Citrus Sinensis ID: 035959

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------34
Protein Sequence
MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccEEEEEEEcccccccHHHHHHHHHHHcccccccccEEEEEcccccccEEEEEccccEEEEEEccEEEEEEEEcccccccccccccccccccccEEEEEEEccccHHHHHHcHHHHHHHHHHHHHHHHcccEEEEEEcccccccccccccccccccccEEEEcHHHHHHHHHHHHHcccEEEEEEccccccHHHHHHHHHHHHccEEEEEEcccccccHHHHHHHHHcccccEEEEEccccccccccHHHHHcccccccccccccccccccHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccEEEEEEEccccccHHHHHHHHHHHHHHHccccccEEEEEcccccccEEEEEccccEEEEEEccEEEEEEEEEEcccccccccccccccccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEcccccccccccEEEcccccccHHHHcccHHHHHHHHHHHHHHHHccEEEEccccccHHHHHHHHHHHccccEEEEEEcEccccHHHHHHHHcccccEEEEEEEcccEEEcccccccccccccccccccccEEEEHHHHHHHccHHHcccccEcc
Coil and Loop (DISEMBL)
MPSMTTVMSVAASAAATFMLIQSYTriylpdevssYFDQKFKNFIARIYSESTLVIEeyddglnrnKLFKAAKlylepkippnvnrikinlpkkesevslsveknqavfdvfngvrlkwkfelkpapdqelcnngnymfkdrvpcfelrfhkkhketvlGTYIPHILKKSKELSKKKKTLKLFTLNCnrinhdtrqsaildhpstfdtlamDTDMKKMIMDDLERAWKRgyllfgppgtgksSLIAAMANYLHFDvydlelssvegNKHLRKVLIATENKSILVVGDIDCCTELQDRsaqartaspdwhspkrdqitlsgllnftdglwsscgderii
Flexible Loop (DISEMBL)
MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKlylepkippnvnrikinLPKKEsevslsveknqavfdvfnGVRLKWKFELkpapdqelcnnGNYMFKDRVPCFELRFHKKhketvlgtyiphilKKSKELSKKKKTLKLFTLNCNrinhdtrqsaildhpstfdTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIatenksilvVGDIDCCTELQDRSAQartaspdwhspkrdqitlsgllnftdglwsscgderii
Low Complexity Region (SEG)
MPsmttvmsvaasaaatFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHIlkkskelskkkktlklftlNCNRINHDTRQSAILDHPSTFDTLAmdtdmkkmimddLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII
Disordered region (IsUnstruct)
*********VAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINL********LSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHIL**************LFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTEL*********************ITLSGLLNFTDGLWSSC******
Disordered Region (DISOPRED)
***MTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVN*******************NQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQD****************RDQITLSGLLNFTDGLWSSCGDERII
Disordered Region (DISEMBL)
**********AASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQD*************SPKRDQITLSGLLNFTDGLWSSCGDERII
Disordered Region (DISPRO)
**SMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAP****CN****MFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQD****************RDQITLSGLLNFTDGLWSSCGDER**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII
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	338	2.2.26 [Sep-21-2011]
Q9P6Q3	449	Probable mitochondrial ch	yes	no	0.369	0.278	0.322	1e-12
Q54DY9	458	Probable mitochondrial ch	yes	no	0.502	0.371	0.262	7e-11
P32839	456	Mitochondrial chaperone B	yes	no	0.334	0.247	0.335	2e-10
Q7ZTL7	419	Mitochondrial chaperone B	N/A	no	0.511	0.412	0.276	2e-10
Q54HY8	421	Probable mitochondrial ch	no	no	0.763	0.612	0.264	6e-09
Q7ZV60	420	Mitochondrial chaperone B	yes	no	0.488	0.392	0.262	9e-08
Q5E9H5	419	Mitochondrial chaperone B	yes	no	0.621	0.501	0.239	6e-07
Q9Y276	419	Mitochondrial chaperone B	yes	no	0.621	0.501	0.239	3e-06
Q9CZP5	418	Mitochondrial chaperone B	yes	no	0.621	0.502	0.239	5e-06
P60373	430	Replication factor C larg	yes	no	0.284	0.223	0.293	0.0001

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

 Score = 74.7 bits (182), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 50/155 (32%), Positives = 86/155 (55%), Gaps = 30/155 (19%)

Query: 202 HPST---FDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLI 245
           HP +     ++ +++++KKMI DD+                ++RGYLL+GPPG+GK+S +
Sbjct: 200 HPRSKRMLSSVVLESNVKKMITDDVHDFLRNSQWYDTRGIPYRRGYLLYGPPGSGKTSFL 259

Query: 246 AAMANYLHFDVYDLELSSVEG--NKHLRKVLIATENKSILVVGDIDCCTELQDRSAQART 303
            A+A  L +D+  L L+  +G  +  L  +L     K+++++ D+D   + ++RS +   
Sbjct: 260 YALAGELDYDICVLNLAE-KGLTDDRLNHLLSNVPPKAVVLLEDVDSAFQGRERSGEV-- 316

Query: 304 ASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
               +H+     +T SGLLN  DG+ SS  DERII
Sbjct: 317 ---GFHA----NVTFSGLLNALDGVTSS--DERII 342

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 = 68.6 bits (166), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 102/217 (47%), Gaps = 47/217 (21%)

Query: 157 TVLGT---YIPHILKKSKELSKKK---KTLKLFTLNCN--RINHDTRQSAILDHPSTFDT 208
           T LGT      ++++++KE++ +K   KTL   ++  +  R  H  R+  I        +
Sbjct: 156 TTLGTGRQVFQNLIEEAKEMALEKEEGKTLIYTSMGTDWRRFGHPRRKRPI-------SS 208

Query: 209 LAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFD 255
           + +D    ++I+ D+++              ++RGYLL+GPPGTGKSS I A+A  L   
Sbjct: 209 VILDKGKSELIIQDVKKFLNNSDWYNDRGIPYRRGYLLYGPPGTGKSSFITALAGELQLS 268

Query: 256 VYDLELSSVE-GNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPD------- 307
           +  L L+     +  L ++L     +SI+++ DID   +  +    A++ S +       
Sbjct: 269 ICILNLAGKSVSDTSLNQLLATAPQRSIILLEDIDSAIQTGNHDLSAKSNSANAPSISSG 328

Query: 308 -------WHSPK----RDQITLSGLLNFTDGLWSSCG 333
                  + +P        +T SGLLN  DG+ +S G
Sbjct: 329 GLQYQGYYGNPSVSSGGSALTFSGLLNALDGVAASEG 365

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 = 67.0 bits (162), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/140 (33%), Positives = 77/140 (55%), Gaps = 27/140 (19%)

Query: 208 TLAMDTDMKKMIMDDL-----------ERA--WKRGYLLFGPPGTGKSSLIAAMANYLHF 254
           ++ +D+ +K+ I+DD+           +R   ++RGYLL+GPPG+GK+S I A+A  L +
Sbjct: 227 SVILDSGIKEGILDDVYDFMKNGKWYSDRGIPYRRGYLLYGPPGSGKTSFIQALAGELDY 286

Query: 255 DVYDLELSSVEGN---KHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSP 311
           ++  L LS  E N     L  ++     +SIL++ DID        + +++T    +HS 
Sbjct: 287 NICILNLS--ENNLTDDRLNHLMNNMPERSILLLEDIDAAF-----NKRSQTGEQGFHS- 338

Query: 312 KRDQITLSGLLNFTDGLWSS 331
               +T SGLLN  DG+ SS
Sbjct: 339 ---SVTFSGLLNALDGVTSS 355

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

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

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

 Score = 66.6 bits (161), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/199 (27%), Positives = 96/199 (48%), Gaps = 26/199 (13%)

Query: 157 TVLGT---YIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDT 213
           T LGT      +IL++++EL+ K++  K  T+  N +  + RQ           ++ ++ 
Sbjct: 138 TALGTNRNIFFNILQEARELALKQQVGK--TVMYNAVGAEWRQFGFPRRRRPLSSVVLEQ 195

Query: 214 DMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDV-YDL 259
            + + I+ D++               ++RGYLL+GPPG GKSS I A+A  L + +    
Sbjct: 196 GISEKIVQDVKGFIENPKWYSDRGIPYRRGYLLYGPPGCGKSSFITALAGELEYSICLMS 255

Query: 260 ELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLS 319
              S   +  L  +L     +SI+++ D+D     +D + Q  TA          ++T S
Sbjct: 256 LSDSSLSDDRLNHLLSVAPQQSIILLEDVDAAFVSRDLNKQNPTAYQG-----MGRLTFS 310

Query: 320 GLLNFTDGLWSSCGDERII 338
           GLLN  DG+ S+  + RI+
Sbjct: 311 GLLNALDGVAST--EARIV 327

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

Xenopus laevis (taxid: 8355)

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

 Score = 62.0 bits (149), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 135/302 (44%), Gaps = 44/302 (14%)

Query: 68  LFKAAKLYLEPKIPPNVN-RIKINLPKKESEV---------SLSVEKNQAVFDVFNGVRL 117
           +FK    Y+  +I  N+  RI ++   K  E          S+ V  +     V+N V  
Sbjct: 30  IFKNVGQYILNRINSNIYYRIDVDSKDKSFEWLLYWLSENDSIKVSNHLNAETVYNLVGK 89

Query: 118 KWKFELKPAPDQE-LCNNGNYMFKDRV--PCFELRFHKKHKETVLGTY------IPHILK 168
             K  L P+  +  +   G +++ DRV    F++      +   + TY      I  +L+
Sbjct: 90  NPKVILVPSVGKHRIVYKGKWIWIDRVRDQQFDMGAGAPFESISISTYKSNAQLINQLLQ 149

Query: 169 KSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLA---MDTDMKKMIMDDLE- 224
           ++  LS  +   K        IN          +P +  +L+   +  D+K  +++D++ 
Sbjct: 150 EAMTLSLNRDIGKTVIY----INGGNGNWERFGNPRSIRSLSSVILADDLKSKLIEDIKS 205

Query: 225 ----RAW--------KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-GNKHLR 271
                +W        +RGYLL+G PG GKSSLI A+A  L+ D+  + LSS +  +K + 
Sbjct: 206 FITNESWYRNRGIPYRRGYLLYGEPGNGKSSLINAIAGELNLDICIVSLSSKDIDDKQIN 265

Query: 272 KVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS 331
            +L     KSIL++ DID       +S +    S + +S   + +T SGLLN  DG+ S 
Sbjct: 266 HLLNNAPPKSILLIEDIDAAF----KSHRDNVDSNNNNSNNNNSLTYSGLLNALDGVASQ 321

Query: 332 CG 333
            G
Sbjct: 322 EG 323

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

Dictyostelium discoideum (taxid: 44689)

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

 Score = 58.2 bits (139), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 49/187 (26%), Positives = 93/187 (49%), Gaps = 22/187 (11%)

Query: 166 ILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER 225
           IL++++EL+ K++  +  T+    +  + R            ++ +++ + + I+DD++ 
Sbjct: 150 ILQEARELALKQEEGR--TVMYTAMGAEWRPFGFPRRRRPLSSVVLESGVAERIVDDVKE 207

Query: 226 -------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-GNKHLR 271
                         ++RGYLL+GPPG GKSS I A+A  L + +  + LS     +  L 
Sbjct: 208 FIGNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELGYSICLMSLSDRSLSDDRLN 267

Query: 272 KVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS 331
            +L     +SI+++ D+D     ++      T +P  +     ++T SGLLN  DG+ SS
Sbjct: 268 HLLSVAPQQSIILLEDVDAAFVSRELLP---TENPLAYQ-GMGRLTFSGLLNALDGVASS 323

Query: 332 CGDERII 338
             + RI+
Sbjct: 324 --EARIV 328

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 = 55.5 bits (132), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 60/251 (23%), Positives = 114/251 (45%), Gaps = 41/251 (16%)

Query: 116 RLKWKFELKPAPDQE-LCNNGNYMFKDR---VPCFELRFHKKHKE---TVLGT---YIPH 165
           R+  KFE  P+P    +   G ++  +R   +   +L+     +    T LGT      +
Sbjct: 90  RISTKFEFVPSPGNHFIWYQGKWIRVERSREMQMIDLQTGTPWESVTFTALGTDRKVFFN 149

Query: 166 ILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER 225
           IL++++EL+ +++  K  T+    +  + R           +++ ++  + + I+ D+  
Sbjct: 150 ILEEARELALQQEEGK--TVMYTAVGSEWRPFGYPRRRRPLNSVVLEQGVTERIVRDIRE 207

Query: 226 -------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDV-YDLELSSVEGNKHLR 271
                         ++RGYLL+GPPG GKSS I A+A  L   +       S   +  L 
Sbjct: 208 FIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELQHSICLLSLTDSSLSDDRLN 267

Query: 272 KVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQ----ITLSGLLNFTDG 327
            +L     +S++++ D+D     +D +A+         +P + Q    +T SGLLN  DG
Sbjct: 268 HLLSVAPQQSLVLLEDVDAAFLSRDLAAE---------NPIKYQGLGRLTFSGLLNALDG 318

Query: 328 LWSSCGDERII 338
           + S+  + RI+
Sbjct: 319 VAST--EARIV 327

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

 Score = 53.1 bits (126), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/251 (23%), Positives = 112/251 (44%), Gaps = 41/251 (16%)

Query: 116 RLKWKFELKPAPDQE-LCNNGNYMFKDR---VPCFELRFHKKHKE---TVLGT---YIPH 165
           R+  KFE  P+P    +   G ++  +R   +   +L+     +    T LGT      +
Sbjct: 90  RISTKFEFVPSPGNHFIWYRGKWIRVERSREMQMIDLQTGTPWESVTFTALGTDRKVFFN 149

Query: 166 ILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER 225
           IL++++EL+ +++  K  T+    +  + R           +++ +   +   I+ D++ 
Sbjct: 150 ILEEARELALQQEEGK--TVMYTAVGSEWRPFGYPRRRRPLNSVVLQQGLADRIVRDVQE 207

Query: 226 -------------AWKRGYLLFGPPGTGKSSLIAAMANYL-HFDVYDLELSSVEGNKHLR 271
                         ++RGYLL+GPPG GKSS I A+A  L H         S   +  L 
Sbjct: 208 FIDNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSSLSDDRLN 267

Query: 272 KVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQ----ITLSGLLNFTDG 327
            +L     +S++++ D+D     +D + +         +P + Q    +T SGLLN  DG
Sbjct: 268 HLLSVAPQQSLVLLEDVDAAFLSRDLAVE---------NPVKYQGLGRLTFSGLLNALDG 318

Query: 328 LWSSCGDERII 338
           + S+  + RI+
Sbjct: 319 VAST--EARIV 327

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

Homo sapiens (taxid: 9606)

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

 Score = 52.4 bits (124), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 60/251 (23%), Positives = 110/251 (43%), Gaps = 41/251 (16%)

Query: 116 RLKWKFELKPAPDQE-LCNNGNYMFKDR---VPCFELRFHKKHKE---TVLGT---YIPH 165
           R+  KFE  P+P    +   G ++  +R   +   +L+     +    T LGT      +
Sbjct: 90  RISTKFEFIPSPGNHFIWYQGKWIRVERNRDMQMVDLQTGTPWESVTFTALGTDRKVFFN 149

Query: 166 ILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER 225
           IL++++ L+ +++  K  T+    +  + R           D++ +   +   I+ D+  
Sbjct: 150 ILEEARALALQQEEGK--TVMYTAVGSEWRTFGYPRRRRPLDSVVLQQGLADRIVKDIRE 207

Query: 226 -------------AWKRGYLLFGPPGTGKSSLIAAMANYL-HFDVYDLELSSVEGNKHLR 271
                         ++RGYLL+GPPG GKSS I A+A  L H         S   +  L 
Sbjct: 208 FIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSSLSDDRLN 267

Query: 272 KVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQ----ITLSGLLNFTDG 327
            +L     +S++++ D+D     +D + +         +P + Q    +T SGLLN  DG
Sbjct: 268 HLLSVAPQQSLVLLEDVDAAFLSRDLAVE---------NPIKYQGLGRLTFSGLLNALDG 318

Query: 328 LWSSCGDERII 338
           + S+  + RI+
Sbjct: 319 VAST--EARIV 327

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|P60373|RFCL_NANEQ Replication factor C large subunit OS=Nanoarchaeum equitans (strain Kin4-M) GN=rfcL PE=3 SV=1

 Score = 47.8 bits (112), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 57/109 (52%), Gaps = 13/109 (11%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRGY-----LLFGPPGTGKSSLIAAMANYLHFDVY 257
           P T D +  + +  K I+ D    +K+ Y     LL+GPPGTGK+S + A+AN L ++V 
Sbjct: 39  PKTLDEVE-NQEQAKQILRDYVINYKKKYKGKALLLYGPPGTGKTSSVYALANELGYEVL 97

Query: 258 DLELSSVEGNKHLRKVLI-ATENK------SILVVGDIDCCTELQDRSA 299
           ++  S      H+  ++  A++ K       I++V ++D  +  +DR  
Sbjct: 98  EVNASDERDAIHIHHIVGEASKGKPLFHKGRIILVDEVDGLSGKEDRGG 146

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Nanoarchaeum equitans (strain Kin4-M) (taxid: 228908)

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	338
225428414	488	PREDICTED: ATP-dependent zinc metallopro	0.991	0.686	0.530	8e-96
255543747	501	ATP binding protein, putative [Ricinus c	0.982	0.662	0.567	2e-94
225428416	494	PREDICTED: ATP-dependent zinc metallopro	0.997	0.682	0.519	4e-94
224105359	457	predicted protein [Populus trichocarpa]	0.997	0.737	0.562	2e-93
118486313	539	unknown [Populus trichocarpa]	0.997	0.625	0.559	6e-93
255561048	528	ATP binding protein, putative [Ricinus c	0.997	0.638	0.466	9e-87
449464546	480	PREDICTED: uncharacterized protein LOC10	0.994	0.7	0.471	4e-86
449464544	501	PREDICTED: uncharacterized protein LOC10	0.994	0.670	0.471	4e-86
449520948	480	PREDICTED: uncharacterized protein LOC10	0.994	0.7	0.471	4e-86
449520946	501	PREDICTED: uncharacterized protein LOC10	0.994	0.670	0.471	4e-86

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

 Score =  356 bits (914), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 189/356 (53%), Positives = 246/356 (69%), Gaps = 21/356 (5%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           MPS  T++S AAS A + MLI+S  R  +P E+  Y   +F+  +    SE TLVIEE+D
Sbjct: 1   MPSTKTMISAAASLAGSAMLIRSIIRDLIPPELQHYLFSRFRGLLGSFTSEFTLVIEEFD 60

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
            G   N+LF+AA++YL   I PN  R+++ LP KES++S+++++N+ V D FNGV LKW 
Sbjct: 61  -GFGHNQLFRAAEVYLGSVISPNAQRLRVTLPNKESKMSVTMDRNEDVADTFNGVSLKWT 119

Query: 121 FELKPAPDQELCNNGNY--MFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKK 178
           F  +  P +   +  NY  M K  +  F+L FHKKHK+TVL  Y+P++L+K K + +  K
Sbjct: 120 FISRSIPTRYFNDPDNYYSMAKSELKFFQLSFHKKHKQTVLEAYLPYVLEKYKAMKETNK 179

Query: 179 TLKLFTLNCNRI---NHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER---------- 225
           TLK+ TL   R+   + D  QS  LDHP+TFDTLAMD+++K+ +M+DLER          
Sbjct: 180 TLKIHTLKFERLQGGSSDPWQSVKLDHPATFDTLAMDSELKRTLMNDLERFVRRKGFYRK 239

Query: 226 ---AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSI 282
              AWKRGYLLFGPPGTGKSSLIAAMANYL+FD+YDLEL+ +  N  LRK+LI+T N+SI
Sbjct: 240 VGKAWKRGYLLFGPPGTGKSSLIAAMANYLNFDIYDLELTDLRCNSELRKLLISTANRSI 299

Query: 283 LVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
           LVV DIDC  ELQDR AQAR  +P  H  +  Q+TLSGLLNF DGLWSSCGDERII
Sbjct: 300 LVVEDIDCSLELQDRLAQARMMNP--HRYQTSQVTLSGLLNFIDGLWSSCGDERII 353

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  352 bits (902), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 206/363 (56%), Positives = 254/363 (69%), Gaps = 31/363 (8%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           +PS   ++S AASAAAT ML+++  + YLP E+  Y   K KNF     SE T VIEEYD
Sbjct: 10  IPSTKAILSTAASAAATAMLLRTVAKDYLPSELRHYIYDKVKNFFNSFSSELTFVIEEYD 69

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
           + LN N LF+AA+LYLEP IPPN+ R+KI+LPKKES+V++S+E+N+ + D FNGV LKWK
Sbjct: 70  N-LNDNHLFRAAELYLEPIIPPNLKRLKISLPKKESKVTVSLERNEEIIDTFNGVTLKWK 128

Query: 121 F---ELK----PAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKEL 173
           F   E++    P+PD       N M       FEL FH KHK+ VL  YI H+++KSKE+
Sbjct: 129 FISREVRVKYIPSPDHY-----NSMPVTDHRFFELTFHNKHKDMVLDAYIKHVIQKSKEI 183

Query: 174 SKKKKTLKLFTLNCNRINH---DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER----- 225
             KKKTLKLFTL  +R+     D  QS  L+HP+TFDTLAMD D+K++IM+DLER     
Sbjct: 184 KDKKKTLKLFTLGQDRMTGRRGDAWQSVNLEHPATFDTLAMDMDVKRVIMEDLERFVKRK 243

Query: 226 --------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIAT 277
                   AWKRGYLLFGPPGTGKSSLIAAMANYL FD+YDLEL+ +  N  LR++LI+T
Sbjct: 244 EFYKRVGKAWKRGYLLFGPPGTGKSSLIAAMANYLKFDIYDLELTDLRTNSDLRRLLIST 303

Query: 278 ENKSILVVGDIDCCTELQDRSAQARTASP-DWHSPKRD-QITLSGLLNFTDGLWSSCGDE 335
            NKSILVV DIDC  ELQ+R  +AR  +    H   RD Q+TLSGLLNF DGLWSSCGDE
Sbjct: 304 GNKSILVVEDIDCSIELQNRITEARALNARQGHGYVRDNQVTLSGLLNFVDGLWSSCGDE 363

Query: 336 RII 338
           R+I
Sbjct: 364 RVI 366

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  350 bits (899), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 187/360 (51%), Positives = 245/360 (68%), Gaps = 23/360 (6%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           MPS  T++S AAS A + MLI+S  R  +P E+  Y   +F+  +    SE TLVIEE+D
Sbjct: 1   MPSTKTMISAAASLAGSAMLIRSIIRDLIPPELQHYLFSRFRGLLGSFTSEFTLVIEEFD 60

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
            G   N+LF+AA++YL   I PN  R+++ LP KES++S+++++N+ V D FNGV LKW 
Sbjct: 61  -GFGHNQLFRAAEVYLGSVISPNAQRLRVTLPNKESKMSVTMDRNEDVADTFNGVSLKWT 119

Query: 121 FELKPAPDQELCNNGNY--MFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKK 178
           F  +  P +   +  NY  M K  +  F+L FHKKHK+TVL  Y+P++L+K K + +  K
Sbjct: 120 FISRSIPTRYFNDPDNYYSMAKSELKFFQLSFHKKHKQTVLEAYLPYVLEKYKAMKETNK 179

Query: 179 TLKLFTLNCNRI---NHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER---------- 225
           TLK+ TL   R+   + D  QS  LDHP+TFDTLAMD+++K+ +M+DLER          
Sbjct: 180 TLKIHTLKFERLQGGSSDPWQSVKLDHPATFDTLAMDSELKRTLMNDLERFVRRKGFYRK 239

Query: 226 ---AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSI 282
              AWKRGYLLFGPPGTGKSSLIAAMANYL+FD+YDLEL+ +  N  LRK+LI+T N+SI
Sbjct: 240 VGKAWKRGYLLFGPPGTGKSSLIAAMANYLNFDIYDLELTDLRCNSELRKLLISTANRSI 299

Query: 283 LVVGDIDCCTELQDRSAQARTASPDWHSPKR----DQITLSGLLNFTDGLWSSCGDERII 338
           LVV DIDC  ELQDR AQAR  +P  +   +      +TLSGLLNF DGLWSSCGDERII
Sbjct: 300 LVVEDIDCSLELQDRLAQARMMNPHRYQTSQVHLSKSVTLSGLLNFIDGLWSSCGDERII 359

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  348 bits (892), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 202/359 (56%), Positives = 252/359 (70%), Gaps = 22/359 (6%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           +PS  T++S AASAAAT +L +S  + +LP E  SY   K K  I    SE TLVIEEYD
Sbjct: 7   IPSAKTMISAAASAAATIVLFRSLVKEHLPYEFQSYIFYKLKTLINSFSSEFTLVIEEYD 66

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
           + LN N LFKAA+LYLEP IPP+  ++KI+L KKES+ S S+++NQ + D FNG+ LKWK
Sbjct: 67  N-LNHNNLFKAAELYLEPIIPPDAKKLKISLTKKESKFSFSLDRNQEIVDTFNGITLKWK 125

Query: 121 FELKPAPDQELC--NNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKK 178
           F  K  P + +   +N N M K     FEL FHKKHK+ V+  Y+ H+++KSKE  ++KK
Sbjct: 126 FISKQVPIKYIPSPDNFNSMPKSEDKFFELSFHKKHKDVVIDVYLKHVIEKSKETKEEKK 185

Query: 179 TLKLFTLNCNRINH---DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER---------- 225
           +LKLF+L  +R++    D  QS  L HP+TFDTLAMD + K++IM+DLER          
Sbjct: 186 SLKLFSLRHDRMSGRRGDVWQSVNLHHPATFDTLAMDMEGKRVIMEDLERFVKRREFYRR 245

Query: 226 ---AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSI 282
              AWKRGYLLFGPPGTGKSSLIAA+ANYL FD+YDLEL+ +  N  LR +LI+TENKS+
Sbjct: 246 VGKAWKRGYLLFGPPGTGKSSLIAAIANYLKFDIYDLELTDLRTNSELRNLLISTENKSV 305

Query: 283 LVVGDIDCCTELQDRSAQARTASPDWHSP---KRDQITLSGLLNFTDGLWSSCGDERII 338
           LVV DIDC  ELQDR AQAR   P  H P   + +Q+TLSGLLNF DGLWSSCGDERII
Sbjct: 306 LVVEDIDCSIELQDRLAQARAMMPSRHHPPYNQANQVTLSGLLNFVDGLWSSCGDERII 364

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  347 bits (889), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 202/361 (55%), Positives = 251/361 (69%), Gaps = 24/361 (6%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           +PS  T++S AASAAAT +L +S  + +LP E  SY   K K  I    SE TLVIEEYD
Sbjct: 10  IPSAKTMISAAASAAATIVLFRSLVKEHLPYEFQSYIFYKLKTLINSFSSEFTLVIEEYD 69

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
           + LN N LFKAA+LYLEP IPP+  ++KI+L KKES+ S S+++NQ + D FNG+ LKWK
Sbjct: 70  N-LNHNNLFKAAELYLEPIIPPDAKKLKISLTKKESKFSFSLDRNQEIVDTFNGITLKWK 128

Query: 121 FELKPAPDQELC--NNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKK 178
           F  K  P + +   +N N M K     FEL FHKKHK+ V+  Y+ H+++KSKE  ++KK
Sbjct: 129 FISKQVPIKYIPSPDNFNSMPKSEDKFFELSFHKKHKDVVIDVYLKHVIEKSKETKEEKK 188

Query: 179 TLKLFTLNCNRINH---DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER---------- 225
           +LKLF+L  +R++    D  QS  L HP+TFDTLAMD + K++IM+DLER          
Sbjct: 189 SLKLFSLRHDRMSGRRGDVWQSVNLHHPATFDTLAMDMEGKRVIMEDLERFVKRREFYRR 248

Query: 226 ---AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSI 282
              AWKRGYLLFGPPGTGKSSLIAA+ANYL FD+YDLEL+ +  N  LR +LI+TENKS+
Sbjct: 249 VGKAWKRGYLLFGPPGTGKSSLIAAIANYLKFDIYDLELTDLRTNSELRNLLISTENKSV 308

Query: 283 LVVGDIDCCTELQDRSAQARTASPDWHSPKRD-----QITLSGLLNFTDGLWSSCGDERI 337
           LVV DIDC  ELQDR AQAR   P  H P  +     Q+TLSGLLNF DGLWSSCGDERI
Sbjct: 309 LVVEDIDCSIELQDRLAQARAMMPSRHHPPYNQANQYQVTLSGLLNFVDGLWSSCGDERI 368

Query: 338 I 338
           I
Sbjct: 369 I 369

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  326 bits (836), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 166/356 (46%), Positives = 231/356 (64%), Gaps = 19/356 (5%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           + +  TV+S AAS AAT ML +S  +  LP E   YF    +  + R  S+ T+V++E+D
Sbjct: 10  LATAKTVLSTAASVAATVMLARSVAQDILPYEFHDYFLFNIRKILGRFSSQITMVVDEFD 69

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
            G   N++++AA+ YL   I P+  R K++ P+KE  +++ +E N+ + DV+ GV+ KW 
Sbjct: 70  -GFVHNQIYEAAETYLASNISPSTRRFKVSKPEKEKNLTVKMEGNEEIIDVYRGVKFKWI 128

Query: 121 FELKPAPDQELCN--NGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKK 178
           F       + L +  + N   +  V  FE+ F KKHKE  L +Y+PHI+++++ + ++KK
Sbjct: 129 FVCSQVESRNLHHPFDHNATLRSEVRSFEVSFPKKHKEMALESYLPHIVREAESMVQEKK 188

Query: 179 TLKLFTLNCNRIN---HDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER---------- 225
           TL++F+++ + I     D  +   LDHP+TF TLA+D  +K  I++DLER          
Sbjct: 189 TLRIFSVDYDNIYGNLADAWKPVNLDHPATFQTLALDAQLKGTILEDLERFVKRKDYYRK 248

Query: 226 ---AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSI 282
              AWKRGYLL+GPPGTGKSSLIAAMANYL FD+YDLEL+ +  N  LRK+LIAT N+SI
Sbjct: 249 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDIYDLELTELRCNSELRKLLIATANRSI 308

Query: 283 LVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
           LVV DIDC  E QDR A+A  A    H P + Q+TLSGLLNF DGLWSSCGDERII
Sbjct: 309 LVVEDIDCTIEFQDRLAEANAAEFHAHYPPQKQVTLSGLLNFIDGLWSSCGDERII 364

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464546|ref|XP_004149990.1| PREDICTED: uncharacterized protein LOC101205613 isoform 2 [Cucumis sativus]

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 167/354 (47%), Positives = 230/354 (64%), Gaps = 18/354 (5%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           +P+   +++ AAS AAT +L++S     LP E   YF    +   +R  S+ T+V++E D
Sbjct: 12  LPNAKAILTAAASFAATVLLLRSIANDLLPSEFREYFYDGIRTIFSRFSSQLTMVVDEMD 71

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
            GL  N++++AA++YL  KI P+  R+K++ P+KE  ++ +VE+N+ V D FNGV+  W 
Sbjct: 72  -GLGPNQIYEAAEIYLATKISPSTARLKVSKPEKEDNITTAVERNEEVVDTFNGVKFHWV 130

Query: 121 FELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTL 180
              +    +E  +N    ++  +  FEL FHKKH+E VL +Y+PHIL ++KEL ++ KTL
Sbjct: 131 LVCEQV-QRENFHNPRSPYRSVIRSFELCFHKKHREMVLKSYLPHILHQAKELKQQTKTL 189

Query: 181 KLFTLNCNRINHDTRQSAI---LDHPSTFDTLAMDTDMKKMIMDDLER------------ 225
           K++T +   +        I   LDHPSTF+ LAMD+++K  I++DLER            
Sbjct: 190 KIYTFDYQNMYGSISDLWIPTNLDHPSTFEKLAMDSEIKHFILNDLERFVKRKKYYEKVG 249

Query: 226 -AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILV 284
            AWKRGYLL+GPPGTGKSSLIAAMANYL FDVYDLEL+ VE N  LRK+L+   N+SILV
Sbjct: 250 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELTGVECNSDLRKLLMGIANRSILV 309

Query: 285 VGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
           V DIDC  E QDR ++         S +R  +TLSGLLNF DGLWSSCGDERII
Sbjct: 310 VEDIDCSVEFQDRDSEKDEEEDPSTSRRRRLVTLSGLLNFIDGLWSSCGDERII 363

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464544|ref|XP_004149989.1| PREDICTED: uncharacterized protein LOC101205613 isoform 1 [Cucumis sativus]

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 167/354 (47%), Positives = 230/354 (64%), Gaps = 18/354 (5%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           +P+   +++ AAS AAT +L++S     LP E   YF    +   +R  S+ T+V++E D
Sbjct: 12  LPNAKAILTAAASFAATVLLLRSIANDLLPSEFREYFYDGIRTIFSRFSSQLTMVVDEMD 71

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
            GL  N++++AA++YL  KI P+  R+K++ P+KE  ++ +VE+N+ V D FNGV+  W 
Sbjct: 72  -GLGPNQIYEAAEIYLATKISPSTARLKVSKPEKEDNITTAVERNEEVVDTFNGVKFHWV 130

Query: 121 FELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTL 180
              +    +E  +N    ++  +  FEL FHKKH+E VL +Y+PHIL ++KEL ++ KTL
Sbjct: 131 LVCEQV-QRENFHNPRSPYRSVIRSFELCFHKKHREMVLKSYLPHILHQAKELKQQTKTL 189

Query: 181 KLFTLNCNRINHDTRQSAI---LDHPSTFDTLAMDTDMKKMIMDDLER------------ 225
           K++T +   +        I   LDHPSTF+ LAMD+++K  I++DLER            
Sbjct: 190 KIYTFDYQNMYGSISDLWIPTNLDHPSTFEKLAMDSEIKHFILNDLERFVKRKKYYEKVG 249

Query: 226 -AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILV 284
            AWKRGYLL+GPPGTGKSSLIAAMANYL FDVYDLEL+ VE N  LRK+L+   N+SILV
Sbjct: 250 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELTGVECNSDLRKLLMGIANRSILV 309

Query: 285 VGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
           V DIDC  E QDR ++         S +R  +TLSGLLNF DGLWSSCGDERII
Sbjct: 310 VEDIDCSVEFQDRDSEKDEEEDPSTSRRRRLVTLSGLLNFIDGLWSSCGDERII 363

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520948|ref|XP_004167494.1| PREDICTED: uncharacterized protein LOC101229933 isoform 2 [Cucumis sativus]

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 167/354 (47%), Positives = 230/354 (64%), Gaps = 18/354 (5%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           +P+   +++ AAS AAT +L++S     LP E   YF    +   +R  S+ T+V++E D
Sbjct: 12  LPNAKAILTAAASFAATVLLLRSIANDLLPSEFREYFYDGIRTIFSRFSSQLTMVVDEMD 71

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
            GL  N++++AA++YL  KI P+  R+K++ P+KE  ++ +VE+N+ V D FNGV+  W 
Sbjct: 72  -GLGPNQIYEAAEIYLATKISPSTARLKVSKPEKEDNITTAVERNEEVVDTFNGVKFHWV 130

Query: 121 FELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTL 180
              +    +E  +N    ++  +  FEL FHKKH+E VL +Y+PHIL ++KEL ++ KTL
Sbjct: 131 LVCEQV-QRENFHNPRSPYRSVIRSFELCFHKKHREMVLKSYLPHILHQAKELKQQTKTL 189

Query: 181 KLFTLNCNRINHDTRQSAI---LDHPSTFDTLAMDTDMKKMIMDDLER------------ 225
           K++T +   +        I   LDHPSTF+ LAMD+++K  I++DLER            
Sbjct: 190 KIYTFDYQNMYGSISDLWIPTNLDHPSTFEKLAMDSEIKHFILNDLERFVKRKKYYEKVG 249

Query: 226 -AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILV 284
            AWKRGYLL+GPPGTGKSSLIAAMANYL FDVYDLEL+ VE N  LRK+L+   N+SILV
Sbjct: 250 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELTGVECNSDLRKLLMGIANRSILV 309

Query: 285 VGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
           V DIDC  E QDR ++         S +R  +TLSGLLNF DGLWSSCGDERII
Sbjct: 310 VEDIDCSVEFQDRDSEKDEEEDPSTSRRRRLVTLSGLLNFIDGLWSSCGDERII 363

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520946|ref|XP_004167493.1| PREDICTED: uncharacterized protein LOC101229933 isoform 1 [Cucumis sativus]

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 167/354 (47%), Positives = 230/354 (64%), Gaps = 18/354 (5%)

Query: 1   MPSMTTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYD 60
           +P+   +++ AAS AAT +L++S     LP E   YF    +   +R  S+ T+V++E D
Sbjct: 12  LPNAKAILTAAASFAATVLLLRSIANDLLPSEFREYFYDGIRTIFSRFSSQLTMVVDEMD 71

Query: 61  DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWK 120
            GL  N++++AA++YL  KI P+  R+K++ P+KE  ++ +VE+N+ V D FNGV+  W 
Sbjct: 72  -GLGPNQIYEAAEIYLATKISPSTARLKVSKPEKEDNITTAVERNEEVVDTFNGVKFHWV 130

Query: 121 FELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELSKKKKTL 180
              +    +E  +N    ++  +  FEL FHKKH+E VL +Y+PHIL ++KEL ++ KTL
Sbjct: 131 LVCEQV-QRENFHNPRSPYRSVIRSFELCFHKKHREMVLKSYLPHILHQAKELKQQTKTL 189

Query: 181 KLFTLNCNRINHDTRQSAI---LDHPSTFDTLAMDTDMKKMIMDDLER------------ 225
           K++T +   +        I   LDHPSTF+ LAMD+++K  I++DLER            
Sbjct: 190 KIYTFDYQNMYGSISDLWIPTNLDHPSTFEKLAMDSEIKHFILNDLERFVKRKKYYEKVG 249

Query: 226 -AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILV 284
            AWKRGYLL+GPPGTGKSSLIAAMANYL FDVYDLEL+ VE N  LRK+L+   N+SILV
Sbjct: 250 KAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELTGVECNSDLRKLLMGIANRSILV 309

Query: 285 VGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
           V DIDC  E QDR ++         S +R  +TLSGLLNF DGLWSSCGDERII
Sbjct: 310 VEDIDCSVEFQDRDSEKDEEEDPSTSRRRRLVTLSGLLNFIDGLWSSCGDERII 363

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	338
TAIR|locus:2078007	451	AT3G50940 [Arabidopsis thalian	0.920	0.689	0.411	8.1e-60
TAIR|locus:2175956	533	AT5G17740 [Arabidopsis thalian	0.937	0.594	0.385	8e-53
TAIR|locus:1005716649	495	AT2G18193 [Arabidopsis thalian	0.896	0.612	0.388	2.7e-52
TAIR|locus:2175946	470	AT5G17730 [Arabidopsis thalian	0.920	0.661	0.369	1.9e-51
TAIR|locus:2053109	494	AT2G18190 [Arabidopsis thalian	0.905	0.619	0.370	2.3e-48
TAIR|locus:2174502	520	AT5G57480 [Arabidopsis thalian	0.822	0.534	0.337	5.3e-45
TAIR|locus:2077997	576	BCS1 "cytochrome BC1 synthesis	0.600	0.352	0.472	1.2e-44
TAIR|locus:2175976	392	AT5G17750 [Arabidopsis thalian	0.754	0.650	0.391	1.9e-44
TAIR|locus:2175986	505	AT5G17760 [Arabidopsis thalian	0.550	0.368	0.480	2.8e-41
TAIR|locus:2095512	500	AT3G28580 [Arabidopsis thalian	0.855	0.578	0.328	2.6e-40

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

 Score = 613 (220.8 bits), Expect = 8.1e-60, P = 8.1e-60
 Identities = 138/335 (41%), Positives = 191/335 (57%)

Query:    19 MLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEP 78
             +L +S  + Y+P+EV  Y    F+ F +    + T VIEE+  G   N++F+AA+ YL  
Sbjct:    27 ILARSVVQDYMPNEVHEYISHGFRRFFSYFSYQMTAVIEEFG-GFEHNQVFEAAEAYLST 85

Query:    79 KIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCN--NGN 136
             KI  +  RIK+N  +K+S  S++VE+++ V D+F+GV+L W    +    ++  N  + N
Sbjct:    86 KISNSTRRIKVNKLEKQSNYSVTVERDEEVVDIFDGVKLSWILVCRHVDKKDFRNPRDLN 145

Query:   137 YMFKDRVPCFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRINHDTRQ 196
                K  V  +EL F KK K  VL +Y+P +                   +   +      
Sbjct:   146 STLKSEVRSYELSFRKKFKNMVLESYLPFVVEQAASIKQKFKTLKIFTVDSYSVEWT--- 202

Query:   197 SAILDHPSTFDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPGTGKSS 243
             S  LDHPSTF TLA            L+R             AWKRGYLL+GPPGTGKSS
Sbjct:   203 SVTLDHPSTFRTLALDPEVKKNLVEDLDRFVQRKGFYGRVGKAWKRGYLLYGPPGTGKSS 262

Query:   244 LIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQART 303
             LIAA+AN+L+FD+YDL+L+S+  N  LR++L++T N+SILVV DIDC  EL+DRS     
Sbjct:   263 LIAAIANHLNFDIYDLDLTSLNNNAELRRLLMSTANRSILVVEDIDCSIELKDRSTDQEN 322

Query:   304 ASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
                  + P    +TLSGLLNF DGLWSSCG+ERII
Sbjct:   323 -----NDPLHKTVTLSGLLNFVDGLWSSCGNERII 352

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:2175956 AT5G17740 [Arabidopsis thaliana (taxid:3702)]

 Score = 547 (197.6 bits), Expect = 8.0e-53, P = 8.0e-53
 Identities = 129/335 (38%), Positives = 179/335 (53%)

Query:    19 MLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEP 78
             M+I+      +P  V ++     K+F     S  TL I++       ++L+ AA+ YL  
Sbjct:    25 MIIKPMINTIIPRPVQNFVFSYLKSFAGSRSSTLTLTIDQMSSMYIPDELYAAAQAYLST 84

Query:    79 KIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNG-NY 137
             KI PN  R+ +     E +V L +   + V DV+NG++LKW+F  +   +  +   G +Y
Sbjct:    85 KISPNSVRLIMARDPAEKKVKLYLSDGEVVSDVYNGIKLKWRFLARNKNNTMVEEYGQSY 144

Query:   138 MFKDRVPCFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRINHDTRQS 197
                 +    EL F KKH++ V+ +YIP++                   +C      T QS
Sbjct:   145 QGNIQRESLELSFDKKHRDLVVNSYIPYVESKAKEVNNKRRILKM---HCYSHMAQTWQS 201

Query:   198 AILDHPSTFDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPGTGKSSL 244
                 HPSTFDT+A            L+R             AWKRGYLL+GPPGTGKSSL
Sbjct:   202 VNFKHPSTFDTMAMNDDLKRSMIEDLDRFVGRKDFYKRVGKAWKRGYLLYGPPGTGKSSL 261

Query:   245 IAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDR-SAQART 303
             +AAMANYL FD+YDL+L+SV+G+ HLR +L+AT N SIL++ DIDC  +L  R      T
Sbjct:   262 VAAMANYLKFDIYDLQLASVQGDAHLRSLLLATNNSSILLIEDIDCSVDLPTRLQPPTET 321

Query:   304 ASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
             + P         +TLSGLLN  DGLWSSCG+ERII
Sbjct:   322 SQPLGAVQVSKPLTLSGLLNCIDGLWSSCGNERII 356

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 = 542 (195.9 bits), Expect = 2.7e-52, P = 2.7e-52
 Identities = 132/340 (38%), Positives = 186/340 (54%)

Query:    19 MLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEP 78
             ML +S    ++P+++ SYF      F        T++I+E + GLNRN++F AA++YL  
Sbjct:    26 MLFRSMLHDFVPEKLRSYFSSLLDRFFTPKSKYLTVIIDE-NFGLNRNQVFDAAEMYLRS 84

Query:    79 KIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYM 138
             KI P   R+++    K+   ++S+E+ + + D F    +KW +       Q     G   
Sbjct:    85 KIGPETERLRVGKIPKQKHFTISIERGEEILDTFEESEVKWSYV------QSENEKG--- 135

Query:   139 FKDRVP-CFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRINHDTRQS 197
               D+V   +EL F KK ++ VL +Y+ H+                   +    + D   +
Sbjct:   136 --DKVKRYYELTFEKKLRDKVLNSYLTHVVAESEEIKRNLRVVKLYSRDVYASDDDDGMA 193

Query:   198 A------ILDHPSTFDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPG 238
                     L+HPSTFDTLA            LER             AWKRGYLL+GPPG
Sbjct:   194 GGNWGCINLEHPSTFDTLAMDPNAKKKIIDDLERFLKRKEFYKRVGKAWKRGYLLYGPPG 253

Query:   239 TGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRS 298
             TGKSSLIAAMANYL FDV+DLELSS+  N  L++VL++T N+SILV+ DIDC  E++DR 
Sbjct:   254 TGKSSLIAAMANYLKFDVFDLELSSIYDNGELKRVLLSTTNRSILVIEDIDCNAEVRDRE 313

Query:   299 AQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
             A+ +    D     + ++TLSG+LNF DGLWSS GDERII
Sbjct:   314 AENQE---D--EQIKGKVTLSGILNFIDGLWSSFGDERII 348

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:2175946 AT5G17730 [Arabidopsis thaliana (taxid:3702)]

 Score = 534 (193.0 bits), Expect = 1.9e-51, P = 1.9e-51
 Identities = 124/336 (36%), Positives = 181/336 (53%)

Query:    19 MLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEP 78
             M+I+ +  + +P  + +Y      +F+    S  TL+I+++      N+L+ AA++Y+  
Sbjct:    25 MMIKPFLEMTIPPPLQNYMISYLNSFLHSTPSTLTLIIDDHIKNGMYNELYGAAQVYIST 84

Query:    79 KIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYM 138
             K+  N  R++I+  + E  V++     + V D++ G+ +KW+F +       +   G + 
Sbjct:    85 KVNHNAERLRISRDRSEKNVNIHFSVGEVVSDIYQGIEVKWRFCVDSNKSNMVHYFGEH- 143

Query:   139 FK---DRVPCFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRINHDTR 195
             FK   DR  C EL F KKH E VL +YIP++                    C  +     
Sbjct:   144 FKLNPDR-ECVELSFEKKHTELVLNSYIPYVESKAKVINNERKILKMYSYCCMYLKW--- 199

Query:   196 QSAILDHPSTFDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPGTGKS 242
             QS  L+HPSTFDT+A            L+R              WKRGYLL+GPPGTGK+
Sbjct:   200 QSVNLEHPSTFDTMAMNEELKRSVMGDLDRFIRRKDFYKRVGKPWKRGYLLYGPPGTGKT 259

Query:   243 SLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQAR 302
             SL+AA+ANYL FD+YDL+L+SV  +  LR++L+ T N SIL+V DIDC  +L  R  Q +
Sbjct:   260 SLVAAIANYLKFDIYDLQLASVREDADLRRLLLGTTNSSILLVEDIDCAVDLHTR-LQPK 318

Query:   303 TASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
             T      S     +TLSGLL   DGLWSSCGDERI+
Sbjct:   319 TQDDTKGS---SMLTLSGLLTCIDGLWSSCGDERIV 351

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:2053109 AT2G18190 [Arabidopsis thaliana (taxid:3702)]

 Score = 505 (182.8 bits), Expect = 2.3e-48, P = 2.3e-48
 Identities = 126/340 (37%), Positives = 176/340 (51%)

Query:    19 MLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEP 78
             ML +S     +P+ + SY       F        T+VI+E   G  RN++F AA++YL  
Sbjct:    27 MLFRSLFNDEVPERLRSYITDLLNRFFTPKSKNLTMVIDEII-GFKRNQVFDAAEVYLRN 85

Query:    79 KIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYM 138
             KI P   R+++    K+   ++ +EK + + D F    L+W +      + E  N  +  
Sbjct:    86 KIGPETARLRVGKLPKQKHFTIYIEKGEEILDTFENSELRWTYV-----ESE--NEASQK 138

Query:   139 FKDRVPCFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRINHDTRQSA 198
              K R   +EL F KK ++ V+ +Y+ H+                   +      D   + 
Sbjct:   139 EK-RY--YELTFEKKLRDKVMNSYLSHVVAESEETKRDLRAVKLYSRDVRASKDDDGMAG 195

Query:   199 I------LDHPSTFDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPGT 239
                    L+HPSTF+TLA            +ER             AWKRGYLL+GPPGT
Sbjct:   196 AGWGCINLEHPSTFETLAMDPGAKKKIIDDMERFLKRREFYKRVGKAWKRGYLLYGPPGT 255

Query:   240 GKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCT-ELQDRS 298
             GKSSLIAAMANYL FDV+DLELSS+  N  L+ +L++T N+SILV+ DIDC + E+ DR 
Sbjct:   256 GKSSLIAAMANYLKFDVFDLELSSIYENAQLKSILLSTTNRSILVIEDIDCSSAEVVDRE 315

Query:   299 AQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
             A       ++      ++TLSGLLNF DGLWSS GDERII
Sbjct:   316 ADEYQ---EYEEGYYGRVTLSGLLNFVDGLWSSFGDERII 352

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:2174502 AT5G57480 [Arabidopsis thaliana (taxid:3702)]

 Score = 383 (139.9 bits), Expect = 5.3e-45, Sum P(2) = 5.3e-45
 Identities = 102/302 (33%), Positives = 143/302 (47%)

Query:    22 QSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLV-IEEYDDGLNRNKLFKAAKLYLEPKI 80
             QS  +   P E+   F  KF N I  ++S      I E D G+N N+L+ A +LYL   +
Sbjct:    19 QSLMQSIFPPELRFAF-LKFFNRIFHVFSSYCYFDITEID-GVNTNELYNAVQLYLSSSV 76

Query:    81 PPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFK 140
                 NR+ +      S ++  +  N ++ D FNGV + W+  +     Q           
Sbjct:    77 SIAGNRLSLTRAVNSSSITFGLSNNDSIVDTFNGVTVLWEHVVTQRQTQTFAWRP---LP 133

Query:   141 DRVPCFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXX----XXXXXXNCNRINHDTRQ 196
             +    F LR  KK K  +L +Y+ +I                       + +   H   +
Sbjct:   134 EEKRGFTLRIKKKDKTLILNSYLDYIMERANEIRRKNQDRLLYTNSRGGSLDSRGHPW-E 192

Query:   197 SAILDHPSTFDTLAXXXXXXXXXXXXLE-------------RAWKRGYLLFGPPGTGKSS 243
             S    HPSTF+TLA            L+             RAWKRGYLL+GPPGTGKSS
Sbjct:   193 SVPFKHPSTFETLAMDPRKKQQIMDDLKDFAEGQVFYQKTGRAWKRGYLLYGPPGTGKSS 252

Query:   244 LIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQART 303
             +IAAMANYL +D+YDLEL+ V  N  LRK+L+ T +KSI+V+ DIDC   L +R   +  
Sbjct:   253 MIAAMANYLGYDIYDLELTEVHSNSELRKLLMKTSSKSIIVIEDIDCSINLTNRKKNSSN 312

Query:   304 AS 305
              S
Sbjct:   313 VS 314

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0009407 "toxin catabolic process" evidence=RCA

GO:0010583 "response to cyclopentenone" evidence=RCA

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

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 104/220 (47%), Positives = 131/220 (59%)

Query:   136 NYMFKDRVPCFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRI--NH- 192
             N   +  V  FEL FHKK K+  L +Y+P +                   +   +  N+ 
Sbjct:   191 NSTLRSEVRSFELNFHKKFKDVALESYLPFMVKRATLMKQEKKTLKIFTLSPENMYGNYS 250

Query:   193 DTRQSAILDHPSTFDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPGT 239
             D   S  LDHPSTF TLA            L++             AWKRGYLL+GPPGT
Sbjct:   251 DAWTSVTLDHPSTFKTLAMDSDVKTSVMEDLDKFVKRRDFYKRVGKAWKRGYLLYGPPGT 310

Query:   240 GKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSA 299
             GKSSLIAAMAN+L+FD+YDLEL++V  N  LR++LIAT N+SIL+V DIDC  EL+DR++
Sbjct:   311 GKSSLIAAMANHLNFDIYDLELTAVNNNSELRRLLIATANRSILIVEDIDCSLELKDRTS 370

Query:   300 -QARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
              +    S D   P+  ++TLSGLLNF DGLWSSCGDERII
Sbjct:   371 DEPPRESDDIEDPRYKKVTLSGLLNFIDGLWSSCGDERII 410

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:2175976 AT5G17750 [Arabidopsis thaliana (taxid:3702)]

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 110/281 (39%), Positives = 155/281 (55%)

Query:    75 YLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNN 134
             YL  KI P+ +++++        V+L + + + V DV+ G+ LKW++ L+   +++    
Sbjct:    57 YLSSKISPDASKLRMTRDPNNKNVNLHLSQGEVVSDVYKGIELKWRY-LE-GRNKKTTVV 114

Query:   135 GNYMFKDRV--PCFELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRINH 192
             G    +  V   CFEL F KKHK+ V+ +YI ++                   +   +  
Sbjct:   115 GEETEEAIVNWQCFELSFDKKHKDLVVKSYIAYVERKAKVIKEERRIIKMHSYSSYTLRW 174

Query:   193 DTRQSAILDHPSTFDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPGT 239
                QS   +HPSTF T+A            L+R             AWKR Y L+GPPGT
Sbjct:   175 ---QSVKFEHPSTFHTMAMTPKLKSSVMEDLDRFIKRKDYYKRVGKAWKRSYFLYGPPGT 231

Query:   240 GKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSA 299
             GKSSL+AAMANYL FD+YDL+L++V+G+  LR +L+AT N SIL+V DIDC  +L  R  
Sbjct:   232 GKSSLVAAMANYLKFDIYDLQLANVQGDAQLRSLLLATNNSSILLVEDIDCSVDLPTRLQ 291

Query:   300 QARTA--SPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
              A T   +P   +P    +TLSGLLN  DGLWSSCGDERI+
Sbjct:   292 PATTTLGAPKGSTP----LTLSGLLNCIDGLWSSCGDERIV 328

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:2175986 AT5G17760 [Arabidopsis thaliana (taxid:3702)]

 Score = 438 (159.2 bits), Expect = 2.8e-41, P = 2.8e-41
 Identities = 99/206 (48%), Positives = 123/206 (59%)

Query:   146 FELRFHKKHKETVLGTYIPHIXXXXXXXXXXXXXXXXXXXNCNRINHDTRQSAILDHPST 205
             FEL F KKHK+ +L +Y+P+I                   N  R      +S IL+HPST
Sbjct:   163 FELSFDKKHKDLILNSYVPYIESKAKEIRDERRILMLHSLNSLRW-----ESVILEHPST 217

Query:   206 FDTLAXXXXXXXXXXXXLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYL 252
             F+T+A            L+R             AWKRGYLL+GPPGTGKSSL+AAMANYL
Sbjct:   218 FETMAMEDDLKRDVIEDLDRFIRRKEFYKRVGKAWKRGYLLYGPPGTGKSSLVAAMANYL 277

Query:   253 HFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPK 312
              FDVYDL+L+SV  +  LR++L+AT N+SILV+ DIDC  +L +R  Q         S  
Sbjct:   278 KFDVYDLQLASVMRDSDLRRLLLATRNRSILVIEDIDCAVDLPNRIEQPVEGKNRGES-- 335

Query:   313 RDQITLSGLLNFTDGLWSSCGDERII 338
             +  +TLSGLLNF DGLWSSCGDERII
Sbjct:   336 QGPLTLSGLLNFIDGLWSSCGDERII 361

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:2095512 AT3G28580 [Arabidopsis thaliana (taxid:3702)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 106/323 (32%), Positives = 159/323 (49%)

Query:    47 RIYSESTLVIEEYD-DGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKN 105
             R Y    +   EY  +   R++ +   + YL         ++K N  K    + LS++  
Sbjct:    46 RFYPYIQITFHEYSGEHFKRSEAYLGIQSYLSKDSSARAKKLKANTTKGSKSIVLSMDDK 105

Query:   106 QAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPH 165
             + + D F G+R+ W+ + + A  Q       Y   +    + LRFH++ +E ++  Y+ H
Sbjct:   106 EEITDDFEGIRVWWQSKKEGATRQSF---SFYPEANEKRYYMLRFHRRDREVIIERYLEH 162

Query:   166 IXXXXXXXXXXXXXXXXXXXNCNRIN-HDTRQSAI-LDHPSTFDTLAXXXXXXXXXXXXL 223
             +                      + + ++++ S +  +HP+TFDTLA            L
Sbjct:   163 VMREGKTIEQKNRERKLYSNTPGQSHGNNSKWSHVTFEHPATFDTLAMEENKKEEIKSDL 222

Query:   224 -------------ERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHL 270
                           +AWKRGYLLFGPPGTGKS++IAAMAN+L +DVYDLEL++V+ N HL
Sbjct:   223 IKFSKSKDYYKKIGKAWKRGYLLFGPPGTGKSTMIAAMANFLEYDVYDLELTTVKDNTHL 282

Query:   271 RKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSP---------------KRDQ 315
             R++LI T  KSI+V+ DIDC   L  +  +      D                   K  +
Sbjct:   283 RRLLIETSAKSIIVIEDIDCSLNLTGQRKKKEEEEEDGDDKNTIEKKMMMKNEGENKESK 342

Query:   316 ITLSGLLNFTDGLWSSCGDERII 338
             +TLSGLLNF DGLWS+CG ERII
Sbjct:   343 VTLSGLLNFIDGLWSACGGERII 365

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00036345001 SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (487 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	338
pfam14363	100	pfam14363, AAA_assoc, Domain associated at C-termi	5e-25
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	1e-09
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	3e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-05
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	7e-05
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-04
smart00382	148	smart00382, AAA, ATPases associated with a variety	8e-04
COG1484	254	COG1484, DnaC, DNA replication protein [DNA replic	9e-04
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	0.001
PRK08116	268	PRK08116, PRK08116, hypothetical protein; Validate	0.002
pfam13207	114	pfam13207, AAA_17, AAA domain	0.003
pfam00006	213	pfam00006, ATP-synt_ab, ATP synthase alpha/beta fa	0.003
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	0.004
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	0.004

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

 Score = 96.9 bits (242), Expect = 5e-25
 Identities = 36/97 (37%), Positives = 53/97 (54%), Gaps = 4/97 (4%)

Query: 28  YLPDEVSSYFDQKFKNFIA-RIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNR 86
            LP E+  Y     +     R     T+VI+EYD G +RN+L+ AA+ YL  KI P+  R
Sbjct: 1   LLPHELREYLSSLLRRLFGSRFSPYLTIVIDEYD-GFSRNQLYDAAEAYLSTKISPSARR 59

Query: 87  IKINLPK--KESEVSLSVEKNQAVFDVFNGVRLKWKF 121
           +K +  K  K S + LS++  + V DVF GV++ W  
Sbjct: 60  LKASKAKKSKNSSLVLSLDDGEEVTDVFEGVKVWWTS 96

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

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

 Score = 55.3 bits (134), Expect = 1e-09
 Identities = 31/116 (26%), Positives = 50/116 (43%), Gaps = 19/116 (16%)

Query: 231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV------EGNKHLRKVL--IATENKSI 282
            LL+GPPGTGK++L  A+A  L     ++  S +      E  K LR++          +
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60

Query: 283 LVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII 338
           + + +I       D  A +R +  D  S    +  ++ LL   DG  SS     +I
Sbjct: 61  IFIDEI-------DALAGSRGSGGDSES----RRVVNQLLTELDGFTSSLSKVIVI 105

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

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

 Score = 45.1 bits (108), Expect = 3e-05
 Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 7/57 (12%)

Query: 223 LERAWKRGYL----LFGPPGTGKSSLIAAMANYLHFDVYDLELSSV-EGNKHLRKVL 274
           L R  + G L    L+GPPGTGK++L   +A           LS+V  G K LR+V+
Sbjct: 27  LRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFE--ALSAVTSGVKDLREVI 81

Length = 413

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

 Score = 44.1 bits (105), Expect = 6e-05
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 6/62 (9%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRGY-----LLFGPPGTGKSSLIAAMANYLHFDVY 257
           P T   +  +   K+ + + +E +W +G      LL+GPPG GK+SL  A+AN   ++V 
Sbjct: 10  PKTLSDVVGNEKAKEQLREWIE-SWLKGKPKKALLLYGPPGVGKTSLAHALANDYGWEVI 68

Query: 258 DL 259
           +L
Sbjct: 69  EL 70

Length = 482

>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 = 42.1 bits (99), Expect = 7e-05
 Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 14/81 (17%)

Query: 223 LERAWKRGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSVEG-----------NK 268
           LE    +  LL+GPPGTGK++L  A+AN L         L  S +               
Sbjct: 14  LELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLV 73

Query: 269 HLRKVLIATENKSILVVGDID 289
            L   L       +L + +ID
Sbjct: 74  RLLFELAEKAKPGVLFIDEID 94

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

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

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 39/144 (27%), Positives = 61/144 (42%), Gaps = 47/144 (32%)

Query: 200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDL 259
           + HP  F+ L ++                +G LL+GPPGTGK+ L  A+AN        +
Sbjct: 198 MKHPELFEHLGIEP--------------PKGVLLYGPPGTGKTLLAKAVANEAGAYFISI 243

Query: 260 ---ELSSV---EGNKHLRKVLI-ATENK-SILVVGDIDCCTELQDRSAQARTASPDWHSP 311
              E+ S    E  + LR++   A EN  SI+ + +ID                    +P
Sbjct: 244 NGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAI------------------AP 285

Query: 312 KRDQIT-------LSGLLNFTDGL 328
           KR+++T       ++ LL   DGL
Sbjct: 286 KREEVTGEVEKRVVAQLLTLMDGL 309

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

 Score = 39.3 bits (91), Expect = 8e-04
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 228 KRGYLLFGPPGTGKSSLIAAMANYL 252
               L+ GPPG+GK++L  A+A  L
Sbjct: 2   GEVILIVGPPGSGKTTLARALAREL 26

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

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

 Score = 40.1 bits (94), Expect = 9e-04
 Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 13/81 (16%)

Query: 185 LNCNRINHDTR------QSAILDHPSTFDTLAMDTD---MKKMIMD--DLERAWKRGY-- 231
           L   ++  + R      +SA      TF+    +      KK + D   L   ++RG   
Sbjct: 49  LEEEKLAREARKIERRLRSASFPAKKTFEEFDFEFQPGIDKKALEDLASLVEFFERGENL 108

Query: 232 LLFGPPGTGKSSLIAAMANYL 252
           +L GPPG GK+ L  A+ N L
Sbjct: 109 VLLGPPGVGKTHLAIAIGNEL 129

Length = 254

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

 Score = 40.3 bits (95), Expect = 0.001
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 233 LFGPPGTGKSSLIAAMANYLHFDVYDLELSSV-EGNKHLRKVLIATEN 279
           L+GPPGTGK++L   +A   +       LS+V  G K LR+++     
Sbjct: 53  LWGPPGTGKTTLARLIAGTTNAAFE--ALSAVTSGVKDLREIIEEARK 98

Length = 436

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

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 229 RGYLLFGPPGTGKSSLIAAMANYL 252
            G LL+G  GTGK+ L A +AN L
Sbjct: 115 VGLLLWGSVGTGKTYLAACIANEL 138

Length = 268

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

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE 260
            L+ GPPG+GKS+L   +A  L   V  L+
Sbjct: 2   ILITGPPGSGKSTLAKKLAEKLGIPVISLD 31

Length = 114

>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain

 Score = 37.8 bits (89), Expect = 0.003
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 28/88 (31%)

Query: 232 LLFGPPGTGKSSLIAAMANYLHFDVYD------------LE-LSSVEGNKHLRKVLIATE 278
            +FG  GTGK+ L+  +A     DV +             E +  + G   L        
Sbjct: 19  GIFGGSGTGKTVLLGMIARNAKADVVEVYVLIGERGREVAEFIEELLGEGAL-------- 70

Query: 279 NKSILVVGDIDCCTELQDRSAQARTASP 306
            ++++V           D     R  +P
Sbjct: 71  KRTVVVAA-------TSDEPPAERYLAP 91

This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213

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

 Score = 38.3 bits (89), Expect = 0.004
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 6/52 (11%)

Query: 229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV------EGNKHLRKVL 274
           +G LL+GPPGTGK+ L  A+A         ++ S +      E  K++R++ 
Sbjct: 277 KGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELF 328

Length = 494

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

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 42/122 (34%), Positives = 60/122 (49%), Gaps = 25/122 (20%)

Query: 229 RGYLLFGPPGTGKSSLIAAMAN-----YLHFDVYDLEL---SSVEGNKHLRKVL-IATEN 279
           +G +L+GPPGTGK+ L  A+AN     +L   V   EL      +G K +R++  +A EN
Sbjct: 218 KGVILYGPPGTGKTLLAKAVANETSATFLR--VVGSELIQKYLGDGPKLVRELFRVAEEN 275

Query: 280 K-SILVVGDIDCCTELQDRSAQARTASPDWHS--PKRDQITLSGLLNFTDGLWSSCGDER 336
             SI+ + +ID             T   D  S   K  Q T+  LLN  DG + S GD +
Sbjct: 276 APSIVFIDEIDAIG----------TKRYDATSGGEKEIQRTMLELLNQLDG-FDSRGDVK 324

Query: 337 II 338
           +I
Sbjct: 325 VI 326

Length = 438

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	338
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	100.0
PF14363	98	AAA_assoc: Domain associated at C-terminal with AA	99.96
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.86
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.78
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.77
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.74
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.74
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.71
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.71
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	99.7
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.7
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.69
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.69
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.69
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.65
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.64
CHL00195	489	ycf46 Ycf46; Provisional	99.61
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.59
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.59
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.59
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.59
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.58
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.58
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.57
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.55
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.55
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.52
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.52
CHL00176	638	ftsH cell division protein; Validated	99.52
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.51
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.49
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.48
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.45
PF00004	132	AAA: ATPase family associated with various cellula	99.45
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.44
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.43
CHL00206	2281	ycf2 Ycf2; Provisional	99.41
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.39
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.38
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.33
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.31
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.29
PRK04195	482	replication factor C large subunit; Provisional	99.28
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.27
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.26
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.25
PRK07952	244	DNA replication protein DnaC; Validated	99.24
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.24
PLN03025	319	replication factor C subunit; Provisional	99.19
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.19
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.17
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.17
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.16
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.16
PRK13342	413	recombination factor protein RarA; Reviewed	99.15
PRK06893	229	DNA replication initiation factor; Validated	99.15
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.15
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.14
PHA02544	316	44 clamp loader, small subunit; Provisional	99.14
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.12
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.12
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.11
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.11
PRK08727	233	hypothetical protein; Validated	99.11
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.11
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.1
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.08
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.07
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.06
PRK12377	248	putative replication protein; Provisional	99.05
PRK08181	269	transposase; Validated	99.04
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.03
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.03
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.02
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.02
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.02
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.02
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.02
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.01
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.01
PRK08084	235	DNA replication initiation factor; Provisional	99.0
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.0
PRK06526	254	transposase; Provisional	99.0
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.0
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.0
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.0
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.99
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.98
PRK10865	857	protein disaggregation chaperone; Provisional	98.98
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.97
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	98.97
CHL00181	287	cbbX CbbX; Provisional	98.96
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	98.96
PRK08939	306	primosomal protein DnaI; Reviewed	98.95
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.95
PRK12402	337	replication factor C small subunit 2; Reviewed	98.94
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.93
PRK05642	234	DNA replication initiation factor; Validated	98.93
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.93
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.93
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	98.93
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.92
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.91
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	98.91
KOG2028	554	consensus ATPase related to the helicase subunit o	98.9
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.9
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.9
PRK13341	725	recombination factor protein RarA/unknown domain f	98.9
CHL00095	821	clpC Clp protease ATP binding subunit	98.89
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.89
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.88
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.88
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.88
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.86
PRK08116	268	hypothetical protein; Validated	98.86
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.86
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.86
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.85
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	98.85
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	98.85
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.84
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.84
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.84
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.82
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.81
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.8
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.8
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	98.79
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	98.79
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.78
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	98.78
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.78
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.76
PRK09183	259	transposase/IS protein; Provisional	98.75
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.75
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.74
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	98.73
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.73
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.72
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	98.72
PHA02244	383	ATPase-like protein	98.71
PRK12422	445	chromosomal replication initiation protein; Provis	98.71
PRK06620	214	hypothetical protein; Validated	98.71
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.7
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	98.68
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	98.67
PF07726	131	AAA_3: ATPase family associated with various cellu	98.67
smart00382	148	AAA ATPases associated with a variety of cellular	98.67
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	98.64
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	98.64
PRK06835	329	DNA replication protein DnaC; Validated	98.64
PRK06921	266	hypothetical protein; Provisional	98.63
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.63
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.61
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.61
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	98.6
PF08740	187	BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA A	98.58
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.57
COG0714	329	MoxR-like ATPases [General function prediction onl	98.53
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.51
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.5
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	98.49
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.49
PRK09087	226	hypothetical protein; Validated	98.48
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	98.46
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.45
CHL00095	821	clpC Clp protease ATP binding subunit	98.44
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.43
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.43
PRK10865	857	protein disaggregation chaperone; Provisional	98.42
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	98.42
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.41
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	98.4
PRK11608	326	pspF phage shock protein operon transcriptional ac	98.4
PHA00729	226	NTP-binding motif containing protein	98.39
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.38
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	98.37
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	98.35
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.33
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.32
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.31
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.31
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.28
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.27
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	98.27
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	98.27
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.27
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.26
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.26
PRK13531	498	regulatory ATPase RavA; Provisional	98.25
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.25
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.25
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.23
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	98.23
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.2
PF13173	128	AAA_14: AAA domain	98.2
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	98.2
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.17
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.16
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	98.13
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.11
KOG0736	953	consensus Peroxisome assembly factor 2 containing	98.09
PRK08058	329	DNA polymerase III subunit delta'; Validated	98.09
PHA02624	647	large T antigen; Provisional	98.01
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.98
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	97.97
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.95
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	97.93
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.9
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	97.9
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	97.89
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.87
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.86
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.83
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	97.83
PHA02774	613	E1; Provisional	97.82
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.81
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.76
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	97.75
PRK15455	644	PrkA family serine protein kinase; Provisional	97.73
PRK08118	167	topology modulation protein; Reviewed	97.71
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	97.71
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.7
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.69
PRK00131	175	aroK shikimate kinase; Reviewed	97.68
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	97.68
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	97.66
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	97.65
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	97.64
PF05729	166	NACHT: NACHT domain	97.62
smart00350	509	MCM minichromosome maintenance proteins.	97.61
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	97.6
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	97.6
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.6
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.59
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.58
PRK08699	325	DNA polymerase III subunit delta'; Validated	97.56
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	97.53
PRK13947	171	shikimate kinase; Provisional	97.51
PRK03839	180	putative kinase; Provisional	97.51
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.49
PRK15115	444	response regulator GlrR; Provisional	97.48
COG4650	531	RtcR Sigma54-dependent transcription regulator con	97.48
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.47
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.47
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.45
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.45
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.43
) 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	97.43
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.43
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.43
PRK00625	173	shikimate kinase; Provisional	97.42
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	97.42
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.42
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	97.42
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.42
PRK07261	171	topology modulation protein; Provisional	97.38
PRK13949	169	shikimate kinase; Provisional	97.37
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.33
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.33
PRK04132	846	replication factor C small subunit; Provisional	97.33
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.32
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.32
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.31
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.3
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.29
COG1855	604	ATPase (PilT family) [General function prediction	97.28
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.28
PRK06217	183	hypothetical protein; Validated	97.28
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.27
PRK13765	637	ATP-dependent protease Lon; Provisional	97.26
PRK13764	602	ATPase; Provisional	97.26
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.26
cd01128	249	rho_factor Transcription termination factor rho is	97.25
PRK14532	188	adenylate kinase; Provisional	97.24
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.23
COG2204	464	AtoC Response regulator containing CheY-like recei	97.23
PRK13948	182	shikimate kinase; Provisional	97.23
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	97.22
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.22
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.22
PRK14531	183	adenylate kinase; Provisional	97.21
PRK05917	290	DNA polymerase III subunit delta'; Validated	97.21
PRK13946	184	shikimate kinase; Provisional	97.2
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.19
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	97.19
PF13245	76	AAA_19: Part of AAA domain	97.18
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.18
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.18
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.18
COG0606	490	Predicted ATPase with chaperone activity [Posttran	97.17
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.17
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	97.17
PRK05057	172	aroK shikimate kinase I; Reviewed	97.16
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.16
PRK03731	171	aroL shikimate kinase II; Reviewed	97.16
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.15
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.13
PRK06547	172	hypothetical protein; Provisional	97.13
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.11
PRK06762	166	hypothetical protein; Provisional	97.1
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	97.07
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.07
PRK14530	215	adenylate kinase; Provisional	97.06
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	97.06
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.04
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	97.02
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	97.0
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	97.0
PRK11823	446	DNA repair protein RadA; Provisional	97.0
PF14516	331	AAA_35: AAA-like domain	97.0
PRK02496	184	adk adenylate kinase; Provisional	96.98
PRK14528	186	adenylate kinase; Provisional	96.97
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.96
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	96.96
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	96.96
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.95
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	96.95
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.95
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.94
PF13479	213	AAA_24: AAA domain	96.92
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.92
PRK10365	441	transcriptional regulatory protein ZraR; Provision	96.92
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.92
PRK04296	190	thymidine kinase; Provisional	96.92
PLN03210	1153	Resistant to P. syringae 6; Provisional	96.92
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.92
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.91
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.91
PRK09376	416	rho transcription termination factor Rho; Provisio	96.88
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.87
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.87
PTZ00088	229	adenylate kinase 1; Provisional	96.87
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.87
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.86
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.85
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.84
PRK09862	506	putative ATP-dependent protease; Provisional	96.82
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.81
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.81
PRK00279	215	adk adenylate kinase; Reviewed	96.81
PTZ00202	550	tuzin; Provisional	96.78
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.77
PRK04182	180	cytidylate kinase; Provisional	96.76
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.75
PRK14527	191	adenylate kinase; Provisional	96.75
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	96.73
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.72
PLN02200	234	adenylate kinase family protein	96.72
PRK06696	223	uridine kinase; Validated	96.71
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	96.7
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.69
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.69
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.69
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.69
PRK04040	188	adenylate kinase; Provisional	96.68
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.67
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	96.67
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	96.66
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.65
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	96.65
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.65
PLN02199	303	shikimate kinase	96.65
PRK01184	184	hypothetical protein; Provisional	96.64
TIGR00767	415	rho transcription termination factor Rho. Members	96.63
PHA02530	300	pseT polynucleotide kinase; Provisional	96.61
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.61
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.58
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	96.58
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.56
PRK14526	211	adenylate kinase; Provisional	96.56
PRK08233	182	hypothetical protein; Provisional	96.55
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	96.55
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.54
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.52
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.5
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	96.49
PRK10436	462	hypothetical protein; Provisional	96.48
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.45
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.45
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.45
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.43
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.43
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.42
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.42
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.4
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.4
PRK12608	380	transcription termination factor Rho; Provisional	96.37
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.37
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.37
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.36
COG4178	604	ABC-type uncharacterized transport system, permeas	96.36
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.36
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.35
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.35
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.34
PRK14529	223	adenylate kinase; Provisional	96.33
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	96.31
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.3
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.29
PRK09825	176	idnK D-gluconate kinase; Provisional	96.28
PRK05541	176	adenylylsulfate kinase; Provisional	96.28
PRK00889	175	adenylylsulfate kinase; Provisional	96.28
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	96.27
PRK10646	153	ADP-binding protein; Provisional	96.27
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.26
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	96.25
PF13555	62	AAA_29: P-loop containing region of AAA domain	96.24
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.23
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	96.23
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.23
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.23
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	96.23
PLN02674	244	adenylate kinase	96.22
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.21
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	96.21
PRK04841	903	transcriptional regulator MalT; Provisional	96.2
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.19
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.19
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	96.18
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	96.17
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	96.15
PRK07132	299	DNA polymerase III subunit delta'; Validated	96.12
PRK10536	262	hypothetical protein; Provisional	96.12
PRK05480	209	uridine/cytidine kinase; Provisional	96.11
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.1
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.1
PRK14974	336	cell division protein FtsY; Provisional	96.09
PRK04328	249	hypothetical protein; Provisional	96.09
PLN02165	334	adenylate isopentenyltransferase	96.08
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	96.08
PRK12338	319	hypothetical protein; Provisional	96.07
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.06
PRK06067	234	flagellar accessory protein FlaH; Validated	96.06
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.05
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.05
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.02
PRK11545	163	gntK gluconate kinase 1; Provisional	96.01
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	96.01
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	96.0
PRK06851	367	hypothetical protein; Provisional	95.98
PLN02459	261	probable adenylate kinase	95.98
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.98
PRK14730	195	coaE dephospho-CoA kinase; Provisional	95.98
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.96
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.95
PRK05973	237	replicative DNA helicase; Provisional	95.93
PRK06761	282	hypothetical protein; Provisional	95.92
PRK13889	988	conjugal transfer relaxase TraA; Provisional	95.92
PRK09354	349	recA recombinase A; Provisional	95.91
PRK13808	333	adenylate kinase; Provisional	95.9
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	95.9
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.9
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	95.89
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	95.87
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	95.84
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	95.83
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.83
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.81
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.77
PRK00081	194	coaE dephospho-CoA kinase; Reviewed	95.77
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.75
PRK00300	205	gmk guanylate kinase; Provisional	95.75
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.74
PRK14737	186	gmk guanylate kinase; Provisional	95.74
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.73
PRK04301	317	radA DNA repair and recombination protein RadA; Va	95.73
PRK14021	542	bifunctional shikimate kinase/3-dehydroquinate syn	95.73
COG0802	149	Predicted ATPase or kinase [General function predi	95.72
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.72
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	95.71
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	95.71
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.7
PRK05818	261	DNA polymerase III subunit delta'; Validated	95.7
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.68
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	95.68
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	95.68
PRK07667	193	uridine kinase; Provisional	95.68
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.67
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.67
COG1485	367	Predicted ATPase [General function prediction only	95.66
PRK13975	196	thymidylate kinase; Provisional	95.66
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	95.66
PRK13951	488	bifunctional shikimate kinase/3-dehydroquinate syn	95.64
PRK06851	367	hypothetical protein; Provisional	95.64
PHA00350	399	putative assembly protein	95.63
PRK00023	225	cmk cytidylate kinase; Provisional	95.63
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	95.63
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.63
PRK04220	301	2-phosphoglycerate kinase; Provisional	95.62
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	95.62
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	95.61
PRK14738	206	gmk guanylate kinase; Provisional	95.61
TIGR00152	188	dephospho-CoA kinase. This model produces scores i	95.58
PRK13826	1102	Dtr system oriT relaxase; Provisional	95.56
KOG1808	1856	consensus AAA ATPase containing von Willebrand fac	95.55
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.53
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.52
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	95.51
PRK08356	195	hypothetical protein; Provisional	95.51

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

Probab=100.00  E-value=2.1e-77  Score=573.66  Aligned_cols=324  Identities=42%  Similarity=0.711  Sum_probs=300.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCCHhHHHHHHHHHHHHhhccCCCcEEEEeccCCCCCccHHHHHHHHHhCCCCCCCC
Q 035959            5 TTVMSVAASAAATFMLIQSYTRIYLPDEVSSYFDQKFKNFIARIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNV   84 (338)
Q Consensus         5 ~~~~~~~~S~~a~~~l~~~~~~~~~P~~l~~~~~~~~~~l~~~~~~~~ti~i~e~~~~~~~n~~y~a~~~YLs~~~~~~~   84 (338)
                      +++|+.+||++|++|++|+|+++++|.+++.|+.+++++|++++++|.++.|.|+ +|+.+|++|.|+|.||++++++.+
T Consensus         1 ~~~~~~~~s~~~~~~~~~~~~~~~~p~~~~~y~~~~~~~l~g~~s~~~~~~~~e~-~g~~~n~~~~aie~yl~~k~~~~~   79 (457)
T KOG0743|consen    1 SSVFTAYASLLGSLMFIKSMLQDIIPPSINPYFISALRGLFGVFSSYALIRIGEQ-DGVFRNQLYVAIEVYLSSKSSAIA   79 (457)
T ss_pred             CCccchhHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHhhccCcccEEEEeehh-ccchHHHHHHHHHHhhhccchhhh
Confidence            3579999999999999999999999999999999999999999999999999999 889999999999999999999999


Q ss_pred             CeeEeecCCCCCceEEEccCCceEEEeecCeEEEEEEEeecCCCCCcCCCCCCCCCCCcceEEEEEcCcchhhHHhhhhH
Q 035959           85 NRIKINLPKKESEVSLSVEKNQAVFDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIP  164 (338)
Q Consensus        85 ~rL~~~~~~~~~~~~~~l~~ge~v~D~f~G~~~~W~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~~~~~~~vl~~~l~  164 (338)
                      +|++.++..+++++++.++++++|.|+|+||+++|++++..+..+...     +...++|+|+|+|++++|+.|+.+||+
T Consensus        80 ~rl~~~~~~~s~~~~l~~~~~~~i~d~f~gv~~~w~~~~~~~~~~~~~-----~~~~~~r~~~L~f~k~~~e~V~~syl~  154 (457)
T KOG0743|consen   80 KRLTQNLSKNSKSLVLGLDDNEEISDEFEGVPVKWRHFVDYNEKWIFV-----EREREKRYFELTFHKKPRELVTLSYLP  154 (457)
T ss_pred             hhhhhhhccccccceEEecCCcEEEEEEeceEEEEEEEEEecCccccc-----ccCCcceEEEEEecCccHHHhHHhHHH
Confidence            999999999999999999999999999999999999998877665332     224688999999999999999999999


Q ss_pred             HHHHHhHHHHHhccceeeeeccCc--cC--CCCccccccCCCCCccccccCChhHHHHHHHHHHh-------------hh
Q 035959          165 HILKKSKELSKKKKTLKLFTLNCN--RI--NHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER-------------AW  227 (338)
Q Consensus       165 ~v~~~~~~~~~~~~~~~l~~~~~~--~~--~~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~-------------~~  227 (338)
                      |+.+++++|.++++.+++|++++.  .+  .+..|..++++||++|++++|++++|++|++||++             ||
T Consensus       155 ~v~~~~k~I~~~~r~~kl~t~~~~~~~~~~~~~~W~~v~f~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkaw  234 (457)
T KOG0743|consen  155 YVVSKAKEILEENRELKLYTNSGKTVIYTAKGGEWRSVGFPHPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAW  234 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCcccccccCCcceecCCCCCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcch
Confidence            999999999999999999999843  22  47799999999999999999999999999999998             89


Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPD  307 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~  307 (338)
                      +|||||||||||||||+++|||+++++++|+++++++..+++|+++|..+++++||+||||||.+.++.|.+....+.+ 
T Consensus       235 KRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n~dLr~LL~~t~~kSIivIEDIDcs~~l~~~~~~~~~~~~-  313 (457)
T KOG0743|consen  235 KRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLDSDLRHLLLATPNKSILLIEDIDCSFDLRERRKKKKENFE-  313 (457)
T ss_pred             hccceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCcHHHHHHHHhCCCCcEEEEeeccccccccccccccccccc-
Confidence            9999999999999999999999999999999999999999999999999999999999999999998887766542211 


Q ss_pred             CCCCCcchhhHHHHHHHhcCCcCCCCCcccC
Q 035959          308 WHSPKRDQITLSGLLNFTDGLWSSCGDERII  338 (338)
Q Consensus       308 ~~~~~~~~~~ls~lLn~iDgl~s~~g~erii  338 (338)
                         ...+++|||||||+||||||+||+||||
T Consensus       314 ---~~~~~VTlSGLLNfiDGlwSscg~ERIi  341 (457)
T KOG0743|consen  314 ---GDLSRVTLSGLLNFLDGLWSSCGDERII  341 (457)
T ss_pred             ---CCcceeehHHhhhhhccccccCCCceEE
Confidence               1357899999999999999999999997

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

Probab=99.96  E-value=1.7e-29  Score=200.59  Aligned_cols=97  Identities=36%  Similarity=0.662  Sum_probs=93.6

Q ss_pred             hCCHhHHHHHHHHHHHHhh-ccCCCcEEEEeccCCCCCccHHHHHHHHHhCCCCCCCCCeeEeecCCCCCceEEEccCCc
Q 035959           28 YLPDEVSSYFDQKFKNFIA-RIYSESTLVIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQ  106 (338)
Q Consensus        28 ~~P~~l~~~~~~~~~~l~~-~~~~~~ti~i~e~~~~~~~n~~y~a~~~YLs~~~~~~~~rL~~~~~~~~~~~~~~l~~ge  106 (338)
                      |||++||+|+.+++++++. +++||+||+|+|+ +|+.+|++|+||++||+++++++++||++++++++++++++|++||
T Consensus         1 ~~P~~lr~~~~~~~~~~~~~~~s~~~ti~I~E~-~g~~~N~ly~a~~~YL~s~~s~~a~rL~~~~~~~~~~~~l~l~~~e   79 (98)
T PF14363_consen    1 LLPHELRSYLRSLLRRLFSSRFSPYLTIVIPEF-DGLSRNELYDAAQAYLSSKISPSARRLKASKSKNSKNLVLSLDDGE   79 (98)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCCcEEEEEEeC-CCccccHHHHHHHHHHhhccCcccceeeecccCCCCceEEecCCCC
Confidence            6899999999999998886 8999999999999 7999999999999999999999999999999999999999999999


Q ss_pred             eEEEeecCeEEEEEEEeec
Q 035959          107 AVFDVFNGVRLKWKFELKP  125 (338)
Q Consensus       107 ~v~D~f~G~~~~W~~~~~~  125 (338)
                      +|.|+|+||+|||++++++
T Consensus        80 ~V~D~F~Gv~v~W~~~~~e   98 (98)
T PF14363_consen   80 EVVDVFEGVKVWWSSVCTE   98 (98)
T ss_pred             EEEEEECCEEEEEEEEccC
Confidence            9999999999999999864

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

Probab=99.86  E-value=2.5e-22  Score=188.55  Aligned_cols=120  Identities=30%  Similarity=0.458  Sum_probs=98.8

Q ss_pred             ccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-----CchHH
Q 035959          196 QSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-----GNKHL  270 (338)
Q Consensus       196 ~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-----~~~~l  270 (338)
                      ..+|+.||..|+.++.+|+              +|+|||||||||||.||+|+|++.+..|+.+..+++.     ..+.|
T Consensus       167 VELPL~~PElF~~~GI~PP--------------KGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSElVqKYiGEGaRl  232 (406)
T COG1222         167 VELPLKNPELFEELGIDPP--------------KGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGARL  232 (406)
T ss_pred             hcccccCHHHHHHcCCCCC--------------CceEeeCCCCCcHHHHHHHHHhccCceEEEeccHHHHHHHhccchHH
Confidence            3578888888888888775              9999999999999999999999999999999999876     24555


Q ss_pred             -HHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCcccC
Q 035959          271 -RKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII  338 (338)
Q Consensus       271 -~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~erii  338 (338)
                       +.+|.-+  .+||||||||||++..  +|.....      +.+...++|+-+|||+|||..+. |+.+||
T Consensus       233 VRelF~lArekaPsIIFiDEIDAIg~--kR~d~~t------~gDrEVQRTmleLL~qlDGFD~~-~nvKVI  294 (406)
T COG1222         233 VRELFELAREKAPSIIFIDEIDAIGA--KRFDSGT------SGDREVQRTMLELLNQLDGFDPR-GNVKVI  294 (406)
T ss_pred             HHHHHHHHhhcCCeEEEEechhhhhc--ccccCCC------CchHHHHHHHHHHHHhccCCCCC-CCeEEE
Confidence             4444433  3899999999999998  7765544      23567899999999999999864 787775

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

Probab=99.78  E-value=2.4e-19  Score=177.53  Aligned_cols=116  Identities=24%  Similarity=0.371  Sum_probs=98.7

Q ss_pred             ccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC------
Q 035959          205 TFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG------  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~------  266 (338)
                      .|+++++.+....++.+.+..            .++||+|||||||||||+||+|+|++++.+++.++..++.+      
T Consensus       188 ~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApeivSGvSGES  267 (802)
T KOG0733|consen  188 SFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVSGVSGES  267 (802)
T ss_pred             chhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchhhhcccCccc
Confidence            688888877776666665554            46799999999999999999999999999999999998873      


Q ss_pred             chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                      +..++.+|.++.  .|||+||||||++.+  +|.....         .-.++.+++||+.|||+.-.
T Consensus       268 EkkiRelF~~A~~~aPcivFiDeIDAI~p--kRe~aqr---------eMErRiVaQLlt~mD~l~~~  323 (802)
T KOG0733|consen  268 EKKIRELFDQAKSNAPCIVFIDEIDAITP--KREEAQR---------EMERRIVAQLLTSMDELSNE  323 (802)
T ss_pred             HHHHHHHHHHHhccCCeEEEeeccccccc--chhhHHH---------HHHHHHHHHHHHhhhccccc
Confidence            678999999885  799999999999999  7765433         35689999999999999643

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

Probab=99.77  E-value=7.7e-19  Score=177.66  Aligned_cols=119  Identities=24%  Similarity=0.375  Sum_probs=103.7

Q ss_pred             CCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-----  265 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-----  265 (338)
                      .-.|+++++-+++|.+|.+-++-            ..+.|+|||||||||||.+|+|+|-++...++.|...++.     
T Consensus       668 nV~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGPELLNMYVG  747 (953)
T KOG0736|consen  668 NVSWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGPELLNMYVG  747 (953)
T ss_pred             ccchhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCHHHHHHHhc
Confidence            34899999999999999998887            2356999999999999999999999999999999888865     


Q ss_pred             -CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          266 -GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       266 -~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                       +++++|++|.++.  +|||||+||+|++++.+.|.+++         .++..+.+|+||..|||+..
T Consensus       748 qSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~sGDS---------GGVMDRVVSQLLAELDgls~  806 (953)
T KOG0736|consen  748 QSEENVREVFERARSAAPCVIFFDELDSLAPNRGRSGDS---------GGVMDRVVSQLLAELDGLSD  806 (953)
T ss_pred             chHHHHHHHHHHhhccCCeEEEeccccccCccCCCCCCc---------cccHHHHHHHHHHHhhcccC
Confidence             5789999999985  89999999999999944444443         36889999999999999974

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

Probab=99.74  E-value=2e-18  Score=172.79  Aligned_cols=117  Identities=25%  Similarity=0.400  Sum_probs=100.8

Q ss_pred             CCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE----  265 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~----  265 (338)
                      ..+|+++++.+++|+++.+.+..             ..++|+|||||||||||++++|+|++.+.+++.+.+.++.    
T Consensus       430 ~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~sk~v  509 (693)
T KOG0730|consen  430 NVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFSKYV  509 (693)
T ss_pred             CCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHHHHhc
Confidence            44889999999999888877665             4578999999999999999999999999999999988876    


Q ss_pred             --CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          266 --GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       266 --~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                        ++..++++|.++.  .|||||+||||++..  .|+++.         .+...+.|++||+.|||+-.
T Consensus       510 GeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~--~R~g~~---------~~v~~RVlsqLLtEmDG~e~  567 (693)
T KOG0730|consen  510 GESERAIREVFRKARQVAPCIIFFDEIDALAG--SRGGSS---------SGVTDRVLSQLLTEMDGLEA  567 (693)
T ss_pred             CchHHHHHHHHHHHhhcCCeEEehhhHHhHhh--ccCCCc---------cchHHHHHHHHHHHcccccc
Confidence              3677999999885  789999999999988  776432         25778999999999999964

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

Probab=99.74  E-value=2.8e-18  Score=162.63  Aligned_cols=119  Identities=24%  Similarity=0.434  Sum_probs=98.7

Q ss_pred             ccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----  266 (338)
                      .|+++++..+.|+-+.+.+.-             || +|+|++||||||||.||+|+|.+++..++.|+.+.+.+     
T Consensus       210 kW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPW-kgvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstltSKwRGe  288 (491)
T KOG0738|consen  210 KWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPW-KGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKWRGE  288 (491)
T ss_pred             ChHhhcchHHHHHHHHHHHhhhhhhHHHHhhccccc-ceeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhhhhhccc
Confidence            678888877777766665554             56 69999999999999999999999999999999998874     


Q ss_pred             chHHHHHHHhcC---CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCC
Q 035959          267 NKHLRKVLIATE---NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGD  334 (338)
Q Consensus       267 ~~~l~~~l~~~~---~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~  334 (338)
                      .+.|.++|++++   .|++|||||||++..  .|++..+        +..+++.-+.||-+|||+-...-+
T Consensus       289 SEKlvRlLFemARfyAPStIFiDEIDslcs--~RG~s~E--------HEaSRRvKsELLvQmDG~~~t~e~  349 (491)
T KOG0738|consen  289 SEKLVRLLFEMARFYAPSTIFIDEIDSLCS--QRGGSSE--------HEASRRVKSELLVQMDGVQGTLEN  349 (491)
T ss_pred             hHHHHHHHHHHHHHhCCceeehhhHHHHHh--cCCCccc--------hhHHHHHHHHHHHHhhcccccccc
Confidence            456778887775   899999999999988  6655433        678899999999999999765443

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

Probab=99.71  E-value=4.1e-18  Score=156.33  Aligned_cols=119  Identities=29%  Similarity=0.437  Sum_probs=92.2

Q ss_pred             cccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-----CchHH-
Q 035959          197 SAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-----GNKHL-  270 (338)
Q Consensus       197 ~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-----~~~~l-  270 (338)
                      ++|+.||..++.++..|              +.|++|||+||||||.||+|+||.....++.+-.+++.     +...| 
T Consensus       202 ELPLthPE~YeemGikp--------------PKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvGseLiQkylGdGpklv  267 (440)
T KOG0726|consen  202 ELPLTHPEYYEEMGIKP--------------PKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLV  267 (440)
T ss_pred             cCCCCCHHHHHHcCCCC--------------CCeeEEeCCCCCchhHHHHHHhcccchhhhhhhhHHHHHHHhccchHHH
Confidence            35566666666665554              48999999999999999999999999999888888765     23444 


Q ss_pred             HHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCcccC
Q 035959          271 RKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII  338 (338)
Q Consensus       271 ~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~erii  338 (338)
                      +++|.-+  .+|+|+||||||++..  +|-+.++      +.....++|+-.|||++||..|. |+..||
T Consensus       268 RqlF~vA~e~apSIvFiDEIdAiGt--KRyds~S------ggerEiQrtmLELLNQldGFdsr-gDvKvi  328 (440)
T KOG0726|consen  268 RELFRVAEEHAPSIVFIDEIDAIGT--KRYDSNS------GGEREIQRTMLELLNQLDGFDSR-GDVKVI  328 (440)
T ss_pred             HHHHHHHHhcCCceEEeehhhhhcc--ccccCCC------ccHHHHHHHHHHHHHhccCcccc-CCeEEE
Confidence            4555444  3899999999999988  7755544      23467789999999999999974 777664

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

Probab=99.71  E-value=2e-17  Score=164.08  Aligned_cols=114  Identities=23%  Similarity=0.327  Sum_probs=95.9

Q ss_pred             ccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC------
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE------  265 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~------  265 (338)
                      +|++++.-.+++.++...+..             ..+.|+|||||||||||.||+|+||+.|.+++.|-..++.      
T Consensus       509 tW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPELlNkYVGE  588 (802)
T KOG0733|consen  509 TWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPELLNKYVGE  588 (802)
T ss_pred             ChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHHHHHHHhhh
Confidence            678888777777777766665             2367999999999999999999999999999999988875      


Q ss_pred             CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          266 GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       266 ~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                      ++..++++|.++.  .|||||+||||++.+  .|....         ...+.+.+++||..|||+-
T Consensus       589 SErAVR~vFqRAR~saPCVIFFDEiDaL~p--~R~~~~---------s~~s~RvvNqLLtElDGl~  643 (802)
T KOG0733|consen  589 SERAVRQVFQRARASAPCVIFFDEIDALVP--RRSDEG---------SSVSSRVVNQLLTELDGLE  643 (802)
T ss_pred             HHHHHHHHHHHhhcCCCeEEEecchhhcCc--ccCCCC---------chhHHHHHHHHHHHhcccc
Confidence            3566899999885  799999999999998  664433         3567899999999999994

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

Probab=99.70  E-value=2.5e-17  Score=148.72  Aligned_cols=124  Identities=27%  Similarity=0.341  Sum_probs=94.8

Q ss_pred             ccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----  266 (338)
                      ++.++++-+-.|+++.+.++-             .++||+|||||||||||+|++|+|++....++.+..++...     
T Consensus       153 sy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~firvvgsefvqkylge  232 (408)
T KOG0727|consen  153 SYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE  232 (408)
T ss_pred             cccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHHHHHHHhcc
Confidence            566666666666666665554             35799999999999999999999999999999999888652     


Q ss_pred             -chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCccc
Q 035959          267 -NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERI  337 (338)
Q Consensus       267 -~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~eri  337 (338)
                       ..-++.+|.-+  ..|+||||||||+++.  +|-....      +.+...++.|-.|||+|||.... .+..+
T Consensus       233 gprmvrdvfrlakenapsiifideidaiat--krfdaqt------gadrevqril~ellnqmdgfdq~-~nvkv  297 (408)
T KOG0727|consen  233 GPRMVRDVFRLAKENAPSIIFIDEIDAIAT--KRFDAQT------GADREVQRILIELLNQMDGFDQT-TNVKV  297 (408)
T ss_pred             CcHHHHHHHHHHhccCCcEEEeehhhhHhh--hhccccc------cccHHHHHHHHHHHHhccCcCcc-cceEE
Confidence             22345555444  4799999999999988  7755544      23567899999999999999743 34433

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

Probab=99.70  E-value=4.4e-17  Score=159.51  Aligned_cols=119  Identities=27%  Similarity=0.404  Sum_probs=98.2

Q ss_pred             CccccccCChhHHHH---HHHHHHh---------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----
Q 035959          204 STFDTLAMDTDMKKM---IMDDLER---------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----  266 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~---i~~~l~~---------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----  266 (338)
                      -+|+++-+-++.|++   |++.|..         ..++|+||.||||||||.||+|+|.+.+.+++....++...     
T Consensus       301 v~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdEm~VGv  380 (752)
T KOG0734|consen  301 VTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMFVGV  380 (752)
T ss_pred             cccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhhhhhcc
Confidence            379999887777754   5555555         45789999999999999999999999999999999888652     


Q ss_pred             -chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCC
Q 035959          267 -NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCG  333 (338)
Q Consensus       267 -~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g  333 (338)
                       -..++.+|..+.  .||||||||||++..  +|.....         ...+.|+++||-.|||.-..+|
T Consensus       381 GArRVRdLF~aAk~~APcIIFIDEiDavG~--kR~~~~~---------~y~kqTlNQLLvEmDGF~qNeG  439 (752)
T KOG0734|consen  381 GARRVRDLFAAAKARAPCIIFIDEIDAVGG--KRNPSDQ---------HYAKQTLNQLLVEMDGFKQNEG  439 (752)
T ss_pred             cHHHHHHHHHHHHhcCCeEEEEechhhhcc--cCCccHH---------HHHHHHHHHHHHHhcCcCcCCc
Confidence             467899998875  799999999999988  6755432         2678999999999999976543

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

Probab=99.69  E-value=7.2e-18  Score=152.77  Aligned_cols=159  Identities=21%  Similarity=0.296  Sum_probs=117.4

Q ss_pred             cCcchhhHHhhhhHHHHHHhHHHHHhccceeeeeccCccCCC----CccccccCCCCCccccccCChhHHHHHHHHHHhh
Q 035959          151 HKKHKETVLGTYIPHILKKSKELSKKKKTLKLFTLNCNRINH----DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERA  226 (338)
Q Consensus       151 ~~~~~~~vl~~~l~~v~~~~~~~~~~~~~~~l~~~~~~~~~~----~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~  226 (338)
                      -.++...|++...+..-...+++....+...-|+..++.+..    ..--.+|..|+..|++++..|+            
T Consensus       138 vnKDsyliletLP~eyDsrVkaMevDekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pP------------  205 (424)
T KOG0652|consen  138 VNKDSYLILETLPSEYDSRVKAMEVDEKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPP------------  205 (424)
T ss_pred             ecCCceeehhcCChhhhhhcceeeeccCCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCC------------
Confidence            345556677777777777777777777777777765443211    1122367889999999988775            


Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-----CchHH-HHHHHhc--CCCcEEEEcCCCccCCccccc
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-----GNKHL-RKVLIAT--ENKSILVVGDIDCCTELQDRS  298 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-----~~~~l-~~~l~~~--~~~~Il~iDeiD~~~~~~~r~  298 (338)
                        .|+|+|||||||||.+++|.|...+..+..+-...+.     +...| +..|.-+  ..|+||||||+|++..  +|-
T Consensus       206 --KGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGt--KRf  281 (424)
T KOG0652|consen  206 --KGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGT--KRF  281 (424)
T ss_pred             --CceEeeCCCCCcHHHHHHHHHHhccchHHHhcchHHHhhhhcchHHHHHHHHHHhhccCCeEEEEechhhhcc--ccc
Confidence              8999999999999999999999998877766555443     23443 4444433  4799999999999988  776


Q ss_pred             ccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          299 AQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                      .+..+      .+...++|+-.|||++||..|.
T Consensus       282 DSek~------GDREVQRTMLELLNQLDGFss~  308 (424)
T KOG0652|consen  282 DSEKA------GDREVQRTMLELLNQLDGFSSD  308 (424)
T ss_pred             ccccc------ccHHHHHHHHHHHHhhcCCCCc
Confidence            65542      3567899999999999999874

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

Probab=99.69  E-value=3.8e-17  Score=147.98  Aligned_cols=122  Identities=25%  Similarity=0.436  Sum_probs=98.0

Q ss_pred             CCCccccccCChhHHH---HHHHHHHhh-----h-cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC------
Q 035959          202 HPSTFDTLAMDTDMKK---MIMDDLERA-----W-KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG------  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~---~i~~~l~~~-----~-~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~------  266 (338)
                      ...+|++++++++.|+   -|++.|..|     | ++++|+|||||||||++|+|+|++++.+++.+..+++..      
T Consensus       116 ~~it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp~l~vkat~liGehVGdg  195 (368)
T COG1223         116 SDITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDG  195 (368)
T ss_pred             ccccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCceEEechHHHHHHHhhhH
Confidence            3458999999988774   466777762     3 589999999999999999999999999999999988763      


Q ss_pred             chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCC
Q 035959          267 NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCG  333 (338)
Q Consensus       267 ~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g  333 (338)
                      ...++++...+.  .|||+||||+|+++-  +|+=++-        .+...-.++.||..|||+-..+|
T Consensus       196 ar~Ihely~rA~~~aPcivFiDE~DAiaL--dRryQel--------RGDVsEiVNALLTelDgi~eneG  254 (368)
T COG1223         196 ARRIHELYERARKAAPCIVFIDELDAIAL--DRRYQEL--------RGDVSEIVNALLTELDGIKENEG  254 (368)
T ss_pred             HHHHHHHHHHHHhcCCeEEEehhhhhhhh--hhhHHHh--------cccHHHHHHHHHHhccCcccCCc
Confidence            345777877775  899999999999976  6644332        34456789999999999986554

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

Probab=99.69  E-value=2.3e-17  Score=148.70  Aligned_cols=113  Identities=27%  Similarity=0.451  Sum_probs=92.1

Q ss_pred             cccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----chHH-
Q 035959          197 SAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----NKHL-  270 (338)
Q Consensus       197 ~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----~~~l-  270 (338)
                      .+|..||..|+.++...+              .|+|||||||||||.|++|+|.+....++.++.+++..     .+.+ 
T Consensus       164 eLPvKHPELF~aLGIaQP--------------KGvlLygppgtGktLlaraVahht~c~firvsgselvqk~igegsrmv  229 (404)
T KOG0728|consen  164 ELPVKHPELFEALGIAQP--------------KGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKYIGEGSRMV  229 (404)
T ss_pred             hccccCHHHHHhcCCCCC--------------cceEEecCCCCchhHHHHHHHhhcceEEEEechHHHHHHHhhhhHHHH
Confidence            578999999999987654              89999999999999999999999999999999988762     3344 


Q ss_pred             HHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          271 RKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       271 ~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                      +.+|.-+  ..|+|||+||||++..  .|..++.      +.++..++|+-.|||++||.-+.
T Consensus       230 relfvmarehapsiifmdeidsigs--~r~e~~~------ggdsevqrtmlellnqldgfeat  284 (404)
T KOG0728|consen  230 RELFVMAREHAPSIIFMDEIDSIGS--SRVESGS------GGDSEVQRTMLELLNQLDGFEAT  284 (404)
T ss_pred             HHHHHHHHhcCCceEeeeccccccc--ccccCCC------CccHHHHHHHHHHHHhccccccc
Confidence            4444433  3899999999999988  5544333      23567899999999999999865

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

Probab=99.65  E-value=4.4e-16  Score=159.95  Aligned_cols=122  Identities=26%  Similarity=0.372  Sum_probs=100.7

Q ss_pred             CCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-----  265 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-----  265 (338)
                      +-+|+++++-++.|++|.+-+.-            ..++|+||+||||||||.||+|+|.+.|.|++.++.++..     
T Consensus       307 ~V~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE~~~g  386 (774)
T KOG0731|consen  307 GVKFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEMFVG  386 (774)
T ss_pred             CCccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHHHHhcc
Confidence            35899999999999887765554            4689999999999999999999999999999999999865     


Q ss_pred             -CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          266 -GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       266 -~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                       ..+.++.+|..+.  .|||++|||||.+..  .|.+...     .+.+.....||++||-.|||..+.
T Consensus       387 ~~asrvr~lf~~ar~~aP~iifideida~~~--~r~G~~~-----~~~~~e~e~tlnQll~emDgf~~~  448 (774)
T KOG0731|consen  387 VGASRVRDLFPLARKNAPSIIFIDEIDAVGR--KRGGKGT-----GGGQDEREQTLNQLLVEMDGFETS  448 (774)
T ss_pred             cchHHHHHHHHHhhccCCeEEEecccccccc--ccccccc-----CCCChHHHHHHHHHHHHhcCCcCC
Confidence             2567888888775  799999999999987  6642111     122445678999999999999876

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

Probab=99.64  E-value=5e-16  Score=148.25  Aligned_cols=93  Identities=17%  Similarity=0.189  Sum_probs=75.5

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC------chHHHHHHHhcC-------CCcEEEEcCCCccC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG------NKHLRKVLIATE-------NKSILVVGDIDCCT  292 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~------~~~l~~~l~~~~-------~~~Il~iDeiD~~~  292 (338)
                      ..+++++||||||||||.+++|+|+++|.+++.++..++.+      +..++++|..+.       +||||||||||.++
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~  225 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGA  225 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcC
Confidence            56789999999999999999999999999999999998873      567888887653       69999999999998


Q ss_pred             CcccccccccCCCCCCCCCCcchhhHHHHHHHhcCC
Q 035959          293 ELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL  328 (338)
Q Consensus       293 ~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl  328 (338)
                      +  .|+....        ....++..+.|||.+||+
T Consensus       226 g--~r~~~~~--------tv~~qiV~~tLLnl~D~p  251 (413)
T PLN00020        226 G--RFGTTQY--------TVNNQMVNGTLMNIADNP  251 (413)
T ss_pred             C--CCCCCCc--------chHHHHHHHHHHHHhcCC
Confidence            8  5542211        123456668999999874

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.61  E-value=2.6e-15  Score=150.52  Aligned_cols=115  Identities=18%  Similarity=0.287  Sum_probs=90.7

Q ss_pred             CCccccccCChhHHHHHHHHHHh----------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC------C
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER----------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE------G  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~----------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~------~  266 (338)
                      ..+|+++++-+.+|+.+.+....          +.++|+|||||||||||++++|+|++++.+++.++++.+.      +
T Consensus       224 ~~~~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~l~~~~vGes  303 (489)
T CHL00195        224 NEKISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGES  303 (489)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHHhcccccChH
Confidence            34799999988888877654322          4578999999999999999999999999999999987654      2


Q ss_pred             chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcC
Q 035959          267 NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDG  327 (338)
Q Consensus       267 ~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDg  327 (338)
                      +..++++|..+  .+||||+|||||.++.  ++....        ..+...+.++.||+.|+.
T Consensus       304 e~~l~~~f~~A~~~~P~IL~IDEID~~~~--~~~~~~--------d~~~~~rvl~~lL~~l~~  356 (489)
T CHL00195        304 ESRMRQMIRIAEALSPCILWIDEIDKAFS--NSESKG--------DSGTTNRVLATFITWLSE  356 (489)
T ss_pred             HHHHHHHHHHHHhcCCcEEEehhhhhhhc--cccCCC--------CchHHHHHHHHHHHHHhc
Confidence            45678888754  4899999999999876  332221        134567889999999985

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

Probab=99.59  E-value=2.6e-15  Score=151.23  Aligned_cols=123  Identities=20%  Similarity=0.345  Sum_probs=101.5

Q ss_pred             cccCCCCC--ccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          197 SAILDHPS--TFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       197 ~~~~~~p~--~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .+.+..+.  .|+++++-.+.|+.+.+-+.-             .-+.|+|||||||||||+|+.|+|..++..++.+-.
T Consensus       655 ~ik~~k~tgi~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fisvKG  734 (952)
T KOG0735|consen  655 GIKLVKSTGIRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFISVKG  734 (952)
T ss_pred             hccccccCCCCceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEEecC
Confidence            34444443  678888888888877777765             235689999999999999999999999999999988


Q ss_pred             CCcC------CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          262 SSVE------GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       262 ~~~~------~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                      .++.      ++..++.+|.++.  +|||||+||+|++++  +|+.++.         ++..+.+++||..|||.-.
T Consensus       735 PElL~KyIGaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAP--kRGhDsT---------GVTDRVVNQlLTelDG~Eg  800 (952)
T KOG0735|consen  735 PELLSKYIGASEQNVRDLFERAQSAKPCILFFDEFDSIAP--KRGHDST---------GVTDRVVNQLLTELDGAEG  800 (952)
T ss_pred             HHHHHHHhcccHHHHHHHHHHhhccCCeEEEeccccccCc--ccCCCCC---------CchHHHHHHHHHhhccccc
Confidence            8765      4677999998874  899999999999998  7765544         6788999999999999865

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

Probab=99.59  E-value=1.1e-15  Score=138.98  Aligned_cols=119  Identities=27%  Similarity=0.377  Sum_probs=92.7

Q ss_pred             ccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----chHH
Q 035959          196 QSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----NKHL  270 (338)
Q Consensus       196 ~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----~~~l  270 (338)
                      .++|+-||..|-.++.+|+              .|+|||||||||||.+++|+||..+.-++.+=.+++..     ...+
T Consensus       193 ve~pll~perfv~lgidpp--------------kgvllygppgtgktl~aravanrtdacfirvigselvqkyvgegarm  258 (435)
T KOG0729|consen  193 VELPLLHPERFVNLGIDPP--------------KGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGARM  258 (435)
T ss_pred             HhccccCHHHHhhcCCCCC--------------CceEEeCCCCCchhHHHHHHhcccCceEEeehhHHHHHHHhhhhHHH
Confidence            3567788888888888775              89999999999999999999999999999998887652     3444


Q ss_pred             -HHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCccc
Q 035959          271 -RKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERI  337 (338)
Q Consensus       271 -~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~eri  337 (338)
                       +.+|.-+  .+.||||+||||++..  .|-.+..      +.+...++|+-.|+|++||... .|+..+
T Consensus       259 vrelf~martkkaciiffdeidaigg--arfddg~------ggdnevqrtmleli~qldgfdp-rgnikv  319 (435)
T KOG0729|consen  259 VRELFEMARTKKACIIFFDEIDAIGG--ARFDDGA------GGDNEVQRTMLELINQLDGFDP-RGNIKV  319 (435)
T ss_pred             HHHHHHHhcccceEEEEeeccccccC--ccccCCC------CCcHHHHHHHHHHHHhccCCCC-CCCeEE
Confidence             4444433  3679999999999988  6644432      2245679999999999999984 476554

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

Probab=99.59  E-value=2.4e-15  Score=138.68  Aligned_cols=114  Identities=25%  Similarity=0.420  Sum_probs=88.2

Q ss_pred             ccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----  266 (338)
                      .|+++++-+..|+.+.+.+.-             || +|+|||||||||||.|++|+|-+.+..++.++-+++.+     
T Consensus       131 kWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~Pw-rgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLvSKWmGE  209 (439)
T KOG0739|consen  131 KWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPW-RGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGE  209 (439)
T ss_pred             chhhhccchhHHHHHHhheeecccchhhhcCCCCcc-eeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHHHHHHhcc
Confidence            456677777777776665544             34 79999999999999999999999999999999988774     


Q ss_pred             chHH-HHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 NKHL-RKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ~~~l-~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                      .+.| ..+|.-+  .+|+||||||||.+..  .|+..+         ...+++.-..||-+|.|+--
T Consensus       210 SEkLVknLFemARe~kPSIIFiDEiDslcg--~r~enE---------seasRRIKTEfLVQMqGVG~  265 (439)
T KOG0739|consen  210 SEKLVKNLFEMARENKPSIIFIDEIDSLCG--SRSENE---------SEASRRIKTEFLVQMQGVGN  265 (439)
T ss_pred             HHHHHHHHHHHHHhcCCcEEEeehhhhhcc--CCCCCc---------hHHHHHHHHHHHHhhhcccc
Confidence            3344 4444433  3899999999998877  554433         34678999999999999964

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

Probab=99.59  E-value=3.5e-15  Score=146.34  Aligned_cols=122  Identities=26%  Similarity=0.318  Sum_probs=94.1

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      +..+|+++++.+..++++.+.+..             .+++|+|||||||||||++++++|++++.+++.+..+++..  
T Consensus       140 p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l~~k~  219 (398)
T PTZ00454        140 PDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKY  219 (398)
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHHHHh
Confidence            345789999998888888877653             35789999999999999999999999999999988765431  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                          ...++.+|..+  ..|+||||||||.++.  +|.+...      +.+...++.+..||+.|||+...
T Consensus       220 ~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~--~r~~~~~------~~d~~~~r~l~~LL~~ld~~~~~  282 (398)
T PTZ00454        220 LGEGPRMVRDVFRLARENAPSIIFIDEVDSIAT--KRFDAQT------GADREVQRILLELLNQMDGFDQT  282 (398)
T ss_pred             cchhHHHHHHHHHHHHhcCCeEEEEECHhhhcc--ccccccC------CccHHHHHHHHHHHHHhhccCCC
Confidence                23456666554  4789999999999987  5533221      11234578899999999998754

>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=99.58  E-value=8.7e-15  Score=131.45  Aligned_cols=94  Identities=23%  Similarity=0.329  Sum_probs=70.2

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhc-----CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHH
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWK-----RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVL  274 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~-----~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l  274 (338)
                      .-.|.+|++++++++++..+.-.+.....     ..+|||||||+|||+||..+|++++.++..++...+....++..++
T Consensus        17 ~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i~k~~dl~~il   96 (233)
T PF05496_consen   17 RLRPKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAIEKAGDLAAIL   96 (233)
T ss_dssp             HTS-SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC--SCHHHHHHH
T ss_pred             hcCCCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCCeEeccchhhhhHHHHHHHH
Confidence            35688999999999998876655554332     3589999999999999999999999999999988777788899999


Q ss_pred             HhcCCCcEEEEcCCCccCC
Q 035959          275 IATENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 ~~~~~~~Il~iDeiD~~~~  293 (338)
                      ..+..+.||||||||.+..
T Consensus        97 ~~l~~~~ILFIDEIHRlnk  115 (233)
T PF05496_consen   97 TNLKEGDILFIDEIHRLNK  115 (233)
T ss_dssp             HT--TT-EEEECTCCC--H
T ss_pred             HhcCCCcEEEEechhhccH
Confidence            9999999999999999954

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.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.58  E-value=4.4e-15  Score=150.09  Aligned_cols=123  Identities=26%  Similarity=0.379  Sum_probs=95.2

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC---
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE---  265 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~---  265 (338)
                      .+..+|+++++.++.|+++.+.+..            ..++|+|||||||||||++++++|++++.+++.++++++.   
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~~~  128 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMF  128 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHHHHH
Confidence            3455899999999888777654442            3467999999999999999999999999999999887653   


Q ss_pred             ---CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          266 ---GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       266 ---~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                         ....++++|..+.  .|+||||||||.+..  +|.....      +.+.....+++.||+.|||+.+.
T Consensus       129 ~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~--~r~~~~~------~~~~~~~~~~~~lL~~~d~~~~~  191 (495)
T TIGR01241       129 VGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGR--QRGAGLG------GGNDEREQTLNQLLVEMDGFGTN  191 (495)
T ss_pred             hcccHHHHHHHHHHHHhcCCCEEEEechhhhhh--ccccCcC------CccHHHHHHHHHHHhhhccccCC
Confidence               2456788887763  689999999999987  5533211      11234468899999999999654

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.57  E-value=6.2e-15  Score=147.93  Aligned_cols=120  Identities=22%  Similarity=0.329  Sum_probs=87.3

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCc----------EEE
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFD----------VYD  258 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~----------~~~  258 (338)
                      ++.+|+++++-+..++++.+.+..             ++++|+|||||||||||++++++|++++.+          ++.
T Consensus       177 p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~  256 (512)
T TIGR03689       177 PDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLN  256 (512)
T ss_pred             CCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEe
Confidence            356899999888888888877654             467899999999999999999999998755          223


Q ss_pred             EecCCcCC------chHHHHHHHhcC------CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhc
Q 035959          259 LELSSVEG------NKHLRKVLIATE------NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTD  326 (338)
Q Consensus       259 l~~~~~~~------~~~l~~~l~~~~------~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iD  326 (338)
                      +..+++.+      ...++.+|..+.      .++||||||+|.++.  .|+....        ....+..+++||+.||
T Consensus       257 v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~--~R~~~~s--------~d~e~~il~~LL~~LD  326 (512)
T TIGR03689       257 IKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFR--TRGSGVS--------SDVETTVVPQLLSELD  326 (512)
T ss_pred             ccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhc--ccCCCcc--------chHHHHHHHHHHHHhc
Confidence            33333321      234556655442      589999999999987  5533211        1234678899999999


Q ss_pred             CCcCC
Q 035959          327 GLWSS  331 (338)
Q Consensus       327 gl~s~  331 (338)
                      |+.+.
T Consensus       327 gl~~~  331 (512)
T TIGR03689       327 GVESL  331 (512)
T ss_pred             ccccC
Confidence            99864

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

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

Probab=99.55  E-value=1e-14  Score=147.32  Aligned_cols=122  Identities=26%  Similarity=0.370  Sum_probs=98.9

Q ss_pred             CCCccccccCChhHHHHHHHH---HHh---------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC----
Q 035959          202 HPSTFDTLAMDTDMKKMIMDD---LER---------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE----  265 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~---l~~---------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~----  265 (338)
                      ..-+|.++++.++.|+++.+-   |..         ..++|+||+||||||||.|++|+|.+.+.|++.++.++..    
T Consensus       145 ~~v~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FVemfV  224 (596)
T COG0465         145 VKVTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFV  224 (596)
T ss_pred             cCcChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCceeccchhhhhhhc
Confidence            345899999988888766554   443         3478999999999999999999999999999999999865    


Q ss_pred             --CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          266 --GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       266 --~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                        ..+..+.+|.++.  .|||+||||||++..  .|.....      +.+.....||++||..|||.-+.
T Consensus       225 GvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr--~Rg~g~G------ggnderEQTLNQlLvEmDGF~~~  286 (596)
T COG0465         225 GVGASRVRDLFEQAKKNAPCIIFIDEIDAVGR--QRGAGLG------GGNDEREQTLNQLLVEMDGFGGN  286 (596)
T ss_pred             CCCcHHHHHHHHHhhccCCCeEEEehhhhccc--ccCCCCC------CCchHHHHHHHHHHhhhccCCCC
Confidence              3678899999886  599999999999987  5543321      22445567999999999999753

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.55  E-value=1.4e-14  Score=142.15  Aligned_cols=120  Identities=24%  Similarity=0.348  Sum_probs=92.6

Q ss_pred             CCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC---
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG---  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~---  266 (338)
                      ..+|+++++-++.++++.+.+..             ..++|+|||||||||||++++++|++++.+++.++++++..   
T Consensus       127 ~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~~l~~~~~  206 (389)
T PRK03992        127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFI  206 (389)
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCCEEEeehHHHhHhhc
Confidence            34788999988888888877654             34678999999999999999999999999999998887642   


Q ss_pred             ---chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ---NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ---~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                         ...++.+|..+.  .++||||||||.+..  .|.+....      .+...+.++..||+.+||+.+
T Consensus       207 g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~--~r~~~~~~------~~~~~~~~l~~lL~~ld~~~~  267 (389)
T PRK03992        207 GEGARLVRELFELAREKAPSIIFIDEIDAIAA--KRTDSGTS------GDREVQRTLMQLLAEMDGFDP  267 (389)
T ss_pred             cchHHHHHHHHHHHHhcCCeEEEEechhhhhc--ccccCCCC------ccHHHHHHHHHHHHhccccCC
Confidence               234566666543  689999999999987  55433221      123456789999999999864

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

Probab=99.52  E-value=1.7e-14  Score=142.75  Aligned_cols=123  Identities=26%  Similarity=0.310  Sum_probs=92.5

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-  266 (338)
                      .++.+|+++++-+..++++.+.+..             .+++|+|||||||||||++++++|+.++.+++.+..+++.. 
T Consensus       177 ~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~seL~~k  256 (438)
T PTZ00361        177 APLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQK  256 (438)
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEecchhhhh
Confidence            3456888888888888777776653             34679999999999999999999999999999998877642 


Q ss_pred             -----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 -----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 -----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                           ...++.+|..+  ..++||||||||.+..  +|.....      +.....+.++..||+.|||+...
T Consensus       257 ~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~--kR~~~~s------gg~~e~qr~ll~LL~~Ldg~~~~  320 (438)
T PTZ00361        257 YLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGT--KRYDATS------GGEKEIQRTMLELLNQLDGFDSR  320 (438)
T ss_pred             hcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhc--cCCCCCC------cccHHHHHHHHHHHHHHhhhccc
Confidence                 22355666544  3789999999999986  5543222      11234567889999999998643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.52  E-value=3.1e-14  Score=150.19  Aligned_cols=117  Identities=23%  Similarity=0.356  Sum_probs=95.5

Q ss_pred             CccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-----
Q 035959          204 STFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-----  265 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-----  265 (338)
                      .+|+++++.+..|+.+.+.+..             ..++|+|||||||||||++++|+|++++.+++.++.+++.     
T Consensus       450 ~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~~~vG  529 (733)
T TIGR01243       450 VRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVG  529 (733)
T ss_pred             cchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhhcccC
Confidence            3788999999999888887653             3567899999999999999999999999999999987754     


Q ss_pred             -CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          266 -GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       266 -~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                       ++..++++|..+.  .++||||||||.+++  .|+....        .....+.++.||+.|||+..
T Consensus       530 ese~~i~~~f~~A~~~~p~iifiDEid~l~~--~r~~~~~--------~~~~~~~~~~lL~~ldg~~~  587 (733)
T TIGR01243       530 ESEKAIREIFRKARQAAPAIIFFDEIDAIAP--ARGARFD--------TSVTDRIVNQLLTEMDGIQE  587 (733)
T ss_pred             cHHHHHHHHHHHHHhcCCEEEEEEChhhhhc--cCCCCCC--------ccHHHHHHHHHHHHhhcccC
Confidence             2456888887764  789999999999987  5543222        23457899999999999864

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.

