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      ...++-||..|+|||+.+
T Consensus        83 n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          83 NVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             ccceeeeeccCCcccccc
Confidence            456889999999999876

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=85.47  E-value=0.28  Score=37.65  Aligned_cols=22  Identities=18%  Similarity=0.301  Sum_probs=19.5

Q ss_pred             eEEecCCCCChHHHHHHHHHHc
Q 024550           34 YLLYGPPGTGKSSLIAAMANYL   55 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~   55 (266)
                      |-+.|.|++|||||+.+|....
T Consensus         8 IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           8 VSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCccHHHHHHHHHhhc
Confidence            7788999999999999997654

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=85.01  E-value=0.2  Score=41.71  Aligned_cols=18  Identities=33%  Similarity=0.565  Sum_probs=15.5

Q ss_pred             CceeEEecCCCCChHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la   48 (266)
                      ...++-||+.|+|||+..
T Consensus        75 n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          75 NVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             EEEEEEECSTTSSHHHHH
T ss_pred             ceeeeccccCCCCccccc
Confidence            456999999999999875

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {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 YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=84.57  E-value=0.69  Score=36.47  Aligned_cols=23  Identities=39%  Similarity=0.537  Sum_probs=20.4

Q ss_pred             ceeEEecCCCCChHHHHHHHHHH
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANY   54 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~   54 (266)
                      -.+.+.|-|.+||||++.++.+.
T Consensus       113 ~~v~vvG~PNvGKSsliN~L~~~  135 (273)
T d1puja_         113 IRALIIGIPNVGKSTLINRLAKK  135 (273)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             eEEEEEecCccchhhhhhhhhcc
Confidence            34899999999999999999864

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=84.13  E-value=1.4  Score=36.98  Aligned_cols=36  Identities=28%  Similarity=0.303  Sum_probs=30.9

Q ss_pred             ceeEEecCCCCChHHHHHHHHHHcCCcEEEEeCCcc
Q 024550           32 RGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNL   67 (266)
Q Consensus        32 ~~iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~   67 (266)
                      +...|.|.+|+||+.++.+++...+.+++.+..+..
T Consensus        29 ~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~~~~   64 (408)
T d1c4oa1          29 RFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNKI   64 (408)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESSHH
T ss_pred             CcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeCCHH
Confidence            347999999999999999999999999988765443

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {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: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=84.05  E-value=0.29  Score=40.65  Aligned_cols=19  Identities=26%  Similarity=0.590  Sum_probs=15.9

Q ss_pred             CCceeEEecCCCCChHHHH
Q 024550           30 WKRGYLLYGPPGTGKSSLI   48 (266)
Q Consensus        30 ~~~~iLl~GppGtGKT~la   48 (266)
                      ....++-||+.|+|||+..
T Consensus       124 ~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         124 YNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             CEEEEEEECSTTSSHHHHH
T ss_pred             cceeEEeeccCCCccceEe
Confidence            3556999999999999865

>d2axpa1 c.37.1.1 (A:2-165) Hypothetical protein YorR {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: Nucleotide and nucleoside kinases
domain: Hypothetical protein YorR
species: Bacillus subtilis [TaxId: 1423]

Probab=84.01  E-value=1.1  Score=30.11  Aligned_cols=59  Identities=20%  Similarity=0.273  Sum_probs=44.9

Q ss_pred             eEEecCCCCChHHHHHHHHHHcCCcEEEEeCCccc--ChhhHHHHHHHcccCCeeeeecch
Q 024550           34 YLLYGPPGTGKSSLIAAMANYLKFDVYDLELSNLL--GNNDLRHILIATENKSILVVEDID   92 (266)
Q Consensus        34 iLl~GppGtGKT~la~ala~~~~~~~~~i~~~~~~--~~~~l~~~~~~~~~~~vl~iDeid   92 (266)
                      +++-||--|=||+++..+.+++..|++.-+...+.  ++..+-+-|.+.....-++||.+-
T Consensus         3 iilegpdccfkstvaaklskelkypiikgssfelaksgneklfehfnkladednviidrfv   63 (164)
T d2axpa1           3 IILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFV   63 (164)
T ss_dssp             EEEECCSSSCHHHHHHHHHHHHTCCEEECCCHHHHHHCHHHHHHHHHHHTTCCSEEEESCH
T ss_pred             EEEeCCchhhHHHHHHHHHhhhcCceecCchhhhhhccCHHHHHHHHhhccccceeeehhh
Confidence            67899999999999999999999998876544443  445566667777666666677654

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=83.98  E-value=0.3  Score=40.53  Aligned_cols=19  Identities=32%  Similarity=0.649  Sum_probs=16.0

Q ss_pred             CceeEEecCCCCChHHHHH
Q 024550           31 KRGYLLYGPPGTGKSSLIA   49 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~   49 (266)
                      ...++-||..|+|||+++.
T Consensus       114 n~tifaYGqTGSGKTyTm~  132 (362)
T d1v8ka_         114 KATCFAYGQTGSGKTHTMG  132 (362)
T ss_dssp             EEEEEEEESTTSSHHHHHH
T ss_pred             CceEEeeccCCCCCceeee
Confidence            4568999999999998863

>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=83.18  E-value=0.34  Score=36.29  Aligned_cols=33  Identities=27%  Similarity=0.152  Sum_probs=22.4

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcCCcEEEEe
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLE   63 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~~~~~~i~   63 (266)
                      .+.+++.-|.|+|||.......-......+.+.
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~~~~~~~~~~v~   72 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVS   72 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHSSSEEEEEC
T ss_pred             CCCEEEEcCCCCCCcchhhhhhhhccCceEEec
Confidence            457999999999999876554444444434333

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) 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: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.65  E-value=0.4  Score=39.43  Aligned_cols=26  Identities=19%  Similarity=0.217  Sum_probs=22.2

Q ss_pred             CceeEEecCCCCChHHHHHHHHHHcC
Q 024550           31 KRGYLLYGPPGTGKSSLIAAMANYLK   56 (266)
Q Consensus        31 ~~~iLl~GppGtGKT~la~ala~~~~   56 (266)
                      -|+|-+.|..|+|||||+.++....|
T Consensus        17 IRNI~iiGhvd~GKTTL~d~Ll~~~g   42 (341)
T d1n0ua2          17 VRNMSVIAHVDHGKSTLTDSLVQRAG   42 (341)
T ss_dssp             EEEEEEECCGGGTHHHHHHHHHHHHB
T ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHCC
Confidence            46799999999999999999975553