>CHL00176 ftsH cell division protein; Validated

Probab=99.52  E-value=3.7e-14  Score=146.34  Aligned_cols=123  Identities=26%  Similarity=0.375  Sum_probs=93.6

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC---
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE---  265 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~---  265 (338)
                      ...-+|+++++.++.++++.+.+..            ..++|+||+||||||||++++++|++++.+++.++++++.   
T Consensus       177 ~~~~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~~~~  256 (638)
T CHL00176        177 DTGITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMF  256 (638)
T ss_pred             CCCCCHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHHHHh
Confidence            3345899999988888766554432            2467999999999999999999999999999999887654   


Q ss_pred             ---CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          266 ---GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       266 ---~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                         ....++.+|..+.  .||||||||||++..  .|.....      +.+.....++..||+.|||+...
T Consensus       257 ~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~--~r~~~~~------~~~~e~~~~L~~LL~~~dg~~~~  319 (638)
T CHL00176        257 VGVGAARVRDLFKKAKENSPCIVFIDEIDAVGR--QRGAGIG------GGNDEREQTLNQLLTEMDGFKGN  319 (638)
T ss_pred             hhhhHHHHHHHHHHHhcCCCcEEEEecchhhhh--cccCCCC------CCcHHHHHHHHHHHhhhccccCC
Confidence               2345677777664  789999999999976  5532211      11334568899999999998754

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

Probab=99.51  E-value=5e-14  Score=142.35  Aligned_cols=118  Identities=25%  Similarity=0.365  Sum_probs=95.8

Q ss_pred             CCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC---
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG---  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~---  266 (338)
                      .-+|+++++....|+.+.+.+..             ..++|+|||||||||||+|++|+|++++.+++.++.+++.+   
T Consensus       238 ~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~sk~v  317 (494)
T COG0464         238 DVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWV  317 (494)
T ss_pred             CcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHHHhcccc
Confidence            34788888877777777766655             23468999999999999999999999999999999997764   


Q ss_pred             ---chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ---NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ---~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                         +..++++|..+.  .+|||||||+|.+++  .|.....         +...+.+++||..|||+-..
T Consensus       318 Gesek~ir~~F~~A~~~~p~iiFiDEiDs~~~--~r~~~~~---------~~~~r~~~~lL~~~d~~e~~  376 (494)
T COG0464         318 GESEKNIRELFEKARKLAPSIIFIDEIDSLAS--GRGPSED---------GSGRRVVGQLLTELDGIEKA  376 (494)
T ss_pred             chHHHHHHHHHHHHHcCCCcEEEEEchhhhhc--cCCCCCc---------hHHHHHHHHHHHHhcCCCcc
Confidence               567888888875  799999999999998  6644332         22369999999999999754

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

Probab=99.49  E-value=4.1e-14  Score=131.13  Aligned_cols=112  Identities=28%  Similarity=0.423  Sum_probs=86.8

Q ss_pred             cccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----chH-H
Q 035959          197 SAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----NKH-L  270 (338)
Q Consensus       197 ~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----~~~-l  270 (338)
                      .+|+..|..|-.+...+              +.|++||||||||||.+++++|..+|.+++.+..+++.+     .+. +
T Consensus       149 elpl~np~lf~rvgIk~--------------Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~lv~kyiGEsaRlI  214 (388)
T KOG0651|consen  149 ELPLTNPELFLRVGIKP--------------PKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKYIGESARLI  214 (388)
T ss_pred             EeeccCchhccccCCCC--------------CceeEEeCCCCCchhHHHHHHHHhcCCceEEeeHhhhhhhhcccHHHHH
Confidence            35566666666655544              489999999999999999999999999999999988874     223 4


Q ss_pred             HHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          271 RKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       271 ~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                      ++.+..+.  .+||||+||||++..  .|..+..      ..+...++||-.|||+|||.-.
T Consensus       215 Remf~yA~~~~pciifmdeiDAigG--Rr~se~T------s~dreiqrTLMeLlnqmdgfd~  268 (388)
T KOG0651|consen  215 RDMFRYAREVIPCIIFMDEIDAIGG--RRFSEGT------SSDREIQRTLMELLNQMDGFDT  268 (388)
T ss_pred             HHHHHHHhhhCceEEeehhhhhhcc--EEecccc------chhHHHHHHHHHHHHhhccchh
Confidence            55665554  689999999999987  4533322      2356779999999999999864

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

Probab=99.48  E-value=5.4e-14  Score=133.19  Aligned_cols=122  Identities=24%  Similarity=0.420  Sum_probs=94.2

Q ss_pred             ccccccCChhHHHHHHHHHHh--------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER--------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~--------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----  266 (338)
                      +|+++++-+.+++.+.+.+.-              ..++|+|||||||||||.+|+|+|.+.|..++.|..+.+.+    
T Consensus        90 ~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~KWfg  169 (386)
T KOG0737|consen   90 SFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTSKWFG  169 (386)
T ss_pred             ehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccchhhHH
Confidence            677777777766666655443              34689999999999999999999999999999999998875    


Q ss_pred             -chHHHHHHHhcC---CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCcccC
Q 035959          267 -NKHLRKVLIATE---NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII  338 (338)
Q Consensus       267 -~~~l~~~l~~~~---~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~erii  338 (338)
                       ...+.+.++..+   +|+||+|||||.++.  .| +..        .+......-.+|...=||+.|. +++||+
T Consensus       170 E~eKlv~AvFslAsKl~P~iIFIDEvds~L~--~R-~s~--------dHEa~a~mK~eFM~~WDGl~s~-~~~rVl  233 (386)
T KOG0737|consen  170 EAQKLVKAVFSLASKLQPSIIFIDEVDSFLG--QR-RST--------DHEATAMMKNEFMALWDGLSSK-DSERVL  233 (386)
T ss_pred             HHHHHHHHHHhhhhhcCcceeehhhHHHHHh--hc-ccc--------hHHHHHHHHHHHHHHhccccCC-CCceEE
Confidence             234545544444   799999999999987  55 221        2456678888999999999976 556764

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

Probab=99.45  E-value=5.9e-14  Score=130.75  Aligned_cols=120  Identities=24%  Similarity=0.422  Sum_probs=90.7

Q ss_pred             ccccccCChhHHHHHHHHHHh--------------hhcCceeeeCCCCCCcHHHHHHHHHHhC---------CcEEEEec
Q 035959          205 TFDTLAMDTDMKKMIMDDLER--------------AWKRGYLLFGPPGTGKSSLIAAMANYLH---------FDVYDLEL  261 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~--------------~~~~g~LL~GppGtGKT~l~~aia~~l~---------~~~~~l~~  261 (338)
                      .|++++.+.++|++++.....              .|.|-+|||||||||||+|++|+|.++-         -.++++++
T Consensus       140 lWEsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins  219 (423)
T KOG0744|consen  140 LWESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS  219 (423)
T ss_pred             hHHHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh
Confidence            568899999999999988776              5788899999999999999999999983         24567777


Q ss_pred             CCcCC------chHHHHHHHhcC-------CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCC
Q 035959          262 SSVEG------NKHLRKVLIATE-------NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL  328 (338)
Q Consensus       262 ~~~~~------~~~l~~~l~~~~-------~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl  328 (338)
                      .++.+      ..-+.++|++..       .-.+++|||+++++.  .|......++     +...-+.++.||.+||.+
T Consensus       220 hsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~--aR~s~~S~~E-----psDaIRvVNalLTQlDrl  292 (423)
T KOG0744|consen  220 HSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAA--ARTSASSRNE-----PSDAIRVVNALLTQLDRL  292 (423)
T ss_pred             hHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHH--HHHhhhcCCC-----CchHHHHHHHHHHHHHHh
Confidence            76653      233455555542       345788999999987  6644433222     334578999999999999


Q ss_pred             cCC
Q 035959          329 WSS  331 (338)
Q Consensus       329 ~s~  331 (338)
                      -.+
T Consensus       293 K~~  295 (423)
T KOG0744|consen  293 KRY  295 (423)
T ss_pred             ccC
Confidence            754

>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=99.45  E-value=9.2e-14  Score=114.35  Aligned_cols=90  Identities=30%  Similarity=0.469  Sum_probs=72.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC------chHHHHHHHhc--CC-CcEEEEcCCCccCCcccccccc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG------NKHLRKVLIAT--EN-KSILVVGDIDCCTELQDRSAQA  301 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~------~~~l~~~l~~~--~~-~~Il~iDeiD~~~~~~~r~~~~  301 (338)
                      +||+||||||||++++++|+.++.+++.+++.++.+      ...+..++..+  .. ++||+|||+|.+..  +. ...
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~--~~-~~~   77 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFP--KS-QPS   77 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSH--HC-STS
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccc--cc-ccc
Confidence            589999999999999999999999999999998762      34567777765  24 89999999999987  33 111


Q ss_pred             cCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          302 RTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       302 ~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                              ........+..|++.||.....
T Consensus        78 --------~~~~~~~~~~~L~~~l~~~~~~   99 (132)
T PF00004_consen   78 --------SSSFEQRLLNQLLSLLDNPSSK   99 (132)
T ss_dssp             --------SSHHHHHHHHHHHHHHHTTTTT
T ss_pred             --------cccccccccceeeecccccccc
Confidence                    1345678899999999998865

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=99.44  E-value=2.9e-13  Score=124.36  Aligned_cols=93  Identities=28%  Similarity=0.385  Sum_probs=84.8

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcC-----ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHH
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKR-----GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLI  275 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~-----g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~  275 (338)
                      -.|+.|+++++++.+|+.+.-.+.++..|     .+|||||||.|||+||..+|+++|..+...+...+....+|..++.
T Consensus        20 lRP~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK~gDlaaiLt   99 (332)
T COG2255          20 LRPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPGDLAAILT   99 (332)
T ss_pred             cCcccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccccChhhHHHHHh
Confidence            45889999999999999988888875554     4899999999999999999999999998888888888899999999


Q ss_pred             hcCCCcEEEEcCCCccCC
Q 035959          276 ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 ~~~~~~Il~iDeiD~~~~  293 (338)
                      .+...+||||||||.+.+
T Consensus       100 ~Le~~DVLFIDEIHrl~~  117 (332)
T COG2255         100 NLEEGDVLFIDEIHRLSP  117 (332)
T ss_pred             cCCcCCeEEEehhhhcCh
Confidence            999999999999999975

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.43  E-value=3e-13  Score=131.58  Aligned_cols=121  Identities=24%  Similarity=0.341  Sum_probs=90.0

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      +..+|+++++.+..++++.+.+..             ..++|+|||||||||||++++++|+.++.+++.+...++..  
T Consensus       117 p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~~~~l~~~~  196 (364)
T TIGR01242       117 PNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKY  196 (364)
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEecchHHHHHHh
Confidence            344788999989888888887754             23678999999999999999999999999988887665432  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                          ...++.++..+  ..++||+|||+|.+..  .|.+...      +.+...+.++..+|+.+||+..
T Consensus       197 ~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~--~~~~~~~------~~~~~~~~~l~~ll~~ld~~~~  258 (364)
T TIGR01242       197 IGEGARLVREIFELAKEKAPSIIFIDEIDAIAA--KRTDSGT------SGDREVQRTLMQLLAELDGFDP  258 (364)
T ss_pred             hhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhcc--ccccCCC------CccHHHHHHHHHHHHHhhCCCC
Confidence                12345555544  3689999999999976  5533222      1123456789999999999753

Many proteins may score above the trusted cutoff because an internal

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.41  E-value=2.7e-13  Score=149.04  Aligned_cols=95  Identities=20%  Similarity=0.245  Sum_probs=72.8

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCc--------------------------------------
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGN--------------------------------------  267 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~--------------------------------------  267 (338)
                      ..++|+||+||||||||.||+|+|.+++.+++.++++++...                                      
T Consensus      1628 ~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~~n~ 1707 (2281)
T CHL00206       1628 SPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMMNA 1707 (2281)
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhhhcch
Confidence            446999999999999999999999999999999988765420                                      


Q ss_pred             ---------h--HHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCC
Q 035959          268 ---------K--HLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGD  334 (338)
Q Consensus       268 ---------~--~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~  334 (338)
                               .  .++.+|..+  .+||||+|||||.+..  +               .....+++.|||.|||....|..
T Consensus      1708 ~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~--~---------------ds~~ltL~qLLneLDg~~~~~s~ 1770 (2281)
T CHL00206       1708 LTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNV--N---------------ESNYLSLGLLVNSLSRDCERCST 1770 (2281)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCC--C---------------ccceehHHHHHHHhccccccCCC
Confidence                     1  145556655  3799999999999975  1               11246799999999998644444


Q ss_pred             ccc
Q 035959          335 ERI  337 (338)
Q Consensus       335 eri  337 (338)
                      +.|
T Consensus      1771 ~~V 1773 (2281)
T CHL00206       1771 RNI 1773 (2281)
T ss_pred             CCE
Confidence            444

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

Probab=99.39  E-value=5.1e-13  Score=130.25  Aligned_cols=122  Identities=28%  Similarity=0.408  Sum_probs=91.5

Q ss_pred             ccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----c
Q 035959          205 TFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----N  267 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----~  267 (338)
                      .|+++.+....|+.+.+.+.-            +..+|+||.||||||||.|++|+|.+.+..++.+..+++.+     .
T Consensus       151 ~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr~p~rglLLfGPpgtGKtmL~~aiAsE~~atff~iSassLtsK~~Ge~  230 (428)
T KOG0740|consen  151 GWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLREPVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSLTSKYVGES  230 (428)
T ss_pred             cccCCcchhhHHHHhhhhhhhcccchHhhhccccccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHhhhhccChH
Confidence            344555555555554444433            44579999999999999999999999999999999998874     2


Q ss_pred             hHHHHHHHhc---CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCcccC
Q 035959          268 KHLRKVLIAT---ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDERII  338 (338)
Q Consensus       268 ~~l~~~l~~~---~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~erii  338 (338)
                      +.+.+.+...   .+|+|+||||||.++.  +|...         .+..+++....+|..+||..++ ++.||+
T Consensus       231 eK~vralf~vAr~~qPsvifidEidslls--~Rs~~---------e~e~srr~ktefLiq~~~~~s~-~~drvl  292 (428)
T KOG0740|consen  231 EKLVRALFKVARSLQPSVIFIDEIDSLLS--KRSDN---------EHESSRRLKTEFLLQFDGKNSA-PDDRVL  292 (428)
T ss_pred             HHHHHHHHHHHHhcCCeEEEechhHHHHh--hcCCc---------ccccchhhhhHHHhhhccccCC-CCCeEE
Confidence            2444444433   3899999999999998  77222         2467789999999999999987 555764

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.38  E-value=1.1e-12  Score=138.59  Aligned_cols=118  Identities=26%  Similarity=0.409  Sum_probs=92.9

Q ss_pred             CCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC---
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG---  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~---  266 (338)
                      ..+|+++++.+..++.+.+.+..             ..++|+|||||||||||++++++|++++.+++.+++.++.+   
T Consensus       174 ~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~~~~~  253 (733)
T TIGR01243       174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYY  253 (733)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHhcccc
Confidence            34899999999888888777654             34578999999999999999999999999999998876542   


Q ss_pred             ---chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ---NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ---~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                         ...++.+|..+.  .++||||||||.+..  +|....         ....+..++.||+.|||+...
T Consensus       254 g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~--~r~~~~---------~~~~~~~~~~Ll~~ld~l~~~  312 (733)
T TIGR01243       254 GESEERLREIFKEAEENAPSIIFIDEIDAIAP--KREEVT---------GEVEKRVVAQLLTLMDGLKGR  312 (733)
T ss_pred             cHHHHHHHHHHHHHHhcCCcEEEeehhhhhcc--cccCCc---------chHHHHHHHHHHHHhhccccC
Confidence               345777777653  679999999999987  443221         123467889999999999653

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.33  E-value=3.4e-12  Score=132.65  Aligned_cols=122  Identities=25%  Similarity=0.369  Sum_probs=92.2

Q ss_pred             CCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-----  265 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-----  265 (338)
                      ..+|+++.+.+..++++.+.+..            ..++|+||+||||||||++++++|++++.+++.++++++.     
T Consensus       148 ~~~~~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~~~~g  227 (644)
T PRK10733        148 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVG  227 (644)
T ss_pred             hCcHHHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHHhhhc
Confidence            45788888877777766554432            2367899999999999999999999999999999987643     


Q ss_pred             -CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCC
Q 035959          266 -GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSC  332 (338)
Q Consensus       266 -~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~  332 (338)
                       ....++.+|..+.  .|+||||||||.+..  .|.....      +.+.....+++.||+.|||+.+.+
T Consensus       228 ~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~--~r~~~~~------g~~~~~~~~ln~lL~~mdg~~~~~  289 (644)
T PRK10733        228 VGASRVRDMFEQAKKAAPCIIFIDEIDAVGR--QRGAGLG------GGHDEREQTLNQMLVEMDGFEGNE  289 (644)
T ss_pred             ccHHHHHHHHHHHHhcCCcEEEehhHhhhhh--ccCCCCC------CCchHHHHHHHHHHHhhhcccCCC
Confidence             2345677776653  789999999999986  5543211      112345679999999999997643

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

Probab=99.31  E-value=1.4e-12  Score=131.25  Aligned_cols=93  Identities=30%  Similarity=0.456  Sum_probs=80.8

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC------CchHHHHHHHhcC--C-CcEEEEcCCCccCCccc
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE------GNKHLRKVLIATE--N-KSILVVGDIDCCTELQD  296 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~------~~~~l~~~l~~~~--~-~~Il~iDeiD~~~~~~~  296 (338)
                      ++++|+|+|||||||||.+++|+|++.+..++.+++.++.      +++.|++.|..+.  + |+|++|||+|.+.+  +
T Consensus       216 ~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p--~  293 (693)
T KOG0730|consen  216 KPPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGPELISKFPGETESNLRKAFAEALKFQVPSIIFIDELDALCP--K  293 (693)
T ss_pred             CCCCCccccCCCCCChHHHHHHHHHHhCceeEecccHHHHHhcccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCC--c
Confidence            5679999999999999999999999999999999998775      4678999999885  4 99999999999998  6


Q ss_pred             ccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          297 RSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       297 r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                      |.+..          ...+++.++|+..|||+-+
T Consensus       294 r~~~~----------~~e~Rv~sqlltL~dg~~~  317 (693)
T KOG0730|consen  294 REGAD----------DVESRVVSQLLTLLDGLKP  317 (693)
T ss_pred             ccccc----------hHHHHHHHHHHHHHhhCcC
Confidence            64432          2568999999999999973

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.29  E-value=9.9e-12  Score=119.30  Aligned_cols=94  Identities=22%  Similarity=0.324  Sum_probs=79.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-----hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHH
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-----AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVL  274 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-----~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l  274 (338)
                      ...|.+|+++++.++.++.+...+..     ...+++|||||||||||++++++|+.++.++..++...+.....+..++
T Consensus        18 ~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~~~~~~l~~~l   97 (328)
T PRK00080         18 SLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPGDLAAIL   97 (328)
T ss_pred             hcCcCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccccChHHHHHHH
Confidence            34588999999999998888776654     2235799999999999999999999999998888777666667788888


Q ss_pred             HhcCCCcEEEEcCCCccCC
Q 035959          275 IATENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 ~~~~~~~Il~iDeiD~~~~  293 (338)
                      .....+++|||||||.+..
T Consensus        98 ~~l~~~~vl~IDEi~~l~~  116 (328)
T PRK00080         98 TNLEEGDVLFIDEIHRLSP  116 (328)
T ss_pred             HhcccCCEEEEecHhhcch
Confidence            8888899999999999864

>PRK04195 replication factor C large subunit; Provisional

Probab=99.28  E-value=1.8e-11  Score=123.38  Aligned_cols=95  Identities=24%  Similarity=0.415  Sum_probs=79.5

Q ss_pred             cCCCCCccccccCChhHHHHHHHHHHhhh----cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHH
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDLERAW----KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVL  274 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l~~~~----~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l  274 (338)
                      ..+.|.+|+++++++..++.+...+....    ++.+||+||||||||++++++|++++++++.++.++......+..++
T Consensus         6 eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~r~~~~i~~~i   85 (482)
T PRK04195          6 EKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVA   85 (482)
T ss_pred             hhcCCCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEcccccccHHHHHHHH
Confidence            47889999999999999999888887522    57899999999999999999999999999999998877655555554


Q ss_pred             Hhc--------CCCcEEEEcCCCccCC
Q 035959          275 IAT--------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 ~~~--------~~~~Il~iDeiD~~~~  293 (338)
                      ...        ..+.||||||+|.+..
T Consensus        86 ~~~~~~~sl~~~~~kvIiIDEaD~L~~  112 (482)
T PRK04195         86 GEAATSGSLFGARRKLILLDEVDGIHG  112 (482)
T ss_pred             HHhhccCcccCCCCeEEEEecCccccc
Confidence            433        1578999999999864

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.27  E-value=1.5e-11  Score=116.41  Aligned_cols=89  Identities=21%  Similarity=0.307  Sum_probs=74.6

Q ss_pred             ccccccCChhHHHHHHHHHHh-----hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCC
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-----AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATEN  279 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-----~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~  279 (338)
                      +|+++++.++.++.+...+..     ...++++|+||||||||++++++|+.++.++..+..........+...+.....
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~   81 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNLEE   81 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcCchhHHHHHHhccc
Confidence            688999999999888877764     223568999999999999999999999998887776666666677777877788


Q ss_pred             CcEEEEcCCCccCC
Q 035959          280 KSILVVGDIDCCTE  293 (338)
Q Consensus       280 ~~Il~iDeiD~~~~  293 (338)
                      +.+|||||||.+.+
T Consensus        82 ~~vl~iDEi~~l~~   95 (305)
T TIGR00635        82 GDVLFIDEIHRLSP   95 (305)
T ss_pred             CCEEEEehHhhhCH
Confidence            89999999999865

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.

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

Probab=99.26  E-value=8.8e-12  Score=119.44  Aligned_cols=158  Identities=19%  Similarity=0.214  Sum_probs=109.3

Q ss_pred             cchhhHHhhhhHHHHHHhHHHHHhccceeeeecc-C-ccC--CCCccccccCCCCCccccccCChhHHHHHHHHHHh---
Q 035959          153 KHKETVLGTYIPHILKKSKELSKKKKTLKLFTLN-C-NRI--NHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER---  225 (338)
Q Consensus       153 ~~~~~vl~~~l~~v~~~~~~~~~~~~~~~l~~~~-~-~~~--~~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~---  225 (338)
                      +.-..|..+|+..++.....+++..+...-+... . ...  .+  -..........|+.++..|.++++|.+....   
T Consensus       299 keg~~V~w~yi~r~LGqPSLiREsSrg~~pw~gsls~~k~~i~~--~~~~s~~gk~pl~~ViL~psLe~Rie~lA~aTaN  376 (630)
T KOG0742|consen  299 KEGTLVTWRYIERRLGQPSLIRESSRGRFPWIGSLSALKHPIQG--SRSASSRGKDPLEGVILHPSLEKRIEDLAIATAN  376 (630)
T ss_pred             cccchhHHHHHHHHcCCchhhhhhccccCCCcccHHHHhchhhh--hHhhhhcCCCCcCCeecCHHHHHHHHHHHHHhcc
Confidence            3445688899999998888777766644222111 0 000  00  0011122233699999999998888765554   


Q ss_pred             -----hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----chHHHHHHHhcC---CCcEEEEcCCCccC
Q 035959          226 -----AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----NKHLRKVLIATE---NKSILVVGDIDCCT  292 (338)
Q Consensus       226 -----~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----~~~l~~~l~~~~---~~~Il~iDeiD~~~  292 (338)
                           ..-|++|+|||||||||..++-+|.+.|.++-.+...++..     ...+.++|+-..   +.-+|||||.|.++
T Consensus       377 TK~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS~rGLllFIDEADAFL  456 (630)
T KOG0742|consen  377 TKKHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFL  456 (630)
T ss_pred             cccccchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCccccchHHHHHHHHHHHHHhhcccceEEEehhhHHHH
Confidence                 34578999999999999999999999999988888877763     456778887553   67899999999998


Q ss_pred             CcccccccccCCCCCCCCCCcchhhHHHHH
Q 035959          293 ELQDRSAQARTASPDWHSPKRDQITLSGLL  322 (338)
Q Consensus       293 ~~~~r~~~~~~~~~~~~~~~~~~~~ls~lL  322 (338)
                      .  +|+....        ....+..|+.||
T Consensus       457 c--eRnktym--------SEaqRsaLNAlL  476 (630)
T KOG0742|consen  457 C--ERNKTYM--------SEAQRSALNALL  476 (630)
T ss_pred             H--Hhchhhh--------cHHHHHHHHHHH
Confidence            7  7766544        223455666655

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

Probab=99.25  E-value=1.2e-11  Score=118.60  Aligned_cols=92  Identities=24%  Similarity=0.424  Sum_probs=72.1

Q ss_pred             CCCCccccccCChhHH---HHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhc
Q 035959          201 DHPSTFDTLAMDTDMK---KMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIAT  277 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k---~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~  277 (338)
                      -.|.+++++++++++.   .-+...++...-...+|||||||||||+++.||..++.++..++... .+..+++.+++++
T Consensus        18 mRP~~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~-~gvkdlr~i~e~a   96 (436)
T COG2256          18 LRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVT-SGVKDLREIIEEA   96 (436)
T ss_pred             hCCCCHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhhCCceEEecccc-ccHHHHHHHHHHH
Confidence            3588999999987764   23333343333456899999999999999999999999999998754 3467788888776


Q ss_pred             C------CCcEEEEcCCCccCC
Q 035959          278 E------NKSILVVGDIDCCTE  293 (338)
Q Consensus       278 ~------~~~Il~iDeiD~~~~  293 (338)
                      .      ++.||||||||.+..
T Consensus        97 ~~~~~~gr~tiLflDEIHRfnK  118 (436)
T COG2256          97 RKNRLLGRRTILFLDEIHRFNK  118 (436)
T ss_pred             HHHHhcCCceEEEEehhhhcCh
Confidence            2      589999999999954

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.24  E-value=1.3e-11  Score=113.60  Aligned_cols=118  Identities=19%  Similarity=0.321  Sum_probs=79.9

Q ss_pred             HhHHHHHhccceeeeeccCccCCCCccccccCCCCCccccccCChhHHHHHHHHHHh------hhcCceeeeCCCCCCcH
Q 035959          169 KSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER------AWKRGYLLFGPPGTGKS  242 (338)
Q Consensus       169 ~~~~~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~------~~~~g~LL~GppGtGKT  242 (338)
                      .+.++.++++..++++..      ..|.-.+..+..+|+++...++..+.++..+..      ....+++|+|+||||||
T Consensus        40 ~~~~i~~~~~q~~~~~~~------~~s~i~~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKT  113 (244)
T PRK07952         40 RSAALERENRAMKMQRTF------NRSGIRPLHQNCSFENYRVECEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKN  113 (244)
T ss_pred             HHHHHHHHHHHHHHHHHH------HHcCCCccccCCccccccCCCchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHH
Confidence            344456666665555442      123222355677999987765444444444443      11258999999999999


Q ss_pred             HHHHHHHHHh---CCcEEEEecCCcCC---------chHHHHHHHhcCCCcEEEEcCCCccC
Q 035959          243 SLIAAMANYL---HFDVYDLELSSVEG---------NKHLRKVLIATENKSILVVGDIDCCT  292 (338)
Q Consensus       243 ~l~~aia~~l---~~~~~~l~~~~~~~---------~~~l~~~l~~~~~~~Il~iDeiD~~~  292 (338)
                      ||+.|+|+++   +..+..++..++..         +....+++..+...++|||||+++..
T Consensus       114 hLa~aia~~l~~~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~~~dlLvIDDig~~~  175 (244)
T PRK07952        114 HLAAAICNELLLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEIGVQT  175 (244)
T ss_pred             HHHHHHHHHHHhcCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhccCCEEEEeCCCCCC
Confidence            9999999998   67888887766542         12334667777789999999999875

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

Probab=99.24  E-value=8.1e-12  Score=122.87  Aligned_cols=96  Identities=25%  Similarity=0.431  Sum_probs=76.0

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCC-cEEEEecCCcC------CchHHHHHHHhcC----------CCcEEEEcCC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHF-DVYDLELSSVE------GNKHLRKVLIATE----------NKSILVVGDI  288 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~-~~~~l~~~~~~------~~~~l~~~l~~~~----------~~~Il~iDei  288 (338)
                      ++-+|+|||||||||||.+|+-+..-++. +--.++..++.      ++++++++|.+++          .-.||++|||
T Consensus       254 ~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEi  333 (744)
T KOG0741|consen  254 KHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEI  333 (744)
T ss_pred             cceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhh
Confidence            56689999999999999999999998864 34455665554      4788999998873          4579999999


Q ss_pred             CccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          289 DCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       289 D~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                      |+++.  .|++..+       ..++....+++||.-|||+-+
T Consensus       334 DAICK--qRGS~~g-------~TGVhD~VVNQLLsKmDGVeq  366 (744)
T KOG0741|consen  334 DAICK--QRGSMAG-------STGVHDTVVNQLLSKMDGVEQ  366 (744)
T ss_pred             HHHHH--hcCCCCC-------CCCccHHHHHHHHHhcccHHh
Confidence            99987  6654433       245677899999999999864

>PLN03025 replication factor C subunit; Provisional

Probab=99.19  E-value=5.4e-11  Score=113.79  Aligned_cols=95  Identities=24%  Similarity=0.311  Sum_probs=71.6

Q ss_pred             cCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh-C----CcEEEEecCCcCCchHHHHH
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL-H----FDVYDLELSSVEGNKHLRKV  273 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l-~----~~~~~l~~~~~~~~~~l~~~  273 (338)
                      ..+.|.+|+++++++++.+.+...+.......+|||||||||||+++.++|+++ +    ..+..++.++......++..
T Consensus         5 ~kyrP~~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~sd~~~~~~vr~~   84 (319)
T PLN03025          5 EKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVVRNK   84 (319)
T ss_pred             hhcCCCCHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecccccccHHHHHHH
Confidence            378899999999999988887776665444569999999999999999999997 2    24666666655444445544


Q ss_pred             HHhc---------CCCcEEEEcCCCccCC
Q 035959          274 LIAT---------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 l~~~---------~~~~Il~iDeiD~~~~  293 (338)
                      +...         ....|++|||+|.+..
T Consensus        85 i~~~~~~~~~~~~~~~kviiiDE~d~lt~  113 (319)
T PLN03025         85 IKMFAQKKVTLPPGRHKIVILDEADSMTS  113 (319)
T ss_pred             HHHHHhccccCCCCCeEEEEEechhhcCH
Confidence            3321         2467999999999965

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

Probab=99.19  E-value=3.6e-11  Score=127.24  Aligned_cols=124  Identities=25%  Similarity=0.346  Sum_probs=90.0

Q ss_pred             CCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCc
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSV  264 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~  264 (338)
                      -..|+++++-......+.+.+.-             ..+||+|+|||||||||++++|+|..+.     ..++.-..++.
T Consensus       261 ~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkgaD~  340 (1080)
T KOG0732|consen  261 SVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKGADC  340 (1080)
T ss_pred             ccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcCchh
Confidence            34788888766655555554443             3579999999999999999999999983     23333333333


Q ss_pred             C------CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCcc
Q 035959          265 E------GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDER  336 (338)
Q Consensus       265 ~------~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~er  336 (338)
                      .      .+.+++.+|.++.  .|+|+++||||-+++  .|.....         ......+|.||-.|||+-+. |...
T Consensus       341 lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlap--vrSskqE---------qih~SIvSTLLaLmdGldsR-gqVv  408 (1080)
T KOG0732|consen  341 LSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAP--VRSSKQE---------QIHASIVSTLLALMDGLDSR-GQVV  408 (1080)
T ss_pred             hccccCcHHHHHHHHHHHHhccCceEEeccccccccc--cccchHH---------HhhhhHHHHHHHhccCCCCC-CceE
Confidence            2      3567888888885  799999999999999  5533322         23457889999999999865 6555


Q ss_pred             cC
Q 035959          337 II  338 (338)
Q Consensus       337 ii  338 (338)
                      +|
T Consensus       409 vi  410 (1080)
T KOG0732|consen  409 VI  410 (1080)
T ss_pred             EE
Confidence            43

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

Probab=99.17  E-value=4.3e-11  Score=111.23  Aligned_cols=98  Identities=30%  Similarity=0.443  Sum_probs=70.3

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC------cEEEEecCCcCCc
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF------DVYDLELSSVEGN  267 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~------~~~~l~~~~~~~~  267 (338)
                      .|.  ..+.|.+|+++++++.+.+.+.+.+.+.-...||||||||||||+.|.|+|.++.-      .+..++.++....
T Consensus        25 swt--eKYrPkt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGi  102 (346)
T KOG0989|consen   25 SWT--EKYRPKTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGI  102 (346)
T ss_pred             chH--HHhCCCcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccc
Confidence            354  47899999999999999999988888744457899999999999999999999853      2344444443321


Q ss_pred             h-------HHHHHHHhc--------CCCcEEEEcCCCccCC
Q 035959          268 K-------HLRKVLIAT--------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~-------~l~~~l~~~--------~~~~Il~iDeiD~~~~  293 (338)
                      +       ...++....        +..-|+||||+|.+..
T Consensus       103 svvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmts  143 (346)
T KOG0989|consen  103 SVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTS  143 (346)
T ss_pred             cchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhH
Confidence            1       111222111        1347999999999964

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

Probab=99.17  E-value=8e-11  Score=119.79  Aligned_cols=84  Identities=25%  Similarity=0.360  Sum_probs=67.3

Q ss_pred             cCChhHHHHHHHHHHhh-----hc-CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHH------------
Q 035959          210 AMDTDMKKMIMDDLERA-----WK-RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLR------------  271 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~~-----~~-~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~------------  271 (338)
                      .+-+.+|++|++.|.-.     .+ .-++|.||||+|||||++++|+.++..++.+++..+.++++++            
T Consensus       326 YGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHRRTYIGamPG  405 (782)
T COG0466         326 YGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPG  405 (782)
T ss_pred             cCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhccccccccccCCh
Confidence            34567899999988761     12 2357999999999999999999999999999999999876654            


Q ss_pred             HHH---Hhc-CCCcEEEEcCCCccCC
Q 035959          272 KVL---IAT-ENKSILVVGDIDCCTE  293 (338)
Q Consensus       272 ~~l---~~~-~~~~Il~iDeiD~~~~  293 (338)
                      +++   ..+ ..+.+++|||||.+..
T Consensus       406 rIiQ~mkka~~~NPv~LLDEIDKm~s  431 (782)
T COG0466         406 KIIQGMKKAGVKNPVFLLDEIDKMGS  431 (782)
T ss_pred             HHHHHHHHhCCcCCeEEeechhhccC
Confidence            233   333 3688999999999987

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.16  E-value=8.9e-11  Score=117.71  Aligned_cols=94  Identities=27%  Similarity=0.491  Sum_probs=72.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++++++++.+...+.... +.++|||||||||||++|+++|+.++.                        
T Consensus         7 kyRP~~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~   86 (472)
T PRK14962          7 KYRPKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFM   86 (472)
T ss_pred             HHCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCC
Confidence            5679999999999999888877776533 345899999999999999999998753                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++.+.-.....++++....      ....||||||+|.+..
T Consensus        87 dv~el~aa~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~  131 (472)
T PRK14962         87 DVIELDAASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTK  131 (472)
T ss_pred             ccEEEeCcccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhHH
Confidence            57777776444445566555443      2467999999999853

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.16  E-value=1.3e-10  Score=118.16  Aligned_cols=97  Identities=23%  Similarity=0.340  Sum_probs=83.3

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHh----------------------------------hhcCceeeeCCCCC
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLER----------------------------------AWKRGYLLFGPPGT  239 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~----------------------------------~~~~g~LL~GppGt  239 (338)
                      .|.  ....|..|.+|..++..-+.++.+|..                                  |.++-+||+||||-
T Consensus       260 LWV--dky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGl  337 (877)
T KOG1969|consen  260 LWV--DKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGL  337 (877)
T ss_pred             eee--cccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCC
Confidence            574  478899999999999999999999987                                  45567899999999


Q ss_pred             CcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhc----------CCCcEEEEcCCCccC
Q 035959          240 GKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIAT----------ENKSILVVGDIDCCT  292 (338)
Q Consensus       240 GKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~----------~~~~Il~iDeiD~~~  292 (338)
                      |||+||+.+|+++||.+++++.++-.+...++..+..+          .+|.+|||||||-..
T Consensus       338 GKTTLAHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~  400 (877)
T KOG1969|consen  338 GKTTLAHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAP  400 (877)
T ss_pred             ChhHHHHHHHHhcCceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCc
Confidence            99999999999999999999999988866665554433          379999999999875

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.15  E-value=1.1e-10  Score=115.54  Aligned_cols=93  Identities=25%  Similarity=0.384  Sum_probs=73.8

Q ss_pred             CCCCCccccccCChhHHHH---HHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHh
Q 035959          200 LDHPSTFDTLAMDTDMKKM---IMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIA  276 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~---i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~  276 (338)
                      ..+|.+|+++++.++....   +...+.......++|+||||||||++++++|+.++.+++.++.... ....++.++..
T Consensus         5 ~~RP~~l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~~-~~~~ir~ii~~   83 (413)
T PRK13342          5 RMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTS-GVKDLREVIEE   83 (413)
T ss_pred             hhCCCCHHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEecccc-cHHHHHHHHHH
Confidence            4678999999999887544   6666766555689999999999999999999999999999987653 33455555554


Q ss_pred             c------CCCcEEEEcCCCccCC
Q 035959          277 T------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ~------~~~~Il~iDeiD~~~~  293 (338)
                      .      ..+.+|||||||.+..
T Consensus        84 ~~~~~~~g~~~vL~IDEi~~l~~  106 (413)
T PRK13342         84 ARQRRSAGRRTILFIDEIHRFNK  106 (413)
T ss_pred             HHHhhhcCCceEEEEechhhhCH
Confidence            4      2678999999999854

>PRK06893 DNA replication initiation factor; Validated

Probab=99.15  E-value=1.6e-10  Score=105.58  Aligned_cols=94  Identities=17%  Similarity=0.236  Sum_probs=62.6

Q ss_pred             ccCCCCCccccccCChhHH--HHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHH
Q 035959          198 AILDHPSTFDTLAMDTDMK--KMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRK  272 (338)
Q Consensus       198 ~~~~~p~~f~~l~~~~~~k--~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~  272 (338)
                      ++...+.+|++++..++..  ..+.+.........++||||||||||||++|+|+++   +..+.++++....  ....+
T Consensus         7 ~~~~~~~~fd~f~~~~~~~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~~--~~~~~   84 (229)
T PRK06893          7 IHQIDDETLDNFYADNNLLLLDSLRKNFIDLQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQ--YFSPA   84 (229)
T ss_pred             CCCCCcccccccccCChHHHHHHHHHHhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHhh--hhhHH
Confidence            4456677999998655432  112122211222346899999999999999999987   4566677664322  11234


Q ss_pred             HHHhcCCCcEEEEcCCCccCC
Q 035959          273 VLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       273 ~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ++....+..+|+||||+.+..
T Consensus        85 ~~~~~~~~dlLilDDi~~~~~  105 (229)
T PRK06893         85 VLENLEQQDLVCLDDLQAVIG  105 (229)
T ss_pred             HHhhcccCCEEEEeChhhhcC
Confidence            556667789999999999864

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.15  E-value=1.3e-10  Score=118.78  Aligned_cols=94  Identities=21%  Similarity=0.376  Sum_probs=75.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      .++|++|+++++.+++++.+.+.+.. ..+..|||+||+|||||++++++|+.++.                        
T Consensus         9 KYRPqtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~   88 (700)
T PRK12323          9 KWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEID   88 (700)
T ss_pred             HhCCCcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHH
Confidence            56899999999999999998888876 33456899999999999999999998864                        


Q ss_pred             -----cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 -----DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 -----~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                           +++.++..+-...+++++++...      .+..|+||||+|.+..
T Consensus        89 aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~  138 (700)
T PRK12323         89 AGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTN  138 (700)
T ss_pred             cCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCH
Confidence                 55666665544556677777654      2567999999999954

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.14  E-value=1.5e-10  Score=118.58  Aligned_cols=94  Identities=19%  Similarity=0.390  Sum_probs=75.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++.+.+++.+...+... .+..|||+||||||||++|+++|+.++.                        
T Consensus         8 KyRPktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hp   87 (702)
T PRK14960          8 KYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFI   87 (702)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCC
Confidence            467999999999999999998888763 3467899999999999999999998853                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++-....+++.++...      .+..|+||||+|.+..
T Consensus        88 DviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~  132 (702)
T PRK14960         88 DLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLST  132 (702)
T ss_pred             ceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCH
Confidence            56777776555556777777655      2567999999998854

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.14  E-value=3.3e-10  Score=107.81  Aligned_cols=98  Identities=18%  Similarity=0.195  Sum_probs=75.6

Q ss_pred             CCccccccCCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHH
Q 035959          192 HDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHL  270 (338)
Q Consensus       192 ~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l  270 (338)
                      ...|.  ..+.|.+|+++++++..++.+...+.... +..+||+||||+|||+++.++|+.++.+++.+++.+ .....+
T Consensus         8 ~~~w~--~kyrP~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~~~~-~~~~~i   84 (316)
T PHA02544          8 EFMWE--QKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSD-CRIDFV   84 (316)
T ss_pred             CCcce--eccCCCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCccceEeccCc-ccHHHH
Confidence            34675  37889999999999999999988887643 345667999999999999999999999999999887 322223


Q ss_pred             HHHH----Hhc---CCCcEEEEcCCCccC
Q 035959          271 RKVL----IAT---ENKSILVVGDIDCCT  292 (338)
Q Consensus       271 ~~~l----~~~---~~~~Il~iDeiD~~~  292 (338)
                      +..+    ...   ..+.+|+|||+|.+.
T Consensus        85 ~~~l~~~~~~~~~~~~~~vliiDe~d~l~  113 (316)
T PHA02544         85 RNRLTRFASTVSLTGGGKVIIIDEFDRLG  113 (316)
T ss_pred             HHHHHHHHHhhcccCCCeEEEEECccccc
Confidence            2322    222   367899999999883

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.12  E-value=1.6e-10  Score=115.11  Aligned_cols=94  Identities=19%  Similarity=0.393  Sum_probs=71.1

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++.+++.+.+...+.... +..+||+||||||||++|+++|+.++.                        
T Consensus        11 KyRP~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~   90 (484)
T PRK14956         11 KYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISS   90 (484)
T ss_pred             HhCCCCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCc
Confidence            5679999999999999888888777633 345899999999999999999998864                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++...-...++++.+...+      ....|+||||+|.+..
T Consensus        91 dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~  135 (484)
T PRK14956         91 DVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTD  135 (484)
T ss_pred             cceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCH
Confidence            35556654433344555554433      2567999999999954

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.12  E-value=2.2e-10  Score=115.93  Aligned_cols=94  Identities=16%  Similarity=0.369  Sum_probs=76.2

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++.+++.+.+.+.+.... +..|||+||||||||++|+++|+.++.                        
T Consensus         9 kyRP~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~   88 (509)
T PRK14958          9 KWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFP   88 (509)
T ss_pred             HHCCCCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCc
Confidence            5679999999999999999999887743 456899999999999999999998843                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++-...++++.++....      +..|+||||+|.+..
T Consensus        89 d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~  133 (509)
T PRK14958         89 DLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSG  133 (509)
T ss_pred             eEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCH
Confidence            367777765555667777776542      467999999999864

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

Probab=99.11  E-value=3e-10  Score=112.08  Aligned_cols=116  Identities=21%  Similarity=0.286  Sum_probs=78.6

Q ss_pred             cccc-ccCChhHHHHHHHHHHh----------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-
Q 035959          205 TFDT-LAMDTDMKKMIMDDLER----------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-  266 (338)
Q Consensus       205 ~f~~-l~~~~~~k~~i~~~l~~----------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-  266 (338)
                      .++. +++.++.++.+...+..                ..+.++||+||||||||++++++|..++.+++.++++.+.. 
T Consensus        68 ~L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~  147 (412)
T PRK05342         68 HLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEA  147 (412)
T ss_pred             HHhhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccC
Confidence            3443 67888888776544422                12467999999999999999999999999999999987642 


Q ss_pred             -------chHHHHHHHh------cCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCC
Q 035959          267 -------NKHLRKVLIA------TENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL  328 (338)
Q Consensus       267 -------~~~l~~~l~~------~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl  328 (338)
                             ...+..++..      ...++||||||||.+..  ++.+...      ..+-....+...||..|||-
T Consensus       148 gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~--~~~~~~~------~~d~s~~~vQ~~LL~~Leg~  214 (412)
T PRK05342        148 GYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIAR--KSENPSI------TRDVSGEGVQQALLKILEGT  214 (412)
T ss_pred             CcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhcc--ccCCCCc------CCCcccHHHHHHHHHHHhcC
Confidence                   1123333322      23689999999999976  3211111      00111234778999999985

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.11  E-value=2e-10  Score=118.84  Aligned_cols=94  Identities=19%  Similarity=0.357  Sum_probs=74.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      .++|.+|+++++++++++.+.+.+... .+..|||+||+|||||++++++|+.++.                        
T Consensus         9 KYRPqtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~   88 (830)
T PRK07003          9 KWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFV   88 (830)
T ss_pred             HhCCCcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCc
Confidence            467999999999999999998888763 3456899999999999999999998853                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++..+-....++++++...      .+..|+||||+|.+..
T Consensus        89 DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~  133 (830)
T PRK07003         89 DYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTN  133 (830)
T ss_pred             eEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCH
Confidence            46666665444455677777654      2568999999999954

>PRK08727 hypothetical protein; Validated

Probab=99.11  E-value=4.2e-10  Score=103.02  Aligned_cols=94  Identities=22%  Similarity=0.247  Sum_probs=66.7

Q ss_pred             ccCCCCCccccccCChhHHHHHHHHHH-hhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHH
Q 035959          198 AILDHPSTFDTLAMDTDMKKMIMDDLE-RAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKV  273 (338)
Q Consensus       198 ~~~~~p~~f~~l~~~~~~k~~i~~~l~-~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~  273 (338)
                      ++.....+|++++..+...-.....+. ..+...++|+||+|||||||++|+|+++   +..+.++++.+..  ..+.+.
T Consensus        10 ~~~~~~~~f~~f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~~--~~~~~~   87 (233)
T PRK08727         10 LRYPSDQRFDSYIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAA--GRLRDA   87 (233)
T ss_pred             CCCCCcCChhhccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHhh--hhHHHH
Confidence            345556699998876643322222322 2334568999999999999999998876   5677777765533  345566


Q ss_pred             HHhcCCCcEEEEcCCCccCC
Q 035959          274 LIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 l~~~~~~~Il~iDeiD~~~~  293 (338)
                      +....+..+|+|||+|.+..
T Consensus        88 ~~~l~~~dlLiIDDi~~l~~  107 (233)
T PRK08727         88 LEALEGRSLVALDGLESIAG  107 (233)
T ss_pred             HHHHhcCCEEEEeCcccccC
Confidence            77777889999999998865

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.11  E-value=3e-10  Score=113.93  Aligned_cols=94  Identities=17%  Similarity=0.339  Sum_probs=76.0

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHh------------------------CC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYL------------------------HF  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l------------------------~~  254 (338)
                      .+.|.+|+++++++.+.+.+.+.+.. ..++.+||+||||||||++|+++|+.+                        ..
T Consensus         6 KyRP~~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~   85 (491)
T PRK14964          6 KYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHP   85 (491)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCC
Confidence            46799999999999988888777665 334689999999999999999999865                        24


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++-....+++.++...      ....|+||||+|.+..
T Consensus        86 Dv~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~  130 (491)
T PRK14964         86 DVIEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSN  130 (491)
T ss_pred             CEEEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCH
Confidence            67888887766667788777665      2568999999998854

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.10  E-value=2.9e-10  Score=105.77  Aligned_cols=87  Identities=15%  Similarity=0.266  Sum_probs=61.9

Q ss_pred             cccccCChhHHHHHHHHHHh---------------hhcCceeeeCCCCCCcHHHHHHHHHHh---C----CcEEEEecCC
Q 035959          206 FDTLAMDTDMKKMIMDDLER---------------AWKRGYLLFGPPGTGKSSLIAAMANYL---H----FDVYDLELSS  263 (338)
Q Consensus       206 f~~l~~~~~~k~~i~~~l~~---------------~~~~g~LL~GppGtGKT~l~~aia~~l---~----~~~~~l~~~~  263 (338)
                      ++++++-+++|+++.+....               +...+++|+||||||||++|+++|+.+   +    ..++.+++++
T Consensus         5 l~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~~   84 (261)
T TIGR02881         5 LSRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERAD   84 (261)
T ss_pred             HHHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHHH
Confidence            56788888888777654433               122457999999999999999999875   2    3566666655


Q ss_pred             cCC------chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          264 VEG------NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       264 ~~~------~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      +..      ...+..++..+ .++||||||+|.+..
T Consensus        85 l~~~~~g~~~~~~~~~~~~a-~~~VL~IDE~~~L~~  119 (261)
T TIGR02881        85 LVGEYIGHTAQKTREVIKKA-LGGVLFIDEAYSLAR  119 (261)
T ss_pred             hhhhhccchHHHHHHHHHhc-cCCEEEEechhhhcc
Confidence            432      23456666554 468999999999853

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.08  E-value=5.1e-10  Score=109.00  Aligned_cols=94  Identities=17%  Similarity=0.310  Sum_probs=70.7

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|++++++++..+.+...+.. ..+..+||+||||||||++++++|+.+..                        
T Consensus         9 kyrP~~~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~   88 (363)
T PRK14961          9 KWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCL   88 (363)
T ss_pred             HhCCCchhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCC
Confidence            45789999999999999888887776 33456899999999999999999998742                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++-.....++.++....      ...|+||||+|.+..
T Consensus        89 d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~  133 (363)
T PRK14961         89 DLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSR  133 (363)
T ss_pred             ceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCH
Confidence            345555443233455666665532      457999999998853

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

Probab=99.07  E-value=1e-09  Score=100.12  Aligned_cols=98  Identities=23%  Similarity=0.292  Sum_probs=83.5

Q ss_pred             CCccccccCCCCCccccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCc
Q 035959          192 HDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSV  264 (338)
Q Consensus       192 ~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~  264 (338)
                      ++...+++...|..+++|++-+..|+.+++...+    ....++||||++|||||++++|+.+++   |..++.++-.++
T Consensus        12 ~~~l~~i~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~L   91 (249)
T PF05673_consen   12 SGYLEPIKHPDPIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKEDL   91 (249)
T ss_pred             CCcEEecCCCCCCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHHh
Confidence            3456667777778999999999999999988877    455789999999999999999999977   678888888888


Q ss_pred             CCchHHHHHHHhcCCCcEEEEcCCC
Q 035959          265 EGNKHLRKVLIATENKSILVVGDID  289 (338)
Q Consensus       265 ~~~~~l~~~l~~~~~~~Il~iDeiD  289 (338)
                      .+-..+...+...+.+-|||+||+.
T Consensus        92 ~~l~~l~~~l~~~~~kFIlf~DDLs  116 (249)
T PF05673_consen   92 GDLPELLDLLRDRPYKFILFCDDLS  116 (249)
T ss_pred             ccHHHHHHHHhcCCCCEEEEecCCC
Confidence            8888888888888889999999854

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.06  E-value=7e-10  Score=111.95  Aligned_cols=94  Identities=20%  Similarity=0.394  Sum_probs=73.8

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|++|+++++.+.+.+.+...+.. ..+..+||+||||||||++|+++|+.++.                        
T Consensus        14 kyRP~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~   93 (507)
T PRK06645         14 KYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNN   93 (507)
T ss_pred             hhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhc
Confidence            57899999999999988888776665 33468999999999999999999998842                        


Q ss_pred             ----cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 ----DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ----~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                          +++.++..+-....+++.++..+.      ...|+||||+|.+..
T Consensus        94 ~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~  142 (507)
T PRK06645         94 HNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSK  142 (507)
T ss_pred             CCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCH
Confidence                455666554445567777776652      568999999998853

>PRK12377 putative replication protein; Provisional

Probab=99.05  E-value=7.5e-10  Score=102.19  Aligned_cols=89  Identities=22%  Similarity=0.323  Sum_probs=62.0

Q ss_pred             CccccccCChhHHHHHHHHHHh------hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC--------
Q 035959          204 STFDTLAMDTDMKKMIMDDLER------AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG--------  266 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~------~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~--------  266 (338)
                      .+|+++....+..+.++..+..      ....+++|+||||||||||+.|+|+++   +..+..++..++..        
T Consensus        71 ~tFdnf~~~~~~~~~a~~~a~~~a~~~~~~~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~~~l~~~~~~  150 (248)
T PRK12377         71 CSFANYQVQNDGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVMSRLHESYDN  150 (248)
T ss_pred             CCcCCcccCChhHHHHHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHHHHHHHHHhc
Confidence            4788876544333333332222      223579999999999999999999988   57787887766542        


Q ss_pred             chHHHHHHHhcCCCcEEEEcCCCccC
Q 035959          267 NKHLRKVLIATENKSILVVGDIDCCT  292 (338)
Q Consensus       267 ~~~l~~~l~~~~~~~Il~iDeiD~~~  292 (338)
                      ......++..+...++|+|||+....
T Consensus       151 ~~~~~~~l~~l~~~dLLiIDDlg~~~  176 (248)
T PRK12377        151 GQSGEKFLQELCKVDLLVLDEIGIQR  176 (248)
T ss_pred             cchHHHHHHHhcCCCEEEEcCCCCCC
Confidence            11234567777899999999997654

>PRK08181 transposase; Validated

Probab=99.04  E-value=4.8e-10  Score=104.65  Aligned_cols=67  Identities=28%  Similarity=0.431  Sum_probs=52.9

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-------chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-------NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-------~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      .+.+++|+||||||||||+.|+|+++   |+.+++++..++..       +..+.+.+....+..+|||||++....
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~~~  181 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYVTK  181 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEeccccccC
Confidence            35679999999999999999999866   77888887765442       233556677777899999999998754

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.03  E-value=1e-09  Score=111.70  Aligned_cols=94  Identities=19%  Similarity=0.389  Sum_probs=72.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++.+++++.+...+.. ..+..|||+||||+|||++++++|+.++.                        
T Consensus         9 k~rP~~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~   88 (527)
T PRK14969          9 KWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFV   88 (527)
T ss_pred             HhCCCcHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCC
Confidence            35689999999999999988888876 33456899999999999999999998843                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++.+.-....+++.++..+.      +..|+||||+|.+..
T Consensus        89 d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~  133 (527)
T PRK14969         89 DLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSK  133 (527)
T ss_pred             ceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCH
Confidence            455666554344556777766542      467999999998853

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

Probab=99.03  E-value=5e-10  Score=118.30  Aligned_cols=92  Identities=25%  Similarity=0.396  Sum_probs=78.2

Q ss_pred             CCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC-----
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG-----  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~-----  266 (338)
                      .|..++.+++.++..+++++-|.+..+.+++|+||||||||++++++|..+          +..++.++++.+..     
T Consensus       177 r~~~l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~  256 (731)
T TIGR02639       177 KNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYR  256 (731)
T ss_pred             hcCCCCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhcccc
Confidence            566888999998888888888887778899999999999999999999987          67888998876653     


Q ss_pred             ---chHHHHHHHhcC--CCcEEEEcCCCccCC
Q 035959          267 ---NKHLRKVLIATE--NKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ---~~~l~~~l~~~~--~~~Il~iDeiD~~~~  293 (338)
                         +..+++++..+.  .++||||||||.+..
T Consensus       257 g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~  288 (731)
T TIGR02639       257 GDFEERLKAVVSEIEKEPNAILFIDEIHTIVG  288 (731)
T ss_pred             chHHHHHHHHHHHHhccCCeEEEEecHHHHhc
Confidence               256888888764  588999999999986

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.02  E-value=8.3e-10  Score=116.17  Aligned_cols=94  Identities=18%  Similarity=0.338  Sum_probs=69.6

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCCc-----------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHFD-----------------------  255 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~~-----------------------  255 (338)
                      ..+|.+|+++++.+.+++.+.+.+.. ..+..|||+||||||||++++++|+.++..                       
T Consensus         9 KyRP~tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~   88 (944)
T PRK14949          9 KWRPATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFV   88 (944)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCc
Confidence            46789999999999999888877765 334567999999999999999999988542                       


Q ss_pred             -EEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          256 -VYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       256 -~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                       ++.++..+-.....++.++...      .+..|+||||+|.+..
T Consensus        89 DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~  133 (944)
T PRK14949         89 DLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSR  133 (944)
T ss_pred             eEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCH
Confidence             2334443322334566665544      2467999999999953

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.02  E-value=7.8e-10  Score=114.10  Aligned_cols=94  Identities=17%  Similarity=0.326  Sum_probs=72.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++.+.+.+.+...+.. ..+..|||+||+|||||++++++|+.++.                        
T Consensus         9 KyRP~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~   88 (647)
T PRK07994          9 KWRPQTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFV   88 (647)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCC
Confidence            35799999999999999988888876 33455899999999999999999998854                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++..+-...++++.++....      ...|+||||+|.+..
T Consensus        89 D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~  133 (647)
T PRK07994         89 DLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSR  133 (647)
T ss_pred             CceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCH
Confidence            455666554334456676665542      567999999999854

>TIGR00763 lon ATP-dependent protease La

Probab=99.02  E-value=1.1e-09  Score=116.46  Aligned_cols=85  Identities=22%  Similarity=0.277  Sum_probs=65.0

Q ss_pred             ccCChhHHHHHHHHHHhh------hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCc---------------
Q 035959          209 LAMDTDMKKMIMDDLERA------WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGN---------------  267 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~------~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~---------------  267 (338)
                      +.+.+..++++.+.+...      ....++|+||||||||++++++|+.++.+++.+++....+.               
T Consensus       322 ~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~  401 (775)
T TIGR00763       322 HYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMP  401 (775)
T ss_pred             cCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCCCC
Confidence            567788888888866542      22358999999999999999999999999999987664322               


Q ss_pred             hHHHHHHHhc-CCCcEEEEcCCCccCC
Q 035959          268 KHLRKVLIAT-ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l~~~-~~~~Il~iDeiD~~~~  293 (338)
                      ..+.+.+... ..+.||+|||||.+..
T Consensus       402 g~i~~~l~~~~~~~~villDEidk~~~  428 (775)
T TIGR00763       402 GRIIQGLKKAKTKNPLFLLDEIDKIGS  428 (775)
T ss_pred             chHHHHHHHhCcCCCEEEEechhhcCC
Confidence            2344555543 3556999999999975

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.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.02  E-value=7.5e-10  Score=100.05  Aligned_cols=94  Identities=20%  Similarity=0.253  Sum_probs=66.3

Q ss_pred             ccCCCCCccccccC--ChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHH
Q 035959          198 AILDHPSTFDTLAM--DTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRK  272 (338)
Q Consensus       198 ~~~~~p~~f~~l~~--~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~  272 (338)
                      ++...+.+|++++.  +....+.+...+....++.++|+||||||||++++++++++   +.+++.+++..+...  ...
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~~~--~~~   83 (226)
T TIGR03420         6 VGLPDDPTFDNFYAGGNAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQA--DPE   83 (226)
T ss_pred             CCCCCchhhcCcCcCCcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHHHh--HHH
Confidence            34555668999874  23344444444433445679999999999999999999887   467888888776532  234


Q ss_pred             HHHhcCCCcEEEEcCCCccCC
Q 035959          273 VLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       273 ~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ++.......+|+|||+|.+..
T Consensus        84 ~~~~~~~~~lLvIDdi~~l~~  104 (226)
T TIGR03420        84 VLEGLEQADLVCLDDVEAIAG  104 (226)
T ss_pred             HHhhcccCCEEEEeChhhhcC
Confidence            444455678999999999864

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.02  E-value=8.9e-10  Score=113.33  Aligned_cols=94  Identities=18%  Similarity=0.373  Sum_probs=73.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++++.+.+.+.+.+... .+..|||+||+|||||++++++|+.++.                        
T Consensus         9 KyRP~~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~   88 (618)
T PRK14951          9 KYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDID   88 (618)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHH
Confidence            567999999999999988888888763 3356899999999999999999998753                        


Q ss_pred             -----cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 -----DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 -----~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                           +++.++..+-...++++.++....      +..|+||||+|.+..
T Consensus        89 ~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~  138 (618)
T PRK14951         89 SGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTN  138 (618)
T ss_pred             cCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCH
Confidence                 455665554444556777776542      467999999999864

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.01  E-value=1e-09  Score=103.38  Aligned_cols=106  Identities=18%  Similarity=0.168  Sum_probs=70.7

Q ss_pred             cccCChhHHHHHHHHHHh---------------hhcCceeeeCCCCCCcHHHHHHHHHHhC-------CcEEEEecCCcC
Q 035959          208 TLAMDTDMKKMIMDDLER---------------AWKRGYLLFGPPGTGKSSLIAAMANYLH-------FDVYDLELSSVE  265 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~---------------~~~~g~LL~GppGtGKT~l~~aia~~l~-------~~~~~l~~~~~~  265 (338)
                      .+++-+++|+++.+....               ....+++|+||||||||++|+++|..+.       .+++.+++.++.
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~  102 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLV  102 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHHh
Confidence            577777788776553332               1234789999999999999999998773       257777765543


Q ss_pred             ------CchHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcC
Q 035959          266 ------GNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDG  327 (338)
Q Consensus       266 ------~~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDg  327 (338)
                            +...+..++..+ .+++|||||+|.+..  .++.           ..........|++.||.
T Consensus       103 ~~~~g~~~~~~~~~~~~a-~~gvL~iDEi~~L~~--~~~~-----------~~~~~~~~~~Ll~~le~  156 (284)
T TIGR02880       103 GQYIGHTAPKTKEILKRA-MGGVLFIDEAYYLYR--PDNE-----------RDYGQEAIEILLQVMEN  156 (284)
T ss_pred             HhhcccchHHHHHHHHHc-cCcEEEEechhhhcc--CCCc-----------cchHHHHHHHHHHHHhc
Confidence                  123455566654 458999999999854  2211           11234566778888874

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.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.01  E-value=1.2e-09  Score=112.69  Aligned_cols=93  Identities=23%  Similarity=0.435  Sum_probs=73.0

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++.+.+++.+...+... .+.+|||+||+|||||++++++|+.++.                        
T Consensus         9 KYRP~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~   88 (709)
T PRK08691          9 KWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYV   88 (709)
T ss_pred             HhCCCCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCcc
Confidence            467999999999999999998888863 3567999999999999999999998642                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCT  292 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~  292 (338)
                      +++.++..+-.....++.++...      .+..||||||+|.+.
T Consensus        89 DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls  132 (709)
T PRK08691         89 DLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLS  132 (709)
T ss_pred             ceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccC
Confidence            34556655444455677777643      356899999999874

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.00  E-value=1.5e-09  Score=99.51  Aligned_cols=90  Identities=21%  Similarity=0.306  Sum_probs=59.2

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCCcCCchHHHH
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSVEGNKHLRK  272 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~~~~~~~l~~  272 (338)
                      +....+|++++...+  +.++..+.+    +..+.++||||||||||||++|+|+++.   ..+.++++.....  ...+
T Consensus        15 ~~~~~~fd~f~~~~n--~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~~--~~~~   90 (235)
T PRK08084         15 LPDDETFASFYPGDN--DSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRAW--FVPE   90 (235)
T ss_pred             CCCcCCccccccCcc--HHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHhh--hhHH
Confidence            455568999874421  223333333    3335789999999999999999998764   4566666654322  1223


Q ss_pred             HHHhcCCCcEEEEcCCCccCC
Q 035959          273 VLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       273 ~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ++....+..+|+||||+.+..
T Consensus        91 ~~~~~~~~dlliiDdi~~~~~  111 (235)
T PRK08084         91 VLEGMEQLSLVCIDNIECIAG  111 (235)
T ss_pred             HHHHhhhCCEEEEeChhhhcC
Confidence            344444568999999999864

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.00  E-value=1.4e-09  Score=110.60  Aligned_cols=94  Identities=19%  Similarity=0.365  Sum_probs=71.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++.+...+.+...+... .+..+||+||||||||++++++|+.+..                        
T Consensus         9 KyRP~~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~   88 (546)
T PRK14957          9 KYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFI   88 (546)
T ss_pred             HHCcCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCC
Confidence            457899999999999998888877752 3346899999999999999999998752                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++...-....+++.++...      ....|+||||+|.+..
T Consensus        89 dlieidaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~  133 (546)
T PRK14957         89 DLIEIDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSK  133 (546)
T ss_pred             ceEEeecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccH
Confidence            55566654433444555555543      2567999999999854

>PRK06526 transposase; Provisional

Probab=99.00  E-value=5.6e-10  Score=103.50  Aligned_cols=121  Identities=15%  Similarity=0.238  Sum_probs=74.4

Q ss_pred             hhhHHHHHHhHHHHHhccceeeeeccCccCCCCccccccCCCCCccccccCC--hhHHHHHHHHHHh----hhcCceeee
Q 035959          161 TYIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMD--TDMKKMIMDDLER----AWKRGYLLF  234 (338)
Q Consensus       161 ~~l~~v~~~~~~~~~~~~~~~l~~~~~~~~~~~~w~~~~~~~p~~f~~l~~~--~~~k~~i~~~l~~----~~~~g~LL~  234 (338)
                      ++|..+++..-+.+++++..+..+..            .++.+.+|+++-..  +...+..+..+..    ..+.+++|+
T Consensus        37 e~l~~ll~~E~~~R~~~~~~~~lk~a------------~~p~~~~le~fd~~~~~~~~~~~~~~l~~~~fi~~~~nlll~  104 (254)
T PRK06526         37 EFLAACLQREVAARESHGGEGRIRAA------------RFPARKSLEEFDFDHQRSLKRDTIAHLGTLDFVTGKENVVFL  104 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhC------------CCCCCCChhhccCccCCCcchHHHHHHhcCchhhcCceEEEE
Confidence            56666666665555555544343332            13333455544322  2333334444433    235689999


Q ss_pred             CCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-------chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          235 GPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-------NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       235 GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-------~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ||||||||||+.+++.++   |+.++.+...++..       ...+.+.+....+..+|||||++....
T Consensus       105 Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~~  173 (254)
T PRK06526        105 GPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIPF  173 (254)
T ss_pred             eCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCCC
Confidence            999999999999999876   66666665554321       223445566667889999999998753

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.00  E-value=1.7e-09  Score=105.33  Aligned_cols=94  Identities=17%  Similarity=0.417  Sum_probs=71.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------cEEEEecCCcCC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------DVYDLELSSVEG  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------~~~~l~~~~~~~  266 (338)
                      ..+|.+|+++++.+...+.+.+.+.. ..++++|||||||+|||+++.++|+.+..            .+++++......
T Consensus        10 k~rP~~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~   89 (367)
T PRK14970         10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNS   89 (367)
T ss_pred             HHCCCcHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCC
Confidence            57799999999999999989888876 34568999999999999999999998742            334444333333


Q ss_pred             chHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      ...++.++..+      ..+.||+|||+|.+..
T Consensus        90 ~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~  122 (367)
T PRK14970         90 VDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSS  122 (367)
T ss_pred             HHHHHHHHHHHhhccccCCcEEEEEeChhhcCH
Confidence            45677776643      2467999999998753

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.00  E-value=1.7e-09  Score=110.73  Aligned_cols=94  Identities=24%  Similarity=0.382  Sum_probs=72.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhC-------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLH-------------------------  253 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~-------------------------  253 (338)
                      ...|.+|+++++++.+.+.+...+.... +..|||+||+|||||++++++|+.+.                         
T Consensus         6 kyRP~~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~   85 (584)
T PRK14952          6 KYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPG   85 (584)
T ss_pred             HhCCCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCC
Confidence            4679999999999999998888887632 34589999999999999999998764                         


Q ss_pred             -CcEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          254 -FDVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       254 -~~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                       .+++.++.++....++++.+....      ....|+||||+|.+..
T Consensus        86 ~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~  132 (584)
T PRK14952         86 SIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTT  132 (584)
T ss_pred             CceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCH
Confidence             246666665544455565554433      3577999999999854

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.00  E-value=1.8e-09  Score=110.55  Aligned_cols=94  Identities=20%  Similarity=0.419  Sum_probs=75.2

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------C
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------F  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~  254 (338)
                      ...|.+|+++++.+++.+.+.+.+.. ..++.|||+||+|||||++++.+|+.+.                        .
T Consensus         9 k~rP~~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~   88 (559)
T PRK05563          9 KWRPQTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLM   88 (559)
T ss_pred             HhCCCcHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCC
Confidence            45799999999999999988888876 3456799999999999999999999873                        4


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++-.....++.+...+.      ...|+||||+|.+..
T Consensus        89 dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~  133 (559)
T PRK05563         89 DVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLST  133 (559)
T ss_pred             CeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCH
Confidence            677777765455556777766542      567999999998854

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.99  E-value=1.5e-09  Score=115.05  Aligned_cols=95  Identities=22%  Similarity=0.365  Sum_probs=73.6

Q ss_pred             cCCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhC------------------------
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLH------------------------  253 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~------------------------  253 (338)
                      ..+.|.+|+++++++.+++.|...+... ....|||+||+|||||++++++|+.+.                        
T Consensus         7 ~KyRP~~f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~   86 (824)
T PRK07764          7 RRYRPATFAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGP   86 (824)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCC
Confidence            3678999999999999999988888863 335689999999999999999999884                        


Q ss_pred             --CcEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          254 --FDVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       254 --~~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                        .+++.++..+....++++.+....      ....|+||||+|.+..
T Consensus        87 ~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~  134 (824)
T PRK07764         87 GSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTP  134 (824)
T ss_pred             CCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCH
Confidence              245666655444455666654432      3678999999999964

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.98  E-value=1.9e-09  Score=108.96  Aligned_cols=93  Identities=19%  Similarity=0.400  Sum_probs=70.0

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC-----------------------c
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF-----------------------D  255 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~-----------------------~  255 (338)
                      ...|.+|++++++++.++.+...+... .+..+||+||||||||++++++|+.+..                       +
T Consensus         7 KyRP~~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~d   86 (504)
T PRK14963          7 RARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPD   86 (504)
T ss_pred             hhCCCCHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCc
Confidence            467999999999999988888887763 2345699999999999999999998842                       3


Q ss_pred             EEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccC
Q 035959          256 VYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCT  292 (338)
Q Consensus       256 ~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~  292 (338)
                      ++.++..+......++.+...+      ..+.||||||+|.+.
T Consensus        87 v~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls  129 (504)
T PRK14963         87 VLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMS  129 (504)
T ss_pred             eEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccC
Confidence            6666665434444555554333      257899999999774

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.98  E-value=1.6e-09  Score=116.13  Aligned_cols=93  Identities=20%  Similarity=0.372  Sum_probs=77.9

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC----
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG----  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~----  266 (338)
                      -.|..++.+++.++..+++++-|.+..+.+.+|+||||||||+++.++|..+          +.+++.+++..+..    
T Consensus       172 ~r~~~l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~  251 (857)
T PRK10865        172 AEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKY  251 (857)
T ss_pred             HhcCCCCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccch
Confidence            3456789999999988999998888778899999999999999999999988          67899998887652    


Q ss_pred             ----chHHHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                          +..+++++...   ..++||||||+|.+..
T Consensus       252 ~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~  285 (857)
T PRK10865        252 RGEFEERLKGVLNDLAKQEGNVILFIDELHTMVG  285 (857)
T ss_pred             hhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhcc
Confidence                23577777654   3678999999999986

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.97  E-value=2.5e-09  Score=105.33  Aligned_cols=94  Identities=14%  Similarity=0.314  Sum_probs=70.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++++.+++.+...+... .+..+||+||||+|||++|.++|+.+..                        
T Consensus         9 k~RP~~~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~   88 (397)
T PRK14955          9 KYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCR   88 (397)
T ss_pred             hcCCCcHhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHH
Confidence            467999999999999999888888763 3456999999999999999999998843                        


Q ss_pred             --------cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 --------DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 --------~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                              +++.++..+....++++.+...+      ....|+||||+|.+..
T Consensus        89 ~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~  141 (397)
T PRK14955         89 DFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSI  141 (397)
T ss_pred             HHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCH
Confidence                    23344443333345666665555      2567999999999863

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

Probab=98.97  E-value=2.1e-09  Score=109.23  Aligned_cols=84  Identities=17%  Similarity=0.332  Sum_probs=66.4

Q ss_pred             cCChhHHHHHHHHHHhh------hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchH--------------
Q 035959          210 AMDTDMKKMIMDDLERA------WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKH--------------  269 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~~------~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~--------------  269 (338)
                      .+-.++|++|++.+.-.      ...-+.|+||||+||||++++||..+|..+++++...+.+.++              
T Consensus       414 Ygm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHRRTYVGAMPG  493 (906)
T KOG2004|consen  414 YGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYVGAMPG  493 (906)
T ss_pred             cchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhcccceeeeccCCh
Confidence            34467899999988761      1223679999999999999999999999999999988876443              


Q ss_pred             -HHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          270 -LRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       270 -l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                       +.+.+.... .+.+++|||||.+..
T Consensus       494 kiIq~LK~v~t~NPliLiDEvDKlG~  519 (906)
T KOG2004|consen  494 KIIQCLKKVKTENPLILIDEVDKLGS  519 (906)
T ss_pred             HHHHHHHhhCCCCceEEeehhhhhCC
Confidence             445555553 788999999999974

>CHL00181 cbbX CbbX; Provisional

Probab=98.96  E-value=2.8e-09  Score=100.56  Aligned_cols=107  Identities=18%  Similarity=0.217  Sum_probs=70.1

Q ss_pred             ccccCChhHHHHHHHHHHh-------------hhcCc--eeeeCCCCCCcHHHHHHHHHHhC-------CcEEEEecCCc
Q 035959          207 DTLAMDTDMKKMIMDDLER-------------AWKRG--YLLFGPPGTGKSSLIAAMANYLH-------FDVYDLELSSV  264 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~-------------~~~~g--~LL~GppGtGKT~l~~aia~~l~-------~~~~~l~~~~~  264 (338)
                      +++++.+++|+++.+....             +...|  ++|+||||||||++|+++|..+.       .+++.++..++
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~l  102 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDL  102 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHHH
Confidence            4688888888877654332             11223  79999999999999999998762       24777776554


Q ss_pred             CC------chHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcC
Q 035959          265 EG------NKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDG  327 (338)
Q Consensus       265 ~~------~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDg  327 (338)
                      ..      ......++..+ .+.||||||+|.+..  .+..           ....+.....|+..||.
T Consensus       103 ~~~~~g~~~~~~~~~l~~a-~ggVLfIDE~~~l~~--~~~~-----------~~~~~e~~~~L~~~me~  157 (287)
T CHL00181        103 VGQYIGHTAPKTKEVLKKA-MGGVLFIDEAYYLYK--PDNE-----------RDYGSEAIEILLQVMEN  157 (287)
T ss_pred             HHHHhccchHHHHHHHHHc-cCCEEEEEccchhcc--CCCc-----------cchHHHHHHHHHHHHhc
Confidence            31      22345556554 568999999999864  2211           11234566677777764

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

Probab=98.96  E-value=3.8e-09  Score=103.99  Aligned_cols=118  Identities=22%  Similarity=0.299  Sum_probs=77.4

Q ss_pred             cccc-ccCChhHHHHHHHHHHh-----------h-------hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC
Q 035959          205 TFDT-LAMDTDMKKMIMDDLER-----------A-------WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE  265 (338)
Q Consensus       205 ~f~~-l~~~~~~k~~i~~~l~~-----------~-------~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~  265 (338)
                      .++. ++++++.++.+...+..           +       .+..+||+||||||||++++++|..++.++..++++.+.
T Consensus        74 ~L~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L~  153 (413)
T TIGR00382        74 HLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLT  153 (413)
T ss_pred             HhcceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhcc
Confidence            3444 46677777766544421           0       124699999999999999999999999999988887654


Q ss_pred             C--------chHHHHHHHhc------CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          266 G--------NKHLRKVLIAT------ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       266 ~--------~~~l~~~l~~~------~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                      .        ...+..++...      ..++||+|||||.+..  ++...+-..      +-...-+...||..|||...
T Consensus       154 ~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~--~~~~~s~~~------dvsg~~vq~~LL~iLeG~~~  224 (413)
T TIGR00382       154 EAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISR--KSENPSITR------DVSGEGVQQALLKIIEGTVA  224 (413)
T ss_pred             ccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhch--hhccccccc------cccchhHHHHHHHHhhccce
Confidence            2        12233443322      3578999999999976  332211100      11112467889999999764

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.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.95  E-value=1.4e-09  Score=103.48  Aligned_cols=89  Identities=25%  Similarity=0.347  Sum_probs=63.4

Q ss_pred             CCccccccCChhHHHHH----HHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-----
Q 035959          203 PSTFDTLAMDTDMKKMI----MDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-----  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i----~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-----  266 (338)
                      ..+|+++..++..+..+    .+.+..    +..+|++|+||||||||||+.|+|+++   |..+..+...++..     
T Consensus       123 ~atf~~~~~~~~~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~~lk~~  202 (306)
T PRK08939        123 QASLADIDLDDRDRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIRELKNS  202 (306)
T ss_pred             cCcHHHhcCCChHHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHHHHHHH
Confidence            35777776554333222    223332    245699999999999999999999998   78888887765431     


Q ss_pred             --chHHHHHHHhcCCCcEEEEcCCCcc
Q 035959          267 --NKHLRKVLIATENKSILVVGDIDCC  291 (338)
Q Consensus       267 --~~~l~~~l~~~~~~~Il~iDeiD~~  291 (338)
                        +..+.+.+.......+|||||+..-
T Consensus       203 ~~~~~~~~~l~~l~~~dlLiIDDiG~e  229 (306)
T PRK08939        203 ISDGSVKEKIDAVKEAPVLMLDDIGAE  229 (306)
T ss_pred             HhcCcHHHHHHHhcCCCEEEEecCCCc
Confidence              2345667777889999999999765

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.95  E-value=2.8e-09  Score=96.77  Aligned_cols=90  Identities=18%  Similarity=0.228  Sum_probs=61.3

Q ss_pred             ccCCCCCccccccCCh--hHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHH
Q 035959          198 AILDHPSTFDTLAMDT--DMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLR  271 (338)
Q Consensus       198 ~~~~~p~~f~~l~~~~--~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~  271 (338)
                      ++...|.+|++++...  .....+.+.... ...++++|+||||||||||++++++++   +..+..+++.+...     
T Consensus         9 ~~~~~~~~~d~f~~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~~~-----   83 (227)
T PRK08903          9 LGPPPPPTFDNFVAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPLL-----   83 (227)
T ss_pred             CCCCChhhhcccccCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHhHH-----
Confidence            4556677899987432  222222222221 234679999999999999999999976   66788888766432     


Q ss_pred             HHHHhcCCCcEEEEcCCCccCC
Q 035959          272 KVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       272 ~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                       .+.......+|+|||+|.+..
T Consensus        84 -~~~~~~~~~~liiDdi~~l~~  104 (227)
T PRK08903         84 -AFDFDPEAELYAVDDVERLDD  104 (227)
T ss_pred             -HHhhcccCCEEEEeChhhcCc
Confidence             123344678999999998743

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.94  E-value=2.5e-09  Score=102.38  Aligned_cols=69  Identities=16%  Similarity=0.296  Sum_probs=55.2

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCc
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSV  264 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~  264 (338)
                      .|.  ..+.|.+|+++++.++.++.+...+......+++|+||||||||++++++|+++.     .++..+++.+.
T Consensus         4 ~w~--~ky~P~~~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~~~~   77 (337)
T PRK12402          4 LWT--EKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADF   77 (337)
T ss_pred             chH--HhhCCCcHHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEechhhh
Confidence            464  3678999999999999888888877764334799999999999999999999884     34567776543

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.93  E-value=3.3e-09  Score=108.29  Aligned_cols=94  Identities=18%  Similarity=0.415  Sum_probs=72.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------C
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------F  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~  254 (338)
                      ..+|.+|+++++++...+.+...+.. ..++.+||+||||+|||++|.++|+.+.                        .
T Consensus         9 KyRP~~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~   88 (605)
T PRK05896          9 KYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSV   88 (605)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCC
Confidence            56899999999999999888888765 3346799999999999999999999873                        2


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++..+.....+++.+.....      ...|++|||+|.+..
T Consensus        89 DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~  133 (605)
T PRK05896         89 DIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLST  133 (605)
T ss_pred             ceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCH
Confidence            556666554344455666655432      467999999998853

>PRK05642 DNA replication initiation factor; Validated

Probab=98.93  E-value=3.5e-09  Score=97.01  Aligned_cols=92  Identities=21%  Similarity=0.293  Sum_probs=63.4

Q ss_pred             ccCCCCCccccccCChhHHHHHHHHHHh------hh-cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCc
Q 035959          198 AILDHPSTFDTLAMDTDMKKMIMDDLER------AW-KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGN  267 (338)
Q Consensus       198 ~~~~~p~~f~~l~~~~~~k~~i~~~l~~------~~-~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~  267 (338)
                      ++.....+|++++....  ...++.+.+      .| .+.++||||+|||||||++|+|+++   +..+.+++..++...
T Consensus        10 ~~~~~~~tfdnF~~~~~--~~a~~~~~~~~~~~~~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~~~   87 (234)
T PRK05642         10 VRLRDDATFANYYPGAN--AAALGYVERLCEADAGWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDR   87 (234)
T ss_pred             CCCCCcccccccCcCCh--HHHHHHHHHHhhccccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHHhh
Confidence            34555669999874432  333444432      23 2578999999999999999999865   567888887765432


Q ss_pred             hHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 KHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                        ...++.......+|+|||++.+..
T Consensus        88 --~~~~~~~~~~~d~LiiDDi~~~~~  111 (234)
T PRK05642         88 --GPELLDNLEQYELVCLDDLDVIAG  111 (234)
T ss_pred             --hHHHHHhhhhCCEEEEechhhhcC
Confidence              234444455668999999998854

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.93  E-value=5.6e-09  Score=100.80  Aligned_cols=94  Identities=21%  Similarity=0.461  Sum_probs=70.8

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhC------------------------C
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLH------------------------F  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~  254 (338)
                      ...|.+|+++++.+..++.+.+.+... .+..+|||||||+|||+++.++|+.+.                        .
T Consensus         7 ~~rp~~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~   86 (355)
T TIGR02397         7 KYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSL   86 (355)
T ss_pred             HhCCCcHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCC
Confidence            467899999999999999988888763 345689999999999999999998873                        2


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++.........+++++..+.      .+.||+|||+|.+..
T Consensus        87 ~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~  131 (355)
T TIGR02397        87 DVIEIDAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSK  131 (355)
T ss_pred             CEEEeeccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCH
Confidence            355555543333345666665542      456999999998843

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.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.93  E-value=3.7e-09  Score=108.41  Aligned_cols=94  Identities=20%  Similarity=0.336  Sum_probs=71.1

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++++.+++.+...+... ....|||+||||||||++|.++|+.+..                        
T Consensus         9 KyRP~sf~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hp   88 (624)
T PRK14959          9 RYRPQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHV   88 (624)
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCC
Confidence            578999999999999988888888763 3567999999999999999999998853                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++...-...++++.+....      ....||||||+|.+..
T Consensus        89 Dv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~  133 (624)
T PRK14959         89 DVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTR  133 (624)
T ss_pred             ceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCH
Confidence            26666654333334455443322      2567999999999953

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.93  E-value=3.7e-09  Score=108.78  Aligned_cols=94  Identities=19%  Similarity=0.400  Sum_probs=73.2

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++.+++++.+...+... .+..||||||+|||||+++.++|+.+..                        
T Consensus         9 k~RP~~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~   88 (576)
T PRK14965          9 KYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSV   88 (576)
T ss_pred             HhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCC
Confidence            456999999999999999998888763 4567899999999999999999998742                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++..+.....+++.+.....      ...|+||||+|.+..
T Consensus        89 d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~  133 (576)
T PRK14965         89 DVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLST  133 (576)
T ss_pred             CeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCH
Confidence            356666555444556666665542      467999999998854

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.92  E-value=3.1e-09  Score=113.72  Aligned_cols=93  Identities=18%  Similarity=0.324  Sum_probs=77.2

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC----
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG----  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~----  266 (338)
                      -.|..++.+++.++..+++++.|.+..+.+.+|+||||||||+++.++|..+          +..++.++++.+..    
T Consensus       181 ~r~~~ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~~~  260 (852)
T TIGR03345       181 AREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASV  260 (852)
T ss_pred             hcCCCCCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhccccc
Confidence            3567889999999988889888888778899999999999999999999986          25678888876542    


Q ss_pred             ----chHHHHHHHhcC---CCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIATE---NKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~~---~~~Il~iDeiD~~~~  293 (338)
                          +..+++++..+.   .+.||||||||.+..
T Consensus       261 ~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~  294 (852)
T TIGR03345       261 KGEFENRLKSVIDEVKASPQPIILFIDEAHTLIG  294 (852)
T ss_pred             chHHHHHHHHHHHHHHhcCCCeEEEEeChHHhcc
Confidence                256778887663   578999999999986

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.

>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=98.91  E-value=5e-09  Score=86.23  Aligned_cols=79  Identities=28%  Similarity=0.412  Sum_probs=58.6

Q ss_pred             hhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHH-----------HHHhcC
Q 035959          213 TDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRK-----------VLIATE  278 (338)
Q Consensus       213 ~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~-----------~l~~~~  278 (338)
                      +...+.+...+.....+.++++||||||||++++++++.+   +.+++.+++...........           ......
T Consensus         4 ~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (151)
T cd00009           4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKA   83 (151)
T ss_pred             HHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccC
Confidence            3445555555554556789999999999999999999999   88999999887664332221           122234


Q ss_pred             CCcEEEEcCCCcc
Q 035959          279 NKSILVVGDIDCC  291 (338)
Q Consensus       279 ~~~Il~iDeiD~~  291 (338)
                      .+.+|+|||++.+
T Consensus        84 ~~~~lilDe~~~~   96 (151)
T cd00009          84 KPGVLFIDEIDSL   96 (151)
T ss_pred             CCeEEEEeChhhh
Confidence            7899999999987

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=98.91  E-value=6.1e-09  Score=97.01  Aligned_cols=38  Identities=26%  Similarity=0.206  Sum_probs=34.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE  265 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~  265 (338)
                      .+.+||.||||||||++|+++|+.+|.+++.+++..-.
T Consensus        21 g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~   58 (262)
T TIGR02640        21 GYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAEL   58 (262)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccC
Confidence            46799999999999999999999999999999887633

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

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

Probab=98.90  E-value=3e-09  Score=101.11  Aligned_cols=93  Identities=24%  Similarity=0.410  Sum_probs=64.3

Q ss_pred             CCCCccccccCChhHHH---HHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCc-EEEEecCCcCC-chHHHHHHH
Q 035959          201 DHPSTFDTLAMDTDMKK---MIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFD-VYDLELSSVEG-NKHLRKVLI  275 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~---~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~-~~~l~~~~~~~-~~~l~~~l~  275 (338)
                      -.|.++++++++.++.-   -+...+++..-..++||||||||||+|++.+++....+ +..|+++.... ..+++.+|+
T Consensus       132 mRPktL~dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~t~dvR~ife  211 (554)
T KOG2028|consen  132 MRPKTLDDYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAKTNDVRDIFE  211 (554)
T ss_pred             cCcchHHHhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccccchHHHHHHHH
Confidence            45677777777655431   22223333333568999999999999999999988654 44455554443 456788887


Q ss_pred             hc-------CCCcEEEEcCCCccCC
Q 035959          276 AT-------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 ~~-------~~~~Il~iDeiD~~~~  293 (338)
                      +.       .++.|||||||+.+..
T Consensus       212 ~aq~~~~l~krkTilFiDEiHRFNk  236 (554)
T KOG2028|consen  212 QAQNEKSLTKRKTILFIDEIHRFNK  236 (554)
T ss_pred             HHHHHHhhhcceeEEEeHHhhhhhh
Confidence            66       3789999999999954

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.90  E-value=6e-09  Score=107.53  Aligned_cols=94  Identities=17%  Similarity=0.334  Sum_probs=70.6

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhC-------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLH-------------------------  253 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~-------------------------  253 (338)
                      ...|.+|+++++.+..++.+...+... ....|||+||||+|||++++++|+.+.                         
T Consensus         9 kyRP~~~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~~~~~   88 (585)
T PRK14950          9 KWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSA   88 (585)
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHhcCCC
Confidence            567999999999999999888877753 234579999999999999999998873                         


Q ss_pred             CcEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          254 FDVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       254 ~~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      .+++.++........+++.+...+      ....||||||+|.+..
T Consensus        89 ~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~  134 (585)
T PRK14950         89 VDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLST  134 (585)
T ss_pred             CeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCH
Confidence            234555554434445566655433      2578999999998853

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.90  E-value=5.5e-09  Score=108.68  Aligned_cols=94  Identities=22%  Similarity=0.454  Sum_probs=71.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC---------------------cEE
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF---------------------DVY  257 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~---------------------~~~  257 (338)
                      ..+|.+|+++++.+.+.+.+...+.. ..++.|||+||||||||++|+++|+.+..                     +++
T Consensus        11 KyRP~~f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvi   90 (725)
T PRK07133         11 KYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDII   90 (725)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEE
Confidence            57899999999999999888888876 34567999999999999999999988742                     234


Q ss_pred             EEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          258 DLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       258 ~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      .++..+-....+++.+...+.      ...|+||||+|.+..
T Consensus        91 eidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~  132 (725)
T PRK07133         91 EMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSK  132 (725)
T ss_pred             EEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCH
Confidence            444433223445666665542      567999999998853

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.90  E-value=3.1e-09  Score=111.52  Aligned_cols=93  Identities=20%  Similarity=0.362  Sum_probs=67.0

Q ss_pred             CCCCCccccccCChhHHH---HHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHh
Q 035959          200 LDHPSTFDTLAMDTDMKK---MIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIA  276 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~---~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~  276 (338)
                      ..+|.+|+++++.++...   .+...+.......++||||||||||++++++|+.++..++.+++... ...+++..+..
T Consensus        21 k~RP~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~~~-~i~dir~~i~~   99 (725)
T PRK13341         21 RLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVLA-GVKDLRAEVDR   99 (725)
T ss_pred             hcCCCcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhcCcceeehhhhh-hhHHHHHHHHH
Confidence            456999999999887653   34444443333578999999999999999999999988888876532 22233333322


Q ss_pred             -------cCCCcEEEEcCCCccCC
Q 035959          277 -------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 -------~~~~~Il~iDeiD~~~~  293 (338)
                             .....+|||||||.+..
T Consensus       100 a~~~l~~~~~~~IL~IDEIh~Ln~  123 (725)
T PRK13341        100 AKERLERHGKRTILFIDEVHRFNK  123 (725)
T ss_pred             HHHHhhhcCCceEEEEeChhhCCH
Confidence                   23567999999999864

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.89  E-value=2.2e-09  Score=114.81  Aligned_cols=89  Identities=20%  Similarity=0.358  Sum_probs=74.5

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC--------
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG--------  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~--------  266 (338)
                      .++.+++.+...+++++.|.+..+++++|+||||||||+++.++|..+          +..++.++++.+..        
T Consensus       177 ~~~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~  256 (821)
T CHL00095        177 NLDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEF  256 (821)
T ss_pred             CCCCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHH
Confidence            567788888888999999988888899999999999999999999987          36889999876542        


Q ss_pred             chHHHHHHHhcC--CCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIATE--NKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~~--~~~Il~iDeiD~~~~  293 (338)
                      +..+..++..+.  .+.||||||||.+..
T Consensus       257 e~rl~~i~~~~~~~~~~ILfiDEih~l~~  285 (821)
T CHL00095        257 EERLKRIFDEIQENNNIILVIDEVHTLIG  285 (821)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEecHHHHhc
Confidence            346777887653  578999999999986

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.89  E-value=7.3e-09  Score=106.86  Aligned_cols=94  Identities=15%  Similarity=0.332  Sum_probs=71.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++++.+++.+...+.. ..+..|||+||||||||++|.++|+.+..                        
T Consensus         9 kyRP~~f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~   88 (620)
T PRK14954          9 KYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCR   88 (620)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHH
Confidence            45799999999999999888887766 44567999999999999999999998854                        


Q ss_pred             --------cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 --------DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 --------~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                              ++..++..+....++++.+...+      ..+.|+||||+|.+..
T Consensus        89 ~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~  141 (620)
T PRK14954         89 DFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLST  141 (620)
T ss_pred             HHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCH
Confidence                    23334433333345666666555      3578999999999854

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.88  E-value=7.7e-09  Score=105.89  Aligned_cols=94  Identities=19%  Similarity=0.365  Sum_probs=71.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|.+|+++++++..++.+...+... .++.||||||||+|||++++++|+.+..                        
T Consensus         9 kyRP~~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~   88 (563)
T PRK06647          9 KRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSL   88 (563)
T ss_pred             HhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCC
Confidence            467999999999999999998888763 3456999999999999999999998742                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++..+-....+++.+...+      ....|+||||+|.+..
T Consensus        89 dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~  133 (563)
T PRK06647         89 DVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSN  133 (563)
T ss_pred             CeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCH
Confidence            34555544323344566655332      3678999999998853

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.88  E-value=5e-09  Score=97.14  Aligned_cols=86  Identities=24%  Similarity=0.417  Sum_probs=61.0

Q ss_pred             cccCChhHHHHHHHHHHh-----hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-------chHH-H
Q 035959          208 TLAMDTDMKKMIMDDLER-----AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-------NKHL-R  271 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~-----~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-------~~~l-~  271 (338)
                      ++-..+...+..+..+..     +.+.+++|+||||||||||+.|||+++   |..++.+...++..       +... .
T Consensus        80 d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~~Lk~~~~~~~~~~  159 (254)
T COG1484          80 DFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLEE  159 (254)
T ss_pred             cccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhcCchHH
Confidence            344444444444444443     345789999999999999999999988   67888998887653       1122 2


Q ss_pred             HHHHhcCCCcEEEEcCCCccCC
Q 035959          272 KVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       272 ~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ++...+.+..+|||||+-....
T Consensus       160 ~l~~~l~~~dlLIiDDlG~~~~  181 (254)
T COG1484         160 KLLRELKKVDLLIIDDIGYEPF  181 (254)
T ss_pred             HHHHHhhcCCEEEEecccCccC
Confidence            3444477899999999988654

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.88  E-value=5.1e-09  Score=112.35  Aligned_cols=92  Identities=20%  Similarity=0.378  Sum_probs=75.9

Q ss_pred             CCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC-----
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG-----  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~-----  266 (338)
                      .|..++.+++.++..+++++-|.+..+++.+|+||||||||+++.++|..+          +.+++.+++..+..     
T Consensus       168 ~~~~~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~  247 (852)
T TIGR03346       168 REGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYR  247 (852)
T ss_pred             hCCCCCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhhcchhh
Confidence            456788899999888889988888778899999999999999999999986          67788888776542     


Q ss_pred             ---chHHHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          267 ---NKHLRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ---~~~l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                         +..+.+++..+   ..+.||||||||.+..
T Consensus       248 g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~  280 (852)
T TIGR03346       248 GEFEERLKAVLNEVTKSEGQIILFIDELHTLVG  280 (852)
T ss_pred             hhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhc
Confidence               23567777665   3589999999999976

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.86  E-value=1.1e-08  Score=105.87  Aligned_cols=94  Identities=23%  Similarity=0.399  Sum_probs=72.8

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++.+.+++.+...+... ....+||+||||||||++|+++|+.+..                        
T Consensus         9 kyRP~~f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~   88 (620)
T PRK14948          9 KYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGN   88 (620)
T ss_pred             HhCCCcHhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCC
Confidence            567899999999999998888887763 3467899999999999999999998753                        


Q ss_pred             --cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 --DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 --~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                        +++.++.........++.++..+.      ...|+||||+|.+..
T Consensus        89 h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~  135 (620)
T PRK14948         89 ALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLST  135 (620)
T ss_pred             CccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCH
Confidence              455555543334456777776552      457999999998853

>PRK08116 hypothetical protein; Validated

Probab=98.86  E-value=7.1e-09  Score=96.89  Aligned_cols=62  Identities=27%  Similarity=0.448  Sum_probs=47.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC----------chHHHHHHHhcCCCcEEEEcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG----------NKHLRKVLIATENKSILVVGDIDC  290 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~----------~~~l~~~l~~~~~~~Il~iDeiD~  290 (338)
                      .|++|+|+||||||||+.|+|+++   +.+++.++..++..          ......++.......+|+|||+..
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~  189 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNADLLILDDLGA  189 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCCCEEEEecccC
Confidence            569999999999999999999987   67888888765431          012234555666788999999964

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=98.86  E-value=4.1e-09  Score=95.67  Aligned_cols=91  Identities=20%  Similarity=0.307  Sum_probs=61.1

Q ss_pred             CCccccccCChh--HHHHHHHHHHhh-hc--CceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCC------
Q 035959          203 PSTFDTLAMDTD--MKKMIMDDLERA-WK--RGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEG------  266 (338)
Q Consensus       203 p~~f~~l~~~~~--~k~~i~~~l~~~-~~--~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~------  266 (338)
                      .-+|++++..+.  .--.....+... ..  ..++||||+|+|||||++|+++++     +..+.++++.+...      
T Consensus         4 ~~tFdnfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~   83 (219)
T PF00308_consen    4 KYTFDNFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIREFADAL   83 (219)
T ss_dssp             T-SCCCS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHH
T ss_pred             CCccccCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHHHHHHH
Confidence            348999865432  223333444332 21  358999999999999999999876     56788888765432      


Q ss_pred             -chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          267 -NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 -~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                       ...+..+........+|+|||||.+..
T Consensus        84 ~~~~~~~~~~~~~~~DlL~iDDi~~l~~  111 (219)
T PF00308_consen   84 RDGEIEEFKDRLRSADLLIIDDIQFLAG  111 (219)
T ss_dssp             HTTSHHHHHHHHCTSSEEEEETGGGGTT
T ss_pred             HcccchhhhhhhhcCCEEEEecchhhcC
Confidence             233455666777899999999999865

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.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.86  E-value=1.2e-08  Score=96.83  Aligned_cols=99  Identities=21%  Similarity=0.287  Sum_probs=70.4

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCcCCc
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSVEGN  267 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~~~~  267 (338)
                      ..|.  ..+.|.+|+++++.++..+.+...+.......++|+||||||||++++++++.+.     ..++.++.++....
T Consensus         5 ~~w~--~kyrP~~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~   82 (319)
T PRK00440          5 EIWV--EKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDWRENFLELNASDERGI   82 (319)
T ss_pred             Cccc--hhhCCCcHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEEeccccccch
Confidence            3575  4788999999999999998888888764445689999999999999999999873     23445544443322


Q ss_pred             hHHHHHH----Hhc----CCCcEEEEcCCCccCC
Q 035959          268 KHLRKVL----IAT----ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l----~~~----~~~~Il~iDeiD~~~~  293 (338)
                      ..+...+    ...    ..+.+|+|||+|.+..
T Consensus        83 ~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~  116 (319)
T PRK00440         83 DVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS  116 (319)
T ss_pred             HHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH
Confidence            2222222    211    2356999999998854

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.85  E-value=1e-08  Score=105.54  Aligned_cols=94  Identities=20%  Similarity=0.439  Sum_probs=72.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      .+.|.+|+++++++.+++.+...+... .+..+||+||+|+|||++++++|+.+..                        
T Consensus        17 KyRP~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~   96 (598)
T PRK09111         17 KYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIM   96 (598)
T ss_pred             hhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHh
Confidence            578999999999999999888888763 3457999999999999999999998753                        


Q ss_pred             -----cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 -----DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 -----~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                           +++.++..+.....+++.++..+.      ...|+||||+|.+..
T Consensus        97 ~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~  146 (598)
T PRK09111         97 EGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLST  146 (598)
T ss_pred             cCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCH
Confidence                 233444443334556777765552      578999999999853

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=98.85  E-value=1.3e-09  Score=91.29  Aligned_cols=64  Identities=33%  Similarity=0.422  Sum_probs=48.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHH---------------hcCCCcEEEEcCCCccCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLI---------------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~---------------~~~~~~Il~iDeiD~~~~  293 (338)
                      +++|+||||||||++++.+|..++.+++.+.+....+..+|.....               ....+.+++||||+.+.+
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            4799999999999999999999999999999988766554431111               001578999999998753

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.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=98.85  E-value=2.9e-09  Score=95.78  Aligned_cols=98  Identities=22%  Similarity=0.311  Sum_probs=73.7

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh-C----CcEEEEecCCcCCch
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL-H----FDVYDLELSSVEGNK  268 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l-~----~~~~~l~~~~~~~~~  268 (338)
                      .|.  ..+.|..+.+++++++.-.++.-......-.++++.||||||||+-+.++|..+ |    -.+.+++.++-..-.
T Consensus        16 ~wV--eKYrP~~l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGID   93 (333)
T KOG0991|consen   16 PWV--EKYRPSVLQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGID   93 (333)
T ss_pred             hHH--HhhCchHHHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccH
Confidence            364  588999999999999877766655555444578999999999999999999987 3    346788888766544


Q ss_pred             HHH---HHHHhc------CCCcEEEEcCCCccCC
Q 035959          269 HLR---KVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       269 ~l~---~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      -++   +.|.+.      .+..|+++||.|++..
T Consensus        94 vVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~  127 (333)
T KOG0991|consen   94 VVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTA  127 (333)
T ss_pred             HHHHHHHHHHHhhccCCCCceeEEEeeccchhhh
Confidence            443   333332      1467999999999976

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.84  E-value=1.2e-08  Score=102.89  Aligned_cols=94  Identities=18%  Similarity=0.359  Sum_probs=70.5

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++.+.+.+.+...+.. ..+..||||||||+|||++++++|..++.                        
T Consensus         9 kyRP~~f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~   88 (486)
T PRK14953          9 KYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFP   88 (486)
T ss_pred             hhCCCcHHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCC
Confidence            46799999999999999988888876 34456899999999999999999998742                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++-....+++.+...+      ..+.|++|||+|.+..
T Consensus        89 d~~eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~  133 (486)
T PRK14953         89 DLIEIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTK  133 (486)
T ss_pred             cEEEEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcCH
Confidence            35555554433334455544433      2567999999998853

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.84  E-value=1.2e-08  Score=103.27  Aligned_cols=94  Identities=23%  Similarity=0.393  Sum_probs=72.6

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------C
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------F  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~  254 (338)
                      .++|.+|+++++++.+++.+...+.. ..+..||||||||+|||++++++|+.+.                        .
T Consensus         7 KyRP~~fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~   86 (535)
T PRK08451          7 KYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHI   86 (535)
T ss_pred             HHCCCCHHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCC
Confidence            56799999999999999988888876 3345689999999999999999999872                        2


Q ss_pred             cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++-....+++.++...      ....|++|||+|.+..
T Consensus        87 dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~  131 (535)
T PRK08451         87 DIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTK  131 (535)
T ss_pred             eEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCH
Confidence            46666654433445677776553      2467999999998854

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.84  E-value=1.2e-08  Score=101.99  Aligned_cols=94  Identities=22%  Similarity=0.361  Sum_probs=70.0

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++.+..++.+...+.. ..+..+|||||||+|||+++.++|+.+..                        
T Consensus        10 kyRP~~~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~   89 (451)
T PRK06305         10 KYRPQTFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTS   89 (451)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCC
Confidence            46789999999999999888888876 34567999999999999999999998732                        


Q ss_pred             -cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          255 -DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 -~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                       +++.++.......++++.+....      ..+.|+||||+|.+..
T Consensus        90 ~d~~~i~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt~  135 (451)
T PRK06305         90 LDVLEIDGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLTK  135 (451)
T ss_pred             CceEEeeccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCH
Confidence             35555544333334454443322      3678999999998854

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.82  E-value=2.3e-09  Score=94.19  Aligned_cols=65  Identities=26%  Similarity=0.470  Sum_probs=48.9

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC-------CchHHHHHHHhcCCCcEEEEcCCCccC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE-------GNKHLRKVLIATENKSILVVGDIDCCT  292 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~-------~~~~l~~~l~~~~~~~Il~iDeiD~~~  292 (338)
                      +.+++|+||||||||||+.|+++++   |+.+.+++..++.       ......+.+.......+|||||+....
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~~  121 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYEP  121 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS-
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCccccccEecccccceee
Confidence            5789999999999999999999877   7888888887654       123345566667788999999997553

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.81  E-value=8.4e-09  Score=103.25  Aligned_cols=95  Identities=18%  Similarity=0.307  Sum_probs=62.3

Q ss_pred             cCCCCCccccccCChhHH---HHHHHHHHhh--hcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCc-
Q 035959          199 ILDHPSTFDTLAMDTDMK---KMIMDDLERA--WKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGN-  267 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k---~~i~~~l~~~--~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~-  267 (338)
                      ++.+..+|++++..+...   ..+......+  ..++++||||||||||||++|+|+++     +..++++++.++... 
T Consensus       114 ~l~~~~tfd~fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~~  193 (450)
T PRK00149        114 PLNPKYTFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKFTNDF  193 (450)
T ss_pred             CCCCCCcccccccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHH
Confidence            455666899976543222   2222222222  12468999999999999999999998     456888887664321 


Q ss_pred             ------hHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 ------KHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ------~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                            .....+.......++|+|||||.+..
T Consensus       194 ~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~  225 (450)
T PRK00149        194 VNALRNNTMEEFKEKYRSVDVLLIDDIQFLAG  225 (450)
T ss_pred             HHHHHcCcHHHHHHHHhcCCEEEEehhhhhcC
Confidence                  11223334445788999999999865

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.80  E-value=1.1e-08  Score=101.04  Aligned_cols=94  Identities=18%  Similarity=0.290  Sum_probs=59.8

Q ss_pred             CCCCCccccccCChhHH---HHHHHHHHhhh--cCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCC---
Q 035959          200 LDHPSTFDTLAMDTDMK---KMIMDDLERAW--KRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEG---  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k---~~i~~~l~~~~--~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~---  266 (338)
                      +....+|++++..+...   ..+.+....+.  .++++||||||||||||++|+|+++     +..++++++.++..   
T Consensus       103 l~~~~tfd~fi~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~~~  182 (405)
T TIGR00362       103 LNPKYTFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTNDFV  182 (405)
T ss_pred             CCCCCcccccccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHHHHHH
Confidence            45556899865433221   12222222221  2468999999999999999999987     56788888765431   


Q ss_pred             ----chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                          ...+..+.......++|+|||||.+..
T Consensus       183 ~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~  213 (405)
T TIGR00362       183 NALRNNKMEEFKEKYRSVDLLLIDDIQFLAG  213 (405)
T ss_pred             HHHHcCCHHHHHHHHHhCCEEEEehhhhhcC
Confidence                011222333344678999999998865

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).

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.80  E-value=2.2e-08  Score=103.54  Aligned_cols=94  Identities=17%  Similarity=0.423  Sum_probs=75.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC-------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH-------------------------  253 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~-------------------------  253 (338)
                      .+.|.+|+++++.+.+++.+...+.. ..+..||||||+|+|||+++.++|+.+.                         
T Consensus        10 kyRP~~f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~   89 (614)
T PRK14971         10 KYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRS   89 (614)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCC
Confidence            57899999999999999999888876 3445699999999999999999999874                         


Q ss_pred             CcEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          254 FDVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       254 ~~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      .+++.++..+.....+++.++..+.      ..-|+||||+|.+..
T Consensus        90 ~n~~~ld~~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~  135 (614)
T PRK14971         90 YNIHELDAASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQ  135 (614)
T ss_pred             CceEEecccccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCH
Confidence            4666777665445567777775542      567999999999854

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

Probab=98.79  E-value=2.3e-08  Score=105.99  Aligned_cols=85  Identities=21%  Similarity=0.255  Sum_probs=66.1

Q ss_pred             ccCChhHHHHHHHHHHh------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchH-------------
Q 035959          209 LAMDTDMKKMIMDDLER------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKH-------------  269 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~-------------  269 (338)
                      ..+.+.+|++|++.+..      .....++|+||||+|||++++++|..++.+++.++++.+.+...             
T Consensus       324 ~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~  403 (784)
T PRK10787        324 HYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMP  403 (784)
T ss_pred             ccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccchhccCCCCC
Confidence            67788899999988875      12235789999999999999999999999999999887654332             


Q ss_pred             --HHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          270 --LRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       270 --l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                        +.+.+.... .+.|++|||||.+..
T Consensus       404 G~~~~~l~~~~~~~~villDEidk~~~  430 (784)
T PRK10787        404 GKLIQKMAKVGVKNPLFLLDEIDKMSS  430 (784)
T ss_pred             cHHHHHHHhcCCCCCEEEEEChhhccc
Confidence              223344433 567999999999975

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=98.79  E-value=4.4e-09  Score=91.88  Aligned_cols=89  Identities=21%  Similarity=0.386  Sum_probs=64.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC----cEEEEecCCcCC----chHHHHHHHhcC------CCcEEEEcCCCccCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF----DVYDLELSSVEG----NKHLRKVLIATE------NKSILVVGDIDCCTEL  294 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~----~~~~l~~~~~~~----~~~l~~~l~~~~------~~~Il~iDeiD~~~~~  294 (338)
                      ..+||.||+|||||.+++++|..+..    ++..+|++....    ..-+.+++....      ...||+|||||.+.+ 
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~~-   82 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAHP-   82 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCSH-
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhHHHhhccc-
Confidence            46799999999999999999999996    999999999887    444555555443      346999999999976 


Q ss_pred             ccccccccCCCCCCCCCCcchhhHHHHHHHhcCC
Q 035959          295 QDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL  328 (338)
Q Consensus       295 ~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl  328 (338)
                       . .+.        +.+.........||..||+=
T Consensus        83 -~-~~~--------~~~v~~~~V~~~LL~~le~g  106 (171)
T PF07724_consen   83 -S-NSG--------GADVSGEGVQNSLLQLLEGG  106 (171)
T ss_dssp             -T-TTT--------CSHHHHHHHHHHHHHHHHHS
T ss_pred             -c-ccc--------cchhhHHHHHHHHHHHhccc
Confidence             1 110        01112235577788888753

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 ....

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

Probab=98.78  E-value=1.8e-08  Score=106.17  Aligned_cols=99  Identities=14%  Similarity=0.325  Sum_probs=72.8

Q ss_pred             ccCChhHHHHHHHHHHhh--------hc-CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHH-----
Q 035959          209 LAMDTDMKKMIMDDLERA--------WK-RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVL-----  274 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~--------~~-~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l-----  274 (338)
                      ++++++..+.+.+.+...        .+ ..+||+||||||||.+++++|..++.+++.+++++......+.+++     
T Consensus       460 ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~LiG~~~g  539 (758)
T PRK11034        460 VFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPG  539 (758)
T ss_pred             EeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHcCCCCC
Confidence            677888888888777741        12 3489999999999999999999999999999998765322222221     


Q ss_pred             ----------Hh---cCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhc-CCc
Q 035959          275 ----------IA---TENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTD-GLW  329 (338)
Q Consensus       275 ----------~~---~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iD-gl~  329 (338)
                                .+   ..+.+||+|||||.+.+                      ...+.||+.|| |..
T Consensus       540 yvg~~~~g~L~~~v~~~p~sVlllDEieka~~----------------------~v~~~LLq~ld~G~l  586 (758)
T PRK11034        540 YVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHP----------------------DVFNLLLQVMDNGTL  586 (758)
T ss_pred             cccccccchHHHHHHhCCCcEEEeccHhhhhH----------------------HHHHHHHHHHhcCee
Confidence                      11   13568999999999954                      35677888887 543

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

Probab=98.78  E-value=2.2e-08  Score=90.47  Aligned_cols=97  Identities=24%  Similarity=0.293  Sum_probs=82.3

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE  265 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~  265 (338)
                      +...+++-.+|-.+.++++-+..|+.+++...+    ....++||||..|||||||++|+-+++   +...+.|+-.++.
T Consensus        46 ~~L~pv~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k~dl~  125 (287)
T COG2607          46 GYLEPVPDPDPIDLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDKEDLA  125 (287)
T ss_pred             CcccCCCCCCCcCHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcHHHHh
Confidence            345567777778899999999999999888777    445789999999999999999999887   5678888888888


Q ss_pred             CchHHHHHHHhcCCCcEEEEcCCC
Q 035959          266 GNKHLRKVLIATENKSILVVGDID  289 (338)
Q Consensus       266 ~~~~l~~~l~~~~~~~Il~iDeiD  289 (338)
                      +-..|...+...+.+-|||+||+-
T Consensus       126 ~Lp~l~~~Lr~~~~kFIlFcDDLS  149 (287)
T COG2607         126 TLPDLVELLRARPEKFILFCDDLS  149 (287)
T ss_pred             hHHHHHHHHhcCCceEEEEecCCC
Confidence            878888888888899999999974

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.78  E-value=1.4e-08  Score=103.86  Aligned_cols=94  Identities=20%  Similarity=0.280  Sum_probs=62.3

Q ss_pred             CCCCCccccccCChhHH---HHHHHHHHhh--hcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCC---
Q 035959          200 LDHPSTFDTLAMDTDMK---KMIMDDLERA--WKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEG---  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k---~~i~~~l~~~--~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~---  266 (338)
                      +....+|++++..+...   ..+...+..+  +.+.++|||++|||||||++|+|+++     ++.++++++.++..   
T Consensus       281 L~~~~TFDnFvvG~sN~~A~aaa~avae~~~~~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~  360 (617)
T PRK14086        281 LNPKYTFDTFVIGASNRFAHAAAVAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFI  360 (617)
T ss_pred             CCCCCCHhhhcCCCccHHHHHHHHHHHhCccccCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHH
Confidence            44445899987654322   1222222221  23458999999999999999999987     56788888866542   


Q ss_pred             ----chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                          ...+..+.....+.++|+||||+.+..
T Consensus       361 ~al~~~~~~~f~~~y~~~DLLlIDDIq~l~g  391 (617)
T PRK14086        361 NSIRDGKGDSFRRRYREMDILLVDDIQFLED  391 (617)
T ss_pred             HHHHhccHHHHHHHhhcCCEEEEehhccccC
Confidence                111223333445689999999999865

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.76  E-value=2.9e-08  Score=97.52  Aligned_cols=89  Identities=26%  Similarity=0.376  Sum_probs=66.4

Q ss_pred             ccccccCChhHHHHHHHHHHhh----------hcCceeeeCCCCCCcHHHHHHHHHHhCC--------------------
Q 035959          205 TFDTLAMDTDMKKMIMDDLERA----------WKRGYLLFGPPGTGKSSLIAAMANYLHF--------------------  254 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~----------~~~g~LL~GppGtGKT~l~~aia~~l~~--------------------  254 (338)
                      .|+++++.+..++.+.+.+...          .+++|||+||||+|||+++.++|+.+..                    
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~   82 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAG   82 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcC
Confidence            5889999999999998888874          4577999999999999999999987632                    


Q ss_pred             ---cEEEEecCCc-CCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 ---DVYDLELSSV-EGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ---~~~~l~~~~~-~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                         +++.+..... ...++++.++..+.      +..|+||||+|.+..
T Consensus        83 ~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~  131 (394)
T PRK07940         83 THPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTE  131 (394)
T ss_pred             CCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCH
Confidence               2334433211 23455677666542      456999999999964

>PRK09183 transposase/IS protein; Provisional

Probab=98.75  E-value=2.6e-08  Score=92.72  Aligned_cols=66  Identities=18%  Similarity=0.255  Sum_probs=48.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-------chHHHHHHHh-cCCCcEEEEcCCCccCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-------NKHLRKVLIA-TENKSILVVGDIDCCTE  293 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-------~~~l~~~l~~-~~~~~Il~iDeiD~~~~  293 (338)
                      ..+++|+||||||||||+.+++..+   |+.+..++..++..       ...+...+.. ...+++|+|||++....
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~~dlLiiDdlg~~~~  178 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYLPF  178 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcCCCEEEEcccccCCC
Confidence            4578999999999999999998764   77888877665431       1224445544 45778999999987643

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.75  E-value=2.1e-08  Score=100.08  Aligned_cols=95  Identities=15%  Similarity=0.295  Sum_probs=60.4

Q ss_pred             cCCCCCccccccCChhHH---HHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCc--
Q 035959          199 ILDHPSTFDTLAMDTDMK---KMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGN--  267 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k---~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~--  267 (338)
                      ++.+..+|++++..+...   ..+.+....+ +.++++||||||+|||||++|+|+++     +..++++++.++...  
T Consensus        97 ~l~~~~tFdnFv~g~~n~~a~~~~~~~~~~~~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f~~~~~  176 (440)
T PRK14088         97 PLNPDYTFENFVVGPGNSFAYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLV  176 (440)
T ss_pred             CCCCCCcccccccCCchHHHHHHHHHHHhCcCCCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHH
Confidence            345566899987544322   1222222222 23568999999999999999999986     456788877653311  


Q ss_pred             -----hHHHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          268 -----KHLRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       268 -----~~l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                           ..+........ ++.+|+|||++.+.+
T Consensus       177 ~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~  208 (440)
T PRK14088        177 DSMKEGKLNEFREKYRKKVDVLLIDDVQFLIG  208 (440)
T ss_pred             HHHhcccHHHHHHHHHhcCCEEEEechhhhcC
Confidence                 11222222222 588999999998865

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

Probab=98.74  E-value=1.3e-08  Score=107.33  Aligned_cols=89  Identities=24%  Similarity=0.368  Sum_probs=68.2

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC--------
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG--------  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~--------  266 (338)
                      .++.+++.++..+++++.|.+..+.++||+||||||||++++++|..+          +..++.+++..+..        
T Consensus       184 ~~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~  263 (758)
T PRK11034        184 GIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDF  263 (758)
T ss_pred             CCCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhH
Confidence            456678888888888888887667889999999999999999999875          45566666554432        


Q ss_pred             chHHHHHHHhc--CCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIAT--ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~--~~~~Il~iDeiD~~~~  293 (338)
                      +..++.++..+  ..+.||||||||.+..
T Consensus       264 e~rl~~l~~~l~~~~~~ILfIDEIh~L~g  292 (758)
T PRK11034        264 EKRFKALLKQLEQDTNSILFIDEIHTIIG  292 (758)
T ss_pred             HHHHHHHHHHHHhcCCCEEEeccHHHHhc
Confidence            23456666544  3578999999999987

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=98.73  E-value=2.9e-08  Score=94.59  Aligned_cols=84  Identities=23%  Similarity=0.290  Sum_probs=62.4

Q ss_pred             cccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHH---------------
Q 035959          208 TLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRK---------------  272 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~---------------  272 (338)
                      +...+++..+.++..+.  ..+.+||.||||||||++++++|..++.+++.+++....+..++..               
T Consensus        46 ~y~f~~~~~~~vl~~l~--~~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f  123 (327)
T TIGR01650        46 AYLFDKATTKAICAGFA--YDRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEF  123 (327)
T ss_pred             CccCCHHHHHHHHHHHh--cCCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEE
Confidence            46677777777776664  3578999999999999999999999999999998887554322110               


Q ss_pred             ----HHHhcCCCcEEEEcCCCccCC
Q 035959          273 ----VLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       273 ----~l~~~~~~~Il~iDeiD~~~~  293 (338)
                          +......+.+|++||||.+-+
T Consensus       124 ~~GpL~~A~~~g~illlDEin~a~p  148 (327)
T TIGR01650       124 RDGILPWALQHNVALCFDEYDAGRP  148 (327)
T ss_pred             ecCcchhHHhCCeEEEechhhccCH
Confidence                001113567899999998854

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.

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

Probab=98.73  E-value=4.7e-08  Score=91.59  Aligned_cols=66  Identities=27%  Similarity=0.459  Sum_probs=56.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--------chHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--------NKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--------~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +.++||.||+|+|||.||+.+|+.++.|+-..|++.+..        +.-+.+++..+.      .+.|++|||||.++.
T Consensus        97 KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIar  176 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIAR  176 (408)
T ss_pred             eccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhc
Confidence            578999999999999999999999999999999988763        233566666653      689999999999965

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

Probab=98.72  E-value=4.3e-08  Score=103.71  Aligned_cols=85  Identities=16%  Similarity=0.329  Sum_probs=62.9

Q ss_pred             cccCChhHHHHHHHHHHhh--------hcC-ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCch----------
Q 035959          208 TLAMDTDMKKMIMDDLERA--------WKR-GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNK----------  268 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~--------~~~-g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~----------  268 (338)
                      .+++.++..+.+.+.+...        .+. .+||+||||||||++++++|..++.+++.+++++.....          
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~~~~lig~~~  534 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPP  534 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhcccHHHHhcCCC
Confidence            4677777777777777651        123 379999999999999999999999999999988754321          


Q ss_pred             ---------HHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          269 ---------HLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       269 ---------~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                               .+.+.+. ..+.+||+|||||.+.+
T Consensus       535 gyvg~~~~~~l~~~~~-~~p~~VvllDEieka~~  567 (731)
T TIGR02639       535 GYVGFEQGGLLTEAVR-KHPHCVLLLDEIEKAHP  567 (731)
T ss_pred             CCcccchhhHHHHHHH-hCCCeEEEEechhhcCH
Confidence                     1222222 23679999999998854

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=98.72  E-value=3.7e-08  Score=100.52  Aligned_cols=64  Identities=17%  Similarity=0.336  Sum_probs=53.2

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSS  263 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~  263 (338)
                      ...|.+|+++++.++..+.+...+..+.+..+||+||||||||++|+++++++          +.+++.++++.
T Consensus        58 ~~rp~~f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~  131 (531)
T TIGR02902        58 KTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATT  131 (531)
T ss_pred             hhCcCCHHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEcccc
Confidence            56789999999999888888776665666789999999999999999998753          35788888864

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.

>PHA02244 ATPase-like protein

Probab=98.71  E-value=6.9e-08  Score=93.25  Aligned_cols=66  Identities=20%  Similarity=0.349  Sum_probs=48.6

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC----c----CCchHH--HHHHHhcCCCcEEEEcCCCccCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS----V----EGNKHL--RKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~----~----~~~~~l--~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ...+||+||||||||+++++||..++.+++.++...    +    .....+  ..++.......+|+||||+.+.+
T Consensus       119 ~~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~~~GgvLiLDEId~a~p  194 (383)
T PHA02244        119 NIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAFKKGGLFFIDEIDASIP  194 (383)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHhhcCCEEEEeCcCcCCH
Confidence            467999999999999999999999999999887421    0    001111  13334456789999999998854

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.71  E-value=4e-08  Score=98.12  Aligned_cols=94  Identities=20%  Similarity=0.332  Sum_probs=60.5

Q ss_pred             CCCCCccccccCChhHHH--HHHHHHHh-h-----h-cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-
Q 035959          200 LDHPSTFDTLAMDTDMKK--MIMDDLER-A-----W-KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~--~i~~~l~~-~-----~-~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-  266 (338)
                      +.+..+|++++..+....  .....+.. +     + .++++||||||+|||||++|+|+++   +..+.+++...+.. 
T Consensus       104 l~~~~tFdnFv~g~~N~~a~~~a~~~a~~~~~~~~~~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~  183 (445)
T PRK12422        104 LDPLMTFANFLVTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEH  183 (445)
T ss_pred             CCccccccceeeCCcHHHHHHHHHHHHhccccccCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHH
Confidence            445568999875433221  23333322 1     1 2568999999999999999999987   57888887654321 


Q ss_pred             ------chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          267 ------NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ------~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                            ...+..+.......++|+||||+.+..
T Consensus       184 ~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~  216 (445)
T PRK12422        184 LVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSG  216 (445)
T ss_pred             HHHHHhcchHHHHHHHcccCCEEEEcchhhhcC
Confidence                  111222222245788999999999854

>PRK06620 hypothetical protein; Validated

Probab=98.71  E-value=3e-08  Score=89.66  Aligned_cols=82  Identities=17%  Similarity=0.220  Sum_probs=49.7

Q ss_pred             CCCCCccccccCChhHH--HHHHHHHHhhh-----cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHH
Q 035959          200 LDHPSTFDTLAMDTDMK--KMIMDDLERAW-----KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRK  272 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k--~~i~~~l~~~~-----~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~  272 (338)
                      ..+.-+|++++..+.-.  -.........|     .+.++||||||||||||++|+|+..+..  .+.....  ..   .
T Consensus         9 ~~~~~tfd~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~--~~~~~~~--~~---~   81 (214)
T PRK06620          9 TSSKYHPDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAY--IIKDIFF--NE---E   81 (214)
T ss_pred             CCCCCCchhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhccCCE--Ecchhhh--ch---h
Confidence            34445899987655221  12222222223     2558999999999999999999988752  2221111  11   1


Q ss_pred             HHHhcCCCcEEEEcCCCcc
Q 035959          273 VLIATENKSILVVGDIDCC  291 (338)
Q Consensus       273 ~l~~~~~~~Il~iDeiD~~  291 (338)
                      .   ....++|+|||||.+
T Consensus        82 ~---~~~~d~lliDdi~~~   97 (214)
T PRK06620         82 I---LEKYNAFIIEDIENW   97 (214)
T ss_pred             H---HhcCCEEEEeccccc
Confidence            1   134589999999954

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.70  E-value=4.4e-08  Score=97.98  Aligned_cols=91  Identities=15%  Similarity=0.326  Sum_probs=59.8

Q ss_pred             CCccccccCChhHHH---HHHHHHHhh--hcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCc-----
Q 035959          203 PSTFDTLAMDTDMKK---MIMDDLERA--WKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGN-----  267 (338)
Q Consensus       203 p~~f~~l~~~~~~k~---~i~~~l~~~--~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~-----  267 (338)
                      +.+|++++..+....   .+......+  ..++++|||++|+|||||++|+++++     +..++++++.++...     
T Consensus       111 ~~tFdnFv~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l  190 (450)
T PRK14087        111 ENTFENFVIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDIL  190 (450)
T ss_pred             ccchhcccCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHH
Confidence            468888875543221   111111212  12568999999999999999999965     467788877664421     


Q ss_pred             ----hHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 ----KHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ----~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                          ..+..........++|+||||+.+..
T Consensus       191 ~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~  220 (450)
T PRK14087        191 QKTHKEIEQFKNEICQNDVLIIDDVQFLSY  220 (450)
T ss_pred             HHhhhHHHHHHHHhccCCEEEEeccccccC
Confidence                22333444456788999999998864

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

Probab=98.68  E-value=7.7e-08  Score=83.79  Aligned_cols=83  Identities=19%  Similarity=0.225  Sum_probs=58.7

Q ss_pred             cCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh--------
Q 035959          210 AMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA--------  276 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~--------  276 (338)
                      ++..+.-+++++.+..  ..+..+||+|++||||+.+|++|.+..   +.+++.++|+.+.. +.+...+..        
T Consensus         2 iG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~-~~~e~~LFG~~~~~~~~   80 (168)
T PF00158_consen    2 IGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPE-ELLESELFGHEKGAFTG   80 (168)
T ss_dssp             S--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-H-HHHHHHHHEBCSSSSTT
T ss_pred             EeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhc-chhhhhhhccccccccc
Confidence            4455556667777776  556789999999999999999999976   46899999998753 334333332        


Q ss_pred             ----------cCCCcEEEEcCCCccCC
Q 035959          277 ----------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ----------~~~~~Il~iDeiD~~~~  293 (338)
                                ......|+||||+.+..
T Consensus        81 ~~~~~~G~l~~A~~GtL~Ld~I~~L~~  107 (168)
T PF00158_consen   81 ARSDKKGLLEQANGGTLFLDEIEDLPP  107 (168)
T ss_dssp             TSSEBEHHHHHTTTSEEEEETGGGS-H
T ss_pred             cccccCCceeeccceEEeecchhhhHH
Confidence                      13678999999999975

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 ....

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=98.67  E-value=2.4e-08  Score=100.26  Aligned_cols=94  Identities=22%  Similarity=0.458  Sum_probs=75.0

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ..+|..|+++++.+.+.+.+.+.+.. .-..+|||.||.|||||++++.+|+.++.                        
T Consensus         9 KyRP~~F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~~   88 (515)
T COG2812           9 KYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLI   88 (515)
T ss_pred             HhCcccHHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhcCCcc
Confidence            35699999999999999988888877 34578999999999999999999998742                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++++|..+-...++++.+.++..      +.-|++|||+|.+..
T Consensus        89 DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~  133 (515)
T COG2812          89 DVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSK  133 (515)
T ss_pred             cchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhH
Confidence            344444444445677888888773      678999999999864

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=98.67  E-value=1.1e-08  Score=84.48  Aligned_cols=75  Identities=24%  Similarity=0.271  Sum_probs=46.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHH--HHhc----------CCCcEEEEcCCCccCCcccc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKV--LIAT----------ENKSILVVGDIDCCTELQDR  297 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~--l~~~----------~~~~Il~iDeiD~~~~~~~r  297 (338)
                      .+||+|+||+|||++++++|..++.++.+|.++.-...+++.-.  +...          --..|+++|||.+..+    
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNrapp----   76 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRAPP----   76 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS-H----
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccCCH----
Confidence            47999999999999999999999999999988643322222110  0000          1257999999999876    


Q ss_pred             cccccCCCCCCCCCCcchhhHHHHHHHhc
Q 035959          298 SAQARTASPDWHSPKRDQITLSGLLNFTD  326 (338)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~ls~lLn~iD  326 (338)
                                        .+.|.||.+|.
T Consensus        77 ------------------ktQsAlLeam~   87 (131)
T PF07726_consen   77 ------------------KTQSALLEAME   87 (131)
T ss_dssp             ------------------HHHHHHHHHHH
T ss_pred             ------------------HHHHHHHHHHH
Confidence                              67788888874

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.67  E-value=3.9e-08  Score=79.91  Aligned_cols=66  Identities=26%  Similarity=0.408  Sum_probs=49.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCc---EEEEecCCcCC--------------------chHHHHHHHhcC--CCcE
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFD---VYDLELSSVEG--------------------NKHLRKVLIATE--NKSI  282 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~---~~~l~~~~~~~--------------------~~~l~~~l~~~~--~~~I  282 (338)
                      ++.++|+||||||||++++++|..+...   ++.+++.....                    ......++..+.  .+.+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            3578999999999999999999999765   88887765321                    122333333333  3599


Q ss_pred             EEEcCCCccCC
Q 035959          283 LVVGDIDCCTE  293 (338)
Q Consensus       283 l~iDeiD~~~~  293 (338)
                      |+|||++.+..
T Consensus        82 iiiDei~~~~~   92 (148)
T smart00382       82 LILDEITSLLD   92 (148)
T ss_pred             EEEECCcccCC
Confidence            99999999976

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.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=98.64  E-value=8.1e-08  Score=94.11  Aligned_cols=37  Identities=22%  Similarity=0.466  Sum_probs=33.8

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV  264 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~  264 (338)
                      ++++||+||||||||++++++|..++.+++.++.+.+
T Consensus        47 p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~~   83 (441)
T TIGR00390        47 PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKF   83 (441)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCeEEEeeccee
Confidence            4789999999999999999999999999999997644

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=98.64  E-value=7.2e-08  Score=94.50  Aligned_cols=57  Identities=21%  Similarity=0.450  Sum_probs=46.2

Q ss_pred             ccCChhHHHHHHHHHHhhh--------------cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC
Q 035959          209 LAMDTDMKKMIMDDLERAW--------------KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE  265 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~~--------------~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~  265 (338)
                      +++.++.|+.+...+...|              +.++||+||||||||++++++|..++.+++.++++.+.
T Consensus        17 IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~f~   87 (443)
T PRK05201         17 IIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFT   87 (443)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchhhc
Confidence            6777777877776664421              46899999999999999999999999999999876443

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.64  E-value=1e-07  Score=91.57  Aligned_cols=65  Identities=25%  Similarity=0.316  Sum_probs=50.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------chHHHHHHHhcCCCcEEEEcCCCccC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------NKHLRKVLIATENKSILVVGDIDCCT  292 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------~~~l~~~l~~~~~~~Il~iDeiD~~~  292 (338)
                      ..+++|+||||||||||+.|+|+++   |..+.+++..++..         ..+....+..+....+|||||+....
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e~  259 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTEK  259 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCCC
Confidence            4789999999999999999999987   77888887766532         11222235556678999999998764

>PRK06921 hypothetical protein; Provisional

Probab=98.63  E-value=7.3e-08  Score=90.03  Aligned_cols=63  Identities=29%  Similarity=0.386  Sum_probs=47.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCCcCCc-----hHHHHHHHhcCCCcEEEEcCCCc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSSVEGN-----KHLRKVLIATENKSILVVGDIDC  290 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~~~~~-----~~l~~~l~~~~~~~Il~iDeiD~  290 (338)
                      ..+++|+||||||||||+.|+|+++    +..+++++..++...     ..+...+......++|||||++.
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            4679999999999999999999987    567777776543221     12233445556789999999955

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.63  E-value=1.4e-07  Score=91.52  Aligned_cols=86  Identities=15%  Similarity=0.273  Sum_probs=60.9

Q ss_pred             ccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHhC---------CcEEEEecCCcCCchH----
Q 035959          207 DTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYLH---------FDVYDLELSSVEGNKH----  269 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l~---------~~~~~l~~~~~~~~~~----  269 (338)
                      +.+.+.++..+.+...+..    ..+..++++||||||||++++++++++.         ..++.+++....+...    
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~   94 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVE   94 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHH
Confidence            4677888878777777765    2335789999999999999999998763         4678888876543111    


Q ss_pred             ----------------------HHHHHHh---cCCCcEEEEcCCCccC
Q 035959          270 ----------------------LRKVLIA---TENKSILVVGDIDCCT  292 (338)
Q Consensus       270 ----------------------l~~~l~~---~~~~~Il~iDeiD~~~  292 (338)
                                            +..++..   ..++.||+|||+|.+.
T Consensus        95 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~  142 (365)
T TIGR02928        95 LANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLV  142 (365)
T ss_pred             HHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhc
Confidence                                  1111121   2356799999999996

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.61  E-value=2.7e-07  Score=90.40  Aligned_cols=86  Identities=21%  Similarity=0.278  Sum_probs=59.3

Q ss_pred             ccccCChhHHHHHHHHHHhh----hcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCc----------
Q 035959          207 DTLAMDTDMKKMIMDDLERA----WKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGN----------  267 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~----~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~----------  267 (338)
                      +.+.+.++..+++...+...    .+..++++||||||||++++.+++.+     +..++.+++....+.          
T Consensus        30 ~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~  109 (394)
T PRK00411         30 ENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQ  109 (394)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHH
Confidence            45667776667777766542    23568999999999999999999887     467888888654321          


Q ss_pred             -------------hHH-HH---HHHhcCCCcEEEEcCCCccC
Q 035959          268 -------------KHL-RK---VLIATENKSILVVGDIDCCT  292 (338)
Q Consensus       268 -------------~~l-~~---~l~~~~~~~Il~iDeiD~~~  292 (338)
                                   .++ ..   .+.....+.||+|||+|.+.
T Consensus       110 l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~  151 (394)
T PRK00411        110 LFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLF  151 (394)
T ss_pred             hcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhh
Confidence                         111 11   11122345799999999996

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

Probab=98.61  E-value=1.5e-07  Score=91.45  Aligned_cols=66  Identities=26%  Similarity=0.448  Sum_probs=57.9

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--------chHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--------NKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--------~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +.++||.||+|+|||.|++.+|+-++.|+...||+.+..        ++-+.+++..+.      +..|++|||+|.+..
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~  305 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITK  305 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcc
Confidence            578999999999999999999999999999999999873        345677777663      789999999999984

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

Probab=98.60  E-value=1.4e-07  Score=96.20  Aligned_cols=87  Identities=25%  Similarity=0.413  Sum_probs=62.8

Q ss_pred             ccccCChhHHHHHHHHHHhh--hcCceeeeCCCCCCcHHHHHHHHHHhC----CcEEEEecCCcCCc--hHHHHH----H
Q 035959          207 DTLAMDTDMKKMIMDDLERA--WKRGYLLFGPPGTGKSSLIAAMANYLH----FDVYDLELSSVEGN--KHLRKV----L  274 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~--~~~g~LL~GppGtGKT~l~~aia~~l~----~~~~~l~~~~~~~~--~~l~~~----l  274 (338)
                      .+++..+..|+...++...|  ....+||+||+|+|||.|++++++++-    +.+..++|+.+...  +.+.+.    |
T Consensus       408 ~d~i~~~s~kke~~n~~~spv~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vf  487 (952)
T KOG0735|consen  408 HDFIQVPSYKKENANQELSPVFRHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVF  487 (952)
T ss_pred             CceeecchhhhhhhhhhcccccccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchhHHHHHHHHHHHH
Confidence            34555566666666555443  335689999999999999999999985    45678888887742  333333    3


Q ss_pred             Hhc--CCCcEEEEcCCCccCC
Q 035959          275 IAT--ENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 ~~~--~~~~Il~iDeiD~~~~  293 (338)
                      .+.  -.|+||++||+|+++.
T Consensus       488 se~~~~~PSiIvLDdld~l~~  508 (952)
T KOG0735|consen  488 SEALWYAPSIIVLDDLDCLAS  508 (952)
T ss_pred             HHHHhhCCcEEEEcchhhhhc
Confidence            333  3899999999999987

>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=98.58  E-value=6.1e-06  Score=72.77  Aligned_cols=136  Identities=9%  Similarity=0.189  Sum_probs=94.7

Q ss_pred             cEEEEeccCCCCCccHHHHHHHHHhCCC-CCCCCCeeEeecCC----------------------CCCceEEEccCCceE
Q 035959           52 STLVIEEYDDGLNRNKLFKAAKLYLEPK-IPPNVNRIKINLPK----------------------KESEVSLSVEKNQAV  108 (338)
Q Consensus        52 ~ti~i~e~~~~~~~n~~y~a~~~YLs~~-~~~~~~rL~~~~~~----------------------~~~~~~~~l~~ge~v  108 (338)
                      .|+.|++.      +++|+.+..||+.+ ....++++.+.+..                      +...+.+.+..|. .
T Consensus        27 ~sv~I~~~------D~~Y~~lm~Wls~q~~~~~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~G~-h   99 (187)
T PF08740_consen   27 SSVEIPSD------DEAYDWLMRWLSSQPFSKRSRHLSATTRSNSSWDDDESDDEDSWDTNTSDDKKKPIRFTPSPGT-H   99 (187)
T ss_pred             EEEEECCC------CHHHHHHHHHHhhCCcccccceeEEEeecccccccccccccchhccccccCCcCCeEEEeCCCC-E
Confidence            57777765      69999999999998 67778888887732                      3567889999994 4


Q ss_pred             EEeecCeEEEEEEEeecCCCCCcCCCCCCCCCCCcceEEEEEcCcchhhHHhhhhHHHHHHhHHH--HHhccceeeeecc
Q 035959          109 FDVFNGVRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKEL--SKKKKTLKLFTLN  186 (338)
Q Consensus       109 ~D~f~G~~~~W~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~~~~~~~vl~~~l~~v~~~~~~~--~~~~~~~~l~~~~  186 (338)
                      ...|+|   +|..+.+..+......   .. ..+.+.++|++....++ +    |..+++++++.  +++.....||...
T Consensus       100 ~F~y~G---~~~~~~R~~~~~~~~~---~~-~~~~e~l~l~~lg~s~~-~----l~~ll~ear~~~~~~~~~~t~Iy~~~  167 (187)
T PF08740_consen  100 WFWYKG---RWFWFSRQRESNSYNS---WT-GAPDETLTLSCLGRSPK-P----LKDLLEEAREYYLKKQKGKTTIYRAD  167 (187)
T ss_pred             EEEECC---EEEEEEEEeccccccc---cC-CCCceEEEEEEecCCHH-H----HHHHHHHHHHHHHHhcCCcEEEEeCC
Confidence            558999   5787777764332221   11 34589999999998765 4    44555666554  3344445699985


Q ss_pred             CccCCCCccccccCCCCCccccc
Q 035959          187 CNRINHDTRQSAILDHPSTFDTL  209 (338)
Q Consensus       187 ~~~~~~~~w~~~~~~~p~~f~~l  209 (338)
                      +..   ..|....-+++++++++
T Consensus       168 ~~~---~~W~~~~~r~~RplsTV  187 (187)
T PF08740_consen  168 GSE---YRWRRVASRPKRPLSTV  187 (187)
T ss_pred             CCC---CCCcCCCCcCCCCCCCC
Confidence            211   15999887888888764

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.57  E-value=2.3e-07  Score=96.29  Aligned_cols=64  Identities=16%  Similarity=0.366  Sum_probs=53.6

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCc
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSV  264 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~  264 (338)
                      ..|.+|+++++..+..+.+++.+..+.+..++|+||||||||++++++++..          +.+++.+++..+
T Consensus       148 ~rp~~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l  221 (615)
T TIGR02903       148 LRPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL  221 (615)
T ss_pred             cCcCcHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhc
Confidence            4588999999988888888888876777789999999999999999998766          346788887765

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

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

Probab=98.53  E-value=3.4e-07  Score=88.01  Aligned_cols=95  Identities=22%  Similarity=0.252  Sum_probs=65.0

Q ss_pred             ccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHH------HHHH--Hh----
Q 035959          209 LAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHL------RKVL--IA----  276 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l------~~~l--~~----  276 (338)
                      +++.+.....+...+.  ..+.+||-||||||||.+++++|..++.+++.++|..-...+++      ....  ..    
T Consensus        26 ~~g~~~~~~~~l~a~~--~~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~  103 (329)
T COG0714          26 VVGDEEVIELALLALL--AGGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRF  103 (329)
T ss_pred             eeccHHHHHHHHHHHH--cCCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEE
Confidence            3444444444333332  35789999999999999999999999999999999975543332      1111  00    


Q ss_pred             cC---CC---cEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcC
Q 035959          277 TE---NK---SILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDG  327 (338)
Q Consensus       277 ~~---~~---~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDg  327 (338)
                      ..   -.   +|+++|||+...+                      .+.+.||..|+.
T Consensus       104 ~~gpl~~~~~~ill~DEInra~p----------------------~~q~aLl~~l~e  138 (329)
T COG0714         104 VPGPLFAAVRVILLLDEINRAPP----------------------EVQNALLEALEE  138 (329)
T ss_pred             ecCCcccccceEEEEeccccCCH----------------------HHHHHHHHHHhC
Confidence            01   12   3999999999865                      566777877764

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.51  E-value=7e-07  Score=87.06  Aligned_cols=53  Identities=26%  Similarity=0.462  Sum_probs=46.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ..+|++++++++.+..++.+.+.+.. ..+..+||+||+|+||++++.++|+.+
T Consensus        12 ~~~P~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~L   65 (365)
T PRK07471         12 APHPRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFL   65 (365)
T ss_pred             CCCCCchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            36899999999999999999888877 335679999999999999999999977

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.50  E-value=3.7e-07  Score=97.94  Aligned_cols=86  Identities=19%  Similarity=0.362  Sum_probs=62.1

Q ss_pred             ccccCChhHHHHHHHHHHhh--------hcCc-eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCch------
Q 035959          207 DTLAMDTDMKKMIMDDLERA--------WKRG-YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNK------  268 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~--------~~~g-~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~------  268 (338)
                      +.+++.++..+.+.+.+...        .+.| +||+||||||||++++++|..+   ...++.+++++.....      
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~  645 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLK  645 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhcccc
Confidence            34678888888887777651        2334 7999999999999999999998   3467888887654221      


Q ss_pred             -------------HHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          269 -------------HLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       269 -------------~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                   .|...+.. .+.+||+|||||.+.+
T Consensus       646 g~~~gyvg~~~~g~L~~~v~~-~p~svvllDEieka~~  682 (852)
T TIGR03345       646 GSPPGYVGYGEGGVLTEAVRR-KPYSVVLLDEVEKAHP  682 (852)
T ss_pred             CCCCCcccccccchHHHHHHh-CCCcEEEEechhhcCH
Confidence                         23333333 5779999999997654

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.

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=98.49  E-value=3.3e-07  Score=88.12  Aligned_cols=52  Identities=31%  Similarity=0.468  Sum_probs=42.7

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +.|..|+.+++.++.++.+.-.+..+...++||.||||||||++++++|..+
T Consensus         2 ~~~~~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          2 KKPFPFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            3577899999999888877654443334679999999999999999999988

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

Probab=98.49  E-value=2.5e-07  Score=96.61  Aligned_cols=97  Identities=20%  Similarity=0.348  Sum_probs=75.7

Q ss_pred             cccCChhHHHHHHHHHHh------hh--c-CceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCCcCCchHHHHHHH
Q 035959          208 TLAMDTDMKKMIMDDLER------AW--K-RGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSVEGNKHLRKVLI  275 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~------~~--~-~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~~~~~~~l~~~l~  275 (338)
                      .++++++.-..+.+.+.+      ..  | ..+||.||+|+|||-|++++|..+.   -.++.+|+++......+.+++-
T Consensus       492 rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLIG  571 (786)
T COG0542         492 RVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIG  571 (786)
T ss_pred             ceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHhC
Confidence            467777777777776666      11  2 2468999999999999999999996   7899999999887666666654


Q ss_pred             hc------------------CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhc
Q 035959          276 AT------------------ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTD  326 (338)
Q Consensus       276 ~~------------------~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iD  326 (338)
                      ..                  .+.|||++|||+..-+                      ..++-||+.+|
T Consensus       572 aPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHp----------------------dV~nilLQVlD  618 (786)
T COG0542         572 APPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHP----------------------DVFNLLLQVLD  618 (786)
T ss_pred             CCCCCceeccccchhHhhhcCCCeEEEechhhhcCH----------------------HHHHHHHHHhc
Confidence            33                  2579999999999865                      67788888887

>PRK09087 hypothetical protein; Validated

Probab=98.48  E-value=3e-07  Score=83.88  Aligned_cols=85  Identities=18%  Similarity=0.230  Sum_probs=52.0

Q ss_pred             cCCCCCccccccCChhHHHHHHHHHHh--hhcC-ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHH
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDLER--AWKR-GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLI  275 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l~~--~~~~-g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~  275 (338)
                      +.....+|++++..+.-. .++..+.+  .|.. .++|+||+|+|||||++++|+..+..  +++...+..     ..+.
T Consensus        13 ~~~~~~~~~~Fi~~~~N~-~a~~~l~~~~~~~~~~l~l~G~~GsGKThLl~~~~~~~~~~--~i~~~~~~~-----~~~~   84 (226)
T PRK09087         13 SHDPAYGRDDLLVTESNR-AAVSLVDHWPNWPSPVVVLAGPVGSGKTHLASIWREKSDAL--LIHPNEIGS-----DAAN   84 (226)
T ss_pred             CCCCCCChhceeecCchH-HHHHHHHhcccCCCCeEEEECCCCCCHHHHHHHHHHhcCCE--EecHHHcch-----HHHH
Confidence            344446899988633222 23334443  2333 48999999999999999999887654  343332211     1112


Q ss_pred             hcCCCcEEEEcCCCccC
Q 035959          276 ATENKSILVVGDIDCCT  292 (338)
Q Consensus       276 ~~~~~~Il~iDeiD~~~  292 (338)
                      ... ..+|+|||+|.+.
T Consensus        85 ~~~-~~~l~iDDi~~~~  100 (226)
T PRK09087         85 AAA-EGPVLIEDIDAGG  100 (226)
T ss_pred             hhh-cCeEEEECCCCCC
Confidence            221 2689999999863

>TIGR00602 rad24 checkpoint protein rad24

Probab=98.46  E-value=1.6e-07  Score=97.03  Aligned_cols=63  Identities=27%  Similarity=0.295  Sum_probs=51.7

Q ss_pred             CCccccccCCCCCccccccCChhHHHHHHHHHHhh-----hcCceeeeCCCCCCcHHHHHHHHHHhCCcE
Q 035959          192 HDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERA-----WKRGYLLFGPPGTGKSSLIAAMANYLHFDV  256 (338)
Q Consensus       192 ~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~-----~~~g~LL~GppGtGKT~l~~aia~~l~~~~  256 (338)
                      ...|.  ....|.++++++++++..+.+...+...     ..+.++|+||||||||++++++|+.++..+
T Consensus        71 ~~pW~--eKyrP~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~  138 (637)
T TIGR00602        71 NEPWV--EKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQV  138 (637)
T ss_pred             cCchH--HHhCCCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHH
Confidence            34685  4889999999999998888888777761     223489999999999999999999998654

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.45  E-value=1.2e-06  Score=85.08  Aligned_cols=54  Identities=22%  Similarity=0.354  Sum_probs=47.0

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ..||+.|+.+++..+.++.+...+... .+..+||+||+|+|||+++.++|+.+.
T Consensus        16 ~~~P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Ll   70 (351)
T PRK09112         16 VPSPSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHIL   70 (351)
T ss_pred             CCCCCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHc
Confidence            369999999999999999998888763 345699999999999999999999873

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.44  E-value=5.6e-07  Score=96.48  Aligned_cols=86  Identities=19%  Similarity=0.350  Sum_probs=60.8

Q ss_pred             ccccCChhHHHHHHHHHHhh--------hcC-ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchH-----
Q 035959          207 DTLAMDTDMKKMIMDDLERA--------WKR-GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKH-----  269 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~--------~~~-g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~-----  269 (338)
                      +.++++++..+.+...+...        .+. .+||+||||||||++++++|..+   +.+++.+++++......     
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l~  588 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLI  588 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccHHHhc
Confidence            34678888888787777641        112 37899999999999999999987   35788888877543221     


Q ss_pred             --------------HHHHHHhcCCCcEEEEcCCCccCC
Q 035959          270 --------------LRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       270 --------------l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                    |...+.. .+.+||+|||||.+.+
T Consensus       589 g~~~gyvg~~~~~~l~~~~~~-~p~~VvllDeieka~~  625 (821)
T CHL00095        589 GSPPGYVGYNEGGQLTEAVRK-KPYTVVLFDEIEKAHP  625 (821)
T ss_pred             CCCCcccCcCccchHHHHHHh-CCCeEEEECChhhCCH
Confidence                          2222222 3568999999998854

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.43  E-value=8.4e-07  Score=95.44  Aligned_cols=87  Identities=16%  Similarity=0.393  Sum_probs=62.7

Q ss_pred             ccccCChhHHHHHHHHHHhhh--------c-CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHH
Q 035959          207 DTLAMDTDMKKMIMDDLERAW--------K-RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVL  274 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~~--------~-~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l  274 (338)
                      +.+++++...+.+...+....        + ..+||+||||||||++|+++|..+   +.+++.+++++........+++
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l~  644 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLI  644 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchHHHhc
Confidence            457788888888888777621        2 247899999999999999999987   4678899988765432222221


Q ss_pred             ----------------H--hcCCCcEEEEcCCCccCC
Q 035959          275 ----------------I--ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 ----------------~--~~~~~~Il~iDeiD~~~~  293 (338)
                                      .  ...+.+||+||||+.+.+
T Consensus       645 g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka~~  681 (852)
T TIGR03346       645 GAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAHP  681 (852)
T ss_pred             CCCCCccCcccccHHHHHHHcCCCcEEEEeccccCCH
Confidence                            1  123568999999998854

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.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.43  E-value=1.1e-06  Score=89.59  Aligned_cols=91  Identities=16%  Similarity=0.219  Sum_probs=67.8

Q ss_pred             CCCccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHH-
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLI-  275 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~-  275 (338)
                      ...+|+++++.....+++++.+.+  .....+||+|++||||+++|+++....   +.+++.++|+.+.. ..+...++ 
T Consensus       199 ~~~~f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~~-~~~e~elFG  277 (520)
T PRK10820        199 DDSAFSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPD-DVVESELFG  277 (520)
T ss_pred             ccccccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCCH-HHHHHHhcC
Confidence            345788998888777778887775  344679999999999999999987665   35899999998753 23332221 


Q ss_pred             -----------------hcCCCcEEEEcCCCccCC
Q 035959          276 -----------------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 -----------------~~~~~~Il~iDeiD~~~~  293 (338)
                                       +......|+|||||.+..
T Consensus       278 ~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~  312 (520)
T PRK10820        278 HAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSP  312 (520)
T ss_pred             CCCCCcCCcccCCCChhhhcCCCEEEEeChhhCCH
Confidence                             123467899999999965

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.42  E-value=7.5e-07  Score=95.71  Aligned_cols=88  Identities=15%  Similarity=0.397  Sum_probs=61.9

Q ss_pred             cccccCChhHHHHHHHHHHhhh------c---CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHH
Q 035959          206 FDTLAMDTDMKKMIMDDLERAW------K---RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKV  273 (338)
Q Consensus       206 f~~l~~~~~~k~~i~~~l~~~~------~---~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~  273 (338)
                      ++.+++.+...+.+...+....      .   ..+||+||||||||++|+++|..+   +.+++.+++++........++
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~L  646 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRL  646 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHHH
Confidence            4567888887777777776521      1   247899999999999999999987   456888888876532222222


Q ss_pred             H---------------H---hcCCCcEEEEcCCCccCC
Q 035959          274 L---------------I---ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 l---------------~---~~~~~~Il~iDeiD~~~~  293 (338)
                      +               .   ...+.++|+||||+.+.+
T Consensus       647 iG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~~  684 (857)
T PRK10865        647 VGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHP  684 (857)
T ss_pred             hCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCCH
Confidence            2               1   112458999999997754

>TIGR01817 nifA Nif-specific regulatory protein

Probab=98.42  E-value=1e-06  Score=90.12  Aligned_cols=89  Identities=16%  Similarity=0.184  Sum_probs=69.3

Q ss_pred             CccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh--
Q 035959          204 STFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA--  276 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~--  276 (338)
                      .+|+.+++.....+++++.+..  .....+||+|++||||+++|+++....   +.+++.++|..+.. ..+...++.  
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~~-~~~~~~lfg~~  271 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSE-TLLESELFGHE  271 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCCH-HHHHHHHcCCC
Confidence            4788999988888888888887  344579999999999999999999875   56899999998743 333333311  


Q ss_pred             ----------------cCCCcEEEEcCCCccCC
Q 035959          277 ----------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ----------------~~~~~Il~iDeiD~~~~  293 (338)
                                      ......|+|||||.+..
T Consensus       272 ~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~  304 (534)
T TIGR01817       272 KGAFTGAIAQRKGRFELADGGTLFLDEIGEISP  304 (534)
T ss_pred             CCccCCCCcCCCCcccccCCCeEEEechhhCCH
Confidence                            23467899999999865

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.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=98.41  E-value=8e-07  Score=88.04  Aligned_cols=86  Identities=20%  Similarity=0.334  Sum_probs=55.6

Q ss_pred             cccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCc-----EEEEecCCcCC--------------
Q 035959          206 FDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFD-----VYDLELSSVEG--------------  266 (338)
Q Consensus       206 f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~-----~~~l~~~~~~~--------------  266 (338)
                      ++++.++++..+.++..+..  +++++|+||||||||++|+++|..+...     +..+....-.+              
T Consensus       174 l~d~~i~e~~le~l~~~L~~--~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vg  251 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTI--KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVG  251 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhc--CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCC
Confidence            45566666666666666653  5789999999999999999999988531     22222221000              


Q ss_pred             ----chHHHHHHHhc----CCCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIAT----ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~----~~~~Il~iDeiD~~~~  293 (338)
                          ...+.+++..+    ..+.+||||||+....
T Consensus       252 y~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani  286 (459)
T PRK11331        252 FRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANL  286 (459)
T ss_pred             eEecCchHHHHHHHHHhcccCCcEEEEehhhccCH
Confidence                11222333333    3679999999998764

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=98.40  E-value=8.6e-07  Score=84.10  Aligned_cols=84  Identities=21%  Similarity=0.322  Sum_probs=60.6

Q ss_pred             cCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------CcEEEEecCC
Q 035959          210 AMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------FDVYDLELSS  263 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~~~~~l~~~~  263 (338)
                      ++..+....+......  ..+..+||+||||||||+++.++|+.+.                        .+++.++.++
T Consensus         4 ~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~   83 (325)
T COG0470           4 VPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSD   83 (325)
T ss_pred             ccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccc
Confidence            3444444555555553  1233599999999999999999999986                        6889998888


Q ss_pred             cCC----chHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          264 VEG----NKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       264 ~~~----~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      ...    .+.++.+.....      ..-|++|||+|.+..
T Consensus        84 ~~~~~i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~  123 (325)
T COG0470          84 LRKIDIIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTE  123 (325)
T ss_pred             cCCCcchHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhH
Confidence            765    234555544432      468999999999975

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=98.40  E-value=1.5e-06  Score=83.58  Aligned_cols=88  Identities=15%  Similarity=0.236  Sum_probs=67.1

Q ss_pred             ccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHH----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLI----  275 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~----  275 (338)
                      .++++++.....+.+++.+.+  .....+||.|++||||+++|+++....   +.+++.++|..+.. ..+...++    
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~-~~~~~~lfg~~~   82 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-NLLDSELFGHEA   82 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCH-HHHHHHHccccc
Confidence            467788888888888888887  334579999999999999999998765   36899999998753 33333321    


Q ss_pred             --------------hcCCCcEEEEcCCCccCC
Q 035959          276 --------------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 --------------~~~~~~Il~iDeiD~~~~  293 (338)
                                    .......|+|||||.+..
T Consensus        83 ~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L~~  114 (326)
T PRK11608         83 GAFTGAQKRHPGRFERADGGTLFLDELATAPM  114 (326)
T ss_pred             cccCCcccccCCchhccCCCeEEeCChhhCCH
Confidence                          223567899999999964

>PHA00729 NTP-binding motif containing protein

Probab=98.39  E-value=6.8e-07  Score=81.12  Aligned_cols=37  Identities=19%  Similarity=0.334  Sum_probs=28.1

Q ss_pred             HHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          218 MIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       218 ~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      .+++.+.......++++|+|||||||+|.++|+.++.
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~~   43 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVFW   43 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3444454433346899999999999999999998763

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

Probab=98.38  E-value=7.9e-07  Score=92.97  Aligned_cols=91  Identities=24%  Similarity=0.420  Sum_probs=78.2

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC--------
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG--------  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~--------  266 (338)
                      .++.+++.++..+++++.|.+..+++-+|.|+||+|||.++..+|...          +..++.+|+..+..        
T Consensus       168 klDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~LvAGakyRGeF  247 (786)
T COG0542         168 KLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEF  247 (786)
T ss_pred             CCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecHHHHhccccccCcH
Confidence            567789999999999999999888899999999999999999999876          56789999988774        


Q ss_pred             chHHHHHHHhcC--CCcEEEEcCCCccCCcc
Q 035959          267 NKHLRKVLIATE--NKSILVVGDIDCCTELQ  295 (338)
Q Consensus       267 ~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~  295 (338)
                      ++.|+.++.+..  .+.||||||||.+....
T Consensus       248 EeRlk~vl~ev~~~~~vILFIDEiHtiVGAG  278 (786)
T COG0542         248 EERLKAVLKEVEKSKNVILFIDEIHTIVGAG  278 (786)
T ss_pred             HHHHHHHHHHHhcCCCeEEEEechhhhcCCC
Confidence            567778887774  48999999999998743

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=98.37  E-value=2.2e-06  Score=82.56  Aligned_cols=83  Identities=16%  Similarity=0.260  Sum_probs=60.2

Q ss_pred             cCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHH----------
Q 035959          210 AMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVL----------  274 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l----------  274 (338)
                      ++.....+.+++.+.+  .....+||+|++||||+++|+++....   +.+++.++|..+.. ..+...+          
T Consensus         2 iG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~-~~l~~~lfG~~~g~~~g   80 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSE-NLLDSELFGHEAGAFTG   80 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCCh-HHHHHHHhccccccccC
Confidence            3444555666776766  334679999999999999999998766   36899999998653 3333333          


Q ss_pred             --------HhcCCCcEEEEcCCCccCC
Q 035959          275 --------IATENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 --------~~~~~~~Il~iDeiD~~~~  293 (338)
                              ........|||||||.+..
T Consensus        81 a~~~~~G~~~~a~gGtL~Ldei~~L~~  107 (329)
T TIGR02974        81 AQKRHQGRFERADGGTLFLDELATASL  107 (329)
T ss_pred             cccccCCchhhCCCCEEEeCChHhCCH
Confidence                    1223578999999999864

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

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=98.35  E-value=4.9e-07  Score=87.33  Aligned_cols=50  Identities=26%  Similarity=0.410  Sum_probs=45.7

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+|..+++.++.|..++..+..+.-.|+||.||+|||||+++++++..+.
T Consensus        14 ~pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~   63 (350)
T CHL00081         14 FPFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLP   63 (350)
T ss_pred             CCHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHh
Confidence            37999999999999999999888778999999999999999999988773

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.33  E-value=2.1e-06  Score=87.59  Aligned_cols=89  Identities=13%  Similarity=0.125  Sum_probs=68.8

Q ss_pred             CccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHH-----------hCCcEEEEecCCcCCchHH
Q 035959          204 STFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANY-----------LHFDVYDLELSSVEGNKHL  270 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~-----------l~~~~~~l~~~~~~~~~~l  270 (338)
                      .+|+++++..+..+++.+.+..  .....+||+|++||||+.+|+++.+.           .+.+++.++|..+.. ..+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e-~ll  294 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAE-SLL  294 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCCh-hhH
Confidence            4688899988888888888776  34567999999999999999999987           357899999998753 333


Q ss_pred             HHHHHh-------------------cCCCcEEEEcCCCccCC
Q 035959          271 RKVLIA-------------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       271 ~~~l~~-------------------~~~~~Il~iDeiD~~~~  293 (338)
                      ...++.                   ......||||||+.+..
T Consensus       295 eseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~  336 (538)
T PRK15424        295 EAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPL  336 (538)
T ss_pred             HHHhcCCccccccCccccccCCchhccCCCEEEEcChHhCCH
Confidence            333222                   23567899999999965

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.32  E-value=3.4e-06  Score=80.52  Aligned_cols=89  Identities=19%  Similarity=0.369  Sum_probs=65.8

Q ss_pred             ccccccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC--------CcEEEEecC--CcCCchHHHHH
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH--------FDVYDLELS--SVEGNKHLRKV  273 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~--------~~~~~l~~~--~~~~~~~l~~~  273 (338)
                      +|+++++.+..++.+...+.. ..++.|||+||+|+|||++|.++|+.+-        .+++.+...  .....++++.+
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir~~   81 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIRNI   81 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHHHH
Confidence            588999999999999888876 3456789999999999999999999762        144444331  11234567766


Q ss_pred             HHhc------CCCcEEEEcCCCccCC
Q 035959          274 LIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      ...+      ...-|++|||+|.+..
T Consensus        82 ~~~~~~~p~~~~~kv~iI~~ad~m~~  107 (313)
T PRK05564         82 IEEVNKKPYEGDKKVIIIYNSEKMTE  107 (313)
T ss_pred             HHHHhcCcccCCceEEEEechhhcCH
Confidence            6643      2567999999998854

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.31  E-value=2.8e-06  Score=74.90  Aligned_cols=66  Identities=26%  Similarity=0.405  Sum_probs=45.9

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------cEEEEecCCc-CCchHHHHHHHhcC----
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------DVYDLELSSV-EGNKHLRKVLIATE----  278 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~------------------------~~~~l~~~~~-~~~~~l~~~l~~~~----  278 (338)
                      +..+||+||||+|||+++.++++.+..                        ++..++...- ...+.++.++..+.    
T Consensus        14 ~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~~~   93 (188)
T TIGR00678        14 AHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTPQ   93 (188)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccCcc
Confidence            456999999999999999999998732                        2344433221 12345655555442    


Q ss_pred             --CCcEEEEcCCCccCC
Q 035959          279 --NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 --~~~Il~iDeiD~~~~  293 (338)
                        .+.|+||||+|.+..
T Consensus        94 ~~~~kviiide~~~l~~  110 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNE  110 (188)
T ss_pred             cCCeEEEEEechhhhCH
Confidence              567999999999864

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.

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.31  E-value=8e-07  Score=74.53  Aligned_cols=75  Identities=25%  Similarity=0.324  Sum_probs=52.1

Q ss_pred             hhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhCC---cEEEEecCCcCCchHHHHHHHhcCCCcEEEEcC
Q 035959          213 TDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLHF---DVYDLELSSVEGNKHLRKVLIATENKSILVVGD  287 (338)
Q Consensus       213 ~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~~---~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDe  287 (338)
                      ...-+++.+.+..  .....++|+|+|||||+++|+++....+.   +++.+++....     .+++..+ ....|+|+|
T Consensus         4 S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-----~~~l~~a-~~gtL~l~~   77 (138)
T PF14532_consen    4 SPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-----AELLEQA-KGGTLYLKN   77 (138)
T ss_dssp             CHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-----HHHHHHC-TTSEEEEEC
T ss_pred             CHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-----HHHHHHc-CCCEEEECC
Confidence            3445666666666  34567999999999999999999998764   34444444432     3344444 778899999


Q ss_pred             CCccCC
Q 035959          288 IDCCTE  293 (338)
Q Consensus       288 iD~~~~  293 (338)
                      ||.+..
T Consensus        78 i~~L~~   83 (138)
T PF14532_consen   78 IDRLSP   83 (138)
T ss_dssp             GCCS-H
T ss_pred             hHHCCH
Confidence            999965

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.28  E-value=1.4e-06  Score=88.48  Aligned_cols=67  Identities=30%  Similarity=0.381  Sum_probs=56.0

Q ss_pred             CCCccccccCCCCCccccccCChhHHHHHHHHHHhh-----hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          191 NHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERA-----WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       191 ~~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~-----~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +...|.  ....|.+.++|+..+...+++..+|+..     .++-+||+||||||||++++++|+++|+.+.+-
T Consensus         5 ~~~~W~--~ky~P~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~Ew   76 (519)
T PF03215_consen    5 ESEPWV--EKYAPKTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQEW   76 (519)
T ss_pred             ccCccc--hhcCCCCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEEe
Confidence            456785  4889999999999998888888888872     234578999999999999999999999877653

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.27  E-value=2.6e-06  Score=82.27  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=50.4

Q ss_pred             CCCccc-cccCChhHHHHHHHHHHhh------hcCceeeeCCCCCCcHHHHHHHHHHhCC-------cEEEEec
Q 035959          202 HPSTFD-TLAMDTDMKKMIMDDLERA------WKRGYLLFGPPGTGKSSLIAAMANYLHF-------DVYDLEL  261 (338)
Q Consensus       202 ~p~~f~-~l~~~~~~k~~i~~~l~~~------~~~g~LL~GppGtGKT~l~~aia~~l~~-------~~~~l~~  261 (338)
                      +-.-|+ ++.+.++.+.++++.+...      .++.++|+||||||||+++.++|+.++.       ++|.+..
T Consensus        45 ~y~~F~~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~  118 (361)
T smart00763       45 RYRFFDHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKW  118 (361)
T ss_pred             eccccchhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEe
Confidence            334566 7888888999999998872      2466799999999999999999999975       8999987

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=98.27  E-value=2.9e-06  Score=89.42  Aligned_cols=89  Identities=18%  Similarity=0.259  Sum_probs=67.7

Q ss_pred             CccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHH----
Q 035959          204 STFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVL----  274 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l----  274 (338)
                      ..|+++++.....+.+++.+..  .....+||+|++|||||++|+++....   +.+++.++|..+.. ..+...+    
T Consensus       373 ~~~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~-~~~~~~lfg~~  451 (686)
T PRK15429        373 SEFGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPA-GLLESDLFGHE  451 (686)
T ss_pred             ccccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCCh-hHhhhhhcCcc
Confidence            4688899988888888888887  334579999999999999999999865   56899999988643 1111111    


Q ss_pred             --------------HhcCCCcEEEEcCCCccCC
Q 035959          275 --------------IATENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 --------------~~~~~~~Il~iDeiD~~~~  293 (338)
                                    .....+..|+||||+.+..
T Consensus       452 ~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L~~  484 (686)
T PRK15429        452 RGAFTGASAQRIGRFELADKSSLFLDEVGDMPL  484 (686)
T ss_pred             cccccccccchhhHHHhcCCCeEEEechhhCCH
Confidence                          1234568999999999864

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=98.27  E-value=2.4e-06  Score=89.11  Aligned_cols=48  Identities=25%  Similarity=0.347  Sum_probs=41.0

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .|..+++.+..+..+.-.+..+.-.++||.||||||||+++++++..+
T Consensus         2 pf~~ivGq~~~~~al~~~av~~~~g~vli~G~~GtgKs~lar~l~~~l   49 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAVDPRIGGVLIRGEKGTAKSTAARGLAALL   49 (633)
T ss_pred             CcchhcChHHHHHHHHHHhhCCCCCeEEEEcCCCCcHHHHHHHHHHhC
Confidence            477889999888887776666655689999999999999999999987

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.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.27  E-value=3.2e-06  Score=88.34  Aligned_cols=88  Identities=18%  Similarity=0.177  Sum_probs=67.0

Q ss_pred             ccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHH-HHHH---
Q 035959          205 TFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLR-KVLI---  275 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~-~~l~---  275 (338)
                      +|+.+++.....+++++.+..  .....+||+|++||||+++|+++.+..   +.+++.++|..+.. +.+. .+|.   
T Consensus       323 ~~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~-~~~~~elfg~~~  401 (638)
T PRK11388        323 TFDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPD-EALAEEFLGSDR  401 (638)
T ss_pred             cccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCCh-HHHHHHhcCCCC
Confidence            578888877777778887777  334569999999999999999999876   36899999998764 2222 2322   


Q ss_pred             -----------hcCCCcEEEEcCCCccCC
Q 035959          276 -----------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 -----------~~~~~~Il~iDeiD~~~~  293 (338)
                                 +......||||||+.+..
T Consensus       402 ~~~~~~~~g~~~~a~~GtL~ldei~~l~~  430 (638)
T PRK11388        402 TDSENGRLSKFELAHGGTLFLEKVEYLSP  430 (638)
T ss_pred             cCccCCCCCceeECCCCEEEEcChhhCCH
Confidence                       123568899999999865

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=98.26  E-value=4.2e-06  Score=76.58  Aligned_cols=66  Identities=26%  Similarity=0.292  Sum_probs=56.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                      ..|-.++||+|||||.+++++|+.+|..++.++|++-.+...+.+++..+. ..+.+++||++++..
T Consensus        32 ~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~~~~l~ril~G~~~~GaW~cfdefnrl~~   98 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMDYQSLSRILKGLAQSGAWLCFDEFNRLSE   98 (231)
T ss_dssp             TTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-HHHHHHHHHHHHHHT-EEEEETCCCSSH
T ss_pred             CCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccccHHHHHHHHHHHhhcCchhhhhhhhhhhH
Confidence            456689999999999999999999999999999999988888999998875 689999999999854

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.26  E-value=9e-07  Score=71.12  Aligned_cols=63  Identities=22%  Similarity=0.340  Sum_probs=40.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ++||||||+|||+++..+|..+...+-.-....+-....-.+.+.......++++||+.....
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~~q~vvi~DD~~~~~~   63 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQGQPVVIIDDFGQDND   63 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccCCCcEEEEeecCcccc
Confidence            479999999999999998887742221000011111111224555666789999999998864

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

>PRK13531 regulatory ATPase RavA; Provisional

Probab=98.25  E-value=2e-06  Score=86.01  Aligned_cols=81  Identities=19%  Similarity=0.213  Sum_probs=50.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCC--cEE--EEecC---CcCCchHHHH-----HHHh-----cCCCcEEEEcCCCc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHF--DVY--DLELS---SVEGNKHLRK-----VLIA-----TENKSILVVGDIDC  290 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~--~~~--~l~~~---~~~~~~~l~~-----~l~~-----~~~~~Il~iDeiD~  290 (338)
                      ...+||+||||||||++|++++...+.  ++.  .+.++   ++.....+..     .+..     .+...+||+|||..
T Consensus        39 g~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~r  118 (498)
T PRK13531         39 GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWK  118 (498)
T ss_pred             CCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcCcHHHhhhhhcCchhhhcCCccccccEEeeccccc
Confidence            467999999999999999999998753  222  22221   1111111111     1111     12345999999986


Q ss_pred             cCCcccccccccCCCCCCCCCCcchhhHHHHHHHh-cCCcC
Q 035959          291 CTELQDRSAQARTASPDWHSPKRDQITLSGLLNFT-DGLWS  330 (338)
Q Consensus       291 ~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~i-Dgl~s  330 (338)
                      +.+                      .+.+.||..| ++...
T Consensus       119 asp----------------------~~QsaLLeam~Er~~t  137 (498)
T PRK13531        119 AGP----------------------AILNTLLTAINERRFR  137 (498)
T ss_pred             CCH----------------------HHHHHHHHHHHhCeEe
Confidence            654                      6778888888 45543

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.25  E-value=7.9e-07  Score=73.01  Aligned_cols=37  Identities=41%  Similarity=0.626  Sum_probs=29.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh--------CCcEEEEecCCcC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL--------HFDVYDLELSSVE  265 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l--------~~~~~~l~~~~~~  265 (338)
                      +.++++||||+|||+++..++..+        ..+++.+++....
T Consensus         5 ~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   49 (131)
T PF13401_consen    5 RILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSR   49 (131)
T ss_dssp             --EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHS
T ss_pred             cccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCC
Confidence            567899999999999999999987        6778888776655

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

Probab=98.25  E-value=1.8e-06  Score=77.17  Aligned_cols=46  Identities=28%  Similarity=0.489  Sum_probs=36.2

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +|+++++++..|+.+.-....  ..++|++||||||||++++++..-+
T Consensus         1 Df~dI~GQe~aKrAL~iAAaG--~h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAAG--GHHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHHC--C--EEEES-CCCTHHHHHHHHHHCS
T ss_pred             ChhhhcCcHHHHHHHHHHHcC--CCCeEEECCCCCCHHHHHHHHHHhC
Confidence            478899999988887665543  5789999999999999999999876

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.

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

Probab=98.23  E-value=3.8e-06  Score=81.89  Aligned_cols=85  Identities=18%  Similarity=0.309  Sum_probs=60.4

Q ss_pred             ccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHhCCc-----EEEEecCCcCCchH-HHHH-----
Q 035959          209 LAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYLHFD-----VYDLELSSVEGNKH-LRKV-----  273 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l~~~-----~~~l~~~~~~~~~~-l~~~-----  273 (338)
                      +...++..+++...+..    ..+..+++|||||||||..++-++.++...     ++++||....+... +.++     
T Consensus        19 l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~   98 (366)
T COG1474          19 LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLG   98 (366)
T ss_pred             ccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcC
Confidence            55556666666655555    334559999999999999999999998543     89999988765222 1222     


Q ss_pred             -------------------HHhcCCCcEEEEcCCCccCC
Q 035959          274 -------------------LIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 -------------------l~~~~~~~Il~iDeiD~~~~  293 (338)
                                         +.......||+|||+|.+..
T Consensus        99 ~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~  137 (366)
T COG1474          99 KVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVD  137 (366)
T ss_pred             CCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhcc
Confidence                               22223578999999999986

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=98.23  E-value=2.9e-06  Score=81.81  Aligned_cols=48  Identities=27%  Similarity=0.443  Sum_probs=42.8

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .|..+++.++.|+.++-.+..+...+++|.|+||||||+++++++..+
T Consensus         2 pf~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             CccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            478889999999988887777777889999999999999999999877

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=98.20  E-value=3.7e-06  Score=82.46  Aligned_cols=94  Identities=18%  Similarity=0.248  Sum_probs=58.3

Q ss_pred             cCCCCCccccccCChhHH--HHHHHHHHh-h--hcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCcCC--
Q 035959          199 ILDHPSTFDTLAMDTDMK--KMIMDDLER-A--WKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSVEG--  266 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k--~~i~~~l~~-~--~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~~~--  266 (338)
                      .+....+|++++..+...  ..+...+.. +  ....++||||.|.|||||++|++++..     ..++++.......  
T Consensus        79 ~l~~~ytFdnFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~  158 (408)
T COG0593          79 GLNPKYTFDNFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDF  158 (408)
T ss_pred             cCCCCCchhheeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHH
Confidence            345556999987765432  222222222 2  235689999999999999999999883     2355554433211  


Q ss_pred             -----chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          267 -----NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 -----~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                           +..+.+.=... +-.+|+||||+.+..
T Consensus       159 v~a~~~~~~~~Fk~~y-~~dlllIDDiq~l~g  189 (408)
T COG0593         159 VKALRDNEMEKFKEKY-SLDLLLIDDIQFLAG  189 (408)
T ss_pred             HHHHHhhhHHHHHHhh-ccCeeeechHhHhcC
Confidence                 11122222223 678999999999976

>PF13173 AAA_14: AAA domain

Probab=98.20  E-value=2.5e-06  Score=70.63  Aligned_cols=65  Identities=18%  Similarity=0.391  Sum_probs=49.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC--CcEEEEecCCcCCch----HHHHHHHhc--CCCcEEEEcCCCccCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH--FDVYDLELSSVEGNK----HLRKVLIAT--ENKSILVVGDIDCCTE  293 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~--~~~~~l~~~~~~~~~----~l~~~l~~~--~~~~Il~iDeiD~~~~  293 (338)
                      +.++|+||+|+|||+++..++..+.  ..+..+++.+.....    ++.+.+.+.  ..+.+||||||+.+..
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEiq~~~~   75 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLADPDLLEYFLELIKPGKKYIFIDEIQYLPD   75 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHhhhhhHHHHHHhhccCCcEEEEehhhhhcc
Confidence            4578999999999999999998886  788899888765321    133444443  3679999999999864

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=98.20  E-value=5.1e-06  Score=84.64  Aligned_cols=91  Identities=15%  Similarity=0.201  Sum_probs=69.9

Q ss_pred             CCCccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA  276 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~  276 (338)
                      ...+|+++++..+..+.+.+.+..  .....+||.|++||||+++|+++.+..   +.+++.++|..+.. ..+...++.
T Consensus       207 ~~~~f~~iiG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~e-~lleseLFG  285 (526)
T TIGR02329       207 TRYRLDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAE-SLLEAELFG  285 (526)
T ss_pred             cccchhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCCh-hHHHHHhcC
Confidence            345788999988888888888876  345679999999999999999999765   56899999998753 333333322


Q ss_pred             -------------------cCCCcEEEEcCCCccCC
Q 035959          277 -------------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 -------------------~~~~~Il~iDeiD~~~~  293 (338)
                                         ......||||||+.+..
T Consensus       286 ~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~  321 (526)
T TIGR02329       286 YEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPL  321 (526)
T ss_pred             CcccccccccccccccchhhcCCceEEecChHhCCH
Confidence                               23467899999999965

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.17  E-value=7.2e-06  Score=86.45  Aligned_cols=86  Identities=26%  Similarity=0.369  Sum_probs=55.1

Q ss_pred             cccCChhHHHHHHHHHHh----hhcCc-eeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCCc-----
Q 035959          208 TLAMDTDMKKMIMDDLER----AWKRG-YLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEGN-----  267 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~----~~~~g-~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~~-----  267 (338)
                      .|.+.++..++|...|..    ..+.+ ++++|+||||||.+++.+...+          ...++.|+|..+...     
T Consensus       756 ~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYq  835 (1164)
T PTZ00112        756 YLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQ  835 (1164)
T ss_pred             cCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHH
Confidence            344555444555444443    12223 4699999999999999998776          256789998654432     


Q ss_pred             ------------------hHHHHHHHhcC----CCcEEEEcCCCccCC
Q 035959          268 ------------------KHLRKVLIATE----NKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ------------------~~l~~~l~~~~----~~~Il~iDeiD~~~~  293 (338)
                                        ..+..++....    ...||||||||.+..
T Consensus       836 vI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~k  883 (1164)
T PTZ00112        836 VLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLIT  883 (1164)
T ss_pred             HHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCc
Confidence                              12233333321    356999999999975

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.16  E-value=8.9e-06  Score=82.83  Aligned_cols=88  Identities=14%  Similarity=0.139  Sum_probs=67.7

Q ss_pred             ccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHH----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLI----  275 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~----  275 (338)
                      .+..+++.....+.+.+.+..  +....+||+|++||||+++++++....   +.+++.++|..+.. ..+...++    
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~-~~~e~~lfG~~~  263 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPE-SLAESELFGHVK  263 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCCh-HHHHHHhcCccc
Confidence            467788888888888888887  445679999999999999999999875   46899999998753 22222221    


Q ss_pred             --------------hcCCCcEEEEcCCCccCC
Q 035959          276 --------------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 --------------~~~~~~Il~iDeiD~~~~  293 (338)
                                    .......|||||||.+..
T Consensus       264 g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~~  295 (509)
T PRK05022        264 GAFTGAISNRSGKFELADGGTLFLDEIGELPL  295 (509)
T ss_pred             cccCCCcccCCcchhhcCCCEEEecChhhCCH
Confidence                          123567899999999965

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=98.13  E-value=2.6e-05  Score=67.36  Aligned_cols=82  Identities=18%  Similarity=0.323  Sum_probs=57.1

Q ss_pred             ChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC-----------------------CcEEEEecCCc---
Q 035959          212 DTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH-----------------------FDVYDLELSSV---  264 (338)
Q Consensus       212 ~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~-----------------------~~~~~l~~~~~---  264 (338)
                      ++...+.+.+.+.. ..+..+||+||+|+||+++|.++|+.+-                       .+++.++....   
T Consensus         2 q~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~   81 (162)
T PF13177_consen    2 QEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKS   81 (162)
T ss_dssp             -HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSS
T ss_pred             cHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccch
Confidence            34455555555554 3345689999999999999999998761                       35667766654   


Q ss_pred             CCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          265 EGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       265 ~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      ...++++.+.....      ..-|++|||+|.+..
T Consensus        82 i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~  116 (162)
T PF13177_consen   82 IKIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTE  116 (162)
T ss_dssp             BSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-H
T ss_pred             hhHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhH
Confidence            24567777777663      567999999999964

...

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.11  E-value=8.2e-06  Score=79.86  Aligned_cols=90  Identities=13%  Similarity=0.167  Sum_probs=71.1

Q ss_pred             CccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCCcCCchHHHHHHHhc
Q 035959          204 STFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSSVEGNKHLRKVLIAT  277 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~~~~~~~l~~~l~~~  277 (338)
                      ..++.+++....-+++++.+.+  +....+|++|++||||+.+|++|....    +.+++.+||+.+..+-....+|-..
T Consensus        75 ~~~~~LIG~~~~~~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~eLFG~~  154 (403)
T COG1221          75 EALDDLIGESPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFGHE  154 (403)
T ss_pred             hhhhhhhccCHHHHHHHHHHHhhCCCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHHHHhccc
Confidence            4678899988888888888888  334568999999999999999988543    5689999999988765554443211


Q ss_pred             -----------------CCCcEEEEcCCCccCC
Q 035959          278 -----------------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       278 -----------------~~~~Il~iDeiD~~~~  293 (338)
                                       .....||+|||+.+..
T Consensus       155 kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~  187 (403)
T COG1221         155 KGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPP  187 (403)
T ss_pred             cceeecccCCcCchheecCCCEEehhhhhhCCH
Confidence                             3578999999999976

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

Probab=98.09  E-value=5.6e-06  Score=85.47  Aligned_cols=64  Identities=22%  Similarity=0.491  Sum_probs=55.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC------chHHHHHHHhcC--CCcEEEEcCCCccCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG------NKHLRKVLIATE--NKSILVVGDIDCCTE  293 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~------~~~l~~~l~~~~--~~~Il~iDeiD~~~~  293 (338)
                      .+||+|+||||||++++++|.++|.+++.++|.++.+      +..+...+..+.  .|+|||+-++|.+.-
T Consensus       433 ~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~i  504 (953)
T KOG0736|consen  433 SVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGI  504 (953)
T ss_pred             EEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeee
Confidence            3799999999999999999999999999999998874      455666676664  799999999999974

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=98.09  E-value=1.2e-05  Score=77.29  Aligned_cols=89  Identities=22%  Similarity=0.302  Sum_probs=61.2

Q ss_pred             ccccccC-ChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------CcEEE
Q 035959          205 TFDTLAM-DTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------FDVYD  258 (338)
Q Consensus       205 ~f~~l~~-~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~~~~~  258 (338)
                      .|+++.+ .+.+.+.+...+.. ..+..|||+||+|+||++++.++|+.+-                        .++..
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~   82 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHL   82 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEE
Confidence            4667777 67777777777765 3456789999999999999999998862                        13444


Q ss_pred             EecCCc-CCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          259 LELSSV-EGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       259 l~~~~~-~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +....- ...++++.+.....      ...|++|||+|.+..
T Consensus        83 i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~  124 (329)
T PRK08058         83 VAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTA  124 (329)
T ss_pred             eccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCH
Confidence            433211 12345666655432      567999999999854

>PHA02624 large T antigen; Provisional

Probab=98.01  E-value=2.5e-05  Score=79.77  Aligned_cols=88  Identities=19%  Similarity=0.257  Sum_probs=57.1

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTAS  305 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~  305 (338)
                      |.++.++|+||||||||+++.++++.++..+..++...-    .+.--|.-+...-+++|||+-.-.-. +..       
T Consensus       429 PKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt~----ks~FwL~pl~D~~~~l~dD~t~~~~~-~~~-------  496 (647)
T PHA02624        429 PKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPPD----KLNFELGCAIDQFMVVFEDVKGQPAD-NKD-------  496 (647)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCcc----hhHHHhhhhhhceEEEeeeccccccc-ccc-------
Confidence            667789999999999999999999999666666664332    22223333346689999999754431 010       


Q ss_pred             CCCCCCCcchhhHHHHHHHhcCC
Q 035959          306 PDWHSPKRDQITLSGLLNFTDGL  328 (338)
Q Consensus       306 ~~~~~~~~~~~~ls~lLn~iDgl  328 (338)
                         -..+..-..|..|=|.+||-
T Consensus       497 ---Lp~G~~~dNl~~lRn~LDG~  516 (647)
T PHA02624        497 ---LPSGQGMNNLDNLRDYLDGS  516 (647)
T ss_pred             ---CCcccccchhhHHHhhcCCC
Confidence               00112223356677888886

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

Probab=97.98  E-value=8.6e-06  Score=81.07  Aligned_cols=65  Identities=31%  Similarity=0.439  Sum_probs=51.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec-CCcC--C----chHHHHHHHhcC--CCcEEEEcCCCccCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL-SSVE--G----NKHLRKVLIATE--NKSILVVGDIDCCTE  293 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~-~~~~--~----~~~l~~~l~~~~--~~~Il~iDeiD~~~~  293 (338)
                      ..+||+||||+|||.||+.+|..-++|++.+-- .++.  +    ...+.+.|.++-  .-+||++|||+.+++
T Consensus       539 vSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD  612 (744)
T KOG0741|consen  539 VSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLD  612 (744)
T ss_pred             eEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhc
Confidence            357999999999999999999999999887633 2332  1    235778888874  679999999999875

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=97.97  E-value=3.3e-06  Score=79.40  Aligned_cols=99  Identities=19%  Similarity=0.218  Sum_probs=68.5

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC----c--EEEEecCCcCC
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF----D--VYDLELSSVEG  266 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~----~--~~~l~~~~~~~  266 (338)
                      -.|.  +.+.|..+++++...+....+.+......-...|+|||||||||+.+.|.|..+-.    .  +..+++++-..
T Consensus        29 ~pwv--ekyrP~~l~dv~~~~ei~st~~~~~~~~~lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaSd~rg  106 (360)
T KOG0990|consen   29 QPWV--EKYRPPFLGIVIKQEPIWSTENRYSGMPGLPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNASDDRG  106 (360)
T ss_pred             CCCc--cCCCCchhhhHhcCCchhhHHHHhccCCCCCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhccCccC
Confidence            3564  57889999999998887777776655544458999999999999999999987732    1  33445554332


Q ss_pred             c---hHHHHHHHhc---------CCCcEEEEcCCCccCC
Q 035959          267 N---KHLRKVLIAT---------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~---~~l~~~l~~~---------~~~~Il~iDeiD~~~~  293 (338)
                      -   ..-.+.+..+         ....++++||.|.+..
T Consensus       107 id~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT~  145 (360)
T KOG0990|consen  107 IDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTR  145 (360)
T ss_pred             CcchHHHHHHHHhhccceeccccCceeEEEecchhHhhH
Confidence            1   1122333333         2567999999999863

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.95  E-value=4.3e-05  Score=73.09  Aligned_cols=48  Identities=19%  Similarity=0.322  Sum_probs=42.6

Q ss_pred             ccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          205 TFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .|+++++.+..++.+...+... -+..|||+||+|+||++++.++|+.+
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~l   50 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGL   50 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            4789999999999999988773 35789999999999999999999986

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=97.93  E-value=1.6e-05  Score=74.47  Aligned_cols=67  Identities=31%  Similarity=0.486  Sum_probs=43.8

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCCc---EEEEecCCcCCchHHHHHHHhc-------------CCCcEEEEcCCCc
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHFD---VYDLELSSVEGNKHLRKVLIAT-------------ENKSILVVGDIDC  290 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~~---~~~l~~~~~~~~~~l~~~l~~~-------------~~~~Il~iDeiD~  290 (338)
                      .++.+||.||+|||||.+++..-..+...   +..++++...+...+.++++..             .++.|++|||++.
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDDlN~  111 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDDLNM  111 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEETTT-
T ss_pred             cCCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecccCC
Confidence            46789999999999999998877666432   3456665544444444443322             2567999999998


Q ss_pred             cCC
Q 035959          291 CTE  293 (338)
Q Consensus       291 ~~~  293 (338)
                      -..
T Consensus       112 p~~  114 (272)
T PF12775_consen  112 PQP  114 (272)
T ss_dssp             S--
T ss_pred             CCC
Confidence            765

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.90  E-value=9.2e-05  Score=72.26  Aligned_cols=63  Identities=25%  Similarity=0.343  Sum_probs=45.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh----C-CcEEEEecCCc----------------------CCchHHHHHHHhcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL----H-FDVYDLELSSV----------------------EGNKHLRKVLIATENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l----~-~~~~~l~~~~~----------------------~~~~~l~~~l~~~~~~~  281 (338)
                      ..++|.||+|+|||+++..+|..+    | ..+..+.....                      .+..++...+.+.....
T Consensus       138 ~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~~D  217 (374)
T PRK14722        138 GVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELRNKH  217 (374)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhcCCC
Confidence            357899999999999999999864    3 34555544432                      12345666677777889


Q ss_pred             EEEEcCCCcc
Q 035959          282 ILVVGDIDCC  291 (338)
Q Consensus       282 Il~iDeiD~~  291 (338)
                      +|+||.....
T Consensus       218 lVLIDTaG~~  227 (374)
T PRK14722        218 MVLIDTIGMS  227 (374)
T ss_pred             EEEEcCCCCC
Confidence            9999998655

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

Probab=97.90  E-value=1.7e-05  Score=80.37  Aligned_cols=90  Identities=31%  Similarity=0.501  Sum_probs=67.5

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC------chHHHHHHHhcC--CCcEEEEcCCCccCCcccccc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG------NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSA  299 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~------~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~  299 (338)
                      +++++++||||||||.+++++|+. +.....++...+..      ...++.++....  .++++++||+|.+.+  .|..
T Consensus        18 ~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~d~~~~~~~--~~~~   94 (494)
T COG0464          18 PKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAP--KRSS   94 (494)
T ss_pred             CCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEeechhhhccc--Cccc
Confidence            489999999999999999999998 44334444444332      345666666654  569999999999988  5544


Q ss_pred             cccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          300 QARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                      ..         .......++.|+..+||+-
T Consensus        95 ~~---------~~~~~~v~~~l~~~~d~~~  115 (494)
T COG0464          95 DQ---------GEVERRVVAQLLALMDGLK  115 (494)
T ss_pred             cc---------cchhhHHHHHHHHhccccc
Confidence            11         2456788999999999997

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=97.89  E-value=2.8e-05  Score=74.98  Aligned_cols=72  Identities=26%  Similarity=0.380  Sum_probs=49.0

Q ss_pred             cccccCChhHHHH--HHHHHHhh---hcCceeeeCCCCCCcHHHHHHHHHHhC--CcEEEEecCCcCCc-----hHHHHH
Q 035959          206 FDTLAMDTDMKKM--IMDDLERA---WKRGYLLFGPPGTGKSSLIAAMANYLH--FDVYDLELSSVEGN-----KHLRKV  273 (338)
Q Consensus       206 f~~l~~~~~~k~~--i~~~l~~~---~~~g~LL~GppGtGKT~l~~aia~~l~--~~~~~l~~~~~~~~-----~~l~~~  273 (338)
                      .+.++++.+.+++  ++-++...   ..+++||.||||||||.|+.+||.++|  .|+..++.+++.+.     +.|.+.
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~isgSEiyS~e~kKTE~L~qa  102 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVSISGSEIYSSEVKKTEALTQA  102 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEEEEGGGG-BTTC-HHHHHHHH
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeEcccceeeecccCchHHHHHH
Confidence            3568888777654  23333332   358899999999999999999999997  68899999888742     336666


Q ss_pred             HHhc
Q 035959          274 LIAT  277 (338)
Q Consensus       274 l~~~  277 (338)
                      |.+.
T Consensus       103 ~Rra  106 (398)
T PF06068_consen  103 FRRA  106 (398)
T ss_dssp             HHCS
T ss_pred             HHHh
Confidence            6654

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.

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.87  E-value=1.1e-05  Score=65.54  Aligned_cols=31  Identities=39%  Similarity=0.712  Sum_probs=28.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      +++.||||+|||++++.+|+.+|+.++.++-
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEecc
Confidence            6899999999999999999999998877765

...

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.86  E-value=4.7e-05  Score=73.30  Aligned_cols=66  Identities=23%  Similarity=0.402  Sum_probs=48.6

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------cEEEEecCC---cCCchHHHHHHHhcC--
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------DVYDLELSS---VEGNKHLRKVLIATE--  278 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~------------------------~~~~l~~~~---~~~~~~l~~~l~~~~--  278 (338)
                      +..+||+||+|+||+++|.++|+.+..                        +++.+....   ....++++.+...+.  
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~~~~~  101 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSFVVQT  101 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHHHhhc
Confidence            467999999999999999999998731                        556664432   223456776665542  


Q ss_pred             ----CCcEEEEcCCCccCC
Q 035959          279 ----NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 ----~~~Il~iDeiD~~~~  293 (338)
                          ...|++||++|.+..
T Consensus       102 ~~~~~~kv~iI~~a~~m~~  120 (328)
T PRK05707        102 AQLGGRKVVLIEPAEAMNR  120 (328)
T ss_pred             cccCCCeEEEECChhhCCH
Confidence                567899999999964

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=97.83  E-value=7.6e-05  Score=69.08  Aligned_cols=43  Identities=28%  Similarity=0.326  Sum_probs=31.0

Q ss_pred             CChhHHHHHHHHHHhh--hcC-ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          211 MDTDMKKMIMDDLERA--WKR-GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       211 ~~~~~k~~i~~~l~~~--~~~-g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ......++++..+...  .+. -++|+||+|+|||++++.+++.+.
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcC
Confidence            3344445566666542  223 478999999999999999999876

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.

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=97.83  E-value=7.5e-05  Score=74.99  Aligned_cols=87  Identities=14%  Similarity=0.171  Sum_probs=62.1

Q ss_pred             cccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh----
Q 035959          206 FDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA----  276 (338)
Q Consensus       206 f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~----  276 (338)
                      +..+++.....+.+...+..  +....+++.|++||||+++++++....   +.+++.++|..+.. ..+...+..    
T Consensus       137 ~~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~-~~~~~~lfg~~~g  215 (469)
T PRK10923        137 TTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPK-DLIESELFGHEKG  215 (469)
T ss_pred             cccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCH-HHHHHHhcCCCCC
Confidence            44566666556666666654  334568999999999999999999876   46899999998743 333333322    


Q ss_pred             --------------cCCCcEEEEcCCCccCC
Q 035959          277 --------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 --------------~~~~~Il~iDeiD~~~~  293 (338)
                                    ...+..|||||||.+..
T Consensus       216 ~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~  246 (469)
T PRK10923        216 AFTGANTIRQGRFEQADGGTLFLDEIGDMPL  246 (469)
T ss_pred             CCCCCCcCCCCCeeECCCCEEEEeccccCCH
Confidence                          22467899999999865

>PHA02774 E1; Provisional

Probab=97.82  E-value=4.6e-05  Score=77.52  Aligned_cols=63  Identities=25%  Similarity=0.353  Sum_probs=44.0

Q ss_pred             HHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCCcE-EEEecCCcCCchHHHHHHHhcCCCcEEEEcCC
Q 035959          219 IMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHFDV-YDLELSSVEGNKHLRKVLIATENKSILVVGDI  288 (338)
Q Consensus       219 i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~~~-~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDei  288 (338)
                      +...+.. |.+++++|+||||||||+++.+|++.++..+ ..++..+   .    --+..+....|++|||+
T Consensus       424 lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s---~----FwLqpl~d~ki~vlDD~  488 (613)
T PHA02774        424 LKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKS---H----FWLQPLADAKIALLDDA  488 (613)
T ss_pred             HHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECcc---c----cccchhccCCEEEEecC
Confidence            3333433 4457889999999999999999999997554 3455421   1    11344456689999999

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=97.81  E-value=3.4e-05  Score=68.98  Aligned_cols=43  Identities=30%  Similarity=0.433  Sum_probs=31.9

Q ss_pred             CChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          211 MDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       211 ~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.....+.+.+.+.....+.++|+||+|+|||+|++.+.+.+.
T Consensus         3 gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~   45 (234)
T PF01637_consen    3 GREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELK   45 (234)
T ss_dssp             S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhh
Confidence            4445556666666554457789999999999999999999883

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.76  E-value=6.3e-05  Score=63.22  Aligned_cols=63  Identities=19%  Similarity=0.341  Sum_probs=42.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-----------------------------chHHH---HHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-----------------------------NKHLR---KVLI  275 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-----------------------------~~~l~---~~l~  275 (338)
                      ++++||||+|||+++.+++..+   +.++..++......                             ...+.   ..+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATADDPAAARLLSKAERLR   81 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcchHHHHHHHhhhhhccccccEEEEEcCCCCCcHHHHHHHHHHHH
Confidence            5799999999999999999887   45566665542211                             01111   1223


Q ss_pred             hcCCCcEEEEcCCCccCC
Q 035959          276 ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 ~~~~~~Il~iDeiD~~~~  293 (338)
                      ....+.+++|||+..+.+
T Consensus        82 ~~~~~~~lviDe~~~~~~   99 (165)
T cd01120          82 ERGGDDLIILDELTRLVR   99 (165)
T ss_pred             hCCCCEEEEEEcHHHHHH
Confidence            334788999999998865

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.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.75  E-value=5.1e-05  Score=72.53  Aligned_cols=71  Identities=27%  Similarity=0.424  Sum_probs=50.0

Q ss_pred             ccccCChhHHHH---HHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhC--CcEEEEecCCcCC-----chHHHHHH
Q 035959          207 DTLAMDTDMKKM---IMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLH--FDVYDLELSSVEG-----NKHLRKVL  274 (338)
Q Consensus       207 ~~l~~~~~~k~~---i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~--~~~~~l~~~~~~~-----~~~l~~~l  274 (338)
                      +-++++.+.++.   +++.+++  -..+|+|+.||||||||.||-++|.++|  .||..++.+++-+     .+-|.+.|
T Consensus        39 dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~isgsEiYS~E~kKTE~L~qa~  118 (450)
T COG1224          39 DGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQAL  118 (450)
T ss_pred             CcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCceeeccceeeeecccHHHHHHHHH
Confidence            456777665542   3344443  3458899999999999999999999997  5677888887764     23355555


Q ss_pred             Hhc
Q 035959          275 IAT  277 (338)
Q Consensus       275 ~~~  277 (338)
                      .+.
T Consensus       119 Rra  121 (450)
T COG1224         119 RRA  121 (450)
T ss_pred             HHh
Confidence            544

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.73  E-value=5.3e-05  Score=77.09  Aligned_cols=61  Identities=23%  Similarity=0.349  Sum_probs=49.3

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh------hhcCceeeeCCCCCCcHHHHHHHHHHh-CCcEEEEec
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER------AWKRGYLLFGPPGTGKSSLIAAMANYL-HFDVYDLEL  261 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~------~~~~g~LL~GppGtGKT~l~~aia~~l-~~~~~~l~~  261 (338)
                      .+-.-|+++.+.++.+++|++.+..      ..++-++|.||||+|||+|++++|+.+ .+++|.+..
T Consensus        70 ~ry~fF~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~kg  137 (644)
T PRK15455         70 KRYPAFEEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMERVPIYVLKA  137 (644)
T ss_pred             ccccchhcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHhCcceeecC
Confidence            3344688888999999999999955      234457899999999999999999988 467887755

>PRK08118 topology modulation protein; Reviewed

Probab=97.71  E-value=6.2e-05  Score=65.39  Aligned_cols=32  Identities=31%  Similarity=0.523  Sum_probs=29.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .+++.||||+|||++++.+++.++.+++.+|.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~   34 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDA   34 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecch
Confidence            47899999999999999999999999887763

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

Probab=97.71  E-value=0.00013  Score=73.20  Aligned_cols=92  Identities=20%  Similarity=0.256  Sum_probs=70.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHH
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVL  274 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l  274 (338)
                      +.++.+|+++++..+.-.++++.+.+  +....+|+.|++||||..+|++|.+.-   +.+++.+||+.+-. .-|...|
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe-~LlESEL  316 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPE-TLLESEL  316 (560)
T ss_pred             cccccchhhhccCCHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCCH-HHHHHHH
Confidence            44566899999988877777777776  445679999999999999999999876   57999999998752 2222222


Q ss_pred             Hhc-------------------CCCcEEEEcCCCccC
Q 035959          275 IAT-------------------ENKSILVVGDIDCCT  292 (338)
Q Consensus       275 ~~~-------------------~~~~Il~iDeiD~~~  292 (338)
                      +..                   +...-||||||..+.
T Consensus       317 FGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgemp  353 (560)
T COG3829         317 FGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMP  353 (560)
T ss_pred             hCcCCccccccccCCCCcceeeccCCeEEehhhccCC
Confidence            222                   356789999999885

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.70  E-value=0.00019  Score=67.73  Aligned_cols=65  Identities=14%  Similarity=0.259  Sum_probs=45.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC---------CcEEEEecCCcCCchHHH-HHHHhc---------------------
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH---------FDVYDLELSSVEGNKHLR-KVLIAT---------------------  277 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~---------~~~~~l~~~~~~~~~~l~-~~l~~~---------------------  277 (338)
                      .++||+|++|.|||++++..+....         .+++.+....--++..+- .++..+                     
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            5799999999999999999987552         467777765544332221 111111                     


Q ss_pred             --CCCcEEEEcCCCccCC
Q 035959          278 --ENKSILVVGDIDCCTE  293 (338)
Q Consensus       278 --~~~~Il~iDeiD~~~~  293 (338)
                        -..-+|+|||+|.++.
T Consensus       142 r~~~vrmLIIDE~H~lLa  159 (302)
T PF05621_consen  142 RRLGVRMLIIDEFHNLLA  159 (302)
T ss_pred             HHcCCcEEEeechHHHhc
Confidence              2567999999999876

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.69  E-value=0.0003  Score=62.66  Aligned_cols=75  Identities=24%  Similarity=0.357  Sum_probs=44.1

Q ss_pred             HHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC----------chHHHHHHHhc--------
Q 035959          219 IMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG----------NKHLRKVLIAT--------  277 (338)
Q Consensus       219 i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~----------~~~l~~~l~~~--------  277 (338)
                      .+..+.....+.+++.||||||||+++.+++..+   +..++.+..+.-..          ...+..++...        
T Consensus         9 a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~~~~   88 (196)
T PF13604_consen    9 AVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKTGIEAQTIHSFLYRIPNGDDEGR   88 (196)
T ss_dssp             HHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHTS-EEEHHHHTTEECCEECCSS
T ss_pred             HHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhhCcchhhHHHHHhcCCccccccc
Confidence            3333433334567899999999999999988766   56666665543211          01122222211        


Q ss_pred             ---CCCcEEEEcCCCccCC
Q 035959          278 ---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       278 ---~~~~Il~iDeiD~~~~  293 (338)
                         .+..+|||||+..+..
T Consensus        89 ~~~~~~~vliVDEasmv~~  107 (196)
T PF13604_consen   89 PELPKKDVLIVDEASMVDS  107 (196)
T ss_dssp             CC-TSTSEEEESSGGG-BH
T ss_pred             ccCCcccEEEEecccccCH
Confidence               2358999999988753

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.68  E-value=3.7e-05  Score=66.10  Aligned_cols=33  Identities=30%  Similarity=0.447  Sum_probs=29.8

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +..++|+||||||||++++++|..++.++++.+
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d   36 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD   36 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            467899999999999999999999999888764

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.68  E-value=4.8e-05  Score=76.17  Aligned_cols=68  Identities=22%  Similarity=0.319  Sum_probs=55.8

Q ss_pred             CCCccccccCCCCCccccccCChhHHHHHHHHHHh-------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          191 NHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLER-------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       191 ~~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~-------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ++..|.  ....|++.++|+..+....++..+|+.       ...+-+||+||+|||||+.++.||.++|+.+..-.
T Consensus        68 ~~elW~--eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew~  142 (634)
T KOG1970|consen   68 EFELWV--EKYKPRTLEELAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIEWS  142 (634)
T ss_pred             ccchhH--HhcCcccHHHHhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhhCceeeeec
Confidence            456785  478899999999988888888888883       22345799999999999999999999998876543

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=97.66  E-value=0.00018  Score=71.93  Aligned_cols=85  Identities=16%  Similarity=0.190  Sum_probs=59.3

Q ss_pred             cccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh------
Q 035959          208 TLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA------  276 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~------  276 (338)
                      .+++.....+.+.+.+..  .....++++|++||||+++++++....   +.+++.++|..+.. ..+...+..      
T Consensus       144 ~ii~~S~~~~~~~~~~~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~-~~~~~~lfg~~~~~~  222 (457)
T PRK11361        144 HILTNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPE-SLLESELFGHEKGAF  222 (457)
T ss_pred             ceecccHHHhHHHHHHHHHcCCCcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCH-HHHHHHhcCCCCCCC
Confidence            345544444555555554  334568999999999999999998765   46899999998753 333333322      


Q ss_pred             ------------cCCCcEEEEcCCCccCC
Q 035959          277 ------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ------------~~~~~Il~iDeiD~~~~  293 (338)
                                  .....+|+|||||.+..
T Consensus       223 ~~~~~~~~g~~~~a~~gtl~ld~i~~l~~  251 (457)
T PRK11361        223 TGAQTLRQGLFERANEGTLLLDEIGEMPL  251 (457)
T ss_pred             CCCCCCCCCceEECCCCEEEEechhhCCH
Confidence                        12467999999999965

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=97.65  E-value=0.00024  Score=70.77  Aligned_cols=86  Identities=19%  Similarity=0.214  Sum_probs=60.3

Q ss_pred             ccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh-----
Q 035959          207 DTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA-----  276 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~-----  276 (338)
                      ..+++.....+.+...+..  .....++++|++||||+++++++....   +.+++.++|..+.. ..+...++.     
T Consensus       139 ~~lig~s~~~~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~-~~~~~~lfg~~~~~  217 (445)
T TIGR02915       139 RGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPE-NLLESELFGYEKGA  217 (445)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCCh-HHHHHHhcCCCCCC
Confidence            3445554455556665554  334678999999999999999998776   35899999998743 334433322     


Q ss_pred             -------------cCCCcEEEEcCCCccCC
Q 035959          277 -------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 -------------~~~~~Il~iDeiD~~~~  293 (338)
                                   ......|+||||+.+..
T Consensus       218 ~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~  247 (445)
T TIGR02915       218 FTGAVKQTLGKIEYAHGGTLFLDEIGDLPL  247 (445)
T ss_pred             cCCCccCCCCceeECCCCEEEEechhhCCH
Confidence                         13567899999999965

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).

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=97.64  E-value=9.9e-05  Score=76.43  Aligned_cols=78  Identities=22%  Similarity=0.226  Sum_probs=49.0

Q ss_pred             HHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEecCCcC----CchHHHHHHHh-----------cC
Q 035959          216 KKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLELSSVE----GNKHLRKVLIA-----------TE  278 (338)
Q Consensus       216 k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~~~~~----~~~~l~~~l~~-----------~~  278 (338)
                      |..+.-....|.-.++||.|+||||||+++++++..++.  ++..+.+....    ..-++...+..           ..
T Consensus         4 ~~Al~l~av~p~~g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A   83 (589)
T TIGR02031         4 KLALTLLAVDPSLGGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEA   83 (589)
T ss_pred             HHHHHHhccCCCcceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeC
Confidence            333333333344468999999999999999999998864  46666642111    11112211111           12


Q ss_pred             CCcEEEEcCCCccCC
Q 035959          279 NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 ~~~Il~iDeiD~~~~  293 (338)
                      ...+|+||||+.+.+
T Consensus        84 ~~GvL~lDEi~rl~~   98 (589)
T TIGR02031        84 PRGVLYVDMANLLDD   98 (589)
T ss_pred             CCCcEeccchhhCCH
Confidence            457999999999965

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.

>PF05729 NACHT: NACHT domain

Probab=97.62  E-value=0.00012  Score=61.85  Aligned_cols=65  Identities=25%  Similarity=0.448  Sum_probs=42.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC---------cEEEEecCCcCCch---HHHHHH------------------HhcC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF---------DVYDLELSSVEGNK---HLRKVL------------------IATE  278 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~---------~~~~l~~~~~~~~~---~l~~~l------------------~~~~  278 (338)
                      |-++++|+||+|||++++.++..+..         -++.+.+.+.....   .+...+                  ....
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKN   80 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcC
Confidence            34789999999999999999987721         12344444333211   222222                  2224


Q ss_pred             CCcEEEEcCCCccCC
Q 035959          279 NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 ~~~Il~iDeiD~~~~  293 (338)
                      .+.+|+||.+|.+..
T Consensus        81 ~~~llilDglDE~~~   95 (166)
T PF05729_consen   81 KRVLLILDGLDELEE   95 (166)
T ss_pred             CceEEEEechHhccc
Confidence            678999999999976

>smart00350 MCM minichromosome maintenance proteins

Probab=97.61  E-value=7.5e-05  Score=76.06  Aligned_cols=84  Identities=23%  Similarity=0.282  Sum_probs=51.0

Q ss_pred             ccCChhHHHHHHHHHHhhh---------cC---ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE----ecCCcCCchHHHH
Q 035959          209 LAMDTDMKKMIMDDLERAW---------KR---GYLLFGPPGTGKSSLIAAMANYLHFDVYDL----ELSSVEGNKHLRK  272 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~~---------~~---g~LL~GppGtGKT~l~~aia~~l~~~~~~l----~~~~~~~~~~l~~  272 (338)
                      +.+.+..|..++-.+....         -+   .+||+|+||||||.+++++++......+..    ++..+.. ..++.
T Consensus       205 i~G~~~~k~~l~l~l~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~~l~~-~~~~~  283 (509)
T smart00350      205 IYGHEDIKKAILLLLFGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTA-AVTRD  283 (509)
T ss_pred             ccCcHHHHHHHHHHHhCCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcCCccc-cceEc
Confidence            4556666766666654411         01   599999999999999999999876443322    1111111 00000


Q ss_pred             ----------HHHhcCCCcEEEEcCCCccCC
Q 035959          273 ----------VLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       273 ----------~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                -....+...+++|||+|.+.+
T Consensus       284 ~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~~  314 (509)
T smart00350      284 PETREFTLEGGALVLADNGVCCIDEFDKMDD  314 (509)
T ss_pred             cCcceEEecCccEEecCCCEEEEechhhCCH
Confidence                      001123578999999999864

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=97.60  E-value=7.5e-05  Score=72.74  Aligned_cols=65  Identities=18%  Similarity=0.319  Sum_probs=41.9

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCC-cEEEEecCCcC------------CchHHHHHHHhcCCC-cEEEEcCCCcc
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHF-DVYDLELSSVE------------GNKHLRKVLIATENK-SILVVGDIDCC  291 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~-~~~~l~~~~~~------------~~~~l~~~l~~~~~~-~Il~iDeiD~~  291 (338)
                      .++|++||||+|+|||+|..+..+.+.. .-..+......            ....+..+.....+. .+|++||++.-
T Consensus        61 ~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~~~~~lLcfDEF~V~  139 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELAKESRLLCFDEFQVT  139 (362)
T ss_pred             CCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHHhcCCEEEEeeeecc
Confidence            3689999999999999999999988753 11111111110            122344445555444 49999999865

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

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

Probab=97.60  E-value=0.00028  Score=75.18  Aligned_cols=85  Identities=20%  Similarity=0.340  Sum_probs=57.8

Q ss_pred             ccCChhHHHHHHHHHHh-------h-hcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-----------
Q 035959          209 LAMDTDMKKMIMDDLER-------A-WKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-----------  266 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~-------~-~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-----------  266 (338)
                      ++++++....|-+.+..       + ..--+||.||.|+|||-|++|+|.++   .-.++.+|+++...           
T Consensus       564 V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskligsp~gy  643 (898)
T KOG1051|consen  564 VIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGSPPGY  643 (898)
T ss_pred             ccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhccCCCccc
Confidence            45555555555555544       1 12237899999999999999999988   34688999986221           


Q ss_pred             --chHHHHHHHhc--CCCcEEEEcCCCccCC
Q 035959          267 --NKHLRKVLIAT--ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 --~~~l~~~l~~~--~~~~Il~iDeiD~~~~  293 (338)
                        ....-++-..+  .+.+||+|||||..-+
T Consensus       644 vG~e~gg~LteavrrrP~sVVLfdeIEkAh~  674 (898)
T KOG1051|consen  644 VGKEEGGQLTEAVKRRPYSVVLFEEIEKAHP  674 (898)
T ss_pred             ccchhHHHHHHHHhcCCceEEEEechhhcCH
Confidence              22233333333  3679999999998865

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.60  E-value=6.2e-05  Score=74.10  Aligned_cols=65  Identities=14%  Similarity=0.218  Sum_probs=42.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHH-hCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANY-LHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~-l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      +.++++.|||||||||++.+++.+ .-..-.....+.+..+-. .+.+......++|+|||+..+.-
T Consensus       209 ~~Nli~lGp~GTGKThla~~l~~~~a~~sG~f~T~a~Lf~~L~-~~~lg~v~~~DlLI~DEvgylp~  274 (449)
T TIGR02688       209 NYNLIELGPKGTGKSYIYNNLSPYVILISGGTITVAKLFYNIS-TRQIGLVGRWDVVAFDEVATLKF  274 (449)
T ss_pred             CCcEEEECCCCCCHHHHHHHHhHHHHHHcCCcCcHHHHHHHHH-HHHHhhhccCCEEEEEcCCCCcC
Confidence            467999999999999999998887 211111222222221111 14445556889999999999654

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.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.59  E-value=4.2e-05  Score=69.38  Aligned_cols=63  Identities=24%  Similarity=0.390  Sum_probs=38.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC-------------c---CCchHHHHHHHhc----CCCcEEEEcCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS-------------V---EGNKHLRKVLIAT----ENKSILVVGDI  288 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~-------------~---~~~~~l~~~l~~~----~~~~Il~iDei  288 (338)
                      .-+|+||+||+|||++++.++...  -++..+.+.             +   ..-..+...+..+    .....||||.|
T Consensus        13 ~~~liyG~~G~GKtt~a~~~~~~~--~~~~~d~~~~~l~g~~~~~v~~~d~~~~~~~~~d~l~~~~~~~~~ydtVVIDsI   90 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKYLPGKT--LVLSFDMSSKVLIGDENVDIADHDDMPPIQAMVEFYVMQNIQAVKYDNIVIDNI   90 (220)
T ss_pred             cEEEEECCCCCCHHHHHHhcCCCC--EEEeccccchhccCCCCCceeecCCCCCHHHHHHHHHHHHhccccCCEEEEecH
Confidence            458999999999999999987421  112222211             0   0112333333322    35789999999


Q ss_pred             CccCC
Q 035959          289 DCCTE  293 (338)
Q Consensus       289 D~~~~  293 (338)
                      +.+..
T Consensus        91 ~~l~~   95 (220)
T TIGR01618        91 SALQN   95 (220)
T ss_pred             HHHHH
Confidence            99753

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.58  E-value=0.00044  Score=65.19  Aligned_cols=59  Identities=25%  Similarity=0.375  Sum_probs=43.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----C-CcEEEEecCCcC----------------------CchHHHHHHHhcCCCcE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----H-FDVYDLELSSVE----------------------GNKHLRKVLIATENKSI  282 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----~-~~~~~l~~~~~~----------------------~~~~l~~~l~~~~~~~I  282 (338)
                      -++|.||+|+|||+++..+|.++    + ..+..+++....                      +..++.+.+..+...++
T Consensus       196 vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~~~~d~  275 (282)
T TIGR03499       196 VIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRLRDKDL  275 (282)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHccCCCE
Confidence            46799999999999999999876    3 677777665521                      23456677777777889


Q ss_pred             EEEcCC
Q 035959          283 LVVGDI  288 (338)
Q Consensus       283 l~iDei  288 (338)
                      ||||..
T Consensus       276 vliDt~  281 (282)
T TIGR03499       276 ILIDTA  281 (282)
T ss_pred             EEEeCC
Confidence            998864

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=97.56  E-value=0.00027  Score=68.01  Aligned_cols=66  Identities=17%  Similarity=0.246  Sum_probs=48.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhC-------------------------CcEEEEecCC----------cCCchHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLH-------------------------FDVYDLELSS----------VEGNKHLRK  272 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~-------------------------~~~~~l~~~~----------~~~~~~l~~  272 (338)
                      +..+||+||+|+|||+++.++|+.+.                         .+++.++...          ....++++.
T Consensus        21 ~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~iR~  100 (325)
T PRK08699         21 PNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDAVRE  100 (325)
T ss_pred             ceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHHHHH
Confidence            46799999999999999999998862                         3566676532          123455666


Q ss_pred             HHHhcC------CCcEEEEcCCCccCC
Q 035959          273 VLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       273 ~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +...+.      ...|++||++|.+..
T Consensus       101 l~~~~~~~p~~~~~kV~iiEp~~~Ld~  127 (325)
T PRK08699        101 IIDNVYLTSVRGGLRVILIHPAESMNL  127 (325)
T ss_pred             HHHHHhhCcccCCceEEEEechhhCCH
Confidence            665542      567999999999964

>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=97.53  E-value=0.00022  Score=66.46  Aligned_cols=79  Identities=24%  Similarity=0.240  Sum_probs=49.4

Q ss_pred             hHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHH--hC--Cc-EEEEecCCcCCchH-----------------
Q 035959          214 DMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANY--LH--FD-VYDLELSSVEGNKH-----------------  269 (338)
Q Consensus       214 ~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~--l~--~~-~~~l~~~~~~~~~~-----------------  269 (338)
                      ...++|.+.|..  ...+-+.|+|++|+|||+||..+++.  ..  ++ ++.+++....+...                 
T Consensus         3 ~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~   82 (287)
T PF00931_consen    3 KEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSIS   82 (287)
T ss_dssp             HHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSS
T ss_pred             HHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccc
Confidence            345677777776  33455789999999999999999977  32  32 44555544332111                 


Q ss_pred             -------HHHHHHh-c-CCCcEEEEcCCCccC
Q 035959          270 -------LRKVLIA-T-ENKSILVVGDIDCCT  292 (338)
Q Consensus       270 -------l~~~l~~-~-~~~~Il~iDeiD~~~  292 (338)
                             +.+.+.+ + .++++|||||++...
T Consensus        83 ~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~  114 (287)
T PF00931_consen   83 DPKDIEELQDQLRELLKDKRCLLVLDDVWDEE  114 (287)
T ss_dssp             CCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHH
T ss_pred             cccccccccccchhhhccccceeeeeeecccc
Confidence                   1111111 1 358999999998765

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.

>PRK13947 shikimate kinase; Provisional

Probab=97.51  E-value=9.3e-05  Score=63.82  Aligned_cols=32  Identities=31%  Similarity=0.438  Sum_probs=29.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .++|.|+||||||++++.+|+.+++++++.+.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d~   34 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTDK   34 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECch
Confidence            48899999999999999999999999987764

>PRK03839 putative kinase; Provisional

Probab=97.51  E-value=8.4e-05  Score=64.89  Aligned_cols=30  Identities=30%  Similarity=0.574  Sum_probs=27.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ++|.|+||+|||++++.+|+.++++++.++
T Consensus         3 I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            789999999999999999999999887654

>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=97.49  E-value=0.00011  Score=62.05  Aligned_cols=31  Identities=29%  Similarity=0.451  Sum_probs=28.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .++|+|+||+|||++++++|..++++++..+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d   31 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD   31 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            3789999999999999999999999988765

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.

>PRK15115 response regulator GlrR; Provisional

Probab=97.48  E-value=0.00045  Score=68.86  Aligned_cols=84  Identities=15%  Similarity=0.207  Sum_probs=57.5

Q ss_pred             ccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh-------
Q 035959          209 LAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA-------  276 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~-------  276 (338)
                      +++.....+.+++.+..  .....++++|++||||+++++++....   +.+++.++|..+.. ..+...+..       
T Consensus       136 lig~s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~-~~~~~~lfg~~~~~~~  214 (444)
T PRK15115        136 IVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPE-QLLESELFGHARGAFT  214 (444)
T ss_pred             ccccCHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCH-HHHHHHhcCCCcCCCC
Confidence            34444444445554443  334568999999999999999998875   46899999998743 333333221       


Q ss_pred             -----------cCCCcEEEEcCCCccCC
Q 035959          277 -----------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 -----------~~~~~Il~iDeiD~~~~  293 (338)
                                 ......|||||||.+..
T Consensus       215 ~~~~~~~g~~~~a~~gtl~l~~i~~l~~  242 (444)
T PRK15115        215 GAVSNREGLFQAAEGGTLFLDEIGDMPA  242 (444)
T ss_pred             CCccCCCCcEEECCCCEEEEEccccCCH
Confidence                       23467899999999865

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=97.48  E-value=0.00065  Score=63.66  Aligned_cols=77  Identities=18%  Similarity=0.330  Sum_probs=58.9

Q ss_pred             HHHHHHHHh---hhcCceeeeCCCCCCcHHHHHHHHH------HhCCcEEEEecCCcCCchHHHHHHHhc----------
Q 035959          217 KMIMDDLER---AWKRGYLLFGPPGTGKSSLIAAMAN------YLHFDVYDLELSSVEGNKHLRKVLIAT----------  277 (338)
Q Consensus       217 ~~i~~~l~~---~~~~g~LL~GppGtGKT~l~~aia~------~l~~~~~~l~~~~~~~~~~l~~~l~~~----------  277 (338)
                      .+.++++++   ..+..+||.||.|.|||.|++-+..      .+.-+++.++|..+..+..+..+|...          
T Consensus       194 nrmieqierva~rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~  273 (531)
T COG4650         194 NRMIEQIERVAIRSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARES  273 (531)
T ss_pred             HHHHHHHHHHHhhccCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhh
Confidence            344555554   3446799999999999999998764      345689999999999877777766544          


Q ss_pred             -------CCCcEEEEcCCCccCC
Q 035959          278 -------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       278 -------~~~~Il~iDeiD~~~~  293 (338)
                             ....+||+|||..+..
T Consensus       274 r~gllrsadggmlfldeigelga  296 (531)
T COG4650         274 REGLLRSADGGMLFLDEIGELGA  296 (531)
T ss_pred             hhhhhccCCCceEehHhhhhcCc
Confidence                   3578999999998864

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.47  E-value=0.00071  Score=64.99  Aligned_cols=80  Identities=20%  Similarity=0.236  Sum_probs=54.9

Q ss_pred             hHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------CcEEEEecC--CcCC
Q 035959          214 DMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------FDVYDLELS--SVEG  266 (338)
Q Consensus       214 ~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~~~~~l~~~--~~~~  266 (338)
                      ..++.+...+.+ .-+.++||+||+|+||+.++.++|+.+-                        .+++.+...  .-..
T Consensus         9 ~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~I~   88 (325)
T PRK06871          9 PTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKDIG   88 (325)
T ss_pred             HHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCCCC
Confidence            345566666655 3356899999999999999999998772                        235555432  1123


Q ss_pred             chHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      .++++.+...+.      ..-|++||++|.+..
T Consensus        89 id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~  121 (325)
T PRK06871         89 VDQVREINEKVSQHAQQGGNKVVYIQGAERLTE  121 (325)
T ss_pred             HHHHHHHHHHHhhccccCCceEEEEechhhhCH
Confidence            456666655542      567999999999964

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.47  E-value=0.00062  Score=65.74  Aligned_cols=80  Identities=20%  Similarity=0.262  Sum_probs=56.2

Q ss_pred             hHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------CcEEEEecCC---cC
Q 035959          214 DMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------FDVYDLELSS---VE  265 (338)
Q Consensus       214 ~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~~~~~l~~~~---~~  265 (338)
                      ...++++..+.. .-+..+||+||+|+||+.+|.++|..+-                        -+++.+....   ..
T Consensus         9 ~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I   88 (334)
T PRK07993          9 PDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKSSL   88 (334)
T ss_pred             HHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccC
Confidence            345566666655 3456899999999999999999998871                        2455554332   23


Q ss_pred             CchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          266 GNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       266 ~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      ..++++.+...+.      ..-|++||++|.+..
T Consensus        89 ~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~  122 (334)
T PRK07993         89 GVDAVREVTEKLYEHARLGGAKVVWLPDAALLTD  122 (334)
T ss_pred             CHHHHHHHHHHHhhccccCCceEEEEcchHhhCH
Confidence            4556666665542      567999999999964

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=97.45  E-value=6.2e-05  Score=62.70  Aligned_cols=27  Identities=44%  Similarity=0.682  Sum_probs=23.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      +++.||||+||||+++.++..++..++
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~~~i   28 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGAVVI   28 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCEEE
Confidence            589999999999999999999984443

...

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=97.45  E-value=0.00013  Score=65.26  Aligned_cols=24  Identities=46%  Similarity=0.855  Sum_probs=19.4

Q ss_pred             Cc-eeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RG-YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g-~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+ .+++||||||||+++.+++..+
T Consensus        17 ~~~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   17 NGITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             SE-EEEE-STTSSHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCChHHHHHHHHHHh
Confidence            44 7899999999999888877776

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.43  E-value=0.00011  Score=63.70  Aligned_cols=56  Identities=25%  Similarity=0.328  Sum_probs=34.6

Q ss_pred             ccCChhHHHHHHHHHHh---hhcCceeeeCCCCCCcHHHHHHHHHHhCCc---EEEEecCCc
Q 035959          209 LAMDTDMKKMIMDDLER---AWKRGYLLFGPPGTGKSSLIAAMANYLHFD---VYDLELSSV  264 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~---~~~~g~LL~GppGtGKT~l~~aia~~l~~~---~~~l~~~~~  264 (338)
                      +++.++..+++...+..   ..++.++++||+|+|||++++++...+...   ++.+++...
T Consensus         2 fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    2 FVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             -TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            35566666666666632   234678999999999999999988877433   666666555

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.43  E-value=0.00022  Score=58.86  Aligned_cols=45  Identities=18%  Similarity=0.210  Sum_probs=33.7

Q ss_pred             cccCChhHHHHHHHHHHh-----hhcCce--eeeCCCCCCcHHHHHHHHHHh
Q 035959          208 TLAMDTDMKKMIMDDLER-----AWKRGY--LLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~-----~~~~g~--LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+.+++-..+.+++.+..     .+++.+  .|+||||||||++++.||+.+
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            467777667777766666     122333  499999999999999999986

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

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.43  E-value=0.00077  Score=65.21  Aligned_cols=37  Identities=22%  Similarity=0.218  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          215 MKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       215 ~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .++++... ...-+.++||+||+|+||++++.++|+.+
T Consensus         9 ~~~~l~~~-~~rl~ha~Lf~Gp~G~GK~~lA~~~A~~L   45 (342)
T PRK06964          9 DWNRLQAL-RARLPHALLLHGQAGIGKLDFAQHLAQGL   45 (342)
T ss_pred             HHHHHHHh-cCCcceEEEEECCCCCCHHHHHHHHHHHH
Confidence            34444442 22345789999999999999999999877

>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=97.43  E-value=0.00036  Score=64.98  Aligned_cols=89  Identities=19%  Similarity=0.377  Sum_probs=57.4

Q ss_pred             CCccccccCChhHHHHHHHHHHhh--hcCceeeeCCCCCCcHHHHHHHHHHhCC---cEEEEecC-CcC-----------
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERA--WKRGYLLFGPPGTGKSSLIAAMANYLHF---DVYDLELS-SVE-----------  265 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~--~~~g~LL~GppGtGKT~l~~aia~~l~~---~~~~l~~~-~~~-----------  265 (338)
                      +-+++++...+...+.+.+.+...  .+..+++.||+|+|||+++.++..++..   .++.++-. ++.           
T Consensus       100 ~~sle~l~~~~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~~l~~~~~~~~~~  179 (270)
T PF00437_consen  100 PFSLEDLGESGSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPELRLPGPNQIQIQT  179 (270)
T ss_dssp             --CHCCCCHTHHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S--SCSSEEEEEE
T ss_pred             cccHhhccCchhhHHHHHHHHhhccccceEEEEECCCccccchHHHHHhhhccccccceEEeccccceeecccceEEEEe
Confidence            337788877776666666666653  3567899999999999999999998843   34444321 111           


Q ss_pred             --CchHHHHHHHhc--CCCcEEEEcCCCcc
Q 035959          266 --GNKHLRKVLIAT--ENKSILVVGDIDCC  291 (338)
Q Consensus       266 --~~~~l~~~l~~~--~~~~Il~iDeiD~~  291 (338)
                        ....+.+++..+  ..|++|++.||...
T Consensus       180 ~~~~~~~~~~l~~~LR~~pD~iiigEiR~~  209 (270)
T PF00437_consen  180 RRDEISYEDLLKSALRQDPDVIIIGEIRDP  209 (270)
T ss_dssp             ETTTBSHHHHHHHHTTS--SEEEESCE-SC
T ss_pred             ecCcccHHHHHHHHhcCCCCcccccccCCH
Confidence              122455666554  37899999999764

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 ....

>PRK00625 shikimate kinase; Provisional

Probab=97.42  E-value=0.00013  Score=63.87  Aligned_cols=32  Identities=31%  Similarity=0.530  Sum_probs=29.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .++|.|+||+|||++++.+|+.++++++++|-
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D~   33 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTDD   33 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhhH
Confidence            47899999999999999999999999988863

>TIGR00368 Mg chelatase-related protein

Probab=97.42  E-value=0.00021  Score=72.53  Aligned_cols=47  Identities=28%  Similarity=0.453  Sum_probs=36.1

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+|+++.+....++.+.-.+  .....++|.||||||||+++++++..+
T Consensus       189 ~d~~dv~Gq~~~~~al~~aa--~~g~~vlliG~pGsGKTtlar~l~~ll  235 (499)
T TIGR00368       189 LDLKDIKGQQHAKRALEIAA--AGGHNLLLFGPPGSGKTMLASRLQGIL  235 (499)
T ss_pred             CCHHHhcCcHHHHhhhhhhc--cCCCEEEEEecCCCCHHHHHHHHhccc
Confidence            47888888887766554433  223569999999999999999999754

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.42  E-value=0.00031  Score=77.91  Aligned_cols=65  Identities=26%  Similarity=0.363  Sum_probs=50.6

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCch-------------HH----HHHHHhcCCCcEEEEcCCCc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNK-------------HL----RKVLIATENKSILVVGDIDC  290 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~-------------~l----~~~l~~~~~~~Il~iDeiD~  290 (338)
                      .+++||-|.||+|||+|+.|+|+..|...+.+++++-.+--             +.    ..++..+.+..-+++||+..
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            57899999999999999999999999999999998743210             00    12344455788999999986


Q ss_pred             cC
Q 035959          291 CT  292 (338)
Q Consensus       291 ~~  292 (338)
                      ..
T Consensus      1623 aS 1624 (4600)
T COG5271        1623 AS 1624 (4600)
T ss_pred             hH
Confidence            53

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=97.42  E-value=0.00066  Score=67.99  Aligned_cols=85  Identities=15%  Similarity=0.192  Sum_probs=60.0

Q ss_pred             cccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh------
Q 035959          208 TLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA------  276 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~------  276 (338)
                      .+++..+..+++...+..  .....+++.|++||||+++++++....   +.+++.++|..+.. +.+...+..      
T Consensus       135 ~lig~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~-~~~~~~lfg~~~~~~  213 (463)
T TIGR01818       135 ELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPK-DLIESELFGHEKGAF  213 (463)
T ss_pred             ceeecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCH-HHHHHHhcCCCCCCC
Confidence            355555555666666654  334568999999999999999998875   46899999998743 333333321      


Q ss_pred             ------------cCCCcEEEEcCCCccCC
Q 035959          277 ------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ------------~~~~~Il~iDeiD~~~~  293 (338)
                                  ...+..|+|||||.+..
T Consensus       214 ~~~~~~~~g~~~~a~~gtl~l~ei~~l~~  242 (463)
T TIGR01818       214 TGANTRRQGRFEQADGGTLFLDEIGDMPL  242 (463)
T ss_pred             CCcccCCCCcEEECCCCeEEEEchhhCCH
Confidence                        12467899999999865

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.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.42  E-value=0.00031  Score=61.22  Aligned_cols=64  Identities=17%  Similarity=0.177  Sum_probs=47.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCch-----------------------HHHHHHHh-cCCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNK-----------------------HLRKVLIA-TENKSILVV  285 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~-----------------------~l~~~l~~-~~~~~Il~i  285 (338)
                      -+++.|+||+|||+++..++..++.+++++.......++                       +|..++.. ..+..+++|
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            378999999999999999999988777777665543321                       34444544 345678999


Q ss_pred             cCCCccCC
Q 035959          286 GDIDCCTE  293 (338)
Q Consensus       286 DeiD~~~~  293 (338)
                      |-+..+..
T Consensus        83 D~Lt~~~~   90 (170)
T PRK05800         83 DCLTTWVT   90 (170)
T ss_pred             hhHHHHHH
Confidence            98888754

>PRK07261 topology modulation protein; Provisional

Probab=97.38  E-value=0.00027  Score=61.51  Aligned_cols=31  Identities=26%  Similarity=0.441  Sum_probs=27.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      +++.|+||+|||+|++.++..++.+++.+|.
T Consensus         3 i~i~G~~GsGKSTla~~l~~~~~~~~i~~D~   33 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKLSQHYNCPVLHLDT   33 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCeEecCC
Confidence            6899999999999999999999888776653

>PRK13949 shikimate kinase; Provisional

Probab=97.37  E-value=0.00015  Score=63.04  Aligned_cols=33  Identities=33%  Similarity=0.477  Sum_probs=29.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      +.++|.||||+|||++++.+|+.+++++++.|.
T Consensus         2 ~~I~liG~~GsGKstl~~~La~~l~~~~id~D~   34 (169)
T PRK13949          2 ARIFLVGYMGAGKTTLGKALARELGLSFIDLDF   34 (169)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCCeecccH
Confidence            358999999999999999999999999888763

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.33  E-value=0.0002  Score=60.69  Aligned_cols=32  Identities=31%  Similarity=0.566  Sum_probs=28.6

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +.++|+.|-||||||+++..+|..+++..+.+
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~~i~i   38 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLEYIEI   38 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCceEeh
Confidence            35799999999999999999999999887655

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.33  E-value=0.0004  Score=59.66  Aligned_cols=23  Identities=35%  Similarity=0.677  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.++|+||+|||+++.-+++.+
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             EEEEeCCCCccHHHHHHHHHHHH
Confidence            47899999999999999999887

>PRK04132 replication factor C small subunit; Provisional

Probab=97.33  E-value=0.0004  Score=74.19  Aligned_cols=62  Identities=19%  Similarity=0.278  Sum_probs=51.0

Q ss_pred             eeeC--CCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCchHHHHHHHhcC--------CCcEEEEcCCCccCC
Q 035959          232 LLFG--PPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGNKHLRKVLIATE--------NKSILVVGDIDCCTE  293 (338)
Q Consensus       232 LL~G--ppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~~~l~~~l~~~~--------~~~Il~iDeiD~~~~  293 (338)
                      +..|  |++.||||+|.|+|+++     +.+++.+++++....+.+++.+....        +..|+||||+|.+..
T Consensus       568 ~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~  644 (846)
T PRK04132        568 FIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ  644 (846)
T ss_pred             hhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCCH
Confidence            5668  99999999999999998     56899999999777677777765431        236999999999964

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.32  E-value=0.0014  Score=62.87  Aligned_cols=80  Identities=16%  Similarity=0.153  Sum_probs=55.1

Q ss_pred             hHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC-----------------------CcEEEEecCC---cCC
Q 035959          214 DMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH-----------------------FDVYDLELSS---VEG  266 (338)
Q Consensus       214 ~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~-----------------------~~~~~l~~~~---~~~  266 (338)
                      +.++.+...+.. .-+..+||+||.|+||+.++.++|..+-                       .+++.+....   ...
T Consensus        10 ~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~   89 (319)
T PRK06090         10 PVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGKSIT   89 (319)
T ss_pred             HHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCCcCC
Confidence            445566665554 3346799999999999999999998761                       2566665432   223


Q ss_pred             chHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      .++++.+...+      ....|++||++|.+..
T Consensus        90 vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~  122 (319)
T PRK06090         90 VEQIRQCNRLAQESSQLNGYRLFVIEPADAMNE  122 (319)
T ss_pred             HHHHHHHHHHHhhCcccCCceEEEecchhhhCH
Confidence            45566554443      2467999999999964

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.32  E-value=0.00035  Score=65.54  Aligned_cols=86  Identities=19%  Similarity=0.354  Sum_probs=54.0

Q ss_pred             cccCChhHHHHHHHHHHhhh-----cCc--eeeeCCCCCCcHHHHHHHHHHh---CCc--EE-----EEecCCcCC----
Q 035959          208 TLAMDTDMKKMIMDDLERAW-----KRG--YLLFGPPGTGKSSLIAAMANYL---HFD--VY-----DLELSSVEG----  266 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~~-----~~g--~LL~GppGtGKT~l~~aia~~l---~~~--~~-----~l~~~~~~~----  266 (338)
                      .+.++.-.++.|+..+...|     ++.  +-|||+|||||++.++.+|+.+   |..  ++     ..++..-..    
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~Y  162 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIEDY  162 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHHHHH
Confidence            36777777888888887722     233  3499999999999999999987   221  10     111111111    


Q ss_pred             chHHHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                      ..+|..-+.+.   -+++|.|+||+|.+.+
T Consensus       163 k~eL~~~v~~~v~~C~rslFIFDE~DKmp~  192 (344)
T KOG2170|consen  163 KEELKNRVRGTVQACQRSLFIFDEVDKLPP  192 (344)
T ss_pred             HHHHHHHHHHHHHhcCCceEEechhhhcCH
Confidence            12233222222   2789999999999864

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.31  E-value=0.0012  Score=63.28  Aligned_cols=80  Identities=18%  Similarity=0.241  Sum_probs=52.6

Q ss_pred             hHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC---------------------CcEEEEe--cCCc-----
Q 035959          214 DMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH---------------------FDVYDLE--LSSV-----  264 (338)
Q Consensus       214 ~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~---------------------~~~~~l~--~~~~-----  264 (338)
                      ..++.+...+.. ..+..+||+||+|+||+.+|.++|+.+-                     -+++.++  ...-     
T Consensus        11 ~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~   90 (319)
T PRK08769         11 RAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLR   90 (319)
T ss_pred             HHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCccccccc
Confidence            445566666554 3345799999999999999999998661                     2455553  1110     


Q ss_pred             --CCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          265 --EGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       265 --~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                        ...+.++.+...+.      ..-|+|||++|.+..
T Consensus        91 ~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~  127 (319)
T PRK08769         91 TEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINR  127 (319)
T ss_pred             ccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCH
Confidence              12345555555442      457999999999964

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.30  E-value=0.00067  Score=60.50  Aligned_cols=35  Identities=23%  Similarity=0.406  Sum_probs=28.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      .-++++||||+|||+++..++...   +..+.+++...
T Consensus        13 ~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~   50 (209)
T TIGR02237        13 TITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG   50 (209)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            346899999999999998888654   66788888875

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.29  E-value=0.0013  Score=64.68  Aligned_cols=65  Identities=23%  Similarity=0.457  Sum_probs=46.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh-------CCcEEEEecCCcC----------------------CchHHHHHHHhcC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL-------HFDVYDLELSSVE----------------------GNKHLRKVLIATE  278 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l-------~~~~~~l~~~~~~----------------------~~~~l~~~l~~~~  278 (338)
                      ++-++|+||+|+|||++++.+|..+       +..+..+++....                      ...++...+....
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~~  253 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQSK  253 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHhC
Confidence            3457899999999999999999876       2445545443321                      1234555566667


Q ss_pred             CCcEEEEcCCCccC
Q 035959          279 NKSILVVGDIDCCT  292 (338)
Q Consensus       279 ~~~Il~iDeiD~~~  292 (338)
                      ...+|+||.+....
T Consensus       254 ~~DlVLIDTaGr~~  267 (388)
T PRK12723        254 DFDLVLVDTIGKSP  267 (388)
T ss_pred             CCCEEEEcCCCCCc
Confidence            78999999998775

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=97.28  E-value=0.0003  Score=69.15  Aligned_cols=44  Identities=25%  Similarity=0.590  Sum_probs=39.0

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ++++...++.+++++.+..     +|+|+.||||.|||++++|+|.++.
T Consensus       245 ~ledY~L~dkl~eRL~era-----eGILIAG~PGaGKsTFaqAlAefy~  288 (604)
T COG1855         245 SLEDYGLSDKLKERLEERA-----EGILIAGAPGAGKSTFAQALAEFYA  288 (604)
T ss_pred             chhhcCCCHHHHHHHHhhh-----cceEEecCCCCChhHHHHHHHHHHH
Confidence            6788888998888887754     7999999999999999999999884

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.28  E-value=0.00023  Score=62.05  Aligned_cols=29  Identities=24%  Similarity=0.500  Sum_probs=25.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +++.||||+|||++++.+|..++...+..
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is~   30 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLSA   30 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            57999999999999999999998755443

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.

>PRK06217 hypothetical protein; Validated

Probab=97.28  E-value=0.00024  Score=62.34  Aligned_cols=31  Identities=29%  Similarity=0.426  Sum_probs=27.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .++|.|+||+|||++++++++.++.+++.+|
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcC
Confidence            3789999999999999999999998877664

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.27  E-value=0.0002  Score=62.29  Aligned_cols=33  Identities=30%  Similarity=0.407  Sum_probs=30.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      +.+.|.|++|+|||++.+++|+.+++++++.|-
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D~   35 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTDQ   35 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccchH
Confidence            568999999999999999999999999998864

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.26  E-value=0.00063  Score=70.84  Aligned_cols=49  Identities=31%  Similarity=0.468  Sum_probs=41.8

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      |..|+.+++.++.++.+...+..  ++.++|+||||||||+++++++..+.
T Consensus        27 ~~~~~~vigq~~a~~~L~~~~~~--~~~~l~~G~~G~GKttla~~l~~~l~   75 (637)
T PRK13765         27 ERLIDQVIGQEHAVEVIKKAAKQ--RRHVMMIGSPGTGKSMLAKAMAELLP   75 (637)
T ss_pred             cccHHHcCChHHHHHHHHHHHHh--CCeEEEECCCCCcHHHHHHHHHHHcC
Confidence            67899999998888877765654  35899999999999999999999875

>PRK13764 ATPase; Provisional

Probab=97.26  E-value=0.00077  Score=69.60  Aligned_cols=83  Identities=17%  Similarity=0.329  Sum_probs=51.5

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC---cEEEEe------cCC-cCC------
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF---DVYDLE------LSS-VEG------  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~---~~~~l~------~~~-~~~------  266 (338)
                      +.+++++..++.+++.+.     ..+.++|+.||||+||||+++|++.++..   .+..++      +.. +..      
T Consensus       237 ~~~Le~l~l~~~l~~~l~-----~~~~~ILIsG~TGSGKTTll~AL~~~i~~~~riV~TiEDp~El~~~~~i~q~~~~~~  311 (602)
T PRK13764        237 KLSLEDYNLSEKLKERLE-----ERAEGILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQVPPEITQYSKLEG  311 (602)
T ss_pred             CCCHHHhCCCHHHHHHHH-----hcCCEEEEECCCCCCHHHHHHHHHHHHhhCCCEEEEECCCccccCCCcceEEeeccc
Confidence            346788877665544433     23578999999999999999999998852   232221      111 010      


Q ss_pred             -chHHHHHHHhcCCCcEEEEcCCCcc
Q 035959          267 -NKHLRKVLIATENKSILVVGDIDCC  291 (338)
Q Consensus       267 -~~~l~~~l~~~~~~~Il~iDeiD~~  291 (338)
                       ...+.+.+. ..+|+++++||+-..
T Consensus       312 ~~~~~~~~lL-R~rPD~IivGEiRd~  336 (602)
T PRK13764        312 SMEETADILL-LVRPDYTIYDEMRKT  336 (602)
T ss_pred             cHHHHHHHHH-hhCCCEEEECCCCCH
Confidence             012222221 247999999999754

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.26  E-value=0.00025  Score=59.84  Aligned_cols=29  Identities=31%  Similarity=0.394  Sum_probs=24.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.|+||+|||++++.++..++..++..
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~~   30 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFIDG   30 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEeC
Confidence            57999999999999999999988765543

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

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=97.25  E-value=0.0011  Score=61.47  Aligned_cols=26  Identities=31%  Similarity=0.575  Sum_probs=23.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ..+++.||+|+|||+|++.+++.+..
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccc
Confidence            45799999999999999999998754

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.

>PRK14532 adenylate kinase; Provisional

Probab=97.24  E-value=0.00027  Score=62.09  Aligned_cols=30  Identities=23%  Similarity=0.438  Sum_probs=26.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .+++.||||+|||++++.+|..+|+..+..
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            378999999999999999999999876654

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.23  E-value=0.00026  Score=60.66  Aligned_cols=29  Identities=31%  Similarity=0.550  Sum_probs=24.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.++..++..++..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v~~   29 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFIEG   29 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEEeC
Confidence            46899999999999999999998665443

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.

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

Probab=97.23  E-value=0.0011  Score=66.20  Aligned_cols=87  Identities=16%  Similarity=0.171  Sum_probs=65.6

Q ss_pred             ccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh---
Q 035959          205 TFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA---  276 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~---  276 (338)
                      .+..+++..+.-+++.+.+.+  +....+|++|++||||..+|++|...-   +.+++.+||..+-.+ -+...|+.   
T Consensus       139 ~~~~liG~S~am~~l~~~i~kvA~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~-l~ESELFGhek  217 (464)
T COG2204         139 LGGELVGESPAMQQLRRLIAKVAPSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPEN-LLESELFGHEK  217 (464)
T ss_pred             ccCCceecCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHH-HHHHHhhcccc
Confidence            455677777777777777776  445679999999999999999999877   459999999987632 23332322   


Q ss_pred             ---------------cCCCcEEEEcCCCccC
Q 035959          277 ---------------TENKSILVVGDIDCCT  292 (338)
Q Consensus       277 ---------------~~~~~Il~iDeiD~~~  292 (338)
                                     .+....||||||..+.
T Consensus       218 GAFTGA~~~r~G~fE~A~GGTLfLDEI~~mp  248 (464)
T COG2204         218 GAFTGAITRRIGRFEQANGGTLFLDEIGEMP  248 (464)
T ss_pred             cCcCCcccccCcceeEcCCceEEeeccccCC
Confidence                           1357899999999875

>PRK13948 shikimate kinase; Provisional

Probab=97.23  E-value=0.00031  Score=61.94  Aligned_cols=34  Identities=26%  Similarity=0.197  Sum_probs=31.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      ++.++|.|++|+|||++++.+|+.+++++++.|.
T Consensus        10 ~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D~   43 (182)
T PRK13948         10 VTWVALAGFMGTGKSRIGWELSRALMLHFIDTDR   43 (182)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHcCCCEEECCH
Confidence            4778999999999999999999999999988773

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=97.22  E-value=0.00078  Score=70.07  Aligned_cols=50  Identities=34%  Similarity=0.480  Sum_probs=40.3

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      ..++.+++.++.++.+...+..  +++++|+||||||||++++++++.++..
T Consensus        15 ~~~~~viG~~~a~~~l~~a~~~--~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        15 RLIDQVIGQEEAVEIIKKAAKQ--KRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             hhHhhccCHHHHHHHHHHHHHc--CCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            3567888888877766666654  3689999999999999999999999643

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>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=97.22  E-value=0.0003  Score=58.61  Aligned_cols=30  Identities=30%  Similarity=0.459  Sum_probs=27.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +.+.|+||+|||++++.+|..++.+++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            578999999999999999999999988776

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.22  E-value=0.0015  Score=67.34  Aligned_cols=64  Identities=17%  Similarity=0.369  Sum_probs=46.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCCchH----------------------HHHHHH--
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEGNKH----------------------LRKVLI--  275 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~~~~----------------------l~~~l~--  275 (338)
                      ++++.|-||||||.++..+-+.+          .++++.|+.-.+.+..+                      |..-|.  
T Consensus       424 ~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~  503 (767)
T KOG1514|consen  424 CMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFTVP  503 (767)
T ss_pred             eEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccC
Confidence            57899999999999999999866          36777887776664222                      112222  


Q ss_pred             -hcCCCcEEEEcCCCccCC
Q 035959          276 -ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 -~~~~~~Il~iDeiD~~~~  293 (338)
                       .-..++||+|||+|.+..
T Consensus       504 k~~~~~~VvLiDElD~Lvt  522 (767)
T KOG1514|consen  504 KPKRSTTVVLIDELDILVT  522 (767)
T ss_pred             CCCCCCEEEEeccHHHHhc
Confidence             012579999999999986

>PRK14531 adenylate kinase; Provisional

Probab=97.21  E-value=0.00033  Score=61.54  Aligned_cols=31  Identities=26%  Similarity=0.485  Sum_probs=27.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +-+++.||||+|||++++.+|..+|...+..
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            4589999999999999999999998876543

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=97.21  E-value=0.0023  Score=60.39  Aligned_cols=80  Identities=11%  Similarity=0.099  Sum_probs=54.6

Q ss_pred             hHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC----------------CcEEEEecCC---cCCchHHHHH
Q 035959          214 DMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH----------------FDVYDLELSS---VEGNKHLRKV  273 (338)
Q Consensus       214 ~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~----------------~~~~~l~~~~---~~~~~~l~~~  273 (338)
                      ...+.+...+.. .-+..|||+||+|+||+.+|.++|..+-                .+++.+....   ....+.++.+
T Consensus         4 ~~~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l   83 (290)
T PRK05917          4 AAWEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAI   83 (290)
T ss_pred             HHHHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHH
Confidence            345556666655 3456899999999999999999998762                2455553322   1234455655


Q ss_pred             HHhcC------CCcEEEEcCCCccCC
Q 035959          274 LIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       274 l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      ...+.      ..-|++||++|.+..
T Consensus        84 ~~~~~~~p~e~~~kv~ii~~ad~mt~  109 (290)
T PRK05917         84 KKQIWIHPYESPYKIYIIHEADRMTL  109 (290)
T ss_pred             HHHHhhCccCCCceEEEEechhhcCH
Confidence            55542      467999999999965

>PRK13946 shikimate kinase; Provisional

Probab=97.20  E-value=0.00029  Score=61.94  Aligned_cols=34  Identities=32%  Similarity=0.439  Sum_probs=31.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      ++.++|.|+||+|||++++.+|+.+|+++++.|.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D~   43 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDADT   43 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcCH
Confidence            3678999999999999999999999999988774

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.19  E-value=0.0017  Score=60.57  Aligned_cols=88  Identities=19%  Similarity=0.334  Sum_probs=54.6

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEe------cCCcC-----C--
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLE------LSSVE-----G--  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~------~~~~~-----~--  266 (338)
                      +.+++++.+.++..+.+.+.+.. ....+++.||+|+|||+++.++..++.   ..++.++      +..+.     .  
T Consensus        56 ~~~l~~lg~~~~~~~~l~~~~~~-~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~~~~~~q~~v~~~~  134 (264)
T cd01129          56 ILDLEKLGLKPENLEIFRKLLEK-PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQIPGINQVQVNEKA  134 (264)
T ss_pred             CCCHHHcCCCHHHHHHHHHHHhc-CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceecCCCceEEEeCCcC
Confidence            34678888877766655444432 223478999999999999999987774   2344332      11111     0  


Q ss_pred             chHHHHHHHhc--CCCcEEEEcCCCcc
Q 035959          267 NKHLRKVLIAT--ENKSILVVGDIDCC  291 (338)
Q Consensus       267 ~~~l~~~l~~~--~~~~Il~iDeiD~~  291 (338)
                      ...+..++..+  ..|++|+++||..-
T Consensus       135 ~~~~~~~l~~~lR~~PD~i~vgEiR~~  161 (264)
T cd01129         135 GLTFARGLRAILRQDPDIIMVGEIRDA  161 (264)
T ss_pred             CcCHHHHHHHHhccCCCEEEeccCCCH
Confidence            11233333333  37999999999654

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.

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=97.19  E-value=0.0014  Score=64.12  Aligned_cols=50  Identities=26%  Similarity=0.290  Sum_probs=43.0

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -.|.-+++.+..|..+.-....|.-.|+|+-|+.|||||++++|+|..|.
T Consensus        14 ~pf~aivGqd~lk~aL~l~av~P~iggvLI~G~kGtaKSt~~Rala~LLp   63 (423)
T COG1239          14 LPFTAIVGQDPLKLALGLNAVDPQIGGALIAGEKGTAKSTLARALADLLP   63 (423)
T ss_pred             cchhhhcCchHHHHHHhhhhcccccceeEEecCCCccHHHHHHHHHHhCC
Confidence            35677788888998888877667778999999999999999999999884

>PF13245 AAA_19: Part of AAA domain

Probab=97.18  E-value=0.00059  Score=51.42  Aligned_cols=33  Identities=36%  Similarity=0.578  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHH-HHHHHh------CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIA-AMANYL------HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~-aia~~l------~~~~~~l~~~  262 (338)
                      -+++.||||||||+++. .++..+      +..+..+..+
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            35569999999996544 444444      4455555443

>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=97.18  E-value=0.00034  Score=61.40  Aligned_cols=29  Identities=31%  Similarity=0.555  Sum_probs=25.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +++.||||+|||++++.+|..++..++.+
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~   30 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHIST   30 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            68999999999999999999998776554

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.18  E-value=0.0013  Score=58.66  Aligned_cols=65  Identities=15%  Similarity=0.252  Sum_probs=42.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH-----hCCcEE-----------EEecCC---cC---C-----chHHHHHHHhcC--C
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY-----LHFDVY-----------DLELSS---VE---G-----NKHLRKVLIATE--N  279 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~-----l~~~~~-----------~l~~~~---~~---~-----~~~l~~~l~~~~--~  279 (338)
                      +.++|.||+|+|||++++.++..     .|.++-           ....+.   +.   +     -.++..++....  .
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~l~~~~s~~~~e~~~~~~iL~~~~~~~  105 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKGE  105 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcccceEEEeccchhccccccChHHHHHHHHHHHHHhccCCC
Confidence            57899999999999999999843     343320           111110   00   0     134567777777  8


Q ss_pred             CcEEEEcCCCccCC
Q 035959          280 KSILVVGDIDCCTE  293 (338)
Q Consensus       280 ~~Il~iDeiD~~~~  293 (338)
                      +.++++||.-.-.+
T Consensus       106 p~llllDEp~~glD  119 (199)
T cd03283         106 PVLFLLDEIFKGTN  119 (199)
T ss_pred             CeEEEEecccCCCC
Confidence            99999999865544

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

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=97.18  E-value=0.0012  Score=63.49  Aligned_cols=61  Identities=26%  Similarity=0.408  Sum_probs=48.9

Q ss_pred             ccc-cccCChhHHHHHHHHHHh------hhcCceeeeCCCCCCcHHHHHHHHHHh-CCcEEEEecCCcC
Q 035959          205 TFD-TLAMDTDMKKMIMDDLER------AWKRGYLLFGPPGTGKSSLIAAMANYL-HFDVYDLELSSVE  265 (338)
Q Consensus       205 ~f~-~l~~~~~~k~~i~~~l~~------~~~~g~LL~GppGtGKT~l~~aia~~l-~~~~~~l~~~~~~  265 (338)
                      .|+ .+.+-++...++++.+..      ..++-++|.||+|+|||+++..+.+.+ .+++|.+..+.+.
T Consensus        58 ~f~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~y~~Y~l~~~Pm~  126 (358)
T PF08298_consen   58 FFEDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLEEYPIYTLKGCPMH  126 (358)
T ss_pred             CccccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhheEEEEEecCCccc
Confidence            455 677788889999999887      345568999999999999999999988 4678877665554

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=97.17  E-value=0.00031  Score=69.65  Aligned_cols=48  Identities=29%  Similarity=0.461  Sum_probs=39.2

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ..+|.++.+++..|+.+.-..  +-.+++|++||||||||+++.-+..-+
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAA--AGgHnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAA--AGGHNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHH--hcCCcEEEecCCCCchHHhhhhhcccC
Confidence            448999999999888775443  446789999999999999999887655

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.17  E-value=0.00067  Score=54.70  Aligned_cols=24  Identities=33%  Similarity=0.357  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++++++||+|+|||.++.+.+..+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~   24 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILEL   24 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHH
Confidence            368999999999999887777655

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=97.17  E-value=0.0024  Score=61.41  Aligned_cols=99  Identities=16%  Similarity=0.205  Sum_probs=72.6

Q ss_pred             cccccCCCCCccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchH
Q 035959          195 RQSAILDHPSTFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKH  269 (338)
Q Consensus       195 w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~  269 (338)
                      ...++..+-..|+.++.....-+.++....+  .....+|+.|++||||-.+|+|.....   ..++.-++|+.+-.+..
T Consensus       192 ~~~~~~~~~~~F~~~v~~S~~mk~~v~qA~k~AmlDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNCA~lPe~~a  271 (511)
T COG3283         192 LQNVAAQDVSGFEQIVAVSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLPEDAA  271 (511)
T ss_pred             HhhcccccccchHHHhhccHHHHHHHHHHHHhhccCCCeEEecCCCchHHHHHHHHhhcCcccCCCeeEeecCCCchhHh
Confidence            4445667777899999888777777776665  445679999999999999999865544   57899999998875332


Q ss_pred             HHHHH------------HhcCCCcEEEEcCCCccCC
Q 035959          270 LRKVL------------IATENKSILVVGDIDCCTE  293 (338)
Q Consensus       270 l~~~l------------~~~~~~~Il~iDeiD~~~~  293 (338)
                      -..+|            .+.+...-+++|||-.+.+
T Consensus       272 EsElFG~apg~~gk~GffE~AngGTVlLDeIgEmSp  307 (511)
T COG3283         272 ESELFGHAPGDEGKKGFFEQANGGTVLLDEIGEMSP  307 (511)
T ss_pred             HHHHhcCCCCCCCccchhhhccCCeEEeehhhhcCH
Confidence            22333            3334567889999988865

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.16  E-value=0.0004  Score=60.51  Aligned_cols=33  Identities=36%  Similarity=0.665  Sum_probs=30.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      ..++|.||+|+|||++++.+|+.+++++++.+.
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~l~~~~vd~D~   37 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQ   37 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHHcCCcEEECCc
Confidence            568999999999999999999999999887764

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.16  E-value=0.0011  Score=59.89  Aligned_cols=33  Identities=24%  Similarity=0.420  Sum_probs=28.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      -++++||||+|||+++..+|...   +..++++++.
T Consensus        25 i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         25 ITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            36899999999999999998755   6788888877

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.16  E-value=0.00044  Score=59.72  Aligned_cols=32  Identities=28%  Similarity=0.481  Sum_probs=29.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ..++|.|+||+|||++++.+|..+|+++++.|
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~~~~d~D   34 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGYRFVDTD   34 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEEcc
Confidence            35789999999999999999999999988775

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.15  E-value=0.0015  Score=56.82  Aligned_cols=63  Identities=16%  Similarity=0.165  Sum_probs=45.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----------------------chHHHHHHHhcCCCcEEEEcC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----------------------NKHLRKVLIATENKSILVVGD  287 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----------------------~~~l~~~l~~~~~~~Il~iDe  287 (338)
                      +|+.|+||+|||+++..++...+.+++++......+                       ..++.+.+.+...+.+|+||-
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            589999999999999999988777887776654332                       123444444434567899998


Q ss_pred             CCccCC
Q 035959          288 IDCCTE  293 (338)
Q Consensus       288 iD~~~~  293 (338)
                      +..+..
T Consensus        82 lt~~~~   87 (169)
T cd00544          82 LTLWVT   87 (169)
T ss_pred             HhHHHH
Confidence            888765

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.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.13  E-value=0.0034  Score=52.54  Aligned_cols=26  Identities=31%  Similarity=0.424  Sum_probs=23.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      .-++|.|+.|+|||++++++++.++.
T Consensus        23 ~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        23 TVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            34689999999999999999999864

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.

>PRK06547 hypothetical protein; Provisional

Probab=97.13  E-value=0.00065  Score=59.36  Aligned_cols=33  Identities=30%  Similarity=0.461  Sum_probs=27.6

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ..-+++.|++|+|||++++.+++.++..++..+
T Consensus        15 ~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         15 MITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            345788999999999999999999887766544

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.11  E-value=0.00075  Score=64.42  Aligned_cols=49  Identities=29%  Similarity=0.331  Sum_probs=37.1

Q ss_pred             ChhHHHHHHHHHHh--------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          212 DTDMKKMIMDDLER--------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       212 ~~~~k~~i~~~l~~--------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +++.++.+.+.++.        ..+..+.|.|+||+|||++++.+|..+|+++++++
T Consensus       109 ~~~~~~~~~~~l~~~~~~~~~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~id~D  165 (309)
T PRK08154        109 SPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARLGVPFVELN  165 (309)
T ss_pred             CHHHHHHHHHHHHHHHhhhhhccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEeHH
Confidence            44444444444444        33456899999999999999999999999998765

>PRK06762 hypothetical protein; Provisional

Probab=97.10  E-value=0.00055  Score=58.79  Aligned_cols=33  Identities=15%  Similarity=0.235  Sum_probs=27.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .-+++.|+||+|||++++.+++.++..++.++.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~~   35 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERLGRGTLLVSQ   35 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEEecH
Confidence            457899999999999999999999656655543

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=97.07  E-value=0.00072  Score=72.28  Aligned_cols=64  Identities=22%  Similarity=0.319  Sum_probs=39.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC-------cEEEEecCCcCC-c----hH--HHHHHHhcCCCcEEEEcCCCccCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF-------DVYDLELSSVEG-N----KH--LRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~-------~~~~l~~~~~~~-~----~~--l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      .+||.|+||||||.+++++++....       +...+.++.... .    ..  +..=....+...+++|||+|.+..
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            5899999999999999999986532       333333332211 0    00  000001123578999999999864

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.07  E-value=0.002  Score=61.30  Aligned_cols=64  Identities=22%  Similarity=0.347  Sum_probs=41.4

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecC-CcC-------------CchHHHHHHHhc--CCCcEEEE
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELS-SVE-------------GNKHLRKVLIAT--ENKSILVV  285 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~-~~~-------------~~~~l~~~l~~~--~~~~Il~i  285 (338)
                      .+.++++.||+|+|||++++|++.++.     ..++.++-. ++.             ....+.+++..+  ..|+.|++
T Consensus       131 ~~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v~~~~~~~~~~~~~~l~~aLR~~pD~iiv  210 (299)
T TIGR02782       131 ARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQLRTSDDAISMTRLLKATLRLRPDRIIV  210 (299)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEEEEEecCCCCCHHHHHHHHhcCCCCEEEE
Confidence            356899999999999999999998862     223322111 000             011344555443  37899999


Q ss_pred             cCCCc
Q 035959          286 GDIDC  290 (338)
Q Consensus       286 DeiD~  290 (338)
                      .||-.
T Consensus       211 GEiR~  215 (299)
T TIGR02782       211 GEVRG  215 (299)
T ss_pred             eccCC
Confidence            99864

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK14530 adenylate kinase; Provisional

Probab=97.06  E-value=0.00056  Score=61.62  Aligned_cols=29  Identities=28%  Similarity=0.483  Sum_probs=26.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      ..++|.||||+|||++++.+|..++++.+
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~~~~i   32 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFGVEHV   32 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEE
Confidence            45889999999999999999999998766

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=97.06  E-value=0.00045  Score=73.94  Aligned_cols=98  Identities=26%  Similarity=0.361  Sum_probs=68.7

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh---------------hcC-ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA---------------WKR-GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS  263 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~---------------~~~-g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~  263 (338)
                      .+.|.....+.+....-..+.+.+...               ... .++++||||+|||+.+.++|..+|+.++..|.+.
T Consensus       313 k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g~~v~E~Nas~  392 (871)
T KOG1968|consen  313 KYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELGFKVVEKNASD  392 (871)
T ss_pred             ccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhcccceeecCccc
Confidence            344444455555444444555555541               112 3589999999999999999999999999999999


Q ss_pred             cCCchHHHHHHHhcC--------------------CCcEEEEcCCCccCCccccc
Q 035959          264 VEGNKHLRKVLIATE--------------------NKSILVVGDIDCCTELQDRS  298 (338)
Q Consensus       264 ~~~~~~l~~~l~~~~--------------------~~~Il~iDeiD~~~~~~~r~  298 (338)
                      ..+...+...+..+.                    ..-||++||+|-+.. .+|+
T Consensus       393 ~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~-~dRg  446 (871)
T KOG1968|consen  393 VRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG-EDRG  446 (871)
T ss_pred             cccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc-hhhh
Confidence            887666554444321                    133999999999987 4564

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.04  E-value=0.00062  Score=59.32  Aligned_cols=31  Identities=19%  Similarity=0.387  Sum_probs=26.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+++.||||+|||++++.++..+|+..+..
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~g~~~~~~   34 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKYGFTHLST   34 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            3468999999999999999999998765544

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.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=97.02  E-value=0.0035  Score=61.36  Aligned_cols=43  Identities=21%  Similarity=0.341  Sum_probs=32.6

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +++++...+...+.+.    . ....+|+.||+|+|||++++++..++
T Consensus       131 ~l~~lgl~~~~~~~l~----~-~~GlilI~G~TGSGKTT~l~al~~~i  173 (372)
T TIGR02525       131 DLKQMGIEPDLFNSLL----P-AAGLGLICGETGSGKSTLAASIYQHC  173 (372)
T ss_pred             CHHHcCCCHHHHHHHH----h-cCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            6788887776544433    2 23346899999999999999999887

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>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=97.00  E-value=0.00067  Score=60.93  Aligned_cols=34  Identities=38%  Similarity=0.552  Sum_probs=26.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~  263 (338)
                      -++++||+|||||.++-++|+.+|.+++.+|--.
T Consensus         3 v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Driq   36 (233)
T PF01745_consen    3 VYLIVGPTGTGKTALAIALAQKTGAPVISLDRIQ   36 (233)
T ss_dssp             EEEEE-STTSSHHHHHHHHHHHH--EEEEE-SGG
T ss_pred             EEEEECCCCCChhHHHHHHHHHhCCCEEEeccee
Confidence            3689999999999999999999999998886544

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.00  E-value=0.00099  Score=61.95  Aligned_cols=124  Identities=18%  Similarity=0.244  Sum_probs=76.8

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh-CCc-----------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL-HFD-----------------------  255 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l-~~~-----------------------  255 (338)
                      ...|.+++.+....+....+........-..+++|||+|+||-+.+.++-+++ |..                       
T Consensus         6 kyrpksl~~l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEist   85 (351)
T KOG2035|consen    6 KYRPKSLDELIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEIST   85 (351)
T ss_pred             hcCcchhhhcccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEE
Confidence            56788898888877776666655543223579999999999999999998887 311                       


Q ss_pred             -----EEEEecCCcCCchH--HHHHHHhcC-----------CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhh
Q 035959          256 -----VYDLELSSVEGNKH--LRKVLIATE-----------NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQIT  317 (338)
Q Consensus       256 -----~~~l~~~~~~~~~~--l~~~l~~~~-----------~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~  317 (338)
                           ..+++.++....++  +..++.+++           .-.+++|-|+|.+..    ..+           ...++|
T Consensus        86 vsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~----dAQ-----------~aLRRT  150 (351)
T KOG2035|consen   86 VSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTR----DAQ-----------HALRRT  150 (351)
T ss_pred             ecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhH----HHH-----------HHHHHH
Confidence                 11223333332221  345554442           346999999999964    221           234666


Q ss_pred             HHHHHHHhcCCcCCCCCcccC
Q 035959          318 LSGLLNFTDGLWSSCGDERII  338 (338)
Q Consensus       318 ls~lLn~iDgl~s~~g~erii  338 (338)
                      +.-.-+.+-=+.+|..-.|||
T Consensus       151 MEkYs~~~RlIl~cns~SriI  171 (351)
T KOG2035|consen  151 MEKYSSNCRLILVCNSTSRII  171 (351)
T ss_pred             HHHHhcCceEEEEecCcccch
Confidence            666666555555444334443

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.00  E-value=0.0015  Score=65.60  Aligned_cols=64  Identities=25%  Similarity=0.333  Sum_probs=44.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC--------------------chHHHHHHHhc--CCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG--------------------NKHLRKVLIAT--ENKSILV  284 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~--------------------~~~l~~~l~~~--~~~~Il~  284 (338)
                      -++|+||||+|||+|+..+|...   +.++++++..+-..                    +.++.+++...  .++.+||
T Consensus        82 ~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~~~~lVV  161 (446)
T PRK11823         82 VVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEEKPDLVV  161 (446)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccccHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHHhhCCCEEE
Confidence            46899999999999999988765   56788887654211                    11223333332  2678999


Q ss_pred             EcCCCccCC
Q 035959          285 VGDIDCCTE  293 (338)
Q Consensus       285 iDeiD~~~~  293 (338)
                      ||.|..+..
T Consensus       162 IDSIq~l~~  170 (446)
T PRK11823        162 IDSIQTMYS  170 (446)
T ss_pred             Eechhhhcc
Confidence            999998864

>PF14516 AAA_35: AAA-like domain

Probab=97.00  E-value=0.0032  Score=60.68  Aligned_cols=55  Identities=13%  Similarity=0.195  Sum_probs=40.7

Q ss_pred             cCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC
Q 035959          210 AMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE  265 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~  265 (338)
                      +..++.-+.+.+.+.++ ..-+.++||..+||||+...+.+.+   |+....+++..+.
T Consensus        14 i~R~~~e~~~~~~i~~~-G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~   71 (331)
T PF14516_consen   14 IERPPAEQECYQEIVQP-GSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLG   71 (331)
T ss_pred             cCchHHHHHHHHHHhcC-CCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCC
Confidence            34445666677666642 3446799999999999999888766   7888888887754

>PRK02496 adk adenylate kinase; Provisional

Probab=96.98  E-value=0.00065  Score=59.46  Aligned_cols=29  Identities=31%  Similarity=0.644  Sum_probs=25.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +++.||||+|||++++.+|..++...+..
T Consensus         4 i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          4 LIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            78999999999999999999998876644

>PRK14528 adenylate kinase; Provisional

Probab=96.97  E-value=0.00075  Score=59.56  Aligned_cols=29  Identities=24%  Similarity=0.552  Sum_probs=25.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      .+++.||||+|||++++.+|..++++.+.
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~~~~~is   31 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERLSIPQIS   31 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCeee
Confidence            47899999999999999999999877654

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.96  E-value=0.004  Score=62.08  Aligned_cols=62  Identities=23%  Similarity=0.315  Sum_probs=44.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcC----------------------CchHHHHHHHhcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVE----------------------GNKHLRKVLIATENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~----------------------~~~~l~~~l~~~~~~~  281 (338)
                      +.++|.||+|+|||+++..+|..+     +..+..+++....                      +..++...+.......
T Consensus       222 ~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~~~D  301 (424)
T PRK05703        222 GVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLRDCD  301 (424)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhCCCC
Confidence            346899999999999999988754     3567777665421                      1234555666666788


Q ss_pred             EEEEcCCCc
Q 035959          282 ILVVGDIDC  290 (338)
Q Consensus       282 Il~iDeiD~  290 (338)
                      +|+||..-.
T Consensus       302 lVlIDt~G~  310 (424)
T PRK05703        302 VILIDTAGR  310 (424)
T ss_pred             EEEEeCCCC
Confidence            999997644

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=96.96  E-value=0.00073  Score=63.31  Aligned_cols=59  Identities=31%  Similarity=0.358  Sum_probs=40.7

Q ss_pred             cccCChhHHH--HHHHHHHh---hhcCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEecCCcCC
Q 035959          208 TLAMDTDMKK--MIMDDLER---AWKRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLELSSVEG  266 (338)
Q Consensus       208 ~l~~~~~~k~--~i~~~l~~---~~~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~~~~~~  266 (338)
                      .++++.+.++  -++-++..   -..|++||.||||||||.|+-||+.++|.  ++.-+-.+++.+
T Consensus        39 g~vGQ~~AReAagiivdlik~KkmaGravLlaGppgtGKTAlAlaisqELG~kvPFcpmvgSEvyS  104 (456)
T KOG1942|consen   39 GFVGQENAREAAGIIVDLIKSKKMAGRAVLLAGPPGTGKTALALAISQELGPKVPFCPMVGSEVYS  104 (456)
T ss_pred             ccccchhhhhhhhHHHHHHHhhhccCcEEEEecCCCCchhHHHHHHHHHhCCCCCcccccchhhhh
Confidence            4566555543  23444443   34578999999999999999999999975  555555555544

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

Probab=96.96  E-value=0.0022  Score=64.03  Aligned_cols=90  Identities=13%  Similarity=0.160  Sum_probs=67.5

Q ss_pred             CccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---chHHH----
Q 035959          204 STFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---NKHLR----  271 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---~~~l~----  271 (338)
                      ..+..+++..+...++++.++-  +....+||.|++||||..+|+||...-   +.+++.+||+.+-.   +++|-    
T Consensus       220 ~~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPesLlESELFGHeK  299 (550)
T COG3604         220 LEVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPESLLESELFGHEK  299 (550)
T ss_pred             cccccceecCHHHHHHHHHHHHHhcCCCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccchHHHHHHHhcccc
Confidence            3667888888877778777766  455679999999999999999999877   57899999998753   22221    


Q ss_pred             HHHH----------hcCCCcEEEEcCCCccCC
Q 035959          272 KVLI----------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       272 ~~l~----------~~~~~~Il~iDeiD~~~~  293 (338)
                      -.|.          +++...-||+|||.-+.-
T Consensus       300 GAFTGA~~~r~GrFElAdGGTLFLDEIGelPL  331 (550)
T COG3604         300 GAFTGAINTRRGRFELADGGTLFLDEIGELPL  331 (550)
T ss_pred             cccccchhccCcceeecCCCeEechhhccCCH
Confidence            1111          124678999999998853

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.95  E-value=0.0042  Score=63.15  Aligned_cols=63  Identities=21%  Similarity=0.295  Sum_probs=44.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCc----------------------CCchHHHHHHHhcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSV----------------------EGNKHLRKVLIATENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~----------------------~~~~~l~~~l~~~~~~~  281 (338)
                      ..+.|.||+|+|||+++..+|..+     +..+..++....                      .+...+...+.......
T Consensus       351 ~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~~~D  430 (559)
T PRK12727        351 GVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLRDYK  430 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhccCC
Confidence            446799999999999999998754     234554443221                      12345677777777889


Q ss_pred             EEEEcCCCcc
Q 035959          282 ILVVGDIDCC  291 (338)
Q Consensus       282 Il~iDeiD~~  291 (338)
                      +||||..-..
T Consensus       431 LVLIDTaG~s  440 (559)
T PRK12727        431 LVLIDTAGMG  440 (559)
T ss_pred             EEEecCCCcc
Confidence            9999998765

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=96.95  E-value=0.0034  Score=57.08  Aligned_cols=34  Identities=32%  Similarity=0.572  Sum_probs=25.2

Q ss_pred             HHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          219 IMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       219 i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++.++-+...-+.|+.||||||||++++-+|..+
T Consensus       128 li~~ly~~g~lntLiigpP~~GKTTlLRdiaR~~  161 (308)
T COG3854         128 LIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLL  161 (308)
T ss_pred             HHHHHHhcCceeeEEecCCCCChHHHHHHHHHHh
Confidence            3444443323457899999999999999999876

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.95  E-value=0.0033  Score=60.93  Aligned_cols=82  Identities=24%  Similarity=0.437  Sum_probs=47.9

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC----cEEEEecC-C--------------
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF----DVYDLELS-S--------------  263 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~----~~~~l~~~-~--------------  263 (338)
                      +.+++++...+.    +.+.+. ..+..+++.||+|+|||+++.++..++..    .++.+.-. +              
T Consensus       102 ~~~l~~lg~~~~----l~~~~~-~~~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~~~~~~~i~q~e  176 (343)
T TIGR01420       102 IPTFEELGLPPV----LRELAE-RPRGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVHRNKRSLINQRE  176 (343)
T ss_pred             CCCHHHcCCCHH----HHHHHh-hcCcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhccCccceEEccc
Confidence            446677665542    222222 22344689999999999999999987742    23322110 0              


Q ss_pred             cC-CchHHHHHHHhc--CCCcEEEEcCCC
Q 035959          264 VE-GNKHLRKVLIAT--ENKSILVVGDID  289 (338)
Q Consensus       264 ~~-~~~~l~~~l~~~--~~~~Il~iDeiD  289 (338)
                      +. ....+.+.+..+  ..|++|++||+-
T Consensus       177 vg~~~~~~~~~l~~~lr~~pd~i~vgEir  205 (343)
T TIGR01420       177 VGLDTLSFANALRAALREDPDVILIGEMR  205 (343)
T ss_pred             cCCCCcCHHHHHHHhhccCCCEEEEeCCC
Confidence            11 011233444332  489999999995

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.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.94  E-value=0.0008  Score=57.82  Aligned_cols=28  Identities=25%  Similarity=0.494  Sum_probs=25.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      +-+.||||||||++++-+|+++|++++.
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vs   30 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVS   30 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceee
Confidence            4578999999999999999999998765

>PF13479 AAA_24: AAA domain

Probab=96.92  E-value=0.00042  Score=62.47  Aligned_cols=60  Identities=25%  Similarity=0.455  Sum_probs=38.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC-------------CcCCchHHHHHHHhc----CCCcEEEEcCCCccC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS-------------SVEGNKHLRKVLIAT----ENKSILVVGDIDCCT  292 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~-------------~~~~~~~l~~~l~~~----~~~~Il~iDeiD~~~  292 (338)
                      -++||||||+|||+++..+-+-+   +++++..             .+.+-.++...+..+    .....||||-++.+.
T Consensus         5 ~~lIyG~~G~GKTt~a~~~~k~l---~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y~tiVIDsis~~~   81 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASLPKPL---FIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEEDEADYDTIVIDSISWLE   81 (213)
T ss_pred             EEEEECCCCCCHHHHHHhCCCeE---EEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhccCCCCEEEEECHHHHH
Confidence            47999999999999998872111   2222222             111234455555432    477899999998874

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.92  E-value=0.0027  Score=63.65  Aligned_cols=86  Identities=23%  Similarity=0.421  Sum_probs=57.9

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCc-eeeeCCCCCCcHHHHHHHHHHhCCc---EEEE------ecCCcCC---ch--
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRG-YLLFGPPGTGKSSLIAAMANYLHFD---VYDL------ELSSVEG---NK--  268 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g-~LL~GppGtGKT~l~~aia~~l~~~---~~~l------~~~~~~~---~~--  268 (338)
                      -+|+.+++.+...+.+...+..|  .| +|+.||.|+|||++.-++-++++.+   +..+      ....+..   +.  
T Consensus       235 l~l~~Lg~~~~~~~~~~~~~~~p--~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~~~~gI~Q~qVN~k~  312 (500)
T COG2804         235 LDLEKLGMSPFQLARLLRLLNRP--QGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEYQLPGINQVQVNPKI  312 (500)
T ss_pred             CCHHHhCCCHHHHHHHHHHHhCC--CeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeeeecCCcceeeccccc
Confidence            37899999999888888888754  56 4789999999999999999888643   2222      2222210   11  


Q ss_pred             --HHHHHHHhc--CCCcEEEEcCCCcc
Q 035959          269 --HLRKVLIAT--ENKSILVVGDIDCC  291 (338)
Q Consensus       269 --~l~~~l~~~--~~~~Il~iDeiD~~  291 (338)
                        +..+.+...  ..|+||++.||--.
T Consensus       313 gltfa~~LRa~LRqDPDvImVGEIRD~  339 (500)
T COG2804         313 GLTFARALRAILRQDPDVIMVGEIRDL  339 (500)
T ss_pred             CCCHHHHHHHHhccCCCeEEEeccCCH
Confidence              122222222  37999999999754

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=96.92  E-value=0.0035  Score=62.24  Aligned_cols=84  Identities=14%  Similarity=0.220  Sum_probs=58.9

Q ss_pred             ccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh-------
Q 035959          209 LAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA-------  276 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~-------  276 (338)
                      +++.....+.+++++..  .....++++|++||||+++++++....   +.+++.++|..+.. ..+...+..       
T Consensus       141 lig~s~~~~~~~~~i~~~~~~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~-~~~~~~lfg~~~~~~~  219 (441)
T PRK10365        141 MVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNE-SLLESELFGHEKGAFT  219 (441)
T ss_pred             eEecCHHHHHHHHHHhhccCCCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCH-HHHHHHhcCCCCCCcC
Confidence            34444444555555544  334678999999999999999998765   46899999998653 444444322       


Q ss_pred             -----------cCCCcEEEEcCCCccCC
Q 035959          277 -----------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 -----------~~~~~Il~iDeiD~~~~  293 (338)
                                 ...+..|+|||||.+..
T Consensus       220 ~~~~~~~g~~~~a~~gtl~ldei~~l~~  247 (441)
T PRK10365        220 GADKRREGRFVEADGGTLFLDEIGDISP  247 (441)
T ss_pred             CCCcCCCCceeECCCCEEEEeccccCCH
Confidence                       12467899999999965

>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=96.92  E-value=0.0012  Score=57.44  Aligned_cols=32  Identities=28%  Similarity=0.250  Sum_probs=25.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      ++++||||||||+++..++...   |.++.++++.
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            6899999999999998876654   5667666553

A related protein is found in archaea.

>PRK04296 thymidine kinase; Provisional

Probab=96.92  E-value=0.0029  Score=55.99  Aligned_cols=29  Identities=21%  Similarity=0.309  Sum_probs=23.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      .+++||||+|||+++..++..+   +..++.+
T Consensus         5 ~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          5 EFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            5899999999999888887765   5566655

>PLN03210 Resistant to P

Probab=96.92  E-value=0.0025  Score=71.23  Aligned_cols=59  Identities=19%  Similarity=0.173  Sum_probs=43.9

Q ss_pred             cccccCCCCCccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          195 RQSAILDHPSTFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       195 w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      |..+....+..++.+++.+...+++...+..  ...+-+-++||+|+|||+||+++++.+.
T Consensus       172 ~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~  232 (1153)
T PLN03210        172 LGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLS  232 (1153)
T ss_pred             HHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHh
Confidence            4445555667888888877777777766643  2234567999999999999999998774

syringae 6; Provisional

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.92  E-value=0.0015  Score=60.19  Aligned_cols=32  Identities=38%  Similarity=0.540  Sum_probs=26.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      ++|.|+||+|||+++++++..+   +.++..++..
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~~D   36 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTD   36 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEccH
Confidence            5799999999999999999988   4666666543

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.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.91  E-value=0.0015  Score=48.03  Aligned_cols=29  Identities=31%  Similarity=0.387  Sum_probs=23.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh-CCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL-HFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l-~~~~~~l  259 (338)
                      +.+.|+||+|||+++++++..+ +.++..+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l~~~~~~~i   31 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQLGGRSVVVL   31 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCEEEE
Confidence            4688999999999999999986 3444444

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.91  E-value=0.0013  Score=64.32  Aligned_cols=65  Identities=22%  Similarity=0.298  Sum_probs=43.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC--------------------chHHHHHHHhc--CCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG--------------------NKHLRKVLIAT--ENKSIL  283 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~--------------------~~~l~~~l~~~--~~~~Il  283 (338)
                      .-++++||||+|||+|+..+|..+   +.++++++..+-..                    +..+..++...  .++.+|
T Consensus        83 slvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EEs~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~~~~lV  162 (372)
T cd01121          83 SVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEESPEQIKLRADRLGISTENLYLLAETNLEDILASIEELKPDLV  162 (372)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCcCHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHHhcCCcEE
Confidence            346899999999999999988765   35677776543110                    11222333222  378999


Q ss_pred             EEcCCCccCC
Q 035959          284 VVGDIDCCTE  293 (338)
Q Consensus       284 ~iDeiD~~~~  293 (338)
                      +||+|..+..
T Consensus       163 VIDSIq~l~~  172 (372)
T cd01121         163 IIDSIQTVYS  172 (372)
T ss_pred             EEcchHHhhc
Confidence            9999998854

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=96.88  E-value=0.0016  Score=63.73  Aligned_cols=23  Identities=35%  Similarity=0.638  Sum_probs=21.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .++.||||+|||+|++++++...
T Consensus       172 ~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        172 GLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             EEEeCCCCCChhHHHHHHHHHHH
Confidence            68899999999999999999774

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.87  E-value=0.0016  Score=63.28  Aligned_cols=24  Identities=38%  Similarity=0.498  Sum_probs=22.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+++.|.||||||.|+-.++..+
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            457899999999999999999988

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.87  E-value=0.00076  Score=58.67  Aligned_cols=29  Identities=31%  Similarity=0.300  Sum_probs=25.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      +-++|.|+||+|||+++++++..++..++
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~~~~~   31 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLAEPWL   31 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhCCCcc
Confidence            45789999999999999999998876544

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.87  E-value=0.00095  Score=61.01  Aligned_cols=29  Identities=24%  Similarity=0.588  Sum_probs=26.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.+|+.++++.+.+
T Consensus         9 Ivl~G~PGsGK~T~a~~La~~~g~~~is~   37 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSKKENLKHINM   37 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            78999999999999999999998776544

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.87  E-value=0.0027  Score=57.28  Aligned_cols=65  Identities=18%  Similarity=0.249  Sum_probs=40.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH-----HhCCcE---------EEEecCCcCC-----------c---hHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN-----YLHFDV---------YDLELSSVEG-----------N---KHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~-----~l~~~~---------~~l~~~~~~~-----------~---~~l~~~l~~~~~~  280 (338)
                      +.++|.||.|+|||++++.++.     ..|..+         ++-....+..           .   ..+..++..+..+
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a~~~~~~~~d~i~~~l~~~~si~~~~S~f~~el~~l~~~l~~~~~~  109 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRR  109 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEcCCcEEeeeeeeeeeeCCccChhhccchHHHHHHHHHHHHHhCCCC
Confidence            6789999999999999999883     233211         1101111111           1   2233334445689


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      ++++|||+..-.+
T Consensus       110 slvllDE~~~gtd  122 (213)
T cd03281         110 SLVLIDEFGKGTD  122 (213)
T ss_pred             cEEEeccccCCCC
Confidence            9999999987664

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

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.86  E-value=0.00074  Score=58.61  Aligned_cols=28  Identities=29%  Similarity=0.579  Sum_probs=24.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++++|.||||||+++..++ .+|++++.+
T Consensus         3 I~ITGTPGvGKTT~~~~L~-~lg~~~i~l   30 (180)
T COG1936           3 IAITGTPGVGKTTVCKLLR-ELGYKVIEL   30 (180)
T ss_pred             EEEeCCCCCchHHHHHHHH-HhCCceeeH
Confidence            6799999999999999999 888876655

>TIGR01351 adk adenylate kinases

Probab=96.85  E-value=0.00099  Score=59.77  Aligned_cols=29  Identities=28%  Similarity=0.531  Sum_probs=25.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +++.||||+|||++++.+|..+|+..+..
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            68999999999999999999998776544

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.

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.84  E-value=0.00074  Score=54.68  Aligned_cols=22  Identities=32%  Similarity=0.566  Sum_probs=20.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++|.|+||+|||++++.++..+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            5799999999999999999996

...

>PRK09862 putative ATP-dependent protease; Provisional

Probab=96.82  E-value=0.0012  Score=66.90  Aligned_cols=47  Identities=28%  Similarity=0.382  Sum_probs=32.4

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .|..+.+....++.+.-.+  .....++|.||||+|||++++.++..+.
T Consensus       189 d~~~v~Gq~~~~~al~laa--~~G~~llliG~~GsGKTtLak~L~gllp  235 (506)
T PRK09862        189 DLSDVIGQEQGKRGLEITA--AGGHNLLLIGPPGTGKTMLASRINGLLP  235 (506)
T ss_pred             CeEEEECcHHHHhhhheec--cCCcEEEEECCCCCcHHHHHHHHhccCC
Confidence            5666666555444432111  3345689999999999999999998663

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.81  E-value=0.0016  Score=61.04  Aligned_cols=61  Identities=25%  Similarity=0.353  Sum_probs=34.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC----------CchHHHHHHH-----hcCCCcEEEEcCCCcc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE----------GNKHLRKVLI-----ATENKSILVVGDIDCC  291 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~----------~~~~l~~~l~-----~~~~~~Il~iDeiD~~  291 (338)
                      ++|+|.||+|||++++.++.++   +..+..++...+.          .+..++..+.     .+.+..|||+|+..-+
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls~~~iVI~Dd~nYi   82 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALSKDTIVILDDNNYI   82 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHTT-SEEEE-S---S
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhccCeEEEEeCCchH
Confidence            6899999999999999999986   5667666643322          1223333222     2256799999998754

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.81  E-value=0.0047  Score=58.19  Aligned_cols=54  Identities=28%  Similarity=0.468  Sum_probs=39.0

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCce-eeeCCCCCCcHHHHHHHHHHhCC
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGY-LLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~-LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ....+|.+ ..+|+.+..++-+.+ +    . ..++|+ |+.||+|+|||+.++||-++++.
T Consensus        97 vlR~Ip~~-i~~~e~LglP~i~~~-~----~-~~~~GLILVTGpTGSGKSTTlAamId~iN~  151 (353)
T COG2805          97 VLRLIPSK-IPTLEELGLPPIVRE-L----A-ESPRGLILVTGPTGSGKSTTLAAMIDYINK  151 (353)
T ss_pred             EEeccCcc-CCCHHHcCCCHHHHH-H----H-hCCCceEEEeCCCCCcHHHHHHHHHHHHhc
Confidence            34455533 448999988875444 2    2 234675 78999999999999999999963

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.81  E-value=0.0012  Score=59.54  Aligned_cols=29  Identities=28%  Similarity=0.501  Sum_probs=25.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++++||||+|||++++.+|..+++..+.+
T Consensus         3 I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            78999999999999999999999776554

>PTZ00202 tuzin; Provisional

Probab=96.78  E-value=0.0041  Score=61.77  Aligned_cols=62  Identities=19%  Similarity=0.206  Sum_probs=48.3

Q ss_pred             CCCccccccCChhHHHHHHHHHHh---hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER---AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS  263 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~---~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~  263 (338)
                      -|.....+++.+....++...+..   ..++-..|.||+|||||++++.++..++...+.+|...
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNprg  321 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVRG  321 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCCC
Confidence            344566778888777777776654   22345689999999999999999999998888888773

>TIGR02012 tigrfam_recA protein RecA

Probab=96.77  E-value=0.0034  Score=60.19  Aligned_cols=65  Identities=14%  Similarity=0.160  Sum_probs=41.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHHH---hcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVLI---ATENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l~---~~~~~~  281 (338)
                      +-++++||||||||+|+..++...   +..+.+++.....+                     .++....+.   +.....
T Consensus        56 ~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~~~~~~  135 (321)
T TIGR02012        56 RIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVD  135 (321)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhccCCc
Confidence            346899999999999977766544   55666665543111                     111111111   224688


Q ss_pred             EEEEcCCCccCC
Q 035959          282 ILVVGDIDCCTE  293 (338)
Q Consensus       282 Il~iDeiD~~~~  293 (338)
                      +||||-|.++.+
T Consensus       136 lIVIDSv~al~~  147 (321)
T TIGR02012       136 IIVVDSVAALVP  147 (321)
T ss_pred             EEEEcchhhhcc
Confidence            999999999875

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.

>PRK04182 cytidylate kinase; Provisional

Probab=96.76  E-value=0.0013  Score=56.73  Aligned_cols=29  Identities=28%  Similarity=0.520  Sum_probs=26.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +.|.|+||+|||++++++|..+|+++++.
T Consensus         3 I~i~G~~GsGKstia~~la~~lg~~~id~   31 (180)
T PRK04182          3 ITISGPPGSGKTTVARLLAEKLGLKHVSA   31 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCcEecH
Confidence            67999999999999999999999988763

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.75  E-value=0.001  Score=64.92  Aligned_cols=36  Identities=36%  Similarity=0.653  Sum_probs=27.0

Q ss_pred             HHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          219 IMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       219 i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      +++.+....+..+++.||.|||||++++++...+..
T Consensus        13 v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   13 VIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             HHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            333343344566789999999999999999988843

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK14527 adenylate kinase; Provisional

Probab=96.75  E-value=0.001  Score=58.77  Aligned_cols=29  Identities=28%  Similarity=0.568  Sum_probs=25.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      .-+++.||||+|||++++.+|+.++...+
T Consensus         7 ~~i~i~G~pGsGKsT~a~~La~~~~~~~i   35 (191)
T PRK14527          7 KVVIFLGPPGAGKGTQAERLAQELGLKKL   35 (191)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCCC
Confidence            45789999999999999999999886544

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=96.73  E-value=0.001  Score=57.11  Aligned_cols=26  Identities=38%  Similarity=0.626  Sum_probs=20.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      +.|.|+||||||+|++++++. |++++
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            579999999999999999999 76654

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.72  E-value=0.0015  Score=55.99  Aligned_cols=29  Identities=28%  Similarity=0.589  Sum_probs=26.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +.+.|++|+|||++++.+|+.++++++..
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~~~   31 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLISA   31 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCceecH
Confidence            57999999999999999999999887765

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.

>PLN02200 adenylate kinase family protein

Probab=96.72  E-value=0.0015  Score=59.86  Aligned_cols=28  Identities=21%  Similarity=0.396  Sum_probs=24.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDV  256 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~  256 (338)
                      .-+++.||||+|||++++.+|..+|+..
T Consensus        44 ~ii~I~G~PGSGKsT~a~~La~~~g~~h   71 (234)
T PLN02200         44 FITFVLGGPGSGKGTQCEKIVETFGFKH   71 (234)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            3568999999999999999999998754

>PRK06696 uridine kinase; Validated

Probab=96.71  E-value=0.0051  Score=55.76  Aligned_cols=36  Identities=14%  Similarity=0.200  Sum_probs=28.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE  265 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~  265 (338)
                      -+.+.|++|+|||++++.++..+   |.+++.+.+.+..
T Consensus        24 iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~   62 (223)
T PRK06696         24 RVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFH   62 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecccccc
Confidence            35699999999999999999998   6667766655443

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=96.70  E-value=0.0013  Score=59.30  Aligned_cols=22  Identities=36%  Similarity=0.628  Sum_probs=19.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++++|+||+|||++++.++...
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc
Confidence            4789999999999999999883

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

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.69  E-value=0.0016  Score=57.15  Aligned_cols=26  Identities=42%  Similarity=0.767  Sum_probs=22.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      .+++.||||+||||+|+.+|+.++.+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~   27 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLP   27 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCc
Confidence            37899999999999999999996544

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.69  E-value=0.002  Score=54.70  Aligned_cols=31  Identities=35%  Similarity=0.446  Sum_probs=26.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      +++.|+||+|||+++++++..+   +..++.++.
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~~   35 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLDG   35 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcC
Confidence            5789999999999999999998   666666654

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.69  E-value=0.006  Score=54.93  Aligned_cols=34  Identities=24%  Similarity=0.211  Sum_probs=26.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---C------CcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---H------FDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~------~~~~~l~~~~  263 (338)
                      -+.|+||||+|||+++..+|...   +      ..+++++...
T Consensus        21 v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          21 ITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             EEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            36899999999999999988654   2      5667777654

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.69  E-value=0.0075  Score=59.32  Aligned_cols=64  Identities=17%  Similarity=0.219  Sum_probs=42.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC----------------------CchHHHHHHHhcC---CC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE----------------------GNKHLRKVLIATE---NK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~----------------------~~~~l~~~l~~~~---~~  280 (338)
                      +-++|.||+|+|||+++..+|..+   +..+..+++....                      +...+.+.+..+.   ..
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~~~  321 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEARV  321 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhccCC
Confidence            457899999999999999999877   4455555543321                      1234445554443   35


Q ss_pred             cEEEEcCCCccC
Q 035959          281 SILVVGDIDCCT  292 (338)
Q Consensus       281 ~Il~iDeiD~~~  292 (338)
                      ++||||-.-...
T Consensus       322 DvVLIDTaGRs~  333 (436)
T PRK11889        322 DYILIDTAGKNY  333 (436)
T ss_pred             CEEEEeCccccC
Confidence            888888665543

>PRK04040 adenylate kinase; Provisional

Probab=96.68  E-value=0.0016  Score=57.66  Aligned_cols=33  Identities=18%  Similarity=0.516  Sum_probs=26.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh--CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL--HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l--~~~~~~l~~~~  263 (338)
                      .-++++|+||+|||++++.++..+  ++.+  ++..+
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~--~~~g~   37 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLKEDYKI--VNFGD   37 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhccCCeE--Eecch
Confidence            347899999999999999999999  5554  44444

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=96.67  E-value=0.0011  Score=56.16  Aligned_cols=26  Identities=27%  Similarity=0.548  Sum_probs=22.5

Q ss_pred             eeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          233 LFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       233 L~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      +.||||+|||++++.+|..+|+..+.
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            57999999999999999999875443

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 ....

>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=96.67  E-value=0.0029  Score=56.12  Aligned_cols=66  Identities=21%  Similarity=0.245  Sum_probs=32.6

Q ss_pred             eeeeCCCCCCcHHHHHHH-HHHh---CCcEEEEecCCcC-----C--c------------------hHHHHHHHhcCCCc
Q 035959          231 YLLFGPPGTGKSSLIAAM-ANYL---HFDVYDLELSSVE-----G--N------------------KHLRKVLIATENKS  281 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~ai-a~~l---~~~~~~l~~~~~~-----~--~------------------~~l~~~l~~~~~~~  281 (338)
                      ++++|.||+|||..+... ....   |.+++. +...+.     .  .                  .+-.......+..+
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            578999999999987665 4332   455443 433222     0  0                  00111222233789


Q ss_pred             EEEEcCCCccCCcccccc
Q 035959          282 ILVVGDIDCCTELQDRSA  299 (338)
Q Consensus       282 Il~iDeiD~~~~~~~r~~  299 (338)
                      ||||||++...+  .|..
T Consensus        82 liviDEa~~~~~--~r~~   97 (193)
T PF05707_consen   82 LIVIDEAQNFFP--SRSW   97 (193)
T ss_dssp             EEEETTGGGTSB-----T
T ss_pred             EEEEECChhhcC--CCcc
Confidence            999999999988  5544

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.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.66  E-value=0.003  Score=56.51  Aligned_cols=24  Identities=33%  Similarity=0.559  Sum_probs=21.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -++|.|+||+|||++++.+|+.+.
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L~   26 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKELR   26 (261)
T ss_pred             eEEEecCCCCCchHHHHHHHHHHH
Confidence            368999999999999999999984

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.65  E-value=0.0053  Score=60.70  Aligned_cols=64  Identities=19%  Similarity=0.357  Sum_probs=44.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC-CchHHH---HHHHhcC--CCcEEEEcCCCccCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE-GNKHLR---KVLIATE--NKSILVVGDIDCCTE  293 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~-~~~~l~---~~l~~~~--~~~Il~iDeiD~~~~  293 (338)
                      -++++||.+||||++++-+...+.-.++.++..++. ...++.   +.+....  .+..+|||||++.-+
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~~~l~d~~~~~~~~~~~~~~yifLDEIq~v~~  108 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLDEIQNVPD  108 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcchhhHHHHHHHHHHhhccCCceEEEecccCchh
Confidence            678999999999999988888776555555555444 333332   2222222  458999999999864

>PF06431 Polyoma_lg_T_C: Polyomavirus large T antigen C-terminus; InterPro: IPR010932 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []

Probab=96.65  E-value=0.003  Score=60.91  Aligned_cols=71  Identities=23%  Similarity=0.257  Sum_probs=45.6

Q ss_pred             HHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCcc
Q 035959          217 KMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCC  291 (338)
Q Consensus       217 ~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~  291 (338)
                      -++++.+..  |.+|.+|+-||-.||||++|+|+-+.+|-....|++..    +.|.--|.-+-..=.+++||+---
T Consensus       142 ~~iL~~lv~N~PKkRy~lFkGPvNsGKTTlAAAlLdL~gG~~LNvN~p~----dkl~FELG~AiDQfmVvFEDVKGq  214 (417)
T PF06431_consen  142 LEILKCLVENIPKKRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQ  214 (417)
T ss_dssp             HHHHHHHHHTBTTB-EEEEE-STTSSHHHHHHHHHHHH-EEEE-TSS-T----TTHHHHHCCCTT-SEEEEEEE--S
T ss_pred             HHHHHHHhcCCCcceeEEEecCcCCchHHHHHHHHHhcCCceeecCCCh----hhcchhhheeeceEEEEEEecCCC
Confidence            344444444  77789999999999999999999999998888887754    233333333346678888888654

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.65  E-value=0.0078  Score=57.74  Aligned_cols=65  Identities=23%  Similarity=0.381  Sum_probs=40.9

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEec-CCcC------------CchHHHHHHHhc--CCCcEEEEc
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLEL-SSVE------------GNKHLRKVLIAT--ENKSILVVG  286 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~-~~~~------------~~~~l~~~l~~~--~~~~Il~iD  286 (338)
                      .+..+++.|++|+|||+++.|++.+.     ...++.++- .++.            ..-.+.+++..+  -.|+.|++.
T Consensus       147 ~~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El~~~~~~~v~~~~~~~~~~~~ll~~aLR~~PD~IivG  226 (319)
T PRK13894        147 AHRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYVQYHTSIDVNMTALLKTTLRMRPDRILVG  226 (319)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCccccCCCCEEEEecCCCCCHHHHHHHHhcCCCCEEEEe
Confidence            35779999999999999999999874     122222211 1110            012344444443  378999999


Q ss_pred             CCCcc
Q 035959          287 DIDCC  291 (338)
Q Consensus       287 eiD~~  291 (338)
                      ||-.-
T Consensus       227 EiR~~  231 (319)
T PRK13894        227 EVRGP  231 (319)
T ss_pred             ccCCH
Confidence            98753

>PLN02199 shikimate kinase

Probab=96.65  E-value=0.0031  Score=59.63  Aligned_cols=34  Identities=26%  Similarity=0.480  Sum_probs=31.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .+.++|.|.+|+|||++++.+|+.+|+++++.|.
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD~  135 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCDT  135 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEehHH
Confidence            5689999999999999999999999999988764

>PRK01184 hypothetical protein; Provisional

Probab=96.64  E-value=0.0018  Score=56.67  Aligned_cols=29  Identities=24%  Similarity=0.332  Sum_probs=24.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|.||||+|||+++. ++..+|++++..
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            36799999999999876 788899887654

>TIGR00767 rho transcription termination factor Rho

Probab=96.63  E-value=0.0041  Score=61.18  Aligned_cols=24  Identities=29%  Similarity=0.549  Sum_probs=21.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+++.||||+|||+|++++++.+.
T Consensus       170 ~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       170 RGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             EEEEECCCCCChhHHHHHHHHhhc
Confidence            379999999999999999999864

Members of this family differ in the specificity of RNA binding.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.61  E-value=0.0018  Score=61.04  Aligned_cols=29  Identities=28%  Similarity=0.265  Sum_probs=24.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh-CCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL-HFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l-~~~~~  257 (338)
                      .-+++.||||||||++++.++..+ +..++
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l   32 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNV   32 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEE
Confidence            457899999999999999999998 55443

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.61  E-value=0.0063  Score=58.42  Aligned_cols=62  Identities=19%  Similarity=0.335  Sum_probs=40.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecC-CcC------------CchHHHHHHHhc--CCCcEEEEcC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELS-SVE------------GNKHLRKVLIAT--ENKSILVVGD  287 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~-~~~------------~~~~l~~~l~~~--~~~~Il~iDe  287 (338)
                      +.++++.|++|+|||+++.|++.++.     ..++.++-. ++.            ..-.+.+++..+  ..|+.|++-|
T Consensus       144 ~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El~~~~~n~v~l~~~~~~~~~~lv~~aLR~~PD~IivGE  223 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEIQCAAENAVALHTSDTVDMARLLKSTMRLRPDRIIVGE  223 (323)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCcccccCCCCEEEeccCCCcCHHHHHHHHhCCCCCEEEEee
Confidence            56799999999999999999998762     233333211 111            011344444433  3789999988


Q ss_pred             CC
Q 035959          288 ID  289 (338)
Q Consensus       288 iD  289 (338)
                      |-
T Consensus       224 iR  225 (323)
T PRK13833        224 VR  225 (323)
T ss_pred             cC
Confidence            84

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.58  E-value=0.0052  Score=61.42  Aligned_cols=65  Identities=17%  Similarity=0.257  Sum_probs=43.5

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC--c------------------------hHHHHHHHhcC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG--N------------------------KHLRKVLIATE  278 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~--~------------------------~~l~~~l~~~~  278 (338)
                      +.-++++|+||+|||+++..+|..+   |..+..+++.....  .                        ..+.+.+....
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al~~~~  174 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLEKFK  174 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHHhh
Confidence            3457899999999999999999877   55666665543221  0                        11234444444


Q ss_pred             CCcEEEEcCCCccC
Q 035959          279 NKSILVVGDIDCCT  292 (338)
Q Consensus       279 ~~~Il~iDeiD~~~  292 (338)
                      ...+|+||..-...
T Consensus       175 ~~DvVIIDTAGr~~  188 (437)
T PRK00771        175 KADVIIVDTAGRHA  188 (437)
T ss_pred             cCCEEEEECCCccc
Confidence            56889998886553

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=96.58  E-value=0.007  Score=49.95  Aligned_cols=64  Identities=23%  Similarity=0.301  Sum_probs=42.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC--------------------cEEEEecCCcCCchHHHHH--HHhcCCCcEEEEcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF--------------------DVYDLELSSVEGNKHLRKV--LIATENKSILVVGD  287 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~--------------------~~~~l~~~~~~~~~~l~~~--l~~~~~~~Il~iDe  287 (338)
                      -++|.|+=|+|||++++++|..+|.                    +++-+|+-.+.+..++..+  +.......|.+||=
T Consensus        17 vi~L~GdLGaGKTtf~r~l~~~lg~~~~V~SPTF~l~~~Y~~~~~~l~H~DLYRl~~~~e~~~~g~~e~~~~~~i~~IEW   96 (123)
T PF02367_consen   17 VILLSGDLGAGKTTFVRGLARALGIDEEVTSPTFSLVNEYEGGNIPLYHFDLYRLEDPEELEDLGLEEYLFEDGICVIEW   96 (123)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT--S----TTTTSEEEEEETTEEEEEEE-TT-SSTHHHHHCTTTTCSSSSEEEEEES
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCCCcCCCCeEEEEEecCCCceEEEeeccccCCHHHHHHCCchhhhCCCCEEEEEC
Confidence            4689999999999999999999963                    3444555555555544332  22334688888876


Q ss_pred             CCccCC
Q 035959          288 IDCCTE  293 (338)
Q Consensus       288 iD~~~~  293 (338)
                      -+.+..
T Consensus        97 ~e~~~~  102 (123)
T PF02367_consen   97 PERLKE  102 (123)
T ss_dssp             GGGGTT
T ss_pred             cccccc
Confidence            655543

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.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.56  E-value=0.0018  Score=56.87  Aligned_cols=30  Identities=33%  Similarity=0.516  Sum_probs=25.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      ..+.|.||+|+|||++++.++..++.++..
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~~~~~~   32 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQTQLLV   32 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCCCeEEE
Confidence            357899999999999999999988765443

>PRK14526 adenylate kinase; Provisional

Probab=96.56  E-value=0.0022  Score=57.88  Aligned_cols=27  Identities=30%  Similarity=0.716  Sum_probs=24.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      ++|.||||+|||++++.+|..++...+
T Consensus         3 i~l~G~pGsGKsT~a~~La~~~~~~~i   29 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNELNYYHI   29 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcee
Confidence            789999999999999999999886543

>PRK08233 hypothetical protein; Provisional

Probab=96.55  E-value=0.0026  Score=55.00  Aligned_cols=23  Identities=22%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.+.|+||+|||+++..++..++
T Consensus         6 I~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          6 ITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             EEEECCCCCCHHHHHHHHHhhCC
Confidence            56889999999999999999985

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

Probab=96.55  E-value=0.0052  Score=58.76  Aligned_cols=39  Identities=21%  Similarity=0.389  Sum_probs=35.1

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE  265 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~  265 (338)
                      .|.++|+.||+|+|||-+++-+|+..+.|++.+..+...
T Consensus        49 ~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATKfT   87 (444)
T COG1220          49 TPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFT   87 (444)
T ss_pred             CccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeeeee
Confidence            367899999999999999999999999999999887644

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.54  E-value=0.0052  Score=58.97  Aligned_cols=64  Identities=13%  Similarity=0.137  Sum_probs=42.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC---------------------CchHHHHHHH---hcCCCcE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE---------------------GNKHLRKVLI---ATENKSI  282 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~---------------------~~~~l~~~l~---~~~~~~I  282 (338)
                      -+.++||||||||+|+..++...   +..+.+++...-.                     +.+++..++.   ......+
T Consensus        57 iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~s~~~~l  136 (325)
T cd00983          57 IIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSLVRSGAVDL  136 (325)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHHHhccCCCE
Confidence            36899999999999998877544   5667777664311                     1111222222   2246899


Q ss_pred             EEEcCCCccCC
Q 035959          283 LVVGDIDCCTE  293 (338)
Q Consensus       283 l~iDeiD~~~~  293 (338)
                      ||||-|-++.+
T Consensus       137 IVIDSvaal~~  147 (325)
T cd00983         137 IVVDSVAALVP  147 (325)
T ss_pred             EEEcchHhhcc
Confidence            99999999875

RecA couples ATP hydrolysis to DNA strand exchange.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.52  E-value=0.011  Score=62.83  Aligned_cols=79  Identities=16%  Similarity=0.258  Sum_probs=47.1

Q ss_pred             CChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---C--CcEEEEecCCcC----------CchHHHHHHH
Q 035959          211 MDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---H--FDVYDLELSSVE----------GNKHLRKVLI  275 (338)
Q Consensus       211 ~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~--~~~~~l~~~~~~----------~~~~l~~~l~  275 (338)
                      ..+..++.+...+.   .+-.+|.|+||||||++++++...+   +  ..++.+-.+.-.          ....+.+++.
T Consensus       324 l~~~Q~~Ai~~~~~---~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~g~~a~Tih~lL~  400 (720)
T TIGR01448       324 LSEEQKQALDTAIQ---HKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEVTGLTASTIHRLLG  400 (720)
T ss_pred             CCHHHHHHHHHHHh---CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHhcCCccccHHHHhh
Confidence            45555554444332   3467899999999999999987765   3  344433322110          1123444443


Q ss_pred             hc------------CCCcEEEEcCCCccC
Q 035959          276 AT------------ENKSILVVGDIDCCT  292 (338)
Q Consensus       276 ~~------------~~~~Il~iDeiD~~~  292 (338)
                      ..            ....+|||||+..+.
T Consensus       401 ~~~~~~~~~~~~~~~~~~llIvDEaSMvd  429 (720)
T TIGR01448       401 YGPDTFRHNHLEDPIDCDLLIVDESSMMD  429 (720)
T ss_pred             ccCCccchhhhhccccCCEEEEeccccCC
Confidence            21            246899999998774

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.

>cd01394 radB RadB

Probab=96.50  E-value=0.0053  Score=55.13  Aligned_cols=33  Identities=27%  Similarity=0.423  Sum_probs=27.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      -++++||||+|||+++..+|...   +.++.+++..
T Consensus        21 i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~e   56 (218)
T cd01394          21 VTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTE   56 (218)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            37899999999999999988765   5677777654

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=96.49  E-value=0.0037  Score=53.44  Aligned_cols=44  Identities=23%  Similarity=0.343  Sum_probs=33.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKV  273 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~  273 (338)
                      +..+++.|+.|+|||+++++++.+++.++++  ..++.+.++..++
T Consensus        12 k~~i~vmGvsGsGKSTigk~L~~~l~~~F~d--gDd~Hp~~NveKM   55 (191)
T KOG3354|consen   12 KYVIVVMGVSGSGKSTIGKALSEELGLKFID--GDDLHPPANVEKM   55 (191)
T ss_pred             ceeEEEEecCCCChhhHHHHHHHHhCCcccc--cccCCCHHHHHHH
Confidence            4567899999999999999999999988754  4455544444333

>PRK10436 hypothetical protein; Provisional

Probab=96.48  E-value=0.016  Score=58.30  Aligned_cols=86  Identities=23%  Similarity=0.432  Sum_probs=55.1

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCc-eeeeCCCCCCcHHHHHHHHHHhCC---cEEEEe------cCCcC-----C--
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRG-YLLFGPPGTGKSSLIAAMANYLHF---DVYDLE------LSSVE-----G--  266 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g-~LL~GppGtGKT~l~~aia~~l~~---~~~~l~------~~~~~-----~--  266 (338)
                      .+++++++.+...+.+.+.+..  +.| +|+.||+|+|||+++.|+..+++.   .++.++      +..+.     .  
T Consensus       195 ~~L~~LG~~~~~~~~l~~~~~~--~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE~~l~gi~Q~~v~~~~  272 (462)
T PRK10436        195 LDLETLGMTPAQLAQFRQALQQ--PQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVEIPLAGINQTQIHPKA  272 (462)
T ss_pred             CCHHHcCcCHHHHHHHHHHHHh--cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCccccCCCcceEeeCCcc
Confidence            4789999988766666655543  345 689999999999999888777742   233332      11111     0  


Q ss_pred             chHHHHHHHhc--CCCcEEEEcCCCcc
Q 035959          267 NKHLRKVLIAT--ENKSILVVGDIDCC  291 (338)
Q Consensus       267 ~~~l~~~l~~~--~~~~Il~iDeiD~~  291 (338)
                      .......+...  ..|++|+|.||-..
T Consensus       273 g~~f~~~lr~~LR~dPDvI~vGEIRD~  299 (462)
T PRK10436        273 GLTFQRVLRALLRQDPDVIMVGEIRDG  299 (462)
T ss_pred             CcCHHHHHHHHhcCCCCEEEECCCCCH
Confidence            11233444333  37999999998754

>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=96.45  E-value=0.011  Score=50.33  Aligned_cols=65  Identities=22%  Similarity=0.305  Sum_probs=40.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCc--EEEEecCCc-----------------CCchHHHHHHH---hcCCCcEEEEc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFD--VYDLELSSV-----------------EGNKHLRKVLI---ATENKSILVVG  286 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~--~~~l~~~~~-----------------~~~~~l~~~l~---~~~~~~Il~iD  286 (338)
                      .-+.|.||+|+|||+|+++++..+...  -+.++...+                 .+..+.+++..   -+.++.++++|
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~r~~l~~~l~~~~~i~ilD  105 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARALLLNPDLLLLD  105 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCCccEEEECCEEcccCCHHHHHhceEEEeeCCHHHHHHHHHHHHHhcCCCEEEEe
Confidence            457899999999999999999876422  112221111                 11122222211   12478999999


Q ss_pred             CCCccCC
Q 035959          287 DIDCCTE  293 (338)
Q Consensus       287 eiD~~~~  293 (338)
                      |...-.+
T Consensus       106 Ep~~~lD  112 (157)
T cd00267         106 EPTSGLD  112 (157)
T ss_pred             CCCcCCC
Confidence            9998776

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.45  E-value=0.015  Score=59.09  Aligned_cols=87  Identities=23%  Similarity=0.364  Sum_probs=55.8

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCc-eeeeCCCCCCcHHHHHHHHHHhC---CcEEEEec------CCcC-----C-
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRG-YLLFGPPGTGKSSLIAAMANYLH---FDVYDLEL------SSVE-----G-  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g-~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~------~~~~-----~-  266 (338)
                      +.+++++.+.++..+.+...+..  +.| +++.||+|+|||+++.++.+++.   ..++.++-      ..+.     . 
T Consensus       218 ~~~l~~Lg~~~~~~~~l~~~~~~--~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~~~~~~~q~~v~~~  295 (486)
T TIGR02533       218 RLDLETLGMSPELLSRFERLIRR--PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEYQIEGIGQIQVNPK  295 (486)
T ss_pred             CCCHHHcCCCHHHHHHHHHHHhc--CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeeeecCCCceEEEccc
Confidence            45788999888877766665542  355 58999999999999998887774   23333321      1111     0 


Q ss_pred             -chHHHHHHHhc--CCCcEEEEcCCCcc
Q 035959          267 -NKHLRKVLIAT--ENKSILVVGDIDCC  291 (338)
Q Consensus       267 -~~~l~~~l~~~--~~~~Il~iDeiD~~  291 (338)
                       .......+..+  ..|++|++.||-.-
T Consensus       296 ~g~~f~~~lr~~LR~dPDvI~vGEiRd~  323 (486)
T TIGR02533       296 IGLTFAAGLRAILRQDPDIIMVGEIRDL  323 (486)
T ss_pred             cCccHHHHHHHHHhcCCCEEEEeCCCCH
Confidence             01222333322  37999999998754

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=96.45  E-value=0.0081  Score=59.63  Aligned_cols=117  Identities=20%  Similarity=0.230  Sum_probs=67.7

Q ss_pred             ccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCcCCchHH-------
Q 035959          207 DTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSVEGNKHL-------  270 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~~~~~~l-------  270 (338)
                      .++.+.+.....+.+.+..    ...+.+++.|-||||||-+..-+-..+.     ...++++|.++.....+       
T Consensus       150 ~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI~~~  229 (529)
T KOG2227|consen  150 GTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKIFSS  229 (529)
T ss_pred             CCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHHHHH
Confidence            3455555555555444444    3446689999999999998876655542     35588999886642111       


Q ss_pred             --------------HHHHHh-c---CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhc
Q 035959          271 --------------RKVLIA-T---ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTD  326 (338)
Q Consensus       271 --------------~~~l~~-~---~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iD  326 (338)
                                    .+.|.. .   ...-++++||+|.+..   |+...-..--....-..++..|-|+-|.+|
T Consensus       230 ~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~t---r~~~vLy~lFewp~lp~sr~iLiGiANslD  300 (529)
T KOG2227|consen  230 LLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLIT---RSQTVLYTLFEWPKLPNSRIILIGIANSLD  300 (529)
T ss_pred             HHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhh---cccceeeeehhcccCCcceeeeeeehhhhh
Confidence                          111111 1   2367999999999985   221110000011123455677777777776

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.43  E-value=0.013  Score=57.50  Aligned_cols=35  Identities=23%  Similarity=0.266  Sum_probs=27.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      +-++|.||+|+|||+++..+|..+   +..+..+++..
T Consensus       207 ~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDt  244 (407)
T PRK12726        207 RIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDT  244 (407)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCc
Confidence            446899999999999999999876   45565565544

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.43  E-value=0.017  Score=59.76  Aligned_cols=87  Identities=23%  Similarity=0.447  Sum_probs=55.8

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCc-eeeeCCCCCCcHHHHHHHHHHhCC---cEEEEe------cCCcC-----C--
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRG-YLLFGPPGTGKSSLIAAMANYLHF---DVYDLE------LSSVE-----G--  266 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g-~LL~GppGtGKT~l~~aia~~l~~---~~~~l~------~~~~~-----~--  266 (338)
                      .+++++++.++..+.+.+.+..  +.| +|+.||+|+|||+++.++.++++.   .++.++      +..+.     .  
T Consensus       293 ~~l~~lg~~~~~~~~l~~~~~~--~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~~~~~~q~~v~~~~  370 (564)
T TIGR02538       293 LDIDKLGFEPDQKALFLEAIHK--PQGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINLPGINQVNVNPKI  370 (564)
T ss_pred             CCHHHcCCCHHHHHHHHHHHHh--cCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceecCCCceEEEecccc
Confidence            4788999988877777655543  345 589999999999999888888742   233221      11111     0  


Q ss_pred             chHHHHHHHhc--CCCcEEEEcCCCccC
Q 035959          267 NKHLRKVLIAT--ENKSILVVGDIDCCT  292 (338)
Q Consensus       267 ~~~l~~~l~~~--~~~~Il~iDeiD~~~  292 (338)
                      .......+...  ..|++|++.||..--
T Consensus       371 g~~~~~~l~~~LR~dPDvI~vGEiRd~e  398 (564)
T TIGR02538       371 GLTFAAALRSFLRQDPDIIMVGEIRDLE  398 (564)
T ss_pred             CCCHHHHHHHHhccCCCEEEeCCCCCHH
Confidence            11233333333  379999999997543

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=96.42  E-value=0.0055  Score=51.70  Aligned_cols=65  Identities=22%  Similarity=0.258  Sum_probs=40.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCc---EE-----EEecCCcCCchHHHHHHH---hcCCCcEEEEcCCCccCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFD---VY-----DLELSSVEGNKHLRKVLI---ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~---~~-----~l~~~~~~~~~~l~~~l~---~~~~~~Il~iDeiD~~~~  293 (338)
                      ..+.+.||+|+|||+|+++++......   ++     .+....-.+....+++..   -+.++.++++||-..-.+
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~~i~~~~~lS~G~~~rv~laral~~~p~illlDEP~~~LD  102 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQLSGGEKMRLALAKLLLENPNLLLLDEPTNHLD  102 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCeEEEEEEccCCHHHHHHHHHHHHHhcCCCEEEEeCCccCCC
Confidence            457899999999999999999876321   10     111100022333333322   124899999999887765

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.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.42  E-value=0.011  Score=51.90  Aligned_cols=63  Identities=17%  Similarity=0.220  Sum_probs=40.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHH-----HhCCcE--------------EEEecCCcCC---------chHHHHHHHhcCCCcE
Q 035959          231 YLLFGPPGTGKSSLIAAMAN-----YLHFDV--------------YDLELSSVEG---------NKHLRKVLIATENKSI  282 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~-----~l~~~~--------------~~l~~~~~~~---------~~~l~~~l~~~~~~~I  282 (338)
                      ++|+||.|.|||++++.++-     +.|..+              ..+...+-..         -.++..++..+..+++
T Consensus         2 ~~ltG~N~~GKst~l~~i~~~~~la~~G~~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~~l   81 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGLIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATENSL   81 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHHHhCCCeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCCeE
Confidence            68999999999999999883     233211              1111111110         1234455566668999


Q ss_pred             EEEcCCCccCC
Q 035959          283 LVVGDIDCCTE  293 (338)
Q Consensus       283 l~iDeiD~~~~  293 (338)
                      +++||.-.-.+
T Consensus        82 lllDEp~~g~d   92 (185)
T smart00534       82 VLLDELGRGTS   92 (185)
T ss_pred             EEEecCCCCCC
Confidence            99999987665

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=96.40  E-value=0.0094  Score=53.85  Aligned_cols=35  Identities=26%  Similarity=0.357  Sum_probs=25.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~  263 (338)
                      .-+|+.||||||||.++..++...    |.+++++...+
T Consensus        20 s~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee   58 (226)
T PF06745_consen   20 SVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEE   58 (226)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS
T ss_pred             cEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecC
Confidence            457999999999999988766433    78888887654

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 ....

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=96.40  E-value=0.0026  Score=55.30  Aligned_cols=22  Identities=36%  Similarity=0.789  Sum_probs=19.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++|+|+||+||||+++.++..+
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            7899999999999999999988

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.37  E-value=0.0072  Score=58.98  Aligned_cols=23  Identities=30%  Similarity=0.556  Sum_probs=21.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .++.||||||||+|++.+++.+.
T Consensus       136 ~LIvG~pGtGKTTLl~~la~~i~  158 (380)
T PRK12608        136 GLIVAPPRAGKTVLLQQIAAAVA  158 (380)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            69999999999999999998773

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.37  E-value=0.015  Score=52.53  Aligned_cols=34  Identities=24%  Similarity=0.101  Sum_probs=26.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      ..+++.||||+|||+++..++...   +..+..+++.
T Consensus        21 ~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~e   57 (229)
T TIGR03881        21 FFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTTE   57 (229)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            457899999999999998876533   5667777764

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.

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

Probab=96.37  E-value=0.014  Score=62.66  Aligned_cols=88  Identities=20%  Similarity=0.402  Sum_probs=67.6

Q ss_pred             cccccCC-hhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC--------
Q 035959          206 FDTLAMD-TDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG--------  266 (338)
Q Consensus       206 f~~l~~~-~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~--------  266 (338)
                      ++.+++. ++.-+++++-|.+..+++-+|.|.||+|||.++.-+|+..          +..++.+++..+..        
T Consensus       185 ldPvigr~deeirRvi~iL~Rrtk~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~  264 (898)
T KOG1051|consen  185 LDPVIGRHDEEIRRVIEILSRKTKNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEF  264 (898)
T ss_pred             CCCccCCchHHHHHHHHHHhccCCCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHH
Confidence            4556665 5666778888888777899999999999999999999877          24567777765543        


Q ss_pred             chHHHHHHHh---cCCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIA---TENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~---~~~~~Il~iDeiD~~~~  293 (338)
                      +..+..++..   .....||+|||++++..
T Consensus       265 E~rlk~l~k~v~~~~~gvILfigelh~lvg  294 (898)
T KOG1051|consen  265 EERLKELLKEVESGGGGVILFLGELHWLVG  294 (898)
T ss_pred             HHHHHHHHHHHhcCCCcEEEEecceeeeec
Confidence            3456666665   34789999999999987

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.36  E-value=0.0034  Score=56.04  Aligned_cols=28  Identities=29%  Similarity=0.388  Sum_probs=24.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDV  256 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~  256 (338)
                      .-+++.|+||+|||++++.+|..++...
T Consensus         4 ~~i~i~G~~G~GKst~a~~l~~~~~~~~   31 (197)
T PRK12339          4 TIHFIGGIPGVGKTSISGYIARHRAIDI   31 (197)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            4578999999999999999999988653

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=96.36  E-value=0.012  Score=60.73  Aligned_cols=25  Identities=36%  Similarity=0.582  Sum_probs=22.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ...+|+.||+|||||+|.+|+|.-.
T Consensus       419 G~~llI~G~SG~GKTsLlRaiaGLW  443 (604)
T COG4178         419 GERLLITGESGAGKTSLLRALAGLW  443 (604)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccC
Confidence            4558999999999999999999855

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.36  E-value=0.0047  Score=53.08  Aligned_cols=36  Identities=31%  Similarity=0.429  Sum_probs=30.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE  265 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~  265 (338)
                      -+.|.|.||+|||++++++...+   +.+++.++...+.
T Consensus         4 vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~lR   42 (156)
T PF01583_consen    4 VIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGDNLR   42 (156)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcchh
Confidence            36799999999999999999988   7889999877655

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 ....

>TIGR00376 DNA helicase, putative

Probab=96.35  E-value=0.0062  Score=63.80  Aligned_cols=51  Identities=27%  Similarity=0.436  Sum_probs=34.0

Q ss_pred             cCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          210 AMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      ..++..++.+...+..  ...++++||||||||+++.++...+   |..+..+..+
T Consensus       157 ~ln~~Q~~Av~~~l~~--~~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~s  210 (637)
T TIGR00376       157 NLNESQKEAVSFALSS--KDLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPS  210 (637)
T ss_pred             CCCHHHHHHHHHHhcC--CCeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCc
Confidence            3455555555443321  2457899999999999998887765   5666655433

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.35  E-value=0.01  Score=63.36  Aligned_cols=64  Identities=23%  Similarity=0.345  Sum_probs=41.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC----------chHHHHHHHh-------cCCCcEEEEcCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG----------NKHLRKVLIA-------TENKSILVVGDI  288 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~----------~~~l~~~l~~-------~~~~~Il~iDei  288 (338)
                      +-++|.|+||||||+++.++...+   |+.+..+-.+....          ...+.+++..       .....+|||||+
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            456899999999999999987654   66666554333210          1123333221       235789999998


Q ss_pred             CccC
Q 035959          289 DCCT  292 (338)
Q Consensus       289 D~~~  292 (338)
                      -.+.
T Consensus       449 sMv~  452 (744)
T TIGR02768       449 GMVG  452 (744)
T ss_pred             ccCC
Confidence            7654

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.34  E-value=0.0029  Score=54.93  Aligned_cols=25  Identities=28%  Similarity=0.392  Sum_probs=22.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      -+++.||||+|||+++++++..++.
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCc
Confidence            4689999999999999999998753

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.

>PRK14529 adenylate kinase; Provisional

Probab=96.33  E-value=0.0028  Score=57.70  Aligned_cols=27  Identities=30%  Similarity=0.502  Sum_probs=24.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      ++|.||||+|||++++.+|..++...+
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~~~~i   29 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYDLAHI   29 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCc
Confidence            789999999999999999999987654

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=96.31  E-value=0.012  Score=52.32  Aligned_cols=65  Identities=17%  Similarity=0.237  Sum_probs=40.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH-----hCCc--------------EEEEecCCcCC---------chHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY-----LHFD--------------VYDLELSSVEG---------NKHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~-----l~~~--------------~~~l~~~~~~~---------~~~l~~~l~~~~~~  280 (338)
                      +-++|.||.|+|||++++.++.-     .|..              +..+...+...         ...+..++.....+
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~~~~~~~~g~~~~~~~~~i~~~dqi~~~~~~~d~i~~~~s~~~~e~~~l~~i~~~~~~~  109 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPR  109 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHHHHHHHHcCCCccccccccCCcCEEEEEecCcccccCCceeHHHHHHHHHHHHHhccCC
Confidence            45899999999999999999932     2311              11111111000         12344455555689


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      .++++||.-.-.+
T Consensus       110 ~llllDEp~~gld  122 (202)
T cd03243         110 SLVLIDELGRGTS  122 (202)
T ss_pred             eEEEEecCCCCCC
Confidence            9999999977665

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

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.30  E-value=0.009  Score=54.10  Aligned_cols=34  Identities=21%  Similarity=0.237  Sum_probs=26.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~  263 (338)
                      -+.|+||||||||+++..+|...         +..+++++...
T Consensus        21 i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          21 ITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            36899999999999999988553         25677777655

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 .

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.29  E-value=0.01  Score=56.53  Aligned_cols=27  Identities=15%  Similarity=0.497  Sum_probs=23.8

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .+..+++.||+|+|||+++++++..+.
T Consensus       143 ~~~~ili~G~tGsGKTTll~al~~~~~  169 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTFLKSLVDEIP  169 (308)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHccCC
Confidence            356789999999999999999998873

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=96.28  E-value=0.0069  Score=53.01  Aligned_cols=26  Identities=31%  Similarity=0.557  Sum_probs=23.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      -+.+.||+|+|||+++++++..++..
T Consensus         5 ~i~l~G~sGsGKSTl~~~la~~l~~~   30 (176)
T PRK09825          5 SYILMGVSGSGKSLIGSKIAALFSAK   30 (176)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCE
Confidence            47899999999999999999998764

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.28  E-value=0.0048  Score=53.54  Aligned_cols=33  Identities=24%  Similarity=0.299  Sum_probs=26.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~  261 (338)
                      .-++|.|+||+|||++++++++.+.   ..++.++.
T Consensus         8 ~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~~   43 (176)
T PRK05541          8 YVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDG   43 (176)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEec
Confidence            3468999999999999999999885   33555544

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.28  E-value=0.0049  Score=53.45  Aligned_cols=33  Identities=27%  Similarity=0.375  Sum_probs=26.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      -+.|.|+||+|||+++++++..+   +..+..++..
T Consensus         6 ~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id~D   41 (175)
T PRK00889          6 TVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDGD   41 (175)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEcCc
Confidence            46799999999999999999988   4456666553

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=96.27  E-value=0.0033  Score=57.79  Aligned_cols=31  Identities=32%  Similarity=0.723  Sum_probs=22.9

Q ss_pred             eeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          233 LFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       233 L~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      +.||||+|||++++++..++   +.+++.+++..
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~~~~~~vNLDP   34 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNGRDVYIVNLDP   34 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT-S-EEEEE--T
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCceEEEcch
Confidence            46999999999999999988   56677776654

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK10646 ADP-binding protein; Provisional

Probab=96.27  E-value=0.038  Score=47.34  Aligned_cols=42  Identities=17%  Similarity=0.235  Sum_probs=29.9

Q ss_pred             hhHHHHHHHHHHhhhcC--ceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          213 TDMKKMIMDDLERAWKR--GYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       213 ~~~k~~i~~~l~~~~~~--g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ++.-+++-+.+....+.  -++|.|+=|+|||++++++++.+|.
T Consensus        11 ~~~t~~l~~~la~~l~~g~vi~L~GdLGaGKTtf~rgl~~~Lg~   54 (153)
T PRK10646         11 EQATLDLGARVAKACDGATVIYLYGDLGAGKTTFSRGFLQALGH   54 (153)
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            33334444455443333  3789999999999999999999973

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.26  E-value=0.006  Score=52.72  Aligned_cols=33  Identities=33%  Similarity=0.431  Sum_probs=27.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      +++.||||+|||+++..+|..+   +..+..+++..
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D~   38 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADT   38 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcCC
Confidence            5789999999999999998876   66777776653

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.

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=96.25  E-value=0.0044  Score=54.15  Aligned_cols=29  Identities=31%  Similarity=0.406  Sum_probs=25.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +.|+|+||+|||+++..+++ +|++++..|
T Consensus         2 i~itG~~gsGKst~~~~l~~-~g~~~i~~D   30 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE-LGIPVIDAD   30 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH-CCCCEEecC
Confidence            57899999999999999999 788776554

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=96.24  E-value=0.005  Score=44.51  Aligned_cols=22  Identities=45%  Similarity=0.791  Sum_probs=19.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+|+||.|+|||+++.|+.-.+
T Consensus        26 tli~G~nGsGKSTllDAi~~~L   47 (62)
T PF13555_consen   26 TLITGPNGSGKSTLLDAIQTVL   47 (62)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7999999999999999987654

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.23  E-value=0.0085  Score=56.15  Aligned_cols=25  Identities=32%  Similarity=0.607  Sum_probs=22.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .++++.||||+|||+|+++++..+.
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccC
Confidence            4789999999999999999999874

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.

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=96.23  E-value=0.01  Score=52.73  Aligned_cols=21  Identities=24%  Similarity=0.506  Sum_probs=19.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia  249 (338)
                      +-++|.||.|+|||++++.++
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            458999999999999999988

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

>TIGR00416 sms DNA repair protein RadA

Probab=96.23  E-value=0.0072  Score=60.80  Aligned_cols=64  Identities=23%  Similarity=0.277  Sum_probs=42.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC--------------------chHHHHHHHhc--CCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG--------------------NKHLRKVLIAT--ENKSILV  284 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~--------------------~~~l~~~l~~~--~~~~Il~  284 (338)
                      -+++.|+||+|||+|+..+|..+   +.++++++..+-..                    +.++..+...+  .++.+|+
T Consensus        96 vilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EEs~~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i~~~~~~~vV  175 (454)
T TIGR00416        96 LILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICANIEEENPQACV  175 (454)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcCCHHHHHHHHHHcCCChHHeEEcCCCCHHHHHHHHHhcCCcEEE
Confidence            46899999999999999887755   45677776643210                    11222222222  3688999


Q ss_pred             EcCCCccCC
Q 035959          285 VGDIDCCTE  293 (338)
Q Consensus       285 iDeiD~~~~  293 (338)
                      ||.|..+..
T Consensus       176 IDSIq~l~~  184 (454)
T TIGR00416       176 IDSIQTLYS  184 (454)
T ss_pred             Eecchhhcc
Confidence            999998753

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)).

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=96.23  E-value=0.013  Score=54.93  Aligned_cols=64  Identities=22%  Similarity=0.386  Sum_probs=47.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----chHHHHHHHhcC---CCcEEEEcCCCcc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----NKHLRKVLIATE---NKSILVVGDIDCC  291 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----~~~l~~~l~~~~---~~~Il~iDeiD~~  291 (338)
                      +...||.|.+|+||.++++..|--.++.++.+..+.--+    .++|+.++..+.   ++.+++|+|-+-.
T Consensus        31 ~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~y~~~~f~~dLk~~~~~ag~~~~~~vfll~d~qi~  101 (268)
T PF12780_consen   31 RGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITKGYSIKDFKEDLKKALQKAGIKGKPTVFLLTDSQIV  101 (268)
T ss_dssp             TEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTSTTTHHHHHHHHHHHHHHHHHCS-S-EEEEEECCCSS
T ss_pred             CCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeCCcCHHHHHHHHHHHHHHHhccCCCeEEEecCcccc
Confidence            345899999999999999988888899999888765332    245667666553   6788998886644

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=96.23  E-value=0.0041  Score=55.29  Aligned_cols=38  Identities=18%  Similarity=0.311  Sum_probs=29.3

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh-CCcEEEEecCCcC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL-HFDVYDLELSSVE  265 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l-~~~~~~l~~~~~~  265 (338)
                      |.-+++.|+||+|||+++..+...+ +..++.++...+.
T Consensus        15 P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~r   53 (199)
T PF06414_consen   15 PTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEFR   53 (199)
T ss_dssp             -EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGGG
T ss_pred             CEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHHH
Confidence            4668899999999999999999988 7778888777654

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.

>PLN02674 adenylate kinase

Probab=96.22  E-value=0.0082  Score=55.38  Aligned_cols=29  Identities=24%  Similarity=0.510  Sum_probs=25.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      ..++|.||||+||+++++.+|..+++..+
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~~~~~hi   60 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDEYCLCHL   60 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHcCCcEE
Confidence            55899999999999999999999986543

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.21  E-value=0.023  Score=49.03  Aligned_cols=29  Identities=17%  Similarity=0.217  Sum_probs=23.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      +.+|+++|+||||+|.++|-..   |..+..+
T Consensus         5 i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~v   36 (159)
T cd00561           5 IQVYTGNGKGKTTAALGLALRALGHGYRVGVV   36 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            4689999999999999988655   5666654

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=96.21  E-value=0.0048  Score=53.88  Aligned_cols=36  Identities=31%  Similarity=0.463  Sum_probs=31.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE  265 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~  265 (338)
                      -+.|+|.+|+|||++|.|+...|   |+.+|.+|...+.
T Consensus        25 viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDGDnvR   63 (197)
T COG0529          25 VIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGDNVR   63 (197)
T ss_pred             EEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecChhHh
Confidence            45799999999999999999988   8899999887665

>PRK04841 transcriptional regulator MalT; Provisional

Probab=96.20  E-value=0.019  Score=62.18  Aligned_cols=58  Identities=24%  Similarity=0.278  Sum_probs=39.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      +.+|..-..++..+.+.+    .+... ..+-.++.||+|.|||+++...+...+ ++..+++.
T Consensus         7 ~~~p~~~~~~~~R~rl~~----~l~~~~~~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l~   65 (903)
T PRK04841          7 LSRPVRLHNTVVRERLLA----KLSGANNYRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSLD   65 (903)
T ss_pred             cCCCCCccccCcchHHHH----HHhcccCCCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEecC
Confidence            445555556666665444    44432 234579999999999999999887777 77666664

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.19  E-value=0.0067  Score=59.12  Aligned_cols=45  Identities=27%  Similarity=0.499  Sum_probs=32.7

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +.+++++..++..    .+.+. .....+++.||+|+|||+++++++.++
T Consensus       114 ~~~l~~l~~~~~~----~~~~~-~~~glilI~GpTGSGKTTtL~aLl~~i  158 (358)
T TIGR02524       114 PPKLSKLDLPAAI----IDAIA-PQEGIVFITGATGSGKSTLLAAIIREL  158 (358)
T ss_pred             CCCHHHcCCCHHH----HHHHh-ccCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4478888776543    33332 223447899999999999999999887

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=96.19  E-value=0.0088  Score=52.48  Aligned_cols=65  Identities=18%  Similarity=0.264  Sum_probs=39.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCc--EEEEec-------CCc-CCchHHHHHHH---hcCCCcEEEEcCCCccCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFD--VYDLEL-------SSV-EGNKHLRKVLI---ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~--~~~l~~-------~~~-~~~~~l~~~l~---~~~~~~Il~iDeiD~~~~  293 (338)
                      .-+.|.||.|+|||+|++.++..+..+  -+.++.       ... .+...-+++..   -+.++.++++||--.-++
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~~~p~lllLDEPts~LD  103 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAYLD  103 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHhcCCCEEEEECCcccCC
Confidence            346799999999999999999876321  111111       111 12222222211   124789999999887765

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.

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=96.18  E-value=0.015  Score=60.21  Aligned_cols=91  Identities=19%  Similarity=0.088  Sum_probs=60.9

Q ss_pred             hHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEecCC----cCCchHHHHHHHhc---------
Q 035959          214 DMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLELSS----VEGNKHLRKVLIAT---------  277 (338)
Q Consensus       214 ~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~~~----~~~~~~l~~~l~~~---------  277 (338)
                      ..|..+.-....| .-.|++|-|++|||||+++++++..+..  ++..+..+.    +...-+|...+..-         
T Consensus        10 ~~~~Al~l~av~p~~~gGv~i~g~~G~~ks~~~r~l~~llp~~~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~~pGll   89 (584)
T PRK13406         10 DAALAAALLAVDPAGLGGVVLRARAGPVRDRWLAALRALLPAGTPLRRLPPGIADDRLLGGLDLAATLRAGRPVAQRGLL   89 (584)
T ss_pred             HHHHHHHHhCcCccccceEEEEcCCCcHHHHHHHHHHHhcCCCCCcccCCCCCcHHHccCCchHHhHhhcCCcCCCCCce
Confidence            3444444333334 4478999999999999999999998864  555444332    11223344444322         


Q ss_pred             --CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhc
Q 035959          278 --ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTD  326 (338)
Q Consensus       278 --~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iD  326 (338)
                        ..+.||+|||+..+.+                      .+++.||..|+
T Consensus        90 a~Ah~GvL~lDe~n~~~~----------------------~~~~aLleame  118 (584)
T PRK13406         90 AEADGGVLVLAMAERLEP----------------------GTAARLAAALD  118 (584)
T ss_pred             eeccCCEEEecCcccCCH----------------------HHHHHHHHHHh
Confidence              2468999999998864                      67888888876

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=96.17  E-value=0.012  Score=53.24  Aligned_cols=62  Identities=19%  Similarity=0.271  Sum_probs=38.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH-----HhCCcE---------EEEecCCcCC-------c-------hHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN-----YLHFDV---------YDLELSSVEG-------N-------KHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~-----~l~~~~---------~~l~~~~~~~-------~-------~~l~~~l~~~~~~  280 (338)
                      +-++|.||+|+|||++.+.++.     ..|..+         +.--...+..       .       ..+..++....++
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~~~~l~~~g~~vp~~~~~i~~~~~i~~~~~~~~~ls~g~s~f~~e~~~l~~~l~~~~~~  110 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVALIALLAQIGSFVPASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATER  110 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHhccCCeeccccceecceeeEeccCCchhhhccCcchHHHHHHHHHHHHHhCCCC
Confidence            4578999999999999999864     222211         1000111110       0       1355566666789


Q ss_pred             cEEEEcCCCc
Q 035959          281 SILVVGDIDC  290 (338)
Q Consensus       281 ~Il~iDeiD~  290 (338)
                      ++++|||.-.
T Consensus       111 ~llllDEp~~  120 (216)
T cd03284         111 SLVLLDEIGR  120 (216)
T ss_pred             eEEEEecCCC
Confidence            9999999843

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

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=96.15  E-value=0.011  Score=44.85  Aligned_cols=30  Identities=30%  Similarity=0.406  Sum_probs=24.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~  260 (338)
                      +++.|.+|+|||+++..+|..+   |+++..++
T Consensus         2 ~~~~g~~G~Gktt~~~~l~~~l~~~g~~v~~~~   34 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAAALAKRGKRVLLID   34 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEC
Confidence            4688999999999999999987   56665555

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=96.12  E-value=0.045  Score=52.08  Aligned_cols=77  Identities=12%  Similarity=0.161  Sum_probs=51.8

Q ss_pred             HHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHh--------C---C--cEEEEe--cCCcCCchHHHHHHHhcC-
Q 035959          216 KKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYL--------H---F--DVYDLE--LSSVEGNKHLRKVLIATE-  278 (338)
Q Consensus       216 k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l--------~---~--~~~~l~--~~~~~~~~~l~~~l~~~~-  278 (338)
                      ++.+...+.. ..+..|||+|+.|.||+.++.++++.+        .   .  ++..++  ... ...++++.+....+ 
T Consensus         5 ~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~-i~vd~Ir~l~~~~~~   83 (299)
T PRK07132          5 IKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKD-LSKSEFLSAINKLYF   83 (299)
T ss_pred             HHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCc-CCHHHHHHHHHHhcc
Confidence            3444445544 345679999999999999999999887        1   1  344444  222 23456666666552 


Q ss_pred             ------CCcEEEEcCCCccCC
Q 035959          279 ------NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 ------~~~Il~iDeiD~~~~  293 (338)
                            .+-|++||++|.+..
T Consensus        84 ~~~~~~~~KvvII~~~e~m~~  104 (299)
T PRK07132         84 SSFVQSQKKILIIKNIEKTSN  104 (299)
T ss_pred             CCcccCCceEEEEecccccCH
Confidence                  678999999988853

>PRK10536 hypothetical protein; Provisional

Probab=96.12  E-value=0.018  Score=53.45  Aligned_cols=38  Identities=24%  Similarity=0.291  Sum_probs=27.4

Q ss_pred             ChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHH
Q 035959          212 DTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       212 ~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .......++..+..  ..-+++.||+|||||+|+.|+|.+
T Consensus        60 ~n~~Q~~~l~al~~--~~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         60 RNEAQAHYLKAIES--KQLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             CCHHHHHHHHHHhc--CCeEEEECCCCCCHHHHHHHHHHH
Confidence            33444455555543  246789999999999999999985

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.11  E-value=0.008  Score=53.66  Aligned_cols=32  Identities=16%  Similarity=0.172  Sum_probs=24.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC-CcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH-FDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~-~~~~~l~~  261 (338)
                      -+.+.||+|+|||+|+++++..++ ..+..++.
T Consensus         8 iI~I~G~sGsGKTTl~~~l~~~l~~~~~~~i~~   40 (209)
T PRK05480          8 IIGIAGGSGSGKTTVASTIYEELGDESIAVIPQ   40 (209)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceEEEeC
Confidence            467999999999999999999983 34444443

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.10  E-value=0.0046  Score=54.41  Aligned_cols=26  Identities=27%  Similarity=0.668  Sum_probs=23.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ...+++.||+|+|||+++++++..+.
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            45689999999999999999998874

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.10  E-value=0.0071  Score=56.25  Aligned_cols=34  Identities=21%  Similarity=0.125  Sum_probs=26.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .-++++||||||||+++..+|...   |.++.++++.
T Consensus        37 s~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~E   73 (259)
T TIGR03878        37 SVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVE   73 (259)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec
Confidence            446899999999999998876643   5677777665

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK14974 cell division protein FtsY; Provisional

Probab=96.09  E-value=0.017  Score=55.81  Aligned_cols=34  Identities=35%  Similarity=0.428  Sum_probs=26.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .-++|.||||+|||++++.+|..+   +..+..+++.
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~D  177 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGD  177 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            457899999999999999999876   4555555443

>PRK04328 hypothetical protein; Provisional

Probab=96.09  E-value=0.019  Score=52.99  Aligned_cols=45  Identities=24%  Similarity=0.214  Sum_probs=31.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH---hCCcEEEEecCCcCCchHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY---LHFDVYDLELSSVEGNKHLRKVLI  275 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~---l~~~~~~l~~~~~~~~~~l~~~l~  275 (338)
                      ..+|++||||||||.|+..++..   -|.+.++++..+  +...+.+-+.
T Consensus        24 s~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~ee--~~~~i~~~~~   71 (249)
T PRK04328         24 NVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVALEE--HPVQVRRNMR   71 (249)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEeeC--CHHHHHHHHH
Confidence            45789999999999998876543   267888888765  3333444433

>PLN02165 adenylate isopentenyltransferase

Probab=96.08  E-value=0.0049  Score=59.23  Aligned_cols=31  Identities=23%  Similarity=0.438  Sum_probs=26.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+.|.||+|+|||+|+.++|..++..++..
T Consensus        44 ~iivIiGPTGSGKStLA~~LA~~l~~eIIsa   74 (334)
T PLN02165         44 KVVVIMGATGSGKSRLSVDLATRFPSEIINS   74 (334)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHcCCceecC
Confidence            4578999999999999999999998765544

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=96.08  E-value=0.039  Score=52.11  Aligned_cols=22  Identities=32%  Similarity=0.546  Sum_probs=19.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +=|.|+||+|||+|+..+.+.+
T Consensus       107 v~l~G~pGsGKTTLl~~l~~~l  128 (290)
T PRK10463        107 LNLVSSPGSGKTTLLTETLMRL  128 (290)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3488999999999999999876

>PRK12338 hypothetical protein; Provisional

Probab=96.07  E-value=0.0054  Score=58.64  Aligned_cols=28  Identities=25%  Similarity=0.332  Sum_probs=24.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDV  256 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~  256 (338)
                      .-+++.|+||+|||++++++|..++...
T Consensus         5 ~ii~i~G~sGsGKST~a~~la~~l~~~~   32 (319)
T PRK12338          5 YVILIGSASGIGKSTIASELARTLNIKH   32 (319)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCeE
Confidence            4578999999999999999999998654

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.06  E-value=0.013  Score=55.70  Aligned_cols=34  Identities=18%  Similarity=0.208  Sum_probs=27.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~  263 (338)
                      -++++||||+|||+++..+|...         +..+++++..+
T Consensus        97 i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~  139 (310)
T TIGR02236        97 ITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTEN  139 (310)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCC
Confidence            35899999999999999888663         23678887765

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.06  E-value=0.0086  Score=54.51  Aligned_cols=35  Identities=29%  Similarity=0.235  Sum_probs=27.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      ...++++||||||||+++..++...   +..++++++.
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e   62 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE   62 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC
Confidence            3457899999999999999987543   5667666653

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.05  E-value=0.018  Score=52.45  Aligned_cols=65  Identities=18%  Similarity=0.225  Sum_probs=42.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH-Hh----CCc---------E---EEEecC---CcCC--------chHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN-YL----HFD---------V---YDLELS---SVEG--------NKHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~-~l----~~~---------~---~~l~~~---~~~~--------~~~l~~~l~~~~~~  280 (338)
                      +-++|.||.|+|||++.+.++. .+    |..         +   +.....   ++..        -.++..++..+.++
T Consensus        32 ~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~~  111 (222)
T cd03287          32 YCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTSR  111 (222)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCccccccccchHHHHHHHHHHHHHhCCCC
Confidence            4578999999999999999887 22    211         1   111111   1110        13456777778899


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      ++++|||+..-..
T Consensus       112 sLvllDE~~~gT~  124 (222)
T cd03287         112 SLVILDELGRGTS  124 (222)
T ss_pred             eEEEEccCCCCCC
Confidence            9999999866543

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

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.05  E-value=0.012  Score=57.81  Aligned_cols=65  Identities=22%  Similarity=0.319  Sum_probs=43.7

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhC-----C--cEEEEecCCcC--------------------CchHHHHHHHhcCCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLH-----F--DVYDLELSSVE--------------------GNKHLRKVLIATENK  280 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~-----~--~~~~l~~~~~~--------------------~~~~l~~~l~~~~~~  280 (338)
                      ++-+.|.||+|+|||+.++-+|..+.     .  .++.+|.-.+.                    +..++...+..+...
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            45578999999999998888887664     1  23333333332                    245566666777778


Q ss_pred             cEEEEcCCCccC
Q 035959          281 SILVVGDIDCCT  292 (338)
Q Consensus       281 ~Il~iDeiD~~~  292 (338)
                      ++|++|=+....
T Consensus       283 d~ILVDTaGrs~  294 (407)
T COG1419         283 DVILVDTAGRSQ  294 (407)
T ss_pred             CEEEEeCCCCCc
Confidence            899888665543

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.02  E-value=0.0084  Score=55.53  Aligned_cols=36  Identities=25%  Similarity=0.249  Sum_probs=29.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      .+-+|++|+||||||.++..++...   |.+++++...+
T Consensus        23 g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e   61 (260)
T COG0467          23 GSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEE   61 (260)
T ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence            3557999999999999988877654   67788887765

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=96.01  E-value=0.0051  Score=53.08  Aligned_cols=27  Identities=33%  Similarity=0.545  Sum_probs=22.7

Q ss_pred             eCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          234 FGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       234 ~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .||||+|||+++++++..++..+++-+
T Consensus         1 ~G~sGsGKSTla~~la~~l~~~~~~~d   27 (163)
T PRK11545          1 MGVSGSGKSAVASEVAHQLHAAFLDGD   27 (163)
T ss_pred             CCCCCCcHHHHHHHHHHHhCCeEEeCc
Confidence            499999999999999999987555444

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=96.01  E-value=0.0098  Score=58.00  Aligned_cols=33  Identities=30%  Similarity=0.559  Sum_probs=28.5

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      |.+.++++||||.||||.++..+-..++-.++.
T Consensus       260 PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViS  292 (432)
T PF00519_consen  260 PKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVIS  292 (432)
T ss_dssp             TTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-
T ss_pred             CcccEEEEECCCCCchhHHHHHHHHHhCCEEEE
Confidence            667788999999999999999999999877654

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.

>cd04159 Arl10_like Arl10-like subfamily

Probab=96.00  E-value=0.012  Score=48.60  Aligned_cols=21  Identities=29%  Similarity=0.463  Sum_probs=19.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +.|.||+|+|||+|+.++...
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            578999999999999999875

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>PRK06851 hypothetical protein; Provisional

Probab=95.98  E-value=0.0098  Score=58.03  Aligned_cols=38  Identities=37%  Similarity=0.514  Sum_probs=32.2

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      ...+-++|.|+||||||+|+..++..+   |+++....|+.
T Consensus       212 ~~~~~~~i~G~pG~GKstl~~~i~~~a~~~G~~v~~~hC~~  252 (367)
T PRK06851        212 GVKNRYFLKGRPGTGKSTMLKKIAKAAEERGFDVEVYHCGF  252 (367)
T ss_pred             ccceEEEEeCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCCC
Confidence            445789999999999999999999988   77777777764

>PLN02459 probable adenylate kinase

Probab=95.98  E-value=0.0071  Score=56.27  Aligned_cols=28  Identities=21%  Similarity=0.509  Sum_probs=24.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      ++|.||||+|||+++..+|..+++..+.
T Consensus        32 ii~~G~PGsGK~T~a~~la~~~~~~~is   59 (261)
T PLN02459         32 WVFLGCPGVGKGTYASRLSKLLGVPHIA   59 (261)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEe
Confidence            7789999999999999999999876543

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.98  E-value=0.0083  Score=52.60  Aligned_cols=32  Identities=25%  Similarity=0.462  Sum_probs=25.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH---FDVYDLELS  262 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~  262 (338)
                      +.+.|+||+|||++++.++..++   .++..++..
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~~~~~~~i~~D   36 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLD   36 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEehh
Confidence            46899999999999999999873   455555443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=95.98  E-value=0.0068  Score=53.94  Aligned_cols=30  Identities=23%  Similarity=0.180  Sum_probs=25.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.++|++|+|||++++.+++.+|.++++.
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~~g~~~i~~   32 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQKGIPILDA   32 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCeEeeC
Confidence            367999999999999999999888877644

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.96  E-value=0.011  Score=54.14  Aligned_cols=36  Identities=28%  Similarity=0.253  Sum_probs=27.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHH---hCCcEEEEecCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANY---LHFDVYDLELSS  263 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~---l~~~~~~l~~~~  263 (338)
                      ...+|++||||||||.++..++..   -|.+++++.+.+
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~ee   59 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALEE   59 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEeeC
Confidence            345799999999999998875543   266777777654

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.

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.95  E-value=0.0048  Score=53.51  Aligned_cols=24  Identities=33%  Similarity=0.490  Sum_probs=21.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -++|.||+|+|||++++.+++...
T Consensus         3 ii~l~G~~GsGKsTl~~~L~~~~~   26 (180)
T TIGR03263         3 LIVISGPSGVGKSTLVKALLEEDP   26 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHccCc
Confidence            468999999999999999999764

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.

>PRK05973 replicative DNA helicase; Provisional

Probab=95.93  E-value=0.0091  Score=54.84  Aligned_cols=89  Identities=19%  Similarity=0.062  Sum_probs=49.0

Q ss_pred             hhhHHHHHHhHHHHHhccceeeeeccCcc--CCC-CccccccC--CCCCccccccCChhHHHHHHHHHHhhhcCceeeeC
Q 035959          161 TYIPHILKKSKELSKKKKTLKLFTLNCNR--INH-DTRQSAIL--DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFG  235 (338)
Q Consensus       161 ~~l~~v~~~~~~~~~~~~~~~l~~~~~~~--~~~-~~w~~~~~--~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~G  235 (338)
                      ..+.++-.+|+.+..+.. +.++..-...  .+| ..|..+..  ..+.+.+.+.+.=            +...-+++.|
T Consensus         5 ~~~~~~~~~a~~~~~~~~-~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~~~l~GGl------------~~Gsl~LIaG   71 (237)
T PRK05973          5 APIYHLKRKAKLLSRAQN-IPLHEALDRIAAEEGFSSWSLLAAKAAATTPAEELFSQL------------KPGDLVLLGA   71 (237)
T ss_pred             hHHHHHHHHHHHHHHhcC-CcHHHHHHHHHHHhccchHHHHHHhccCCCCHHHhcCCC------------CCCCEEEEEe
Confidence            445566677777764432 2232221000  022 36876543  2233455543211            1123478999


Q ss_pred             CCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          236 PPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       236 ppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      +||+|||+++..++...   |.+++++++.
T Consensus        72 ~PG~GKT~lalqfa~~~a~~Ge~vlyfSlE  101 (237)
T PRK05973         72 RPGHGKTLLGLELAVEAMKSGRTGVFFTLE  101 (237)
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence            99999999988877654   6666666544

>PRK06761 hypothetical protein; Provisional

Probab=95.92  E-value=0.0078  Score=56.69  Aligned_cols=31  Identities=23%  Similarity=0.365  Sum_probs=25.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +-+++.||||+|||++++.+++.+....+.+
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~g~~v   34 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQNGIEV   34 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcCceEE
Confidence            3478999999999999999999997544443

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=95.92  E-value=0.031  Score=61.13  Aligned_cols=63  Identities=17%  Similarity=0.322  Sum_probs=41.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC----------CchHHHHHHHh-------cCCCcEEEEcCCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE----------GNKHLRKVLIA-------TENKSILVVGDID  289 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~----------~~~~l~~~l~~-------~~~~~Il~iDeiD  289 (338)
                      -++|.|+||||||+++.++...+   |+.+.-+-.+...          ....+..++..       .....+|||||+-
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            46799999999999988876544   6666655443221          11234444422       2356899999998


Q ss_pred             ccC
Q 035959          290 CCT  292 (338)
Q Consensus       290 ~~~  292 (338)
                      .+.
T Consensus       444 Mv~  446 (988)
T PRK13889        444 MVG  446 (988)
T ss_pred             cCC
Confidence            764

>PRK09354 recA recombinase A; Provisional

Probab=95.91  E-value=0.015  Score=56.45  Aligned_cols=64  Identities=11%  Similarity=0.160  Sum_probs=41.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHH---HhcCCCcE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVL---IATENKSI  282 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l---~~~~~~~I  282 (338)
                      -++++||||||||+|+..++...   |..+.+++...-.+                     .++...++   .+.....+
T Consensus        62 IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~s~~~~l  141 (349)
T PRK09354         62 IVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDL  141 (349)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhcCCCCE
Confidence            36899999999999988766543   55666666544111                     11111111   12246889


Q ss_pred             EEEcCCCccCC
Q 035959          283 LVVGDIDCCTE  293 (338)
Q Consensus       283 l~iDeiD~~~~  293 (338)
                      ||||-|-++.+
T Consensus       142 IVIDSvaaL~~  152 (349)
T PRK09354        142 IVVDSVAALVP  152 (349)
T ss_pred             EEEeChhhhcc
Confidence            99999998875

>PRK13808 adenylate kinase; Provisional

Probab=95.90  E-value=0.0072  Score=58.18  Aligned_cols=29  Identities=24%  Similarity=0.490  Sum_probs=25.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|+||||+|||+++..||..+++..+.+
T Consensus         3 Iiv~GpPGSGK~T~a~~LA~~ygl~~is~   31 (333)
T PRK13808          3 LILLGPPGAGKGTQAQRLVQQYGIVQLST   31 (333)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceecc
Confidence            78999999999999999999998866554

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=95.90  E-value=0.019  Score=48.58  Aligned_cols=22  Identities=18%  Similarity=0.501  Sum_probs=19.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+..+...
T Consensus         1 ~i~~vG~~~~GKstLi~~l~~~   22 (167)
T cd04160           1 SVLILGLDNAGKTTFLEQLKTL   22 (167)
T ss_pred             CEEEEecCCCCHHHHHHHHhhh
Confidence            3689999999999999998754

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.90  E-value=0.0065  Score=54.11  Aligned_cols=23  Identities=48%  Similarity=0.901  Sum_probs=21.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +++.||+|+|||+++.+++.++.
T Consensus         4 ilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhh
Confidence            58999999999999999998874

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=95.89  E-value=0.011  Score=52.27  Aligned_cols=22  Identities=23%  Similarity=0.419  Sum_probs=20.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +.|.||+|+|||+++++++..+
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999987

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.

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=95.87  E-value=0.0066  Score=62.59  Aligned_cols=84  Identities=24%  Similarity=0.330  Sum_probs=50.9

Q ss_pred             cCChhHHHHHHHHHHh-------h---hc--CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC-------cC-CchH
Q 035959          210 AMDTDMKKMIMDDLER-------A---WK--RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS-------VE-GNKH  269 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~-------~---~~--~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~-------~~-~~~~  269 (338)
                      ...++.|+.++-.|-.       .   .+  -++||+|.||||||.|++.+++-+..-+|.---.+       .. -+.+
T Consensus       432 ye~edvKkglLLqLfGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVtrd~d  511 (804)
T KOG0478|consen  432 YELEDVKKGLLLQLFGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVTKDPD  511 (804)
T ss_pred             hcccchhhhHHHHHhcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEEecCc
Confidence            3445566666555543       1   11  24899999999999999999988754433221110       00 0112


Q ss_pred             HHHHHHhc-----CCCcEEEEcCCCccCC
Q 035959          270 LRKVLIAT-----ENKSILVVGDIDCCTE  293 (338)
Q Consensus       270 l~~~l~~~-----~~~~Il~iDeiD~~~~  293 (338)
                      -++++.+.     +...|-+|||+|.+..
T Consensus       512 tkqlVLesGALVLSD~GiCCIDEFDKM~d  540 (804)
T KOG0478|consen  512 TRQLVLESGALVLSDNGICCIDEFDKMSD  540 (804)
T ss_pred             cceeeeecCcEEEcCCceEEchhhhhhhH
Confidence            23333333     4688999999999954

>TIGR00017 cmk cytidylate kinase

Probab=95.84  E-value=0.0089  Score=54.16  Aligned_cols=29  Identities=34%  Similarity=0.506  Sum_probs=25.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      -+.+.||+|+|||++++.+|..+++.++.
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~~~~~~~~   32 (217)
T TIGR00017         4 IIAIDGPSGAGKSTVAKAVAEKLGYAYLD   32 (217)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            35689999999999999999999977654

This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.

>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=95.83  E-value=0.0055  Score=54.65  Aligned_cols=35  Identities=31%  Similarity=0.419  Sum_probs=25.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      +-++|.||+|+|||+.+.-+|.++   +..+-.+.+..
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~D~   39 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLKGKKVALISADT   39 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEEST
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhccccceeecCCC
Confidence            457899999999999999999877   45555554443

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 ....

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.83  E-value=0.0082  Score=50.25  Aligned_cols=24  Identities=33%  Similarity=0.573  Sum_probs=21.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      +.|.||+|+|||++++.++..+..
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~~   25 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFDP   25 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCCc
Confidence            578999999999999999998643

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.

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.81  E-value=0.011  Score=51.46  Aligned_cols=30  Identities=30%  Similarity=0.461  Sum_probs=25.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~  260 (338)
                      +.|.|++|+|||++++.+++.+   |+.+..+.
T Consensus         3 I~ieG~~GsGKtT~~~~L~~~l~~~g~~v~~~~   35 (200)
T cd01672           3 IVFEGIDGAGKTTLIELLAERLEARGYEVVLTR   35 (200)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            5688999999999999999998   66665553

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.77  E-value=0.017  Score=51.82  Aligned_cols=65  Identities=20%  Similarity=0.253  Sum_probs=39.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH-----HhCCcE------------E--EEecCC-cCC--------chHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN-----YLHFDV------------Y--DLELSS-VEG--------NKHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~-----~l~~~~------------~--~l~~~~-~~~--------~~~l~~~l~~~~~~  280 (338)
                      +-++|.||.|+|||++++.++.     ++|..+            +  .+...+ +..        -.++..++..+.++
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~~~~la~~G~~vpa~~~~l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~~il~~~~~~  109 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADGD  109 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCcchhhcCccChhheeEecCCccccchhhhHHHHHHHHHHHHHHhcCCC
Confidence            4589999999999999999873     333221            0  011110 100        11334445555689


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      +++++||+..-.+
T Consensus       110 ~lvllDE~~~gt~  122 (204)
T cd03282         110 SLVLIDELGRGTS  122 (204)
T ss_pred             cEEEeccccCCCC
Confidence            9999999866543

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

>PRK00081 coaE dephospho-CoA kinase; Reviewed

Probab=95.77  E-value=0.01  Score=52.66  Aligned_cols=30  Identities=33%  Similarity=0.325  Sum_probs=25.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      -+.|+|++|+|||+++..+++ +|+++++.|
T Consensus         4 ~i~ltG~~gsGKst~~~~l~~-~g~~~i~~D   33 (194)
T PRK00081          4 IIGLTGGIGSGKSTVANLFAE-LGAPVIDAD   33 (194)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-cCCEEEEec
Confidence            478999999999999999998 888776554

>TIGR00235 udk uridine kinase

Probab=95.75  E-value=0.0079  Score=53.77  Aligned_cols=23  Identities=22%  Similarity=0.304  Sum_probs=20.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.+.||+|+|||||+++++..++
T Consensus         9 i~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         9 IGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            45999999999999999999875

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.75  E-value=0.0081  Score=53.29  Aligned_cols=25  Identities=36%  Similarity=0.477  Sum_probs=22.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||+|+|||+|++.++..+.
T Consensus         6 ~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          6 LLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCc
Confidence            4578999999999999999999875

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=95.74  E-value=0.0082  Score=48.01  Aligned_cols=22  Identities=32%  Similarity=0.531  Sum_probs=19.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +++.|++|+|||+|++.++...
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            6789999999999999999654

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.74  E-value=0.0077  Score=53.22  Aligned_cols=25  Identities=24%  Similarity=0.406  Sum_probs=22.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++-++|.||+|+|||+|++.+.+..
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcC
Confidence            3557899999999999999998875

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.73  E-value=0.042  Score=58.33  Aligned_cols=63  Identities=24%  Similarity=0.305  Sum_probs=42.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----C-CcEEEEecCCcC----------------------CchHHHHHHHhcCCCcE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----H-FDVYDLELSSVE----------------------GNKHLRKVLIATENKSI  282 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----~-~~~~~l~~~~~~----------------------~~~~l~~~l~~~~~~~I  282 (338)
                      -++|.||+|+|||+++..||..+    | ..+..+......                      +..++.+.+.......+
T Consensus       187 Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~~~~~D~  266 (767)
T PRK14723        187 VLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAALGDKHL  266 (767)
T ss_pred             EEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHHhcCCCE
Confidence            46899999999999999999765    2 244444332211                      23456666777777788


Q ss_pred             EEEcCCCccC
Q 035959          283 LVVGDIDCCT  292 (338)
Q Consensus       283 l~iDeiD~~~  292 (338)
                      ||||=.-...
T Consensus       267 VLIDTAGRs~  276 (767)
T PRK14723        267 VLIDTVGMSQ  276 (767)
T ss_pred             EEEeCCCCCc
Confidence            9888666543

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=95.73  E-value=0.021  Score=54.59  Aligned_cols=34  Identities=15%  Similarity=0.204  Sum_probs=26.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~  263 (338)
                      -++++||||+|||.++..+|...         +..+++++..+
T Consensus       104 vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~  146 (317)
T PRK04301        104 ITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEG  146 (317)
T ss_pred             EEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCC
Confidence            35799999999999999988653         23677777655

>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=95.73  E-value=0.0093  Score=61.34  Aligned_cols=33  Identities=18%  Similarity=0.341  Sum_probs=30.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      ..++|.|.||+|||++.+.+|+.++++++++|-
T Consensus         7 ~~i~LiG~~GaGKttvg~~LA~~L~~~fiD~D~   39 (542)
T PRK14021          7 PQAVIIGMMGAGKTRVGKEVAQMMRLPFADADV   39 (542)
T ss_pred             ccEEEECCCCCCHHHHHHHHHHHhCCCEEEchH
Confidence            357899999999999999999999999998874

>COG0802 Predicted ATPase or kinase [General function prediction only]

Probab=95.72  E-value=0.074  Score=45.22  Aligned_cols=38  Identities=29%  Similarity=0.347  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhhh--cCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          216 KKMIMDDLERAW--KRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       216 k~~i~~~l~~~~--~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ..++-+.+....  ..-++|.|+=|.|||+++++++..++
T Consensus        11 t~~lg~~l~~~l~~g~Vv~L~GdLGAGKTtf~rgi~~~Lg   50 (149)
T COG0802          11 TLALGERLAEALKAGDVVLLSGDLGAGKTTLVRGIAKGLG   50 (149)
T ss_pred             HHHHHHHHHhhCCCCCEEEEEcCCcCChHHHHHHHHHHcC
Confidence            344444444433  23468999999999999999999986

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.72  E-value=0.0097  Score=52.72  Aligned_cols=23  Identities=22%  Similarity=0.303  Sum_probs=20.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.+.|+||+|||++++.++..++
T Consensus         2 i~i~G~sgsGKTtla~~l~~~~~   24 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRILP   24 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            46789999999999999999983

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.

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=95.71  E-value=0.01  Score=56.70  Aligned_cols=31  Identities=23%  Similarity=0.464  Sum_probs=26.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+++.||+|+|||+++..+|..++..++..
T Consensus         5 ~~i~i~GptgsGKt~la~~la~~~~~~iis~   35 (307)
T PRK00091          5 KVIVIVGPTASGKTALAIELAKRLNGEIISA   35 (307)
T ss_pred             eEEEEECCCCcCHHHHHHHHHHhCCCcEEec
Confidence            4578999999999999999999987655444

>PF00488 MutS_V: MutS domain V C-terminus

Probab=95.71  E-value=0.036  Score=50.83  Aligned_cols=65  Identities=23%  Similarity=0.361  Sum_probs=41.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh-----CC------------cE--EEEecC-CcCC--------chHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL-----HF------------DV--YDLELS-SVEG--------NKHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l-----~~------------~~--~~l~~~-~~~~--------~~~l~~~l~~~~~~  280 (338)
                      +.++|+||...|||++++.+|-..     |.            +-  ..+... ++..        -.++..++....++
T Consensus        44 ~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~  123 (235)
T PF00488_consen   44 RIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAESAEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNATEK  123 (235)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSEEEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH--TT
T ss_pred             eEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecccccccccEEEeecccccccccccccHHHhHHHHHhhhhhcccc
Confidence            568999999999999999987533     32            11  111111 1111        13566778888899


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      ++|+|||+-.-..
T Consensus       124 sLvliDE~g~gT~  136 (235)
T PF00488_consen  124 SLVLIDELGRGTN  136 (235)
T ss_dssp             EEEEEESTTTTSS
T ss_pred             eeeecccccCCCC
Confidence            9999999987655

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.70  E-value=0.015  Score=53.08  Aligned_cols=33  Identities=27%  Similarity=0.233  Sum_probs=23.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      .-+++.||||||||+++..++..+   |..+.+++.
T Consensus        25 ~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~   60 (230)
T PRK08533         25 SLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVST   60 (230)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeC
Confidence            457999999999999975554433   556666654

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=95.70  E-value=0.044  Score=50.96  Aligned_cols=66  Identities=12%  Similarity=0.091  Sum_probs=44.7

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhC----------------------CcEEEEecCC-cCCchHHHHHHHhc---C---
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLH----------------------FDVYDLELSS-VEGNKHLRKVLIAT---E---  278 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~----------------------~~~~~l~~~~-~~~~~~l~~~l~~~---~---  278 (338)
                      +..+||+||+|+||..+|.++|..+-                      .+++.+.... ....++++++....   +   
T Consensus         7 ~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s~e~   86 (261)
T PRK05818          7 THPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPSVES   86 (261)
T ss_pred             CcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCchhc
Confidence            47899999999999999999998761                      2344442221 12234455554433   1   


Q ss_pred             -CCcEEEEcCCCccCC
Q 035959          279 -NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 -~~~Il~iDeiD~~~~  293 (338)
                       ..-|++|+++|.+..
T Consensus        87 ~~~KV~II~~ae~m~~  102 (261)
T PRK05818         87 NGKKIYIIYGIEKLNK  102 (261)
T ss_pred             CCCEEEEeccHhhhCH
Confidence             368999999999864

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.68  E-value=0.026  Score=55.96  Aligned_cols=33  Identities=27%  Similarity=0.387  Sum_probs=25.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSS  263 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~  263 (338)
                      +++.||+|+|||+++..+|..+    |..+..+++..
T Consensus       226 i~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt  262 (432)
T PRK12724        226 VFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDN  262 (432)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccc
Confidence            6799999999999999999754    45566665544

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=95.68  E-value=0.012  Score=55.64  Aligned_cols=30  Identities=27%  Similarity=0.576  Sum_probs=25.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +++.||+|+|||+++..+|..++..++.+|
T Consensus         2 i~i~G~t~~GKs~la~~l~~~~~~~iis~D   31 (287)
T TIGR00174         2 IFIMGPTAVGKSQLAIQLAKKLNAEIISVD   31 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCcEEEec
Confidence            578999999999999999999886665553

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=95.68  E-value=0.013  Score=60.47  Aligned_cols=34  Identities=29%  Similarity=0.283  Sum_probs=27.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC----cEEEEecCCc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF----DVYDLELSSV  264 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~----~~~~l~~~~~  264 (338)
                      ++|.|+||+|||++++++|..++.    +++.++...+
T Consensus       395 Ivl~Gl~GSGKSTia~~La~~L~~~~g~~~~~lD~D~v  432 (568)
T PRK05537        395 VFFTGLSGAGKSTIAKALMVKLMEMRGRPVTLLDGDVV  432 (568)
T ss_pred             EEEECCCCChHHHHHHHHHHHhhhccCceEEEeCCcHH
Confidence            578899999999999999999875    4566655443

>PRK07667 uridine kinase; Provisional

Probab=95.68  E-value=0.024  Score=50.14  Aligned_cols=33  Identities=12%  Similarity=0.254  Sum_probs=25.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSS  263 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~  263 (338)
                      +.+.|+||+|||+++..++..++   .++..++..+
T Consensus        20 IgI~G~~gsGKStla~~L~~~l~~~~~~~~~i~~Dd   55 (193)
T PRK07667         20 LGIDGLSRSGKTTFVANLKENMKQEGIPFHIFHIDD   55 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEEcCc
Confidence            46899999999999999999873   4555555544

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.67  E-value=0.029  Score=56.93  Aligned_cols=47  Identities=17%  Similarity=0.148  Sum_probs=33.5

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHH----hCCcEEEEecCCcCCchHHHHHHHh
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANY----LHFDVYDLELSSVEGNKHLRKVLIA  276 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~----l~~~~~~l~~~~~~~~~~l~~~l~~  276 (338)
                      .+.+|+.||||||||+++..++..    .|.+.+++.+.+  +..++.+-...
T Consensus        21 g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~eE--~~~~l~~~~~~   71 (484)
T TIGR02655        21 GRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFEE--SPQDIIKNARS   71 (484)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEec--CHHHHHHHHHH
Confidence            466899999999999999987543    267888888753  34444444433

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.67  E-value=0.014  Score=52.99  Aligned_cols=34  Identities=18%  Similarity=0.227  Sum_probs=27.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~  263 (338)
                      -++|.|+||+|||+++..+|...    +.+++++++..
T Consensus        15 l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~   52 (242)
T cd00984          15 LIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEM   52 (242)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCC
Confidence            46899999999999988877654    77888877543

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.

>COG1485 Predicted ATPase [General function prediction only]

Probab=95.66  E-value=0.029  Score=54.04  Aligned_cols=27  Identities=33%  Similarity=0.468  Sum_probs=23.9

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ++|++|||+-|.|||+|.......+..
T Consensus        65 ~~GlYl~GgVGrGKT~LMD~Fy~~lp~   91 (367)
T COG1485          65 VRGLYLWGGVGRGKTMLMDLFYESLPG   91 (367)
T ss_pred             CceEEEECCCCccHHHHHHHHHhhCCc
Confidence            589999999999999999998877743

>PRK13975 thymidylate kinase; Provisional

Probab=95.66  E-value=0.0092  Score=52.46  Aligned_cols=27  Identities=22%  Similarity=0.175  Sum_probs=23.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDV  256 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~  256 (338)
                      -+.+.|++|+|||++++.+|..++...
T Consensus         4 ~I~ieG~~GsGKtT~~~~L~~~l~~~~   30 (196)
T PRK13975          4 FIVFEGIDGSGKTTQAKLLAEKLNAFW   30 (196)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCe
Confidence            467999999999999999999998643

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=95.66  E-value=0.0078  Score=53.25  Aligned_cols=23  Identities=35%  Similarity=0.631  Sum_probs=21.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-+.||+|+|||+++++++..++
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            45899999999999999999996

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 ....

>PRK13951 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=95.64  E-value=0.01  Score=60.23  Aligned_cols=32  Identities=25%  Similarity=0.435  Sum_probs=28.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .+.|.|+||+|||++++.+|..+++++++.|.
T Consensus         2 ~I~l~G~~GsGKSTv~~~La~~lg~~~id~D~   33 (488)
T PRK13951          2 RIFLVGMMGSGKSTIGKRVSEVLDLQFIDMDE   33 (488)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcCCeEEECcH
Confidence            37899999999999999999999999887753

>PRK06851 hypothetical protein; Provisional

Probab=95.64  E-value=0.015  Score=56.70  Aligned_cols=32  Identities=41%  Similarity=0.649  Sum_probs=26.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      .+-++|.|+||||||++++.++..+   |+++-.+
T Consensus        30 ~~~~il~G~pGtGKStl~~~i~~~~~~~g~~Ve~~   64 (367)
T PRK06851         30 NRIFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFL   64 (367)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            4678999999999999999999887   4554444

>PHA00350 putative assembly protein

Probab=95.63  E-value=0.024  Score=55.87  Aligned_cols=61  Identities=18%  Similarity=0.233  Sum_probs=36.6

Q ss_pred             eeeeCCCCCCcHHHHHH--HHHHh--CCcEEEEecCCcCCchHHHHH---------------------------HHhcCC
Q 035959          231 YLLFGPPGTGKSSLIAA--MANYL--HFDVYDLELSSVEGNKHLRKV---------------------------LIATEN  279 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~a--ia~~l--~~~~~~l~~~~~~~~~~l~~~---------------------------l~~~~~  279 (338)
                      ++++|.||+|||..+-.  +-..+  |..++ .+...+. .+.+.+.                           +.-.+.
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~GR~V~-TNI~Gl~-le~i~~~~~~~p~~~~li~i~~~~~~~~~~~~~~~~w~p~   81 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKDGRKVI-TNIPGLN-LDVFEKVFGEFPSTARLIRIVDRNLEGFESMNRPFSWRPR   81 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHCCCEEE-ECCCCCC-HHHHHhhcccCcccceeEEeccccccchhhhccccccCCC
Confidence            57999999999997665  33333  54443 2333221 0111111                           111347


Q ss_pred             CcEEEEcCCCccCC
Q 035959          280 KSILVVGDIDCCTE  293 (338)
Q Consensus       280 ~~Il~iDeiD~~~~  293 (338)
                      .++|||||+..+.+
T Consensus        82 gaLIViDEaq~~~p   95 (399)
T PHA00350         82 GALYVIDEAQMIFP   95 (399)
T ss_pred             CCEEEEECchhhcC
Confidence            78999999999988

>PRK00023 cmk cytidylate kinase; Provisional

Probab=95.63  E-value=0.0094  Score=54.28  Aligned_cols=32  Identities=28%  Similarity=0.420  Sum_probs=27.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-+.+.||||+|||++++.+|+.+|++++..+
T Consensus         5 ~~i~i~g~~gsGksti~~~la~~~~~~~~~~~   36 (225)
T PRK00023          5 IVIAIDGPAGSGKGTVAKILAKKLGFHYLDTG   36 (225)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCcccCc
Confidence            34679999999999999999999998776543

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=95.63  E-value=0.016  Score=64.42  Aligned_cols=64  Identities=25%  Similarity=0.389  Sum_probs=49.0

Q ss_pred             hhcCceeeeCCCCCCcHH-HHHHHHHHhCCcEEEEecCCcCCchHHHHHHH-hc------------C----CCcEEEEcC
Q 035959          226 AWKRGYLLFGPPGTGKSS-LIAAMANYLHFDVYDLELSSVEGNKHLRKVLI-AT------------E----NKSILVVGD  287 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~-l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~-~~------------~----~~~Il~iDe  287 (338)
                      ...|+|+++||||+|||. ++.++-+..-+++..++.+.-.+......++. .+            +    +.-||+.||
T Consensus      1492 nt~R~~i~cGppGSgK~mlM~~sLrs~~~~ev~~~Nfs~~t~T~s~ls~Ler~t~yy~~tg~~~l~PK~~vK~lVLFcDe 1571 (3164)
T COG5245        1492 NTLRSYIYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMTPSKLSVLERETEYYPNTGVVRLYPKPVVKDLVLFCDE 1571 (3164)
T ss_pred             hccceEEEECCCCCccchhcchhhhhhhheeeeEEeeccccCCHHHHHHHHhhceeeccCCeEEEccCcchhheEEEeec
Confidence            346999999999999999 47888889999999999987665443333333 33            1    346899999


Q ss_pred             CC
Q 035959          288 ID  289 (338)
Q Consensus       288 iD  289 (338)
                      |.
T Consensus      1572 In 1573 (3164)
T COG5245        1572 IN 1573 (3164)
T ss_pred             cC
Confidence            99

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.63  E-value=0.022  Score=54.95  Aligned_cols=27  Identities=22%  Similarity=0.332  Sum_probs=24.3

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .+.++++.||+|+|||+++.|+..++.
T Consensus       159 ~~~nili~G~tgSGKTTll~aL~~~ip  185 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTFTNAALREIP  185 (332)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHhhCC
Confidence            357899999999999999999999885

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=95.62  E-value=0.012  Score=55.89  Aligned_cols=26  Identities=27%  Similarity=0.360  Sum_probs=24.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      -+++.|++|||||+++..+|..++.+
T Consensus        94 iIlI~G~sgsGKStlA~~La~~l~~~  119 (301)
T PRK04220         94 IILIGGASGVGTSTIAFELASRLGIR  119 (301)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            46899999999999999999999876

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=95.62  E-value=0.019  Score=48.18  Aligned_cols=21  Identities=29%  Similarity=0.461  Sum_probs=18.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|+||+|||+|+.+++..
T Consensus         3 i~~vG~~~vGKTsli~~l~~~   23 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEG   23 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999998864

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.

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=95.61  E-value=0.01  Score=63.00  Aligned_cols=29  Identities=41%  Similarity=0.650  Sum_probs=25.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +.+.||||||||++++.+|..+|+.+++.
T Consensus         4 i~I~G~~GsGKST~ak~la~~l~~~~~~~   32 (712)
T PRK09518          4 VAIDGPAGVGKSSVSRALAQYLGYAYLDT   32 (712)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEeec
Confidence            57899999999999999999999775543

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.61  E-value=0.008  Score=53.87  Aligned_cols=23  Identities=30%  Similarity=0.521  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      +-++|.||+|+|||+|+.++.+.
T Consensus        14 ~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         14 LLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             eEEEEECcCCCCHHHHHHHHHhc
Confidence            55789999999999999999754

>TIGR00152 dephospho-CoA kinase

Probab=95.58  E-value=0.012  Score=51.77  Aligned_cols=30  Identities=37%  Similarity=0.509  Sum_probs=25.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +.|+|.+|+|||++++.++...++++++.|
T Consensus         2 i~itG~~gsGKst~~~~l~~~~~~~~i~~D   31 (188)
T TIGR00152         2 IGLTGGIGSGKSTVANYLADKYHFPVIDAD   31 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCeEEeCC
Confidence            568999999999999999998777776553

This model produces scores in the range of 0-25 bits against adenylate, guanylate, uridine, and thymidylate kinases.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=95.56  E-value=0.049  Score=60.04  Aligned_cols=65  Identities=18%  Similarity=0.302  Sum_probs=42.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC----------CchHHHHHHHh-------cCCCcEEEEcC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE----------GNKHLRKVLIA-------TENKSILVVGD  287 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~----------~~~~l~~~l~~-------~~~~~Il~iDe  287 (338)
                      .+-.++.|++|||||++++++...+   |+.++-+-++.-.          ....+..++..       +..+.||||||
T Consensus       397 ~r~~~v~G~AGTGKTt~l~~~~~~~e~~G~~V~g~ApTgkAA~~L~e~~Gi~a~TIas~ll~~~~~~~~l~~~~vlVIDE  476 (1102)
T PRK13826        397 ARIAAVVGRAGAGKTTMMKAAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRDQLDNKTVFVLDE  476 (1102)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEcCcHHHHHHHHHhhCCCeeeHHHHHhhhccCccCCCCCcEEEEEC
Confidence            3556899999999999999987754   6666655333211          11234443222       23568999999


Q ss_pred             CCccC
Q 035959          288 IDCCT  292 (338)
Q Consensus       288 iD~~~  292 (338)
                      +-.+.
T Consensus       477 AsMv~  481 (1102)
T PRK13826        477 AGMVA  481 (1102)
T ss_pred             cccCC
Confidence            98764

>KOG1808 consensus AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=95.55  E-value=0.055  Score=61.92  Aligned_cols=91  Identities=18%  Similarity=0.211  Sum_probs=60.6

Q ss_pred             CCcccc-ccCChhHHHHHHHHHHhhh--cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHH---------
Q 035959          203 PSTFDT-LAMDTDMKKMIMDDLERAW--KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHL---------  270 (338)
Q Consensus       203 p~~f~~-l~~~~~~k~~i~~~l~~~~--~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l---------  270 (338)
                      +..+++ ++.-+.+++-+.+....-.  +-.+||-||.|+|||+++.-+|...|..+..++..+..+-.++         
T Consensus       412 ~~~~~~~~i~T~~vq~~la~~~~a~~~~~~pillqG~tssGKtsii~~la~~~g~~~vrinnhehtd~qeyig~y~~~~~  491 (1856)
T KOG1808|consen  412 LTSEATHYIITPRVQKNLADLARAISSGKFPILLQGPTSSGKTSIIKELARATGKNIVRINNHEHTDLQEYIGTYVADDN  491 (1856)
T ss_pred             cccccceeeccHHHHHHHHHHHHHHhcCCCCeEEecCcCcCchhHHHHHHHHhccCceehhccccchHHHHHHhhhcCCC
Confidence            345555 5555555544443333322  2368999999999999999999999999998877664432111         


Q ss_pred             -------HHHHHhcCCCcEEEEcCCCccCC
Q 035959          271 -------RKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       271 -------~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                             -.+...+.+.+.+++|++.....
T Consensus       492 g~l~freg~LV~Alr~G~~~vlD~lnla~~  521 (1856)
T KOG1808|consen  492 GDLVFREGVLVQALRNGDWIVLDELNLAPH  521 (1856)
T ss_pred             CCeeeehhHHHHHHHhCCEEEeccccccch
Confidence                   12233334789999999887653

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.53  E-value=0.024  Score=55.56  Aligned_cols=64  Identities=23%  Similarity=0.320  Sum_probs=45.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh--CCcEEEEecCCcC--------------------CchHHHHHHHhc--CCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL--HFDVYDLELSSVE--------------------GNKHLRKVLIAT--ENKSILVV  285 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l--~~~~~~l~~~~~~--------------------~~~~l~~~l~~~--~~~~Il~i  285 (338)
                      -+|+-|.||.|||+|+--+|..+  ..++.++...+-.                    .+.++..++..+  .+|.+++|
T Consensus        95 ~iLIgGdPGIGKSTLLLQva~~lA~~~~vLYVsGEES~~QiklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~p~lvVI  174 (456)
T COG1066          95 VILIGGDPGIGKSTLLLQVAARLAKRGKVLYVSGEESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAELEQEKPDLVVI  174 (456)
T ss_pred             EEEEccCCCCCHHHHHHHHHHHHHhcCcEEEEeCCcCHHHHHHHHHHhCCCccceEEehhcCHHHHHHHHHhcCCCEEEE
Confidence            36899999999999877777665  2378888765522                    133444444444  48999999


Q ss_pred             cCCCccCC
Q 035959          286 GDIDCCTE  293 (338)
Q Consensus       286 DeiD~~~~  293 (338)
                      |-|..+..
T Consensus       175 DSIQT~~s  182 (456)
T COG1066         175 DSIQTLYS  182 (456)
T ss_pred             eccceeec
Confidence            99999976

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=95.52  E-value=0.023  Score=52.68  Aligned_cols=50  Identities=32%  Similarity=0.394  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhhhcCce--eeeCCCCCCcHHHHHHHHHHh---C--CcEEEEecCCcC
Q 035959          216 KKMIMDDLERAWKRGY--LLFGPPGTGKSSLIAAMANYL---H--FDVYDLELSSVE  265 (338)
Q Consensus       216 k~~i~~~l~~~~~~g~--LL~GppGtGKT~l~~aia~~l---~--~~~~~l~~~~~~  265 (338)
                      .+++++.+....++.+  =++||||.|||+|+.+++.++   |  ..++-+|.++..
T Consensus        15 ~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~   71 (266)
T PF03308_consen   15 ARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPF   71 (266)
T ss_dssp             HHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGC
T ss_pred             HHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCC
Confidence            3445555543223333  389999999999999999887   2  346777777654

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=95.51  E-value=0.032  Score=47.02  Aligned_cols=21  Identities=29%  Similarity=0.501  Sum_probs=18.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|+||+|||+|+.++...
T Consensus         3 i~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        3 LVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999999863

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PRK08356 hypothetical protein; Provisional

Probab=95.51  E-value=0.013  Score=51.82  Aligned_cols=25  Identities=16%  Similarity=0.139  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      -++|.||||+|||+++..++. .|+.
T Consensus         7 ~i~~~G~~gsGK~t~a~~l~~-~g~~   31 (195)
T PRK08356          7 IVGVVGKIAAGKTTVAKFFEE-KGFC   31 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCc
Confidence            367899999999999999964 6665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	338
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		9e-05
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		1e-04
3vfd_A	389	Human Spastin Aaa Domain Length = 389		2e-04
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		8e-04

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 47/85 (55%), Gaps = 11/85 (12%)
Query: 229 RGYLLFGPPGTGKSSLIAAMA----NYLHFDVYDLELSSV---EGNKHLRKVL-IATENK 280
           RG LLFGPPGTGKS L  A+A    N   F +   +L S    E  K ++ +  +A ENK
Sbjct: 168 RGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENK 227
Query: 281 -SILVVGDID--CCTELQDRSAQAR 302
            SI+ + +ID  C +  ++ S  AR
Sbjct: 228 PSIIFIDEIDSLCGSRSENESEAAR 252

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 47/85 (55%), Gaps = 11/85 (12%)
Query: 229 RGYLLFGPPGTGKSSLIAAMA----NYLHFDVYDLELSS---VEGNKHLRKVL-IATENK 280
           RG LLFGPPGTGKS L  A+A    N   F +   +L S    E  K ++ +  +A ENK
Sbjct: 46  RGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENK 105
Query: 281 -SILVVGDID--CCTELQDRSAQAR 302
            SI+ + +ID  C +  ++ S  AR
Sbjct: 106 PSIIFIDEIDSLCGSRSENESEAAR 130

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/124 (31%), Positives = 60/124 (48%), Gaps = 24/124 (19%)
Query: 225 RAWKRGYLLFGPPGTGKSSL---IAAMANYLHFDVYDLELSSV---EGNKHLRKVL-IAT 277
           RA  RG LLFGPPG GK+ L   +AA +N   F++    L+S    EG K +R +  +A 
Sbjct: 145 RAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVAR 204
Query: 278 E-NKSILVVGDIDC--CTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGD 334
           E   SI+ +  +D   C   +     +R    ++            L+ F DG+  S GD
Sbjct: 205 ELQPSIIFIDQVDSLLCERREGEHDASRRLKTEF------------LIEF-DGVQ-SAGD 250
Query: 335 ERII 338
           +R++
Sbjct: 251 DRVL 254

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 41/71 (57%), Gaps = 8/71 (11%)
Query: 230 GYLLFGPPGTGKSSL---IAAMANYLHFDVYDLELSS---VEGNKHLRKVL-IATENK-S 281
           G LL+GPPGTGKS L   +A  AN   F V   +L S    E  K ++++  +A ENK S
Sbjct: 62  GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPS 121
Query: 282 ILVVGDIDCCT 292
           I+ + ++D  T
Sbjct: 122 IIFIDEVDALT 132

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	338
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05
2qgz_A	308	Helicase loader, putative primosome component; str	6e-06
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-05
2chg_A	226	Replication factor C small subunit; DNA-binding pr	9e-05
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	1e-04
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	1e-04
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	1e-04
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	2e-04
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	2e-04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	2e-04
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	2e-04
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	3e-04
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	3e-04
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	5e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.2 bits (111), Expect = 6e-06
 Identities = 46/265 (17%), Positives = 81/265 (30%), Gaps = 67/265 (25%)

Query: 128 DQELCNNGNYMFKDRVPCFELRFHK----KH-----KETVLGTYIPHILKKSKE------ 172
           D E      Y +KD +  FE  F      K      K  +    I HI+           
Sbjct: 8   DFET-GEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66

Query: 173 -----LSKKKKTLKLF---TLNCN------RINHDTRQSAIL--DHPSTFDTLAMDTD-M 215
                LSK+++ ++ F    L  N       I  + RQ +++   +    D L  D    
Sbjct: 67  LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126

Query: 216 KKM------IMDDLERAWKR-----GYLLFGPPGTGKSSLIAAMAN------YLHFDVYD 258
            K           L +A          L+ G  G+GK+ +   +         + F ++ 
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 259 LELSSVEGNKHLRKVLIATENKSILVVGDIDC-CTELQDRSAQARTASPDWHSPKRDQIT 317
           L L     N +  + ++    K +     ID   T   D S+  +       +  R  + 
Sbjct: 187 LNL----KNCNSPETVLEMLQKLLY---QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 318 LS----GLLNFTDGLWSSCGDERII 338
                  LL     +     + +  
Sbjct: 240 SKPYENCLL-VLLNVQ----NAKAW 259

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.7 bits (102), Expect = 7e-05
 Identities = 48/332 (14%), Positives = 101/332 (30%), Gaps = 118/332 (35%)

Query: 4   MTT----VMSVAASAAATFMLIQSYTRIYLPDEV----SSYFDQKFKNFIARIYSESTLV 55
           +TT    V    ++A  T + +  ++    PDEV      Y D + ++    + + +   
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329

Query: 56  I----EEYDDGLNR---------NKLFKAAKL---YLEP-----------------KIPP 82
           +    E   DGL           +KL    +     LEP                  IP 
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389

Query: 83  NVNRIKI---NLPKKESEVSLS-------VEKNQA-----VFDVFNGVRLKWKFELKPA- 126
            +  + +   ++ K +  V ++       VEK        +  ++  + LK K E + A 
Sbjct: 390 IL--LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY--LELKVKLENEYAL 445

Query: 127 ---------PDQELCNNG-------NYMFK------------DRVPCFE-----LRFHK- 152
                      +   ++         Y +             +R+  F       RF + 
Sbjct: 446 HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQ 505

Query: 153 --KHKET-------------VLGTYIPHILKKSKELSKKKKTLKLFTLNCNRINHDTRQS 197
             +H  T              L  Y P+I     +  +    +  F          ++ +
Sbjct: 506 KIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYT 565

Query: 198 AILDHPSTFDTLAMDTDMKKMIMDDLERAWKR 229
            +L        +A+  +  + I ++  +  +R
Sbjct: 566 DLLR-------IALMAE-DEAIFEEAHKQVQR 589

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 46.4 bits (110), Expect = 6e-06
 Identities = 33/198 (16%), Positives = 69/198 (34%), Gaps = 28/198 (14%)

Query: 55  VIEEYDDGLNRNKLFKAAKLYLEPKIPPNVNRIKINLPKKESEVSLSVEKNQAVFDVFNG 114
            + +       N       +  +P++   +++  ++    + +++LS+ K          
Sbjct: 7   TMAKLGQNTRVNSDQLIQTILADPEVASFISQHHLS----QEQINLSLSKFNQFLVERQK 62

Query: 115 VRLKWKFELKPAPDQELCNNGNYMFKDRVPCFELRFHKKHKETVLGTYIPHILKKSKELS 174
            +LK    +       L  N  Y     +   EL   +K             + +  +L 
Sbjct: 63  YQLKDPSYIAKGYQPILAMNEGYADVSYLETKELVEAQKQAA----------ISERIQLV 112

Query: 175 KKKKTLKLFTLNCNRINHDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLF 234
              K+ +   L+   +N+ +R  A                     ++    A ++G  L+
Sbjct: 113 SLPKSYRHIHLSDIDVNNASRMEAF--------------SAILDFVEQYPSAEQKGLYLY 158

Query: 235 GPPGTGKSSLIAAMANYL 252
           G  G GKS L+AAMA+ L
Sbjct: 159 GDMGIGKSYLLAAMAHEL 176

>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 = 42.2 bits (100), Expect = 9e-05
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 11/66 (16%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRGY----LLFGPPGTGKSSLIAAMANYLHFDVYD 258
           P T D +    ++ +     L+   +R      L  GPPGTGK++   A+A  L  + + 
Sbjct: 13  PRTLDEVVGQDEVIQR----LKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWR 68

Query: 259 ---LEL 261
              +E+
Sbjct: 69  DNFIEM 74

>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 = 42.9 bits (101), Expect = 1e-04
 Identities = 31/115 (26%), Positives = 48/115 (41%), Gaps = 33/115 (28%)

Query: 229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV------EGNKHLRKVLI-ATENK- 280
           RG LL+GPPGTGK+ +  A+AN      + +    +      E   +LRK    A +N  
Sbjct: 239 RGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAP 298

Query: 281 SILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQI-------TLSGLLNFTDGL 328
           +I+ + ++D                     PKR++         +S LL   DGL
Sbjct: 299 AIIFIDELDAIA------------------PKREKTHGEVERRIVSQLLTLMDGL 335

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 224 ERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL--SSVEGNKHLR-KVLIATENK 280
                R  +L+GPPG GK++    +A  L +D+  LE   S V     L   V  A +N 
Sbjct: 73  GSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI--LEQNASDVRSKTLLNAGVKNALDNM 130

Query: 281 SIL 283
           S++
Sbjct: 131 SVV 133

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 9/75 (12%)

Query: 223 LERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV------EGNKHLRKV-LI 275
           L    + G LLFGPPG GK+ L  A+A   +   +++  +S+      EG K +R +  +
Sbjct: 144 LRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAV 202

Query: 276 ATENK-SILVVGDID 289
           A E + SI+ +  +D
Sbjct: 203 ARELQPSIIFIDQVD 217

>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 = 42.1 bits (99), Expect = 2e-04
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 9/75 (12%)

Query: 223 LERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV------EGNKHLRKV-LI 275
           L    K G LLFGPPGTGK+ +   +A+      + +  SS+      EG K +R +  +
Sbjct: 113 LRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEGEKMVRALFAV 171

Query: 276 ATENK-SILVVGDID 289
           A   + +++ + +ID
Sbjct: 172 ARCQQPAVIFIDEID 186

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 223 LERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV------EGNKHLRKV-LI 275
           L    K G LLFGPPG GK+ L  A+A        ++  +S+      +G K +R +  +
Sbjct: 50  LRAPAK-GLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSKYVGDGEKLVRALFAV 108

Query: 276 ATENK-SILVVGDID 289
           A   + SI+ + ++D
Sbjct: 109 ARHMQPSIIFIDEVD 123

>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 = 41.5 bits (98), Expect = 2e-04
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 11/66 (16%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRGY----LLFGPPGTGKSSLIAAMANYLHFDVYD 258
           P T D +    ++ +     L+   +R      L  GPPGTGK++   A+A  L  + + 
Sbjct: 13  PRTLDEVVGQDEVIQR----LKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWR 68

Query: 259 ---LEL 261
              +E+
Sbjct: 69  DNFIEM 74

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A* Length = 180

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 10/56 (17%), Positives = 17/56 (30%), Gaps = 7/56 (12%)

Query: 204 STFDTLAMDTDMKKMIM-------DDLERAWKRGYLLFGPPGTGKSSLIAAMANYL 252
           +  DT       +   +        +      +G    G PG GK+ L  A    +
Sbjct: 7   ANLDTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAI 62

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 41.2 bits (97), Expect = 3e-04
 Identities = 16/26 (61%), Positives = 18/26 (69%), Gaps = 1/26 (3%)

Query: 225 RAWKRGYLLFGPPGTGKSSLIAAMAN 250
             W+ G LLFGPPGTGKS L  A+A 
Sbjct: 43  TPWR-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 = 40.8 bits (96), Expect = 3e-04
 Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 1/26 (3%)

Query: 225 RAWKRGYLLFGPPGTGKSSLIAAMAN 250
           +    G LL+GPPGTGKS L  A+A 
Sbjct: 49  KPTS-GILLYGPPGTGKSYLAKAVAT 73

>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 = 40.4 bits (95), Expect = 5e-04
 Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 11/66 (16%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRGY----LLFGPPGTGKSSLIAAMANYLHFDVYD 258
           P   D +     + K     L+   K G     L  GPPG GK++   A+A  L  + + 
Sbjct: 21  PQRLDDIVGQEHIVKR----LKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWR 76

Query: 259 ---LEL 261
              LEL
Sbjct: 77  HNFLEL 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	338
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.83
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.82
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.82
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.81
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.81
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.65
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.64
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.62
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.61
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.55
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.55
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.55
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.54
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.54
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.53
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.51
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.51
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.51
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.5
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.49
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.46
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.44
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.41
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.39
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.36
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.34
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.3
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.29
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.29
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.28
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.26
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.25
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.25
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.24
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.24
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.23
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.22
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.22
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.2
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.2
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.17
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.16
3pvs_A	447	Replication-associated recombination protein A; ma	99.14
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.12
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.12
3co5_A	143	Putative two-component system transcriptional RES	99.1
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.09
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.09
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.08
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.06
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.06
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.05
3bos_A	242	Putative DNA replication factor; P-loop containing	99.04
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.04
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.02
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.0
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.0
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.98
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.96
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.93
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	98.93
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.93
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.92
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.91
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.91
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.91
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.86
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	98.84
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.84
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.82
2qgz_A	308	Helicase loader, putative primosome component; str	98.82
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.81
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.78
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.77
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.77
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.76
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	98.75
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.72
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.72
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.64
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.64
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.61
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	98.61
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	98.5
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.38
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.37
2fna_A	357	Conserved hypothetical protein; structural genomic	98.35
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.28
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.22
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.21
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	98.19
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.17
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	98.12
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.09
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.08
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.08
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	97.91
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	97.9
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	97.77
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.57
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.56
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.53
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.52
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	97.46
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	97.43
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	97.42
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.38
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.37
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.35
1via_A	175	Shikimate kinase; structural genomics, transferase	97.34
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.34
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.33
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.3
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.3
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.29
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.27
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.24
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.22
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.22
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.22
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.21
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.21
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.21
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.18
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.16
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.15
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.15
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.12
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.1
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.1
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.1
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.09
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.09
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.07
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	97.07
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.05
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.04
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.04
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.02
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.02
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.01
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.0
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.99
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.99
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.98
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.98
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.97
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.95
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.94
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.93
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.92
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.91
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	96.89
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.87
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.85
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.83
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.83
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.83
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.82
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	96.81
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.77
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.75
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	96.75
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	96.75
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.75
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.75
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.75
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.74
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.74
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.73
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.72
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.71
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.69
3f8t_A	506	Predicted ATPase involved in replication control,	96.68
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.68
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.66
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.66
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.65
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.63
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.62
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.61
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.58
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.55
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.53
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.52
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.51
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	96.51
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.47
3io5_A	333	Recombination and repair protein; storage dimer, i	96.46
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.42
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.42
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.41
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.37
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.36
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.35
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.31
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.3
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.28
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.28
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.27
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.26
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.24
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.23
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	96.21
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.18
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.17
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.16
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	96.0
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	96.0
3b6e_A	216	Interferon-induced helicase C domain-containing P;	95.99
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.98
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.97
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.96
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.95
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.94
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.94
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.94
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.93
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.92
1p9r_A	418	General secretion pathway protein E; bacterial typ	95.92
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.88
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.85
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.85
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.85
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.84
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.81
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	95.8
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	95.77
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.75
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.73
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.72
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.7
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.66
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.64
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.61
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.57
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	95.54
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.46
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.39
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.39
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.38
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.38
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	95.32
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	95.32
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.3
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	95.3
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.28
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.25
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.24
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.23
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	95.2
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	95.2
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.2
2ewv_A	372	Twitching motility protein PILT; pilus retraction	95.18
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.16
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.16
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.14
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.12
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.11
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	95.1
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.06
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	95.04
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	95.03
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.02
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	95.0
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.95
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.84
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	94.82
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	94.82
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	94.8
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.79
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.77
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	94.74
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.72
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	94.71
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.69
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.68
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.67
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	94.66
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	94.65
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.62
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	94.57
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.56
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.53
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.51
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.51
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.51
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	94.5
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.49
2hf9_A	226	Probable hydrogenase nickel incorporation protein	94.43
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.37
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	94.36
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.35
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.3
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.26
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	94.2
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.17
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.16
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	94.16
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.16
1nrj_B	218	SR-beta, signal recognition particle receptor beta	94.14
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	94.14
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	94.12
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	94.11
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.11
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.1
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.09
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.09
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.02
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	94.0
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	93.99
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.97
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	93.97
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.88
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.87
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	93.85
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.84
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	93.83
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.82
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.82
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.82
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.81
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	93.8
2wji_A	165	Ferrous iron transport protein B homolog; membrane	93.8
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	93.8
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	93.79
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	93.77
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	93.75
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	93.74
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.7
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	93.69
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	93.66
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.66
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	93.64
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	93.63
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	93.63
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.63
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.63
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.63
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	93.59
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.59
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.56
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.56
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	93.53
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	93.51
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.49
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.46
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.46
1sgw_A	214	Putative ABC transporter; structural genomics, P p	93.46
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	93.45
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.42
2og2_A	359	Putative signal recognition particle receptor; nuc	93.41
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	93.4
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	93.38
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	93.36
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.32
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	93.32
1b0u_A	262	Histidine permease; ABC transporter, transport pro	93.31
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.28
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	93.26
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	93.26
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	93.24
1g6h_A	257	High-affinity branched-chain amino acid transport	93.24
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	93.24
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	93.23
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	93.17
1ji0_A	240	ABC transporter; ATP binding protein, structural g	93.13
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.11
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	93.11
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.09
2xxa_A	433	Signal recognition particle protein; protein trans	93.09
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.07
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.05
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.04
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.03
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	93.03
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.03
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.03
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	93.01
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.96
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	92.94
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	92.93
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	92.92
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.9
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	92.89
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	92.87
2ghi_A	260	Transport protein; multidrug resistance protein, M	92.86
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	92.82
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	92.81
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	92.8
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	92.79
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	92.78
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	92.75
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	92.75
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	92.74
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.73
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	92.73
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	92.72
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	92.71
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	92.71
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	92.7
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	92.69
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	92.68
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	92.68
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	92.67
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	92.64
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.64
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	92.63
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	92.62
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	92.61
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	92.61
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	92.6
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	92.59
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	92.58
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.56
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	92.54
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	92.54
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	92.54
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	92.53
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	92.49
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	92.47
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	92.47
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.45
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	92.39
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	92.39
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	92.32
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	92.31
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	92.3
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	92.29
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.26
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	92.25
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	92.23
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	92.2
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	92.19
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	92.18
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.16
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	92.09
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.07
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	92.05
2fh5_B	214	SR-beta, signal recognition particle receptor beta	92.05
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	91.98
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	91.95
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	91.94
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	91.91
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	91.89
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	91.87
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	91.84
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	91.74
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	91.72
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	91.72
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	91.72
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	91.62
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	91.59
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	91.57
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	91.57
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	91.55
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	91.53
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	91.52
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	91.51
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	91.51
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	91.5
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	91.49
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	91.48
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	91.45
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	91.44
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	91.4
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	91.4
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	91.39
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	91.36
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	91.35
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	91.34
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	91.34
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	91.33
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	91.31
1qhl_A	227	Protein (cell division protein MUKB); SMC, chromos	91.29
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	91.27
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	91.25
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	91.25
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	91.25
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	91.24
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	91.24
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	91.19
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	91.17
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	91.14
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	91.13
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	91.12
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	91.02
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	90.97
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	90.96
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	90.89
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	90.89
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	90.86
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	90.84
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	90.78
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	90.78
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	90.72
3qkt_A	339	DNA double-strand break repair RAD50 ATPase; RECA-	90.68
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	90.65
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	90.64

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.83  E-value=1.7e-20  Score=182.21  Aligned_cols=122  Identities=28%  Similarity=0.373  Sum_probs=101.1

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      +.-+|+++++-++.|+++.+.+.-             ++++|+|||||||||||++|+|+|++++.+++.++++++.+  
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l~sk~  222 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQKY  222 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGGSCSS
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHhhccc
Confidence            345899999999999988887765             46799999999999999999999999999999999998874  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                          +..++.+|..+  .+||||||||||+++.  .|.....      +.+...++++++||+.|||+.+.
T Consensus       223 vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~--~R~~~~~------~~~~~~~~~l~~lL~~lDg~~~~  285 (405)
T 4b4t_J          223 IGEGSRMVRELFVMAREHAPSIIFMDEIDSIGS--TRVEGSG------GGDSEVQRTMLELLNQLDGFETS  285 (405)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTT--SCSCSSS------GGGGHHHHHHHHHHHHHHTTTCC
T ss_pred             cchHHHHHHHHHHHHHHhCCceEeeecchhhcc--CCCCCCC------CCcHHHHHHHHHHHHhhhccCCC
Confidence                45678888776  3799999999999987  5543322      11345678999999999999865

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.9e-20  Score=183.67  Aligned_cols=125  Identities=27%  Similarity=0.331  Sum_probs=103.9

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-  266 (338)
                      .+..+|+++++-++.|+++.+.+..             ++++|+|||||||||||++|+|+|++++.+++.++++++.+ 
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l~~~  245 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVHK  245 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGTCCS
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchhhcc
Confidence            3345899999999999999888775             57899999999999999999999999999999999998764 


Q ss_pred             -----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCC
Q 035959          267 -----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCG  333 (338)
Q Consensus       267 -----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g  333 (338)
                           ...++.+|..+  ..||||||||+|+++.  .|.....      ..+...++++++||+.|||+.+.++
T Consensus       246 ~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~--~R~~~~~------~~~~~~~r~l~~lL~~ldg~~~~~~  311 (428)
T 4b4t_K          246 YLGEGPRMVRDVFRLARENAPSIIFIDEVDSIAT--KRFDAQT------GSDREVQRILIELLTQMDGFDQSTN  311 (428)
T ss_dssp             SCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHC--SCSSSCS------CCCCHHHHHHHHHHHHHHHSCSSCS
T ss_pred             ccchhHHHHHHHHHHHHHcCCCeeechhhhhhhc--cccCCCC------CCChHHHHHHHHHHHHhhCCCCCCC
Confidence                 45678888766  3799999999999987  6644332      1234567899999999999987643

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.82  E-value=2.2e-20  Score=183.49  Aligned_cols=124  Identities=22%  Similarity=0.324  Sum_probs=102.4

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~  266 (338)
                      -.++.+|+++++.++.|+++.+.+..             ++++|+|||||||||||++|+|+|++++.+++.++++++.+
T Consensus       174 ~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s~l~~  253 (434)
T 4b4t_M          174 EKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQ  253 (434)
T ss_dssp             SSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGGCS
T ss_pred             CCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehhhhhh
Confidence            35566999999999999999887665             56899999999999999999999999999999999998874


Q ss_pred             ------chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ------NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ------~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                            ...++.+|..+.  .||||||||||+++.  +|.....+      .......+++.||+.|||+.+.
T Consensus       254 ~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~--~R~~~~~~------~~~~~~~~~~~lL~~ldg~~~~  318 (434)
T 4b4t_M          254 MYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGT--KRFDSEKS------GDREVQRTMLELLNQLDGFSSD  318 (434)
T ss_dssp             SCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHC--CCSSGGGG------TTHHHHHHHHHHHHHHTTSCSS
T ss_pred             cccchHHHHHHHHHHHHHhcCCeEEeecchhhhhh--ccCCCCCC------CchHHHHHHHHHHHHhhccCCC
Confidence                  345777777654  799999999999987  66544331      1234578999999999999864

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.81  E-value=7e-20  Score=180.03  Aligned_cols=123  Identities=24%  Similarity=0.330  Sum_probs=101.3

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-  266 (338)
                      .+.-+|+++++-++.|+++.+.+..             ++++|+|||||||||||++|+|+|++++.+++.++++++.+ 
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s~l~sk  254 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDK  254 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGTCCS
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehhhhccc
Confidence            3345899999999999998887765             46799999999999999999999999999999999998874 


Q ss_pred             -----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 -----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 -----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                           ...++.+|..+  ..||||||||||+++.  .|.....      ..+.....++++||+.|||+.+.
T Consensus       255 ~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~--~R~~~~~------~~~~~~~~~l~~lL~~lDg~~~~  318 (437)
T 4b4t_L          255 YIGESARIIREMFAYAKEHEPCIIFMDEVDAIGG--RRFSEGT------SADREIQRTLMELLTQMDGFDNL  318 (437)
T ss_dssp             SSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSC--CCSSSCC------SSTTHHHHHHHHHHHHHHSSSCT
T ss_pred             cchHHHHHHHHHHHHHHhcCCceeeeeccccccc--ccccCCC------CcchHHHHHHHHHHHHhhcccCC
Confidence                 34567777665  4899999999999987  6644332      12345678999999999999865

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.81  E-value=5.6e-20  Score=179.28  Aligned_cols=122  Identities=23%  Similarity=0.296  Sum_probs=101.5

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      +..+|+++++-++.|++|.+.+..             ++++|+|||||||||||++|+|+|++++.+++.++++++.+  
T Consensus       177 p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s~l~sk~  256 (437)
T 4b4t_I          177 PTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELIQKY  256 (437)
T ss_dssp             CCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESGGGCCSS
T ss_pred             CCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHHHhhhcc
Confidence            345899999999999999888765             57899999999999999999999999999999999998874  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                          +..++.+|..+  .+||||||||||+++.  .|.....      ..+....+++++||+.|||+.+.
T Consensus       257 vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~--~R~~~~~------~~~~~~~~~l~~LL~~lDg~~~~  319 (437)
T 4b4t_I          257 LGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGT--KRYDSNS------GGEREIQRTMLELLNQLDGFDDR  319 (437)
T ss_dssp             SSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSC--CCSCSSC------SSCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CchHHHHHHHHHHHHHhcCCcEEEEehhhhhcc--cCCCCCC------CccHHHHHHHHHHHHHhhCcCCC
Confidence                34567777766  3799999999999988  6644332      12345678999999999998754

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.78  E-value=5.7e-19  Score=173.64  Aligned_cols=123  Identities=22%  Similarity=0.278  Sum_probs=100.8

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-  266 (338)
                      .+.-+|+++++-++.|++|.+.+..             .+++|+|||||||||||++|+|+|++++.+++.++++++.+ 
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s~L~sk  282 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQK  282 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGGGGCCC
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhHHhhcc
Confidence            3345899999999999999887654             56899999999999999999999999999999999998874 


Q ss_pred             -----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 -----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 -----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                           +..++.+|..+  .+||||||||+|.++.  .|.....      +......++++.||+.|||..+.
T Consensus       283 ~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~--~R~~~~~------~~~~~~~~~l~~lL~~lDg~~~~  346 (467)
T 4b4t_H          283 YVGEGARMVRELFEMARTKKACIIFFDEIDAVGG--ARFDDGA------GGDNEVQRTMLELITQLDGFDPR  346 (467)
T ss_dssp             SSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSB--CCSSSSC------GGGGHHHHHHHHHHHHHHSSCCT
T ss_pred             cCCHHHHHHHHHHHHHHhcCCceEeecccccccc--cccCcCC------CccHHHHHHHHHHHHHhhccCCC
Confidence                 45577777766  4899999999999987  6644322      11345578999999999998754

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.65  E-value=5.4e-17  Score=169.91  Aligned_cols=121  Identities=18%  Similarity=0.345  Sum_probs=93.3

Q ss_pred             CCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE----  265 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~----  265 (338)
                      ..+|+++++-++.|+.+.+.+..             .+++|+|||||||||||++++|+|++++.+++.++.+++.    
T Consensus       473 ~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~l~s~~v  552 (806)
T 3cf2_A          473 QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWF  552 (806)
T ss_dssp             CCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHHHHTTTC
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccchhhcccc
Confidence            34788999999999888877664             3568999999999999999999999999999999988764    


Q ss_pred             --CchHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          266 --GNKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       266 --~~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                        ++..++++|..+.  .||||||||||+++.  .|.....      ..++..++++++||+.|||+.+.
T Consensus       553 Gese~~vr~lF~~Ar~~~P~IifiDEiDsl~~--~R~~~~~------~~~~~~~rv~~~lL~~mdg~~~~  614 (806)
T 3cf2_A          553 GESEANVREIFDKARQAAPCVLFFDELDSIAK--ARGGNIG------DGGGAADRVINQILTEMDGMSTK  614 (806)
T ss_dssp             SSCHHHHHHHHHHHHTTCSEEEECSCGGGCC----------------------CHHHHHHHHHHHSSCSS
T ss_pred             chHHHHHHHHHHHHHHcCCceeechhhhHHhh--ccCCCCC------CCchHHHHHHHHHHHHHhCCCCC
Confidence              3567899998774  799999999999988  6643322      11346679999999999999764

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.64  E-value=1.6e-16  Score=166.33  Aligned_cols=117  Identities=26%  Similarity=0.374  Sum_probs=98.0

Q ss_pred             CccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----
Q 035959          204 STFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----  266 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----  266 (338)
                      -+|+++++-++.+++|.+.+.-             .+++|+|||||||||||+|++|+|++++.+++.++++++.+    
T Consensus       201 v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l~sk~~g  280 (806)
T 3cf2_A          201 VGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG  280 (806)
T ss_dssp             CCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHHHSSCTT
T ss_pred             CChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHhhcccch
Confidence            4899999988888888877654             35689999999999999999999999999999999987653    


Q ss_pred             --chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 --NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 --~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                        +..++.+|..+.  .|+||||||||.+++  +|.+..         ....++++++||+.|||+.+.
T Consensus       281 ese~~lr~lF~~A~~~~PsIIfIDEiDal~~--~r~~~~---------~~~~~riv~~LL~~mdg~~~~  338 (806)
T 3cf2_A          281 ESESNLRKAFEEAEKNAPAIIFIDELDAIAP--KREKTH---------GEVERRIVSQLLTLMDGLKQR  338 (806)
T ss_dssp             HHHHHHHHHHHHHTTSCSEEEEEESGGGTCC--TTTTCC---------CTTHHHHHHHHHTHHHHCCGG
T ss_pred             HHHHHHHHHHHHHHHcCCeEEEEehhccccc--ccCCCC---------ChHHHHHHHHHHHHHhccccc
Confidence              456888888775  799999999999987  664332         245688999999999999754

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.62  E-value=2.1e-15  Score=142.81  Aligned_cols=119  Identities=24%  Similarity=0.327  Sum_probs=94.9

Q ss_pred             CCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHh-CCcEEEEecCCcCC--
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYL-HFDVYDLELSSVEG--  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l-~~~~~~l~~~~~~~--  266 (338)
                      ++.+|+++++.++.|+.+.+.+..            ..++++|||||||||||++++++|+++ +.+++.++++++.+  
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~~~~   86 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKW   86 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSCCSS
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHHhhh
Confidence            345899999999999999887754            234789999999999999999999999 88999999988653  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                          ...++.++..+  .+++||||||||.+..  .|....         .....+.++.||+.|||+...
T Consensus        87 ~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~--~~~~~~---------~~~~~~~~~~ll~~ld~~~~~  146 (322)
T 1xwi_A           87 LGESEKLVKNLFQLARENKPSIIFIDEIDSLCG--SRSENE---------SEAARRIKTEFLVQMQGVGVD  146 (322)
T ss_dssp             CCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGC--CSSSCC---------TTHHHHHHHHHHHHHHCSSSC
T ss_pred             hhHHHHHHHHHHHHHHhcCCcEEEeecHHHhcc--cccccc---------chHHHHHHHHHHHHHhccccc
Confidence                34566666654  4789999999999987  443321         234578899999999998653

>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=99.61  E-value=1.3e-15  Score=144.10  Aligned_cols=126  Identities=21%  Similarity=0.295  Sum_probs=95.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-  266 (338)
                      ..++.+|+++++.+..++.+.+.+..            ..++++|||||||||||++++++|++++.+++.++++++.+ 
T Consensus        11 ~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l~~~   90 (322)
T 3eie_A           11 EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSK   90 (322)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHHHTT
T ss_pred             cCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHHhhc
Confidence            45566899999999999999988853            23468999999999999999999999999999999887643 


Q ss_pred             -----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCCCcc
Q 035959          267 -----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCGDER  336 (338)
Q Consensus       267 -----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g~er  336 (338)
                           ...++.++..+  .+++||||||||.+..  .|....         .......+..||+.|||+....++..
T Consensus        91 ~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~--~~~~~~---------~~~~~~~~~~ll~~l~~~~~~~~~v~  156 (322)
T 3eie_A           91 WMGESEKLVKQLFAMARENKPSIIFIDQVDALTG--TRGEGE---------SEASRRIKTELLVQMNGVGNDSQGVL  156 (322)
T ss_dssp             TGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSC--C---------------CCTHHHHHHHHHHHGGGGTSCCCEE
T ss_pred             ccchHHHHHHHHHHHHHhcCCeEEEechhhhhhc--cCCCCc---------chHHHHHHHHHHHHhccccccCCceE
Confidence                 23455666554  3679999999999987  443221         23557889999999999965444333

>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=99.55  E-value=7.2e-15  Score=137.68  Aligned_cols=121  Identities=18%  Similarity=0.341  Sum_probs=94.1

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC---
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE---  265 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~---  265 (338)
                      ++.+|+++++.++.++.+.+.+..             ..++++||+||||||||++++++|+.++.+++.+++.++.   
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~~~~   89 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMW   89 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHHhhh
Confidence            345899999999999998888765             2457899999999999999999999999999999887653   


Q ss_pred             ---CchHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          266 ---GNKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       266 ---~~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                         ....++.+|..+  ..++||||||||.+..  .|.....      ...+.....++.||+.|||+..
T Consensus        90 ~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~--~~~~~~~------~~~~~~~~~~~~lL~~l~~~~~  151 (301)
T 3cf0_A           90 FGESEANVREIFDKARQAAPCVLFFDELDSIAK--ARGGNIG------DGGGAADRVINQILTEMDGMST  151 (301)
T ss_dssp             HTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHH--HHTTTTC------CSSCSCCHHHHHHHHHHHSSCT
T ss_pred             cCchHHHHHHHHHHHHhcCCeEEEEEChHHHhh--ccCCCcC------CcchHHHHHHHHHHHHhhcccC
Confidence               234566777665  3689999999999976  4433211      0123446788999999999864

>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=99.55  E-value=1.6e-14  Score=142.61  Aligned_cols=122  Identities=23%  Similarity=0.314  Sum_probs=93.3

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHh-CCcEEEEecCCcCC-
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYL-HFDVYDLELSSVEG-  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l-~~~~~~l~~~~~~~-  266 (338)
                      .++.+|+++++.+..++.+.+.+..            ..++++||+||||||||++++++|+.+ +.+++.++++++.+ 
T Consensus       128 ~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~l~~~  207 (444)
T 2zan_A          128 RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSK  207 (444)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC-----
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHHHHhh
Confidence            4456899999999999999887742            234789999999999999999999999 88999999887653 


Q ss_pred             -----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCCCC
Q 035959          267 -----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSCG  333 (338)
Q Consensus       267 -----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~~g  333 (338)
                           ...++.+|..+  ..++||||||||.+..  .|....         .....+.++.||+.|||+....+
T Consensus       208 ~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~--~~~~~~---------~~~~~~~~~~lL~~l~~~~~~~~  270 (444)
T 2zan_A          208 WLGESEKLVKNLFQLARENKPSIIFIDEIDSLCG--SRSENE---------SEAARRIKTEFLVQMQGVGVDND  270 (444)
T ss_dssp             ----CCCTHHHHHHHHHHSCSEEEEESCTTTTCC--CSSCCC---------CGGGHHHHHHHHTTTTCSSCCCS
T ss_pred             hcchHHHHHHHHHHHHHHcCCeEEEEechHhhcc--CCCCcc---------ccHHHHHHHHHHHHHhCcccCCC
Confidence                 33456666554  4789999999999987  443221         24567889999999999865333

>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=99.55  E-value=5.8e-15  Score=141.65  Aligned_cols=119  Identities=22%  Similarity=0.333  Sum_probs=90.4

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      ..+.+|+++++.++.++.+.+.+..            ..++++||+||||||||++++++|++++.+++.+++.++..  
T Consensus        45 ~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~~~l~~~~  124 (355)
T 2qp9_X           45 KPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKW  124 (355)
T ss_dssp             --CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEHHHHHSCC
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeHHHHhhhh
Confidence            3456899999999999998887754            12468999999999999999999999999999999876532  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                          ...++.++..+  ..++||||||||.+..  .|....         ....+..++.||..|||+..
T Consensus       125 ~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~--~r~~~~---------~~~~~~~~~~ll~~l~~~~~  183 (355)
T 2qp9_X          125 MGESEKLVKQLFAMARENKPSIIFIDQVDALTG--TRGEGE---------SEASRRIKTELLVQMNGVGN  183 (355)
T ss_dssp             ---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC-----------------CTHHHHHHHHHHHHHHHCC-
T ss_pred             cchHHHHHHHHHHHHHHcCCeEEEEechHhhcc--cCCCCc---------chHHHHHHHHHHHHhhcccc
Confidence                34456666554  3789999999999987  443321         24557888999999999864

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.54  E-value=1.4e-14  Score=133.59  Aligned_cols=123  Identities=23%  Similarity=0.289  Sum_probs=94.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~  266 (338)
                      ..++.+|+++++.++.++.+.+.+..             ..++++||+||||||||++++++|+.++.+++.+++.++..
T Consensus        10 ~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~   89 (285)
T 3h4m_A           10 ERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVK   89 (285)
T ss_dssp             SSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGGCC
T ss_pred             CCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHHHH
Confidence            34456899999999999999888765             24578999999999999999999999999999999988753


Q ss_pred             ------chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ------NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ------~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                            ...+..++...  ..++||||||||.+..  +|.+...      +.....+..+..+|+.+|++..
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~--~~~~~~~------~~~~~~~~~l~~ll~~~~~~~~  153 (285)
T 3h4m_A           90 KFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAA--KRTDALT------GGDREVQRTLMQLLAEMDGFDA  153 (285)
T ss_dssp             CSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHB--CCSSSCC------GGGGHHHHHHHHHHHHHHTTCS
T ss_pred             hccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcc--cCccccC------CccHHHHHHHHHHHHHhhCCCC
Confidence                  23345555544  3679999999999976  4433211      1123456889999999998754

>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=99.54  E-value=3.7e-14  Score=128.83  Aligned_cols=121  Identities=23%  Similarity=0.329  Sum_probs=83.1

Q ss_pred             CCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----  266 (338)
                      +.+|+++++.++.++.+.+.+..            ..++++||+||||||||++++++|++++.+++.++++++..    
T Consensus         2 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~~   81 (262)
T 2qz4_A            2 GVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGG   81 (262)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSSTT
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhccC
Confidence            35789999999998888765543            34578999999999999999999999999999999988753    


Q ss_pred             --chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 --NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 --~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                        ...+..++..+.  .++||+|||+|.+..  +|......     ......+..+..||+.+|++.+
T Consensus        82 ~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~--~~~~~~~~-----~~~~~~~~~l~~ll~~~~~~~~  142 (262)
T 2qz4_A           82 LGAARVRSLFKEARARAPCIVYIDEIDAVGK--KRSTTMSG-----FSNTEEEQTLNQLLVEMDGMGT  142 (262)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEEECC--------------------------CHHHHHHHHHHHTCCT
T ss_pred             hhHHHHHHHHHHHHhcCCeEEEEeCcchhhc--cccccccC-----ccchhHHHHHHHHHHHhhCcCC
Confidence              234556665543  589999999999976  44322110     0123346788999999998754

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.53  E-value=3.8e-14  Score=131.60  Aligned_cols=120  Identities=23%  Similarity=0.332  Sum_probs=90.8

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhh------------hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERA------------WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~------------~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      ..+.+|+++++.++.++.+.+.+..+            .++++||+||||||||++++++|+.++.+++.++++++..  
T Consensus        15 ~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l~~~~   94 (297)
T 3b9p_A           15 GAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSKY   94 (297)
T ss_dssp             SSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTTSSSS
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHHhhcc
Confidence            45678999999999999998887552            3578999999999999999999999999999999988653  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                          ...++.++...  ..++||||||+|.+..  .|....         ........+.||+.+|++...
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~--~~~~~~---------~~~~~~~~~~ll~~l~~~~~~  154 (297)
T 3b9p_A           95 VGDGEKLVRALFAVARHMQPSIIFIDEVDSLLS--ERSSSE---------HEASRRLKTEFLVEFDGLPGN  154 (297)
T ss_dssp             CSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSB--CC--------------CCSHHHHHHHHHHHHHCC--
T ss_pred             cchHHHHHHHHHHHHHHcCCcEEEeccHHHhcc--ccccCc---------chHHHHHHHHHHHHHhccccc
Confidence                22344444443  4789999999999987  443221         123466778899999988653

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.51  E-value=1.9e-14  Score=134.50  Aligned_cols=95  Identities=17%  Similarity=0.182  Sum_probs=67.1

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC------chHHHHHHHhc------CCCcEEEEcCCCccCC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG------NKHLRKVLIAT------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~------~~~l~~~l~~~------~~~~Il~iDeiD~~~~  293 (338)
                      ..++++|||||||||||++++++|++++.+++.++++++.+      ...++.++..+      ..++||+|||||.+.+
T Consensus        34 ~~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~  113 (293)
T 3t15_A           34 KVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAG  113 (293)
T ss_dssp             CCCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC----
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechhhhcC
Confidence            34679999999999999999999999999999999887653      23456666555      2789999999999876


Q ss_pred             cccccccccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          294 LQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       294 ~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                        .+.+...       .....+...+.||+.||++.
T Consensus       114 --~~~~~~~-------~~~~~~~v~~~Ll~~ld~~~  140 (293)
T 3t15_A          114 --RMGGTTQ-------YTVNNQMVNATLMNIADNPT  140 (293)
T ss_dssp             -------------------CHHHHHHHHHHHHHCCC
T ss_pred             --CCCCCcc-------ccchHHHHHHHHHHHhcccc
Confidence              3332211       12245677899999999764

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.51  E-value=3.4e-14  Score=137.67  Aligned_cols=121  Identities=24%  Similarity=0.325  Sum_probs=91.8

Q ss_pred             cCCCCCccccccCChhHHHHHHHHHHhh------------hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDLERA------------WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG  266 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l~~~------------~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~  266 (338)
                      ...++.+|+++++.+..++.+.+.+..+            ..+++||+||||||||++|+++|+.++.+++.+++.++..
T Consensus       107 ~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l~~  186 (389)
T 3vfd_A          107 DNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTS  186 (389)
T ss_dssp             CCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC--
T ss_pred             ccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHhhc
Confidence            4567889999999999999999888542            2478999999999999999999999999999999988753


Q ss_pred             ------chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ------NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ------~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                            ...+..++..+  ..++||||||||.+..  .|....         .......+..||+.|||+..
T Consensus       187 ~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~--~~~~~~---------~~~~~~~~~~ll~~l~~~~~  247 (389)
T 3vfd_A          187 KYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLC--ERREGE---------HDASRRLKTEFLIEFDGVQS  247 (389)
T ss_dssp             -----CHHHHHHHHHHHHHSSSEEEEEETGGGGC-------------------CTHHHHHHHHHHHHHHHC-
T ss_pred             cccchHHHHHHHHHHHHHhcCCeEEEEECchhhcc--cCCCcc---------chHHHHHHHHHHHHhhcccc
Confidence                  23345555544  3679999999999976  443221         23457888899999998865

>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=99.51  E-value=4.7e-14  Score=140.27  Aligned_cols=120  Identities=25%  Similarity=0.349  Sum_probs=91.5

Q ss_pred             CCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----  266 (338)
                      ..+|+++++.++.++++.+.+..            ..++|+||+||||||||++++++|+.++.+++.++++++..    
T Consensus        12 ~~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~~~~g   91 (476)
T 2ce7_A           12 RVTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVELFVG   91 (476)
T ss_dssp             CCCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTTCCTT
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHHHHhc
Confidence            45899999999988887776554            23578999999999999999999999999999999987653    


Q ss_pred             --chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 --NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 --~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                        ...++.+|..+  ..|+||||||||.+..  +|.....      +.+.....+++.||+.|||+.+
T Consensus        92 ~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~--~r~~~~~------g~~~~~~~~l~~LL~~ld~~~~  151 (476)
T 2ce7_A           92 VGAARVRDLFAQAKAHAPCIVFIDEIDAVGR--HRGAGLG------GGHDEREQTLNQLLVEMDGFDS  151 (476)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEEETGGGTCC--C---------------CHHHHHHHHHHHHHHHSCG
T ss_pred             ccHHHHHHHHHHHHhcCCCEEEEechhhhhh--hcccccC------cCcHHHHHHHHHHHHHHhccCC
Confidence              24566677665  3789999999999987  5543211      1133456789999999998754

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.50  E-value=9e-14  Score=126.63  Aligned_cols=123  Identities=24%  Similarity=0.338  Sum_probs=93.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-  266 (338)
                      ...+.+|+++++.++.++.+.+.+..            ..+++++|+||||||||++++++|+.++.+++.+++.++.. 
T Consensus         5 ~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~~~~   84 (257)
T 1lv7_A            5 DQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM   84 (257)
T ss_dssp             CSSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTS
T ss_pred             cCCCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHHHHH
Confidence            34567899999999998877765443            23578999999999999999999999999999999887653 


Q ss_pred             -----chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 -----NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 -----~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                           ...+..++..+.  .+++++|||||.+..  .|.....      +........+..+|+.+||+..
T Consensus        85 ~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~--~~~~~~~------~~~~~~~~~~~~ll~~l~~~~~  147 (257)
T 1lv7_A           85 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGR--QRGAGLG------GGHDEREQTLNQMLVEMDGFEG  147 (257)
T ss_dssp             CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTC--CCSTTSC------CTTCHHHHHHHHHHHHHHTCCS
T ss_pred             hhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhcc--CCCCCcC------CCchHHHHHHHHHHHHhhCccc
Confidence                 345667776653  578999999999976  4432211      1122345788999999999864

>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=99.49  E-value=7.2e-14  Score=134.00  Aligned_cols=118  Identities=22%  Similarity=0.343  Sum_probs=90.0

Q ss_pred             CCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC---
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG---  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~---  266 (338)
                      .+.+|+++++.+..++.+.+.+..            ..++++||+||||||||++++++|+.++.+++.++++++..   
T Consensus        79 ~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~~~  158 (357)
T 3d8b_A           79 PPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWV  158 (357)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGCCSST
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhhcccc
Confidence            467899999999999999888764            23578999999999999999999999999999999988754   


Q ss_pred             ---chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ---NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ---~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                         ...++.++..+  ..++||||||||.+..  .|....         .......+..||..+||+..
T Consensus       159 g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~--~~~~~~---------~~~~~~~~~~lL~~l~~~~~  216 (357)
T 3d8b_A          159 GEGEKMVRALFAVARCQQPAVIFIDEIDSLLS--QRGDGE---------HESSRRIKTEFLVQLDGATT  216 (357)
T ss_dssp             THHHHHHHHHHHHHHHTCSEEEEEETHHHHTB--C---------------CHHHHHHHHHHHHHHC---
T ss_pred             chHHHHHHHHHHHHHhcCCeEEEEeCchhhhc--cCCCCc---------chHHHHHHHHHHHHHhcccc
Confidence               23345555444  4689999999999986  443211         23457888999999999864

>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=99.46  E-value=1.3e-14  Score=132.77  Aligned_cols=123  Identities=27%  Similarity=0.400  Sum_probs=85.5

Q ss_pred             CCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC---
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG---  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~---  266 (338)
                      .+.+|+++++.++.++.+.+.+..            ..++++||+||||||||++++++|+.++.+++.+++..+..   
T Consensus         6 ~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~~~~   85 (268)
T 2r62_A            6 PNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFV   85 (268)
T ss_dssp             CCCCSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTTTTSCS
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHHHHhhc
Confidence            345789999998888888776653            23578999999999999999999999999999998876542   


Q ss_pred             ---chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 ---NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 ---~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                         ...++.++..+  ..++||||||+|.+..  +|......     .........+..||+.+|+..+.
T Consensus        86 ~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~--~~~~~~~~-----~~~~~~~~~~~~ll~~l~~~~~~  148 (268)
T 2r62_A           86 GLGASRVRDLFETAKKQAPSIIFIDEIDAIGK--SRAAGGVV-----SGNDEREQTLNQLLAEMDGFGSE  148 (268)
T ss_dssp             SSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC-----------------CCCSCSSTTTTTTTTTCSSCS
T ss_pred             chHHHHHHHHHHHHHhcCCeEEEEeChhhhcc--cccccccC-----CCchhHHHHHHHHHHHhhCcccC
Confidence               12233344433  3679999999999987  44322110     01123345678899999987653

>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=99.44  E-value=7.4e-14  Score=139.47  Aligned_cols=118  Identities=25%  Similarity=0.373  Sum_probs=93.9

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      .+.+|+++++..+.++++.+.+..             ..++++||+||||||||++++++|+.++.+++.+++.++.+  
T Consensus       199 ~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~~~~  278 (489)
T 3hu3_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (489)
T ss_dssp             TCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHHTSC
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhhhhh
Confidence            345789999999999988887765             34578999999999999999999999999999999887653  


Q ss_pred             ----chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ----NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ----~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                          ...++.+|..+.  .+++|||||||.+..  +|....         .......++.||+.||++..
T Consensus       279 ~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~--~~~~~~---------~~~~~~~~~~LL~~ld~~~~  337 (489)
T 3hu3_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAP--KREKTH---------GEVERRIVSQLLTLMDGLKQ  337 (489)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCB--CTTSCC---------CHHHHHHHHHHHHHHHHSCT
T ss_pred             cchhHHHHHHHHHHHHhcCCcEEEecchhhhcc--cccccc---------chHHHHHHHHHHHHhhcccc
Confidence                234666676653  678999999999987  443221         13456889999999998864

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.41  E-value=6.4e-13  Score=123.05  Aligned_cols=117  Identities=21%  Similarity=0.321  Sum_probs=83.5

Q ss_pred             CCccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC---
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG---  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~---  266 (338)
                      ..+|+++++.+++|+.+.+.+..             ..++|++|+||||||||+|++++|..++..++.++..++.+   
T Consensus         6 ~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~~~~~   85 (274)
T 2x8a_A            6 NVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLNMYV   85 (274)
T ss_dssp             ------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTCSSTT
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHHhhhh
Confidence            34788999888888888776543             34578999999999999999999999999999999888753   


Q ss_pred             ---chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ---NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ---~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                         ...+..++...  ..++++++||||.+..  .|....         .......++.+++.|||.-.
T Consensus        86 ~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~--~r~~~~---------~~~~~~~~~~~l~~Lsgg~~  143 (274)
T 2x8a_A           86 GESERAVRQVFQRAKNSAPCVIFFDEVDALCP--RRSDRE---------TGASVRVVNQLLTEMDGLEA  143 (274)
T ss_dssp             HHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC--------------------CTTHHHHHHHHHHTCCS
T ss_pred             hHHHHHHHHHHHHHHhcCCCeEeeehhhhhhc--ccCCCc---------chHHHHHHHHHHHhhhcccc
Confidence               23466677664  4789999999999876  443211         12235678999999999854

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.39  E-value=1.9e-12  Score=122.24  Aligned_cols=99  Identities=21%  Similarity=0.289  Sum_probs=82.9

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHhh-----hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCc
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERA-----WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGN  267 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~-----~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~  267 (338)
                      ..|..  ...|.+|+++++.+..++.+...+...     ...++||+||||||||++++++|+.++.+++.+++..+...
T Consensus        17 ~~~~~--~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~~~~~~~~   94 (338)
T 3pfi_A           17 ETYET--SLRPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSANIKTTAAPMIEKS   94 (338)
T ss_dssp             --------CCCCSGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEEGGGCCSH
T ss_pred             hhhhh--ccCCCCHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEecchhccch
Confidence            35653  567889999999999999888888763     23579999999999999999999999999999999988877


Q ss_pred             hHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 KHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ..+...+.....+++|||||||.+..
T Consensus        95 ~~~~~~~~~~~~~~vl~lDEi~~l~~  120 (338)
T 3pfi_A           95 GDLAAILTNLSEGDILFIDEIHRLSP  120 (338)
T ss_dssp             HHHHHHHHTCCTTCEEEEETGGGCCH
T ss_pred             hHHHHHHHhccCCCEEEEechhhcCH
Confidence            88888888888999999999999853

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.36  E-value=2.3e-12  Score=128.78  Aligned_cols=121  Identities=24%  Similarity=0.324  Sum_probs=91.6

Q ss_pred             CCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC---
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG---  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~---  266 (338)
                      .+.+|+++++.++.++++.+.+..            ..++|+||+||||||||+|++++|+.++.+++.+++.++..   
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~~  105 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFV  105 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSCT
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhhh
Confidence            456899999999888877765543            13578999999999999999999999999999999987653   


Q ss_pred             ---chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ---NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ---~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                         ...++.+|....  .++|+||||||.+..  .|.....      ........+++.||+.|||...
T Consensus       106 g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~--~r~~~~~------~~~~e~~~~l~~LL~~Ldg~~~  166 (499)
T 2dhr_A          106 GVGAARVRDLFETAKRHAPCIVFIDEIDAVGR--KRGSGVG------GGNDEREQTLNQLLVEMDGFEK  166 (499)
T ss_dssp             THHHHHHHHHTTTSSSSSSCEEEEECGGGTCC--CSSSSTT------TSSHHHHHHHHHHHHHGGGCCS
T ss_pred             hhHHHHHHHHHHHHHhcCCCEEEEehHHHHHH--hhccCcC------CCcHHHHHHHHHHHHHhccccc
Confidence               234566676654  579999999999976  4432110      1122345789999999998754

>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=99.34  E-value=5.5e-12  Score=118.03  Aligned_cols=94  Identities=28%  Similarity=0.364  Sum_probs=80.7

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhh-----hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHH
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERA-----WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVL  274 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~-----~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l  274 (338)
                      ...|.+|+++++.+..++.+...+...     ...++||+||||||||++++++++.++.+++.+++..+....++...+
T Consensus         5 ~~~p~~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~~l~~~l   84 (324)
T 1hqc_A            5 ALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAIL   84 (324)
T ss_dssp             CCCCCSTTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCCSHHHHHHHH
T ss_pred             ccCcccHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccCChHHHHHHH
Confidence            356779999999998888888777652     336899999999999999999999999999999999888777888877


Q ss_pred             Hh-cCCCcEEEEcCCCccCC
Q 035959          275 IA-TENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 ~~-~~~~~Il~iDeiD~~~~  293 (338)
                      .. ...+.+|||||||.+..
T Consensus        85 ~~~~~~~~~l~lDEi~~l~~  104 (324)
T 1hqc_A           85 ANSLEEGDILFIDEIHRLSR  104 (324)
T ss_dssp             TTTCCTTCEEEETTTTSCCH
T ss_pred             HHhccCCCEEEEECCccccc
Confidence            77 67889999999999864

>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=99.30  E-value=2.7e-12  Score=126.97  Aligned_cols=95  Identities=22%  Similarity=0.208  Sum_probs=75.1

Q ss_pred             CCccccccCChhHHHHHHHHHHh-----hhcCceeeeCCCCCCcHHHHHHHHHHhC--CcEEEEecCCcCC-----chHH
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER-----AWKRGYLLFGPPGTGKSSLIAAMANYLH--FDVYDLELSSVEG-----NKHL  270 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~-----~~~~g~LL~GppGtGKT~l~~aia~~l~--~~~~~l~~~~~~~-----~~~l  270 (338)
                      ...|+++++.++.++.+...+..     ..++++||+||||||||++++++|++++  .+++.++++++.+     ...+
T Consensus        33 ~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~~~~~~~~~~~  112 (456)
T 2c9o_A           33 KQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVL  112 (456)
T ss_dssp             CSEETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGCCSSSCHHHHH
T ss_pred             hhchhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHHHHhhhhhHHH
Confidence            34689999999988866554443     3457899999999999999999999999  8999999988763     2347


Q ss_pred             HHHHHhc-----CCCcEEEEcCCCccCCcccccc
Q 035959          271 RKVLIAT-----ENKSILVVGDIDCCTELQDRSA  299 (338)
Q Consensus       271 ~~~l~~~-----~~~~Il~iDeiD~~~~~~~r~~  299 (338)
                      .++|..+     ..++||||||||.+..  +|..
T Consensus       113 ~~~f~~a~~~~~~~~~il~iDEid~l~~--~r~~  144 (456)
T 2c9o_A          113 MENFRRAIGLRIKETKEVYEGEVTELTP--CETE  144 (456)
T ss_dssp             HHHHHHTEEEEEEEEEEEEEEEEEEEEE--C---
T ss_pred             HHHHHHHHhhhhcCCcEEEEechhhccc--ccCC
Confidence            7778776     3789999999999987  5543

>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=99.29  E-value=3.7e-12  Score=115.65  Aligned_cols=122  Identities=24%  Similarity=0.320  Sum_probs=85.9

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      .++.+|+++++.++.+.++.+....            ..++|++|+||||||||+|++++|+.++..++.++..++..  
T Consensus        10 ~~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~~~~~   89 (254)
T 1ixz_A           10 APKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF   89 (254)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHSC
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHHHHHH
Confidence            3455899999988888776654433            23568999999999999999999999999888888765431  


Q ss_pred             ----chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 ----NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ----~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                          ...+..++....  .++++++||||.+..  .|.....      .........+..+|+.|||...
T Consensus        90 ~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~--~~~~~~~------~~~~~~~~~~~~ll~~l~g~~~  151 (254)
T 1ixz_A           90 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGR--KRGSGVG------GGNDEREQTLNQLLVEMDGFEK  151 (254)
T ss_dssp             TTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC-----------------CHHHHHHHHHHHHHHHTCCT
T ss_pred             hhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhc--ccCcccc------ccchHHHHHHHHHHHHHhCCCC
Confidence                234566777654  579999999999875  3322110      0122345678899999998753

>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=99.29  E-value=8.9e-12  Score=125.14  Aligned_cols=100  Identities=17%  Similarity=0.284  Sum_probs=80.6

Q ss_pred             CCccccccCCCCCccccccCChhHHHHHHHHHHhh-----------------hcCceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          192 HDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERA-----------------WKRGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       192 ~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~-----------------~~~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ...|..  ...|.+|+++++.+..++.+.+.+...                 ..+++||+||||||||++++++|+.++.
T Consensus        26 ~~lW~e--kyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~  103 (516)
T 1sxj_A           26 DKLWTV--KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY  103 (516)
T ss_dssp             CCCHHH--HTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCCccc--ccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            446864  678999999999999999999888761                 2468999999999999999999999999


Q ss_pred             cEEEEecCCcCCchHHHHHHH-------------h-------cCCCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLI-------------A-------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~-------------~-------~~~~~Il~iDeiD~~~~  293 (338)
                      +++.+++++......+...+.             .       ...+.||||||+|.+..
T Consensus       104 ~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~  162 (516)
T 1sxj_A          104 DILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSG  162 (516)
T ss_dssp             EEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCT
T ss_pred             CEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccch
Confidence            999999998776443333222             1       13578999999999975

>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=99.28  E-value=3.1e-12  Score=122.56  Aligned_cols=112  Identities=20%  Similarity=0.293  Sum_probs=81.8

Q ss_pred             ccCChhHHHHHHHHHHh---------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-------
Q 035959          209 LAMDTDMKKMIMDDLER---------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-------  266 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~---------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-------  266 (338)
                      +++.+..++.+...+..               ..+.++||+||||||||++|+++|+.++.+++.++++.+..       
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l~~~~~~g~~   96 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGED   96 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHTTCHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHhccccccccc
Confidence            57888888888877742               13468999999999999999999999999999999987663       


Q ss_pred             -chHHHHHHHhc------CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCC
Q 035959          267 -NKHLRKVLIAT------ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL  328 (338)
Q Consensus       267 -~~~l~~~l~~~------~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl  328 (338)
                       ...+..++...      ..++||||||||.+..  .|.+...+      .........+.||..|||.
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~--~~~~~~~~------~~~~~~~~~~~Ll~~leg~  157 (363)
T 3hws_A           97 VENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISR--KSDNPSIT------RDVSGEGVQQALLKLIEGT  157 (363)
T ss_dssp             HTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCC--CSSCC---------CHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcc--cccccccc------cccchHHHHHHHHHHhcCc
Confidence             22345555544      2578999999999987  44332210      0111234789999999975

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.25  E-value=1.4e-11  Score=102.82  Aligned_cols=84  Identities=14%  Similarity=0.190  Sum_probs=65.1

Q ss_pred             cccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHhcCCCcE
Q 035959          208 TLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIATENKSI  282 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~~~~~~I  282 (338)
                      .+++..+..+++.+.+..  .....+||+||||||||++|+++++..   +.+++ +++..+.....+...+... ...+
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~~~~~~~~~~a-~~g~   79 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNAPQLNDFIALA-QGGT   79 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTSSCHHHHHHHH-TTSC
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcchhhhcHHHHc-CCcE
Confidence            356666667777777765  345679999999999999999999987   67888 9999887665555666554 5589


Q ss_pred             EEEcCCCccCC
Q 035959          283 LVVGDIDCCTE  293 (338)
Q Consensus       283 l~iDeiD~~~~  293 (338)
                      |+|||||.+..
T Consensus        80 l~ldei~~l~~   90 (145)
T 3n70_A           80 LVLSHPEHLTR   90 (145)
T ss_dssp             EEEECGGGSCH
T ss_pred             EEEcChHHCCH
Confidence            99999999854

>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=99.25  E-value=1.3e-11  Score=114.31  Aligned_cols=111  Identities=17%  Similarity=0.285  Sum_probs=79.6

Q ss_pred             cccCChhHHHHHHHHHHhh--------------hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-------
Q 035959          208 TLAMDTDMKKMIMDDLERA--------------WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-------  266 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~--------------~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-------  266 (338)
                      .+++.++.++.+...+..+              .+.++||+||||||||++++++|+.++.+++.++++.+..       
T Consensus        16 ~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~~~~~~~   95 (310)
T 1ofh_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE   95 (310)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGS
T ss_pred             hcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccCCccCcc
Confidence            4678888888888777651              3567999999999999999999999999999999987653       


Q ss_pred             -chHHHHHHHhc-------CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCC
Q 035959          267 -NKHLRKVLIAT-------ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL  328 (338)
Q Consensus       267 -~~~l~~~l~~~-------~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl  328 (338)
                       ...+..++...       ..++||||||+|.+..  ++.....        +.........||+.||+.
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~--~~~~~~~--------~~~~~~~~~~Ll~~le~~  155 (310)
T 1ofh_A           96 VDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICK--KGEYSGA--------DVSREGVQRDLLPLVEGS  155 (310)
T ss_dssp             TTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSC--CSSCCSS--------HHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCc--ccccccc--------chhHHHHHHHHHHHhcCC
Confidence             23355555533       2478999999999976  3211100        111123467788888874

>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=99.24  E-value=4.4e-11  Score=104.25  Aligned_cols=94  Identities=23%  Similarity=0.320  Sum_probs=74.2

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCchHHHHHH
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGNKHLRKVL  274 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~~~l~~~l  274 (338)
                      ...|..|+++++.+..++.+.+.+......+++|+||||||||++++++++.+     ...++.+++........+...+
T Consensus        10 ~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (226)
T 2chg_A           10 KYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKI   89 (226)
T ss_dssp             HTSCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHHH
T ss_pred             hcCCCCHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHHH
Confidence            46788999999999999999888887555569999999999999999999986     3567888887766544444433


Q ss_pred             Hhc--------CCCcEEEEcCCCccCC
Q 035959          275 IAT--------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 ~~~--------~~~~Il~iDeiD~~~~  293 (338)
                      ...        ..+.+|+|||+|.+..
T Consensus        90 ~~~~~~~~~~~~~~~vliiDe~~~l~~  116 (226)
T 2chg_A           90 KEFARTAPIGGAPFKIIFLDEADALTA  116 (226)
T ss_dssp             HHHHTSCCSTTCSCEEEEEETGGGSCH
T ss_pred             HHHhcccCCCccCceEEEEeChhhcCH
Confidence            321        4688999999999854

>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=99.24  E-value=1.6e-11  Score=115.38  Aligned_cols=98  Identities=18%  Similarity=0.207  Sum_probs=78.5

Q ss_pred             CCccccccCCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHH
Q 035959          192 HDTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHL  270 (338)
Q Consensus       192 ~~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l  270 (338)
                      ...|..  ...|.+|+++++.++.++.+.+.+... .+..+|++||||||||++++++|+.++.+++.++++... ...+
T Consensus        13 ~~~~~~--k~rP~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~~~~~~-~~~i   89 (324)
T 3u61_B           13 EHILEQ--KYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDCK-IDFV   89 (324)
T ss_dssp             CSSHHH--HSCCCSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEETTTCC-HHHH
T ss_pred             cchHHH--hhCCCCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEcccccC-HHHH
Confidence            346753  677899999999999999888888863 335678889999999999999999999999999988755 4445


Q ss_pred             HHHHHhc----C---CCcEEEEcCCCccC
Q 035959          271 RKVLIAT----E---NKSILVVGDIDCCT  292 (338)
Q Consensus       271 ~~~l~~~----~---~~~Il~iDeiD~~~  292 (338)
                      +..+...    +   .+.||+|||+|.+.
T Consensus        90 ~~~~~~~~~~~~~~~~~~vliiDEi~~l~  118 (324)
T 3u61_B           90 RGPLTNFASAASFDGRQKVIVIDEFDRSG  118 (324)
T ss_dssp             HTHHHHHHHBCCCSSCEEEEEEESCCCGG
T ss_pred             HHHHHHHHhhcccCCCCeEEEEECCcccC
Confidence            5444332    2   67899999999996

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.23  E-value=1.7e-11  Score=104.50  Aligned_cols=93  Identities=20%  Similarity=0.370  Sum_probs=72.3

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC----
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG----  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~----  266 (338)
                      ..|..|+++++.+...+.+.+.+....+++++|+||||||||++++++++.+          +.+++.+++..+..    
T Consensus        16 ~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (187)
T 2p65_A           16 ARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKY   95 (187)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECHHHHHHHCCS
T ss_pred             HhccccchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeHHHhhcCCCc
Confidence            3467899999999888888888877666789999999999999999999987          67788887765431    


Q ss_pred             ----chHHHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                          ...+.+++..+   ..+.+|+|||+|.+..
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~  129 (187)
T 2p65_A           96 RGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVG  129 (187)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSS
T ss_pred             hhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhcc
Confidence                11234444333   3678999999999975

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.22  E-value=1.5e-11  Score=104.74  Aligned_cols=92  Identities=21%  Similarity=0.382  Sum_probs=72.7

Q ss_pred             CCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC-----
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG-----  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~-----  266 (338)
                      .|..|+++++.++..+.+.+.+....+++++|+||||||||++++++++.+          +.+++.+++..+..     
T Consensus        17 ~~~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (195)
T 1jbk_A           17 EQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYR   96 (195)
T ss_dssp             HTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSH
T ss_pred             hhccccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccCCcc
Confidence            466889999999888889888877666789999999999999999999987          67888888765431     


Q ss_pred             ---chHHHHHHHh---cCCCcEEEEcCCCccCC
Q 035959          267 ---NKHLRKVLIA---TENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ---~~~l~~~l~~---~~~~~Il~iDeiD~~~~  293 (338)
                         ...+..++..   ...+.||+|||+|.+..
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~  129 (195)
T 1jbk_A           97 GEFEERLKGVLNDLAKQEGNVILFIDELHTMVG  129 (195)
T ss_dssp             HHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT
T ss_pred             ccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhc
Confidence               1234444443   34678999999999976

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.20  E-value=3.6e-11  Score=111.83  Aligned_cols=106  Identities=19%  Similarity=0.204  Sum_probs=77.7

Q ss_pred             cccCChhHHHHHHHHHHhh---------------hcCceeeeCCCCCCcHHHHHHHHHHhC-------CcEEEEecCCcC
Q 035959          208 TLAMDTDMKKMIMDDLERA---------------WKRGYLLFGPPGTGKSSLIAAMANYLH-------FDVYDLELSSVE  265 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~---------------~~~g~LL~GppGtGKT~l~~aia~~l~-------~~~~~l~~~~~~  265 (338)
                      ++++.+..++.+.+.+...               ...++||+||||||||++++++|+.++       .+++.+++..+.
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l~  111 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLV  111 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGTC
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHhh
Confidence            5788888888888766541               223599999999999999999999883       378899888765


Q ss_pred             C------chHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcC
Q 035959          266 G------NKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDG  327 (338)
Q Consensus       266 ~------~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDg  327 (338)
                      .      ...+..++... .++||||||+|.+..  .+.+.           ......+..|++.||.
T Consensus       112 ~~~~g~~~~~~~~~~~~~-~~~vl~iDEid~l~~--~~~~~-----------~~~~~~~~~Ll~~l~~  165 (309)
T 3syl_A          112 GQYIGHTAPKTKEVLKRA-MGGVLFIDEAYYLYR--PDNER-----------DYGQEAIEILLQVMEN  165 (309)
T ss_dssp             CSSTTCHHHHHHHHHHHH-TTSEEEEETGGGSCC--CC--------------CCTHHHHHHHHHHHHH
T ss_pred             hhcccccHHHHHHHHHhc-CCCEEEEEChhhhcc--CCCcc-----------cccHHHHHHHHHHHhc
Confidence            3      23455566554 578999999999975  33211           2235677888888885

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.20  E-value=2.5e-11  Score=111.95  Aligned_cols=121  Identities=24%  Similarity=0.320  Sum_probs=85.6

Q ss_pred             CCCCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--  266 (338)
                      .++.+|+++++.++.++++.+....            ..++|++|+||||||||+|++++|..++..++.+++.++..  
T Consensus        34 ~~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~~~~~  113 (278)
T 1iy2_A           34 APKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF  113 (278)
T ss_dssp             CCCCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHST
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHHHHHH
Confidence            3566899999999888777654443            23568999999999999999999999999998888765431  


Q ss_pred             ----chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          267 ----NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       267 ----~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                          ...+..++...  ..++++++||||.+..  .|.....      .........+..+++.|||..
T Consensus       114 ~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~--~~~~~~~------~~~~~~~~~~~~ll~~lsgg~  174 (278)
T 1iy2_A          114 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGR--KRGSGVG------GGNDEREQTLNQLLVEMDGFE  174 (278)
T ss_dssp             TTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHC--C--------------CHHHHHHHHHHHHHHTTCC
T ss_pred             hhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhc--ccccccC------CcchHHHHHHHHHHHHHhCCC
Confidence                23455666665  3579999999999865  3322100      011234567889999999864

>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=99.17  E-value=9.9e-11  Score=107.35  Aligned_cols=92  Identities=23%  Similarity=0.253  Sum_probs=66.8

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-------chHHHHHHHhc--CCCcEEEEcCCCccCCccc
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-------NKHLRKVLIAT--ENKSILVVGDIDCCTELQD  296 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-------~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~  296 (338)
                      ..++++||+||||||||++++++|+.++.+++.+++.+...       ...++.++...  ..+++|+|||||.+..  .
T Consensus        62 ~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~--~  139 (272)
T 1d2n_A           62 TPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLD--Y  139 (272)
T ss_dssp             CSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTT--C
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHHhcCCchHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhc--c
Confidence            34568999999999999999999999999999998765221       13455666654  4689999999999976  3


Q ss_pred             ccccccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          297 RSAQARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       297 r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                      +...          .......+..|+..+++..
T Consensus       140 ~~~~----------~~~~~~~l~~L~~~~~~~~  162 (272)
T 1d2n_A          140 VPIG----------PRFSNLVLQALLVLLKKAP  162 (272)
T ss_dssp             BTTT----------TBCCHHHHHHHHHHTTCCC
T ss_pred             CCCC----------hhHHHHHHHHHHHHhcCcc
Confidence            3211          1223456667777777764

>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=99.16  E-value=1.8e-10  Score=110.69  Aligned_cols=113  Identities=21%  Similarity=0.295  Sum_probs=75.2

Q ss_pred             cccCChhHHHHHHHHHHh------------------------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          208 TLAMDTDMKKMIMDDLER------------------------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~------------------------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      .+++.+..++.+...+..                              ..+.++||+||||||||++++++|+.++.+++
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~~~~~  101 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIA  101 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEE
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            367788888877766621                              02457999999999999999999999999999


Q ss_pred             EEecCCcCC--------chHHHHHHHhcC------CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHH
Q 035959          258 DLELSSVEG--------NKHLRKVLIATE------NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLN  323 (338)
Q Consensus       258 ~l~~~~~~~--------~~~l~~~l~~~~------~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn  323 (338)
                      .+++..+..        ...+..++....      .++||||||||.+..  +|.+....      .+.......+.||.
T Consensus       102 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~--~~~~~~~~------~~~~~~~~~~~Ll~  173 (376)
T 1um8_A          102 ISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISR--LSENRSIT------RDVSGEGVQQALLK  173 (376)
T ss_dssp             EEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC----------------------CHHHHHHHHH
T ss_pred             EecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhh--hcCCCcee------cccchHHHHHHHHH
Confidence            999987642        223445544332      679999999999976  43322110      01112346888999


Q ss_pred             HhcCC
Q 035959          324 FTDGL  328 (338)
Q Consensus       324 ~iDgl  328 (338)
                      .||+-
T Consensus       174 ~le~~  178 (376)
T 1um8_A          174 IVEGS  178 (376)
T ss_dssp             HHHCC
T ss_pred             Hhhcc
Confidence            99964

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.14  E-value=9e-11  Score=115.88  Aligned_cols=93  Identities=24%  Similarity=0.429  Sum_probs=74.0

Q ss_pred             CCCCCccccccCChhHH---HHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHh
Q 035959          200 LDHPSTFDTLAMDTDMK---KMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIA  276 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k---~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~  276 (338)
                      ...|.+|+++++.++..   ..+...+......++|||||||||||++++++|+.++.+++.+++... ...+++.++..
T Consensus        19 r~rP~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~~~-~~~~ir~~~~~   97 (447)
T 3pvs_A           19 RMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYANADVERISAVTS-GVKEIREAIER   97 (447)
T ss_dssp             HTCCCSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETTTC-CHHHHHHHHHH
T ss_pred             HhCCCCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEeccC-CHHHHHHHHHH
Confidence            45688999999999887   667777766555689999999999999999999999999999987653 34455555554


Q ss_pred             c------CCCcEEEEcCCCccCC
Q 035959          277 T------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ~------~~~~Il~iDeiD~~~~  293 (338)
                      .      ..+.||||||||.+..
T Consensus        98 a~~~~~~~~~~iLfIDEI~~l~~  120 (447)
T 3pvs_A           98 ARQNRNAGRRTILFVDEVHRFNK  120 (447)
T ss_dssp             HHHHHHTTCCEEEEEETTTCC--
T ss_pred             HHHhhhcCCCcEEEEeChhhhCH
Confidence            3      3689999999999864

>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=99.12  E-value=1.6e-10  Score=105.44  Aligned_cols=89  Identities=13%  Similarity=0.213  Sum_probs=62.0

Q ss_pred             CccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCCcCCchHHHHHHH---
Q 035959          204 STFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSVEGNKHLRKVLI---  275 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~~~~~~~l~~~l~---  275 (338)
                      .+|+++++..+..+.+.+.+..  ....++||+||||||||++++++++.+.   .+++.++++.+.. ..+...+.   
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~-~~~~~~l~g~~   81 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-NLLDSELFGHE   81 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCH-HHHHHHHHCCC
T ss_pred             cccccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCCh-hHHHHHhcCCc
Confidence            3688888888888888877766  3457899999999999999999999885   6899999988642 22222111   


Q ss_pred             ---------------hcCCCcEEEEcCCCccCC
Q 035959          276 ---------------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 ---------------~~~~~~Il~iDeiD~~~~  293 (338)
                                     ......+|||||||.+..
T Consensus        82 ~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~  114 (265)
T 2bjv_A           82 AGAFTGAQKRHPGRFERADGGTLFLDELATAPM  114 (265)
T ss_dssp             ---------CCCCHHHHTTTSEEEEESGGGSCH
T ss_pred             ccccccccccccchhhhcCCcEEEEechHhcCH
Confidence                           113468999999999854

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.12  E-value=3.3e-10  Score=99.69  Aligned_cols=93  Identities=18%  Similarity=0.322  Sum_probs=70.0

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|..|+++++.+...+.+...+.... ++.++|+||||||||++++++++.++.                        
T Consensus        16 ~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (250)
T 1njg_A           16 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFV   95 (250)
T ss_dssp             HTCCCSGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCS
T ss_pred             ccCCccHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCc
Confidence            4678889999999998888888887632 346899999999999999999998743                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCT  292 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~  292 (338)
                      +++.++.........+..++....      .+.+|+|||+|.+.
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~  139 (250)
T 1njg_A           96 DLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS  139 (250)
T ss_dssp             SEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC
T ss_pred             ceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECccccc
Confidence            334444443233345666666543      46899999999974

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.10  E-value=2.9e-11  Score=100.71  Aligned_cols=82  Identities=12%  Similarity=0.053  Sum_probs=60.9

Q ss_pred             ccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEc
Q 035959          209 LAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVG  286 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iD  286 (338)
                      +++..+..+++.+.+..  ....++||+||||||||++|+++++..+ +++.+++..+... .....+.. ....+|+||
T Consensus         6 ~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~~-~~~~~~~~-a~~~~l~lD   82 (143)
T 3co5_A            6 KLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLID-MPMELLQK-AEGGVLYVG   82 (143)
T ss_dssp             --CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHHH-CHHHHHHH-TTTSEEEEE
T ss_pred             ceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCChH-hhhhHHHh-CCCCeEEEe
Confidence            45566666777777765  3456799999999999999999999888 8888888875421 13344443 457899999


Q ss_pred             CCCccCC
Q 035959          287 DIDCCTE  293 (338)
Q Consensus       287 eiD~~~~  293 (338)
                      |||.+..
T Consensus        83 ei~~l~~   89 (143)
T 3co5_A           83 DIAQYSR   89 (143)
T ss_dssp             ECTTCCH
T ss_pred             ChHHCCH
Confidence            9999864

>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=99.09  E-value=6.9e-11  Score=101.64  Aligned_cols=90  Identities=19%  Similarity=0.231  Sum_probs=61.9

Q ss_pred             CCCccccccCChhHHHHHHHHHHh-------hhcCceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCCcCCc---
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER-------AWKRGYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSSVEGN---  267 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~-------~~~~g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~~~~~---  267 (338)
                      .+.+|++++...+..+.+++.+..       +...+++|+||||||||+|++++++.+    |..+..+++.++...   
T Consensus         5 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~~~~~~~   84 (180)
T 3ec2_A            5 WNANLDTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLIFRLKH   84 (180)
T ss_dssp             TTCCSSSCCCCSHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHHHHHHHH
T ss_pred             hhCccccccCCCHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHH
Confidence            466899988754444555555543       345789999999999999999999987    666777766544310   


Q ss_pred             ----hHHHHHHHhcCCCcEEEEcCCCcc
Q 035959          268 ----KHLRKVLIATENKSILVVGDIDCC  291 (338)
Q Consensus       268 ----~~l~~~l~~~~~~~Il~iDeiD~~  291 (338)
                          .....++....++.+|+|||++..
T Consensus        85 ~~~~~~~~~~~~~~~~~~llilDE~~~~  112 (180)
T 3ec2_A           85 LMDEGKDTKFLKTVLNSPVLVLDDLGSE  112 (180)
T ss_dssp             HHHHTCCSHHHHHHHTCSEEEEETCSSS
T ss_pred             HhcCchHHHHHHHhcCCCEEEEeCCCCC
Confidence                001133444457899999999865

>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=99.09  E-value=1.4e-10  Score=109.48  Aligned_cols=99  Identities=23%  Similarity=0.360  Sum_probs=73.9

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC------CcEEEEecCCcCC
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH------FDVYDLELSSVEG  266 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~------~~~~~l~~~~~~~  266 (338)
                      ..|..  ...|.+|+++++.++.++.+...+......++||+||||||||++++++|+.++      ..+..+++++...
T Consensus        25 ~~~~~--k~~p~~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~  102 (353)
T 1sxj_D           25 QPWVE--KYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERG  102 (353)
T ss_dssp             -CHHH--HTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCC
T ss_pred             ccHHH--hcCCCCHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccc
Confidence            35654  568899999999999998888888764445599999999999999999999864      4688888877554


Q ss_pred             chHHHHHH---Hh---------------cCCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVL---IA---------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l---~~---------------~~~~~Il~iDeiD~~~~  293 (338)
                      ...++..+   ..               ...+.||+|||+|.+..
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~  147 (353)
T 1sxj_D          103 ISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA  147 (353)
T ss_dssp             HHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH
T ss_pred             hHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccCH
Confidence            33333222   11               12457999999999864

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=99.08  E-value=2.3e-10  Score=106.60  Aligned_cols=99  Identities=20%  Similarity=0.314  Sum_probs=73.2

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCcCCc
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSVEGN  267 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~~~~  267 (338)
                      ..|..  ...|.+|+++++.++.++.+...+......++||+||||||||++++++|+.+.     ..++.+++++....
T Consensus        13 ~~~~~--k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~   90 (327)
T 1iqp_A           13 KPWVE--KYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGI   90 (327)
T ss_dssp             SCHHH--HTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHH
T ss_pred             Cchhh--ccCCCCHHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCch
Confidence            35653  578889999999999999888888765444699999999999999999999863     34778887654322


Q ss_pred             hHHHHHHH----hc----CCCcEEEEcCCCccCC
Q 035959          268 KHLRKVLI----AT----ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l~----~~----~~~~Il~iDeiD~~~~  293 (338)
                      ..++..+.    ..    ..+.+|+|||+|.+..
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~  124 (327)
T 1iqp_A           91 NVIREKVKEFARTKPIGGASFKIIFLDEADALTQ  124 (327)
T ss_dssp             HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH
T ss_pred             HHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCH
Confidence            22222222    11    3578999999999854

>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=99.06  E-value=1.3e-10  Score=107.93  Aligned_cols=98  Identities=22%  Similarity=0.296  Sum_probs=73.2

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCch
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGNK  268 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~~  268 (338)
                      .|.  ....|.+|+++++.+..++.+.+.+......++||+||||||||++++++|+.+     +.+++.+++++.....
T Consensus         6 ~~~--~k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~   83 (319)
T 2chq_A            6 IWV--EKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGID   83 (319)
T ss_dssp             CTT--TTTSCSSGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTSTTCTT
T ss_pred             cHH--HhcCCCCHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccccChH
Confidence            454  367889999999999988888887776444459999999999999999999987     3457888887654332


Q ss_pred             HHHHHHH----hc----CCCcEEEEcCCCccCC
Q 035959          269 HLRKVLI----AT----ENKSILVVGDIDCCTE  293 (338)
Q Consensus       269 ~l~~~l~----~~----~~~~Il~iDeiD~~~~  293 (338)
                      .++..+.    ..    ..+.+|+|||+|.+..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~  116 (319)
T 2chq_A           84 VVRHKIKEFARTAPIGGAPFKIIFLDEADALTA  116 (319)
T ss_dssp             TSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCH
T ss_pred             HHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCH
Confidence            2222222    11    3579999999998853

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.06  E-value=3.5e-10  Score=107.66  Aligned_cols=62  Identities=21%  Similarity=0.305  Sum_probs=46.7

Q ss_pred             CCCc-cccccCChhHHHHH---HHHHHhh--hcCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEecCC
Q 035959          202 HPST-FDTLAMDTDMKKMI---MDDLERA--WKRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLELSS  263 (338)
Q Consensus       202 ~p~~-f~~l~~~~~~k~~i---~~~l~~~--~~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~~~  263 (338)
                      .|.. |+++++.+..++.+   .+.+...  .++++||+||||||||++++++|+.++.  +++.+++..
T Consensus        38 ~p~~~~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~  107 (368)
T 3uk6_A           38 EPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSE  107 (368)
T ss_dssp             CBCSEETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGG
T ss_pred             CcCcchhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchh
Confidence            4444 99999999887764   3333332  2368999999999999999999999974  666666544

>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=99.05  E-value=9.4e-10  Score=104.25  Aligned_cols=95  Identities=23%  Similarity=0.324  Sum_probs=75.1

Q ss_pred             cCCCCCccccccCChhHHHHHHHHHHhh-----hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHH
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDLERA-----WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKV  273 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l~~~-----~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~  273 (338)
                      ..-.|.+|+.+++.+..++.+...+...     ....++|+||||||||||++++|+.++.++...+........++..+
T Consensus        17 ~~lr~~~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~~~~~~l~~~   96 (334)
T 1in4_A           17 QFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAI   96 (334)
T ss_dssp             CTTSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSHHHHHHH
T ss_pred             HHcCCccHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHhcCHHHHHHH
Confidence            3466889999998887777766666542     12568999999999999999999999988877776665556667777


Q ss_pred             HHhcCCCcEEEEcCCCccCC
Q 035959          274 LIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 l~~~~~~~Il~iDeiD~~~~  293 (338)
                      +.....+.|++|||+|.+..
T Consensus        97 ~~~~~~~~v~~iDE~~~l~~  116 (334)
T 1in4_A           97 LTSLERGDVLFIDEIHRLNK  116 (334)
T ss_dssp             HHHCCTTCEEEEETGGGCCH
T ss_pred             HHHccCCCEEEEcchhhcCH
Confidence            76666789999999998853

>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=99.04  E-value=1.8e-10  Score=102.23  Aligned_cols=93  Identities=16%  Similarity=0.227  Sum_probs=65.4

Q ss_pred             cCCCCCccccccCC---hhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCCcCCchHHHH
Q 035959          199 ILDHPSTFDTLAMD---TDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSVEGNKHLRK  272 (338)
Q Consensus       199 ~~~~p~~f~~l~~~---~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~~~~~~~l~~  272 (338)
                      ++.++.+|+++++.   ....+.+...+..+..++++|+||||||||++++++++.+.   ..++.+++.++...  +..
T Consensus        20 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~~--~~~   97 (242)
T 3bos_A           20 HLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASI--STA   97 (242)
T ss_dssp             CCCTTCSTTTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGGGS--CGG
T ss_pred             CCCCCCChhhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHH--HHH
Confidence            34555789998863   23344444444334467899999999999999999999874   78888888775431  122


Q ss_pred             HHHhcCCCcEEEEcCCCccCC
Q 035959          273 VLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       273 ~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      .+.....+.+|+|||+|.+..
T Consensus        98 ~~~~~~~~~vliiDe~~~~~~  118 (242)
T 3bos_A           98 LLEGLEQFDLICIDDVDAVAG  118 (242)
T ss_dssp             GGTTGGGSSEEEEETGGGGTT
T ss_pred             HHHhccCCCEEEEeccccccC
Confidence            333445689999999999865

>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=99.04  E-value=3.1e-10  Score=106.68  Aligned_cols=94  Identities=16%  Similarity=0.236  Sum_probs=63.5

Q ss_pred             CCCCCcccccc-CCh--hHHHHHHHHHHhhh--cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCc----
Q 035959          200 LDHPSTFDTLA-MDT--DMKKMIMDDLERAW--KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGN----  267 (338)
Q Consensus       200 ~~~p~~f~~l~-~~~--~~k~~i~~~l~~~~--~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~----  267 (338)
                      +.+..+|++++ +..  .....+...+..+.  .++++|+||||||||++++++++.+   +.+++.+++.++...    
T Consensus         4 l~~~~~f~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~~~~~~~~~   83 (324)
T 1l8q_A            4 LNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEH   83 (324)
T ss_dssp             CCTTCCSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHH
T ss_pred             CCCCCCcccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHH
Confidence            45566899987 322  22333444443332  3689999999999999999999999   899999988765311    


Q ss_pred             ---hHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 ---KHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ---~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                         ..+.........+++|+|||||.+..
T Consensus        84 ~~~~~~~~~~~~~~~~~vL~iDEi~~l~~  112 (324)
T 1l8q_A           84 LKKGTINEFRNMYKSVDLLLLDDVQFLSG  112 (324)
T ss_dssp             HHHTCHHHHHHHHHTCSEEEEECGGGGTT
T ss_pred             HHcCcHHHHHHHhcCCCEEEEcCcccccC
Confidence               00111222223589999999999865

>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=99.02  E-value=1.2e-09  Score=103.89  Aligned_cols=94  Identities=18%  Similarity=0.320  Sum_probs=71.3

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      ...|.+|+++++.+...+.+...+.... ++.+||+||||||||++++++|+.++.                        
T Consensus         9 k~rp~~~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (373)
T 1jr3_A            9 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFV   88 (373)
T ss_dssp             HTCCCSTTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCCS
T ss_pred             hhCCCchhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCCC
Confidence            5678899999999998888888887632 346899999999999999999998853                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++...-.....++.++....      .+.||+|||+|.+..
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~  133 (373)
T 1jr3_A           89 DLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR  133 (373)
T ss_dssp             SCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCH
T ss_pred             ceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcH
Confidence            345555543233345666666553      468999999999853

>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=99.00  E-value=1.3e-10  Score=114.18  Aligned_cols=108  Identities=16%  Similarity=0.262  Sum_probs=61.9

Q ss_pred             cccCChhHHHHHHHHHHhh--------------hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-------
Q 035959          208 TLAMDTDMKKMIMDDLERA--------------WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-------  266 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~--------------~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-------  266 (338)
                      .+++.++.|+.+...+..+              +++++||+||||||||++++++|..++.+++.++++.+..       
T Consensus        16 ~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~~~~~g~vG~d   95 (444)
T 1g41_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE   95 (444)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC----CCCC
T ss_pred             HhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchhhcccceeecc
Confidence            4678888888887766543              3578999999999999999999999999999999876542       


Q ss_pred             -chHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 -NKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 -~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                       ...++.++...  ..++.+||+|.+...  .            .....+++++.||+.|||+.+.
T Consensus        96 ~e~~lr~lf~~a--~~~~~~De~d~~~~~--~------------~~~~e~rvl~~LL~~~dg~~~~  145 (444)
T 1g41_A           96 VDSIIRDLTDSA--MKLVRQQEIAKNRAR--A------------EDVAEERILDALLPPAKNQWGE  145 (444)
T ss_dssp             THHHHHHHHHHH--HHHHHHHHHHSCC---------------------------------------
T ss_pred             HHHHHHHHHHHH--Hhcchhhhhhhhhcc--c------------hhhHHHHHHHHHHHHhhccccc
Confidence             23455555543  223457887766431  1            1234478999999999999754

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.00  E-value=7.7e-10  Score=102.79  Aligned_cols=98  Identities=16%  Similarity=0.232  Sum_probs=75.5

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCch
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGNK  268 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~~  268 (338)
                      .|..  ...|.+|+++++.+..++.+...+.......++|+||||||||++++++|+.+     +.+++.+++.+.....
T Consensus        10 ~~~~--~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~   87 (323)
T 1sxj_B           10 PWVE--KYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGID   87 (323)
T ss_dssp             CHHH--HTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHH
T ss_pred             cHHH--hcCCCCHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChH
Confidence            4643  57788999999999999988888876433449999999999999999999986     3567888887655555


Q ss_pred             HHHHHHHhc--------C-CCcEEEEcCCCccCC
Q 035959          269 HLRKVLIAT--------E-NKSILVVGDIDCCTE  293 (338)
Q Consensus       269 ~l~~~l~~~--------~-~~~Il~iDeiD~~~~  293 (338)
                      .++.++...        . ++.+|+|||+|.+..
T Consensus        88 ~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~  121 (323)
T 1sxj_B           88 VVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA  121 (323)
T ss_dssp             HHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH
T ss_pred             HHHHHHHHHHhccccCCCCCceEEEEECcccCCH
Confidence            555554421        2 478999999999853

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=98.98  E-value=1.6e-09  Score=100.59  Aligned_cols=86  Identities=16%  Similarity=0.348  Sum_probs=62.8

Q ss_pred             ccccCChhHHHHHHHHHHhhh---------cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHH-
Q 035959          207 DTLAMDTDMKKMIMDDLERAW---------KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKV-  273 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~~---------~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~-  273 (338)
                      +.+++....++.+...+....         ...+||+||||||||++++++|+.+   +.+++.++++.+........+ 
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~l~   96 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLI   96 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccHHHhc
Confidence            346677777777777777631         2368999999999999999999998   556999999876543322222 


Q ss_pred             ------------------HHhcCCCcEEEEcCCCccCC
Q 035959          274 ------------------LIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 ------------------l~~~~~~~Il~iDeiD~~~~  293 (338)
                                        +.. ...++|+|||+|.+..
T Consensus        97 g~~~~~~~~~~~~~~~~~~~~-~~~~vl~lDEi~~l~~  133 (311)
T 4fcw_A           97 GAPPGYVGYEEGGQLTEAVRR-RPYSVILFDAIEKAHP  133 (311)
T ss_dssp             CCCTTSTTTTTCCHHHHHHHH-CSSEEEEEETGGGSCH
T ss_pred             CCCCccccccccchHHHHHHh-CCCeEEEEeChhhcCH
Confidence                              221 2468999999998853

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.96  E-value=4.1e-10  Score=98.36  Aligned_cols=91  Identities=20%  Similarity=0.278  Sum_probs=58.8

Q ss_pred             CCCccccccCChhHHHHHHHHHHh----h--h--cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC----
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER----A--W--KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG----  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~----~--~--~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~----  266 (338)
                      .+.+|++++......+.+++.+..    .  +  +++++|+||||||||+|++++++.+   +.++..+++.++..    
T Consensus        20 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~~~~~~   99 (202)
T 2w58_A           20 LRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELKH   99 (202)
T ss_dssp             GCCCTTSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHHHHHHHH
T ss_pred             HcCCHhhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHHHHHHHH
Confidence            356899988755333333333332    2  1  1789999999999999999999988   67787777654321    


Q ss_pred             ---chHHHHHHHhcCCCcEEEEcCCCccC
Q 035959          267 ---NKHLRKVLIATENKSILVVGDIDCCT  292 (338)
Q Consensus       267 ---~~~l~~~l~~~~~~~Il~iDeiD~~~  292 (338)
                         ...+..++.......+|+|||++...
T Consensus       100 ~~~~~~~~~~~~~~~~~~~lilDei~~~~  128 (202)
T 2w58_A          100 SLQDQTMNEKLDYIKKVPVLMLDDLGAEA  128 (202)
T ss_dssp             C---CCCHHHHHHHHHSSEEEEEEECCC-
T ss_pred             HhccchHHHHHHHhcCCCEEEEcCCCCCc
Confidence               11122233333445799999997753

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=98.93  E-value=5.7e-10  Score=105.04  Aligned_cols=89  Identities=12%  Similarity=0.165  Sum_probs=63.6

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHH-h-----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLI-A-----  276 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~-~-----  276 (338)
                      |..++.+++.++.++.+...+..  .+++||+||||||||++++++|+.++.+++.+++.......++..... .     
T Consensus        23 ~~~~~~i~g~~~~~~~l~~~l~~--~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~~~l~g~~~~~~~~~~  100 (331)
T 2r44_A           23 DEVGKVVVGQKYMINRLLIGICT--GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLPSDLIGTMIYNQHKGN  100 (331)
T ss_dssp             HHHTTTCCSCHHHHHHHHHHHHH--TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCHHHHHEEEEEETTTTE
T ss_pred             HHhccceeCcHHHHHHHHHHHHc--CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCChhhcCCceeecCCCCc
Confidence            33556778888888877777664  578999999999999999999999999999998854332222110000 0     


Q ss_pred             --c-C---CCcEEEEcCCCccCC
Q 035959          277 --T-E---NKSILVVGDIDCCTE  293 (338)
Q Consensus       277 --~-~---~~~Il~iDeiD~~~~  293 (338)
                        . .   ..+||||||+|.+.+
T Consensus       101 ~~~~~g~l~~~vl~iDEi~~~~~  123 (331)
T 2r44_A          101 FEVKKGPVFSNFILADEVNRSPA  123 (331)
T ss_dssp             EEEEECTTCSSEEEEETGGGSCH
T ss_pred             eEeccCcccccEEEEEccccCCH
Confidence              0 1   137999999998753

>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=98.93  E-value=2.5e-09  Score=100.81  Aligned_cols=54  Identities=30%  Similarity=0.367  Sum_probs=43.6

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ...|.+|+++++.++.++.+...+..+...++||+||||||||++++++|+.++
T Consensus        17 ~~~~~~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           17 TRPVFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             -CCCCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CCCCCCchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhCc
Confidence            345678999999988777655554445567899999999999999999999886

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.93  E-value=3.2e-09  Score=100.51  Aligned_cols=99  Identities=22%  Similarity=0.314  Sum_probs=72.7

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCcCCc
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSVEGN  267 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~~~~  267 (338)
                      ..|..  ...|..|+.+++.+...+.+...+.......++|+||||||||++++++|+.+.     ..+..++.++....
T Consensus        13 ~~~~~--k~rp~~~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~~~~~~   90 (340)
T 1sxj_C           13 LPWVE--KYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGI   90 (340)
T ss_dssp             CCHHH--HTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSH
T ss_pred             CchHH--HhCCCcHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCcccccH
Confidence            35654  578999999999988888888777753223499999999999999999999873     24677777664444


Q ss_pred             hHHHHHHHhc--------CCCcEEEEcCCCccCC
Q 035959          268 KHLRKVLIAT--------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l~~~--------~~~~Il~iDeiD~~~~  293 (338)
                      ..++..+...        ..+.|++|||+|.+..
T Consensus        91 ~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~  124 (340)
T 1sxj_C           91 DVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN  124 (340)
T ss_dssp             HHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH
T ss_pred             HHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCH
Confidence            4444433221        2478999999998853

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=98.92  E-value=3.6e-09  Score=110.65  Aligned_cols=93  Identities=24%  Similarity=0.352  Sum_probs=74.8

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC----
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG----  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~----  266 (338)
                      ..|..|+.+++.++..+++++.+....+.++||+||||||||++++++|..+          +..++.+++..+..    
T Consensus       180 ~~~~~~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~  259 (758)
T 1r6b_X          180 ARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKY  259 (758)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCC
T ss_pred             HhcCCCCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccc
Confidence            3456899999999999999998887777889999999999999999999987          56677777766542    


Q ss_pred             ----chHHHHHHHhcC--CCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIATE--NKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~~--~~~Il~iDeiD~~~~  293 (338)
                          ...+..++..+.  .++||||||+|.+.+
T Consensus       260 ~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~  292 (758)
T 1r6b_X          260 RGDFEKRFKALLKQLEQDTNSILFIDEIHTIIG  292 (758)
T ss_dssp             SSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTT
T ss_pred             cchHHHHHHHHHHHHHhcCCeEEEEechHHHhh
Confidence                245677777665  479999999999976

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=98.91  E-value=1.9e-09  Score=114.41  Aligned_cols=93  Identities=18%  Similarity=0.360  Sum_probs=69.9

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC----
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG----  266 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~----  266 (338)
                      ..|..|+.+++.++..+++++.+.+..+++++|+||||||||++++++|+.+          +.+++.++++.+..    
T Consensus       164 ~r~~~ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~  243 (854)
T 1qvr_A          164 AAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKY  243 (854)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC---------
T ss_pred             HhcCCCcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccCcc
Confidence            3467899999999999999998887777889999999999999999999998          78899999887752    


Q ss_pred             ----chHHHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          267 ----NKHLRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ----~~~l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                          ...+..++..+   ..++||||||+|.+.+
T Consensus       244 ~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~  277 (854)
T 1qvr_A          244 RGEFEERLKAVIQEVVQSQGEVILFIDELHTVVG  277 (854)
T ss_dssp             --CHHHHHHHHHHHHHTTCSSEEEEECCC-----
T ss_pred             chHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhc
Confidence                23456666655   3578999999999976

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.91  E-value=2.2e-09  Score=102.00  Aligned_cols=89  Identities=18%  Similarity=0.210  Sum_probs=66.2

Q ss_pred             ccccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCCcCCc----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSSVEGN----  267 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~~~~~----  267 (338)
                      .++.+++.+...+.+...+..    ..+++++|+||||||||++++++++.+         +..++.+++....+.    
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   96 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVA   96 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHH
Confidence            337788888888888887754    234679999999999999999999988         788889998764431    


Q ss_pred             ------------------hH-HHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          268 ------------------KH-LRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ------------------~~-l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                                        .. +..++...   ..+.+|+|||+|.+..
T Consensus        97 ~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~  144 (387)
T 2v1u_A           97 SAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPK  144 (387)
T ss_dssp             HHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHH
T ss_pred             HHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcc
Confidence                              12 22222222   3467999999999965

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.91  E-value=1.9e-09  Score=106.16  Aligned_cols=94  Identities=16%  Similarity=0.283  Sum_probs=63.0

Q ss_pred             CCCCCcccccc-CChh--HHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCCc---
Q 035959          200 LDHPSTFDTLA-MDTD--MKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEGN---  267 (338)
Q Consensus       200 ~~~p~~f~~l~-~~~~--~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~~---  267 (338)
                      +.+..+|++++ ++..  ....+......+. ..+++||||||||||||++++|+.+     +.+++.+++..+...   
T Consensus        98 l~~~~tfd~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~~~~~~~  177 (440)
T 2z4s_A           98 LNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVD  177 (440)
T ss_dssp             CCTTCSGGGCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHHHHHHHH
T ss_pred             CCCCCChhhcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHH
Confidence            44455899987 3322  2223333333333 4679999999999999999999998     788999987765310   


Q ss_pred             ----hHHHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          268 ----KHLRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ----~~l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                          .....+..... .++||||||+|.+..
T Consensus       178 ~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~  208 (440)
T 2z4s_A          178 SMKEGKLNEFREKYRKKVDILLIDDVQFLIG  208 (440)
T ss_dssp             HHHTTCHHHHHHHHTTTCSEEEEECGGGGSS
T ss_pred             HHHcccHHHHHHHhcCCCCEEEEeCcccccC
Confidence                01112222334 789999999999975

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.86  E-value=2.6e-09  Score=101.30  Aligned_cols=89  Identities=19%  Similarity=0.297  Sum_probs=65.3

Q ss_pred             ccccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHh------CCcEEEEecCCcCC--------
Q 035959          205 TFDTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYL------HFDVYDLELSSVEG--------  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l------~~~~~~l~~~~~~~--------  266 (338)
                      .++.+++.+...+.+.+.+..    ..++.++|+||||||||++++++++.+      +..++.+++....+        
T Consensus        18 ~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i   97 (386)
T 2qby_A           18 IPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADL   97 (386)
T ss_dssp             CCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHH
Confidence            447788888888888877764    234578999999999999999999988      88888888653221        


Q ss_pred             --------------chH----HHHHHHhcCCCcEEEEcCCCccCC
Q 035959          267 --------------NKH----LRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 --------------~~~----l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                    ..+    +...+.....+.+|+|||+|.+..
T Consensus        98 ~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~  142 (386)
T 2qby_A           98 LESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVK  142 (386)
T ss_dssp             TTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHH
T ss_pred             HHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhc
Confidence                          112    222233333589999999999964

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=98.84  E-value=5.6e-09  Score=97.82  Aligned_cols=85  Identities=14%  Similarity=0.229  Sum_probs=61.7

Q ss_pred             cccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHh------
Q 035959          208 TLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIA------  276 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~------  276 (338)
                      .+++..+..+.+.+.+..  ....++||+||||||||++++++++..   +.+++.++|+.+... .+...+..      
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~-l~~~~lfg~~~g~~   81 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNES-LLESELFGHEKGAF   81 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHH-HHHHHHTCCCSSCC
T ss_pred             CcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChH-HHHHHhcCcccccc
Confidence            456666677777777766  445789999999999999999999976   578999999876431 11111111      


Q ss_pred             ------------cCCCcEEEEcCCCccCC
Q 035959          277 ------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ------------~~~~~Il~iDeiD~~~~  293 (338)
                                  .....+|||||||.+..
T Consensus        82 tg~~~~~~g~~~~a~~g~L~LDEi~~l~~  110 (304)
T 1ojl_A           82 TGADKRREGRFVEADGGTLFLDEIGDISP  110 (304)
T ss_dssp             C---CCCCCHHHHHTTSEEEEESCTTCCH
T ss_pred             CchhhhhcCHHHhcCCCEEEEeccccCCH
Confidence                        12457999999999864

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.84  E-value=9.7e-09  Score=97.08  Aligned_cols=54  Identities=20%  Similarity=0.340  Sum_probs=44.4

Q ss_pred             cCCCCCccccccCChhHHHHHHHHH-HhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDL-ERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l-~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ...+|.+|+++++.++..+.+...+ .......++|+||||||||++++++|+.+
T Consensus         6 ~kyrP~~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l   60 (354)
T 1sxj_E            6 DKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI   60 (354)
T ss_dssp             TTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             hccCCCCHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3678999999999998888887776 44322339999999999999999999964

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.82  E-value=3e-08  Score=94.36  Aligned_cols=86  Identities=16%  Similarity=0.058  Sum_probs=64.1

Q ss_pred             cccccCChhHHHHHHHHHHh----hhcC--ceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCCcCCchH------
Q 035959          206 FDTLAMDTDMKKMIMDDLER----AWKR--GYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSSVEGNKH------  269 (338)
Q Consensus       206 f~~l~~~~~~k~~i~~~l~~----~~~~--g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~~~~~~~------  269 (338)
                      ++.+++.+...+.+...+..    ..+.  .++|+||||||||++++++++.+    +..++.+++....+...      
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCHHHHHHHHH
Confidence            36788888888888887776    2224  78999999999999999999998    57788998776543111      


Q ss_pred             --------------------HHHHHHhcCCCcEEEEcCCCcc
Q 035959          270 --------------------LRKVLIATENKSILVVGDIDCC  291 (338)
Q Consensus       270 --------------------l~~~l~~~~~~~Il~iDeiD~~  291 (338)
                                          +...+.....+.+|+|||+|.+
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l  137 (389)
T 1fnn_A           96 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL  137 (389)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS
T ss_pred             HHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc
Confidence                                1122222345789999999998

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.82  E-value=2e-09  Score=101.18  Aligned_cols=89  Identities=25%  Similarity=0.339  Sum_probs=56.4

Q ss_pred             CCccccccCChhHHHHHHH----HHHhh---hcCceeeeCCCCCCcHHHHHHHHHHhC----CcEEEEecCCcCC-----
Q 035959          203 PSTFDTLAMDTDMKKMIMD----DLERA---WKRGYLLFGPPGTGKSSLIAAMANYLH----FDVYDLELSSVEG-----  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~----~l~~~---~~~g~LL~GppGtGKT~l~~aia~~l~----~~~~~l~~~~~~~-----  266 (338)
                      +.+|+++......+..+++    .+...   ...+++|+||||||||+|+.|+|+.+.    .++..+.+.++..     
T Consensus       120 ~~tfd~f~~~~~~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l~~~l~~~  199 (308)
T 2qgz_A          120 HIHLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKNA  199 (308)
T ss_dssp             SCCGGGSCCCSHHHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHHHHHHHCC
T ss_pred             hCCHhhCcCCChHHHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHHHHHHHHH
Confidence            4689998875533333333    33321   257899999999999999999998765    7777777654311     


Q ss_pred             --chHHHHHHHhcCCCcEEEEcCCCcc
Q 035959          267 --NKHLRKVLIATENKSILVVGDIDCC  291 (338)
Q Consensus       267 --~~~l~~~l~~~~~~~Il~iDeiD~~  291 (338)
                        ...+...+.......+||||||+..
T Consensus       200 ~~~~~~~~~~~~~~~~~lLiiDdig~~  226 (308)
T 2qgz_A          200 ISNGSVKEEIDAVKNVPVLILDDIGAE  226 (308)
T ss_dssp             CC----CCTTHHHHTSSEEEEETCCC-
T ss_pred             hccchHHHHHHHhcCCCEEEEcCCCCC
Confidence              1111122223345689999999764

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.81  E-value=7.2e-09  Score=97.80  Aligned_cols=67  Identities=12%  Similarity=0.238  Sum_probs=51.7

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCCc----------------------hHHHHH
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEGN----------------------KHLRKV  273 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~~----------------------~~l~~~  273 (338)
                      ..+.+++|+||||||||++++++++.+          ++.++.++|..+.+.                      ..+.++
T Consensus        43 ~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~  122 (318)
T 3te6_A           43 SQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFY  122 (318)
T ss_dssp             TCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHH
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Confidence            445679999999999999999999998          356788898765431                      235566


Q ss_pred             HHhc----CCCcEEEEcCCCccC
Q 035959          274 LIAT----ENKSILVVGDIDCCT  292 (338)
Q Consensus       274 l~~~----~~~~Il~iDeiD~~~  292 (338)
                      |...    ..+.||+|||+|.+.
T Consensus       123 f~~~~~~~~~~~ii~lDE~d~l~  145 (318)
T 3te6_A          123 ITNVPKAKKRKTLILIQNPENLL  145 (318)
T ss_dssp             HHHSCGGGSCEEEEEEECCSSSC
T ss_pred             HHHhhhccCCceEEEEecHHHhh
Confidence            6653    357899999999996

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=98.78  E-value=1.8e-08  Score=105.32  Aligned_cols=96  Identities=17%  Similarity=0.320  Sum_probs=71.5

Q ss_pred             cccCChhHHHHHHHHHHhhh--------c-CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCc-----------
Q 035959          208 TLAMDTDMKKMIMDDLERAW--------K-RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGN-----------  267 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~~--------~-~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~-----------  267 (338)
                      .+++.++.++.+...+....        + ..+||+||||||||++++++|+.++.+++.++++++...           
T Consensus       459 ~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~~~l~g~~~  538 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPP  538 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCS
T ss_pred             hccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhHhhhcCCCC
Confidence            46677777777776665421        2 258999999999999999999999999999999876431           


Q ss_pred             --------hHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhc
Q 035959          268 --------KHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTD  326 (338)
Q Consensus       268 --------~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iD  326 (338)
                              ..+...+.. ..++||||||||.+.+                      ..++.||..||
T Consensus       539 g~~g~~~~~~l~~~~~~-~~~~vl~lDEi~~~~~----------------------~~~~~Ll~~le  582 (758)
T 1r6b_X          539 GYVGFDQGGLLTDAVIK-HPHAVLLLDEIEKAHP----------------------DVFNILLQVMD  582 (758)
T ss_dssp             CSHHHHHTTHHHHHHHH-CSSEEEEEETGGGSCH----------------------HHHHHHHHHHH
T ss_pred             CCcCccccchHHHHHHh-CCCcEEEEeCccccCH----------------------HHHHHHHHHhc
Confidence                    123333333 4579999999998743                      46677888877

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.77  E-value=1.6e-08  Score=105.89  Aligned_cols=98  Identities=16%  Similarity=0.291  Sum_probs=73.3

Q ss_pred             ccccCChhHHHHHHHHHHhhh--------cC-ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCc-----hH
Q 035959          207 DTLAMDTDMKKMIMDDLERAW--------KR-GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGN-----KH  269 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~~--------~~-g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~-----~~  269 (338)
                      +.+++.++.++.+...+....        +. .+||+||||||||++++++|+.+   +.+++.++++++...     ..
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~~~~~  570 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHSTSGGQ  570 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCCC---
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhcccccccccch
Confidence            456788888888877777621        11 59999999999999999999998   678999999987642     23


Q ss_pred             HHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcC
Q 035959          270 LRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDG  327 (338)
Q Consensus       270 l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDg  327 (338)
                      +...+.. .+.+||||||||.+.+                      ..++.||+.||.
T Consensus       571 l~~~~~~-~~~~vl~lDEi~~~~~----------------------~~~~~Ll~~le~  605 (758)
T 3pxi_A          571 LTEKVRR-KPYSVVLLDAIEKAHP----------------------DVFNILLQVLED  605 (758)
T ss_dssp             CHHHHHH-CSSSEEEEECGGGSCH----------------------HHHHHHHHHHHH
T ss_pred             hhHHHHh-CCCeEEEEeCccccCH----------------------HHHHHHHHHhcc
Confidence            3333333 4678999999998743                      556778888874

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.77  E-value=1.4e-08  Score=85.19  Aligned_cols=81  Identities=17%  Similarity=0.199  Sum_probs=57.4

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHHhcCCC
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLIATENK  280 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~~~~~~  280 (338)
                      .+|+++....  .+.++..+.......++|+||+|+|||+|++++++.+   |..+..++..++....       ...++
T Consensus        14 ~~~~~f~~g~--n~~~~~~l~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~~-------~~~~~   84 (149)
T 2kjq_A           14 PSFDKFLGTE--NAELVYVLRHKHGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLTD-------AAFEA   84 (149)
T ss_dssp             CCCCCCCSCC--THHHHHHCCCCCCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCCG-------GGGGC
T ss_pred             cchhhcCcCc--cHHHHHHHHhcCCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHHH-------HHhCC
Confidence            3566665422  2233444433334568999999999999999999988   7778888888766541       13468


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      .+|+|||++.+..
T Consensus        85 ~lLilDE~~~~~~   97 (149)
T 2kjq_A           85 EYLAVDQVEKLGN   97 (149)
T ss_dssp             SEEEEESTTCCCS
T ss_pred             CEEEEeCccccCh
Confidence            9999999998654

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.76  E-value=9.7e-09  Score=97.84  Aligned_cols=87  Identities=16%  Similarity=0.210  Sum_probs=63.8

Q ss_pred             ccccCChhHHHHHHHHHHh----hhcCceeeeCCCCCCcHHHHHHHHHHh-----------CCcEEEEecCCcC-Cc---
Q 035959          207 DTLAMDTDMKKMIMDDLER----AWKRGYLLFGPPGTGKSSLIAAMANYL-----------HFDVYDLELSSVE-GN---  267 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~----~~~~g~LL~GppGtGKT~l~~aia~~l-----------~~~~~~l~~~~~~-~~---  267 (338)
                      +.+++.++..+.+...+..    ..+++++|+||||||||++++++++.+           +..++.+++.... +.   
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   99 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAV   99 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHH
Confidence            6788888888888877765    224579999999999999999999988           8899999876543 21   


Q ss_pred             --------------------hH-HHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          268 --------------------KH-LRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       268 --------------------~~-l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                                          .. +..+..... .+.+|+|||+|.+..
T Consensus       100 ~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~  147 (384)
T 2qby_B          100 LSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVK  147 (384)
T ss_dssp             HHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHH
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhcc
Confidence                                11 222222233 233999999999864

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=98.75  E-value=1.1e-08  Score=103.40  Aligned_cols=87  Identities=21%  Similarity=0.275  Sum_probs=62.1

Q ss_pred             ccccCChhHHHHHHHHHHh------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCch------------
Q 035959          207 DTLAMDTDMKKMIMDDLER------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNK------------  268 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~------------  268 (338)
                      +++++.+++++.+.+.+..      .....++|+||||||||++++++|..++.++..+++..+....            
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~g~~~~~ig~  160 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRGHRRTYVGA  160 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC-----------------
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhhhHHHHHhcc
Confidence            4577778888777655443      1134689999999999999999999999999999887754321            


Q ss_pred             ---HHHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          269 ---HLRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       269 ---~l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                         .+...+..+. ...||||||||.+..
T Consensus       161 ~~~~~~~~~~~a~~~~~vl~lDEid~l~~  189 (543)
T 3m6a_A          161 MPGRIIQGMKKAGKLNPVFLLDEIDKMSS  189 (543)
T ss_dssp             ---CHHHHHHTTCSSSEEEEEEESSSCC-
T ss_pred             CchHHHHHHHHhhccCCEEEEhhhhhhhh
Confidence               2334444443 456999999999976

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.72  E-value=1.7e-08  Score=100.03  Aligned_cols=87  Identities=21%  Similarity=0.357  Sum_probs=66.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcC---C
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVE---G  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~---~  266 (338)
                      ...|..|+.+++.++..+.+++.+.+..+.++||+||||||||++++++|..+          +.+++.+++..-.   .
T Consensus       173 ~~r~~~ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~~~~g~~  252 (468)
T 3pxg_A          173 IAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGEF  252 (468)
T ss_dssp             HTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------
T ss_pred             HHhcCCCCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCccccchH
Confidence            35677899999999999999999887777889999999999999999999997          7788888876211   1


Q ss_pred             chHHHHHHHhcC--CCcEEEEc
Q 035959          267 NKHLRKVLIATE--NKSILVVG  286 (338)
Q Consensus       267 ~~~l~~~l~~~~--~~~Il~iD  286 (338)
                      ...+..++..+.  .+.|||||
T Consensus       253 e~~~~~~~~~~~~~~~~iLfiD  274 (468)
T 3pxg_A          253 EDRLKKVMDEIRQAGNIILFID  274 (468)
T ss_dssp             CTTHHHHHHHHHTCCCCEEEEC
T ss_pred             HHHHHHHHHHHHhcCCeEEEEe
Confidence            235566666553  67899999

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=98.72  E-value=2.7e-08  Score=105.51  Aligned_cols=97  Identities=19%  Similarity=0.348  Sum_probs=72.0

Q ss_pred             ccccCChhHHHHHHHHHHhhh--------c-CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCc-------
Q 035959          207 DTLAMDTDMKKMIMDDLERAW--------K-RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGN-------  267 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~~--------~-~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~-------  267 (338)
                      +.+++.++..+.+...+....        + ..+||+||||||||++++++|+.+   +.+++.++++++...       
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~s~l~  637 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLI  637 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC-
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHHHHHc
Confidence            557888888887777776521        1 368999999999999999999999   788999999876542       


Q ss_pred             ------------hHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhc
Q 035959          268 ------------KHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTD  326 (338)
Q Consensus       268 ------------~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iD  326 (338)
                                  ..+...+.. ...++|||||||.+..                      ..++.||..||
T Consensus       638 g~~~~~~G~~~~g~l~~~~~~-~~~~vl~lDEi~~l~~----------------------~~~~~Ll~~l~  685 (854)
T 1qvr_A          638 GAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKAHP----------------------DVFNILLQILD  685 (854)
T ss_dssp             -------------CHHHHHHH-CSSEEEEESSGGGSCH----------------------HHHHHHHHHHT
T ss_pred             CCCCCCcCccccchHHHHHHh-CCCeEEEEecccccCH----------------------HHHHHHHHHhc
Confidence                        112222222 3578999999998743                      46677888887

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.64  E-value=1.1e-08  Score=90.41  Aligned_cols=60  Identities=18%  Similarity=0.276  Sum_probs=41.1

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCcc
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCC  291 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~  291 (338)
                      |.++++|+|||||||||+++.|+|+.+...+...  ..  +...  ..+..+....|++|||+|..
T Consensus        56 Pkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~f--an--s~s~--f~l~~l~~~kIiiLDEad~~  115 (212)
T 1tue_A           56 PKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISF--VN--STSH--FWLEPLTDTKVAMLDDATTT  115 (212)
T ss_dssp             TTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCC--CC--SSSC--GGGGGGTTCSSEEEEEECHH
T ss_pred             CcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeE--Ee--ccch--hhhcccCCCCEEEEECCCch
Confidence            4567899999999999999999999997654322  11  1110  01223345679999999953

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=98.64  E-value=1.4e-07  Score=89.24  Aligned_cols=80  Identities=23%  Similarity=0.298  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhC------------------------CcEEEEecC---CcC
Q 035959          214 DMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLH------------------------FDVYDLELS---SVE  265 (338)
Q Consensus       214 ~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~~~~~l~~~---~~~  265 (338)
                      +..+.+...+.. ..+..+||+||||||||++++++|+.+.                        .+++.++..   .-.
T Consensus         9 ~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~~   88 (334)
T 1a5t_A            9 PDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTL   88 (334)
T ss_dssp             HHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSB
T ss_pred             HHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccccCCCC
Confidence            445556666654 2345699999999999999999999874                        346666654   223


Q ss_pred             CchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          266 GNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       266 ~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      ..+.++.++....      .+.|++|||+|.+..
T Consensus        89 ~i~~ir~l~~~~~~~~~~~~~kvviIdead~l~~  122 (334)
T 1a5t_A           89 GVDAVREVTEKLNEHARLGGAKVVWVTDAALLTD  122 (334)
T ss_dssp             CHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCH
T ss_pred             CHHHHHHHHHHHhhccccCCcEEEEECchhhcCH
Confidence            3456777776653      478999999999854

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.61  E-value=5.1e-08  Score=102.05  Aligned_cols=87  Identities=21%  Similarity=0.368  Sum_probs=67.5

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCc-C--C
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSV-E--G  266 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~-~--~  266 (338)
                      ...|..++.+++.++..+++++.+....+.++||+||||||||++++++|+.+          +..++.+++..- .  .
T Consensus       173 ~~~~~~ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~g~~~~G~~  252 (758)
T 3pxi_A          173 IAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGEF  252 (758)
T ss_dssp             HTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC----------
T ss_pred             HHhhCCCCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecccccccchH
Confidence            34567899999999999999999988777899999999999999999999997          778888877211 1  1


Q ss_pred             chHHHHHHHhc--CCCcEEEEc
Q 035959          267 NKHLRKVLIAT--ENKSILVVG  286 (338)
Q Consensus       267 ~~~l~~~l~~~--~~~~Il~iD  286 (338)
                      ...++.++..+  ..++|||||
T Consensus       253 e~~l~~~~~~~~~~~~~iLfiD  274 (758)
T 3pxi_A          253 EDRLKKVMDEIRQAGNIILFID  274 (758)
T ss_dssp             CTTHHHHHHHHHTCCCCEEEEC
T ss_pred             HHHHHHHHHHHHhcCCEEEEEc
Confidence            33566666655  368999999

>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=98.61  E-value=8.4e-08  Score=89.96  Aligned_cols=81  Identities=15%  Similarity=0.189  Sum_probs=58.8

Q ss_pred             hhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh------CCcEEEEecCC-cCCchHHHHHHHhcC------C
Q 035959          213 TDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL------HFDVYDLELSS-VEGNKHLRKVLIATE------N  279 (338)
Q Consensus       213 ~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l------~~~~~~l~~~~-~~~~~~l~~~l~~~~------~  279 (338)
                      ++..+.+...+.......||||||||||||+++.++|+.+      ..+++.++... -...+.++.++..+.      .
T Consensus         3 ~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~~~~   82 (305)
T 2gno_A            3 KDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYT   82 (305)
T ss_dssp             -CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSS
T ss_pred             HHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccccCC
Confidence            3444555555554334579999999999999999999874      45788888764 334556777766553      4


Q ss_pred             CcEEEEcCCCccCC
Q 035959          280 KSILVVGDIDCCTE  293 (338)
Q Consensus       280 ~~Il~iDeiD~~~~  293 (338)
                      ..|+||||+|.+..
T Consensus        83 ~kvviIdead~lt~   96 (305)
T 2gno_A           83 RKYVIVHDCERMTQ   96 (305)
T ss_dssp             SEEEEETTGGGBCH
T ss_pred             ceEEEeccHHHhCH
Confidence            67999999999954

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=98.50  E-value=1.5e-07  Score=93.98  Aligned_cols=81  Identities=14%  Similarity=0.110  Sum_probs=50.8

Q ss_pred             ccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEecCCcCCchHH-----------HHHHH
Q 035959          209 LAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLELSSVEGNKHL-----------RKVLI  275 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~~~~~~~~~l-----------~~~l~  275 (338)
                      +++.++.++.+...+..  ..++||+||||||||++++++|+.++.  ++..+.+.. .+.+++           ...+.
T Consensus        24 ivGq~~~i~~l~~al~~--~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~-~t~~dL~G~~~~~~~~~~g~~~  100 (500)
T 3nbx_X           24 LYERSHAIRLCLLAALS--GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRF-STPEEVFGPLSIQALKDEGRYE  100 (500)
T ss_dssp             CSSCHHHHHHHHHHHHH--TCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTT-CCHHHHHCCBC----------C
T ss_pred             hHHHHHHHHHHHHHHhc--CCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhc-CCHHHhcCcccHHHHhhchhHH
Confidence            45667766666655543  468999999999999999999998854  344444432 111111           11122


Q ss_pred             hcC-----CCcEEEEcCCCccC
Q 035959          276 ATE-----NKSILVVGDIDCCT  292 (338)
Q Consensus       276 ~~~-----~~~Il~iDeiD~~~  292 (338)
                      ...     .++|||||||+.+.
T Consensus       101 ~~~~g~l~~~~IL~IDEI~r~~  122 (500)
T 3nbx_X          101 RLTSGYLPEAEIVFLDEIWKAG  122 (500)
T ss_dssp             BCCTTSGGGCSEEEEESGGGCC
T ss_pred             hhhccCCCcceeeeHHhHhhhc
Confidence            111     35689999998764

>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=98.38  E-value=1.2e-07  Score=89.30  Aligned_cols=91  Identities=12%  Similarity=0.079  Sum_probs=51.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec--CCcC-----C-chHHHHHHHhcCCCcEEEEcCCCccCCccccccc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL--SSVE-----G-NKHLRKVLIATENKSILVVGDIDCCTELQDRSAQ  300 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~--~~~~-----~-~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~  300 (338)
                      +.++|+||||||||+|+.++|...+..+.++++  .+..     . +..+..+........+||||+|+.+..  .+.+.
T Consensus       124 sviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~LLVIDsI~aL~~--~~~~~  201 (331)
T 2vhj_A          124 GMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIG--AAGGN  201 (331)
T ss_dssp             EEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEECCTTTC--------
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCCEEEEeccccccc--ccccc
Confidence            446999999999999999999887666555555  2211     1 112222333332222999999999865  22211


Q ss_pred             ccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          301 ARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       301 ~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                      ..        .+.....+..+|..|+++.
T Consensus       202 s~--------~G~v~~~lrqlL~~L~~~~  222 (331)
T 2vhj_A          202 TT--------SGGISRGAFDLLSDIGAMA  222 (331)
T ss_dssp             -------------CCHHHHHHHHHHHHHH
T ss_pred             cc--------cchHHHHHHHHHHHHHHHH
Confidence            10        1222456677777776553

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=98.37  E-value=6.2e-07  Score=85.95  Aligned_cols=87  Identities=10%  Similarity=0.122  Sum_probs=60.2

Q ss_pred             ccccCChhHHHHHHHHH-Hh---h---hcCceee--eCCCCCCcHHHHHHHHHHh---------CCcEEEEecCCcCCc-
Q 035959          207 DTLAMDTDMKKMIMDDL-ER---A---WKRGYLL--FGPPGTGKSSLIAAMANYL---------HFDVYDLELSSVEGN-  267 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l-~~---~---~~~g~LL--~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~~~~~-  267 (338)
                      +.+++.+...+.+.+.+ ..   .   .++.+++  +||||||||+|++++++.+         +..++.+++....+. 
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY  101 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHH
Confidence            56788877777777777 43   1   2346789  9999999999999999877         456778886432211 


Q ss_pred             ---------------------hH----HHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 ---------------------KH----LRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ---------------------~~----l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                           ..    +...+.....+.+|+|||+|.+..
T Consensus       102 ~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~  152 (412)
T 1w5s_A          102 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLS  152 (412)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHS
T ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhh
Confidence                                 11    122222224578999999999864

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.35  E-value=1.4e-06  Score=81.34  Aligned_cols=55  Identities=24%  Similarity=0.184  Sum_probs=45.4

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS  263 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~  263 (338)
                      .-+.+++.+...+.+.+ +..   +.++++||+|+|||+|++.+++.++..++.+++..
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~   65 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRK   65 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGG
T ss_pred             CHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchh
Confidence            44667888887788877 664   57899999999999999999999887788888764

>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=98.28  E-value=7.5e-07  Score=99.59  Aligned_cols=94  Identities=13%  Similarity=0.141  Sum_probs=64.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC----------------------CchHHHHHHHh--cCCCcEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE----------------------GNKHLRKVLIA--TENKSIL  283 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~----------------------~~~~l~~~l~~--~~~~~Il  283 (338)
                      +|+|||||||||.|+.++|.+.   |-+..+++.....                      ++..++.++..  ...+++|
T Consensus      1085 ~l~~G~~g~GKT~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~~~~~~i 1164 (1706)
T 3cmw_A         1085 VEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVI 1164 (1706)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSEE
T ss_pred             EEEEcCCCCChHHHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHhcCCeEE
Confidence            9999999999999999999876   4566677665522                      12234444432  3479999


Q ss_pred             EEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          284 VVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       284 ~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                      ++|+||++.+  .|.......+   ...+...+.++++|..|||+.
T Consensus      1165 ~~d~~~al~~--~~~~~g~~~~---~~~~~~~r~~~q~l~~~~~~~ 1205 (1706)
T 3cmw_A         1165 VVDSVAALTP--KAEIEGEIGD---SHMGLAARMMSQAMRKLAGNL 1205 (1706)
T ss_dssp             EESCGGGCCC--HHHHHSCTTC---CCTTHHHHHHHHHHHHHHHHH
T ss_pred             EeCchHhcCc--cccccccccc---ccccHHHHHHHHHHHHHHhhh
Confidence            9999999998  4432211110   112445668999999999954

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.22  E-value=2.8e-06  Score=86.63  Aligned_cols=52  Identities=35%  Similarity=0.385  Sum_probs=43.9

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ...|..|+.+++....++.+...+..  ...++|+||||||||++++++|..+.
T Consensus        34 ~~rp~~l~~i~G~~~~l~~l~~~i~~--g~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           34 EVPEKLIDQVIGQEHAVEVIKTAANQ--KRHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             CCCSSHHHHCCSCHHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             cccccccceEECchhhHhhccccccC--CCEEEEEeCCCCCHHHHHHHHhccCC
Confidence            45678999999998888777666653  36899999999999999999999885

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.21  E-value=5.9e-06  Score=96.12  Aligned_cols=67  Identities=28%  Similarity=0.486  Sum_probs=52.3

Q ss_pred             hhcCceeeeCCCCCCcHHHH-HHHHHHhCCcEEEEecCCcCCchHHHHHHHhc-----------------CCCcEEEEcC
Q 035959          226 AWKRGYLLFGPPGTGKSSLI-AAMANYLHFDVYDLELSSVEGNKHLRKVLIAT-----------------ENKSILVVGD  287 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~-~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~-----------------~~~~Il~iDe  287 (338)
                      ..++++||+||||||||++| +++++..++.+..++++...+...+.+.+...                 .++.||||||
T Consensus      1265 ~~~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDE 1344 (2695)
T 4akg_A         1265 NSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDE 1344 (2695)
T ss_dssp             HHTCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEET
T ss_pred             HCCCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEecc
Confidence            34589999999999999999 55555557889999999888777776666532                 1357999999


Q ss_pred             CCccC
Q 035959          288 IDCCT  292 (338)
Q Consensus       288 iD~~~  292 (338)
                      ||...
T Consensus      1345 inmp~ 1349 (2695)
T 4akg_A         1345 INLPK 1349 (2695)
T ss_dssp             TTCSC
T ss_pred             ccccc
Confidence            99753

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=98.19  E-value=9.8e-08  Score=97.38  Aligned_cols=84  Identities=19%  Similarity=0.252  Sum_probs=51.1

Q ss_pred             ccCChhHHHHHHHHHHhhhc-----------CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec----CCcCC---chHH
Q 035959          209 LAMDTDMKKMIMDDLERAWK-----------RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL----SSVEG---NKHL  270 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~~~-----------~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~----~~~~~---~~~l  270 (338)
                      +++.+.+|+.+...+....+           .++||+||||||||++++++|+.++...+....    ..+..   ....
T Consensus       297 I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~~~~~  376 (595)
T 3f9v_A          297 IYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKG  376 (595)
T ss_dssp             TSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECSSGGG
T ss_pred             hcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceeeeccc
Confidence            45666666666444432211           169999999999999999999998766544221    11110   0000


Q ss_pred             -------HHHHHhcCCCcEEEEcCCCccCC
Q 035959          271 -------RKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       271 -------~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                             ...+. .+.++||+|||||.+.+
T Consensus       377 ~g~~~~~~G~l~-~A~~gil~IDEid~l~~  405 (595)
T 3f9v_A          377 TGEYYLEAGALV-LADGGIAVIDEIDKMRD  405 (595)
T ss_dssp             TSSCSEEECHHH-HHSSSEECCTTTTCCCS
T ss_pred             cccccccCCeeE-ecCCCcEEeehhhhCCH
Confidence                   00111 12468999999999865

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.17  E-value=4.7e-06  Score=77.65  Aligned_cols=55  Identities=22%  Similarity=0.193  Sum_probs=43.4

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      ..-+.+++.+...+.+.+.+..  .+.++++||+|+|||+|++.+++..+  ++.+++.
T Consensus         9 ~~~~~~~gR~~el~~L~~~l~~--~~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~   63 (350)
T 2qen_A            9 TRREDIFDREEESRKLEESLEN--YPLTLLLGIRRVGKSSLLRAFLNERP--GILIDCR   63 (350)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHH--CSEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHH
T ss_pred             CChHhcCChHHHHHHHHHHHhc--CCeEEEECCCcCCHHHHHHHHHHHcC--cEEEEee
Confidence            3446678888888888777764  26789999999999999999999876  6666654

>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=98.12  E-value=6.7e-06  Score=79.22  Aligned_cols=89  Identities=22%  Similarity=0.270  Sum_probs=59.8

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTAS  305 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~  305 (338)
                      +.++.++|+||||+|||+++++++..++..++.++...    ......+....+..++++||++..... .|+-..    
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~~~~----~~~~~~lg~~~q~~~~l~dd~~~~~~~-~r~l~~----  237 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPL----DRLNFELGVAIDQFLVVFEDVKGTGGE-SRDLPS----  237 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCT----TTHHHHHGGGTTCSCEEETTCCCSTTT-TTTCCC----
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEeccc----hhHHHHHHHhcchhHHHHHHHHHHHHH-Hhhccc----
Confidence            45567899999999999999999999887765533222    222223444567788899999998763 221110    


Q ss_pred             CCCCCCCcchhhHHHHHHHhcCCc
Q 035959          306 PDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       306 ~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                            +....+++.+.+.+||..
T Consensus       238 ------~~~~~~~~~l~~~ldG~v  255 (377)
T 1svm_A          238 ------GQGINNLDNLRDYLDGSV  255 (377)
T ss_dssp             ------CSHHHHHHTTHHHHHCSS
T ss_pred             ------cCcchHHHHHHHHhcCCC
Confidence                  011236688899999853

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.09  E-value=6.7e-06  Score=95.67  Aligned_cols=85  Identities=19%  Similarity=0.174  Sum_probs=68.1

Q ss_pred             ccCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcC-CCcEEEEc
Q 035959          209 LAMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATE-NKSILVVG  286 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~-~~~Il~iD  286 (338)
                      ++.-|-..+..+..+.+ ....|.++.||||||||.+++++|+.+|.+++.++|++-.+...+.++|..+. ..+++++|
T Consensus       625 lViTPltdr~~~tl~~Al~~~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~~~lg~~~~g~~~~Gaw~~~D  704 (2695)
T 4akg_A          625 LIYTPLLLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFD  704 (2695)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCHHHHHHHHHHHHHHTCEEEEE
T ss_pred             ceecHHHHHHHHHHHHHHHhCCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCChhHhhHHHHHHHhcCCEeeeh
Confidence            45555544443333333 34578899999999999999999999999999999999888888888887765 57999999


Q ss_pred             CCCccCC
Q 035959          287 DIDCCTE  293 (338)
Q Consensus       287 eiD~~~~  293 (338)
                      |++.+..
T Consensus       705 E~nr~~~  711 (2695)
T 4akg_A          705 EFNRLDE  711 (2695)
T ss_dssp             TTTSSCH
T ss_pred             hhhhcCh
Confidence            9999854

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.08  E-value=4.1e-06  Score=94.80  Aligned_cols=100  Identities=12%  Similarity=0.091  Sum_probs=65.9

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC---------------------CchHHHHHHHhc---CC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE---------------------GNKHLRKVLIAT---EN  279 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~---------------------~~~~l~~~l~~~---~~  279 (338)
                      .+++++|+||||||||+|+.+++...   |..+.+++.....                     ..+++.+.+...   .+
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~~~ 1505 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1505 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHHHhcCC
Confidence            45679999999999999999998775   5678888776532                     112233333333   58


Q ss_pred             CcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          280 KSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       280 ~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                      +++||||+++.+.+..+-++...  +   .......+.++++|..|++....
T Consensus      1506 ~~lVVIDsi~al~p~~~~~g~~~--~---~~~~~~~R~lsqlL~~L~~~~~~ 1552 (2050)
T 3cmu_A         1506 VDVIVVDSVAALTPKAEIEGEIG--D---SHMGLAARMMSQAMRKLAGNLKQ 1552 (2050)
T ss_dssp             CSEEEESCGGGCCCHHHHHSCTT--C---CCTTHHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEcChhHhccccccccccc--c---cccchHHHHHHHHHHHHHHHHHh
Confidence            99999999999987211111111  0   00111356789999999987654

>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=98.08  E-value=5.1e-06  Score=76.20  Aligned_cols=69  Identities=16%  Similarity=0.199  Sum_probs=44.3

Q ss_pred             HHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCccC
Q 035959          217 KMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCT  292 (338)
Q Consensus       217 ~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~~  292 (338)
                      ..+...+..  +++++++||||||||||+++.|+|+.++.- -.++.+..      ...+.....+.|++.||....-
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~~l~-G~vn~~~~------~f~l~~~~~k~i~l~Ee~~~~~  161 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWTNE------NFPFNDCVDKMVIWWEEGKMTA  161 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTTCS------SCTTGGGSSCSEEEECSCCEET
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhhccc-ceeecccc------ccccccccccEEEEeccccchh
Confidence            344444544  335689999999999999999999987652 22233211      1123444566778877776553

>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=97.91  E-value=3.5e-05  Score=74.27  Aligned_cols=85  Identities=14%  Similarity=0.223  Sum_probs=60.0

Q ss_pred             cccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCCcCCchHHHHHHHh------
Q 035959          208 TLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSVEGNKHLRKVLIA------  276 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~~~~~~~l~~~l~~------  276 (338)
                      .+++.....+++.+.+..  .....++++|++||||+.+++++.....   .+++.++|+.+.. ..+...+..      
T Consensus       138 ~~ig~s~~m~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~-~~~~~elfg~~~g~~  216 (387)
T 1ny5_A          138 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPR-DIFEAELFGYEKGAF  216 (387)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCH-HHHHHHHHCBCTTSS
T ss_pred             hhhhccHHhhHHHHHHHHhcCCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCH-HHHHHHhcCCCCCCC
Confidence            445555555666666655  3345789999999999999999998764   6899999998653 222222222      


Q ss_pred             ------------cCCCcEEEEcCCCccCC
Q 035959          277 ------------TENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ------------~~~~~Il~iDeiD~~~~  293 (338)
                                  .....+||||||+.+..
T Consensus       217 tga~~~~~g~~~~a~~gtlfldei~~l~~  245 (387)
T 1ny5_A          217 TGAVSSKEGFFELADGGTLFLDEIGELSL  245 (387)
T ss_dssp             TTCCSCBCCHHHHTTTSEEEEESGGGCCH
T ss_pred             CCcccccCCceeeCCCcEEEEcChhhCCH
Confidence                        13467999999999964

>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=97.90  E-value=6.5e-05  Score=71.93  Aligned_cols=86  Identities=15%  Similarity=0.193  Sum_probs=59.6

Q ss_pred             cccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhCCc--EEEEecCCcCCchHHHHHH---------
Q 035959          208 TLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLHFD--VYDLELSSVEGNKHLRKVL---------  274 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~~~--~~~l~~~~~~~~~~l~~~l---------  274 (338)
                      .+++.....+++.+.+..  +....++++|++||||+.+++++....+..  ++.++|+.+..+---..+|         
T Consensus       130 ~~ig~s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~~lfg~~~g~~tg  209 (368)
T 3dzd_A          130 EFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGHEKGAFTG  209 (368)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHHHHHEECSCSSSS
T ss_pred             cccccchHHHHHHhhhhhhhccchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHHHhcCccccccCC
Confidence            345555555555555544  334578999999999999999999887543  9999999875432222222         


Q ss_pred             --------HhcCCCcEEEEcCCCccCC
Q 035959          275 --------IATENKSILVVGDIDCCTE  293 (338)
Q Consensus       275 --------~~~~~~~Il~iDeiD~~~~  293 (338)
                              .+......||||||+.+..
T Consensus       210 a~~~~~g~~~~a~~gtlfldei~~l~~  236 (368)
T 3dzd_A          210 ALTRKKGKLELADQGTLFLDEVGELDQ  236 (368)
T ss_dssp             CCCCEECHHHHTTTSEEEEETGGGSCH
T ss_pred             cccccCChHhhcCCCeEEecChhhCCH
Confidence                    1123567899999999964

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=97.77  E-value=1.4e-05  Score=70.25  Aligned_cols=64  Identities=16%  Similarity=0.149  Sum_probs=41.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh--------C-CcEEEEecCCcCC---------------------chHHHHHHH-hcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL--------H-FDVYDLELSSVEG---------------------NKHLRKVLI-ATE  278 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l--------~-~~~~~l~~~~~~~---------------------~~~l~~~l~-~~~  278 (338)
                      -+|++|+||||||+++.+++...        | .+++..++.++..                     ...+...+. ...
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            46899999999999988865442        4 6666666554321                     012222211 112


Q ss_pred             CCcEEEEcCCCccCC
Q 035959          279 NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 ~~~Il~iDeiD~~~~  293 (338)
                      ..+||||||++.+.+
T Consensus        87 ~~~vliIDEAq~l~~  101 (199)
T 2r2a_A           87 IGSIVIVDEAQDVWP  101 (199)
T ss_dssp             TTCEEEETTGGGTSB
T ss_pred             CceEEEEEChhhhcc
Confidence            489999999999975

>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=97.57  E-value=9.7e-05  Score=72.62  Aligned_cols=61  Identities=21%  Similarity=0.207  Sum_probs=36.6

Q ss_pred             cCCCCCccccccCChhHHHHHHH---HHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CC-cEEEEecC
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMD---DLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HF-DVYDLELS  262 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~---~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~-~~~~l~~~  262 (338)
                      +...|.+|+.+  .++.++.+..   .+.. ..+.+++.||||||||+++.+++..+   +. .++.+..+
T Consensus        16 ~~~~p~~~~~L--n~~Q~~av~~~~~~i~~-~~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T   83 (459)
T 3upu_A           16 PRGSHMTFDDL--TEGQKNAFNIVMKAIKE-KKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPT   83 (459)
T ss_dssp             -----CCSSCC--CHHHHHHHHHHHHHHHS-SSCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             cccCCCccccC--CHHHHHHHHHHHHHHhc-CCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCc
Confidence            46777888875  4443433332   2222 12378999999999999999999887   33 45555443

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=97.56  E-value=6e-05  Score=62.96  Aligned_cols=31  Identities=23%  Similarity=0.251  Sum_probs=27.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      -++|.||||+|||++++.++..+++.++..+
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            4689999999999999999999998876654

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.53  E-value=4.2e-05  Score=65.12  Aligned_cols=32  Identities=28%  Similarity=0.402  Sum_probs=29.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +.++|.||||+|||++++++|..+++++++.+
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l~~~~i~~d   37 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLTKRILYDSD   37 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            56899999999999999999999999888764

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=97.52  E-value=7.4e-05  Score=63.03  Aligned_cols=33  Identities=21%  Similarity=0.300  Sum_probs=28.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .-++|.|+||+|||+++++++..++.+++.++.
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~~   36 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCeEEecc
Confidence            457899999999999999999999988876543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=97.46  E-value=0.0004  Score=81.79  Aligned_cols=68  Identities=24%  Similarity=0.391  Sum_probs=50.4

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHH-HhCCcEEEEecCCcCCchHHHHHHHhc------------------CCCcEEEEc
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMAN-YLHFDVYDLELSSVEGNKHLRKVLIAT------------------ENKSILVVG  286 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~-~l~~~~~~l~~~~~~~~~~l~~~l~~~------------------~~~~Il~iD  286 (338)
                      ..++.+||+||||||||.++....+ ..+++++.++++.-.+...+...+...                  .+..|+|||
T Consensus      1302 ~~~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiD 1381 (3245)
T 3vkg_A         1302 SEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCD 1381 (3245)
T ss_dssp             HTTCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEET
T ss_pred             HCCCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEec
Confidence            3467899999999999988765444 446778899999888777777666520                  123699999


Q ss_pred             CCCccCC
Q 035959          287 DIDCCTE  293 (338)
Q Consensus       287 eiD~~~~  293 (338)
                      |++.-..
T Consensus      1382 DiNmp~~ 1388 (3245)
T 3vkg_A         1382 EINLPST 1388 (3245)
T ss_dssp             TTTCCCC
T ss_pred             ccCCCCc
Confidence            9997543

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=97.43  E-value=0.00017  Score=61.96  Aligned_cols=25  Identities=28%  Similarity=0.571  Sum_probs=22.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      +.|.||+|+|||+|++.++..++..
T Consensus         3 i~l~G~nGsGKTTLl~~l~g~l~i~   27 (178)
T 1ye8_A            3 IIITGEPGVGKTTLVKKIVERLGKR   27 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCc
Confidence            6789999999999999999987643

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=97.42  E-value=0.00039  Score=81.89  Aligned_cols=67  Identities=18%  Similarity=0.177  Sum_probs=58.8

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcC-CCcEEEEcCCCccCC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATE-NKSILVVGDIDCCTE  293 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~-~~~Il~iDeiD~~~~  293 (338)
                      ...|..+.||+|||||.+++++|+.+|..++.++|++-.+...+.++|..+. ..+..++||++.+-.
T Consensus       603 ~~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~~~~g~i~~G~~~~GaW~cfDEfNrl~~  670 (3245)
T 3vkg_A          603 SRMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLEE  670 (3245)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCHHHHHHHHHHHHHHTCEEEEETTTSSCH
T ss_pred             hcCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCHHHHHHHHhhHhhcCcEEEehhhhcCCH
Confidence            3456789999999999999999999999999999999888778888887765 688999999999854

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.38  E-value=8.5e-05  Score=64.36  Aligned_cols=32  Identities=34%  Similarity=0.421  Sum_probs=28.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ..++|.||||+|||++++++|..+++.+++.+
T Consensus        26 ~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~d   57 (199)
T 3vaa_A           26 VRIFLTGYMGAGKTTLGKAFARKLNVPFIDLD   57 (199)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCCEEcch
Confidence            46889999999999999999999999887654

>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=97.37  E-value=0.00047  Score=59.82  Aligned_cols=35  Identities=17%  Similarity=0.169  Sum_probs=29.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~  263 (338)
                      .-++|.||||+|||+++..+|...+..++.++...
T Consensus        21 ~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~~   55 (220)
T 2cvh_A           21 VLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEG   55 (220)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECCC
Confidence            34689999999999999999986677788887665

>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=97.35  E-value=9.4e-05  Score=62.74  Aligned_cols=32  Identities=28%  Similarity=0.436  Sum_probs=28.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +.++|.|+||+|||+++++++..+++.++..+
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~d   43 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASKSGLKYINVG   43 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHhCCeEEEHH
Confidence            46899999999999999999999998877653

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.34  E-value=9.3e-05  Score=62.54  Aligned_cols=31  Identities=32%  Similarity=0.470  Sum_probs=27.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .++|.||||+|||++++++|..+++++++.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d~d   36 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLDSD   36 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEccc
Confidence            5789999999999999999999998877653

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.34  E-value=0.00045  Score=69.47  Aligned_cols=48  Identities=21%  Similarity=0.231  Sum_probs=37.3

Q ss_pred             CCccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHH
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~  250 (338)
                      |.....+++.+...+.+.+.+..  ...+-+.++||+|+|||+|+..+++
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~  169 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVR  169 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHC
T ss_pred             CCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHh
Confidence            34445688888888888888864  2234578999999999999999874

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.33  E-value=8.2e-05  Score=64.22  Aligned_cols=63  Identities=10%  Similarity=0.116  Sum_probs=38.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC--------cCC----------chHHHHHHHhcC-CCcEEEEcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS--------VEG----------NKHLRKVLIATE-NKSILVVGD  287 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~--------~~~----------~~~l~~~l~~~~-~~~Il~iDe  287 (338)
                      -++++||||+|||+++..++..+   +..++.+....        +.+          ..++..++.... ...+|+|||
T Consensus         5 i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~d~r~~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~dvviIDE   84 (184)
T 2orw_A            5 LTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFIDE   84 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-----CCCEECC----CEECEEESSGGGGGGGCCTTEEEEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeeccccccCcccEEecCCCceeeEEECCHHHHHHHhcCCCCEEEEEC
Confidence            46899999999999986666543   55555442210        000          011222333333 468999999


Q ss_pred             CCccC
Q 035959          288 IDCCT  292 (338)
Q Consensus       288 iD~~~  292 (338)
                      ++.+.
T Consensus        85 ~Q~~~   89 (184)
T 2orw_A           85 VQFFN   89 (184)
T ss_dssp             GGGSC
T ss_pred             cccCC
Confidence            99874

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.30  E-value=0.00012  Score=61.35  Aligned_cols=32  Identities=34%  Similarity=0.516  Sum_probs=29.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ..++|.|+||+|||++++.+|..+|+++++.+
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            46889999999999999999999999988764

>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=97.30  E-value=0.00011  Score=62.35  Aligned_cols=32  Identities=31%  Similarity=0.488  Sum_probs=28.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-++|.|+||+|||++++.+|..+|+++++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~D   34 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALGVGLLDTD   34 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEEeCc
Confidence            34789999999999999999999999887764

>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=97.29  E-value=0.00049  Score=65.63  Aligned_cols=64  Identities=11%  Similarity=0.085  Sum_probs=44.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHHH---hcCCCcE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVLI---ATENKSI  282 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l~---~~~~~~I  282 (338)
                      -++|+||||+|||+|+..+|..+   +..+.+++......                     ..++...+.   ....+.+
T Consensus        63 i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~~~~dl  142 (356)
T 3hr8_A           63 IVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDELVRSGVVDL  142 (356)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTSCCSE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHHHhhhcCCCe
Confidence            36899999999999999999875   56777787665321                     112222222   1246889


Q ss_pred             EEEcCCCccCC
Q 035959          283 LVVGDIDCCTE  293 (338)
Q Consensus       283 l~iDeiD~~~~  293 (338)
                      ++||.+..+.+
T Consensus       143 vVIDSi~~l~~  153 (356)
T 3hr8_A          143 IVVDSVAALVP  153 (356)
T ss_dssp             EEEECTTTCCC
T ss_pred             EEehHhhhhcC
Confidence            99999998875

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.27  E-value=0.00019  Score=60.11  Aligned_cols=31  Identities=39%  Similarity=0.696  Sum_probs=27.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ..+.|.||||+|||++++.+|..++..+++.
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id~   35 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDS   35 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEec
Confidence            4578999999999999999999999866553

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.24  E-value=0.00018  Score=65.16  Aligned_cols=32  Identities=25%  Similarity=0.433  Sum_probs=28.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      -++|.||||+|||++++++|..++..++..|.
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            36899999999999999999999988876644

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.22  E-value=0.00052  Score=64.30  Aligned_cols=35  Identities=17%  Similarity=0.217  Sum_probs=29.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~  263 (338)
                      .-++++||||+|||+++..+|..+         +..+++++...
T Consensus       108 ~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          108 TMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             cEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            447899999999999999999875         55778887765

>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=97.22  E-value=0.00078  Score=64.22  Aligned_cols=65  Identities=15%  Similarity=0.202  Sum_probs=46.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHHHh---cCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVLIA---TENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l~~---~~~~~  281 (338)
                      +-++++||||+|||+|+..+|..+   +..+.++++....+                     ...+..++..   .....
T Consensus        64 ~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~~~~~~  143 (356)
T 1u94_A           64 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  143 (356)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHHHHhccCCC
Confidence            457899999999999999988765   66788888743221                     1223333322   24789


Q ss_pred             EEEEcCCCccCC
Q 035959          282 ILVVGDIDCCTE  293 (338)
Q Consensus       282 Il~iDeiD~~~~  293 (338)
                      +||||.+..+..
T Consensus       144 lVVIDsl~~l~~  155 (356)
T 1u94_A          144 VIVVDSVAALTP  155 (356)
T ss_dssp             EEEEECGGGCCC
T ss_pred             EEEEcCHHHhcc
Confidence            999999999875

>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=97.22  E-value=0.00013  Score=62.46  Aligned_cols=32  Identities=31%  Similarity=0.482  Sum_probs=27.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH-hCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY-LHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~-l~~~~~~l~  260 (338)
                      ..++|.|+||+|||++++.+|.. +|+++++++
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La~~l~g~~~id~d   43 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIAAELDGFQHLEVG   43 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSTTEEEEEHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCCCEEeeHH
Confidence            45889999999999999999999 788777654

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.21  E-value=0.00039  Score=70.43  Aligned_cols=79  Identities=19%  Similarity=0.236  Sum_probs=48.1

Q ss_pred             CChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC----------CchHHHHHHHhc
Q 035959          211 MDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE----------GNKHLRKVLIAT  277 (338)
Q Consensus       211 ~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~----------~~~~l~~~l~~~  277 (338)
                      ..+..++.+...+.   .+.+++.||||||||+++.+++..+   +..+..+..+...          ....+.+++...
T Consensus       190 L~~~Q~~Av~~~~~---~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e~~~~~a~Tih~ll~~~  266 (574)
T 3e1s_A          190 LSEEQASVLDQLAG---HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYG  266 (574)
T ss_dssp             CCHHHHHHHHHHTT---CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTSCEEEHHHHTTEE
T ss_pred             CCHHHHHHHHHHHh---CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHHHHHhHhhhcccHHHHHHHHcCC
Confidence            45555554443332   3567899999999999999998865   5666655433211          011233333211


Q ss_pred             -----------CCCcEEEEcCCCccC
Q 035959          278 -----------ENKSILVVGDIDCCT  292 (338)
Q Consensus       278 -----------~~~~Il~iDeiD~~~  292 (338)
                                 ...++|||||+..+.
T Consensus       267 ~~~~~~~~~~~~~~dvlIIDEasml~  292 (574)
T 3e1s_A          267 PQGFRHNHLEPAPYDLLIVDEVSMMG  292 (574)
T ss_dssp             TTEESCSSSSCCSCSEEEECCGGGCC
T ss_pred             cchhhhhhcccccCCEEEEcCccCCC
Confidence                       145899999998663

>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=97.21  E-value=0.00016  Score=60.62  Aligned_cols=32  Identities=19%  Similarity=0.405  Sum_probs=28.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-++|.|+||+|||++++.++..+++++++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~d   34 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEEccc
Confidence            35789999999999999999999998877654

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=97.21  E-value=0.00013  Score=62.25  Aligned_cols=32  Identities=28%  Similarity=0.423  Sum_probs=27.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-++|.|+||+|||++++.++..+++.++..+
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~~l~~~~i~~D   37 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALATGLRLPLLSKD   37 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCeEecHH
Confidence            35789999999999999999999998876643

>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=97.18  E-value=0.00078  Score=63.98  Aligned_cols=65  Identities=11%  Similarity=0.138  Sum_probs=44.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHHH---hcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVLI---ATENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l~---~~~~~~  281 (338)
                      +-++++||||+|||+|+..+|..+   +..+.+++......                     ..++..++.   ....+.
T Consensus        62 ~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~~~~~~  141 (349)
T 2zr9_A           62 RVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVRSGALD  141 (349)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            347899999999999999988655   56777777654221                     112222222   123689


Q ss_pred             EEEEcCCCccCC
Q 035959          282 ILVVGDIDCCTE  293 (338)
Q Consensus       282 Il~iDeiD~~~~  293 (338)
                      +||||++..+..
T Consensus       142 lIVIDsl~~l~~  153 (349)
T 2zr9_A          142 IIVIDSVAALVP  153 (349)
T ss_dssp             EEEEECGGGCCC
T ss_pred             EEEEcChHhhcc
Confidence            999999999874

>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=97.16  E-value=0.00019  Score=59.59  Aligned_cols=29  Identities=28%  Similarity=0.351  Sum_probs=25.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|.||||+|||++++.+ ..+|++++.+
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            4689999999999999999 8889887664

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.15  E-value=0.00033  Score=62.63  Aligned_cols=60  Identities=18%  Similarity=0.214  Sum_probs=42.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC--------------------------chHHHHHHHhcCCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG--------------------------NKHLRKVLIATENK  280 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~--------------------------~~~l~~~l~~~~~~  280 (338)
                      .+++.|+||+||||++.++|..+   |+++..++...-..                          +.++..++.  .++
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D~q~~~~~~al~~gl~~~~~~~~~~~~~~~~e~~l~~~L~--~~p   85 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVETHGRAETEALLNGLPQQPLLRTEYRGMTLEEMDLDALLK--AAP   85 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCTTCHHHHHHHTTSCBCCCEEEEETTEEEEECCHHHHHH--HCC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeCCCCChhHHHHhcCccccCcceeecCCcccccccHHHHHh--cCC
Confidence            47899999999999999988776   77877666643110                          123444443  368


Q ss_pred             cEEEEcCCCcc
Q 035959          281 SILVVGDIDCC  291 (338)
Q Consensus       281 ~Il~iDeiD~~  291 (338)
                      .+++|||+-..
T Consensus        86 dlvIVDElG~~   96 (228)
T 2r8r_A           86 SLVLVDELAHT   96 (228)
T ss_dssp             SEEEESCTTCB
T ss_pred             CEEEEeCCCCC
Confidence            99999998865

>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=97.15  E-value=0.00021  Score=61.78  Aligned_cols=30  Identities=33%  Similarity=0.554  Sum_probs=27.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|.|+||+|||++++.++..++++++.+
T Consensus        22 ~I~l~G~~GsGKST~a~~La~~l~~~~i~~   51 (201)
T 2cdn_A           22 RVLLLGPPGAGKGTQAVKLAEKLGIPQIST   51 (201)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeh
Confidence            478999999999999999999999887765

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.12  E-value=0.00023  Score=59.31  Aligned_cols=30  Identities=27%  Similarity=0.443  Sum_probs=27.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ++|.|+||+|||++++.++..+++++++.+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d   32 (168)
T 2pt5_A            3 IYLIGFMCSGKSTVGSLLSRSLNIPFYDVD   32 (168)
T ss_dssp             EEEESCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            689999999999999999999998887643

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.10  E-value=0.00023  Score=60.48  Aligned_cols=31  Identities=19%  Similarity=0.348  Sum_probs=27.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-++|.|+||+|||++++.++..++..++..
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   34 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKYGYTHLSA   34 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            4578999999999999999999999877654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.10  E-value=0.00027  Score=61.11  Aligned_cols=32  Identities=25%  Similarity=0.382  Sum_probs=27.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-++|.|+||+|||++++.++..+|..++..+
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~d   50 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEACGYPFIEGD   50 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHHTCCEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCEEEeCC
Confidence            45889999999999999999999998776543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.10  E-value=0.00081  Score=76.48  Aligned_cols=67  Identities=15%  Similarity=0.188  Sum_probs=51.4

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCc------------------------hHHHHHHHhcCC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGN------------------------KHLRKVLIATEN  279 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~------------------------~~l~~~l~~~~~  279 (338)
                      ..+.++++||||||||+|+.+++.+.   |..+.++++.+....                        ..+...+.+..+
T Consensus      1080 ~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~~~~ 1159 (2050)
T 3cmu_A         1080 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1159 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHHhCC
Confidence            44668999999999999999988755   788888888775321                        122334445568


Q ss_pred             CcEEEEcCCCccCC
Q 035959          280 KSILVVGDIDCCTE  293 (338)
Q Consensus       280 ~~Il~iDeiD~~~~  293 (338)
                      +++|+||++..+.+
T Consensus      1160 ~dlvVIDsl~~L~~ 1173 (2050)
T 3cmu_A         1160 VDVIVVDSVAALTP 1173 (2050)
T ss_dssp             CSEEEESCGGGCCC
T ss_pred             CCEEEECCcccccc
Confidence            99999999999976

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.09  E-value=0.0002  Score=60.76  Aligned_cols=30  Identities=30%  Similarity=0.620  Sum_probs=26.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|.|+||+|||++++.+|..+++.++..
T Consensus         6 ~I~l~G~~GsGKST~~~~La~~l~~~~i~~   35 (186)
T 3cm0_A            6 AVIFLGPPGAGKGTQASRLAQELGFKKLST   35 (186)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCEEECH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEecH
Confidence            468999999999999999999999876654

>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=97.09  E-value=0.0002  Score=60.73  Aligned_cols=31  Identities=16%  Similarity=0.385  Sum_probs=26.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l  259 (338)
                      .-++|.||||+|||++++.++..++     ++++.+
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~i~~   39 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSF   39 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcCcceEEEeh
Confidence            3578999999999999999999987     666653

>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=97.07  E-value=0.00026  Score=61.76  Aligned_cols=29  Identities=21%  Similarity=0.327  Sum_probs=26.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.++..++..++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVEKYGIPHIST   31 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHSSCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            67899999999999999999999887765

>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=97.07  E-value=0.0012  Score=62.80  Aligned_cols=82  Identities=26%  Similarity=0.428  Sum_probs=48.8

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC----CcEEEEecC-CcC------------
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH----FDVYDLELS-SVE------------  265 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~----~~~~~l~~~-~~~------------  265 (338)
                      +.+++++...+.     +..+......-+++.||+|+|||+++++++..+.    ..++.+.-. +..            
T Consensus       103 ~~~l~~lg~~~~-----l~~l~~~~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~  177 (356)
T 3jvv_A          103 VLTMEELGMGEV-----FKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQRE  177 (356)
T ss_dssp             CCCTTTTTCCHH-----HHHHHHCSSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEE
T ss_pred             CCCHHHcCChHH-----HHHHHhCCCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeee
Confidence            457788877653     2233222223468999999999999999998773    233332111 100            


Q ss_pred             ---CchHHHHHHHhc--CCCcEEEEcCCC
Q 035959          266 ---GNKHLRKVLIAT--ENKSILVVGDID  289 (338)
Q Consensus       266 ---~~~~l~~~l~~~--~~~~Il~iDeiD  289 (338)
                         ....+...+..+  .+|.+|++||+-
T Consensus       178 ~~~~~~~~~~~La~aL~~~PdvillDEp~  206 (356)
T 3jvv_A          178 VHRDTLGFSEALRSALREDPDIILVGEMR  206 (356)
T ss_dssp             BTTTBSCHHHHHHHHTTSCCSEEEESCCC
T ss_pred             eccccCCHHHHHHHHhhhCcCEEecCCCC
Confidence               011233333332  489999999985

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.05  E-value=0.00025  Score=60.68  Aligned_cols=32  Identities=19%  Similarity=0.359  Sum_probs=27.7

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +.-+.|.|+||+|||++++.++..++..++..
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            34578999999999999999999999877654

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.04  E-value=0.00026  Score=60.44  Aligned_cols=31  Identities=16%  Similarity=0.328  Sum_probs=27.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-++|.|+||+|||++++.+|..++..++..
T Consensus        10 ~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   40 (196)
T 2c95_A           10 NIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   40 (196)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            4578999999999999999999999887654

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.04  E-value=0.00029  Score=61.36  Aligned_cols=29  Identities=21%  Similarity=0.376  Sum_probs=26.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.++..++..++..
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            67899999999999999999999887755

>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=97.02  E-value=0.0016  Score=58.05  Aligned_cols=62  Identities=8%  Similarity=0.224  Sum_probs=40.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC-------cCC-------------chHHHHHHHhc---CCCcEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS-------VEG-------------NKHLRKVLIAT---ENKSILV  284 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~-------~~~-------------~~~l~~~l~~~---~~~~Il~  284 (338)
                      ++++||||+|||+++..++..+   +..++.+....       +.+             ..++...+.+.   .++.+|+
T Consensus        15 ~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvVi   94 (223)
T 2b8t_A           15 EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIG   94 (223)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEEE
Confidence            4789999999999888877665   56676663221       111             12343434332   2478999


Q ss_pred             EcCCCccC
Q 035959          285 VGDIDCCT  292 (338)
Q Consensus       285 iDeiD~~~  292 (338)
                      |||+..+.
T Consensus        95 IDEaQ~l~  102 (223)
T 2b8t_A           95 IDEVQFFD  102 (223)
T ss_dssp             ECSGGGSC
T ss_pred             EecCccCc
Confidence            99999764

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.02  E-value=0.00053  Score=61.76  Aligned_cols=36  Identities=19%  Similarity=0.233  Sum_probs=29.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV  264 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~  264 (338)
                      ..++|.||||+|||++++.++..++..++.++...+
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            347899999999999999999999866666665543

>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=97.01  E-value=0.0015  Score=62.54  Aligned_cols=65  Identities=15%  Similarity=0.201  Sum_probs=45.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHHHh---cCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVLIA---TENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l~~---~~~~~  281 (338)
                      +-++|+||||+|||+|+..+|..+   +..+.++++.....                     ..++...+..   .....
T Consensus        75 ~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~~~~~~  154 (366)
T 1xp8_A           75 RITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVRSGAID  154 (366)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             cEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHhcCCCC
Confidence            447899999999999999888765   56788887764221                     1222223322   24689


Q ss_pred             EEEEcCCCccCC
Q 035959          282 ILVVGDIDCCTE  293 (338)
Q Consensus       282 Il~iDeiD~~~~  293 (338)
                      +||||.+..+..
T Consensus       155 lVVIDsl~~l~~  166 (366)
T 1xp8_A          155 VVVVDSVAALTP  166 (366)
T ss_dssp             EEEEECTTTCCC
T ss_pred             EEEEeChHHhcc
Confidence            999999999874

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.00  E-value=0.00088  Score=61.75  Aligned_cols=33  Identities=33%  Similarity=0.471  Sum_probs=26.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      ..++|.||||+|||+++++++..++..++.++.
T Consensus        34 ~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~   66 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN   66 (287)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHTTTCCEEECT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEEEec
Confidence            347899999999999999999988544556654

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=96.99  E-value=0.00033  Score=61.40  Aligned_cols=30  Identities=27%  Similarity=0.527  Sum_probs=26.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|.|+||+|||++++.+|..++..++..
T Consensus         6 ~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   35 (220)
T 1aky_A            6 RMVLIGPPGAGKGTQAPNLQERFHAAHLAT   35 (220)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCceEEeh
Confidence            468999999999999999999999877654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.99  E-value=0.00035  Score=58.95  Aligned_cols=29  Identities=21%  Similarity=0.197  Sum_probs=22.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      .-++|.|+||+|||++++.++..++.+++
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            34789999999999999999999998876

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=96.98  E-value=0.00028  Score=59.81  Aligned_cols=31  Identities=19%  Similarity=0.348  Sum_probs=27.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-++|.|+||+|||++++.++..++..++..
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~   37 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEeeH
Confidence            3578999999999999999999999877765

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.98  E-value=0.00031  Score=58.97  Aligned_cols=29  Identities=28%  Similarity=0.329  Sum_probs=23.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH-HhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN-YLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~-~l~~~~~  257 (338)
                      .-++|.||||+|||++++.++. .+++.++
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~~~~~~~i   32 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEecCCCCCHHHHHHHHHhhcCCcEEe
Confidence            4578999999999999999998 5665444

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.97  E-value=0.0004  Score=58.40  Aligned_cols=30  Identities=37%  Similarity=0.562  Sum_probs=25.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.|.||||+|||++++.++..+|..+++.
T Consensus        10 ~i~l~G~~GsGKSTl~~~l~~~~g~~~i~~   39 (175)
T 1knq_A           10 IYVLMGVSGSGKSAVASEVAHQLHAAFLDG   39 (175)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHTCEEEEG
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhhCcEEEeC
Confidence            478999999999999999999988766554

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=96.95  E-value=0.0016  Score=61.59  Aligned_cols=34  Identities=18%  Similarity=0.090  Sum_probs=28.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~  263 (338)
                      -++|+||||+|||+|+..+|...         +..+++++...
T Consensus       124 i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          124 ITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             EEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            36899999999999999999873         45677887765

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.94  E-value=0.0007  Score=57.46  Aligned_cols=31  Identities=23%  Similarity=0.268  Sum_probs=27.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      +.|.|+||+|||++++.+++.+   |++++..+-
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d~   36 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYRE   36 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            5799999999999999999998   888887753

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=96.93  E-value=0.0004  Score=61.65  Aligned_cols=31  Identities=26%  Similarity=0.425  Sum_probs=27.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ..++|.|+||+|||++++.+|..++..++..
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            3578999999999999999999999877665

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.92  E-value=0.0004  Score=59.86  Aligned_cols=32  Identities=19%  Similarity=0.327  Sum_probs=27.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-++|.|+||+|||++++.++..++..++..+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~d   47 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG   47 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeHH
Confidence            34789999999999999999999998776643

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.91  E-value=0.00034  Score=61.70  Aligned_cols=31  Identities=16%  Similarity=0.413  Sum_probs=27.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-++|.|+||+|||++++.+|..++..++..
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   38 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITTHFELKHLSS   38 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSSSEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCeEEec
Confidence            4578999999999999999999999877654

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=96.89  E-value=0.00037  Score=61.16  Aligned_cols=30  Identities=20%  Similarity=0.392  Sum_probs=27.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .++|.|+||+|||++++.+|..+++.++..
T Consensus         7 ~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   36 (217)
T 3be4_A            7 NLILIGAPGSGKGTQCEFIKKEYGLAHLST   36 (217)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCceEEeh
Confidence            478999999999999999999999887765

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.87  E-value=0.00039  Score=59.22  Aligned_cols=33  Identities=33%  Similarity=0.432  Sum_probs=27.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .-+.|.||||+|||+++++++..++...+.++.
T Consensus        10 ~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~   42 (191)
T 1zp6_A           10 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   42 (191)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             eEEEEECCCCCCHHHHHHHHHhccCCCeEEEcc
Confidence            347899999999999999999987766666654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.85  E-value=0.0018  Score=66.23  Aligned_cols=50  Identities=26%  Similarity=0.414  Sum_probs=34.2

Q ss_pred             cCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          210 AMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      ..++..++.+...+..  +.-.|++||||||||+++..+..++   +..+..+..
T Consensus       189 ~LN~~Q~~AV~~al~~--~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~  241 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQ--KELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAP  241 (646)
T ss_dssp             TCCHHHHHHHHHHHHC--SSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CCCHHHHHHHHHHhcC--CCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcC
Confidence            4577777777766652  1246899999999999877766554   455555443

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=96.83  E-value=0.002  Score=72.33  Aligned_cols=66  Identities=15%  Similarity=0.180  Sum_probs=49.5

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHHHhc---CCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVLIAT---ENK  280 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l~~~---~~~  280 (338)
                      .+.++|+||||||||+|+.+++...   |..+++++......                     ...+.+++..+   .++
T Consensus        34 G~i~lI~G~pGsGKT~LAlqla~~~~~~G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L~~~~~~  113 (1706)
T 3cmw_A           34 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAV  113 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhCCCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHHHhccCC
Confidence            4568999999999999999988753   67888888876432                     22333444333   578


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      .+||||++..+..
T Consensus       114 ~LVVIDSLt~L~~  126 (1706)
T 3cmw_A          114 DVIVVDSVAALTP  126 (1706)
T ss_dssp             SEEEESCSTTCCC
T ss_pred             CEEEEcchhhhcc
Confidence            9999999999976

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.83  E-value=0.00079  Score=58.18  Aligned_cols=30  Identities=20%  Similarity=0.460  Sum_probs=25.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      .-+.|.||+|+|||+++++++..+|..++.
T Consensus        30 ~~i~l~G~~GsGKSTl~~~L~~~~g~~~i~   59 (200)
T 4eun_A           30 RHVVVMGVSGSGKTTIAHGVADETGLEFAE   59 (200)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCCeEEc
Confidence            457899999999999999999999865544

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=96.83  E-value=0.002  Score=57.54  Aligned_cols=34  Identities=21%  Similarity=0.199  Sum_probs=27.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      +.+++.||+|+|||.++.+++..++..++.+-..
T Consensus       109 ~~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~  142 (237)
T 2fz4_A          109 KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (237)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESS
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCC
Confidence            3489999999999999999998887766666433

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=96.82  E-value=0.001  Score=56.24  Aligned_cols=32  Identities=31%  Similarity=0.520  Sum_probs=28.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      -+.|.|++|+|||++++.++..+   |++++.++.
T Consensus         7 ~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d~   41 (179)
T 2pez_A            7 TVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDG   41 (179)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEECC
Confidence            36799999999999999999998   888887764

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=96.81  E-value=0.0005  Score=60.08  Aligned_cols=29  Identities=17%  Similarity=0.268  Sum_probs=26.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.++..+++.++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~g~~~i~~   31 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            68999999999999999999999887765

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.77  E-value=0.0019  Score=55.54  Aligned_cols=30  Identities=30%  Similarity=0.433  Sum_probs=25.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC--cEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF--DVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~--~~~~l  259 (338)
                      -++|.|+||+|||++++.++..++.  +++..
T Consensus         6 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~   37 (213)
T 2plr_A            6 LIAFEGIDGSGKSSQATLLKDWIELKRDVYLT   37 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHhhcCCEEEe
Confidence            4689999999999999999999876  35443

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.75  E-value=0.00088  Score=57.28  Aligned_cols=28  Identities=29%  Similarity=0.694  Sum_probs=24.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      +.|.|+||+||||+++.++..++..++.
T Consensus         3 I~i~G~~GsGKsT~~~~L~~~l~~~~~~   30 (205)
T 2jaq_A            3 IAIFGTVGAGKSTISAEISKKLGYEIFK   30 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHCCEEEC
T ss_pred             EEEECCCccCHHHHHHHHHHhcCCcEEc
Confidence            6799999999999999999999986543

>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=96.75  E-value=0.003  Score=68.32  Aligned_cols=62  Identities=18%  Similarity=0.122  Sum_probs=45.5

Q ss_pred             CCCccccccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHh-------CCcEEEEecCC
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYL-------HFDVYDLELSS  263 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l-------~~~~~~l~~~~  263 (338)
                      .|.....+++.+...+++.+.|..  ...+-+.|+|++|+|||+||+.+++..       ...++.++++.
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~  189 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK  189 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCS
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECC
Confidence            445556788999888999988854  223446799999999999999988752       22355777655

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=96.75  E-value=0.0056  Score=65.89  Aligned_cols=54  Identities=17%  Similarity=0.190  Sum_probs=40.1

Q ss_pred             cCChhHHHHHHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHH------hCCcEEEEecCC
Q 035959          210 AMDTDMKKMIMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANY------LHFDVYDLELSS  263 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~------l~~~~~~l~~~~  263 (338)
                      ++.+...+++.+.|.. ...+-+.++||+|.|||+||+.+++.      +...++.++++.
T Consensus       131 VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~  191 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN  191 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCC
T ss_pred             CCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCC
Confidence            6777778888888775 22355789999999999999999863      244466666654

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.75  E-value=0.00039  Score=61.07  Aligned_cols=30  Identities=13%  Similarity=0.267  Sum_probs=26.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      .-++|.||||+|||++++.+|..++..++.
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l~~~~i~   35 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKYQLAHIS   35 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceec
Confidence            457899999999999999999999976554

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.75  E-value=0.00073  Score=63.55  Aligned_cols=33  Identities=27%  Similarity=0.532  Sum_probs=29.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      ..++|.||+|+|||+++.++|..++..++.+|.
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds   38 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALPCELISVDS   38 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEEEEEECT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCcEEeccc
Confidence            467899999999999999999999988777753

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.75  E-value=0.00096  Score=58.84  Aligned_cols=29  Identities=24%  Similarity=0.453  Sum_probs=25.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.++..++..++..
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            67999999999999999999999876554

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=96.74  E-value=0.00068  Score=60.78  Aligned_cols=30  Identities=20%  Similarity=0.448  Sum_probs=26.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|.||||+|||++++.++..++..++..
T Consensus        31 ~I~l~G~~GsGKsT~a~~L~~~~g~~~is~   60 (243)
T 3tlx_A           31 RYIFLGAPGSGKGTQSLNLKKSHCYCHLST   60 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            478999999999999999999998877655

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=96.73  E-value=0.00099  Score=58.27  Aligned_cols=29  Identities=38%  Similarity=0.604  Sum_probs=25.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      -+.|.||+|+||||+++.++..+|+++++
T Consensus         7 ~i~i~G~~GsGKSTl~~~L~~~~g~~~~d   35 (227)
T 1cke_A            7 VITIDGPSGAGKGTLCKAMAEALQWHLLD   35 (227)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            46799999999999999999998876544

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.72  E-value=0.0017  Score=58.81  Aligned_cols=33  Identities=30%  Similarity=0.512  Sum_probs=29.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ...+.|.|++|+|||++++.+|..+++++++.+
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            456899999999999999999999999887754

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=96.71  E-value=0.00095  Score=57.30  Aligned_cols=32  Identities=13%  Similarity=0.134  Sum_probs=27.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh-CCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL-HFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l-~~~~~~l~~  261 (338)
                      -+.|.|+||+|||++++.++..+ |++++.++.
T Consensus         6 ~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~~   38 (204)
T 2v54_A            6 LIVFEGLDKSGKTTQCMNIMESIPANTIKYLNF   38 (204)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTSCGGGEEEEES
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHCCCceEEEec
Confidence            46799999999999999999998 677777654

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.69  E-value=0.0027  Score=55.36  Aligned_cols=63  Identities=16%  Similarity=0.229  Sum_probs=41.9

Q ss_pred             ceeeeCCCCCCcH-HHHHHHHHHh--CCcEEEEecC-------CcCC----------chHHHHHHHhcCCCcEEEEcCCC
Q 035959          230 GYLLFGPPGTGKS-SLIAAMANYL--HFDVYDLELS-------SVEG----------NKHLRKVLIATENKSILVVGDID  289 (338)
Q Consensus       230 g~LL~GppGtGKT-~l~~aia~~l--~~~~~~l~~~-------~~~~----------~~~l~~~l~~~~~~~Il~iDeiD  289 (338)
                      -+++|||.|+||| +|++++.++.  +..++.+...       .+.+          ...+..++......++|+|||+.
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlIDEaQ  101 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQ  101 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEESSGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccccCccchhhhhhccCCcccceecCCHHHHHHhccCCCEEEEEchh
Confidence            4689999999999 8999998866  6677777533       1110          01111222223356899999999


Q ss_pred             ccCC
Q 035959          290 CCTE  293 (338)
Q Consensus       290 ~~~~  293 (338)
                      -+ +
T Consensus       102 Ff-k  104 (195)
T 1w4r_A          102 FF-P  104 (195)
T ss_dssp             GC-T
T ss_pred             hh-H
Confidence            98 5

>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=96.68  E-value=0.00079  Score=66.40  Aligned_cols=82  Identities=20%  Similarity=0.140  Sum_probs=50.2

Q ss_pred             ccCChhHHHHHHHHHHhhh--cC---ceeeeCCCCCCcHHHHHHH-HHHhCCcEEEEecCCcCCchHHH-----------
Q 035959          209 LAMDTDMKKMIMDDLERAW--KR---GYLLFGPPGTGKSSLIAAM-ANYLHFDVYDLELSSVEGNKHLR-----------  271 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~~~--~~---g~LL~GppGtGKT~l~~ai-a~~l~~~~~~l~~~~~~~~~~l~-----------  271 (338)
                      +.+.+.+|+.+.-.+....  .+   ++||.|+||| ||.+++++ +..+...++.....  .+...|.           
T Consensus       215 I~G~e~vK~aLll~L~GG~~k~rgdihVLL~G~PGt-KS~Lar~i~~~i~pR~~ft~g~~--ss~~gLt~s~r~~tG~~~  291 (506)
T 3f8t_A          215 LPGAEEVGKMLALQLFSCVGKNSERLHVLLAGYPVV-CSEILHHVLDHLAPRGVYVDLRR--TELTDLTAVLKEDRGWAL  291 (506)
T ss_dssp             STTCHHHHHHHHHHHTTCCSSGGGCCCEEEESCHHH-HHHHHHHHHHHTCSSEEEEEGGG--CCHHHHSEEEEESSSEEE
T ss_pred             cCCCHHHHHHHHHHHcCCccccCCceeEEEECCCCh-HHHHHHHHHHHhCCCeEEecCCC--CCccCceEEEEcCCCccc
Confidence            5677778877776665311  11   5999999999 99999999 76654433321111  0111110           


Q ss_pred             -HHHHhcCCCcEEEEcCCCccCC
Q 035959          272 -KVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       272 -~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                       .=....+...+++||||+.+.+
T Consensus       292 ~~G~l~LAdgGvl~lDEIn~~~~  314 (506)
T 3f8t_A          292 RAGAAVLADGGILAVDHLEGAPE  314 (506)
T ss_dssp             EECHHHHTTTSEEEEECCTTCCH
T ss_pred             CCCeeEEcCCCeeehHhhhhCCH
Confidence             0001124579999999999854

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.68  E-value=0.001  Score=58.99  Aligned_cols=29  Identities=24%  Similarity=0.581  Sum_probs=25.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      +-++|.||||+||++.++.+|..+++..+
T Consensus        30 kiI~llGpPGsGKgTqa~~L~~~~g~~hI   58 (217)
T 3umf_A           30 KVIFVLGGPGSGKGTQCEKLVQKFHFNHL   58 (217)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHHHCCEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            56789999999999999999999987643

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.66  E-value=0.00064  Score=57.55  Aligned_cols=31  Identities=26%  Similarity=0.397  Sum_probs=25.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH---FDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~  260 (338)
                      -++|.|+||+|||++++.++..++   +.+..++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~~   36 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEEE
Confidence            368999999999999999999886   3355554

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=96.66  E-value=0.0012  Score=58.02  Aligned_cols=27  Identities=30%  Similarity=0.547  Sum_probs=24.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      ++|.||||+||++.++.+|..+|+..+
T Consensus         3 Iil~GpPGsGKgTqa~~La~~~g~~~i   29 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKEKGFVHI   29 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEE
Confidence            678999999999999999999987654

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=96.65  E-value=0.00071  Score=58.33  Aligned_cols=29  Identities=31%  Similarity=0.329  Sum_probs=25.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +.|.|++|+|||++++.++. +|.++++.+
T Consensus         4 i~i~G~~GsGKSTl~~~L~~-~g~~~i~~d   32 (204)
T 2if2_A            4 IGLTGNIGCGKSTVAQMFRE-LGAYVLDAD   32 (204)
T ss_dssp             EEEEECTTSSHHHHHHHHHH-TTCEEEEHH
T ss_pred             EEEECCCCcCHHHHHHHHHH-CCCEEEEcc
Confidence            67999999999999999999 887776543

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.63  E-value=0.0016  Score=56.22  Aligned_cols=34  Identities=29%  Similarity=0.298  Sum_probs=26.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .-+.|.||+|+|||++++++|..+   |...+.++..
T Consensus        26 ~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d~d   62 (200)
T 3uie_A           26 CVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILDGD   62 (200)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEecCc
Confidence            346799999999999999999988   5554455543

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=96.62  E-value=0.0015  Score=59.10  Aligned_cols=32  Identities=34%  Similarity=0.429  Sum_probs=27.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH---hCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY---LHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~---l~~~~~~l~~  261 (338)
                      -++|.|+||+|||++++.++..   .|+.++.++.
T Consensus         6 lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~   40 (260)
T 3a4m_A            6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGS   40 (260)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECc
Confidence            4789999999999999999998   6787775543

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=96.61  E-value=0.0014  Score=56.21  Aligned_cols=31  Identities=26%  Similarity=0.238  Sum_probs=27.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      -+.|.|++|+|||++++.+|..+|.++++.+
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            4679999999999999999999998877653

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.58  E-value=0.0032  Score=55.27  Aligned_cols=35  Identities=20%  Similarity=0.191  Sum_probs=27.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH--h-------CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY--L-------HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~--l-------~~~~~~l~~~~  263 (338)
                      .-++|+||||+|||+|+..+|..  +       +..+++++...
T Consensus        25 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           25 SITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            34689999999999999999985  3       45677777655

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=96.55  E-value=0.00096  Score=57.66  Aligned_cols=29  Identities=24%  Similarity=0.303  Sum_probs=25.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.|.||+|+|||++++.++. +|.++++.
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            367999999999999999998 88877654

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=96.53  E-value=0.0016  Score=58.38  Aligned_cols=31  Identities=35%  Similarity=0.354  Sum_probs=26.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+.|.||||+|||++++.+|..+++.+++.
T Consensus        10 ~~i~i~G~~GsGKsTla~~la~~lg~~~~d~   40 (233)
T 3r20_A           10 LVVAVDGPAGTGKSSVSRGLARALGARYLDT   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCcccC
Confidence            3578999999999999999999999776543

>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=96.52  E-value=0.0038  Score=61.01  Aligned_cols=64  Identities=16%  Similarity=0.263  Sum_probs=44.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC--------------------------Cc-hHHHHHHHhcC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE--------------------------GN-KHLRKVLIATE  278 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~--------------------------~~-~~l~~~l~~~~  278 (338)
                      +.+++.|+||+||||++.++|..+   |..+..+++....                          +. .-+.+.+....
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D~~r~~a~~qL~~~~~~~gv~v~~~~~~~~dp~~i~~~~l~~~~  179 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFK  179 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCSCCCTTGGGSSHHHHHHSSCCEECCSSSCCSSSTTHHHHHHTTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeccccCchHHHHHHHhhhccCcceEecCCCCCCHHHHHHHHHHHhh
Confidence            357899999999999999999877   4667766654210                          00 12345566666


Q ss_pred             CCcEEEEcCCCccC
Q 035959          279 NKSILVVGDIDCCT  292 (338)
Q Consensus       279 ~~~Il~iDeiD~~~  292 (338)
                      ...+++||..-.+.
T Consensus       180 ~~D~vIIDT~G~~~  193 (432)
T 2v3c_C          180 KADVLIIDTAGRHK  193 (432)
T ss_dssp             SCSEEEEECCCSCS
T ss_pred             CCCEEEEcCCCCcc
Confidence            77899999876653

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=96.51  E-value=0.0015  Score=58.24  Aligned_cols=29  Identities=24%  Similarity=0.557  Sum_probs=25.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      .-+.|.||||+|||+++++++..+|....
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La~~lg~~~~   56 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIAQNFGLQHL   56 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCCCE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEe
Confidence            45789999999999999999999886543

>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=96.51  E-value=0.0076  Score=60.34  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=33.7

Q ss_pred             cCChhHHHHHHHHHHhh---hcCceeeeCCCCCCcHHHHHHHHH
Q 035959          210 AMDTDMKKMIMDDLERA---WKRGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~~---~~~g~LL~GppGtGKT~l~~aia~  250 (338)
                      ++.+..++++.+.|...   ..+-+.++|++|+|||+||..+++
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            37788888888888654   234567999999999999999997

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=96.47  E-value=0.0013  Score=56.99  Aligned_cols=30  Identities=27%  Similarity=0.270  Sum_probs=26.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.|.|++|+|||++++.++..+|+++++.
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vid~   43 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVVNV   43 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEEEC
Confidence            356999999999999999999999888774

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.46  E-value=0.0064  Score=57.05  Aligned_cols=63  Identities=13%  Similarity=0.083  Sum_probs=42.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh-----CCcEEEEecCCcCC---------------------chHH-HHHHHh---c--C
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL-----HFDVYDLELSSVEG---------------------NKHL-RKVLIA---T--E  278 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l-----~~~~~~l~~~~~~~---------------------~~~l-~~~l~~---~--~  278 (338)
                      ++++||||+|||+|+..++..+     +..+.+++...-..                     .+++ ..++..   .  .
T Consensus        31 teI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~i~~~  110 (333)
T 3io5_A           31 LILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDAIERG  110 (333)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHTCCTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHHhhcc
Confidence            5799999999999977666544     56677887654221                     1122 122222   2  3


Q ss_pred             CCcEEEEcCCCccCC
Q 035959          279 NKSILVVGDIDCCTE  293 (338)
Q Consensus       279 ~~~Il~iDeiD~~~~  293 (338)
                      ++.+||||-|..+.+
T Consensus       111 ~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          111 EKVVVFIDSLGNLAS  125 (333)
T ss_dssp             CCEEEEEECSTTCBC
T ss_pred             CceEEEEeccccccc
Confidence            689999999999974

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=96.42  E-value=0.0053  Score=56.83  Aligned_cols=59  Identities=17%  Similarity=0.246  Sum_probs=41.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCCcCC----------------------chHHHHHHHhcCCCcE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSSVEG----------------------NKHLRKVLIATENKSI  282 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~~~~----------------------~~~l~~~l~~~~~~~I  282 (338)
                      .-++|.||+|+|||+++..+|..+    |..+..++......                      ...++..+.....+.+
T Consensus       106 ~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~~~~~l~~al~~~~~~dl  185 (296)
T 2px0_A          106 KYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRIAAVEQLKTYAELLQAPLEVCYTKEEFQQAKELFSEYDH  185 (296)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCSSTTHHHHHHHHHTTTTCCCCBCSSHHHHHHHHHHGGGSSE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcccchHHHHHHHHHHhcCCCeEecCCHHHHHHHHHHhcCCCE
Confidence            457899999999999999999765    55677666543221                      1234444555567899


Q ss_pred             EEEcC
Q 035959          283 LVVGD  287 (338)
Q Consensus       283 l~iDe  287 (338)
                      |+||-
T Consensus       186 vIiDT  190 (296)
T 2px0_A          186 VFVDT  190 (296)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99993

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.42  E-value=0.00069  Score=58.56  Aligned_cols=26  Identities=23%  Similarity=0.289  Sum_probs=22.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      .-+.|.|+||+|||++++.++..++.
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~l~~   36 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEYLKN   36 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            34689999999999999999998754

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.41  E-value=0.0045  Score=53.97  Aligned_cols=34  Identities=18%  Similarity=0.136  Sum_probs=28.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      ..+++|+++|.||||.|.++|-.+   |+.+..+.+-
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            356899999999999999998766   7888888554

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.37  E-value=0.0069  Score=58.55  Aligned_cols=34  Identities=26%  Similarity=0.176  Sum_probs=25.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~  263 (338)
                      -++|+||||+|||+|+..+|...         +..+++++...
T Consensus       180 i~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~  222 (400)
T 3lda_A          180 ITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEG  222 (400)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             EEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCC
Confidence            36899999999999999776433         23477777665

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=96.36  E-value=0.0023  Score=57.38  Aligned_cols=26  Identities=27%  Similarity=0.245  Sum_probs=23.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      -+.|.|+||+|||++++.++..++.+
T Consensus        24 iI~I~G~~GSGKST~a~~L~~~lg~~   49 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQLLGQN   49 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhh
Confidence            46799999999999999999999876

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=96.35  E-value=0.0014  Score=56.00  Aligned_cols=30  Identities=30%  Similarity=0.478  Sum_probs=26.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      -+.|.|++|+|||++++.++.. |+.+++.+
T Consensus        10 ~I~i~G~~GsGKST~~~~La~~-g~~~id~d   39 (203)
T 1uf9_A           10 IIGITGNIGSGKSTVAALLRSW-GYPVLDLD   39 (203)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHT-TCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHC-CCEEEccc
Confidence            4679999999999999999998 88877654

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=96.31  E-value=0.0026  Score=54.08  Aligned_cols=25  Identities=36%  Similarity=0.567  Sum_probs=21.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      -+.|.||+|+|||++++.++...+.
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            4679999999999999999987654

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=96.30  E-value=0.0059  Score=53.05  Aligned_cols=23  Identities=30%  Similarity=0.423  Sum_probs=20.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+|||+|++.++..+
T Consensus        27 ~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           27 ITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36899999999999999999854

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.28  E-value=0.0027  Score=57.10  Aligned_cols=29  Identities=34%  Similarity=0.571  Sum_probs=25.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      -+.|.||+|+|||++++.+|..+|+.+++
T Consensus        29 ~I~I~G~~GsGKSTl~k~La~~Lg~~~~d   57 (252)
T 4e22_A           29 VITVDGPSGAGKGTLCKALAESLNWRLLD   57 (252)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCCcCC
Confidence            46799999999999999999999876553

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.28  E-value=0.0036  Score=53.07  Aligned_cols=32  Identities=31%  Similarity=0.511  Sum_probs=25.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH---FDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~  261 (338)
                      -++|.|+||+|||++++.+|..++   .++..++.
T Consensus        15 ~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~~   49 (186)
T 2yvu_A           15 VVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDG   49 (186)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEeeH
Confidence            467999999999999999999874   45555543

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.27  E-value=0.0023  Score=55.70  Aligned_cols=31  Identities=29%  Similarity=0.331  Sum_probs=27.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+.|.|++|+|||++++.++..+|+++++.
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~   34 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDT   34 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecC
Confidence            3578999999999999999999999887665

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.26  E-value=0.0017  Score=61.77  Aligned_cols=46  Identities=17%  Similarity=0.369  Sum_probs=33.8

Q ss_pred             hhHHHHHHHHHHhhh----cCceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          213 TDMKKMIMDDLERAW----KRGYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       213 ~~~k~~i~~~l~~~~----~~g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      ..+.+.+++.+...-    ...++|.||||+|||++++++|..++++++.
T Consensus         5 ~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A            5 HKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             HHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            345566666665421    2348899999999999999999999877633

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=96.24  E-value=0.0021  Score=55.99  Aligned_cols=29  Identities=38%  Similarity=0.464  Sum_probs=25.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.|.|++|+|||++++.++. +|+++++.
T Consensus         6 ~I~i~G~~GSGKST~~~~L~~-lg~~~id~   34 (218)
T 1vht_A            6 IVALTGGIGSGKSTVANAFAD-LGINVIDA   34 (218)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-TTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-cCCEEEEc
Confidence            467999999999999999998 88877765

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.23  E-value=0.0024  Score=55.23  Aligned_cols=25  Identities=28%  Similarity=0.533  Sum_probs=22.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-++|.||||+|||++++.++..++
T Consensus        13 ~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           13 PPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCc
Confidence            4578999999999999999999874

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=96.21  E-value=0.0028  Score=61.48  Aligned_cols=29  Identities=24%  Similarity=0.272  Sum_probs=24.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      .-++|.|+||+|||++++.++..+++.++
T Consensus       259 ~lIil~G~pGSGKSTla~~L~~~~~~~~i  287 (416)
T 3zvl_A          259 EVVVAVGFPGAGKSTFIQEHLVSAGYVHV  287 (416)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTGGGTCEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhcCcEEE
Confidence            45789999999999999999998876543

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=96.18  E-value=0.0011  Score=57.26  Aligned_cols=31  Identities=23%  Similarity=0.113  Sum_probs=24.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC---CcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH---FDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l  259 (338)
                      .-+.|.|+||+|||++++.++..++   +++..+
T Consensus        10 ~~I~l~G~~GsGKsT~~~~L~~~l~~~~~~v~~~   43 (215)
T 1nn5_A           10 ALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELL   43 (215)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEe
Confidence            3478999999999999999999864   455433

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.17  E-value=0.0018  Score=61.16  Aligned_cols=32  Identities=31%  Similarity=0.456  Sum_probs=27.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      -++|.||+|+|||+|+..+|..++..++..|-
T Consensus        42 lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds   73 (339)
T 3a8t_A           42 LLVLMGATGTGKSRLSIDLAAHFPLEVINSDK   73 (339)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTTSCEEEEECCS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHCCCcEEcccc
Confidence            47899999999999999999999876655443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.16  E-value=0.005  Score=53.40  Aligned_cols=33  Identities=21%  Similarity=0.066  Sum_probs=25.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      ..++|.||||+|||+|+..++..+   +..+..++.
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~~   59 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVTT   59 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEES
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEEc
Confidence            346899999999999999999654   456666554

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=96.00  E-value=0.0022  Score=58.75  Aligned_cols=30  Identities=27%  Similarity=0.327  Sum_probs=24.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh-CCcEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL-HFDVYD  258 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l-~~~~~~  258 (338)
                      .-++|.|+||+|||++++.++..+ ++.++.
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i~   33 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNIN   33 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEec
Confidence            357899999999999999999874 655443

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=96.00  E-value=0.0046  Score=54.79  Aligned_cols=30  Identities=27%  Similarity=0.422  Sum_probs=26.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.|.|++|+|||++++.+|..+|+++++.
T Consensus        18 ~i~i~G~~gsGKst~~~~l~~~lg~~~~d~   47 (236)
T 1q3t_A           18 QIAIDGPASSGKSTVAKIIAKDFGFTYLDT   47 (236)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCceecC
Confidence            467999999999999999999999776653

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=95.99  E-value=0.0078  Score=51.61  Aligned_cols=25  Identities=20%  Similarity=0.381  Sum_probs=20.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+.+++.+|+|+|||.++...+...
T Consensus        48 ~~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           48 GKNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHH
Confidence            3679999999999999877766543

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.98  E-value=0.0037  Score=53.02  Aligned_cols=25  Identities=16%  Similarity=0.389  Sum_probs=21.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-+.|.||+|+|||+|+++++..+.
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            3467999999999999999998763

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=95.97  E-value=0.0056  Score=52.87  Aligned_cols=25  Identities=36%  Similarity=0.585  Sum_probs=22.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      |.++|.||+|+|||+|++.+.....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            6789999999999999999987753

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.96  E-value=0.0057  Score=53.06  Aligned_cols=23  Identities=43%  Similarity=0.634  Sum_probs=21.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.|.||+|+|||||+++++..+.
T Consensus        25 v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           25 VALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             EEEECCTTSCTHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            56999999999999999999885

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.95  E-value=0.01  Score=51.22  Aligned_cols=46  Identities=13%  Similarity=0.181  Sum_probs=31.7

Q ss_pred             HHHHHHHHh-hhcCc--eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          217 KMIMDDLER-AWKRG--YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       217 ~~i~~~l~~-~~~~g--~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      +.+.+.+.. ..+++  +.|.||+|+|||++++.++..+   +.++..++..
T Consensus         8 ~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d   59 (201)
T 1rz3_A            8 DFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMD   59 (201)
T ss_dssp             HHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             HHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccC
Confidence            344444443 22233  5699999999999999999876   6667666443

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.94  E-value=0.0061  Score=53.52  Aligned_cols=34  Identities=26%  Similarity=0.162  Sum_probs=25.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .-+++.||||+|||+++..+|...   +..++.++..
T Consensus        24 ~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e   60 (247)
T 2dr3_A           24 NVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALE   60 (247)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            346899999999999988776543   5566666554

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=95.94  E-value=0.0033  Score=55.09  Aligned_cols=26  Identities=31%  Similarity=0.411  Sum_probs=23.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .++++|.||+|+|||+|+.+++....
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~   59 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH   59 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC
Confidence            36899999999999999999998764

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=95.94  E-value=0.004  Score=58.17  Aligned_cols=32  Identities=22%  Similarity=0.577  Sum_probs=26.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-+++.||+|+|||+|+..+|..++..++..|
T Consensus        11 ~~i~i~GptgsGKt~la~~La~~~~~~iis~D   42 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIELRKILPVELISVD   42 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEEEEECC
T ss_pred             cEEEEECCCccCHHHHHHHHHHhCCCcEEecc
Confidence            45789999999999999999999986665544

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.93  E-value=0.0036  Score=54.47  Aligned_cols=25  Identities=28%  Similarity=0.345  Sum_probs=22.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||+|+|||++++.++..+.
T Consensus         9 ~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            9 LLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhCC
Confidence            3467999999999999999998874

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.92  E-value=0.0057  Score=55.53  Aligned_cols=43  Identities=33%  Similarity=0.499  Sum_probs=29.5

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +++++...+     +++++.-....-+++.||+|+|||+++++++..+
T Consensus         7 ~l~~l~~~~-----vl~~i~i~~g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A            7 EFKKLGLPD-----KVLELCHRKMGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             CGGGSSCCT-----HHHHGGGCSSEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             ChHHCCCHH-----HHHHHhhCCCCEEEEECCCCccHHHHHHHHHHhC
Confidence            556665542     3444442222336899999999999999999876

>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=95.92  E-value=0.0091  Score=58.02  Aligned_cols=49  Identities=27%  Similarity=0.381  Sum_probs=35.1

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCc-eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRG-YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g-~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.+++++.+....+. ++.++.. .+.+ +++.||+|+|||+++++++..+.
T Consensus       143 ~~~l~~Lg~~~~~~~-~L~~l~~-~~ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          143 RLDLHSLGMTAHNHD-NFRRLIK-RPHGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             CCCGGGSCCCHHHHH-HHHHHHT-SSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             CCCHHHcCCCHHHHH-HHHHHHH-hcCCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            346777777765444 3444432 3344 68999999999999999999885

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.88  E-value=0.0042  Score=53.18  Aligned_cols=24  Identities=33%  Similarity=0.643  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||++++.++..+.
T Consensus         9 ii~l~Gp~GsGKSTl~~~L~~~~~   32 (205)
T 3tr0_A            9 LFIISAPSGAGKTSLVRALVKALA   32 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHhhCC
Confidence            467999999999999999998763

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.85  E-value=0.0037  Score=53.57  Aligned_cols=24  Identities=25%  Similarity=0.321  Sum_probs=21.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||+|+|||++++.++..+
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            346799999999999999999877

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.85  E-value=0.0042  Score=58.73  Aligned_cols=32  Identities=19%  Similarity=0.316  Sum_probs=26.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .-+.+.||+|+|||+++..+|..++..++..|
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            35789999999999999999999985554443

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=95.85  E-value=0.0054  Score=53.28  Aligned_cols=33  Identities=27%  Similarity=0.358  Sum_probs=26.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC----CcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH----FDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~----~~~~~l~~  261 (338)
                      .-++|.|+||+|||++++.++..++    .+++.++.
T Consensus        26 ~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~~   62 (211)
T 1m7g_A           26 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDG   62 (211)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEECC
Confidence            3467999999999999999999775    45666653

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.84  E-value=0.0024  Score=55.18  Aligned_cols=29  Identities=21%  Similarity=0.252  Sum_probs=23.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh-CCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL-HFDVYD  258 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l-~~~~~~  258 (338)
                      -+.|.||||+|||++++.++..+ +..++.
T Consensus        23 ~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~   52 (207)
T 2qt1_A           23 IIGISGVTNSGKTTLAKNLQKHLPNCSVIS   52 (207)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTTSTTEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCcEEEe
Confidence            35799999999999999999987 554443

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.81  E-value=0.0091  Score=58.42  Aligned_cols=35  Identities=26%  Similarity=0.433  Sum_probs=28.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      .-+++.|+||+|||+++..+|.++   |..+..+++..
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~  138 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDT  138 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCC
Confidence            457899999999999999999877   66776666543

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=95.80  E-value=0.0047  Score=53.74  Aligned_cols=29  Identities=14%  Similarity=0.150  Sum_probs=26.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      -+.|.||+|||||++++.+|..+|+++++
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            46799999999999999999999999875

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=95.77  E-value=0.0094  Score=55.34  Aligned_cols=35  Identities=14%  Similarity=0.120  Sum_probs=28.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---------------C----CcEEEEecCCc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---------------H----FDVYDLELSSV  264 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---------------~----~~~~~l~~~~~  264 (338)
                      -++++||||+|||+++..+|...               |    ..+++++....
T Consensus       100 i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~  153 (322)
T 2i1q_A          100 VTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGT  153 (322)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCC
Confidence            46899999999999999998753               2    56778877653

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=95.75  E-value=0.0038  Score=57.18  Aligned_cols=29  Identities=31%  Similarity=0.283  Sum_probs=25.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.|.|+||+|||++++.++ .+|++++..
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            46899999999999999999 678877655

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=95.73  E-value=0.011  Score=55.83  Aligned_cols=34  Identities=24%  Similarity=0.280  Sum_probs=27.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC---------CcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH---------FDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~---------~~~~~l~~~~  263 (338)
                      -+.|+||||+|||+|+..+|....         -.+++++...
T Consensus       133 i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~  175 (349)
T 1pzn_A          133 ITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN  175 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCC
Confidence            468999999999999999998872         3556776654

>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=95.72  E-value=0.0086  Score=61.07  Aligned_cols=39  Identities=28%  Similarity=0.411  Sum_probs=27.4

Q ss_pred             CChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          211 MDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       211 ~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .++..++.+...+.   ...+++.||||||||+++..++..+
T Consensus       181 ln~~Q~~av~~~l~---~~~~li~GppGTGKT~~~~~~i~~l  219 (624)
T 2gk6_A          181 LNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSATIVYHL  219 (624)
T ss_dssp             CCHHHHHHHHHHHT---CSEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhc---CCCeEEECCCCCCHHHHHHHHHHHH
Confidence            45555555544443   3457899999999999888777654

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=95.66  E-value=0.0052  Score=57.51  Aligned_cols=31  Identities=23%  Similarity=0.293  Sum_probs=25.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+++.||+|+|||+|+..+|..++..++..
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~~iis~   34 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNGEVISG   34 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTEEEEEC
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCccceeec
Confidence            3467999999999999999999987554433

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=95.64  E-value=0.017  Score=49.94  Aligned_cols=63  Identities=16%  Similarity=0.236  Sum_probs=40.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC--------cCC----------chHHHHHHHhcC-CCcEEEEcCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS--------VEG----------NKHLRKVLIATE-NKSILVVGDI  288 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~--------~~~----------~~~l~~~l~~~~-~~~Il~iDei  288 (338)
                      ++++||+|+|||+.+..++..+   +..++.+...-        +.+          ..+...++..+. ...+|+|||+
T Consensus        11 ~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~~~~~dvViIDEa   90 (191)
T 1xx6_A           11 EVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEV   90 (191)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEEECSG
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHHhccCCEEEEECC
Confidence            5789999999999888877765   66666553110        000          011124454444 4689999999


Q ss_pred             CccCC
Q 035959          289 DCCTE  293 (338)
Q Consensus       289 D~~~~  293 (338)
                      .-+.+
T Consensus        91 qfl~~   95 (191)
T 1xx6_A           91 QFFDD   95 (191)
T ss_dssp             GGSCT
T ss_pred             CCCCH
Confidence            88643

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.61  E-value=0.0066  Score=52.43  Aligned_cols=24  Identities=38%  Similarity=0.596  Sum_probs=21.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +-+.|.||+|+|||+|++.++..+
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            567899999999999999999865

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.57  E-value=0.013  Score=51.49  Aligned_cols=34  Identities=26%  Similarity=0.222  Sum_probs=26.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH----hCCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY----LHFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~----l~~~~~~l~~~~  263 (338)
                      -++++|+||+|||+++..+|..    .+.+++++++..
T Consensus        32 l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E~   69 (251)
T 2zts_A           32 TVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEE   69 (251)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESSS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecccC
Confidence            4689999999999998876643    266777776653

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=95.54  E-value=0.019  Score=46.37  Aligned_cols=22  Identities=27%  Similarity=0.456  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999998864

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.46  E-value=0.0088  Score=51.58  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=21.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.|.||+|+||||+++.++..++
T Consensus         9 i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            9 IGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            56999999999999999999887

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.39  E-value=0.0085  Score=52.24  Aligned_cols=25  Identities=24%  Similarity=0.442  Sum_probs=22.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-+.|.||+|+|||+|+++++....
T Consensus        20 ~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           20 KTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECcCCCCHHHHHHHHHhhCC
Confidence            4578999999999999999998764

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=95.39  E-value=0.0095  Score=52.85  Aligned_cols=30  Identities=30%  Similarity=0.445  Sum_probs=24.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC--CcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH--FDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~--~~~~~l  259 (338)
                      -+.|.||||+|||++++.++..++  .+++..
T Consensus        28 ~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~~   59 (229)
T 4eaq_A           28 FITFEGPEGSGKTTVINEVYHRLVKDYDVIMT   59 (229)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHhcCCCceee
Confidence            357899999999999999999986  465543

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.38  E-value=0.0097  Score=53.15  Aligned_cols=29  Identities=21%  Similarity=0.415  Sum_probs=25.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +-|.||||+|||++++.++..++++.+..
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            55899999999999999999999877654

>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=95.32  E-value=0.03  Score=52.15  Aligned_cols=64  Identities=13%  Similarity=0.142  Sum_probs=43.4

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHh---CC-cEEEEecCCcCCchHHHHHHHhc------CCCcEEEEcCCCc-cC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYL---HF-DVYDLELSSVEGNKHLRKVLIAT------ENKSILVVGDIDC-CT  292 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l---~~-~~~~l~~~~~~~~~~l~~~l~~~------~~~~Il~iDeiD~-~~  292 (338)
                      .....||||||+|+||++.+.++++.+   +. +...+....   +.++++++..+      ..+.|++|||+|. +.
T Consensus        16 ~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~plf~~~kvvii~~~~~kl~   90 (343)
T 1jr3_D           16 GLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP---NTDWNAIFSLCQAMSLFASRQTLLLLLPENGPN   90 (343)
T ss_dssp             CCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT---TCCHHHHHHHHHHHHHCCSCEEEEEECCSSCCC
T ss_pred             CCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC---CCCHHHHHHHhcCcCCccCCeEEEEECCCCCCC
Confidence            345679999999999999999998866   33 222222222   23445554433      3688999999998 64

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=95.32  E-value=0.013  Score=50.34  Aligned_cols=33  Identities=24%  Similarity=0.241  Sum_probs=28.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV  264 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~  264 (338)
                      +|++|++|+|||+++..+|.. +.+++++.....
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            589999999999999999988 888888877654

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=95.30  E-value=0.011  Score=60.26  Aligned_cols=32  Identities=31%  Similarity=0.520  Sum_probs=28.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      -++|.|+||+|||+++++++..+   |.+++.++.
T Consensus        54 lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lDg   88 (630)
T 1x6v_B           54 TVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDG   88 (630)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEESH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEech
Confidence            36899999999999999999999   999988853

>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=95.30  E-value=0.033  Score=45.16  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=18.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|++|+|||+|+.++...
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            689999999999999999763

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=95.28  E-value=0.015  Score=54.10  Aligned_cols=35  Identities=29%  Similarity=0.455  Sum_probs=27.2

Q ss_pred             HHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          219 IMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       219 i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +++++.-  +....+.|.||+|+|||+|+++|+..+.
T Consensus       115 vL~~vsl~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~~  151 (305)
T 2v9p_A          115 ALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLG  151 (305)
T ss_dssp             HHHHHHHTCTTCSEEEEECSSSSSHHHHHHHHHHHHT
T ss_pred             hhccceEEecCCCEEEEECCCCCcHHHHHHHHhhhcC
Confidence            4555544  3445578999999999999999999873

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.25  E-value=0.026  Score=56.08  Aligned_cols=33  Identities=18%  Similarity=0.334  Sum_probs=27.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      +.+++.|+||+||||++.++|..+   |..+..+++
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            357899999999999999999776   677776665

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=95.24  E-value=0.0035  Score=54.10  Aligned_cols=23  Identities=22%  Similarity=0.447  Sum_probs=21.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.|.|++|+|||++++.++..++
T Consensus         3 I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            57899999999999999999885

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.23  E-value=0.041  Score=50.79  Aligned_cols=34  Identities=26%  Similarity=0.357  Sum_probs=27.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .-+++.|++|+|||+++..+|..+   +..+..+++.
T Consensus        99 ~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D  135 (297)
T 1j8m_F           99 YVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGAD  135 (297)
T ss_dssp             EEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            346788999999999999999877   6677776664

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=95.20  E-value=0.021  Score=46.03  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.+++..
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999999864

>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=95.20  E-value=0.025  Score=45.73  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.++...
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            35789999999999999999864

>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=95.20  E-value=0.016  Score=60.86  Aligned_cols=39  Identities=28%  Similarity=0.411  Sum_probs=27.4

Q ss_pred             CChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          211 MDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       211 ~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .++..++.+...+.   .+-+++.||||||||+++.+++..+
T Consensus       357 Ln~~Q~~Av~~~l~---~~~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          357 LNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             CCHHHHHHHHHHHT---SSEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhcc---CCeEEEEcCCCCCHHHHHHHHHHHH
Confidence            45555555554443   2456899999999999888877654

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=95.18  E-value=0.0098  Score=56.81  Aligned_cols=46  Identities=30%  Similarity=0.478  Sum_probs=30.5

Q ss_pred             CCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.+++++.+.+.     +.++.......+++.||+|+|||+++++++..+.
T Consensus       116 ~~~l~~lg~~~~-----l~~l~~~~g~~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          116 IPEFKKLGLPDK-----VLELCHRKMGLILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             CCCHHHHCCCSS-----HHHHTTSSSEEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             cCCHhHcCCCHH-----HHHHhhcCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            345666665432     2222222223478999999999999999998763

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=95.16  E-value=0.011  Score=52.19  Aligned_cols=25  Identities=40%  Similarity=0.573  Sum_probs=22.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||+|+|||+|+++++....
T Consensus        17 ~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           17 TLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCC
Confidence            3467999999999999999999765

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=95.16  E-value=0.011  Score=49.47  Aligned_cols=23  Identities=30%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||.|+|||+|+++++..+
T Consensus        35 ~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           35 MVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            36799999999999999999987

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.14  E-value=0.011  Score=51.27  Aligned_cols=24  Identities=25%  Similarity=0.487  Sum_probs=21.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++++..+.
T Consensus        22 i~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           22 VVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHST
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCC
Confidence            467999999999999999999874

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.12  E-value=0.011  Score=51.74  Aligned_cols=24  Identities=33%  Similarity=0.628  Sum_probs=21.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||+|+|||+|++.++...
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            457799999999999999999976

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.11  E-value=0.0092  Score=50.20  Aligned_cols=18  Identities=33%  Similarity=0.569  Sum_probs=16.0

Q ss_pred             ceeeeCCCCCCcHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAA  247 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~a  247 (338)
                      -+.|.||+|+|||+|+++
T Consensus        11 i~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A           11 LVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            367999999999999993

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=95.10  E-value=0.026  Score=45.91  Aligned_cols=21  Identities=38%  Similarity=0.626  Sum_probs=19.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+++.|++|+|||+|+.++..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            478999999999999999986

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.06  E-value=0.012  Score=50.74  Aligned_cols=23  Identities=43%  Similarity=0.775  Sum_probs=20.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+|||+|++.++..+
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            36799999999999999999876

>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=95.04  E-value=0.025  Score=45.85  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
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            4789999999999999999863

>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=95.03  E-value=0.033  Score=46.05  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=20.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.+++..
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            45899999999999999999863

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=95.02  E-value=0.018  Score=52.65  Aligned_cols=33  Identities=21%  Similarity=0.101  Sum_probs=26.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL----HFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~  261 (338)
                      .-++|.||||+|||+|+..+|..+    |..+..++.
T Consensus        36 ~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~   72 (296)
T 1cr0_A           36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (296)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            346899999999999999998866    446666654

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=95.00  E-value=0.012  Score=52.24  Aligned_cols=29  Identities=21%  Similarity=0.185  Sum_probs=26.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      -+.+.|++|||||++++.+|..+|+++++
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            46799999999999999999999998765

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=94.95  E-value=0.0099  Score=57.47  Aligned_cols=31  Identities=26%  Similarity=0.379  Sum_probs=25.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+++.||+|+|||+|+..+|..++..++..
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~~~iis~   33 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFNGEVINS   33 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHTEEEEEC
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCCCeEeec
Confidence            3467999999999999999999988655443

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=94.84  E-value=0.012  Score=53.39  Aligned_cols=24  Identities=33%  Similarity=0.382  Sum_probs=20.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-++|+||||+|||+|+..++..+
T Consensus        31 ~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           31 TVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            457899999999999999988654

>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=94.82  E-value=0.026  Score=47.48  Aligned_cols=23  Identities=26%  Similarity=0.509  Sum_probs=20.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.+++.|++|+|||+|+.++...
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            35799999999999999999873

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=94.82  E-value=0.021  Score=60.02  Aligned_cols=38  Identities=26%  Similarity=0.448  Sum_probs=26.1

Q ss_pred             CChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHH
Q 035959          211 MDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       211 ~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .++..++.+...+.   ..-+++.||||||||+++..++..
T Consensus       361 Ln~~Q~~Av~~~l~---~~~~lI~GppGTGKT~~i~~~i~~  398 (802)
T 2xzl_A          361 LNSSQSNAVSHVLQ---RPLSLIQGPPGTGKTVTSATIVYH  398 (802)
T ss_dssp             CCHHHHHHHHHHTT---CSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhc---CCCEEEECCCCCCHHHHHHHHHHH
Confidence            45665555554443   234689999999999987776543

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=94.80  E-value=0.044  Score=45.71  Aligned_cols=24  Identities=17%  Similarity=0.294  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      --+++.|++|+|||+|++.+.+..
T Consensus        15 ~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhc
Confidence            357899999999999998887654

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=94.79  E-value=0.014  Score=49.03  Aligned_cols=24  Identities=29%  Similarity=0.303  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -.+|+||.|+|||+++.||+-.++
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~   51 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLG   51 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHc
Confidence            347999999999999999998775

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.77  E-value=0.024  Score=49.57  Aligned_cols=32  Identities=28%  Similarity=0.362  Sum_probs=24.3

Q ss_pred             HHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHH
Q 035959          218 MIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       218 ~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++++.  ...-+.|.||+|+|||+|+++++..
T Consensus        14 ~~l~~i~--~Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           14 HYVDAID--TNTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             HHHHHHH--HCSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             HHHHhcc--CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4555553  2334679999999999999999975

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=94.74  E-value=0.042  Score=46.40  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
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            35789999999999999999864

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.72  E-value=0.016  Score=51.46  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=22.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      +-|.||+|+||||+++.++..+|..
T Consensus        28 igI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           28 IGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhchh
Confidence            5699999999999999999987743

>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=94.71  E-value=0.037  Score=45.38  Aligned_cols=24  Identities=29%  Similarity=0.515  Sum_probs=20.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ..+++.|++|+|||+|+.++...-
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            358999999999999999998643

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.69  E-value=0.014  Score=53.74  Aligned_cols=35  Identities=14%  Similarity=0.235  Sum_probs=23.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCCc
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSV  264 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~~  264 (338)
                      -+.|.||+|+|||++++.++..++   ..+..+++.++
T Consensus         7 iIgItG~sGSGKSTva~~L~~~lg~~~~~~~vI~~D~~   44 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   44 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCCCeeEeecchh
Confidence            357999999999999999999876   44445554443

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=94.68  E-value=0.036  Score=55.18  Aligned_cols=34  Identities=12%  Similarity=-0.009  Sum_probs=27.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC-----cEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF-----DVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~-----~~~~l~~~~  263 (338)
                      .+.|.|++|+|||++++++|..++.     .+..+|...
T Consensus       397 ~I~l~GlsGsGKSTIa~~La~~L~~~~g~r~~~~lDgD~  435 (511)
T 1g8f_A          397 SIVLGNSLTVSREQLSIALLSTFLQFGGGRYYKIFEHNN  435 (511)
T ss_dssp             EEEECTTCCSCHHHHHHHHHHHHTTSCSCCCEEECCCTT
T ss_pred             EEEecccCCCCHHHHHHHHHHHHHHhhcCcceEEecCCC
Confidence            4679999999999999999999985     345565443

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.67  E-value=0.047  Score=50.62  Aligned_cols=33  Identities=21%  Similarity=0.146  Sum_probs=27.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      -++|.|+||+|||+++..+|...   +.++..+++.
T Consensus        70 l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~slE  105 (315)
T 3bh0_A           70 FVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  105 (315)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEECC
Confidence            47899999999999999988665   4577777765

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=94.66  E-value=0.029  Score=46.62  Aligned_cols=22  Identities=27%  Similarity=0.489  Sum_probs=19.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999999864

>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=94.65  E-value=0.026  Score=57.39  Aligned_cols=25  Identities=36%  Similarity=0.590  Sum_probs=20.9

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+-+++.||||||||+++.++...+
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            4568999999999999988877654

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=94.62  E-value=0.024  Score=55.27  Aligned_cols=34  Identities=21%  Similarity=0.311  Sum_probs=27.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      +-+++.||+|+|||+++..+|..+   |..+..+++.
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D  134 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAAD  134 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecC
Confidence            346899999999999999999877   6666666543

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=94.57  E-value=0.014  Score=49.95  Aligned_cols=24  Identities=38%  Similarity=0.498  Sum_probs=21.8

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+|+||.|++|+|||+++.++...
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc
Confidence            478999999999999999999874

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.56  E-value=0.032  Score=48.15  Aligned_cols=25  Identities=24%  Similarity=0.380  Sum_probs=22.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ..-+++.|++|+|||+|+.+++..+
T Consensus        30 ~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           30 TVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3467899999999999999999876

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=94.53  E-value=0.022  Score=56.12  Aligned_cols=23  Identities=35%  Similarity=0.572  Sum_probs=20.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -++|+||+|+|||+|+..++...
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhhh
Confidence            37899999999999999888764

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.51  E-value=0.012  Score=51.75  Aligned_cols=23  Identities=22%  Similarity=0.359  Sum_probs=14.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHH-HHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMA-NYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia-~~l  252 (338)
                      -+.|.||+|+|||++++.++ ..+
T Consensus        29 ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           29 ILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             EEEEECSCC----CHHHHHHC---
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCC
Confidence            46799999999999999999 765

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=94.51  E-value=0.039  Score=46.82  Aligned_cols=32  Identities=16%  Similarity=0.241  Sum_probs=24.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~  260 (338)
                      .-+.+.|++|+|||+++..++..+   |+.+..+.
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            346799999999999999999876   45544443

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.51  E-value=0.03  Score=46.97  Aligned_cols=23  Identities=26%  Similarity=0.563  Sum_probs=20.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.+++..
T Consensus        49 ~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           49 PSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            35799999999999999999874

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=94.50  E-value=0.031  Score=51.92  Aligned_cols=33  Identities=21%  Similarity=0.238  Sum_probs=26.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      -+++.||+|+|||+++..+|..+   +..+..+++.
T Consensus       106 vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~D  141 (306)
T 1vma_A          106 VIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAAD  141 (306)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEccc
Confidence            46899999999999999999876   5566655543

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=94.49  E-value=0.029  Score=56.01  Aligned_cols=32  Identities=19%  Similarity=0.379  Sum_probs=25.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~  260 (338)
                      .-++|.|.||+|||++++.+|.+++   .+...++
T Consensus        36 ~lIvlvGlpGSGKSTia~~La~~L~~~~~d~~v~s   70 (520)
T 2axn_A           36 TVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFN   70 (520)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCCeEEec
Confidence            4578999999999999999999884   4444443

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=94.43  E-value=0.034  Score=48.13  Aligned_cols=36  Identities=22%  Similarity=0.292  Sum_probs=25.5

Q ss_pred             HHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          217 KMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       217 ~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +.+...+......-+++.|++|+|||+|+..++...
T Consensus        27 ~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           27 DKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            333333333333457888999999999999999875

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=94.37  E-value=0.025  Score=57.12  Aligned_cols=33  Identities=24%  Similarity=0.163  Sum_probs=27.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC----CcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH----FDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~----~~~~~l~~~  262 (338)
                      -++|.|+||+|||+++++++..++    .+++.++..
T Consensus       398 ~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD~D  434 (573)
T 1m8p_A          398 TIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGD  434 (573)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEEHH
T ss_pred             EEEeecCCCCCHHHHHHHHHHHhcccCCceEEEECcH
Confidence            367999999999999999999986    677777643

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=94.36  E-value=0.056  Score=45.81  Aligned_cols=23  Identities=26%  Similarity=0.392  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.++...
T Consensus        29 ~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           29 YKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            45899999999999999999753

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.35  E-value=0.054  Score=51.09  Aligned_cols=32  Identities=34%  Similarity=0.387  Sum_probs=25.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      -+.|.|+||+|||+++.+++..+   |..+..++.
T Consensus        81 ~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~~  115 (355)
T 3p32_A           81 RVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAV  115 (355)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEec
Confidence            46799999999999999999876   555544443

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.30  E-value=0.023  Score=45.84  Aligned_cols=22  Identities=32%  Similarity=0.528  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.+++..
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            4789999999999999999864

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=94.26  E-value=0.023  Score=49.86  Aligned_cols=29  Identities=34%  Similarity=0.360  Sum_probs=24.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      +.|.|++|+|||++++.++..+   +++++..
T Consensus         9 i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~   40 (213)
T 4edh_A            9 VTLEGPEGAGKSTNRDYLAERLRERGIEVQLT   40 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCcccc
Confidence            5688999999999999999988   4566544

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=94.20  E-value=0.045  Score=50.36  Aligned_cols=23  Identities=35%  Similarity=0.469  Sum_probs=20.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.+.||+|+|||++++.++..++
T Consensus        34 i~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           34 IFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhh
Confidence            46999999999999999999885

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=94.17  E-value=0.027  Score=47.87  Aligned_cols=24  Identities=25%  Similarity=0.278  Sum_probs=21.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.+.||+|+|||+++.+++..+
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhc
Confidence            457899999999999999998865

>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=94.16  E-value=0.025  Score=45.90  Aligned_cols=22  Identities=27%  Similarity=0.369  Sum_probs=19.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4789999999999999999874

>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=94.16  E-value=0.097  Score=54.68  Aligned_cols=23  Identities=22%  Similarity=0.495  Sum_probs=18.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.||+|+|||+++..++..
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            45899999999999977776543

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.16  E-value=0.024  Score=48.23  Aligned_cols=22  Identities=32%  Similarity=0.588  Sum_probs=19.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+.|.||+|+|||+|+..++..
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            4689999999999999999975

>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=94.14  E-value=0.024  Score=48.69  Aligned_cols=24  Identities=25%  Similarity=0.511  Sum_probs=21.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ..+++.|++|+|||+|+.+++...
T Consensus        13 ~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           13 PSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            458999999999999999999754

>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=94.14  E-value=0.052  Score=45.53  Aligned_cols=21  Identities=38%  Similarity=0.673  Sum_probs=19.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+++.|++|+|||+|+.++..
T Consensus        10 ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A           10 RVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHc
Confidence            578999999999999999986

>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=94.12  E-value=0.023  Score=46.81  Aligned_cols=22  Identities=45%  Similarity=0.640  Sum_probs=19.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+++||.|+|||+++.||+-.+
T Consensus        26 ~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           26 NLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            4899999999999999998655

>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=94.11  E-value=0.019  Score=48.28  Aligned_cols=24  Identities=21%  Similarity=0.293  Sum_probs=20.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -.+++.|++|+|||+|+.++...-
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            357999999999999999987643

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.11  E-value=0.042  Score=48.79  Aligned_cols=30  Identities=20%  Similarity=0.194  Sum_probs=21.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh-------CCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL-------HFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l-------~~~~~~l~  260 (338)
                      +.|.||+|+|||++++.++..+       |.++....
T Consensus        28 I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~r   64 (227)
T 3v9p_A           28 ITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVTR   64 (227)
T ss_dssp             EEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhhccccceeeeeec
Confidence            5688999999999999999987       66665443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.10  E-value=0.026  Score=52.26  Aligned_cols=23  Identities=26%  Similarity=0.483  Sum_probs=21.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+|||++++.+|..+
T Consensus       102 vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A          102 VIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            46799999999999999999876

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=94.09  E-value=0.027  Score=52.28  Aligned_cols=24  Identities=38%  Similarity=0.634  Sum_probs=21.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||+|+|||++++.+|..+
T Consensus       103 ~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          103 RVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH
Confidence            346799999999999999999877

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.09  E-value=0.026  Score=56.25  Aligned_cols=62  Identities=19%  Similarity=0.419  Sum_probs=40.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEecCC-cC-----------------CchHHHHHHHhc--CCCcEEEE
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLELSS-VE-----------------GNKHLRKVLIAT--ENKSILVV  285 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~~~-~~-----------------~~~~l~~~l~~~--~~~~Il~i  285 (338)
                      +.++++.||+|+|||+++++++..+..  .++.++-.. +.                 ..-.+..++...  ..|+++++
T Consensus       260 g~~i~I~GptGSGKTTlL~aL~~~i~~~~giitied~~E~~~~~~~~v~~~~r~~~~~~~~~~~~~l~~~LR~~PD~iiv  339 (511)
T 2oap_1          260 KFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSIEDTREIKLYHENWIAEVTRTGMGEGEIDMYDLLRAALRQRPDYIIV  339 (511)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCCCSSEEEEECBCCSSSCCBCHHHHHHTTGGGCCSEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEEcCcccccCCCCCeEEEEeecccccCCcCHHHHHHHhhccCCCeEEe
Confidence            456899999999999999999998843  344443221 11                 011233444332  26888899


Q ss_pred             cCCC
Q 035959          286 GDID  289 (338)
Q Consensus       286 DeiD  289 (338)
                      .|+-
T Consensus       340 gEir  343 (511)
T 2oap_1          340 GEVR  343 (511)
T ss_dssp             SCCC
T ss_pred             CCcC
Confidence            9874

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=94.02  E-value=0.04  Score=46.09  Aligned_cols=22  Identities=32%  Similarity=0.536  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.+++..
T Consensus        18 ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           18 RILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999998854

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=94.00  E-value=0.045  Score=51.09  Aligned_cols=33  Identities=36%  Similarity=0.566  Sum_probs=26.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      +-+++.||+|+|||+++..+|..+   +..+..+++
T Consensus       106 ~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~  141 (320)
T 1zu4_A          106 NIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAA  141 (320)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            357899999999999999999876   556666554

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=93.99  E-value=0.027  Score=55.07  Aligned_cols=22  Identities=36%  Similarity=0.534  Sum_probs=18.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.++.|+||||||+++..+++.
T Consensus       163 v~~I~G~aGsGKTt~I~~~~~~  184 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEILSRVNF  184 (446)
T ss_dssp             EEEEEECTTSCHHHHHHHHCCT
T ss_pred             EEEEEcCCCCCHHHHHHHHhcc
Confidence            3579999999999999887753

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.97  E-value=0.029  Score=45.53  Aligned_cols=22  Identities=27%  Similarity=0.502  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999998864

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=93.97  E-value=0.024  Score=48.09  Aligned_cols=23  Identities=30%  Similarity=0.523  Sum_probs=20.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+|||+|+..++...
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            46899999999999999999754

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=93.88  E-value=0.047  Score=54.11  Aligned_cols=30  Identities=27%  Similarity=0.319  Sum_probs=24.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      -+.|.||+|+|||+|++.||..+   +..+...
T Consensus       295 VI~LVGpNGSGKTTLl~~LAgll~~~~G~V~l~  327 (503)
T 2yhs_A          295 VILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA  327 (503)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCcccHHHHHHHHHHHhhhcCCeEEEe
Confidence            36799999999999999999876   3445443

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.87  E-value=0.032  Score=45.39  Aligned_cols=23  Identities=30%  Similarity=0.405  Sum_probs=20.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+++.|++|+|||+|+.++...-
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            47899999999999999998753

>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=93.85  E-value=0.032  Score=52.34  Aligned_cols=64  Identities=16%  Similarity=0.363  Sum_probs=40.9

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEecCCc------C--------CchHHHHHHHhc--CCCcEEEEcCC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLELSSV------E--------GNKHLRKVLIAT--ENKSILVVGDI  288 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~~~~------~--------~~~~l~~~l~~~--~~~~Il~iDei  288 (338)
                      ....+++.||+|+|||+|+++++..+..  ..+.++....      .        .....+..+..+  .+|.+|++||.
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            3456889999999999999999998742  2333432211      0        011223333322  47999999998


Q ss_pred             Cc
Q 035959          289 DC  290 (338)
Q Consensus       289 D~  290 (338)
                      -.
T Consensus       250 ~~  251 (330)
T 2pt7_A          250 RS  251 (330)
T ss_dssp             CS
T ss_pred             Ch
Confidence            75

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=93.84  E-value=0.064  Score=47.23  Aligned_cols=63  Identities=6%  Similarity=0.126  Sum_probs=38.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC--CchHH----------------HHHHHhcC-CCcEEEEcCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE--GNKHL----------------RKVLIATE-NKSILVVGDI  288 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~--~~~~l----------------~~~l~~~~-~~~Il~iDei  288 (338)
                      ++++||.|+|||+.+.-++..+   +..++.+...--.  .+..+                ..++.... ...+|+|||+
T Consensus        31 ~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d~R~ge~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~dvViIDEa  110 (214)
T 2j9r_A           31 EVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAIDEV  110 (214)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC-----------------CCEEECSSGGGGGGGCCSSCCEEEECCG
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCCcchHHHHHhhcCCeeEEeecCCHHHHHHHHhcCCCEEEEECc
Confidence            3589999999999877776554   6777766533111  00011                12222222 3689999999


Q ss_pred             CccCC
Q 035959          289 DCCTE  293 (338)
Q Consensus       289 D~~~~  293 (338)
                      .-+.+
T Consensus       111 QF~~~  115 (214)
T 2j9r_A          111 QFFDG  115 (214)
T ss_dssp             GGSCT
T ss_pred             ccCCH
Confidence            98743

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=93.83  E-value=0.032  Score=51.97  Aligned_cols=23  Identities=22%  Similarity=0.241  Sum_probs=20.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.|.||+|+|||||++.|+..+.
T Consensus        93 vgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           93 IGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEECCCCchHHHHHHHHHhhcc
Confidence            46999999999999999999773

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=93.82  E-value=0.032  Score=45.83  Aligned_cols=22  Identities=36%  Similarity=0.551  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
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            5789999999999999999853

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=93.82  E-value=0.033  Score=45.33  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=19.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            8 KVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4789999999999999999864

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.82  E-value=0.054  Score=52.88  Aligned_cols=33  Identities=18%  Similarity=0.266  Sum_probs=26.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~  262 (338)
                      -+++.|+||+|||+|+..+|..+    |.++..+++.
T Consensus       205 liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E  241 (454)
T 2r6a_A          205 LIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLE  241 (454)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECC
Confidence            36899999999999999988754    5578877654

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=93.81  E-value=0.031  Score=45.79  Aligned_cols=21  Identities=43%  Similarity=0.743  Sum_probs=19.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|+||+|||+|+.++..
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~   26 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAG   26 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCccHHHHHHHHhc
Confidence            478999999999999999875

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=93.80  E-value=0.028  Score=49.38  Aligned_cols=31  Identities=26%  Similarity=0.314  Sum_probs=27.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      .+-|+|..|||||++++.++. +|+++++.|.
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            356999999999999999998 9999887765

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=93.80  E-value=0.03  Score=46.03  Aligned_cols=21  Identities=33%  Similarity=0.623  Sum_probs=19.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+.|.|+||+|||+|+.+++.
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~   25 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTG   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            468999999999999999986

>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=93.80  E-value=0.032  Score=52.39  Aligned_cols=30  Identities=37%  Similarity=0.544  Sum_probs=24.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      -+.|.||+|+||||+++.+|..+   +..+...
T Consensus       131 vi~lvG~nGaGKTTll~~Lag~l~~~~g~V~l~  163 (328)
T 3e70_C          131 VIMFVGFNGSGKTTTIAKLANWLKNHGFSVVIA  163 (328)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEE
Confidence            46799999999999999999877   3444444

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=93.79  E-value=0.029  Score=50.14  Aligned_cols=24  Identities=33%  Similarity=0.645  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++++..+.
T Consensus        26 ~~~liG~nGsGKSTLl~~l~Gl~~   49 (240)
T 2onk_A           26 YCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            467999999999999999998764

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=93.77  E-value=0.045  Score=50.59  Aligned_cols=23  Identities=22%  Similarity=0.297  Sum_probs=21.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-|.||+|+|||++++.++..++
T Consensus        83 igI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           83 ISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            46999999999999999999876

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=93.75  E-value=0.018  Score=56.52  Aligned_cols=25  Identities=24%  Similarity=0.506  Sum_probs=22.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-++|.|.||+|||++++.++..++
T Consensus        40 ~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           40 TLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4578999999999999999999875

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=93.74  E-value=0.06  Score=47.74  Aligned_cols=33  Identities=27%  Similarity=0.573  Sum_probs=26.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh--CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL--HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l--~~~~~~l~~~  262 (338)
                      .+++.|.+|+|||+++..+|..+  |..+..+++.
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            35789999999999999999776  6677666644

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.70  E-value=0.035  Score=45.68  Aligned_cols=23  Identities=30%  Similarity=0.517  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.++...
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35789999999999999998864

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=93.69  E-value=0.035  Score=45.03  Aligned_cols=21  Identities=33%  Similarity=0.567  Sum_probs=19.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+++.|++|+|||+|+.++..
T Consensus         8 ~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            478999999999999999986

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=93.66  E-value=0.064  Score=50.34  Aligned_cols=35  Identities=31%  Similarity=0.437  Sum_probs=25.5

Q ss_pred             HHHHHHHhhhcCc--eeeeCCCCCCcHHHHHHHHHHh
Q 035959          218 MIMDDLERAWKRG--YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       218 ~i~~~l~~~~~~g--~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+++++.-.-+.|  +.|.||||+|||+|+.+++..+
T Consensus        43 ~~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           43 DLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             HHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHhCCcccCCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            3455554322333  5699999999999999999766

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=93.66  E-value=0.03  Score=45.58  Aligned_cols=22  Identities=36%  Similarity=0.581  Sum_probs=19.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5789999999999999999853

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=93.64  E-value=0.052  Score=45.77  Aligned_cols=21  Identities=29%  Similarity=0.651  Sum_probs=18.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+++.|++|+|||+|+.++..
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~   48 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTD   48 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            479999999999999999874

>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=93.63  E-value=0.027  Score=50.17  Aligned_cols=25  Identities=24%  Similarity=0.466  Sum_probs=21.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||.|+|||||+++++....
T Consensus        32 e~~~iiG~nGsGKSTLl~~l~Gl~~   56 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTMLNIIGCLDK   56 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCCC
Confidence            3467999999999999999998764

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=93.63  E-value=0.061  Score=50.81  Aligned_cols=39  Identities=28%  Similarity=0.396  Sum_probs=29.7

Q ss_pred             HHHHHHHhhhcCc--eeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          218 MIMDDLERAWKRG--YLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       218 ~i~~~l~~~~~~g--~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      .+++.+ -+-.+|  +.|.||+|+|||+|++.|++....+..
T Consensus        60 ~ald~l-l~i~~Gq~~gIiG~nGaGKTTLl~~I~g~~~~~~g  100 (347)
T 2obl_A           60 RAIDGL-LTCGIGQRIGIFAGSGVGKSTLLGMICNGASADII  100 (347)
T ss_dssp             HHHHHH-SCEETTCEEEEEECTTSSHHHHHHHHHHHSCCSEE
T ss_pred             EEEEee-eeecCCCEEEEECCCCCCHHHHHHHHhcCCCCCEE
Confidence            356666 444444  679999999999999999999876543

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.63  E-value=0.036  Score=52.60  Aligned_cols=27  Identities=26%  Similarity=0.493  Sum_probs=23.3

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ....++|.||+|+|||+|+++++..+.
T Consensus       174 ~G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          174 LERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             TTCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            345678999999999999999999874

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=93.63  E-value=0.015  Score=52.18  Aligned_cols=24  Identities=17%  Similarity=0.261  Sum_probs=21.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.|++|+|||++++.++..++
T Consensus        26 ~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           26 KISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            357899999999999999999983

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.63  E-value=0.037  Score=48.87  Aligned_cols=24  Identities=17%  Similarity=0.246  Sum_probs=21.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.+.|++|+|||++++.++..++
T Consensus         4 ~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            4 RLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcC
Confidence            467999999999999999999984

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=93.59  E-value=0.024  Score=50.07  Aligned_cols=24  Identities=25%  Similarity=0.329  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++++..+.
T Consensus        32 ~~~iiG~nGsGKSTLl~~l~Gl~~   55 (224)
T 2pcj_A           32 FVSIIGASGSGKSTLLYILGLLDA   55 (224)
T ss_dssp             EEEEEECTTSCHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCC
Confidence            467999999999999999998764

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.59  E-value=0.03  Score=50.97  Aligned_cols=23  Identities=26%  Similarity=0.511  Sum_probs=20.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+.|.||+|+|||||+++++...
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            46789999999999999999876

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=93.56  E-value=0.029  Score=47.06  Aligned_cols=21  Identities=24%  Similarity=0.645  Sum_probs=19.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -++|.|++|+|||+|+..++.
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            478999999999999999886

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=93.56  E-value=0.031  Score=52.83  Aligned_cols=27  Identities=22%  Similarity=0.405  Sum_probs=23.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      .-+.|.||+|+|||+|++.|+..+..+
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            457899999999999999999987543

>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=93.53  E-value=0.028  Score=50.05  Aligned_cols=24  Identities=33%  Similarity=0.434  Sum_probs=21.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||+|+|||+|+++++..+
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            346799999999999999999876

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=93.51  E-value=0.038  Score=45.90  Aligned_cols=23  Identities=26%  Similarity=0.488  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.+++.|++|+|||+|+.++...
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            35799999999999999999863

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.49  E-value=0.037  Score=45.08  Aligned_cols=19  Identities=37%  Similarity=0.681  Sum_probs=17.7

Q ss_pred             eeeeCCCCCCcHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia  249 (338)
                      +++.|+||+|||+|+.++.
T Consensus         5 i~ivG~~~~GKSsli~~l~   23 (169)
T 3q85_A            5 VMLVGESGVGKSTLAGTFG   23 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            6899999999999999986

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.46  E-value=0.057  Score=52.55  Aligned_cols=33  Identities=18%  Similarity=0.198  Sum_probs=26.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~  262 (338)
                      -+++.|+||+|||+++..+|...    |.++..+++.
T Consensus       202 l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE  238 (444)
T 2q6t_A          202 LNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLE  238 (444)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            36899999999999999888654    5678777664

>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=93.46  E-value=0.04  Score=44.87  Aligned_cols=21  Identities=24%  Similarity=0.539  Sum_probs=19.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+++.|++|+|||+|+.++..
T Consensus         9 ~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            9 RILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999999976

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=93.46  E-value=0.031  Score=49.18  Aligned_cols=25  Identities=32%  Similarity=0.672  Sum_probs=21.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||.|+|||+|+++++..+.
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl~~   60 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTYLK   60 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3467999999999999999998764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=93.45  E-value=0.04  Score=46.00  Aligned_cols=22  Identities=27%  Similarity=0.477  Sum_probs=20.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
T Consensus         9 ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            9 KTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999999875

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.42  E-value=0.036  Score=45.60  Aligned_cols=21  Identities=29%  Similarity=0.521  Sum_probs=19.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|++|+|||+|+.++..
T Consensus         8 ki~v~G~~~~GKssl~~~l~~   28 (178)
T 2hxs_A            8 KIVVLGDGASGKTSLTTCFAQ   28 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHG
T ss_pred             EEEEECcCCCCHHHHHHHHHh
Confidence            478999999999999999874

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=93.41  E-value=0.041  Score=52.34  Aligned_cols=23  Identities=26%  Similarity=0.483  Sum_probs=21.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+||||+++.+|..+
T Consensus       159 vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          159 VIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCChHHHHHHHHHhhc
Confidence            36799999999999999999976

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=93.40  E-value=0.042  Score=51.40  Aligned_cols=23  Identities=22%  Similarity=0.247  Sum_probs=21.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-|.||+|+|||++++.++..++
T Consensus        95 igI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           95 IGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            56999999999999999999875

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=93.38  E-value=0.057  Score=50.91  Aligned_cols=33  Identities=24%  Similarity=0.216  Sum_probs=27.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      -++|.|+||+|||+++..+|..+   +.++..+++.
T Consensus        48 LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSlE   83 (338)
T 4a1f_A           48 LVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSLE   83 (338)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence            37899999999999999988764   6777777664

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=93.36  E-value=0.056  Score=47.60  Aligned_cols=30  Identities=23%  Similarity=0.143  Sum_probs=25.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -+.+.|++|+|||++++.++..++.++..+
T Consensus         7 ~i~~eG~~g~GKst~~~~l~~~l~~~~~~~   36 (216)
T 3tmk_A            7 LILIEGLDRTGKTTQCNILYKKLQPNCKLL   36 (216)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHCSSEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcccceEE
Confidence            357899999999999999999998754433

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=93.32  E-value=0.038  Score=49.57  Aligned_cols=22  Identities=41%  Similarity=0.516  Sum_probs=20.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+.|.||+|+|||||+++++..
T Consensus        31 ~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           31 VHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4679999999999999999986

>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=93.32  E-value=0.085  Score=44.89  Aligned_cols=23  Identities=17%  Similarity=0.312  Sum_probs=19.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      --+++.|++|+|||+|+..+...
T Consensus        30 ~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           30 FKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhhC
Confidence            35789999999999999998753

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=93.31  E-value=0.033  Score=50.46  Aligned_cols=24  Identities=21%  Similarity=0.394  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||||+++++..+.
T Consensus        34 ~~~liG~nGsGKSTLlk~l~Gl~~   57 (262)
T 1b0u_A           34 VISIIGSSGSGKSTFLRCINFLEK   57 (262)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCC
Confidence            467999999999999999998764

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.28  E-value=0.041  Score=45.82  Aligned_cols=22  Identities=32%  Similarity=0.554  Sum_probs=19.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+.|.|++|+|||+|+.+++..
T Consensus         9 ~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            9 EIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5789999999999999999873

>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=93.26  E-value=0.047  Score=45.01  Aligned_cols=23  Identities=35%  Similarity=0.531  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus        13 ~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           13 AKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35799999999999999999864

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=93.26  E-value=0.037  Score=45.37  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
T Consensus        16 ~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5789999999999999999853

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=93.24  E-value=0.04  Score=49.98  Aligned_cols=24  Identities=38%  Similarity=0.545  Sum_probs=20.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||.|+|||||+++++...
T Consensus        47 e~~~l~G~NGsGKSTLlk~l~Gl~   70 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLSATLAGRE   70 (267)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTCT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            346799999999999999999863

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=93.24  E-value=0.033  Score=50.17  Aligned_cols=24  Identities=42%  Similarity=0.812  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||.|+|||||+++++..+.
T Consensus        35 ~~~liG~nGsGKSTLlk~l~Gl~~   58 (257)
T 1g6h_A           35 VTLIIGPNGSGKSTLINVITGFLK   58 (257)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            467999999999999999998764

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=93.24  E-value=0.034  Score=49.63  Aligned_cols=23  Identities=26%  Similarity=0.563  Sum_probs=20.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+|||||+++++..+
T Consensus        30 ~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           30 IIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            46799999999999999999876

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=93.23  E-value=0.079  Score=51.67  Aligned_cols=38  Identities=39%  Similarity=0.542  Sum_probs=29.6

Q ss_pred             HHHHHHHhhhcCc--eeeeCCCCCCcHHHHHHHHHHhCCcE
Q 035959          218 MIMDDLERAWKRG--YLLFGPPGTGKSSLIAAMANYLHFDV  256 (338)
Q Consensus       218 ~i~~~l~~~~~~g--~LL~GppGtGKT~l~~aia~~l~~~~  256 (338)
                      .+++.+ -+-.+|  +.|.||+|+|||+|++.|++....+.
T Consensus       146 ~vld~v-l~i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~~~~  185 (438)
T 2dpy_A          146 RAINAL-LTVGRGQRMGLFAGSGVGKSVLLGMMARYTRADV  185 (438)
T ss_dssp             HHHHHH-SCCBTTCEEEEEECTTSSHHHHHHHHHHHSCCSE
T ss_pred             eEEeee-EEecCCCEEEEECCCCCCHHHHHHHHhcccCCCe
Confidence            466666 544444  67999999999999999999986543

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=93.17  E-value=0.036  Score=49.07  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=21.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||.|+|||+|+++++..+.
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCc
Confidence            3467999999999999999998763

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.13  E-value=0.036  Score=49.44  Aligned_cols=24  Identities=29%  Similarity=0.512  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||.|+|||||+++++..+.
T Consensus        34 ~~~l~G~nGsGKSTLl~~l~Gl~~   57 (240)
T 1ji0_A           34 IVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            467999999999999999998764

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.11  E-value=0.036  Score=45.02  Aligned_cols=21  Identities=43%  Similarity=0.735  Sum_probs=18.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|+||+|||+|+.++.+
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            378999999999999999863

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=93.11  E-value=0.11  Score=52.02  Aligned_cols=33  Identities=30%  Similarity=0.320  Sum_probs=26.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~  262 (338)
                      -++|.|+||+|||+++++++..++   .+++.++..
T Consensus       374 ~I~l~G~~GsGKSTia~~La~~L~~~G~~~~~ld~D  409 (546)
T 2gks_A          374 CVWLTGLPCAGKSTIAEILATMLQARGRKVTLLDGD  409 (546)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECHH
T ss_pred             EEEccCCCCCCHHHHHHHHHHHhhhcCCeEEEECch
Confidence            367999999999999999999874   456666543

>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=93.09  E-value=0.049  Score=45.52  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=19.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.+++..
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5789999999999999999864

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.09  E-value=0.076  Score=51.70  Aligned_cols=35  Identities=20%  Similarity=0.349  Sum_probs=29.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~  263 (338)
                      +.+++.|++|+|||+++..+|..+    |..+..+++..
T Consensus       101 ~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A          101 AVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            467888999999999999999776    67788777764

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.07  E-value=0.047  Score=54.86  Aligned_cols=32  Identities=34%  Similarity=0.322  Sum_probs=26.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC----CcEEEEecC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH----FDVYDLELS  262 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~----~~~~~l~~~  262 (338)
                      +.|.|++|+|||++++++|..++    ..+..++..
T Consensus       372 I~LiG~sGSGKSTLar~La~~L~~~~G~~i~~lDgD  407 (552)
T 3cr8_A          372 VFFTGLSGAGKSTLARALAARLMEMGGRCVTLLDGD  407 (552)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHTTCSSCEEEESSH
T ss_pred             EEEECCCCChHHHHHHHHHHhhcccCCceEEEECCc
Confidence            67999999999999999999985    345556543

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.05  E-value=0.048  Score=44.79  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      .-+++.|++|+|||+|+.++..
T Consensus         9 ~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            9 PVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CEEEEESCTTTTHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4578999999999999999975

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=93.04  E-value=0.037  Score=49.60  Aligned_cols=25  Identities=24%  Similarity=0.400  Sum_probs=21.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||+|+|||+|+++++..+.
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl~~   60 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRFYI   60 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3467999999999999999998764

>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=93.03  E-value=0.043  Score=45.07  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.++...
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            35789999999999999999875

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=93.03  E-value=0.038  Score=50.13  Aligned_cols=25  Identities=24%  Similarity=0.515  Sum_probs=21.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||.|+|||+|+++++..+.
T Consensus        51 ei~~liG~NGsGKSTLlk~l~Gl~~   75 (263)
T 2olj_A           51 EVVVVIGPSGSGKSTFLRCLNLLED   75 (263)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEEcCCCCcHHHHHHHHHcCCC
Confidence            3467999999999999999998764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.03  E-value=0.047  Score=44.84  Aligned_cols=21  Identities=43%  Similarity=0.714  Sum_probs=18.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+++.|++|+|||+|+.++..
T Consensus        11 ~i~v~G~~~~GKssl~~~l~~   31 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFAD   31 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999999864

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=93.03  E-value=0.038  Score=49.67  Aligned_cols=24  Identities=46%  Similarity=0.635  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||.|+|||+|+++++..+.
T Consensus        28 ~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           28 ILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCC
Confidence            467999999999999999998764

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=93.01  E-value=0.038  Score=50.47  Aligned_cols=24  Identities=29%  Similarity=0.455  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||||+++++..+.
T Consensus        36 ~~~iiGpnGsGKSTLl~~l~Gl~~   59 (275)
T 3gfo_A           36 VTAILGGNGVGKSTLFQNFNGILK   59 (275)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCC
Confidence            467999999999999999998763

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.96  E-value=0.053  Score=44.62  Aligned_cols=22  Identities=27%  Similarity=0.527  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
T Consensus        12 ~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           12 KVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5789999999999999998863

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=92.94  E-value=0.044  Score=45.48  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      --+++.|++|+|||+|+.++...
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            35789999999999999999864

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=92.93  E-value=0.054  Score=44.88  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
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            5799999999999999999864

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=92.92  E-value=0.053  Score=45.38  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=20.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.++...
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35799999999999999999864

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=92.90  E-value=0.054  Score=44.74  Aligned_cols=22  Identities=18%  Similarity=0.379  Sum_probs=19.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999998853

>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=92.89  E-value=0.041  Score=49.68  Aligned_cols=24  Identities=25%  Similarity=0.585  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||.|+|||||+++++..+.
T Consensus        43 i~~l~G~NGsGKSTLlk~l~Gl~~   66 (256)
T 1vpl_A           43 IFGLIGPNGAGKTTTLRIISTLIK   66 (256)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCC
Confidence            467999999999999999998763

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=92.87  E-value=0.046  Score=45.67  Aligned_cols=22  Identities=23%  Similarity=0.413  Sum_probs=19.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+..++..
T Consensus         9 ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            9 KIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999999874

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=92.86  E-value=0.041  Score=49.73  Aligned_cols=25  Identities=24%  Similarity=0.469  Sum_probs=21.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||+|+|||+|+++++..+.
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl~~   71 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRFYD   71 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhccCC
Confidence            3578999999999999999998763

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=92.82  E-value=0.048  Score=51.74  Aligned_cols=24  Identities=29%  Similarity=0.548  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++||....
T Consensus        43 ~~~llGpnGsGKSTLLr~iaGl~~   66 (355)
T 1z47_A           43 MVGLLGPSGSGKTTILRLIAGLER   66 (355)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCC
Confidence            467999999999999999998763

>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=92.81  E-value=0.044  Score=49.79  Aligned_cols=24  Identities=38%  Similarity=0.728  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++++..+.
T Consensus        39 ~~~liG~nGsGKSTLl~~l~Gl~~   62 (266)
T 4g1u_C           39 MVAIIGPNGAGKSTLLRLLTGYLS   62 (266)
T ss_dssp             EEEEECCTTSCHHHHHHHHTSSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhcCCC
Confidence            467999999999999999998763

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=92.80  E-value=0.042  Score=49.99  Aligned_cols=25  Identities=36%  Similarity=0.602  Sum_probs=21.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||.|+|||+|+++|+..+.
T Consensus        46 e~~~i~G~nGsGKSTLlk~l~Gl~~   70 (271)
T 2ixe_A           46 KVTALVGPNGSGKSTVAALLQNLYQ   70 (271)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3467999999999999999998764

>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=92.79  E-value=0.14  Score=54.56  Aligned_cols=65  Identities=14%  Similarity=0.177  Sum_probs=39.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH-----hCCc----EEEE----------ecCCcC----C-----chHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY-----LHFD----VYDL----------ELSSVE----G-----NKHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~-----l~~~----~~~l----------~~~~~~----~-----~~~l~~~l~~~~~~  280 (338)
                      +-++|.||.|+|||++++.+|.-     .|..    ...+          ...+..    +     -..+..++..+..+
T Consensus       663 ~i~~ItGpNGsGKSTlLr~ial~~~~aq~G~~vpa~~~~~~~~d~i~~~ig~~d~l~~~lStf~~e~~~~a~il~~a~~~  742 (934)
T 3thx_A          663 MFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKD  742 (934)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHHHHTCCBSEEEEEEECCSEEEEECC---------CHHHHHHHHHHHHHHHCCTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHHhcCCccccccccchHHHHHHHhcCchhhHHHhHhhhHHHHHHHHHHHHhccCC
Confidence            45789999999999999998532     2321    1111          111100    0     11234555556789


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      ++|+|||.-.-.+
T Consensus       743 sLlLLDEp~~GlD  755 (934)
T 3thx_A          743 SLIIIDELGRGTS  755 (934)
T ss_dssp             CEEEEESCSCSSC
T ss_pred             cEEEEeCCCCCCC
Confidence            9999999877654

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=92.78  E-value=0.057  Score=45.17  Aligned_cols=22  Identities=41%  Similarity=0.626  Sum_probs=20.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
T Consensus        18 ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           18 KLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5799999999999999999874

>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=92.75  E-value=0.058  Score=45.01  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      --+++.|++|+|||+|+.++...
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            35799999999999999999864

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=92.75  E-value=0.044  Score=50.15  Aligned_cols=24  Identities=29%  Similarity=0.696  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||.|+|||||+++++..+.
T Consensus        49 ~~~liG~NGsGKSTLlk~l~Gl~~   72 (279)
T 2ihy_A           49 KWILYGLNGAGKTTLLNILNAYEP   72 (279)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCC
Confidence            467999999999999999998764

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=92.74  E-value=0.046  Score=45.44  Aligned_cols=22  Identities=41%  Similarity=0.626  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+.|.|+||+|||+|+.+++..
T Consensus         6 ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            6 KVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3689999999999999999864

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=92.73  E-value=0.059  Score=44.40  Aligned_cols=23  Identities=17%  Similarity=0.288  Sum_probs=20.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.+++.|++|+|||+|+.++...
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45789999999999999998853

>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=92.73  E-value=0.058  Score=46.68  Aligned_cols=25  Identities=40%  Similarity=0.522  Sum_probs=21.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      -.+|+||.|+|||+++.||+-.++.
T Consensus        25 ~~~I~G~NgsGKStil~ai~~~l~g   49 (203)
T 3qks_A           25 INLIIGQNGSGKSSLLDAILVGLYW   49 (203)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            3589999999999999999877754

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=92.72  E-value=0.044  Score=49.68  Aligned_cols=25  Identities=32%  Similarity=0.570  Sum_probs=21.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||.|+|||||+++++..+.
T Consensus        34 e~~~liG~nGsGKSTLl~~i~Gl~~   58 (266)
T 2yz2_A           34 ECLLVAGNTGSGKSTLLQIVAGLIE   58 (266)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            3467999999999999999998764

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=92.71  E-value=0.044  Score=49.33  Aligned_cols=24  Identities=25%  Similarity=0.397  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++++..+.
T Consensus        33 ~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           33 ILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             EEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            467999999999999999998763

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=92.71  E-value=0.052  Score=51.65  Aligned_cols=24  Identities=38%  Similarity=0.639  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++||....
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           31 FMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCchHHHHHHHHhcCCC
Confidence            467999999999999999998763

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=92.70  E-value=0.19  Score=45.51  Aligned_cols=21  Identities=33%  Similarity=0.604  Sum_probs=19.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+.|.|+||+|||+|+.+++.
T Consensus         5 kI~lvG~~nvGKSTL~n~L~g   25 (272)
T 3b1v_A            5 EIALIGNPNSGKTSLFNLITG   25 (272)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            468999999999999999986

>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=92.69  E-value=0.044  Score=52.14  Aligned_cols=24  Identities=25%  Similarity=0.602  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++||....
T Consensus        32 ~~~llGpsGsGKSTLLr~iaGl~~   55 (359)
T 3fvq_A           32 ILFIIGASGCGKTTLLRCLAGFEQ   55 (359)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCchHHHHHHHHhcCCC
Confidence            467999999999999999998763

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=92.68  E-value=0.061  Score=45.19  Aligned_cols=22  Identities=27%  Similarity=0.471  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+..+...
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            4799999999999999998864

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=92.68  E-value=0.061  Score=44.99  Aligned_cols=23  Identities=17%  Similarity=0.249  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.++...
T Consensus        21 ~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           21 FKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35799999999999999999853

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=92.67  E-value=0.052  Score=48.45  Aligned_cols=23  Identities=30%  Similarity=0.388  Sum_probs=20.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.|++|+|||++++.++..+
T Consensus        29 ~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           29 FIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             EEEEEESTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            35789999999999999999887

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=92.64  E-value=0.078  Score=51.77  Aligned_cols=32  Identities=22%  Similarity=0.205  Sum_probs=26.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      +++.|+||+|||+++..+|...   |.++..+++.
T Consensus       200 iiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlE  234 (444)
T 3bgw_A          200 VLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  234 (444)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSS
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECC
Confidence            6899999999999998888765   6678777664

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=92.64  E-value=0.062  Score=45.46  Aligned_cols=23  Identities=30%  Similarity=0.540  Sum_probs=20.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            9 LKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35789999999999999999864

>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=92.63  E-value=0.053  Score=51.53  Aligned_cols=24  Identities=29%  Similarity=0.516  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|++++|....
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~   54 (359)
T 2yyz_A           31 FVALLGPSGCGKTTTLLMLAGIYK   54 (359)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEcCCCchHHHHHHHHHCCCC
Confidence            467999999999999999998763

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=92.62  E-value=0.062  Score=45.07  Aligned_cols=22  Identities=23%  Similarity=0.351  Sum_probs=19.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+++.|++|+|||+|+.++...
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            4789999999999999999863

>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=92.61  E-value=0.054  Score=51.72  Aligned_cols=23  Identities=30%  Similarity=0.563  Sum_probs=20.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+|||+|+++||...
T Consensus        39 ~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           39 FLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEECCCCChHHHHHHHHHcCC
Confidence            46799999999999999999876

>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=92.61  E-value=0.047  Score=45.02  Aligned_cols=22  Identities=32%  Similarity=0.347  Sum_probs=19.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+..++..
T Consensus         9 ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            9 RLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEECCGGGCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999999864

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=92.60  E-value=0.055  Score=51.87  Aligned_cols=24  Identities=33%  Similarity=0.549  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++||....
T Consensus        31 ~~~llGpsGsGKSTLLr~iaGl~~   54 (381)
T 3rlf_A           31 FVVFVGPSGCGKSTLLRMIAGLET   54 (381)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEcCCCchHHHHHHHHHcCCC
Confidence            467999999999999999998763

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.59  E-value=0.064  Score=45.24  Aligned_cols=23  Identities=30%  Similarity=0.531  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.+++.|++|+|||+|+.++...
T Consensus        29 ~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           29 VKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45899999999999999999864

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=92.58  E-value=0.046  Score=45.83  Aligned_cols=23  Identities=35%  Similarity=0.430  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           24 PEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45899999999999999998753

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=92.56  E-value=0.046  Score=45.43  Aligned_cols=22  Identities=27%  Similarity=0.419  Sum_probs=19.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
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            3689999999999999998863

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=92.54  E-value=0.049  Score=49.41  Aligned_cols=24  Identities=33%  Similarity=0.786  Sum_probs=21.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||.|+|||||+++++..+
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            346799999999999999999876

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=92.54  E-value=0.11  Score=47.71  Aligned_cols=33  Identities=24%  Similarity=0.314  Sum_probs=25.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      .-+.+.|++|+|||+++..+|..+   +..+..+++
T Consensus        99 ~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~  134 (295)
T 1ls1_A           99 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (295)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecC
Confidence            456788999999999999999876   456665554

>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=92.54  E-value=0.063  Score=45.07  Aligned_cols=23  Identities=30%  Similarity=0.616  Sum_probs=20.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      --+++.|++|+|||+|+.++...
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           22 FKYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            35799999999999999999863

>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=92.53  E-value=0.055  Score=51.63  Aligned_cols=24  Identities=29%  Similarity=0.556  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++||....
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~   54 (372)
T 1g29_1           31 FMILLGPSGCGKTTTLRMIAGLEE   54 (372)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCcHHHHHHHHHHcCCC
Confidence            467999999999999999998763

>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=92.49  E-value=0.069  Score=44.87  Aligned_cols=22  Identities=23%  Similarity=0.237  Sum_probs=19.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+..+...
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999888764

>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=92.47  E-value=0.066  Score=44.98  Aligned_cols=23  Identities=22%  Similarity=0.340  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      --+++.|++|+|||+|+.++...
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            35799999999999999999874

>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=92.47  E-value=0.066  Score=45.51  Aligned_cols=23  Identities=35%  Similarity=0.531  Sum_probs=20.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus        21 ~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           21 MKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35799999999999999999853

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=92.45  E-value=0.056  Score=45.64  Aligned_cols=22  Identities=27%  Similarity=0.528  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      .-+++.|+||+|||+|+.+++.
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            4578999999999999999987

>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=92.39  E-value=0.058  Score=45.40  Aligned_cols=23  Identities=30%  Similarity=0.469  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.+++.|++|+|||+|+.++...
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            35799999999999999999864

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=92.39  E-value=0.029  Score=47.51  Aligned_cols=24  Identities=29%  Similarity=0.451  Sum_probs=21.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .+.+.||+|+|||+|+..++..+.
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            467999999999999999999874

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=92.32  E-value=0.07  Score=50.30  Aligned_cols=22  Identities=45%  Similarity=0.738  Sum_probs=19.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +.|.|+||+|||||+.+++..+
T Consensus        77 v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           77 VGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            5799999999999999999864

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.31  E-value=0.059  Score=45.23  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+++.|++|+|||+|+.++...-
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            47999999999999999998754

>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=92.30  E-value=0.13  Score=48.79  Aligned_cols=34  Identities=18%  Similarity=0.201  Sum_probs=27.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .+.++.||+|+|||++++.++..+   +..++.+|..
T Consensus        36 ~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~~   72 (392)
T 4ag6_A           36 SNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDPE   72 (392)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             CceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence            568999999999999999988764   5667777654

>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=92.29  E-value=0.067  Score=45.21  Aligned_cols=23  Identities=26%  Similarity=0.382  Sum_probs=20.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.+++.|++|+|||+|+.++...
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            35789999999999999998753

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=92.26  E-value=0.061  Score=44.43  Aligned_cols=22  Identities=32%  Similarity=0.436  Sum_probs=19.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      .-+++.|++|+|||+|+.++..
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            3578999999999999999984

>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=92.25  E-value=0.12  Score=54.92  Aligned_cols=65  Identities=17%  Similarity=0.210  Sum_probs=39.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH-----hCC----cEEEE----------ecCCcCC---------chHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY-----LHF----DVYDL----------ELSSVEG---------NKHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~-----l~~----~~~~l----------~~~~~~~---------~~~l~~~l~~~~~~  280 (338)
                      .-+.|.||.|+|||++++.++.-     .|.    .-..+          ...+...         -.++..++..+..+
T Consensus       674 ~i~~ItGPNGaGKSTlLr~i~~i~~~aq~g~~vpa~~~~i~~~d~i~~~ig~~d~l~~~~stfs~em~~~~~il~~a~~p  753 (918)
T 3thx_B          674 RVMIITGPNMGGKSSYIKQVALITIMAQIGSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRKATSQ  753 (918)
T ss_dssp             CEEEEESCCCHHHHHHHHHHHHHHHHHHHTCCBSSSEEEEECCSEEEEEC----------CCHHHHHHHHHHHHHHCCTT
T ss_pred             eEEEEECCCCCchHHHHHHHHHHHHHhhcCccccchhhhhhHHHHHHHhCChHHHHHHhHHHhhHHHHHHHHHHHhccCC
Confidence            45789999999999999988742     221    11111          1111000         12233445556789


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      ++|++||.-.-.+
T Consensus       754 ~LlLLDEP~~GlD  766 (918)
T 3thx_B          754 SLVILDELGRGTS  766 (918)
T ss_dssp             CEEEEESTTTTSC
T ss_pred             CEEEEeCCCCCCC
Confidence            9999999877655

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=92.23  E-value=0.11  Score=51.71  Aligned_cols=32  Identities=22%  Similarity=0.232  Sum_probs=24.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      -++|.||||+|||+|+..++...   |..++.+..
T Consensus       283 i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~~  317 (525)
T 1tf7_A          283 IILATGATGTGKTLLVSRFVENACANKERAILFAY  317 (525)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            46899999999999999998765   444555544

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=92.20  E-value=0.045  Score=45.34  Aligned_cols=23  Identities=26%  Similarity=0.457  Sum_probs=9.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEECCCCC------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35789999999999999998743

>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=92.19  E-value=0.062  Score=45.63  Aligned_cols=23  Identities=35%  Similarity=0.531  Sum_probs=20.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
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            35789999999999999999863

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=92.18  E-value=0.078  Score=46.93  Aligned_cols=28  Identities=25%  Similarity=0.296  Sum_probs=23.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC----cEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF----DVYD  258 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~----~~~~  258 (338)
                      +.+.|++|+|||++++.++..++.    +++.
T Consensus        24 i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~   55 (223)
T 3ld9_A           24 ITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVV   55 (223)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHHHCGGGEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhhccCceeeE
Confidence            568899999999999999997754    5554

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.16  E-value=0.026  Score=48.13  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=19.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+.|.|++|+|||+|+.+++..
T Consensus        28 ~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           28 EVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             EEEEEECTTSSHHHHHTTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4689999999999999988753

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=92.09  E-value=0.057  Score=44.97  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
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            45899999999999999998864

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.07  E-value=0.071  Score=46.74  Aligned_cols=23  Identities=22%  Similarity=0.301  Sum_probs=20.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.|++|+|||+.++.++..+
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            35689999999999999999988

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=92.05  E-value=0.066  Score=45.41  Aligned_cols=23  Identities=26%  Similarity=0.349  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            35799999999999999999874

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=92.05  E-value=0.079  Score=45.26  Aligned_cols=23  Identities=26%  Similarity=0.361  Sum_probs=20.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45899999999999999999864

>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=91.98  E-value=0.047  Score=51.68  Aligned_cols=24  Identities=25%  Similarity=0.674  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+.|.||+|+|||+|+++||....
T Consensus        28 ~~~llGpnGsGKSTLLr~iaGl~~   51 (348)
T 3d31_A           28 YFVILGPTGAGKTLFLELIAGFHV   51 (348)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             EEEEECCCCccHHHHHHHHHcCCC
Confidence            467999999999999999998763

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=91.95  E-value=0.074  Score=44.19  Aligned_cols=22  Identities=18%  Similarity=0.448  Sum_probs=19.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      ..+++.|++|+|||+|+.++..
T Consensus        19 ~~i~v~G~~~~GKssl~~~l~~   40 (186)
T 1ksh_A           19 LRLLMLGLDNAGKTTILKKFNG   40 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4579999999999999999875

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=91.94  E-value=0.078  Score=46.59  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=20.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-++|.|++|+|||+|+.++...
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHcCC
Confidence            45789999999999999999863

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=91.91  E-value=0.083  Score=52.13  Aligned_cols=32  Identities=16%  Similarity=-0.014  Sum_probs=26.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL----HFDVYDLELS  262 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~  262 (338)
                      ++|.|+||+|||+++..+|..+    |.++..+++.
T Consensus       245 ~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E  280 (503)
T 1q57_A          245 IMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLE  280 (503)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESS
T ss_pred             EEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEecc
Confidence            6899999999999999988765    4577777764

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=91.89  E-value=0.42  Score=48.98  Aligned_cols=76  Identities=16%  Similarity=0.163  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHH-------------HHhcCCCcE
Q 035959          216 KKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKV-------------LIATENKSI  282 (338)
Q Consensus       216 k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~-------------l~~~~~~~I  282 (338)
                      .+++++.+........+|.|++|+|||+++..++..+...+ .|......+...|.+.             +.......+
T Consensus       180 Q~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~~~~~~-~vtAP~~~a~~~l~~~~~~~i~~~~Pd~~~~~~~~~dl  258 (671)
T 2zpa_A          180 QQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRIAGRA-IVTAPAKASTDVLAQFAGEKFRFIAPDALLASDEQADW  258 (671)
T ss_dssp             HHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHHSSSCE-EEECSSCCSCHHHHHHHGGGCCBCCHHHHHHSCCCCSE
T ss_pred             HHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHHHHhCc-EEECCCHHHHHHHHHHhhCCeEEeCchhhhhCcccCCE
Confidence            34455555543333468999999999999999888886554 4444444433333332             123345789


Q ss_pred             EEEcCCCccC
Q 035959          283 LVVGDIDCCT  292 (338)
Q Consensus       283 l~iDeiD~~~  292 (338)
                      |||||.-.+.
T Consensus       259 liVDEAAaIp  268 (671)
T 2zpa_A          259 LVVDEAAAIP  268 (671)
T ss_dssp             EEEETGGGSC
T ss_pred             EEEEchhcCC
Confidence            9999998775

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=91.87  E-value=0.13  Score=49.87  Aligned_cols=34  Identities=24%  Similarity=0.309  Sum_probs=27.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      ..+++.||+|+|||+++..+|..+   +..+..+++.
T Consensus        99 ~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~D  135 (425)
T 2ffh_A           99 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAAD  135 (425)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeecc
Confidence            456788999999999999999877   5566666553

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=91.84  E-value=0.077  Score=50.40  Aligned_cols=25  Identities=36%  Similarity=0.519  Sum_probs=21.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||+|+|||||+.+|+....
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            4578999999999999999997654

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=91.74  E-value=0.075  Score=45.64  Aligned_cols=23  Identities=22%  Similarity=0.364  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      --+++.|++|+|||+|+..++..
T Consensus        29 ~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           29 CKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35799999999999999999874

>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=91.72  E-value=0.069  Score=48.11  Aligned_cols=23  Identities=26%  Similarity=0.574  Sum_probs=20.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+.|.|+||+|||+|+.++...
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            45789999999999999999864

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=91.72  E-value=0.17  Score=43.98  Aligned_cols=29  Identities=31%  Similarity=0.548  Sum_probs=24.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh--CCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL--HFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l--~~~~~~l  259 (338)
                      +.|-|+.|+||||+++.++..+  +.+++..
T Consensus         5 I~~EG~dGsGKsTq~~~L~~~L~~~~~v~~~   35 (205)
T 4hlc_A            5 ITFEGPEGSGKTTVINEVYHRLVKDYDVIMT   35 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHCCCCEEEe
Confidence            5688999999999999999988  5565554

>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=91.72  E-value=0.092  Score=44.46  Aligned_cols=21  Identities=38%  Similarity=0.591  Sum_probs=19.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -++|.|+||+|||+|+..++.
T Consensus         8 kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            8 RVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            378999999999999999985

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=91.62  E-value=0.29  Score=42.08  Aligned_cols=17  Identities=29%  Similarity=0.372  Sum_probs=14.9

Q ss_pred             cCceeeeCCCCCCcHHH
Q 035959          228 KRGYLLFGPPGTGKSSL  244 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l  244 (338)
                      .+.+++.+|+|+|||..
T Consensus        51 ~~~~lv~~pTGsGKT~~   67 (224)
T 1qde_A           51 GHDVLAQAQSGTGKTGT   67 (224)
T ss_dssp             TCCEEEECCTTSSHHHH
T ss_pred             CCCEEEECCCCCcHHHH
Confidence            35789999999999976

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=91.59  E-value=0.34  Score=50.62  Aligned_cols=24  Identities=25%  Similarity=0.263  Sum_probs=18.1

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHH
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia  249 (338)
                      ..+..+|+.||+|+|||..+...+
T Consensus       387 ~~~~~~Ll~a~TGSGKTlvall~i  410 (780)
T 1gm5_A          387 EKPMNRLLQGDVGSGKTVVAQLAI  410 (780)
T ss_dssp             SSCCCCEEECCSSSSHHHHHHHHH
T ss_pred             cCCCcEEEEcCCCCCHHHHHHHHH
Confidence            334578999999999998654433

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=91.57  E-value=0.13  Score=49.79  Aligned_cols=22  Identities=32%  Similarity=0.449  Sum_probs=19.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +.|.||+|+|||||+++++...
T Consensus        72 valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           72 VAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             EEEEECTTSSHHHHHHHHHTCC
T ss_pred             EEEECCCCCcHHHHHHHHhCCC
Confidence            5699999999999999999843

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=91.57  E-value=0.095  Score=49.68  Aligned_cols=23  Identities=43%  Similarity=0.547  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -.+|+||.|+|||++..||+-.+
T Consensus        25 ~~~i~G~NGaGKTTll~ai~~al   47 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLFEAISFAL   47 (365)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            35799999999999999998554

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=91.55  E-value=0.092  Score=44.28  Aligned_cols=22  Identities=27%  Similarity=0.453  Sum_probs=19.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      --+++.|++|+|||+|+..+..
T Consensus        21 ~ki~~~G~~~~GKssl~~~l~~   42 (201)
T 2q3h_A           21 VKCVLVGDGAVGKTSLVVSYTT   42 (201)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3578999999999999999874

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=91.53  E-value=0.084  Score=44.26  Aligned_cols=23  Identities=26%  Similarity=0.385  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ..+++.|++|+|||+|+.++...
T Consensus        19 ~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           19 LKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35789999999999999999864

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=91.52  E-value=0.082  Score=45.30  Aligned_cols=23  Identities=26%  Similarity=0.444  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus        27 ~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           27 FKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35799999999999999998864

>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=91.51  E-value=0.051  Score=44.92  Aligned_cols=21  Identities=24%  Similarity=0.539  Sum_probs=18.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia  249 (338)
                      .-+++.|++|+|||+|+.++.
T Consensus        19 ~~i~v~G~~~~GKssli~~l~   39 (183)
T 1moz_A           19 LRILILGLDGAGKTTILYRLQ   39 (183)
T ss_dssp             EEEEEEEETTSSHHHHHHHTC
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            457999999999999999887

>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=91.51  E-value=0.39  Score=42.72  Aligned_cols=62  Identities=13%  Similarity=0.206  Sum_probs=35.6

Q ss_pred             eeeeCCCCCCcHHHHHHHH-HHh--CCcEEEEecCC-------cCC----------chHHHHHHHhcCCCcEEEEcCCCc
Q 035959          231 YLLFGPPGTGKSSLIAAMA-NYL--HFDVYDLELSS-------VEG----------NKHLRKVLIATENKSILVVGDIDC  290 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia-~~l--~~~~~~l~~~~-------~~~----------~~~l~~~l~~~~~~~Il~iDeiD~  290 (338)
                      .+++||.|+|||+.+.-++ ++.  |..++.+...-       +.+          ......++......++|+|||+.-
T Consensus        22 ~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D~Ryg~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvViIDEaQF  101 (234)
T 2orv_A           22 QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQF  101 (234)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCCC-----------CEEEEESSGGGGHHHHTTCSEEEESSGGG
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCCccchHHHHhhcCCeeEEEecCCHHHHHHHhccCCEEEEEchhh
Confidence            5789999999997544444 333  55666554221       000          000011233335678999999998


Q ss_pred             cC
Q 035959          291 CT  292 (338)
Q Consensus       291 ~~  292 (338)
                      +.
T Consensus       102 ~~  103 (234)
T 2orv_A          102 FP  103 (234)
T ss_dssp             CT
T ss_pred             hh
Confidence            73

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=91.50  E-value=0.073  Score=52.25  Aligned_cols=24  Identities=29%  Similarity=0.488  Sum_probs=21.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||.|+|||+|++.+++.+
T Consensus       139 e~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCcc
Confidence            347899999999999999999976

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=91.49  E-value=0.079  Score=44.23  Aligned_cols=22  Identities=14%  Similarity=0.383  Sum_probs=19.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      ..+++.|++|+|||+|+.++..
T Consensus        17 ~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           17 HKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4579999999999999999984

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=91.48  E-value=0.14  Score=47.94  Aligned_cols=23  Identities=35%  Similarity=0.585  Sum_probs=20.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.+.|+||+|||+++.+++..+
T Consensus        58 ~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           58 RLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            35789999999999999998765

>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=91.45  E-value=0.094  Score=44.86  Aligned_cols=21  Identities=24%  Similarity=0.540  Sum_probs=19.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|++|+|||+|+.++..
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~   47 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTD   47 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhc
Confidence            579999999999999999885

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=91.44  E-value=0.31  Score=41.11  Aligned_cols=57  Identities=11%  Similarity=0.159  Sum_probs=39.1

Q ss_pred             eeee-CCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC------------------chHHHHHHHhcC-CCcEEEEcC
Q 035959          231 YLLF-GPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG------------------NKHLRKVLIATE-NKSILVVGD  287 (338)
Q Consensus       231 ~LL~-GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~------------------~~~l~~~l~~~~-~~~Il~iDe  287 (338)
                      +.++ +..|+|||+++..+|..+   |..+..+|+..-.+                  ...+.+.+.... ..++++||=
T Consensus         4 i~v~s~kgG~GKTt~a~~la~~la~~g~~vlliD~D~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~yD~viiD~   83 (206)
T 4dzz_A            4 ISFLNPKGGSGKTTAVINIATALSRSGYNIAVVDTDPQMSLTNWSKAGKAAFDVFTAASEKDVYGIRKDLADYDFAIVDG   83 (206)
T ss_dssp             EEECCSSTTSSHHHHHHHHHHHHHHTTCCEEEEECCTTCHHHHHHTTSCCSSEEEECCSHHHHHTHHHHTTTSSEEEEEC
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEECCCCCCHHHHHhcCCCCCcEEecCcHHHHHHHHHhcCCCCEEEEEC
Confidence            3444 668999999999988776   78888888753221                  134555666554 468888874

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=91.40  E-value=0.087  Score=44.93  Aligned_cols=22  Identities=18%  Similarity=0.465  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      ..+++.|++|+|||+|+.++..
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~   47 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSK   47 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHhc
Confidence            4689999999999999999986

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=91.40  E-value=0.091  Score=48.43  Aligned_cols=24  Identities=33%  Similarity=0.484  Sum_probs=20.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.|.||+|+|||||+++++ ...
T Consensus       166 ~i~~l~G~sG~GKSTLln~l~-~~~  189 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSRLT-GEE  189 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH-SCC
T ss_pred             cEEEEECCCCCCHHHHHHHHH-Hhh
Confidence            446799999999999999999 654

>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=91.39  E-value=0.073  Score=49.58  Aligned_cols=24  Identities=38%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHH
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~  250 (338)
                      ..+|+||.|++|+|||+++.++..
T Consensus       146 ~g~gvli~G~sG~GKStlal~l~~  169 (312)
T 1knx_A          146 FGVGVLLTGRSGIGKSECALDLIN  169 (312)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            457899999999999999998765

>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=91.36  E-value=0.066  Score=49.29  Aligned_cols=24  Identities=29%  Similarity=0.447  Sum_probs=21.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||.|+|||+|+++++..+
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            346799999999999999999876

>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=91.35  E-value=0.047  Score=51.77  Aligned_cols=23  Identities=26%  Similarity=0.631  Sum_probs=20.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||+|+|||+|+++||...
T Consensus        33 ~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           33 RFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTSS
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            46799999999999999999876

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=91.34  E-value=0.074  Score=48.97  Aligned_cols=26  Identities=35%  Similarity=0.434  Sum_probs=22.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      .-+.|.||+|+|||||+++++.....
T Consensus       170 eiv~l~G~sG~GKSTll~~l~g~~~~  195 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAINPGLKL  195 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCCC
T ss_pred             CeEEEECCCCCcHHHHHHHhcccccc
Confidence            44679999999999999999986643

>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=91.34  E-value=0.077  Score=50.98  Aligned_cols=24  Identities=38%  Similarity=0.603  Sum_probs=21.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+.|.||+|+|||+|+++|+...
T Consensus        48 e~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           48 QRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             CEEEEECCCCChHHHHHHHHhCCC
Confidence            346799999999999999999765

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=91.33  E-value=0.33  Score=45.49  Aligned_cols=45  Identities=22%  Similarity=0.229  Sum_probs=35.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCchHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGNKHLRKVLI  275 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~~~l~~~l~  275 (338)
                      ++-+++.|..|+|||+++.++|..+   |..+..+++..   ...+...|.
T Consensus        16 ~~i~~~sgkGGvGKTt~a~~lA~~la~~g~~vllid~D~---~~~l~~~l~   63 (334)
T 3iqw_A           16 LRWIFVGGKGGVGKTTTSCSLAIQLAKVRRSVLLLSTDP---AHNLSDAFS   63 (334)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHTTSSSCEEEEECCS---SCHHHHHHT
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHhCCCcEEEEECCC---CCChhHHhc
Confidence            4566788999999999999999877   67888888773   335666664

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=91.31  E-value=0.099  Score=43.78  Aligned_cols=22  Identities=18%  Similarity=0.371  Sum_probs=19.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      .-+++.|++|+|||+|+.++..
T Consensus        18 ~ki~v~G~~~~GKSsl~~~l~~   39 (199)
T 4bas_A           18 LQVVMCGLDNSGKTTIINQVKP   39 (199)
T ss_dssp             EEEEEECCTTSCHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4589999999999999999874

>1qhl_A Protein (cell division protein MUKB); SMC, chromosome partitioning; 2.20A {Escherichia coli} SCOP: c.37.1.12

Probab=91.29  E-value=0.042  Score=48.79  Aligned_cols=23  Identities=39%  Similarity=0.445  Sum_probs=20.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.|.||+|+|||+|+.+|+..+.
T Consensus        30 ~~i~GpnGsGKSTll~~i~g~~~   52 (227)
T 1qhl_A           30 TTLSGGNGAGKSTTMAAFVTALI   52 (227)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcccc
Confidence            35789999999999999999874

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=91.27  E-value=0.087  Score=46.23  Aligned_cols=28  Identities=29%  Similarity=0.507  Sum_probs=22.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +.|.||.|+|||++++.++.. +..+...
T Consensus        23 i~i~G~~GsGKSTl~~~L~~~-~g~v~~~   50 (230)
T 2vp4_A           23 VLIEGNIGSGKTTYLNHFEKY-KNDICLL   50 (230)
T ss_dssp             EEEECSTTSCHHHHHHTTGGG-TTTEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHhc-cCCeEEE
Confidence            568999999999999999987 5455444

>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=91.25  E-value=0.098  Score=48.76  Aligned_cols=24  Identities=29%  Similarity=0.407  Sum_probs=21.7

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .+|++|.|++|+|||+++.++...
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~  167 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR  167 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc
Confidence            568999999999999999999874

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=91.25  E-value=0.096  Score=50.91  Aligned_cols=21  Identities=38%  Similarity=0.574  Sum_probs=19.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +.|.||+|+|||||+.+|+..
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            679999999999999999875

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=91.25  E-value=0.11  Score=44.97  Aligned_cols=22  Identities=32%  Similarity=0.602  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+.++...
T Consensus        15 ki~v~G~~~vGKSsli~~l~~~   36 (223)
T 3cpj_B           15 KIVLIGDSGVGKSNLLSRFTKN   36 (223)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5789999999999999999863

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=91.24  E-value=0.085  Score=44.78  Aligned_cols=22  Identities=36%  Similarity=0.661  Sum_probs=19.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      -.+++.|++|+|||+|+.++..
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~   47 (200)
T 2o52_A           26 FKFLVIGSAGTGKSCLLHQFIE   47 (200)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            3579999999999999999874

>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=91.24  E-value=0.08  Score=44.94  Aligned_cols=20  Identities=35%  Similarity=0.629  Sum_probs=18.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia  249 (338)
                      -+++.|++|+|||+|+..++
T Consensus        25 ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           25 KVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            47899999999999999985

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=91.19  E-value=0.087  Score=44.93  Aligned_cols=23  Identities=17%  Similarity=0.327  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.+++.|++|+|||+|+..+...
T Consensus        31 ~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           31 IKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHHhC
Confidence            45899999999999999998853

>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=91.17  E-value=0.078  Score=45.66  Aligned_cols=22  Identities=27%  Similarity=0.549  Sum_probs=18.6

Q ss_pred             ceeeeCCCCCCcHHHHHH-HHHH
Q 035959          230 GYLLFGPPGTGKSSLIAA-MANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~a-ia~~  251 (338)
                      -+++.|++|+|||+|+.. +.+.
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            478999999999999998 4443

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=91.14  E-value=0.094  Score=44.48  Aligned_cols=23  Identities=17%  Similarity=0.419  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.++...
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           26 KKLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45899999999999999999863

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=91.13  E-value=0.17  Score=50.28  Aligned_cols=35  Identities=20%  Similarity=0.228  Sum_probs=24.6

Q ss_pred             CceeeeCCCCCCcHHHHHH--HHHHh--CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAA--MANYL--HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~a--ia~~l--~~~~~~l~~~~  263 (338)
                      .-++|.||+|+|||+|++.  ++...  +...+.++..+
T Consensus        40 e~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~g~~   78 (525)
T 1tf7_A           40 RSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE   78 (525)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESSS
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEeC
Confidence            4578999999999999999  44433  33445555443

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=91.12  E-value=0.076  Score=44.12  Aligned_cols=22  Identities=14%  Similarity=0.383  Sum_probs=19.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      -.+++.|++|+|||+|+.++..
T Consensus        22 ~~i~v~G~~~~GKSsli~~l~~   43 (181)
T 2h17_A           22 HKVIIVGLDNAGKTTILYQFSM   43 (181)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            3579999999999999999985

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=91.02  E-value=0.074  Score=45.24  Aligned_cols=21  Identities=19%  Similarity=0.509  Sum_probs=19.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|++|+|||+|+.+++.
T Consensus        27 ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           27 KLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             EEEEEEETTSSHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999999874

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=90.97  E-value=0.1  Score=44.53  Aligned_cols=22  Identities=14%  Similarity=0.311  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+..+...
T Consensus        11 ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A           11 KCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999999853

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=90.96  E-value=0.093  Score=45.61  Aligned_cols=23  Identities=30%  Similarity=0.554  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      .-+++.|++|+|||+|+.+++..
T Consensus        30 ~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           30 KTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45799999999999999998753

>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=90.89  E-value=0.11  Score=49.47  Aligned_cols=24  Identities=33%  Similarity=0.469  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||+|+|||+|+++++....
T Consensus        56 i~~IiGpnGaGKSTLlr~i~GL~~   79 (366)
T 3tui_C           56 IYGVIGASGAGKSTLIRCVNLLER   79 (366)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEcCCCchHHHHHHHHhcCCC
Confidence            467999999999999999998763

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=90.89  E-value=0.098  Score=44.98  Aligned_cols=21  Identities=38%  Similarity=0.635  Sum_probs=19.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|++|+|||+|+.++..
T Consensus        36 ki~vvG~~~vGKSsli~~l~~   56 (214)
T 2j1l_A           36 KVVLVGDGGCGKTSLLMVFAD   56 (214)
T ss_dssp             EEEEEECTTSSHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHc
Confidence            578999999999999999874

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=90.86  E-value=0.092  Score=44.32  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=19.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      --+++.|++|+|||+|+.++..
T Consensus        30 ~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           30 MRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCS
T ss_pred             cEEEEECCCCCCHHHHHHHHHh
Confidence            3589999999999999999863

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=90.84  E-value=0.22  Score=43.94  Aligned_cols=62  Identities=15%  Similarity=0.209  Sum_probs=35.9

Q ss_pred             eeeCCCCCCcHH-HHHHHHHHh--CCcEEEEecCC--------cCC----------chHHHHHHHhc-CCCcEEEEcCCC
Q 035959          232 LLFGPPGTGKSS-LIAAMANYL--HFDVYDLELSS--------VEG----------NKHLRKVLIAT-ENKSILVVGDID  289 (338)
Q Consensus       232 LL~GppGtGKT~-l~~aia~~l--~~~~~~l~~~~--------~~~----------~~~l~~~l~~~-~~~~Il~iDeiD  289 (338)
                      +++||.|+|||+ |++.+-++.  +..++.+...-        +.+          ......++... .+..+|+|||+.
T Consensus        32 vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp~~D~R~~~~~I~Sr~G~~~~a~~v~~~~di~~~i~~~~dvV~IDEaQ  111 (219)
T 3e2i_A           32 CITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPAIDDRYHKEKVVSHNGNAIEAINISKASEIMTHDLTNVDVIGIDEVQ  111 (219)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEEC-----------CBTTBCCEEEEESSGGGGGGSCCTTCSEEEECCGG
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcCCceEEEEeccCCcchhhhHHHhcCCceeeEEeCCHHHHHHHHhcCCCEEEEechh
Confidence            689999999999 555554433  55655553321        100          01111222222 367899999999


Q ss_pred             ccCC
Q 035959          290 CCTE  293 (338)
Q Consensus       290 ~~~~  293 (338)
                      -+.+
T Consensus       112 Ff~~  115 (219)
T 3e2i_A          112 FFDD  115 (219)
T ss_dssp             GSCT
T ss_pred             cCCH
Confidence            8754

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=90.78  E-value=0.24  Score=43.44  Aligned_cols=22  Identities=18%  Similarity=0.409  Sum_probs=17.3

Q ss_pred             cCceeeeCCCCCCcHHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia  249 (338)
                      .+.+++.||+|+|||+++..+.
T Consensus        76 g~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           76 NSVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCcHHhHHHHH
Confidence            4568999999999998655443

>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=90.78  E-value=0.24  Score=41.86  Aligned_cols=24  Identities=21%  Similarity=0.232  Sum_probs=17.7

Q ss_pred             cCceeeeCCCCCCcHHH-HHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSL-IAAMANY  251 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l-~~aia~~  251 (338)
                      .+.+++.+|+|+|||.. +.++...
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~~~   62 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIAER   62 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHH
Confidence            36799999999999986 3334443

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=90.72  E-value=0.13  Score=44.31  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=19.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+..+...
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5799999999999999998864

>3qkt_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATP binding, DNA bindi MRE11, replication; HET: DNA ANP; 1.90A {Pyrococcus furiosus} PDB: 3qku_A* 1ii8_A 3qks_B* 3qkr_B* 1ii8_B

Probab=90.68  E-value=0.11  Score=48.53  Aligned_cols=22  Identities=45%  Similarity=0.640  Sum_probs=19.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .+|+||.|+|||+++.||+-.+
T Consensus        26 ~~i~G~NGsGKS~lleAi~~~l   47 (339)
T 3qkt_A           26 NLIIGQNGSGKSSLLDAILVGL   47 (339)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4799999999999999986544

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=90.65  E-value=0.24  Score=42.57  Aligned_cols=31  Identities=32%  Similarity=0.321  Sum_probs=25.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      +.|-|+.|+||||.++.+++.+   |.++....-
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~tre   36 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVILKRE   36 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEC
Confidence            3578999999999999999988   667665543

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=90.64  E-value=0.38  Score=41.22  Aligned_cols=22  Identities=18%  Similarity=0.250  Sum_probs=17.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia  249 (338)
                      .+.+++.+|+|+|||..+...+
T Consensus        51 ~~~~li~~~TGsGKT~~~~~~~   72 (220)
T 1t6n_A           51 GMDVLCQAKSGMGKTAVFVLAT   72 (220)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHH
T ss_pred             CCCEEEECCCCCchhhhhhHHH
Confidence            3568999999999998654444

---

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	338
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	1e-08
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	2e-08
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	2e-07
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	2e-06
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	2e-05
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	3e-04
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	4e-04
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	6e-04
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	8e-04
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	8e-04
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	0.001
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	0.003
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	0.003
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	0.004

>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 = 52.9 bits (127), Expect = 1e-08
 Identities = 34/149 (22%), Positives = 57/149 (38%), Gaps = 28/149 (18%)

Query: 205 TFDTLAMDTDMKKMIMD------------DLERAWKRGYLLFGPPGTGKSSLIAAMANYL 252
           TF  +A   + K+ + +             L     +G L+ GPPGTGK+ L  A+A   
Sbjct: 10  TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA 69

Query: 253 HFDVYDLELSSV------EGNKHLRKVL-IATENK-SILVVGDIDCCTELQDRSAQARTA 304
               + +  S         G   +R +   A +    I+ + +ID          + R A
Sbjct: 70  KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAV-------GRQRGA 122

Query: 305 SPDWHSPKRDQITLSGLLNFTDGLWSSCG 333
                  +R+Q TL+ +L   DG   + G
Sbjct: 123 GLGGGHDEREQ-TLNQMLVEMDGFEGNEG 150

>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 = 52.2 bits (125), Expect = 2e-08
 Identities = 33/149 (22%), Positives = 54/149 (36%), Gaps = 28/149 (18%)

Query: 205 TFDTLAMDTDMKKMIMDDLE------------RAWKRGYLLFGPPGTGKSSLIAAMANYL 252
           TF  +A   + K+ + + +E                +G LL GPPG GK+ L  A+A   
Sbjct: 7   TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA 66

Query: 253 HFDVYDLELSSV------EGNKHLRKVL-IATENK-SILVVGDIDCCTELQDRSAQARTA 304
                    S         G   +R +   A  +   I+ + +ID          + R +
Sbjct: 67  RVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAV-------GRKRGS 119

Query: 305 SPDWHSPKRDQITLSGLLNFTDGLWSSCG 333
                + +R+Q TL+ LL   DG      
Sbjct: 120 GVGGGNDEREQ-TLNQLLVEMDGFEKDTA 147

>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 = 49.7 bits (118), Expect = 2e-07
 Identities = 21/128 (16%), Positives = 43/128 (33%), Gaps = 20/128 (15%)

Query: 214 DMKKMIMDDLE-----RAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNK 268
            M  ++ D L+        KR +L  GP  +GK++L AA+         ++ L     N 
Sbjct: 135 KMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNF 194

Query: 269 HLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL 328
            L        ++ ++V  D+                         + +    L ++ DG 
Sbjct: 195 ELGV----AIDQFLVVFEDVKGTGGESRDLPSG---------QGINNL--DNLRDYLDGS 239

Query: 329 WSSCGDER 336
                +++
Sbjct: 240 VKVNLEKK 247

>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 = 46.0 bits (108), Expect = 2e-06
 Identities = 24/150 (16%), Positives = 56/150 (37%), Gaps = 29/150 (19%)

Query: 205 TFDTLAMDTDMKKMIMDDLERAWK-------------RGYLLFGPPGTGKSSLIAAMANY 251
           T++ +    D+K+ + + ++   +             +G L +GPPG GK+ L  A+AN 
Sbjct: 5   TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 64

Query: 252 LHFDVYDLELSSV------EGNKHLRKVLIATEN--KSILVVGDIDCCTELQDRSAQART 303
              +   ++   +      E   ++R++          +L   ++D         A+   
Sbjct: 65  CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSI-----AKARGGN 119

Query: 304 ASPDWHSPKRDQITLSGLLNFTDGLWSSCG 333
                 +  R    ++ +L   DG+ +   
Sbjct: 120 IGDGGGAADR---VINQILTEMDGMSTKKN 146

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

 Score = 43.4 bits (101), Expect = 2e-05
 Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 5/99 (5%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRG-----YLLFGPPGTGKSSLIAAMANYLHFDVY 257
           P + D      ++KK +   LE A  RG      LL GPPG GK++L   +A+ L  +++
Sbjct: 5   PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIH 64

Query: 258 DLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQD 296
                 +     +  +L + E   +L + +I    +  +
Sbjct: 65  VTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVE 103

>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 = 39.7 bits (91), Expect = 3e-04
 Identities = 14/51 (27%), Positives = 23/51 (45%)

Query: 220 MDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHL 270
           ++ L+       L+ G   TGKSS+I    N L+     L+L   E   ++
Sbjct: 21  IEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYI 71

>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 = 39.2 bits (90), Expect = 4e-04
 Identities = 32/131 (24%), Positives = 45/131 (34%), Gaps = 10/131 (7%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKR-----GYLLFGPPGTGKSSLIAAMANYLHFDVY 257
           P T D       +K+ +   LE A  R       LLFGPPG GK++L   +A+ L     
Sbjct: 5   PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL----- 59

Query: 258 DLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQIT 317
            + L    G    +   +A    + L  GDI    E+   S QA              I 
Sbjct: 60  GVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIV 119

Query: 318 LSGLLNFTDGL 328
           +          
Sbjct: 120 IGQGPAARTIR 130

>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 = 38.9 bits (90), Expect = 6e-04
 Identities = 14/112 (12%), Positives = 31/112 (27%), Gaps = 18/112 (16%)

Query: 225 RAWKRGYLLFGPPGTGKSSLIAAMANYLHFDV--YDLELSSV------EGNKHLRKVLIA 276
           R      ++ G   +GK+ L+ A+   L        +           + N  +  +  A
Sbjct: 120 RYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARA 179

Query: 277 TENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGL 328
                ++V+  +            A   +       R       LL+    +
Sbjct: 180 MLQHRVIVIDSL-------KNVIGAAGGNTTSGGISR---GAFDLLSDIGAM 221

>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 = 38.1 bits (87), Expect = 8e-04
 Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 227 WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV------EGNKHLRKVLIATENK 280
             RG LL+GPPGTGK+ +  A+AN      + +    +      E   +LRK     E  
Sbjct: 37  PPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKN 96

Query: 281 SILVVGDIDCCTELQDRS 298
           +  ++   +       R 
Sbjct: 97  APAIIFIDELDAIAPKRE 114

>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 = 38.0 bits (87), Expect = 8e-04
 Identities = 18/109 (16%), Positives = 27/109 (24%)

Query: 224 ERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSIL 283
           +R      LL GPP +GK++L A +A   +F    +                A +     
Sbjct: 36  DRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDD 95

Query: 284 VVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSSC 332
                  C  + D                     L  LL          
Sbjct: 96  AYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKL 144

>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 = 38.0 bits (87), Expect = 0.001
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 8/50 (16%)

Query: 212 DTDMKKMIMDDLERAWK--------RGYLLFGPPGTGKSSLIAAMANYLH 253
           D   +  + D+LE   +          +LL G PG+GK+SL +A+     
Sbjct: 8   DKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQ 57

>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 = 36.7 bits (83), Expect = 0.003
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 17/72 (23%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLE-----------------RAWKRGYLLFGPPGTGKSSLI 245
           P+    +  +      + + L                      R  +L+GPPG GK++  
Sbjct: 10  PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA 69

Query: 246 AAMANYLHFDVY 257
             +A  L +D+ 
Sbjct: 70  HLVAQELGYDIL 81

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.3 bits (82), Expect = 0.003
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 9/61 (14%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRG-----YLLFGPPGTGKSSLIAAMANYLHFDVY 257
           P + + L+ + ++       L+    +       LL+GP GTGK +   A+   +     
Sbjct: 7   PKSLNALSHNEELTNF----LKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGV 62

Query: 258 D 258
            
Sbjct: 63  Y 63

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.8 bits (81), Expect = 0.004
 Identities = 16/51 (31%), Positives = 24/51 (47%)

Query: 203 PSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH 253
           P   D +        ++   L+ A     L +GPPGTGK+S I A+   L+
Sbjct: 8   PKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELY 58

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	338
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.76
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.76
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.72
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.69
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.6
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.57
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.57
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.55
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.5
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.41
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.33
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.29
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.28
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.27
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.16
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.1
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.04
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.04
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.03
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.96
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	98.94
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.89
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.78
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.78
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.72
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	98.69
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.63
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.62
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.61
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	98.44
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.32
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.28
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	98.2
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.12
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.96
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.94
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.86
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.82
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.8
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.8
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.75
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	97.74
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.73
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.72
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.7
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.55
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.5
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.45
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.4
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.36
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.36
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	97.36
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.35
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.35
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.34
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.29
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.27
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.24
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.23
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.23
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.22
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.22
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.21
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.19
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.14
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.09
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.07
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.02
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.96
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.94
d1okkd2	207	GTPase domain of the signal recognition particle r	96.93
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.9
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.9
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.85
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.84
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.83
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.77
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.66
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.59
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.56
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.56
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.56
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	96.5
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.49
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.48
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.45
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.44
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.39
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.35
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.33
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.33
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.32
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.22
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.19
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.1
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.1
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.09
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.02
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.87
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	95.84
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.79
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.67
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.63
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	95.63
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.61
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.59
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	95.36
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.32
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.26
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.22
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.21
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	95.2
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.17
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.98
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.94
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.9
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.8
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.74
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	94.72
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.65
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	94.56
d1nrjb_	209	Signal recognition particle receptor beta-subunit	94.51
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.48
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	94.48
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.47
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	94.46
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.36
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.35
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.31
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.28
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.18
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	94.14
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	94.08
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.07
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	94.06
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	94.05
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.01
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	93.99
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.97
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.92
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.91
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.91
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.89
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	93.89
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.87
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.83
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.83
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	93.76
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	93.57
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.56
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.5
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.5
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.5
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.49
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.45
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.45
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.44
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.43
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	93.42
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.38
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.36
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.3
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.22
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	93.19
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	93.11
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.07
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	93.04
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.03
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	92.99
d2awna2	232	Maltose transport protein MalK, N-terminal domain	92.91
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.85
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	92.84
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.82
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	92.79
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.79
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	92.71
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	92.7
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	92.69
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	92.69
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	92.69
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	92.64
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	92.62
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.6
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	92.59
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.58
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.55
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	92.5
d1g2912	240	Maltose transport protein MalK, N-terminal domain	92.49
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	92.46
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	92.42
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.37
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	92.36
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.35
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.22
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	92.22
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	92.18
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	92.17
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.1
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	92.1
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	92.07
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	92.03
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	92.0
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	91.97
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	91.95
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	91.93
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	91.86
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	91.85
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.8
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	91.65
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	91.63
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	91.59
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.51
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	91.39
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.29
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	91.28
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	91.16
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	91.11
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	91.0
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	90.9
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	90.89
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	90.73
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	90.73
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	90.51
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	90.49
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	90.0
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	89.95
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	89.88
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	89.87
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	89.71
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	89.57
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.41
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	89.19
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	89.09
d1xpua3	289	Transcription termination factor Rho, ATPase domai	88.1
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	88.05
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	88.03
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	87.44
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	87.05
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	86.98
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	86.89
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	85.99
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	85.9
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	85.9
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	85.51
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	84.93
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	84.81
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	84.4
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	84.4
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	84.13
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	84.12
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	83.42
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	83.12
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	82.98
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	82.96
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	82.78
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	82.76
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	82.61
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	82.23
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	82.17
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	81.61
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	81.45
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	81.24
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	81.2
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	80.39
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	80.32

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.76  E-value=8.3e-19  Score=159.16  Aligned_cols=121  Identities=24%  Similarity=0.357  Sum_probs=97.5

Q ss_pred             CCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----  266 (338)
                      +-+|+++++.++.|+++.+.+.-            .+++|+|||||||||||++|+++|++++.+++.++++++.+    
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~l~~~~~g   87 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVG   87 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTSCCC
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHHhhhcchh
Confidence            34899999999999888664432            45688999999999999999999999999999999998763    


Q ss_pred             --chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 --NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 --~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                        +..++++|..+  .+||||+|||||.+..  +|.....      +........++.||+.|||+.+.
T Consensus        88 ~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~--~r~~~~~------~~~~~~~~~~~~ll~~~d~~~~~  148 (256)
T d1lv7a_          88 VGASRVRDMFEQAKKAAPCIIFIDEIDAVGR--QRGAGLG------GGHDEREQTLNQMLVEMDGFEGN  148 (256)
T ss_dssp             CCHHHHHHHHHHHHTTCSEEEEETTHHHHTC--CCSTTSC------CTTCHHHHHHHHHHHHHHTCCSS
T ss_pred             HHHHHHHHHHHHHHHcCCEEEEEEChhhhCc--cCCCCCC------CCcHHHHHHHHHHHHHhhCCCCC
Confidence              56788888876  4789999999999987  5544332      11334567899999999999653

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.76  E-value=3.7e-19  Score=160.72  Aligned_cols=120  Identities=24%  Similarity=0.329  Sum_probs=92.2

Q ss_pred             CCccccccCChhHHHHHHHHHHh------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----
Q 035959          203 PSTFDTLAMDTDMKKMIMDDLER------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----  266 (338)
Q Consensus       203 p~~f~~l~~~~~~k~~i~~~l~~------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----  266 (338)
                      +.+|+++++.++.|+++.+.+.-            .+++|+|||||||||||++++++|++++.+++.++++.+.+    
T Consensus         5 ~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~~~g   84 (247)
T d1ixza_           5 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVG   84 (247)
T ss_dssp             SCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHSCTT
T ss_pred             CCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhhcccc
Confidence            45999999999999877654321            45689999999999999999999999999999999988653    


Q ss_pred             --chHHHHHHHhcC--CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 --NKHLRKVLIATE--NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 --~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                        ...++++|..+.  +|+||+|||||.+..  +|.....      +.+......++.||+.|||+.+
T Consensus        85 ~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~--~r~~~~~------~~~~~~~~~~~~ll~~~d~~~~  144 (247)
T d1ixza_          85 VGAARVRDLFETAKRHAPCIVFIDEIDAVGR--KRGSGVG------GGNDEREQTLNQLLVEMDGFEK  144 (247)
T ss_dssp             HHHHHHHHHHHHHTTSSSEEEEEETHHHHHC-----------------CHHHHHHHHHHHHHHHTCCT
T ss_pred             HHHHHHHHHHHHHHHcCCEEEEEEChhhhCc--cCCCCCC------CCcHHHHHHHHHHHHHhhCCCC
Confidence              356788887764  789999999999976  5644322      1123456789999999999864

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=5.7e-18  Score=153.61  Aligned_cols=116  Identities=25%  Similarity=0.369  Sum_probs=95.9

Q ss_pred             ccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-----
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-----  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-----  266 (338)
                      +|+++++-+..|+++.+.+..             ++++|+|||||||||||++++++|++++.+++.++++.+.+     
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~~l~~~~~g~   81 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGE   81 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHHHHTTSCTTH
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEEEEEchhhccccccc
Confidence            689999999999988887543             46799999999999999999999999999999999887653     


Q ss_pred             -chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 -NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 -~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                       ...++++|..+  .+|+||+|||+|.++.  +|....         .+..+..++.+++.+|+..+.
T Consensus        82 ~~~~l~~~f~~A~~~~p~il~iDeid~l~~--~r~~~~---------~~~~~~~~~~~~~~~~~~~~~  138 (258)
T d1e32a2          82 SESNLRKAFEEAEKNAPAIIFIDELDAIAP--KREKTH---------GEVERRIVSQLLTLMDGLKQR  138 (258)
T ss_dssp             HHHHHHHHHHHHHHTCSEEEEESSGGGTCC--HHHHCC---------CTTHHHHHHHHHHHHHTCCCS
T ss_pred             HHHHHHHHHHHHHhcCCeEEEehhhhhhcc--CCCCCC---------CchHHHHHHHhcccccccccc
Confidence             45677777765  4899999999999987  664432         234577899999999998654

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=4e-18  Score=155.34  Aligned_cols=120  Identities=18%  Similarity=0.342  Sum_probs=91.4

Q ss_pred             CccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC----
Q 035959          204 STFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG----  266 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~----  266 (338)
                      .+|+++++.++.|+++.+.+..             ++++|+|||||||||||++++++|++++.+++.++++.+.+    
T Consensus         4 ~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l~~~~~~   83 (265)
T d1r7ra3           4 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFG   83 (265)
T ss_dssp             CSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHHHTSCTT
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHhhhcccc
Confidence            3899999888888888877653             34689999999999999999999999999999999877642    


Q ss_pred             --chHHHHHHHhc--CCCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          267 --NKHLRKVLIAT--ENKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       267 --~~~l~~~l~~~--~~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                        ...++.+|..+  ..||||+|||+|.++.  +|.....+      .......+++.||+.||++.+.
T Consensus        84 ~~~~~l~~~f~~A~~~~p~il~ideid~l~~--~~~~~~~~------~~~~~~~~~~~ll~~l~~~~~~  144 (265)
T d1r7ra3          84 ESEANVREIFDKARQAAPCVLFFDELDSIAK--ARGGNIGD------GGGAADRVINQILTEMDGMSTK  144 (265)
T ss_dssp             THHHHHHHHHHHHHHTCSEEEEESSGGGTCC--HHHHCCCT------THHHHHHHHHHHHHTCC-----
T ss_pred             chHHHHHHHHHHHHhcCCcceeHHhhhhccc--cCCCcCCC------CcHHHHHHHHHHHHHhhCcCCC
Confidence              35677777655  4899999999999987  55443221      1233466889999999999764

>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=99.60  E-value=9.2e-16  Score=138.00  Aligned_cols=93  Identities=23%  Similarity=0.240  Sum_probs=73.9

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC-------chHHHHHHHhcC--CCcEEEEcCCCccCCcccc
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG-------NKHLRKVLIATE--NKSILVVGDIDCCTELQDR  297 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~-------~~~l~~~l~~~~--~~~Il~iDeiD~~~~~~~r  297 (338)
                      +.+++|||||||||||++++++|++++.+++.+++++...       ...++++|..+.  +|+||+|||||.+.+  .+
T Consensus        39 p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~~~~p~il~iDEid~l~~--~~  116 (246)
T d1d2na_          39 PLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLD--YV  116 (246)
T ss_dssp             SEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTT--CB
T ss_pred             CCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccccchhhhhhhhhhhhhhcccceeehhhhhhHhh--hc
Confidence            4578999999999999999999999999999999876431       234677777663  689999999999976  33


Q ss_pred             cccccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          298 SAQARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                      ...          ....+..+..|++.||+....
T Consensus       117 ~~~----------~~~~~~~~~~ll~~l~~~~~~  140 (246)
T d1d2na_         117 PIG----------PRFSNLVLQALLVLLKKAPPQ  140 (246)
T ss_dssp             TTT----------TBCCHHHHHHHHHHTTCCCST
T ss_pred             ccc----------cchhHHHHHHHHHHhcCCCcc
Confidence            221          223468889999999998654

>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=99.57  E-value=4.3e-15  Score=131.60  Aligned_cols=93  Identities=24%  Similarity=0.330  Sum_probs=83.2

Q ss_pred             CCCCccccccCChhHHHHHHHHHHhh-----hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHH
Q 035959          201 DHPSTFDTLAMDTDMKKMIMDDLERA-----WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLI  275 (338)
Q Consensus       201 ~~p~~f~~l~~~~~~k~~i~~~l~~~-----~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~  275 (338)
                      -+|.+|+++++.+++++.+...+..+     ...++|||||||||||++|+++|++++.+++.++........++...+.
T Consensus         3 ~RP~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (238)
T d1in4a2           3 LRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILT   82 (238)
T ss_dssp             TSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCcccccHHHHHHHHH
Confidence            35889999999999999998888753     2457999999999999999999999999999999999888888888888


Q ss_pred             hcCCCcEEEEcCCCccCC
Q 035959          276 ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 ~~~~~~Il~iDeiD~~~~  293 (338)
                      .....++++|||+|.+..
T Consensus        83 ~~~~~~~~~ide~~~~~~  100 (238)
T d1in4a2          83 SLERGDVLFIDEIHRLNK  100 (238)
T ss_dssp             HCCTTCEEEEETGGGCCH
T ss_pred             hhccCCchHHHHHHHhhh
Confidence            888999999999999864

>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=99.57  E-value=3.7e-16  Score=145.31  Aligned_cols=93  Identities=14%  Similarity=0.164  Sum_probs=72.0

Q ss_pred             Cce-eeeCCCCCCcHHHHHHHHHHhC--CcEEEEecCCcCC------chHHHHHHHhcCCCcEEEEcCCCccCCcccccc
Q 035959          229 RGY-LLFGPPGTGKSSLIAAMANYLH--FDVYDLELSSVEG------NKHLRKVLIATENKSILVVGDIDCCTELQDRSA  299 (338)
Q Consensus       229 ~g~-LL~GppGtGKT~l~~aia~~l~--~~~~~l~~~~~~~------~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~  299 (338)
                      +|. ||+||||||||.+++|+|.+++  .+++.++.+++.+      +..++.+|..+..++||||||||.+..  .|.+
T Consensus       123 ~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~~~ilf~DEid~~~~--~r~~  200 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIG--AAGG  200 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEECCTTTC-------
T ss_pred             CceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhhccEEEeehhhhhcc--cccc
Confidence            565 5699999999999999999986  6788999999874      567899999888899999999999988  6644


Q ss_pred             cccCCCCCCCCCCcchhhHHHHHHHhcCCcCC
Q 035959          300 QARTASPDWHSPKRDQITLSGLLNFTDGLWSS  331 (338)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s~  331 (338)
                      ...        .....+++++||+.|||+.+.
T Consensus       201 ~~~--------~~~~~r~v~~lL~e~dg~~~~  224 (321)
T d1w44a_         201 NTT--------SGGISRGAFDLLSDIGAMAAS  224 (321)
T ss_dssp             --------------CCHHHHHHHHHHHHHHHH
T ss_pred             CCC--------CCcchhhhhhhhhhccccccC
Confidence            322        233457999999999998754

>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=99.55  E-value=5.9e-15  Score=136.84  Aligned_cols=112  Identities=16%  Similarity=0.259  Sum_probs=83.4

Q ss_pred             ccCChhHHHHHHHHHHh--------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--------
Q 035959          209 LAMDTDMKKMIMDDLER--------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--------  266 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~--------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--------  266 (338)
                      ++++++.++.+...+..              ..++|+||+||||||||.||+|+|+.++.+++.++++++..        
T Consensus        16 ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~~   95 (309)
T d1ofha_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEV   95 (309)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGST
T ss_pred             ccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEeeec
Confidence            57888888877665521              14589999999999999999999999999999999988752        


Q ss_pred             chHHHHHHHhcC-------CCcEEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCcC
Q 035959          267 NKHLRKVLIATE-------NKSILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLWS  330 (338)
Q Consensus       267 ~~~l~~~l~~~~-------~~~Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~s  330 (338)
                      ...++.++..+.       +++||||||||.+.+  .+.+...        +......++.||..+||.-.
T Consensus        96 ~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~--~~~~~~~--------~~~~~gv~~~LL~~~dg~~~  156 (309)
T d1ofha_          96 DSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICK--KGEYSGA--------DVSREGVQRDLLPLVEGSTV  156 (309)
T ss_dssp             THHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSC--CSSCCSS--------HHHHHHHHHHHHHHHHCCEE
T ss_pred             cccccccchhhhcccccccCCceEEehhhhhhhh--hccCccc--------chhhhHHHHHhhHHhcCCEE
Confidence            345667766653       379999999999986  4322211        01123367889999999643

>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=99.50  E-value=4.1e-14  Score=125.37  Aligned_cols=92  Identities=28%  Similarity=0.400  Sum_probs=76.7

Q ss_pred             CCCccccccCChhHHHHHHHHHHhh-----hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHh
Q 035959          202 HPSTFDTLAMDTDMKKMIMDDLERA-----WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIA  276 (338)
Q Consensus       202 ~p~~f~~l~~~~~~k~~i~~~l~~~-----~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~  276 (338)
                      +|.+|+++++.++.++.+...+...     ...++|||||||||||++|+++|+++++++..++.+...........+..
T Consensus         4 RP~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (239)
T d1ixsb2           4 RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILAN   83 (239)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSHHHHHHHHHT
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccchhhHHHHHh
Confidence            5889999999999999888777652     34689999999999999999999999999999999887765555544444


Q ss_pred             c-CCCcEEEEcCCCccCC
Q 035959          277 T-ENKSILVVGDIDCCTE  293 (338)
Q Consensus       277 ~-~~~~Il~iDeiD~~~~  293 (338)
                      . ...+|++|||+|.+..
T Consensus        84 ~~~~~~i~~iDe~~~~~~  101 (239)
T d1ixsb2          84 SLEEGDILFIDEIHRLSR  101 (239)
T ss_dssp             TCCTTCEEEEETGGGCCH
T ss_pred             hccCCCeeeeecccccch
Confidence            4 3678999999999854

>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=99.41  E-value=2.6e-13  Score=120.57  Aligned_cols=98  Identities=17%  Similarity=0.303  Sum_probs=79.4

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHh-----------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcE
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLER-----------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDV  256 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~-----------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~  256 (338)
                      .|..  .+.|.+|++++++++.++++.+.+..                 ...+++|||||||||||++|+++|++++.++
T Consensus         3 lW~e--ky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~   80 (253)
T d1sxja2           3 LWTV--KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI   80 (253)
T ss_dssp             CHHH--HTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEE
T ss_pred             cccc--CcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhh
Confidence            4653  58899999999999999999888764                 2345799999999999999999999999999


Q ss_pred             EEEecCCcCCchHHHHHHHhc--------------------CCCcEEEEcCCCccCC
Q 035959          257 YDLELSSVEGNKHLRKVLIAT--------------------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       257 ~~l~~~~~~~~~~l~~~l~~~--------------------~~~~Il~iDeiD~~~~  293 (338)
                      +.+++++..+...+...+...                    ....++++||+|.+..
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~  137 (253)
T d1sxja2          81 LEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSG  137 (253)
T ss_dssp             EEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCT
T ss_pred             hccccccchhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeecccccc
Confidence            999999887655554433211                    1467999999999865

>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=99.33  E-value=1e-12  Score=115.60  Aligned_cols=99  Identities=20%  Similarity=0.294  Sum_probs=77.6

Q ss_pred             CccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCcCCc
Q 035959          193 DTRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSVEGN  267 (338)
Q Consensus       193 ~~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~~~~  267 (338)
                      ..|.  ..+.|.+|++++++++.++.+...+.......+||+||||||||++|+++|++++     .+++.+++++....
T Consensus        12 ~~w~--~ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~~~~   89 (231)
T d1iqpa2          12 KPWV--EKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGI   89 (231)
T ss_dssp             SCHH--HHTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHH
T ss_pred             chHH--HHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCcccch
Confidence            3574  4788999999999999999999999876666799999999999999999999874     57888888765433


Q ss_pred             hHHHHHHHhc--------CCCcEEEEcCCCccCC
Q 035959          268 KHLRKVLIAT--------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l~~~--------~~~~Il~iDeiD~~~~  293 (338)
                      ..++......        ..+.|+++||+|.+..
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~  123 (231)
T d1iqpa2          90 NVIREKVKEFARTKPIGGASFKIIFLDEADALTQ  123 (231)
T ss_dssp             HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH
T ss_pred             hHHHHHHHHHHhhhhccCCCceEEeehhhhhcch
Confidence            2222222221        3678999999998865

>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=99.29  E-value=5e-12  Score=110.64  Aligned_cols=98  Identities=23%  Similarity=0.334  Sum_probs=73.2

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCC-----cEEEEecCCcCCch
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHF-----DVYDLELSSVEGNK  268 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~-----~~~~l~~~~~~~~~  268 (338)
                      .|.  ..+.|.+|++++++++.++.+...+.......+|||||||||||++++++|++++.     .++..+.++.....
T Consensus         3 pw~--ekyrP~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~   80 (227)
T d1sxjc2           3 PWV--EKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGID   80 (227)
T ss_dssp             CHH--HHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHH
T ss_pred             chh--hhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCee
Confidence            354  36789999999999999999999888755557999999999999999999998752     36677766655433


Q ss_pred             HHHHHHH---hc-----CCCcEEEEcCCCccCC
Q 035959          269 HLRKVLI---AT-----ENKSILVVGDIDCCTE  293 (338)
Q Consensus       269 ~l~~~l~---~~-----~~~~Il~iDeiD~~~~  293 (338)
                      .......   ..     ....+++|||+|.+..
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~  113 (227)
T d1sxjc2          81 VVRNQIKDFASTRQIFSKGFKLIILDEADAMTN  113 (227)
T ss_dssp             HHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH
T ss_pred             eeecchhhccccccccCCCeEEEEEeccccchh
Confidence            2222211   11     2456999999999864

>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=99.28  E-value=3.3e-12  Score=111.85  Aligned_cols=98  Identities=16%  Similarity=0.228  Sum_probs=78.3

Q ss_pred             ccccccCCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCcCCch
Q 035959          194 TRQSAILDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSVEGNK  268 (338)
Q Consensus       194 ~w~~~~~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~~~~~  268 (338)
                      .|..  .+.|.+|++++++++.++.+...+.......+|||||||||||++|+++|++++     .+++.++.++.....
T Consensus         4 pw~e--KyrP~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~   81 (224)
T d1sxjb2           4 PWVE--KYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGID   81 (224)
T ss_dssp             CHHH--HTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHH
T ss_pred             chHh--HhCCCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCce
Confidence            4653  689999999999999999999988875555799999999999999999999885     458889888877655


Q ss_pred             HHHHHHHhc---------CCCcEEEEcCCCccCC
Q 035959          269 HLRKVLIAT---------ENKSILVVGDIDCCTE  293 (338)
Q Consensus       269 ~l~~~l~~~---------~~~~Il~iDeiD~~~~  293 (338)
                      .+...+...         ....+++|||+|.+..
T Consensus        82 ~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~  115 (224)
T d1sxjb2          82 VVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA  115 (224)
T ss_dssp             HHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH
T ss_pred             ehhhHHHHHHHhhccCCCcceEEEEEecccccch
Confidence            444333321         2457999999999975

>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=99.27  E-value=9.8e-12  Score=110.26  Aligned_cols=94  Identities=18%  Similarity=0.320  Sum_probs=75.7

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhh-cCceeeeCCCCCCcHHHHHHHHHHhCC------------------------
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAW-KRGYLLFGPPGTGKSSLIAAMANYLHF------------------------  254 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~-~~g~LL~GppGtGKT~l~~aia~~l~~------------------------  254 (338)
                      .++|.+|++++++++.++.+...+.... ++.+|||||||||||++|.++++.++.                        
T Consensus         5 KyrP~~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~   84 (239)
T d1njfa_           5 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFV   84 (239)
T ss_dssp             HTCCSSGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCT
T ss_pred             hhCCCCHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCC
Confidence            4679999999999999999988887633 456999999999999999999998742                        


Q ss_pred             cEEEEecCCcCCchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          255 DVYDLELSSVEGNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       255 ~~~~l~~~~~~~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      +++.++.++......++.++....      ...|+||||+|.+..
T Consensus        85 ~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~  129 (239)
T d1njfa_          85 DLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR  129 (239)
T ss_dssp             TEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCH
T ss_pred             eEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCH
Confidence            467777766555666777777663      346999999999853

>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=99.16  E-value=2.7e-11  Score=106.09  Aligned_cols=94  Identities=24%  Similarity=0.387  Sum_probs=71.6

Q ss_pred             CCCCCccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh------CCcEEEEecCCcCCchHHHHH
Q 035959          200 LDHPSTFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL------HFDVYDLELSSVEGNKHLRKV  273 (338)
Q Consensus       200 ~~~p~~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l------~~~~~~l~~~~~~~~~~l~~~  273 (338)
                      .+.|.+|+++++.++.++.+...+.......+||+||||||||++++++|+++      ....+.++.+...........
T Consensus         5 ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (237)
T d1sxjd2           5 KYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREK   84 (237)
T ss_dssp             HTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTH
T ss_pred             hhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHH
Confidence            57899999999999999998888876555669999999999999999999986      567778877666543222111


Q ss_pred             HHh----------------c--CCCcEEEEcCCCccCC
Q 035959          274 LIA----------------T--ENKSILVVGDIDCCTE  293 (338)
Q Consensus       274 l~~----------------~--~~~~Il~iDeiD~~~~  293 (338)
                      +..                .  .+..++||||+|.+..
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~  122 (237)
T d1sxjd2          85 VKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA  122 (237)
T ss_dssp             HHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH
T ss_pred             HHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCH
Confidence            111                1  1345999999999864

>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=99.10  E-value=4.6e-11  Score=112.59  Aligned_cols=94  Identities=20%  Similarity=0.205  Sum_probs=69.1

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCccCCcccccccccCCC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDCCTELQDRSAQARTAS  305 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~~~~~~~r~~~~~~~~  305 (338)
                      |.++++|||||||||||+++.++|++++.+++.+++++..+..    .+.......+.++||++....  .+....    
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~----~l~~~~~~~~~l~d~~~~~~~--~~~~~~----  221 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNF----ELGVAIDQFLVVFEDVKGTGG--ESRDLP----  221 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHH----HHGGGTTCSCEEETTCCCSTT--TTTTCC----
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHH----HHHhHHHHHHHHHHHHHHhhh--hccCCC----
Confidence            7778999999999999999999999999999999988765322    234455778889999998876  222211    


Q ss_pred             CCCCCCCcchhhHHHHHHHhcCCcCCCCC
Q 035959          306 PDWHSPKRDQITLSGLLNFTDGLWSSCGD  334 (338)
Q Consensus       306 ~~~~~~~~~~~~ls~lLn~iDgl~s~~g~  334 (338)
                           ....-..+.+|.+.+||-.+.+.+
T Consensus       222 -----~~~~~DeiD~l~~~~dg~~~~~~~  245 (362)
T d1svma_         222 -----SGQGINNLDNLRDYLDGSVKVNLE  245 (362)
T ss_dssp             -----CCSHHHHHHTTHHHHHCSSCEEEC
T ss_pred             -----CeEEEehHhhcccccCCcchhhhh
Confidence                 122234566788888887655444

>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=99.04  E-value=1.6e-10  Score=100.96  Aligned_cols=92  Identities=15%  Similarity=0.257  Sum_probs=61.4

Q ss_pred             CCCccccccCChhH---HHHHHHHHHhh--hcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC-------
Q 035959          202 HPSTFDTLAMDTDM---KKMIMDDLERA--WKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG-------  266 (338)
Q Consensus       202 ~p~~f~~l~~~~~~---k~~i~~~l~~~--~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~-------  266 (338)
                      +..+|++++..+.-   .+.+.+.++.+  ..+.++||||||||||||++|+|+++   +..+++++..+...       
T Consensus         5 ~~~tFdnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (213)
T d1l8qa2           5 PKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLK   84 (213)
T ss_dssp             TTCCSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHH
T ss_pred             CCCChhhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHHHHHHHHHHH
Confidence            44589997654321   22223333322  22458999999999999999999988   56777887765432       


Q ss_pred             chHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                      ..............++|+|||||.+..
T Consensus        85 ~~~~~~~~~~~~~~dll~iDDi~~i~~  111 (213)
T d1l8qa2          85 KGTINEFRNMYKSVDLLLLDDVQFLSG  111 (213)
T ss_dssp             HTCHHHHHHHHHTCSEEEEECGGGGTT
T ss_pred             ccchhhHHHHHhhccchhhhhhhhhcC
Confidence            112334444455789999999999976

>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=99.04  E-value=5e-10  Score=100.98  Aligned_cols=89  Identities=25%  Similarity=0.372  Sum_probs=71.7

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC--------
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG--------  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~--------  266 (338)
                      .++.+++.++.-+++++-|.+..+++.||.||||+|||+++..+|..+          +..++.++++.+.+        
T Consensus        16 ~ld~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~   95 (268)
T d1r6bx2          16 GIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDF   95 (268)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCH
T ss_pred             CCCcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhH
Confidence            355678888888889999988888999999999999999999999864          56799999988774        


Q ss_pred             chHHHHHHHhcC--CCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIATE--NKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~~--~~~Il~iDeiD~~~~  293 (338)
                      +..+..++..+.  .+.||||||++.++.
T Consensus        96 e~r~~~i~~~~~~~~~iIlfiDeih~l~~  124 (268)
T d1r6bx2          96 EKRFKALLKQLEQDTNSILFIDEIHTIIG  124 (268)
T ss_dssp             HHHHHHHHHHHSSSSCEEEEETTTTTTTT
T ss_pred             HHHHHHHHHHhhccCCceEEecchHHHhc
Confidence            345667777764  568999999999987

>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=99.03  E-value=1.1e-10  Score=100.36  Aligned_cols=89  Identities=21%  Similarity=0.388  Sum_probs=72.8

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC--------
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG--------  266 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~--------  266 (338)
                      .++.+++.++..+++++-|.+..+.+++|.||||+|||+++..+|..+          +..++.++++.+.+        
T Consensus        20 ~ld~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~   99 (195)
T d1jbka_          20 KLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEF   99 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHH
T ss_pred             CCCCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHH
Confidence            345677888888889999988888899999999999999999999865          57899999988763        


Q ss_pred             chHHHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          267 NKHLRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       267 ~~~l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                      +..+..++.++   ..+.||||||++.+..
T Consensus       100 E~rl~~il~e~~~~~~~iILfIDeih~l~~  129 (195)
T d1jbka_         100 EERLKGVLNDLAKQEGNVILFIDELHTMVG  129 (195)
T ss_dssp             HHHHHHHHHHHHHSTTTEEEEEETGGGGTT
T ss_pred             HHHHHHHHHHHhcCCCcEEEEcchHHHHhc
Confidence            34566677665   2467999999999986

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.96  E-value=2.8e-10  Score=100.32  Aligned_cols=54  Identities=20%  Similarity=0.367  Sum_probs=45.4

Q ss_pred             cCCCCCccccccCChhHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          199 ILDHPSTFDTLAMDTDMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       199 ~~~~p~~f~~l~~~~~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ..+.|.+|+++++.++.++.+...+... ...++|||||||||||++|+++|+++
T Consensus         3 eky~P~~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2           3 DKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             TTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             cccCCCCHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            4678999999999998888777666542 23468999999999999999999986

>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=98.94  E-value=2.2e-09  Score=100.94  Aligned_cols=93  Identities=24%  Similarity=0.398  Sum_probs=65.6

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC--------chHHHHHHHhcC------CCcEEEEcCCCccC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG--------NKHLRKVLIATE------NKSILVVGDIDCCT  292 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~--------~~~l~~~l~~~~------~~~Il~iDeiD~~~  292 (338)
                      .+..+||.||+|||||.|++++|..++.+++.++++....        ...+.+++....      +.+|+++||+|.+.
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            3567999999999999999999999999999999998774        455667665543      67999999999987


Q ss_pred             CcccccccccCCCCCCCCCCcchhhHHHHHHHhcC
Q 035959          293 ELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDG  327 (338)
Q Consensus       293 ~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDg  327 (338)
                      +........        .+....-....||+.+||
T Consensus       147 ~~s~~~~~~--------~d~a~~~V~~~lLqild~  173 (364)
T d1um8a_         147 RLSENRSIT--------RDVSGEGVQQALLKIVEG  173 (364)
T ss_dssp             ---------------------CHHHHHHHHHHHHC
T ss_pred             ccccccccc--------ccccchHHHHhhhhhhcC
Confidence            621111100        011224577889999996

>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=98.89  E-value=2.3e-09  Score=98.85  Aligned_cols=85  Identities=13%  Similarity=0.291  Sum_probs=64.5

Q ss_pred             cccCChhHHHHHHHHHHh--------hhcC-ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCc-----------
Q 035959          208 TLAMDTDMKKMIMDDLER--------AWKR-GYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGN-----------  267 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~--------~~~~-g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~-----------  267 (338)
                      .++++++.++.+...+..        ..+. .+||.||||+|||.||+++|..++.+++.+++++....           
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~~l~g~~~  102 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPP  102 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSCCCCS
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhhhhcccCC
Confidence            467888888888777754        1123 47899999999999999999999999999999886531           


Q ss_pred             --------hHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 --------KHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 --------~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                              ..+...+ ...+.+|+++||||.+.+
T Consensus       103 gy~g~~~~~~l~~~~-~~~~~~vvl~DeieKa~~  135 (315)
T d1r6bx3         103 GYVGFDQGGLLTDAV-IKHPHAVLLLDEIEKAHP  135 (315)
T ss_dssp             CSHHHHHTTHHHHHH-HHCSSEEEEEETGGGSCH
T ss_pred             CccccccCChhhHHH-HhCccchhhhcccccccc
Confidence                    1123333 235679999999999864

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.78  E-value=3.2e-09  Score=100.51  Aligned_cols=88  Identities=19%  Similarity=0.385  Sum_probs=64.3

Q ss_pred             cccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh----------CCcEEEEecCCcCC--------c
Q 035959          206 FDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL----------HFDVYDLELSSVEG--------N  267 (338)
Q Consensus       206 f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l----------~~~~~~l~~~~~~~--------~  267 (338)
                      ++.+++.+...+++++-|.+..+.+.+|.||||+|||.++..+|..+          +..++.++++.+..        +
T Consensus        21 ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e  100 (387)
T d1qvra2          21 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFE  100 (387)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHH
T ss_pred             CCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHH
Confidence            56678888888999999998888899999999999999999999865          46799999998874        3


Q ss_pred             hHHHHHHHhc---CCCcEEEEcCCCccCC
Q 035959          268 KHLRKVLIAT---ENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ~~l~~~l~~~---~~~~Il~iDeiD~~~~  293 (338)
                      ..+..++..+   ..+.||||||+|.++.
T Consensus       101 ~r~~~i~~~~~~~~~~~ilfide~h~l~~  129 (387)
T d1qvra2         101 ERLKAVIQEVVQSQGEVILFIDELHTVVG  129 (387)
T ss_dssp             HHHHHHHHHHHTTCSSEEEEECCC-----
T ss_pred             HHHHHHHHHhccCCCceEEEeccHHHHhc
Confidence            3556666655   2467899999999987

>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=98.78  E-value=9e-09  Score=94.77  Aligned_cols=85  Identities=18%  Similarity=0.359  Sum_probs=62.9

Q ss_pred             cccCChhHHHHHHHHHHhh--------hcC-ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCCc--------
Q 035959          208 TLAMDTDMKKMIMDDLERA--------WKR-GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEGN--------  267 (338)
Q Consensus       208 ~l~~~~~~k~~i~~~l~~~--------~~~-g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~~--------  267 (338)
                      .++++++.++.+...+...        .+. .+||+||||||||.+|+++|..+   +.+++.+++++....        
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~~~~L~g  103 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIG  103 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC--
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchhhhhhcC
Confidence            4577888888777766651        123 36889999999999999999998   678999999877642        


Q ss_pred             -----------hHHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 -----------KHLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 -----------~~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                 ..|...+.. .+.+||++||||.+.+
T Consensus       104 ~~~gyvG~~~~~~l~~~~~~-~p~~Vvl~DEieK~~~  139 (315)
T d1qvra3         104 APPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKAHP  139 (315)
T ss_dssp             ------------CHHHHHHH-CSSEEEEESSGGGSCH
T ss_pred             CCCCCcCcccCChHHHHHHh-CCCcEEEEehHhhcCH
Confidence                       124444443 3579999999999864

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.72  E-value=2.8e-09  Score=94.39  Aligned_cols=40  Identities=28%  Similarity=0.384  Sum_probs=35.6

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVE  265 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~  265 (338)
                      ..++++||+||||||||++|+++|++++.+++.++.+++.
T Consensus        30 ~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~~   69 (273)
T d1gvnb_          30 ESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFK   69 (273)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHHH
Confidence            4567899999999999999999999999999999886653

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=98.69  E-value=2.5e-08  Score=91.93  Aligned_cols=48  Identities=33%  Similarity=0.471  Sum_probs=40.5

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +|.++++.+..|+.+.-.+..+...++||.||||||||+++++++.-+
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~iL   52 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALL   52 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             ChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHHhC
Confidence            799999999999877655543445679999999999999999999866

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.63  E-value=2.9e-08  Score=87.65  Aligned_cols=87  Identities=10%  Similarity=0.064  Sum_probs=56.8

Q ss_pred             ccccCChhHHHHHHHHHHhhh-----c----CceeeeCCCCCCcHHHHHHHHHHhC---------CcEEEEecCCcCCc-
Q 035959          207 DTLAMDTDMKKMIMDDLERAW-----K----RGYLLFGPPGTGKSSLIAAMANYLH---------FDVYDLELSSVEGN-  267 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~~~-----~----~g~LL~GppGtGKT~l~~aia~~l~---------~~~~~l~~~~~~~~-  267 (338)
                      +++.+.+...+++.+.+....     +    ..++|+||||||||++++++++.+.         ..+..+++...... 
T Consensus        16 ~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   95 (287)
T d1w5sa2          16 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY   95 (287)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchh
Confidence            566676667777777665411     1    1367899999999999999999873         34455555544321 


Q ss_pred             ---------------------hH----HHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 ---------------------KH----LRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 ---------------------~~----l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                           ..    +...........++++||+|.+..
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~  146 (287)
T d1w5sa2          96 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLS  146 (287)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHS
T ss_pred             hHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEecc
Confidence                                 11    122222334678899999999976

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.62  E-value=8.8e-08  Score=82.54  Aligned_cols=80  Identities=23%  Similarity=0.302  Sum_probs=55.2

Q ss_pred             hHHHHHHHHHHhh-hcCceeeeCCCCCCcHHHHHHHHHHhC------------------------CcEEEEecCCcC---
Q 035959          214 DMKKMIMDDLERA-WKRGYLLFGPPGTGKSSLIAAMANYLH------------------------FDVYDLELSSVE---  265 (338)
Q Consensus       214 ~~k~~i~~~l~~~-~~~g~LL~GppGtGKT~l~~aia~~l~------------------------~~~~~l~~~~~~---  265 (338)
                      +..+++.+.+... .+.++||+||||+|||+++.++|+.+.                        .+++.+....-.   
T Consensus         9 ~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i   88 (207)
T d1a5ta2           9 PDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTL   88 (207)
T ss_dssp             HHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSB
T ss_pred             HHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhccccc
Confidence            3455666666653 356799999999999999999999762                        345555433222   


Q ss_pred             CchHHHHHHHhcC------CCcEEEEcCCCccCC
Q 035959          266 GNKHLRKVLIATE------NKSILVVGDIDCCTE  293 (338)
Q Consensus       266 ~~~~l~~~l~~~~------~~~Il~iDeiD~~~~  293 (338)
                      ....++.+.....      ...|++|||+|.+..
T Consensus        89 ~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~  122 (207)
T d1a5ta2          89 GVDAVREVTEKLNEHARLGGAKVVWVTDAALLTD  122 (207)
T ss_dssp             CHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCH
T ss_pred             ccchhhHHhhhhhhccccCccceEEechhhhhhh
Confidence            2345666666543      466999999999965

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.61  E-value=1.2e-07  Score=83.15  Aligned_cols=87  Identities=16%  Similarity=0.065  Sum_probs=60.0

Q ss_pred             ccccCChhHHHHHHHHHHh------hhcCceeeeCCCCCCcHHHHHHHHHHhC----CcEEEEecCCcCCc---------
Q 035959          207 DTLAMDTDMKKMIMDDLER------AWKRGYLLFGPPGTGKSSLIAAMANYLH----FDVYDLELSSVEGN---------  267 (338)
Q Consensus       207 ~~l~~~~~~k~~i~~~l~~------~~~~g~LL~GppGtGKT~l~~aia~~l~----~~~~~l~~~~~~~~---------  267 (338)
                      +++++.+...+.+.+.|..      ..++++||+||||||||++++++++.+.    ..++.+++......         
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIAR   95 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhhhhhhhhhHH
Confidence            5667877777777777765      1236799999999999999999999883    45666666543321         


Q ss_pred             -------------h----HHHHHHHhcCCCcEEEEcCCCccCC
Q 035959          268 -------------K----HLRKVLIATENKSILVVGDIDCCTE  293 (338)
Q Consensus       268 -------------~----~l~~~l~~~~~~~Il~iDeiD~~~~  293 (338)
                                   .    .+.+.+.......++++|++|.+..
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~  138 (276)
T d1fnna2          96 SLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAP  138 (276)
T ss_dssp             HTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCH
T ss_pred             hhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhh
Confidence                         1    1222223334678888999998764

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.44  E-value=4.4e-07  Score=80.31  Aligned_cols=85  Identities=13%  Similarity=0.196  Sum_probs=61.7

Q ss_pred             ccCChhHHHHHHHHHHh--hhcCceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecCCcCCchHHHHHHH--------
Q 035959          209 LAMDTDMKKMIMDDLER--AWKRGYLLFGPPGTGKSSLIAAMANYLH---FDVYDLELSSVEGNKHLRKVLI--------  275 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~--~~~~g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~~~~~~~~l~~~l~--------  275 (338)
                      +++..+.-+++++.+..  ..+..+||+||+||||+.+|++++....   .+++.+++..+........+|.        
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~lfg~~~~~~~~   81 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTG   81 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHHCBCTTSSTT
T ss_pred             eEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHHhcCcccCCcCC
Confidence            46666677778888877  3456799999999999999999998763   4688888887754332233321        


Q ss_pred             ---------hcCCCcEEEEcCCCccCC
Q 035959          276 ---------ATENKSILVVGDIDCCTE  293 (338)
Q Consensus       276 ---------~~~~~~Il~iDeiD~~~~  293 (338)
                               +..+...|+|||||.+..
T Consensus        82 ~~~~~~g~l~~a~gGtL~l~~i~~L~~  108 (247)
T d1ny5a2          82 AVSSKEGFFELADGGTLFLDEIGELSL  108 (247)
T ss_dssp             CCSCBCCHHHHTTTSEEEEESGGGCCH
T ss_pred             cccccCCHHHccCCCEEEEeChHhCCH
Confidence                     112456899999999964

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=98.32  E-value=5.3e-07  Score=86.36  Aligned_cols=58  Identities=19%  Similarity=0.343  Sum_probs=46.3

Q ss_pred             ccCChhHHHHHHHHHHh--------------hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC
Q 035959          209 LAMDTDMKKMIMDDLER--------------AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG  266 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~--------------~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~  266 (338)
                      ++++++.|+.+--.+-.              ..|.++||.||||||||.||+++|..++.|++.++++.+..
T Consensus        16 VvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fTe   87 (443)
T d1g41a_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE   87 (443)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC-
T ss_pred             ccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceeee
Confidence            46667766655444432              23679999999999999999999999999999999998873

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.28  E-value=1.6e-06  Score=75.53  Aligned_cols=56  Identities=21%  Similarity=0.134  Sum_probs=45.1

Q ss_pred             ccccccCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCc
Q 035959          205 TFDTLAMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSV  264 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~  264 (338)
                      .-+.+++.+...+++.    ...++.++++||+|+|||+|+..+++.++..+..+++...
T Consensus        10 ~~~~f~GR~~el~~l~----~~~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~   65 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLK----GLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKF   65 (283)
T ss_dssp             SGGGSCCCHHHHHHHH----HTCSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             ChhhCCChHHHHHHHH----hccCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccc
Confidence            4578888876555544    4556889999999999999999999999998888876544

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.20  E-value=1.9e-06  Score=73.52  Aligned_cols=68  Identities=15%  Similarity=0.190  Sum_probs=51.6

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhC------CcEEEEecCCc-CCchHHHHHHHhcC------CCcEEEEcCCCccC
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLH------FDVYDLELSSV-EGNKHLRKVLIATE------NKSILVVGDIDCCT  292 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~------~~~~~l~~~~~-~~~~~l~~~l~~~~------~~~Il~iDeiD~~~  292 (338)
                      .....+||+||||||||++|.++++...      .+++.+....- ...++++.+...+.      ..-|++|||+|.+.
T Consensus        13 ~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~   92 (198)
T d2gnoa2          13 SEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMT   92 (198)
T ss_dssp             CSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBC
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCccccc
Confidence            3445799999999999999999999873      36888876432 24566777665542      45699999999995


Q ss_pred             C
Q 035959          293 E  293 (338)
Q Consensus       293 ~  293 (338)
                      .
T Consensus        93 ~   93 (198)
T d2gnoa2          93 Q   93 (198)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=98.12  E-value=8e-07  Score=71.27  Aligned_cols=33  Identities=39%  Similarity=0.713  Sum_probs=29.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ++.++|.|||||||||+++++|..+++++++.+
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            467899999999999999999999999987553

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=97.96  E-value=1.5e-06  Score=70.70  Aligned_cols=30  Identities=30%  Similarity=0.484  Sum_probs=27.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .++|.|||||||||+++++|..++++++.+
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            478999999999999999999999988754

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.94  E-value=1.7e-06  Score=70.71  Aligned_cols=33  Identities=18%  Similarity=0.188  Sum_probs=28.8

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      .+.+++.||||||||||++++|+.++.+++..+
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~   39 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFNTTSAWEY   39 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCEEECCT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCCeEeee
Confidence            367899999999999999999999998876543

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=97.86  E-value=3.1e-06  Score=69.33  Aligned_cols=31  Identities=32%  Similarity=0.470  Sum_probs=28.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +++|.|+||+|||++++++|..+|+++++++
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~~~~~d~d   32 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLDLVFLDSD   32 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEecC
Confidence            5788999999999999999999999999864

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=97.82  E-value=4e-06  Score=69.04  Aligned_cols=32  Identities=19%  Similarity=0.405  Sum_probs=29.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +.++|.|+||+|||++++.+|+.+|+++++.|
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~D   34 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEehh
Confidence            56889999999999999999999999988764

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.80  E-value=3.2e-06  Score=68.96  Aligned_cols=34  Identities=32%  Similarity=0.425  Sum_probs=30.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      +-++|.|||||||||+++++++.+|.+++.++..
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            4478999999999999999999999999988764

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=97.80  E-value=7.6e-06  Score=66.41  Aligned_cols=33  Identities=21%  Similarity=0.283  Sum_probs=29.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ++-++|.||||+|||++++++|+.++.+++.++
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~   35 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFG   35 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCCeEEee
Confidence            356889999999999999999999998887765

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.75  E-value=6e-06  Score=67.26  Aligned_cols=24  Identities=46%  Similarity=0.808  Sum_probs=22.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++++|+||||||||+|+++++..+
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            689999999999999999999987

>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=97.74  E-value=5.1e-05  Score=67.49  Aligned_cols=44  Identities=16%  Similarity=0.147  Sum_probs=34.7

Q ss_pred             ccCChhHHHHHHHHHHh---hhcCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          209 LAMDTDMKKMIMDDLER---AWKRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       209 l~~~~~~k~~i~~~l~~---~~~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +++.+...++|++.|..   ...+-+.|||++|+|||+||+++++..
T Consensus        22 ~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~   68 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKS   68 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             eeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhh
Confidence            45677778889888875   222346799999999999999999874

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.73  E-value=6.5e-06  Score=67.37  Aligned_cols=30  Identities=33%  Similarity=0.543  Sum_probs=27.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      ++|.|+||+|||++++++|..++++++++|
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            667799999999999999999999998765

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.72  E-value=8.3e-06  Score=65.82  Aligned_cols=29  Identities=34%  Similarity=0.616  Sum_probs=25.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      +-++|.||||+||||+++++|..++..++
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            55789999999999999999999987644

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.70  E-value=8.3e-06  Score=66.22  Aligned_cols=32  Identities=34%  Similarity=0.561  Sum_probs=27.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      +-++|.||||||||++++++|..++...+..+
T Consensus         7 ~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d   38 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   38 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeechh
Confidence            44789999999999999999999998776554

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.55  E-value=1.9e-05  Score=65.49  Aligned_cols=37  Identities=19%  Similarity=0.253  Sum_probs=28.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEG  266 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~  266 (338)
                      +.-+++.|+||+||||+++.++...++..  ++..++..
T Consensus        14 p~liil~G~pGsGKST~a~~l~~~~~~~~--i~~D~~~~   50 (172)
T d1yj5a2          14 PEVVVAVGFPGAGKSTFIQEHLVSAGYVH--VNRDTLGS   50 (172)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHTGGGTCEE--EEHHHHCS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhcCCEE--EchHHHHH
Confidence            35678999999999999999988877543  44444444

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=97.50  E-value=3e-05  Score=62.85  Aligned_cols=26  Identities=38%  Similarity=0.529  Sum_probs=23.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      -.++|.||||+||||+++++|..++.
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            34899999999999999999999864

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.45  E-value=4e-05  Score=62.91  Aligned_cols=29  Identities=21%  Similarity=0.356  Sum_probs=26.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+||||+++.+|.++|+..+..
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            68999999999999999999999876653

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=97.40  E-value=1.8e-05  Score=67.33  Aligned_cols=66  Identities=17%  Similarity=0.225  Sum_probs=42.7

Q ss_pred             HHHHHHh-hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCc
Q 035959          219 IMDDLER-AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDC  290 (338)
Q Consensus       219 i~~~l~~-~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~  290 (338)
                      +...|.. |.+++++|+|||+||||.++.++++.++-.++  +...-.+    .--|..+....++++||+-.
T Consensus        43 l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vi--s~~N~~s----~F~Lq~l~~~kv~l~dD~t~  109 (205)
T d1tuea_          43 LKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVI--SFVNSTS----HFWLEPLTDTKVAMLDDATT  109 (205)
T ss_dssp             HHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEEC--CCCCSSS----CGGGGGGTTCSSEEEEEECH
T ss_pred             HHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhCCEEE--eccCCCC----CcccccccCCeEEEEecccc
Confidence            3333433 66677899999999999999999999975432  2221111    12234445667888888644

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.36  E-value=5.9e-05  Score=62.16  Aligned_cols=29  Identities=34%  Similarity=0.584  Sum_probs=26.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+||||+++.+|+.+|+..+.+
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~g~~~i~~   31 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKLGIPQIST   31 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            67889999999999999999999887654

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=97.36  E-value=5.7e-05  Score=62.76  Aligned_cols=30  Identities=27%  Similarity=0.461  Sum_probs=25.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|.||||+|||++++.+|.++|+..+..
T Consensus         5 riil~G~pGSGKsT~a~~La~~~g~~~i~~   34 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   34 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            357889999999999999999999876554

>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=97.36  E-value=5.4e-05  Score=61.66  Aligned_cols=24  Identities=29%  Similarity=0.599  Sum_probs=22.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ++|.||||+|||+|+++++..++.
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCC
Confidence            789999999999999999998854

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.35  E-value=4.2e-05  Score=63.72  Aligned_cols=31  Identities=19%  Similarity=0.348  Sum_probs=26.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-+++.||||+|||++++.+|.++|+..+..
T Consensus         7 ~iI~i~G~pGSGKsT~a~~La~~~g~~~i~~   37 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            4578999999999999999999998765443

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=97.35  E-value=3.7e-05  Score=63.98  Aligned_cols=30  Identities=13%  Similarity=0.267  Sum_probs=26.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      -.++|.||||+|||++++.+|+++|+..+.
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~~~~~is   33 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKYQLAHIS   33 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHCCcEEe
Confidence            458899999999999999999999987653

>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=97.34  E-value=4.4e-05  Score=61.74  Aligned_cols=25  Identities=28%  Similarity=0.442  Sum_probs=22.4

Q ss_pred             Cc--eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RG--YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g--~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +|  ++|.|+||+||||+++++|..++
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~   31 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLN   31 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            55  57889999999999999999985

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.29  E-value=7.1e-05  Score=62.45  Aligned_cols=31  Identities=19%  Similarity=0.346  Sum_probs=26.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      .-++|.||||+|||++++.+|.++|...+..
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            3467899999999999999999998866543

>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=97.27  E-value=8.3e-05  Score=61.35  Aligned_cols=29  Identities=21%  Similarity=0.321  Sum_probs=25.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.+|..+|+..+..
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            67899999999999999999999876653

>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=97.24  E-value=1.6e-05  Score=65.72  Aligned_cols=24  Identities=33%  Similarity=0.544  Sum_probs=21.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ++|.|+||+||||+++++|..++.
T Consensus        22 I~L~G~pGSGKTTiAk~La~~l~~   45 (195)
T d1x6va3          22 VWLTGLSGAGKTTVSMALEEYLVC   45 (195)
T ss_dssp             EEEESSCHHHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            468899999999999999999854

>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=97.23  E-value=8.1e-05  Score=62.13  Aligned_cols=31  Identities=16%  Similarity=0.369  Sum_probs=26.7

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      +.-++|.||||+|||++++.+|..+|+..+.
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~is   38 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTHLS   38 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeeEe
Confidence            3457899999999999999999999876654

>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=97.23  E-value=9.4e-05  Score=61.89  Aligned_cols=29  Identities=17%  Similarity=0.447  Sum_probs=25.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.+|.++|+..+..
T Consensus         9 IiliG~PGSGKtT~a~~La~~~g~~~is~   37 (189)
T d2ak3a1           9 AAIMGAPGSGKGTVSSRITKHFELKHLSS   37 (189)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHBCCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEcH
Confidence            67889999999999999999999776543

>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=97.22  E-value=9.7e-05  Score=61.35  Aligned_cols=28  Identities=21%  Similarity=0.419  Sum_probs=25.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      -++|.||||+||||.++.+|+++|+..+
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~g~~~i   30 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKYGYTHL   30 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceE
Confidence            3689999999999999999999987654

>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=97.22  E-value=9.7e-05  Score=58.52  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=20.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +-++|+||||+|||++++.++...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            457899999999999999987655

>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=97.21  E-value=0.0001  Score=60.82  Aligned_cols=29  Identities=28%  Similarity=0.557  Sum_probs=25.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||++++.+|..+|...+..
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g~~~i~~   33 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFHAAHLAT   33 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceEec
Confidence            67889999999999999999998775544

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=97.19  E-value=0.00011  Score=61.94  Aligned_cols=28  Identities=36%  Similarity=0.570  Sum_probs=24.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      -+.+.||||+||+|+++.+|+.+|++.+
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~gl~~i   32 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEALQWHLL   32 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4578899999999999999999998764

>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=97.14  E-value=0.00012  Score=60.17  Aligned_cols=29  Identities=17%  Similarity=0.268  Sum_probs=25.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      ++|.||||+|||+.++.+|.++++..+..
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~~~~~i~~   31 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceech
Confidence            57899999999999999999999876543

>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=97.09  E-value=0.00015  Score=61.24  Aligned_cols=28  Identities=29%  Similarity=0.479  Sum_probs=24.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      +.+.||||+||||+|+.+|.++|++.+.
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            3477999999999999999999987544

>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=97.07  E-value=0.00028  Score=55.18  Aligned_cols=34  Identities=29%  Similarity=0.335  Sum_probs=27.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      +..+|.+|+|+|||.++..++...+..++.+-..
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcCh
Confidence            4568999999999999887777778777766544

>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=97.02  E-value=0.00027  Score=56.58  Aligned_cols=30  Identities=20%  Similarity=0.148  Sum_probs=24.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      -+.+.|+||+|||||+..+++++   |..+..+
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~   36 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLI   36 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEe
Confidence            36799999999999999999886   4544433

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.96  E-value=0.00029  Score=58.51  Aligned_cols=32  Identities=19%  Similarity=0.450  Sum_probs=25.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC---CcEEEEec
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH---FDVYDLEL  261 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~  261 (338)
                      -+++.|.||+||||+++++|.+++   .++..++.
T Consensus         4 li~l~GlpgsGKSTla~~L~~~l~~~~~~~~~~~~   38 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTRYLNFIGVPTREFNV   38 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCCCeEEcc
Confidence            368999999999999999998874   44544443

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.94  E-value=0.00019  Score=58.20  Aligned_cols=26  Identities=19%  Similarity=0.307  Sum_probs=22.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      +-+++.||||+||||+++.++..++.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~   27 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRK   27 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            45789999999999999999998843

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.93  E-value=0.00057  Score=58.10  Aligned_cols=36  Identities=28%  Similarity=0.337  Sum_probs=28.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSV  264 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~  264 (338)
                      +-++|.||+|+|||+.+.-+|.++   |..+..+.+...
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt~   45 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTF   45 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeccc
Confidence            457899999999999999999877   556666655543

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.90  E-value=0.0005  Score=58.46  Aligned_cols=36  Identities=22%  Similarity=0.293  Sum_probs=28.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVE  265 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~  265 (338)
                      -++|.||+|+|||+.+.-+|.++   +..+..+.+....
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt~R   50 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQR   50 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeccccc
Confidence            46789999999999999999877   5667666665433

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=96.90  E-value=0.0024  Score=51.78  Aligned_cols=62  Identities=19%  Similarity=0.247  Sum_probs=43.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC--------------------cEEEEecCCcCCchHHHHH-HH-hcCCCcEEEEcCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF--------------------DVYDLELSSVEGNKHLRKV-LI-ATENKSILVVGDI  288 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~--------------------~~~~l~~~~~~~~~~l~~~-l~-~~~~~~Il~iDei  288 (338)
                      ++|.|+=|+|||++++++++.+|.                    .++-+|+-.+.+..++..+ +. .....+|++||=-
T Consensus        36 i~L~G~LGaGKTtfvr~~~~~lg~~~~V~SPTF~l~~~Y~~~~~~i~H~DlYRl~~~~El~~lg~~e~~~~~~i~~IEWp  115 (158)
T d1htwa_          36 VYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWS  115 (158)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTCCSCCCCCTTTCEEEEEETTEEEEEEECTTCSCTTHHHHSTHHHHHSSSCEEEEESG
T ss_pred             EEEecCCCccHHHHHHHHHhhcccccccCCCceEEEEeeccCCceEEEEEEeccCChhhhhhCCchhHhccCCEEEEECc
Confidence            679999999999999999999962                    3455566666665554432 22 2245678888866


Q ss_pred             CccC
Q 035959          289 DCCT  292 (338)
Q Consensus       289 D~~~  292 (338)
                      +.+.
T Consensus       116 e~~~  119 (158)
T d1htwa_         116 EKGQ  119 (158)
T ss_dssp             GGGT
T ss_pred             hhhh
Confidence            6554

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.85  E-value=0.00098  Score=56.75  Aligned_cols=36  Identities=22%  Similarity=0.216  Sum_probs=28.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSV  264 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~  264 (338)
                      .-++|.||+|+|||+.+.-+|..+   |..+..+.+...
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~   48 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTF   48 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccc
Confidence            346799999999999999999877   556666655543

>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=96.84  E-value=0.0018  Score=60.29  Aligned_cols=87  Identities=22%  Similarity=0.338  Sum_probs=57.4

Q ss_pred             CccccccCChhHHHHHHHHHHhhhcCc-eeeeCCCCCCcHHHHHHHHHHhC---CcEEEEecC-CcC------------C
Q 035959          204 STFDTLAMDTDMKKMIMDDLERAWKRG-YLLFGPPGTGKSSLIAAMANYLH---FDVYDLELS-SVE------------G  266 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~~~~~g-~LL~GppGtGKT~l~~aia~~l~---~~~~~l~~~-~~~------------~  266 (338)
                      .++++++..+...+.+.+.+..  ++| +|+.||+|+|||+++.++.+++.   .+++.++-. +..            .
T Consensus       135 ~~l~~LG~~~~~~~~l~~l~~~--~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~~~~~q~~v~~~~  212 (401)
T d1p9ra_         135 LDLHSLGMTAHNHDNFRRLIKR--PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDIDGIGQTQVNPRV  212 (401)
T ss_dssp             CCGGGSCCCHHHHHHHHHHHTS--SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCCSSSEEEECBGGG
T ss_pred             hhhhhhcccHHHHHHHHHHHhh--hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccccCCCCeeeecCCc
Confidence            4688998888776666554432  345 68999999999999999999874   345544321 110            0


Q ss_pred             chHHHHHHHhc--CCCcEEEEcCCCccC
Q 035959          267 NKHLRKVLIAT--ENKSILVVGDIDCCT  292 (338)
Q Consensus       267 ~~~l~~~l~~~--~~~~Il~iDeiD~~~  292 (338)
                      .......+..+  ..|+||+|.||-...
T Consensus       213 ~~~~~~~l~~~lR~dPDvi~igEiRd~~  240 (401)
T d1p9ra_         213 DMTFARGLRAILRQDPDVVMVGEIRDLE  240 (401)
T ss_dssp             TBCHHHHHHHHGGGCCSEEEESCCCSHH
T ss_pred             CCCHHHHHHHHHhhcCCEEEecCcCChH
Confidence            11234444433  379999999997553

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.83  E-value=0.00069  Score=57.75  Aligned_cols=35  Identities=26%  Similarity=0.334  Sum_probs=22.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      .-++|.||+|+|||+.+.-+|.++   +..+-.+.+..
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt   50 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADV   50 (211)
T ss_dssp             EEEEEECSCCC----HHHHHHHHHHHTTCCEEEEECCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEeec
Confidence            346789999999999999888876   45665555543

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.77  E-value=0.0011  Score=56.60  Aligned_cols=36  Identities=19%  Similarity=0.204  Sum_probs=27.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSV  264 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~  264 (338)
                      .-++|.||+|+|||+.+.-+|.++   +..+-.+.+...
T Consensus        12 ~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~Dt~   50 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTF   50 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeeccc
Confidence            346899999999999999999876   555655554443

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=96.66  E-value=0.0017  Score=58.71  Aligned_cols=64  Identities=16%  Similarity=0.366  Sum_probs=42.2

Q ss_pred             hcCceeeeCCCCCCcHHHHHHHHHHhCC--cEEEEec-CCcC-------------CchHHHHHHHhc--CCCcEEEEcCC
Q 035959          227 WKRGYLLFGPPGTGKSSLIAAMANYLHF--DVYDLEL-SSVE-------------GNKHLRKVLIAT--ENKSILVVGDI  288 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~~aia~~l~~--~~~~l~~-~~~~-------------~~~~l~~~l~~~--~~~~Il~iDei  288 (338)
                      .++++|+.||+|+|||+++.|++.+...  .++.++- .++.             .+-.+.+++..+  ..|+.|++.|+
T Consensus       165 ~~~nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~l~~~~~~~~~~~~~~~~~~~ll~~~lR~~pd~iivgEi  244 (323)
T d1g6oa_         165 IGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGEL  244 (323)
T ss_dssp             HTCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEESCC
T ss_pred             hCCCEEEEeeccccchHHHHHHhhhcccccceeeccchhhhhcccccccceeccccchhHHHHHHHHhccCCCcccCCcc
Confidence            3567999999999999999999998842  3333321 1111             011344444433  37899999998


Q ss_pred             Cc
Q 035959          289 DC  290 (338)
Q Consensus       289 D~  290 (338)
                      -.
T Consensus       245 R~  246 (323)
T d1g6oa_         245 RS  246 (323)
T ss_dssp             CS
T ss_pred             Cc
Confidence            63

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.59  E-value=0.0048  Score=54.20  Aligned_cols=96  Identities=14%  Similarity=0.128  Sum_probs=55.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHHHH---hcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKVLI---ATENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~l~---~~~~~~  281 (338)
                      +-..++||||||||+++..++..+   |..+.++|...-.+                     .++..+++.   +.....
T Consensus        58 ~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~~~~~  137 (268)
T d1xp8a1          58 RITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVRSGAID  137 (268)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             eEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhcCCCc
Confidence            345799999999999988877765   56778887764322                     112222222   234688


Q ss_pred             EEEEcCCCccCCcccccccccCCCCCCCCCCcchhhHHHHHHHhcCCc
Q 035959          282 ILVVGDIDCCTELQDRSAQARTASPDWHSPKRDQITLSGLLNFTDGLW  329 (338)
Q Consensus       282 Il~iDeiD~~~~~~~r~~~~~~~~~~~~~~~~~~~~ls~lLn~iDgl~  329 (338)
                      +||||=+..+.+..+-.+...     +...+...+.++.++..+-.+.
T Consensus       138 liIiDSi~al~~r~e~~~~~~-----~~~~~~~a~~l~~~lr~l~~~~  180 (268)
T d1xp8a1         138 VVVVDSVAALTPRAEIEGDMG-----DSLPGLQARLMSQALRKLTAIL  180 (268)
T ss_dssp             EEEEECTTTCCCSTTC-------------CCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEecccccccHHHHccccc-----chhHHHHHHHHHHHHHHHHhhh
Confidence            999999999875222211111     0112234556666666555443

>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=96.56  E-value=0.0028  Score=53.19  Aligned_cols=49  Identities=18%  Similarity=0.138  Sum_probs=33.2

Q ss_pred             cCChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEec
Q 035959          210 AMDTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLEL  261 (338)
Q Consensus       210 ~~~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~  261 (338)
                      -..+..++.+...+.   ....++..|+|+|||.++.+++..++.+++.+-.
T Consensus        70 ~Lr~yQ~eav~~~~~---~~~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p  118 (206)
T d2fz4a1          70 SLRDYQEKALERWLV---DKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVP  118 (206)
T ss_dssp             CCCHHHHHHHHHHTT---TSEEEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             CcCHHHHHHHHHHHh---CCCcEEEeCCCCCceehHHhHHHHhcCceeEEEc
Confidence            345555554443332   2345678899999999999999988877665533

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.56  E-value=0.00032  Score=57.03  Aligned_cols=30  Identities=27%  Similarity=0.414  Sum_probs=24.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC---cEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF---DVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~---~~~~l~  260 (338)
                      +++.|+||+||||+++.+|..++.   .+..+.
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~~   36 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            578999999999999999999853   444443

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=96.56  E-value=0.0031  Score=55.28  Aligned_cols=64  Identities=14%  Similarity=0.210  Sum_probs=43.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHH---HHhcCCCcE
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKV---LIATENKSI  282 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~---l~~~~~~~I  282 (338)
                      -..|+||||+|||+++..+|..+   |..++++|...-.+                     .++..+.   +.+..+..+
T Consensus        56 itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~~~~~~l  135 (263)
T d1u94a1          56 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV  135 (263)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             EEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHHHhcCCCCE
Confidence            35899999999999988877665   56677777654321                     1122122   222246789


Q ss_pred             EEEcCCCccCC
Q 035959          283 LVVGDIDCCTE  293 (338)
Q Consensus       283 l~iDeiD~~~~  293 (338)
                      +|||-|..+.+
T Consensus       136 iViDSi~al~~  146 (263)
T d1u94a1         136 IVVDSVAALTP  146 (263)
T ss_dssp             EEEECGGGCCC
T ss_pred             EEEECcccccc
Confidence            99999988764

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=96.50  E-value=0.0012  Score=58.29  Aligned_cols=58  Identities=21%  Similarity=0.251  Sum_probs=40.1

Q ss_pred             hhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecCCcCCchHHHHHHHhcCCCcEEEEcCCCc
Q 035959          226 AWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELSSVEGNKHLRKVLIATENKSILVVGDIDC  290 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~~~~~~~~l~~~l~~~~~~~Il~iDeiD~  290 (338)
                      +.+..++|+|||+||||+++.++++.+|.- ..++-+.  +.-    -+..+....++++||.+.
T Consensus       102 ~k~n~~~l~G~~~tGKS~f~~~i~~~lg~~-~~~~~~~--~~f----~l~~l~~k~~~~~~e~~~  159 (267)
T d1u0ja_         102 GKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWTN--ENF----PFNDCVDKMVIWWEEGKM  159 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTTC--SSC----TTGGGSSCSEEEECSCCE
T ss_pred             CccEEEEEEcCCCCCHHHHHHHHHHHhcch-hhccccC--CCc----cccccCCCEEEEEeCCCc
Confidence            556678999999999999999999999643 2222111  111    134455778899999764

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.49  E-value=0.0014  Score=55.43  Aligned_cols=36  Identities=25%  Similarity=0.418  Sum_probs=29.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecCCcC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELSSVE  265 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~~~~  265 (338)
                      -++|+|.||+|||+++++++..+    +.+++.++...+.
T Consensus        26 vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~iR   65 (208)
T d1m7ga_          26 TIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIR   65 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchHHH
Confidence            36899999999999999999766    6678877766543

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.48  E-value=0.0031  Score=54.32  Aligned_cols=66  Identities=18%  Similarity=0.212  Sum_probs=44.4

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh-----CC------------cEEE--EecCC-cCC--------chHHHHHHHhcCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL-----HF------------DVYD--LELSS-VEG--------NKHLRKVLIATEN  279 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l-----~~------------~~~~--l~~~~-~~~--------~~~l~~~l~~~~~  279 (338)
                      .+.++|+||..+|||++++++|--.     |.            +-+.  +...+ +..        -.++..++....+
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~  120 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE  120 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCT
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHhccc
Confidence            3678999999999999999988533     31            1111  11111 111        2356777888889


Q ss_pred             CcEEEEcCCCccCC
Q 035959          280 KSILVVGDIDCCTE  293 (338)
Q Consensus       280 ~~Il~iDeiD~~~~  293 (338)
                      +++++|||+-+-..
T Consensus       121 ~sLvliDE~~~gT~  134 (234)
T d1wb9a2         121 YSLVLMDEIGRGTS  134 (234)
T ss_dssp             TEEEEEESCCCCSS
T ss_pred             ccEEeecccccCCC
Confidence            99999999987665

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.45  E-value=0.001  Score=56.01  Aligned_cols=35  Identities=26%  Similarity=0.170  Sum_probs=26.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---------CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---------HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---------~~~~~~l~~~~  263 (338)
                      +-++|+||||||||+++..+|...         +..+++++...
T Consensus        35 ~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~   78 (251)
T d1szpa2          35 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEG   78 (251)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSS
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecc
Confidence            457999999999999998887543         34566665544

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.44  E-value=0.0046  Score=54.41  Aligned_cols=65  Identities=14%  Similarity=0.204  Sum_probs=43.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCcCC---------------------chHHHHH---HHhcCCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSVEG---------------------NKHLRKV---LIATENKS  281 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~~~---------------------~~~l~~~---l~~~~~~~  281 (338)
                      +-..|+||||||||+++..+|...   |..++++|...-.+                     .++..++   +....+..
T Consensus        61 ~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~~~~~~  140 (269)
T d1mo6a1          61 RVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALD  140 (269)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTTCEE
T ss_pred             eeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            345899999999999986666544   66777777665222                     1122222   22235688


Q ss_pred             EEEEcCCCccCC
Q 035959          282 ILVVGDIDCCTE  293 (338)
Q Consensus       282 Il~iDeiD~~~~  293 (338)
                      +||||-+..+.+
T Consensus       141 liIiDSi~al~~  152 (269)
T d1mo6a1         141 IVVIDSVAALVP  152 (269)
T ss_dssp             EEEEECSTTCCC
T ss_pred             EEEEeccccccc
Confidence            999999998875

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.39  E-value=0.0011  Score=54.72  Aligned_cols=25  Identities=36%  Similarity=0.585  Sum_probs=22.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      |.++|.||+|+|||+|++.+++...
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~   26 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC
Confidence            5689999999999999999999864

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.35  E-value=0.0012  Score=54.76  Aligned_cols=27  Identities=33%  Similarity=0.447  Sum_probs=23.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      |.++|.||+|+|||++++.++...+..
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~~~~   27 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEHSSI   27 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCCc
Confidence            458899999999999999999987543

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.33  E-value=0.0014  Score=55.76  Aligned_cols=34  Identities=21%  Similarity=0.218  Sum_probs=27.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .-.+++||||+|||+++..+|...   +..+.+++..
T Consensus        27 sl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~e   63 (242)
T d1tf7a2          27 SIILATGATGTGKTLLVSRFVENACANKERAILFAYE   63 (242)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeecc
Confidence            346899999999999999988876   5566666554

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=96.33  E-value=0.0011  Score=50.81  Aligned_cols=17  Identities=29%  Similarity=0.296  Sum_probs=14.5

Q ss_pred             CceeeeCCCCCCcHHHH
Q 035959          229 RGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~  245 (338)
                      +.++|.+|||+|||..+
T Consensus         8 ~~~il~~~tGsGKT~~~   24 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRF   24 (140)
T ss_dssp             CEEEECCCTTSSTTTTH
T ss_pred             CcEEEEcCCCCChhHHH
Confidence            56799999999999655

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=96.32  E-value=0.0037  Score=48.90  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=18.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      ++|.|+||+|||+|+..++..
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999998754

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.22  E-value=0.0026  Score=53.97  Aligned_cols=23  Identities=30%  Similarity=0.423  Sum_probs=20.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -++++||||||||+++..+|...
T Consensus        38 ~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          38 ITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            47899999999999999888765

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.19  E-value=0.0012  Score=53.94  Aligned_cols=24  Identities=25%  Similarity=0.235  Sum_probs=20.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +-++++||||+|||+++..+|...
T Consensus        24 ~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          24 SITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHHH
Confidence            447899999999999999988765

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=96.10  E-value=0.0084  Score=51.67  Aligned_cols=35  Identities=29%  Similarity=0.231  Sum_probs=26.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh-------------CCcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL-------------HFDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l-------------~~~~~~l~~~~  263 (338)
                      .-.+|+|+||+|||+++..+|..+             +.++++++...
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~   77 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAED   77 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSS
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccc
Confidence            346899999999999998888764             23577776554

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.10  E-value=0.0016  Score=53.08  Aligned_cols=30  Identities=20%  Similarity=0.288  Sum_probs=23.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC---CcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH---FDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~---~~~~~l~  260 (338)
                      +-+.||+|+|||++++.++..++   .....++
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~   57 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLREQGISVCVFH   57 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhccccccceecc
Confidence            34999999999999999998774   3444443

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.09  E-value=0.0043  Score=52.41  Aligned_cols=24  Identities=25%  Similarity=0.159  Sum_probs=20.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +-++++||||||||+++..+|...
T Consensus        38 ~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          38 AITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             EEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            347899999999999999998654

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=96.02  E-value=0.003  Score=57.88  Aligned_cols=36  Identities=28%  Similarity=0.306  Sum_probs=24.7

Q ss_pred             ChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHH
Q 035959          212 DTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       212 ~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+..+..+..-+.   .+-.+|.||||||||+++..+..
T Consensus       150 ~~~Q~~A~~~al~---~~~~vI~G~pGTGKTt~i~~~l~  185 (359)
T d1w36d1         150 INWQKVAAAVALT---RRISVISGGPGTGKTTTVAKLLA  185 (359)
T ss_dssp             CCHHHHHHHHHHT---BSEEEEECCTTSTHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHc---CCeEEEEcCCCCCceehHHHHHH
Confidence            3455555555443   35578999999999998865443

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.87  E-value=0.0035  Score=50.26  Aligned_cols=29  Identities=17%  Similarity=0.287  Sum_probs=23.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      +-+.|++|+|||+|+..++.++   |+.+-.+
T Consensus         4 i~I~G~~gSGKTTli~~l~~~L~~~g~~v~vi   35 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVAAAVREGWRVGTV   35 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            4589999999999999999887   4444433

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=95.84  E-value=0.011  Score=50.29  Aligned_cols=65  Identities=18%  Similarity=0.257  Sum_probs=43.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh-----CC------------cEEEEecC--C-cCC--------chHHHHHHHhcCCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL-----HF------------DVYDLELS--S-VEG--------NKHLRKVLIATENK  280 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l-----~~------------~~~~l~~~--~-~~~--------~~~l~~~l~~~~~~  280 (338)
                      +.++|+||...|||+++++++-..     |.            +-+.....  + +..        -.++..++.....+
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~~~~  115 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATEN  115 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHCCTT
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhccCCCC
Confidence            457999999999999999877533     31            11111111  1 111        14567778888899


Q ss_pred             cEEEEcCCCccCC
Q 035959          281 SILVVGDIDCCTE  293 (338)
Q Consensus       281 ~Il~iDeiD~~~~  293 (338)
                      ++++|||+-.-..
T Consensus       116 sLvliDE~~~gT~  128 (224)
T d1ewqa2         116 SLVLLDEVGRGTS  128 (224)
T ss_dssp             EEEEEESTTTTSC
T ss_pred             cEEeecccccCcc
Confidence            9999999987655

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=95.79  E-value=0.0035  Score=50.21  Aligned_cols=22  Identities=14%  Similarity=0.353  Sum_probs=19.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|.||+|||+|+..+...
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4799999999999999998764

>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=95.67  E-value=0.004  Score=54.35  Aligned_cols=35  Identities=17%  Similarity=0.297  Sum_probs=22.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh----C---CcEEEEecCC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL----H---FDVYDLELSS  263 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l----~---~~~~~l~~~~  263 (338)
                      ..+|+.|+||||||+++...+.++    +   ..+..+..+.
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn   56 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTN   56 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSH
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcH
Confidence            458999999999998754432222    3   2566666553

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.63  E-value=0.0028  Score=51.78  Aligned_cols=24  Identities=29%  Similarity=0.567  Sum_probs=21.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +-++|.||+|+|||++++.++...
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            346899999999999999999876

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.63  E-value=0.015  Score=47.47  Aligned_cols=23  Identities=26%  Similarity=0.465  Sum_probs=17.8

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+..|+.+|+|+|||.++..++.
T Consensus        23 ~~n~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          23 ETNCLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             GSCEEEECCTTSCHHHHHHHHHH
T ss_pred             cCCeEEEeCCCCcHHHHHHHHHH
Confidence            46789999999999986554443

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.61  E-value=0.0047  Score=51.43  Aligned_cols=34  Identities=21%  Similarity=0.210  Sum_probs=24.3

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH----hCCcEEEEecC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY----LHFDVYDLELS  262 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~----l~~~~~~l~~~  262 (338)
                      .-++|+|+||+|||+++..+|..    -+..+++++..
T Consensus        27 ~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          27 RSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            44689999999999998765532    24566666543

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.59  E-value=0.0041  Score=52.32  Aligned_cols=33  Identities=30%  Similarity=0.308  Sum_probs=26.2

Q ss_pred             cCcee--eeCCCCCCcHHHHHHHHHHh---CCcEEEEe
Q 035959          228 KRGYL--LFGPPGTGKSSLIAAMANYL---HFDVYDLE  260 (338)
Q Consensus       228 ~~g~L--L~GppGtGKT~l~~aia~~l---~~~~~~l~  260 (338)
                      ++|.+  |.|+.|+||||+++.+++.+   |.++..+.
T Consensus         1 ~rG~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           1 RRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             CCCCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            35655  55999999999999999987   67776654

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=95.36  E-value=0.0045  Score=51.01  Aligned_cols=27  Identities=26%  Similarity=0.354  Sum_probs=23.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      .+|+||.|++|+|||+++.++... |+.
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~-g~~   40 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQR-GHR   40 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHT-TCE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCe
Confidence            378999999999999999988865 554

>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=95.32  E-value=0.007  Score=50.89  Aligned_cols=30  Identities=27%  Similarity=0.630  Sum_probs=23.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh--CCcEEEEe
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL--HFDVYDLE  260 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l--~~~~~~l~  260 (338)
                      +++.||+|+|||||+.++..++  +..+..++
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            4789999999999999999876  34555554

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.26  E-value=0.012  Score=49.05  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=20.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -++|.||||+|||+++..+|..+
T Consensus        36 l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          36 VTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            46899999999999999999765

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.22  E-value=0.0049  Score=51.39  Aligned_cols=24  Identities=29%  Similarity=0.296  Sum_probs=21.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      +-+.||+|+||||++++++..++.
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhch
Confidence            348899999999999999999864

>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=95.21  E-value=0.012  Score=50.86  Aligned_cols=33  Identities=21%  Similarity=0.099  Sum_probs=26.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh----CCcEEEEecC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL----HFDVYDLELS  262 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l----~~~~~~l~~~  262 (338)
                      -+++.|+||+|||+++..+|..+    |.++..+++.
T Consensus        37 l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E   73 (277)
T d1cr2a_          37 VIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (277)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeec
Confidence            36899999999999988887542    6788877664

>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=95.20  E-value=0.0047  Score=48.12  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=19.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      ++|.|+||+|||+|+..+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999998874

>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=95.17  E-value=0.012  Score=53.02  Aligned_cols=33  Identities=36%  Similarity=0.491  Sum_probs=25.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CC--cEEEEecCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HF--DVYDLELSS  263 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~--~~~~l~~~~  263 (338)
                      +=+.||||+|||+|+.+++.++   |.  .++.+|.++
T Consensus        54 igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss   91 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSS   91 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGG
T ss_pred             EeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeeccccc
Confidence            3499999999999999999875   33  355555554

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=94.98  E-value=0.0058  Score=47.94  Aligned_cols=21  Identities=24%  Similarity=0.491  Sum_probs=19.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      ++|.|+||+|||+|+.++...
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            689999999999999998764

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.94  E-value=0.0067  Score=49.68  Aligned_cols=25  Identities=16%  Similarity=0.440  Sum_probs=22.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++.++|.||+|+|||+|++.++...
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhC
Confidence            4678999999999999999998764

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=94.90  E-value=0.014  Score=52.56  Aligned_cols=33  Identities=33%  Similarity=0.512  Sum_probs=24.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CC--cEEEEecCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HF--DVYDLELSS  263 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~--~~~~l~~~~  263 (338)
                      +=+.||||+|||+|+.+++.++   |.  .++.+|.++
T Consensus        57 IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss   94 (327)
T d2p67a1          57 LGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSS   94 (327)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-
T ss_pred             EEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCce
Confidence            4599999999999999999876   33  345555443

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.80  E-value=0.023  Score=46.74  Aligned_cols=18  Identities=33%  Similarity=0.471  Sum_probs=15.5

Q ss_pred             cCceeeeCCCCCCcHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~  245 (338)
                      .+.+++.+|+|+|||..+
T Consensus        40 ~~~~il~apTGsGKT~~a   57 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLA   57 (202)
T ss_dssp             CSCEEEECSSHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHH
Confidence            457899999999999865

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.74  E-value=0.0072  Score=49.98  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      +.++|.|+||+|||+|+.++..
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            4689999999999999999986

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=94.72  E-value=0.0069  Score=49.48  Aligned_cols=26  Identities=27%  Similarity=0.356  Sum_probs=22.3

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      ..|+||.|++|+|||+++.++... |.
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~-g~   40 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR-GH   40 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TC
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CC
Confidence            478999999999999999887765 44

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.65  E-value=0.012  Score=47.14  Aligned_cols=21  Identities=33%  Similarity=0.604  Sum_probs=18.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|+||+|||+|+..+..
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            379999999999999998854

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=94.56  E-value=0.0066  Score=49.99  Aligned_cols=27  Identities=33%  Similarity=0.365  Sum_probs=22.6

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHhCCc
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYLHFD  255 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l~~~  255 (338)
                      .+|+||.||+|+|||+++.++... |+.
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~-G~~   41 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK-NHL   41 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT-TCE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCc
Confidence            378999999999999999888754 543

>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=94.51  E-value=0.0089  Score=49.06  Aligned_cols=24  Identities=25%  Similarity=0.560  Sum_probs=21.1

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      ...++|.|+||+|||+|+.++.+.
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            346899999999999999999865

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.48  E-value=0.0089  Score=48.03  Aligned_cols=21  Identities=33%  Similarity=0.743  Sum_probs=18.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|+||+|||+|+..+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999998753

>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=94.48  E-value=0.011  Score=51.95  Aligned_cols=36  Identities=17%  Similarity=0.536  Sum_probs=23.5

Q ss_pred             cCceeeeCCCCCCcHHHHHH-HHHHh---C---CcEEEEecCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAA-MANYL---H---FDVYDLELSS  263 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~a-ia~~l---~---~~~~~l~~~~  263 (338)
                      ...+++.|+||||||+.+.. +|..+   +   ..+..+..+.
T Consensus        24 ~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~   66 (318)
T d1pjra1          24 EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTN   66 (318)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSH
T ss_pred             CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccH
Confidence            35689999999999986544 44333   1   2456665554

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.47  E-value=0.0097  Score=49.89  Aligned_cols=24  Identities=42%  Similarity=0.599  Sum_probs=21.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -++|.||+|+|||+|++.+.....
T Consensus         4 livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCC
Confidence            367999999999999999998753

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.46  E-value=0.013  Score=47.15  Aligned_cols=20  Identities=40%  Similarity=0.730  Sum_probs=18.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|++|+|||+|+..+.+
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999876

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=94.36  E-value=0.0091  Score=48.73  Aligned_cols=27  Identities=33%  Similarity=0.479  Sum_probs=22.0

Q ss_pred             eeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          232 LLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       232 LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      -++|++|+|||+++..+ ...|++++..
T Consensus         7 gitG~~gSGKstva~~l-~~~g~~~~~~   33 (191)
T d1uf9a_           7 GITGNIGSGKSTVAALL-RSWGYPVLDL   33 (191)
T ss_dssp             EEEECTTSCHHHHHHHH-HHTTCCEEEH
T ss_pred             EEECCCCCCHHHHHHHH-HHCCCeEEEc
Confidence            38899999999999988 4578776643

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.35  E-value=0.015  Score=46.50  Aligned_cols=20  Identities=45%  Similarity=0.790  Sum_probs=17.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|++|+|||+|+..+.+
T Consensus         4 i~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCcCHHHHHHHHhC
Confidence            57899999999999998865

>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=94.31  E-value=0.0092  Score=47.28  Aligned_cols=21  Identities=19%  Similarity=0.477  Sum_probs=18.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|+||+|||+|+..+...
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            789999999999999998763

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=94.28  E-value=0.0066  Score=48.44  Aligned_cols=21  Identities=19%  Similarity=0.509  Sum_probs=18.7

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -++|.|+||+|||+|+.++..
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            378999999999999999864

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=94.18  E-value=0.0062  Score=48.97  Aligned_cols=21  Identities=19%  Similarity=0.430  Sum_probs=18.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|+||+|||+|+..++.
T Consensus        14 kIvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999999874

>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=94.14  E-value=0.058  Score=46.85  Aligned_cols=44  Identities=20%  Similarity=0.181  Sum_probs=30.1

Q ss_pred             HHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHH---hCCcEEEE
Q 035959          216 KKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANY---LHFDVYDL  259 (338)
Q Consensus       216 k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~---l~~~~~~l  259 (338)
                      .++|.+|+....+-.-||+|..|+|||-.+...+..   -|+.+..+
T Consensus        92 i~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m  138 (264)
T d1gm5a3          92 HQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFM  138 (264)
T ss_dssp             HHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEE
T ss_pred             HHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEE
Confidence            345666666566667899999999999976554433   25555544

>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=94.08  E-value=0.036  Score=47.62  Aligned_cols=48  Identities=31%  Similarity=0.399  Sum_probs=36.7

Q ss_pred             HHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          216 KKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       216 k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      ...+.+.+.++.++-+++.|.-|+|||+++.++|..+   |..+..+|+..
T Consensus         8 ~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~Dp   58 (279)
T d1ihua2           8 LSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDP   58 (279)
T ss_dssp             HHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESCC
T ss_pred             HHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCC
Confidence            3455666665555667899999999999988888766   78888887763

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.07  E-value=0.013  Score=46.69  Aligned_cols=20  Identities=35%  Similarity=0.758  Sum_probs=18.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|+||+|||+|+..+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67899999999999999886

>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=94.06  E-value=0.025  Score=44.94  Aligned_cols=20  Identities=30%  Similarity=0.594  Sum_probs=18.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|++|+|||+|+..+..
T Consensus         6 i~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57899999999999998775

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.05  E-value=0.013  Score=46.59  Aligned_cols=21  Identities=29%  Similarity=0.495  Sum_probs=19.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      ++|.|++|+|||+|+..+...
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            689999999999999998863

>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=94.01  E-value=0.013  Score=46.47  Aligned_cols=20  Identities=30%  Similarity=0.491  Sum_probs=18.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|+||+|||+|+..+..
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999998885

>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=93.99  E-value=0.024  Score=49.12  Aligned_cols=16  Identities=38%  Similarity=0.488  Sum_probs=14.1

Q ss_pred             cCceeeeCCCCCCcHH
Q 035959          228 KRGYLLFGPPGTGKSS  243 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~  243 (338)
                      ++..++.+|+|+|||.
T Consensus         9 ~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TCEEEECCCTTSSTTT
T ss_pred             CCcEEEEECCCCCHHH
Confidence            4678999999999995

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.97  E-value=0.024  Score=46.48  Aligned_cols=31  Identities=23%  Similarity=0.359  Sum_probs=25.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      +.+.|+.|+||||+++.+++.+   |.++..+..
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            4578999999999999999977   677766644

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.92  E-value=0.013  Score=46.71  Aligned_cols=21  Identities=33%  Similarity=0.634  Sum_probs=18.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+.+.|+||+|||+|+.++..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            368999999999999999974

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.91  E-value=0.014  Score=46.60  Aligned_cols=21  Identities=29%  Similarity=0.487  Sum_probs=18.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|++|+|||+|+..+...
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            689999999999999998763

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.91  E-value=0.0083  Score=48.27  Aligned_cols=21  Identities=29%  Similarity=0.472  Sum_probs=19.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .++|.|+||+|||||+.++.+
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            368999999999999999975

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=93.89  E-value=0.014  Score=46.23  Aligned_cols=22  Identities=23%  Similarity=0.351  Sum_probs=19.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -++|.|++|+|||+|+..+...
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            3678999999999999998763

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.89  E-value=0.0087  Score=50.07  Aligned_cols=23  Identities=35%  Similarity=0.717  Sum_probs=20.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+.|.||.|+|||+|+++++..+
T Consensus        29 i~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          29 VVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCChHHHHHHHHhccc
Confidence            46799999999999999999876

>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=93.87  E-value=0.012  Score=48.96  Aligned_cols=28  Identities=25%  Similarity=0.353  Sum_probs=23.1

Q ss_pred             eeeCCCCCCcHHHHHHHHHHhCCcEEEEe
Q 035959          232 LLFGPPGTGKSSLIAAMANYLHFDVYDLE  260 (338)
Q Consensus       232 LL~GppGtGKT~l~~aia~~l~~~~~~l~  260 (338)
                      -++|++|+|||+++..+. .+|+++++.|
T Consensus         6 gITG~igSGKStv~~~l~-~~G~~vidaD   33 (205)
T d1jjva_           6 GLTGGIGSGKTTIANLFT-DLGVPLVDAD   33 (205)
T ss_dssp             EEECSTTSCHHHHHHHHH-TTTCCEEEHH
T ss_pred             EEECCCCCCHHHHHHHHH-HCCCeEEEch
Confidence            379999999999999876 5788877653

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.83  E-value=0.015  Score=46.41  Aligned_cols=21  Identities=33%  Similarity=0.631  Sum_probs=18.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      ++|.|++|+|||+|+..+...
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            689999999999999998863

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.83  E-value=0.012  Score=47.00  Aligned_cols=20  Identities=30%  Similarity=0.649  Sum_probs=18.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|++|+|||+|+..+++
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999986

>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=93.76  E-value=0.016  Score=48.34  Aligned_cols=28  Identities=39%  Similarity=0.475  Sum_probs=22.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDL  259 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l  259 (338)
                      +-|+|++|+|||+.+..+. .+|+++++.
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            3489999999999999875 778877653

>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=93.57  E-value=0.042  Score=48.41  Aligned_cols=32  Identities=25%  Similarity=0.305  Sum_probs=24.6

Q ss_pred             eeCCCCCCcHHHHHHHHHHh------CCcEEEEecCCc
Q 035959          233 LFGPPGTGKSSLIAAMANYL------HFDVYDLELSSV  264 (338)
Q Consensus       233 L~GppGtGKT~l~~aia~~l------~~~~~~l~~~~~  264 (338)
                      |.|++|+|||+|+..+...+      +..+..+++.+.
T Consensus        32 i~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~Ddf   69 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDF   69 (286)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGG
T ss_pred             eECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCC
Confidence            78999999999999887765      345666666554

>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=93.56  E-value=0.018  Score=45.71  Aligned_cols=20  Identities=30%  Similarity=0.487  Sum_probs=18.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|.+|+|||+|+..+..
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999875

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.50  E-value=0.019  Score=45.87  Aligned_cols=20  Identities=35%  Similarity=0.695  Sum_probs=18.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|+||+|||+|+..+..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            67999999999999999875

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.50  E-value=0.015  Score=46.38  Aligned_cols=20  Identities=30%  Similarity=0.512  Sum_probs=18.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|.||+|||+|+..+..
T Consensus         8 i~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999999876

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.50  E-value=0.018  Score=46.22  Aligned_cols=20  Identities=35%  Similarity=0.689  Sum_probs=18.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|+||+|||+|+..+.+
T Consensus         7 i~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999865

>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=93.49  E-value=0.018  Score=45.85  Aligned_cols=21  Identities=33%  Similarity=0.521  Sum_probs=18.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|++|+|||+|+..+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            589999999999999998853

>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=93.45  E-value=0.016  Score=46.10  Aligned_cols=21  Identities=29%  Similarity=0.515  Sum_probs=19.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|++|+|||+|+..+.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            689999999999999998864

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.45  E-value=0.019  Score=46.40  Aligned_cols=20  Identities=35%  Similarity=0.710  Sum_probs=18.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|.||+|||+|+..+.+
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999885

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.44  E-value=0.016  Score=46.01  Aligned_cols=21  Identities=38%  Similarity=0.626  Sum_probs=18.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|+||+|||+|+..++..
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998763

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.43  E-value=0.018  Score=46.62  Aligned_cols=20  Identities=25%  Similarity=0.585  Sum_probs=18.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|+||+|||+|+..+.+
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            68899999999999998874

>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=93.42  E-value=0.036  Score=47.81  Aligned_cols=36  Identities=25%  Similarity=0.205  Sum_probs=31.0

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      ++-+++.|.-|+|||+++.++|..+   |..+..+|+..
T Consensus         8 p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~Dp   46 (296)
T d1ihua1           8 PPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTDP   46 (296)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECCT
T ss_pred             CeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCCC
Confidence            5778899999999999999999877   78888888663

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=93.38  E-value=0.015  Score=45.55  Aligned_cols=20  Identities=45%  Similarity=0.737  Sum_probs=18.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|+||+|||+|+.++..
T Consensus         4 I~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            57999999999999999974

>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=93.30  E-value=0.02  Score=45.58  Aligned_cols=20  Identities=40%  Similarity=0.674  Sum_probs=18.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|.+|+|||+|+..+..
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            67899999999999998875

>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=93.22  E-value=0.022  Score=44.91  Aligned_cols=20  Identities=20%  Similarity=0.424  Sum_probs=18.5

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|++|+|||+|+..+..
T Consensus         5 v~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999886

>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=93.19  E-value=0.014  Score=47.52  Aligned_cols=27  Identities=22%  Similarity=0.353  Sum_probs=23.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      +.+.|+.|+||||+++.++++++...+
T Consensus        12 I~ieG~~GsGKTTl~~~L~~~l~~~~~   38 (197)
T d2vp4a1          12 VLIEGNIGSGKTTYLNHFEKYKNDICL   38 (197)
T ss_dssp             EEEECSTTSCHHHHHHTTGGGTTTEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            568899999999999999999875443

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=93.11  E-value=0.014  Score=47.58  Aligned_cols=21  Identities=38%  Similarity=0.513  Sum_probs=18.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+.|.|+||+|||||+.++.+
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            378999999999999999974

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.07  E-value=0.021  Score=47.31  Aligned_cols=22  Identities=23%  Similarity=0.375  Sum_probs=20.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +.+.|++|+||||+++.+++.+
T Consensus         5 IviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           5 IVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            5678999999999999999887

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.04  E-value=0.018  Score=49.26  Aligned_cols=24  Identities=25%  Similarity=0.480  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||+|+|||+|++.++....
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~gl~~   56 (230)
T d1l2ta_          33 FVSIMGPSGSGKSTMLNIIGCLDK   56 (230)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCcchhhHhccCCCC
Confidence            467999999999999999998764

>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=93.03  E-value=0.024  Score=45.13  Aligned_cols=20  Identities=30%  Similarity=0.664  Sum_probs=18.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|++|+|||+|+..+..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999998876

>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=92.99  E-value=0.0086  Score=48.01  Aligned_cols=23  Identities=39%  Similarity=0.445  Sum_probs=20.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+|+||.|+|||+++.||.-.++
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            47899999999999999997763

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.91  E-value=0.023  Score=48.57  Aligned_cols=24  Identities=33%  Similarity=0.549  Sum_probs=21.0

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||+|+|||+|++.++....
T Consensus        28 i~~liGpsGsGKSTLl~~i~Gl~~   51 (232)
T d2awna2          28 FVVFVGPSGCGKSTLLRMIAGLET   51 (232)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCChHHHHHHHHhcCCC
Confidence            467999999999999999998663

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.85  E-value=0.022  Score=45.60  Aligned_cols=20  Identities=30%  Similarity=0.512  Sum_probs=18.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|.+|+|||+|+..+..
T Consensus         9 v~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998875

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.84  E-value=0.022  Score=45.16  Aligned_cols=21  Identities=29%  Similarity=0.382  Sum_probs=18.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -++|.|++|+|||+|+..+..
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478899999999999999875

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.82  E-value=0.027  Score=44.97  Aligned_cols=20  Identities=40%  Similarity=0.647  Sum_probs=18.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|+||+|||+|+..+..
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            68999999999999988875

>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=92.79  E-value=0.025  Score=48.65  Aligned_cols=23  Identities=35%  Similarity=0.730  Sum_probs=20.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-|.||.|+|||+|++.++..+.
T Consensus        27 ~~liGpnGaGKSTll~~i~Gl~~   49 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEECCCCChHHHHHHHHHcCCC
Confidence            34789999999999999998774

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.79  E-value=0.028  Score=47.86  Aligned_cols=34  Identities=29%  Similarity=0.358  Sum_probs=25.1

Q ss_pred             HHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          217 KMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       217 ~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +.+.+.+.   .+...|.|++|+|||||+.++.....
T Consensus        87 ~~L~~~l~---~kt~~~~G~SGVGKSTLiN~L~~~~~  120 (225)
T d1u0la2          87 EELKEYLK---GKISTMAGLSGVGKSSLLNAINPGLK  120 (225)
T ss_dssp             HHHHHHHS---SSEEEEECSTTSSHHHHHHHHSTTCC
T ss_pred             hhHHHHhc---CCeEEEECCCCCCHHHHHHhhcchhh
Confidence            34444443   35678999999999999999976543

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.71  E-value=0.023  Score=45.59  Aligned_cols=22  Identities=27%  Similarity=0.455  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+.|.|.||+|||+|+.++.+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4689999999999999999864

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=92.70  E-value=0.037  Score=47.70  Aligned_cols=23  Identities=30%  Similarity=0.444  Sum_probs=20.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -.++|.|.||+|||+|+.++.+.
T Consensus        33 l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          33 LTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             cEEEEECCCCCcHHHHHHHHhCC
Confidence            35799999999999999999864

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=92.69  E-value=0.039  Score=49.10  Aligned_cols=34  Identities=18%  Similarity=0.159  Sum_probs=26.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC-----CcEEEEecCCc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH-----FDVYDLELSSV  264 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~-----~~~~~l~~~~~  264 (338)
                      +-+.|++|+|||++++.++..+.     ..+..++..+.
T Consensus        83 IGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F  121 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             EEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeee
Confidence            34899999999999999999873     45666665554

>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=92.69  E-value=0.029  Score=44.73  Aligned_cols=20  Identities=30%  Similarity=0.521  Sum_probs=18.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|.+|+|||+|+..+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999875

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.024  Score=44.68  Aligned_cols=20  Identities=30%  Similarity=0.552  Sum_probs=18.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|.+|+|||+|+..+.+
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67889999999999999875

>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=92.62  E-value=0.03  Score=44.37  Aligned_cols=20  Identities=35%  Similarity=0.566  Sum_probs=18.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|.+|+|||+|+..+.+
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68899999999999999875

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.60  E-value=0.024  Score=45.39  Aligned_cols=22  Identities=18%  Similarity=0.339  Sum_probs=19.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      =+++.|++|+|||+|+..+...
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4688899999999999998864

>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=92.59  E-value=0.03  Score=44.37  Aligned_cols=21  Identities=29%  Similarity=0.515  Sum_probs=18.8

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|.+|+|||+|+..+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            689999999999999998753

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.55  E-value=0.025  Score=45.11  Aligned_cols=20  Identities=40%  Similarity=0.777  Sum_probs=18.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|.||+|||+|+..+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999999875

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.50  E-value=0.029  Score=48.21  Aligned_cols=24  Identities=29%  Similarity=0.545  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||+|+|||+|++.++....
T Consensus        34 ~~~liGpsGaGKSTLl~~i~Gl~~   57 (239)
T d1v43a3          34 FLVLLGPSGCGKTTTLRMIAGLEE   57 (239)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCChHHHHHHHHHcCCC
Confidence            467999999999999999998773

>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=92.49  E-value=0.028  Score=48.29  Aligned_cols=23  Identities=30%  Similarity=0.574  Sum_probs=20.5

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+-|.||.|+|||+|+++++...
T Consensus        31 ~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          31 FMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSS
T ss_pred             EEEEECCCCChHHHHHHHHhcCC
Confidence            45699999999999999999866

>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=92.46  E-value=0.019  Score=45.97  Aligned_cols=20  Identities=30%  Similarity=0.644  Sum_probs=8.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|.||+|||+|+..+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67899999999999998775

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=92.42  E-value=0.087  Score=44.83  Aligned_cols=46  Identities=22%  Similarity=0.231  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEe
Q 035959          215 MKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLE  260 (338)
Q Consensus       215 ~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~  260 (338)
                      ..+++.+++..+.+...||+|.+|+|||-++...+...   |..+..+-
T Consensus        63 ~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~  111 (233)
T d2eyqa3          63 AINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLV  111 (233)
T ss_dssp             HHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEEC
T ss_pred             HHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEc
Confidence            34567777776666778999999999999765544433   66665553

>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=92.37  E-value=0.032  Score=44.62  Aligned_cols=20  Identities=40%  Similarity=0.637  Sum_probs=18.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|++|+|||+|+..++.
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999998874

>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=92.36  E-value=0.027  Score=44.82  Aligned_cols=21  Identities=29%  Similarity=0.494  Sum_probs=18.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      .+.|.|.||+|||||+.++.+
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            367999999999999999975

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.35  E-value=0.036  Score=46.53  Aligned_cols=29  Identities=17%  Similarity=0.118  Sum_probs=24.5

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhCCcEE
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLHFDVY  257 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~~~~~  257 (338)
                      +-+.+-|+-|+||||+++.++++++...+
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l~~~~i   31 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTYPEWHV   31 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCTTSEE
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhhcCC
Confidence            45778999999999999999999865443

>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=92.22  E-value=0.036  Score=44.13  Aligned_cols=20  Identities=30%  Similarity=0.502  Sum_probs=18.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|++|+|||+|+..++.
T Consensus         7 i~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            57889999999999999886

>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=92.22  E-value=0.035  Score=44.71  Aligned_cols=21  Identities=19%  Similarity=0.414  Sum_probs=18.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +++.|.+|+|||+|+..+...
T Consensus         8 ivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998763

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=92.18  E-value=0.031  Score=47.02  Aligned_cols=28  Identities=18%  Similarity=0.207  Sum_probs=23.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEE
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYD  258 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~  258 (338)
                      +-|+|+.|||||+++..+++..|+.++.
T Consensus         4 IgiTG~igSGKsTva~~l~e~~g~~~i~   31 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNYSAVKYQ   31 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEECC
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCeEEc
Confidence            4589999999999999999988865543

>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=92.17  E-value=0.012  Score=46.13  Aligned_cols=21  Identities=33%  Similarity=0.645  Sum_probs=19.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +.|.|.||+|||||+.++.+.
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            578999999999999999865

>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=92.10  E-value=0.053  Score=44.22  Aligned_cols=33  Identities=15%  Similarity=0.268  Sum_probs=27.2

Q ss_pred             CceeeeCC-CCCCcHHHHHHHHHHh---CCcEEEEec
Q 035959          229 RGYLLFGP-PGTGKSSLIAAMANYL---HFDVYDLEL  261 (338)
Q Consensus       229 ~g~LL~Gp-pGtGKT~l~~aia~~l---~~~~~~l~~  261 (338)
                      +-|++.|- +|+|||+++..+|..+   |+.+..++.
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            35788898 6999999999999877   788887764

>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=92.10  E-value=0.053  Score=49.61  Aligned_cols=35  Identities=29%  Similarity=0.285  Sum_probs=27.9

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      .+++++.|++|+|||.++..+...+   |..++.+|..
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~k   87 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN   87 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEET
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            3789999999999999987666543   6777777764

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.07  E-value=0.025  Score=49.72  Aligned_cols=25  Identities=28%  Similarity=0.445  Sum_probs=21.8

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+-|.||+|+|||+|+++|+..+.
T Consensus        63 e~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHhCCCc
Confidence            3467999999999999999998773

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.03  E-value=0.024  Score=49.12  Aligned_cols=25  Identities=24%  Similarity=0.559  Sum_probs=21.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+-|.||+|+|||+|+++++..+.
T Consensus        42 e~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             CEEEEECCCCChHHHHHHHHhcccC
Confidence            4578999999999999999998763

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=92.00  E-value=0.024  Score=48.70  Aligned_cols=24  Identities=33%  Similarity=0.469  Sum_probs=21.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||+|+|||+|++.|+....
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~Gl~~   56 (240)
T d3dhwc1          33 IYGVIGASGAGKSTLIRCVNLLER   56 (240)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCcc
Confidence            467999999999999999998764

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=91.97  E-value=0.032  Score=44.76  Aligned_cols=21  Identities=38%  Similarity=0.602  Sum_probs=18.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~  251 (338)
                      +.+.|.||+|||||+.++.+.
T Consensus        11 V~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHHCC
Confidence            678899999999999999853

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.95  E-value=0.058  Score=44.96  Aligned_cols=32  Identities=22%  Similarity=0.217  Sum_probs=26.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      +.+.|+-|+||||+++.+++.+...+..+...
T Consensus         6 I~iEG~DGsGKST~~~~L~~~L~~~~~~~~~p   37 (214)
T d1tmka_           6 ILIEGLDRTGKTTQCNILYKKLQPNCKLLKFP   37 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTTSEEEEESS
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCEEEEEC
Confidence            45889999999999999999998776666443

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=91.93  E-value=0.027  Score=48.36  Aligned_cols=24  Identities=25%  Similarity=0.537  Sum_probs=21.2

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHh
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      .-+-+.||+|+|||||++.++..+
T Consensus        29 e~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          29 SIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            346799999999999999999876

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=91.86  E-value=0.025  Score=48.68  Aligned_cols=25  Identities=24%  Similarity=0.400  Sum_probs=22.0

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+-+.||+|+|||+|+++++..+.
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3478999999999999999998773

>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=91.85  E-value=0.024  Score=48.40  Aligned_cols=24  Identities=25%  Similarity=0.674  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||.|+|||+|+++++....
T Consensus        28 ~~~liGpsGaGKSTll~~l~Gl~~   51 (229)
T d3d31a2          28 YFVILGPTGAGKTLFLELIAGFHV   51 (229)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhcCcC
Confidence            467999999999999999998764

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.80  E-value=0.017  Score=46.19  Aligned_cols=20  Identities=30%  Similarity=0.570  Sum_probs=17.3

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|++|+|||+|+..+++
T Consensus         6 i~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC-
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68899999999999998765

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.65  E-value=0.038  Score=44.72  Aligned_cols=20  Identities=30%  Similarity=0.544  Sum_probs=18.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|.+|+|||+|+..+.+
T Consensus        12 i~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            68999999999999999876

>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=91.63  E-value=0.023  Score=45.71  Aligned_cols=21  Identities=24%  Similarity=0.529  Sum_probs=18.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -+++.|+||+|||+|+..+..
T Consensus        19 KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          19 RILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            378999999999999998753

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.59  E-value=0.034  Score=48.00  Aligned_cols=25  Identities=36%  Similarity=0.571  Sum_probs=21.7

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+-+.||+|+|||||+++++..+.
T Consensus        41 e~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcccC
Confidence            3467999999999999999998763

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.51  E-value=0.039  Score=44.47  Aligned_cols=20  Identities=25%  Similarity=0.519  Sum_probs=18.4

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|++|+|||+|+..+..
T Consensus         5 ivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68999999999999998876

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.39  E-value=0.04  Score=44.88  Aligned_cols=20  Identities=40%  Similarity=0.728  Sum_probs=18.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +++.|++|+|||+|+..+..
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            67899999999999998875

>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=91.29  E-value=0.042  Score=44.60  Aligned_cols=20  Identities=20%  Similarity=0.458  Sum_probs=17.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|++|+|||+|+..+..
T Consensus         6 vvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67899999999999988775

>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=91.28  E-value=0.034  Score=44.67  Aligned_cols=20  Identities=35%  Similarity=0.576  Sum_probs=17.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +-|.|+||+|||||+.++.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            56899999999999999854

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.16  E-value=0.023  Score=47.51  Aligned_cols=25  Identities=16%  Similarity=0.191  Sum_probs=22.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      -+.+-|+-|+||||+++.++..+..
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            4678999999999999999998853

>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=91.11  E-value=0.023  Score=45.17  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=18.9

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      .-+.|.|+|++|||+|+.++..
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            3488999999999999998853

>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=91.00  E-value=0.047  Score=47.38  Aligned_cols=23  Identities=35%  Similarity=0.595  Sum_probs=19.9

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+|+||.|+|||+++.|++-.++
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~lg   49 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWVFG   49 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHTSC
T ss_pred             EEEECCCCCcHHHHHHHHHHHhC
Confidence            47999999999999999976554

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.90  E-value=0.045  Score=47.45  Aligned_cols=23  Identities=22%  Similarity=0.403  Sum_probs=20.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+-|.||.|+|||+|+++++...
T Consensus        30 i~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          30 VISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCCcHHHHHHHHHcCc
Confidence            35699999999999999999765

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=90.89  E-value=0.026  Score=48.55  Aligned_cols=23  Identities=26%  Similarity=0.631  Sum_probs=20.8

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+-|.||+|+|||+|++.++...
T Consensus        33 ~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          33 RFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTSS
T ss_pred             EEEEECCCCCcHHHHHHHHHcCc
Confidence            46799999999999999999866

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=90.73  E-value=0.042  Score=47.06  Aligned_cols=24  Identities=29%  Similarity=0.512  Sum_probs=21.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||.|+|||+|+++++..+.
T Consensus        34 i~~liGpnGaGKSTl~~~i~Gl~~   57 (240)
T d1ji0a_          34 IVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCC
Confidence            356999999999999999998774

>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=90.73  E-value=0.038  Score=47.35  Aligned_cols=23  Identities=26%  Similarity=0.676  Sum_probs=20.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +-|.||.|+|||+|+++++..+.
T Consensus        31 ~glvG~nGaGKSTLl~~l~G~~~   53 (238)
T d1vpla_          31 FGLIGPNGAGKTTTLRIISTLIK   53 (238)
T ss_dssp             EEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEECCCCCCHHHHHHHHhcCCC
Confidence            45999999999999999998774

>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=90.51  E-value=0.05  Score=46.38  Aligned_cols=25  Identities=36%  Similarity=0.538  Sum_probs=19.4

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      +..+|.|++|+|||||+.++.....
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~~~  122 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPELG  122 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC---
T ss_pred             ceEEEECCCCccHHHHHHhhccHhH
Confidence            4567889999999999999886543

>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=90.49  E-value=0.044  Score=43.82  Aligned_cols=20  Identities=55%  Similarity=0.695  Sum_probs=18.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      +.|.|.||+|||||+.++.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67899999999999999964

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=90.00  E-value=0.064  Score=45.56  Aligned_cols=23  Identities=48%  Similarity=0.665  Sum_probs=19.9

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l  252 (338)
                      -+-|.||.|+|||+|+++++...
T Consensus        27 i~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          27 ILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             EEECBCCTTSSHHHHHHHHHTSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            35689999999999999999744

>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=89.95  E-value=0.37  Score=37.27  Aligned_cols=62  Identities=11%  Similarity=0.310  Sum_probs=39.0

Q ss_pred             eeeCCCCCCcHH-HHHHHHH--HhCCcEEEEecCCc-------C-------------CchHHHHHHHhc---CCCcEEEE
Q 035959          232 LLFGPPGTGKSS-LIAAMAN--YLHFDVYDLELSSV-------E-------------GNKHLRKVLIAT---ENKSILVV  285 (338)
Q Consensus       232 LL~GppGtGKT~-l~~aia~--~l~~~~~~l~~~~~-------~-------------~~~~l~~~l~~~---~~~~Il~i  285 (338)
                      +++||-.+|||+ |++.+-+  ..|..+..+....-       .             ...++...+...   ....+|+|
T Consensus         6 ~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dvI~I   85 (139)
T d2b8ta1           6 FITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGI   85 (139)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEEE
T ss_pred             EEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccceEEcccCceeeeEEeccchhhHHHHHhhccccCcCEEEe
Confidence            689999999999 6666533  34777766644311       0             123333333322   25789999


Q ss_pred             cCCCccCC
Q 035959          286 GDIDCCTE  293 (338)
Q Consensus       286 DeiD~~~~  293 (338)
                      ||+.-+.+
T Consensus        86 DE~QFf~d   93 (139)
T d2b8ta1          86 DEVQFFDD   93 (139)
T ss_dssp             CSGGGSCT
T ss_pred             chhhhcch
Confidence            99998743

>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=89.88  E-value=0.088  Score=46.26  Aligned_cols=34  Identities=15%  Similarity=0.266  Sum_probs=23.1

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCCc
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSSV  264 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~~  264 (338)
                      +-+.|++|+|||++++++++.+   +.....++..+.
T Consensus         7 IgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsf   43 (288)
T d1a7ja_           7 ISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   43 (288)
T ss_dssp             EEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCC
Confidence            4599999999999999999877   455555555443

>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=89.87  E-value=0.077  Score=47.73  Aligned_cols=26  Identities=31%  Similarity=0.652  Sum_probs=21.6

Q ss_pred             Cce-eeeCCCCCCcHHHHHHHHHHhCC
Q 035959          229 RGY-LLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       229 ~g~-LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      .|+ +++||.|+|||+++.||+-.+|.
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~~~lg~   51 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAISFVLGV   51 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            354 79999999999999999866653

>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=89.71  E-value=0.19  Score=40.85  Aligned_cols=22  Identities=36%  Similarity=0.387  Sum_probs=17.2

Q ss_pred             cCceeeeCCCCCCcHHHHHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia  249 (338)
                      .+.+++.-|+|+|||.......
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~   61 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPA   61 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCcchhhhhh
Confidence            3679999999999997654433

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=89.57  E-value=0.035  Score=48.08  Aligned_cols=25  Identities=28%  Similarity=0.505  Sum_probs=21.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          229 RGYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      .-+.+.||+|+|||+|++.++..+.
T Consensus        45 e~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHhcCC
Confidence            4578999999999999999987663

>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=89.41  E-value=0.081  Score=42.56  Aligned_cols=19  Identities=37%  Similarity=0.644  Sum_probs=17.3

Q ss_pred             eeeeCCCCCCcHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMA  249 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia  249 (338)
                      ++|.|.+|+|||+|+..+.
T Consensus         5 ivllG~~~vGKTsll~r~~   23 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQMR   23 (200)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6899999999999999983

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=89.19  E-value=0.066  Score=46.14  Aligned_cols=24  Identities=42%  Similarity=0.812  Sum_probs=21.2

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHhC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      -+-|.||.|+|||+|+++++..+.
T Consensus        32 i~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          32 VTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHHCCCc
Confidence            356999999999999999998774

>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=89.09  E-value=0.1  Score=41.76  Aligned_cols=22  Identities=32%  Similarity=0.347  Sum_probs=19.1

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMANY  251 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~  251 (338)
                      -+++.|++|+|||+|+..+...
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3689999999999999988763

>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=88.10  E-value=0.096  Score=46.02  Aligned_cols=35  Identities=29%  Similarity=0.502  Sum_probs=25.9

Q ss_pred             HHHHHHHhhhcCc--eeeeCCCCCCcHHHHHHHHHHhC
Q 035959          218 MIMDDLERAWKRG--YLLFGPPGTGKSSLIAAMANYLH  253 (338)
Q Consensus       218 ~i~~~l~~~~~~g--~LL~GppGtGKT~l~~aia~~l~  253 (338)
                      ++++-+. |-.+|  .++.|++|||||+|+..+++...
T Consensus        32 r~ID~l~-PigrGQr~~I~g~~g~GKT~l~~~i~~~~~   68 (289)
T d1xpua3          32 RVLDLAS-PIGRGQRGLIVAPPKAGKTMLLQNIAQSIA   68 (289)
T ss_dssp             HHHHHHS-CCBTTCEEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             eeeeecc-cccCCCeeeEeCCCCCCHHHHHHHHHHHHh
Confidence            4444443 44444  79999999999999999998663

>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=88.05  E-value=0.17  Score=42.94  Aligned_cols=34  Identities=18%  Similarity=0.257  Sum_probs=27.4

Q ss_pred             ceeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          230 GYLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      -+-++|.=|+|||+++..+|..+   |.++..+|+..
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            45578999999999998888766   78888887753

>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=88.03  E-value=0.11  Score=43.65  Aligned_cols=22  Identities=36%  Similarity=0.465  Sum_probs=19.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +++.|..|+|||||++.+.+..
T Consensus         6 ~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           6 TLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             EEEEESSSSSCHHHHHHHHHSC
T ss_pred             EEEeeCCCCCHHHHHHHHHhcC
Confidence            6899999999999999988754

>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=87.44  E-value=0.12  Score=41.19  Aligned_cols=22  Identities=36%  Similarity=0.501  Sum_probs=19.2

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      ++|.|.+|+|||+|+..+...-
T Consensus         5 iv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            6899999999999999987643

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=87.05  E-value=0.15  Score=42.44  Aligned_cols=21  Identities=33%  Similarity=0.551  Sum_probs=18.3

Q ss_pred             ceeeeCCCCCCcHHHHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~aia~  250 (338)
                      -++|.|++|+|||+|+.-+..
T Consensus         8 KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            379999999999999998753

>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=86.98  E-value=0.77  Score=41.98  Aligned_cols=50  Identities=20%  Similarity=0.292  Sum_probs=38.5

Q ss_pred             ChhHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          212 DTDMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       212 ~~~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      .|..-+.+++.+... .+..+|.|-+|+|||.+++++++..+.+++.|...
T Consensus        16 QP~aI~~l~~~l~~g-~~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n   65 (413)
T d1t5la1          16 QPQAIAKLVDGLRRG-VKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHN   65 (413)
T ss_dssp             HHHHHHHHHHHHHHT-CSEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSS
T ss_pred             CHHHHHHHHHHHhcC-CCcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCC
Confidence            345456677777532 24578999999999999999999999998887544

>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=86.89  E-value=0.15  Score=45.17  Aligned_cols=21  Identities=14%  Similarity=0.464  Sum_probs=16.6

Q ss_pred             hhcCceeeeCCCCCCcHHHHH
Q 035959          226 AWKRGYLLFGPPGTGKSSLIA  246 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~~  246 (338)
                      .+...++-||+.|+|||+.+.
T Consensus        74 G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          74 GYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             TCCEEEEEECSTTSSHHHHHT
T ss_pred             CCCcceeeecccCCCCceecc
Confidence            344457899999999999763

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=85.99  E-value=0.16  Score=45.43  Aligned_cols=24  Identities=33%  Similarity=0.175  Sum_probs=21.7

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      +.+-|+-|+|||++++.++++++.
T Consensus         9 I~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           9 IYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEECCccCCHHHHHHHHHHHhcc
Confidence            578899999999999999999854

>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=85.90  E-value=0.18  Score=45.26  Aligned_cols=19  Identities=26%  Similarity=0.572  Sum_probs=15.3

Q ss_pred             hcCceeeeCCCCCCcHHHH
Q 035959          227 WKRGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~  245 (338)
                      +...++-||++|+|||+.+
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            3345789999999999875

>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=85.90  E-value=0.34  Score=39.59  Aligned_cols=40  Identities=23%  Similarity=0.369  Sum_probs=25.1

Q ss_pred             ccccccCChhHHHHHHHH-------HHh------hhcCceeeeCCCCCCcHHH
Q 035959          205 TFDTLAMDTDMKKMIMDD-------LER------AWKRGYLLFGPPGTGKSSL  244 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~-------l~~------~~~~g~LL~GppGtGKT~l  244 (338)
                      +|+++..++++.+.+.+.       ++.      -..+.+++.+|+|+|||..
T Consensus         2 sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTla   54 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAA   54 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHH
T ss_pred             ChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhh
Confidence            466666666555544332       000      1346799999999999963

>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=85.51  E-value=0.64  Score=38.47  Aligned_cols=32  Identities=31%  Similarity=0.477  Sum_probs=21.7

Q ss_pred             cCceeeeCCCCCCcHHHHHHHHHHh---CCcEEEE
Q 035959          228 KRGYLLFGPPGTGKSSLIAAMANYL---HFDVYDL  259 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~~aia~~l---~~~~~~l  259 (338)
                      .+.+++.+|+|+|||..+...+.+.   +..++.+
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv   92 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVI   92 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEE
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEE
Confidence            4678999999999997655444332   4445444

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.93  E-value=0.26  Score=40.54  Aligned_cols=17  Identities=24%  Similarity=0.327  Sum_probs=14.9

Q ss_pred             cCceeeeCCCCCCcHHH
Q 035959          228 KRGYLLFGPPGTGKSSL  244 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l  244 (338)
                      ++.+++..|+|||||..
T Consensus        38 g~dvl~~A~TGsGKTla   54 (207)
T d1t6na_          38 GMDVLCQAKSGMGKTAV   54 (207)
T ss_dssp             TCCEEEECCTTSCHHHH
T ss_pred             CCCeEEEeccccccccc
Confidence            57799999999999973

>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=84.81  E-value=0.41  Score=39.08  Aligned_cols=32  Identities=28%  Similarity=0.358  Sum_probs=25.7

Q ss_pred             eeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          232 LLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       232 LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      +..|-.|+|||+++..+|..+   |.++..+|+..
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            345889999999999888776   78888887753

>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=84.40  E-value=0.37  Score=39.73  Aligned_cols=40  Identities=20%  Similarity=0.268  Sum_probs=27.0

Q ss_pred             ccccccCChhHHHHHHHHHHh-------------hhcCceeeeCCCCCCcHHH
Q 035959          205 TFDTLAMDTDMKKMIMDDLER-------------AWKRGYLLFGPPGTGKSSL  244 (338)
Q Consensus       205 ~f~~l~~~~~~k~~i~~~l~~-------------~~~~g~LL~GppGtGKT~l  244 (338)
                      +|+++..++++.+.+.+.=-.             -..+.+++..|+|||||..
T Consensus        11 sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a   63 (212)
T d1qdea_          11 KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT   63 (212)
T ss_dssp             CGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             ChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhh
Confidence            677777777666555431100             2356799999999999984

>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=84.40  E-value=0.32  Score=44.30  Aligned_cols=22  Identities=32%  Similarity=0.499  Sum_probs=19.6

Q ss_pred             CceeeeCCCCCCcHHHHHHHHH
Q 035959          229 RGYLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       229 ~g~LL~GppGtGKT~l~~aia~  250 (338)
                      -.+.+.|.||+|||||+.++..
T Consensus        57 l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          57 LNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4578999999999999999974

>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=84.13  E-value=0.27  Score=43.76  Aligned_cols=19  Identities=21%  Similarity=0.534  Sum_probs=15.2

Q ss_pred             hcCceeeeCCCCCCcHHHH
Q 035959          227 WKRGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       227 ~~~g~LL~GppGtGKT~l~  245 (338)
                      +...++-||..|+|||+.+
T Consensus        82 ~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          82 YNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             cccceeeeeccCCcccccc
Confidence            3345678999999999965

>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=84.12  E-value=0.34  Score=41.51  Aligned_cols=33  Identities=21%  Similarity=0.281  Sum_probs=25.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh---CCcEEEEecCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL---HFDVYDLELSS  263 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l---~~~~~~l~~~~  263 (338)
                      +.++|-=|+|||+++..+|..+   |+.+..+|+..
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            4468999999999877776554   88888887753

>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=83.42  E-value=0.25  Score=44.02  Aligned_cols=20  Identities=25%  Similarity=0.544  Sum_probs=16.0

Q ss_pred             hhcCceeeeCCCCCCcHHHH
Q 035959          226 AWKRGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~  245 (338)
                      .....++-||..|+|||+.+
T Consensus        79 G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          79 GYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             TCEEEEEEEECTTSSHHHHH
T ss_pred             cCCceEEeeeeccccceEEe
Confidence            34456789999999999875

>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=83.12  E-value=0.5  Score=38.58  Aligned_cols=32  Identities=25%  Similarity=0.343  Sum_probs=25.5

Q ss_pred             eeee-CCCCCCcHHHHHHHHHHh---CCcEEEEecC
Q 035959          231 YLLF-GPPGTGKSSLIAAMANYL---HFDVYDLELS  262 (338)
Q Consensus       231 ~LL~-GppGtGKT~l~~aia~~l---~~~~~~l~~~  262 (338)
                      +-++ +-.|+|||+++..+|..+   |.++..+|+.
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 669999999999988766   7888888864

>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=82.98  E-value=0.25  Score=44.03  Aligned_cols=24  Identities=21%  Similarity=0.293  Sum_probs=21.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHhCC
Q 035959          231 YLLFGPPGTGKSSLIAAMANYLHF  254 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l~~  254 (338)
                      +.+-|+-|+||||+++.+++++..
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            568899999999999999999864

>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=82.96  E-value=0.59  Score=38.20  Aligned_cols=16  Identities=44%  Similarity=0.482  Sum_probs=14.5

Q ss_pred             cCceeeeCCCCCCcHH
Q 035959          228 KRGYLLFGPPGTGKSS  243 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~  243 (338)
                      .+.+++..|+|||||.
T Consensus        40 g~dvl~~a~TGsGKTl   55 (206)
T d1veca_          40 GRDILARAKNGTGKSG   55 (206)
T ss_dssp             TCCEEEECCSSSTTHH
T ss_pred             CCCEEeeccCcccccc
Confidence            5779999999999996

>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=82.78  E-value=0.44  Score=39.47  Aligned_cols=40  Identities=18%  Similarity=0.237  Sum_probs=28.3

Q ss_pred             CccccccCChhHHHHHHHHHHh--------------hhcCceeeeCCCCCCcHHH
Q 035959          204 STFDTLAMDTDMKKMIMDDLER--------------AWKRGYLLFGPPGTGKSSL  244 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~l~~--------------~~~~g~LL~GppGtGKT~l  244 (338)
                      .+|+++..++.+.+.+.+. .-              -..+.+++..|+|||||..
T Consensus        12 ~sF~~l~L~~~l~~~L~~~-g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTla   65 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYAY-GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTAT   65 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHHH-TCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHH
T ss_pred             CCHHHCCCCHHHHHHHHHC-CCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhh
Confidence            3788888877766655321 11              2357799999999999984

>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=82.76  E-value=0.29  Score=38.60  Aligned_cols=20  Identities=35%  Similarity=0.599  Sum_probs=17.6

Q ss_pred             eeeeCCCCCCcHHHHHHHHH
Q 035959          231 YLLFGPPGTGKSSLIAAMAN  250 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~  250 (338)
                      ++|.|..|+|||+|+.-+..
T Consensus         5 ivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            68999999999999987754

>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=82.61  E-value=1.2  Score=40.46  Aligned_cols=48  Identities=23%  Similarity=0.228  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHHhhhcCceeeeCCCCCCcHHHHHHHHHHhCCcEEEEecC
Q 035959          214 DMKKMIMDDLERAWKRGYLLFGPPGTGKSSLIAAMANYLHFDVYDLELS  262 (338)
Q Consensus       214 ~~k~~i~~~l~~~~~~g~LL~GppGtGKT~l~~aia~~l~~~~~~l~~~  262 (338)
                      ...+++.+.|.. ..+..+|.|.+|++|++++++++...+.+++.|...
T Consensus        15 ~aI~~l~~~L~~-g~~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~~   62 (408)
T d1c4oa1          15 KAIAGLVEALRD-GERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPN   62 (408)
T ss_dssp             HHHHHHHHHHHT-TCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESS
T ss_pred             HHHHHHHHHHhc-CCCcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeCC
Confidence            345666666653 234478999999999999999999999998887543

>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=82.23  E-value=1.7  Score=33.41  Aligned_cols=65  Identities=17%  Similarity=0.306  Sum_probs=38.0

Q ss_pred             Cce--eeeCCCCCCcHHHHHHHHH---HhCCcEEEEecCC--------cCC----------chHHHHHHHhc-CCCcEEE
Q 035959          229 RGY--LLFGPPGTGKSSLIAAMAN---YLHFDVYDLELSS--------VEG----------NKHLRKVLIAT-ENKSILV  284 (338)
Q Consensus       229 ~g~--LL~GppGtGKT~l~~aia~---~l~~~~~~l~~~~--------~~~----------~~~l~~~l~~~-~~~~Il~  284 (338)
                      .|.  ++.||-.+|||+-+-..++   ..|..+..+....        +.+          ..++..++... ....+|+
T Consensus         6 ~G~l~lI~GpMfSGKTteLi~~~~~~~~~g~~vl~i~~~~D~Ry~~~~i~sh~g~~~~a~~~~~~~~~~~~~~~~~dvI~   85 (141)
T d1xx6a1           6 HGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIA   85 (141)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEE
T ss_pred             ceeEEEEEeccccHHHHHHHHHHHHhhhcCCcEEEEEeccccccccceeeecccceEEEEEecchhhhhhhhcccccEEE
Confidence            555  6899999999995444443   3466666554321        110          01122222222 3679999


Q ss_pred             EcCCCccCC
Q 035959          285 VGDIDCCTE  293 (338)
Q Consensus       285 iDeiD~~~~  293 (338)
                      |||+.-+.+
T Consensus        86 IDE~QFf~d   94 (141)
T d1xx6a1          86 IDEVQFFDD   94 (141)
T ss_dssp             ECSGGGSCT
T ss_pred             Eeehhhccc
Confidence            999998754

>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=81.61  E-value=0.26  Score=44.39  Aligned_cols=20  Identities=25%  Similarity=0.506  Sum_probs=16.0

Q ss_pred             hhcCceeeeCCCCCCcHHHH
Q 035959          226 AWKRGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       226 ~~~~g~LL~GppGtGKT~l~  245 (338)
                      .+...++-||..|+|||+..
T Consensus       112 G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         112 GGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             TCEEEEEEEESTTSSHHHHH
T ss_pred             ccCceEEeeccCCCCCceee
Confidence            34455789999999999876

>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=81.45  E-value=0.35  Score=42.82  Aligned_cols=18  Identities=22%  Similarity=0.503  Sum_probs=15.1

Q ss_pred             cCceeeeCCCCCCcHHHH
Q 035959          228 KRGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       228 ~~g~LL~GppGtGKT~l~  245 (338)
                      ...++-||..|+|||+..
T Consensus        85 n~~i~aYGqTGSGKTyTm  102 (330)
T d1ry6a_          85 VCSCFAYGQTGSGKTYTM  102 (330)
T ss_dssp             EEEEEEECCTTSSHHHHH
T ss_pred             CeEEEeeeccccccceee
Confidence            344789999999999986

>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=81.24  E-value=0.27  Score=44.26  Aligned_cols=26  Identities=19%  Similarity=0.411  Sum_probs=18.4

Q ss_pred             HHHHHhhhcCceeeeCCCCCCcHHHH
Q 035959          220 MDDLERAWKRGYLLFGPPGTGKSSLI  245 (338)
Q Consensus       220 ~~~l~~~~~~g~LL~GppGtGKT~l~  245 (338)
                      ++.+-..+...++-||+.|+|||+..
T Consensus        67 v~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          67 VQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCceeeeccccCCCCccccc
Confidence            33333344456789999999999974

>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=81.20  E-value=0.22  Score=44.12  Aligned_cols=18  Identities=39%  Similarity=0.637  Sum_probs=15.4

Q ss_pred             ceeeeCCCCCCcHHHHHH
Q 035959          230 GYLLFGPPGTGKSSLIAA  247 (338)
Q Consensus       230 g~LL~GppGtGKT~l~~a  247 (338)
                      --||+|.+|||||+|...
T Consensus        16 valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             EEEEEECTTSCHHHHTCB
T ss_pred             EEEEEccCCCCccccccC
Confidence            369999999999998754

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=80.39  E-value=0.39  Score=41.65  Aligned_cols=22  Identities=41%  Similarity=0.631  Sum_probs=20.0

Q ss_pred             eeeeCCCCCCcHHHHHHHHHHh
Q 035959          231 YLLFGPPGTGKSSLIAAMANYL  252 (338)
Q Consensus       231 ~LL~GppGtGKT~l~~aia~~l  252 (338)
                      +++.|++|+|||+|+.-+++..
T Consensus        71 ~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          71 IGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEeeCCCCCCHHHHHHHHHHHH
Confidence            8999999999999999998764

>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=80.32  E-value=0.62  Score=38.72  Aligned_cols=40  Identities=30%  Similarity=0.466  Sum_probs=27.9

Q ss_pred             CccccccCChhHHHHHHHH-HHh------------hhcCceeeeCCCCCCcHH
Q 035959          204 STFDTLAMDTDMKKMIMDD-LER------------AWKRGYLLFGPPGTGKSS  243 (338)
Q Consensus       204 ~~f~~l~~~~~~k~~i~~~-l~~------------~~~~g~LL~GppGtGKT~  243 (338)
                      .+|+++..++.+.+.+.+. ...            -..+.++...|+|||||.
T Consensus        17 ~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          17 PTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             CSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHH
T ss_pred             CCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhh
Confidence            3788888777766655432 000            235779999999999997