Citrus Sinensis ID: 045120

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370----
Protein Sequence
MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEAKEKGEEIEEKVEKWLTRYQLSKKAKTEVKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLVHTTAA
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHccccHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccEEEEEcccccccccccccccccccccccEEEEEcccccccEEcccccHHHHHHHHHHHcccccccccHHHHHHHHHHHcccccHHHHHHHHHcccccccccHHHHHHHcccccHHHHHHHcccccccccccccccccHHHcccccccHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHcccHHHHHHHHHHHHcccccccHHHHHHHHHccccHHccccEEEEEEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccEEEEEEEccccHccHHHHcccccccccccEEEEEEccccccEEEccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccHHHHHHHHHcccHHHHHcHcccHHHHcHcEEcccccccccHHHHHHHHHcccEEEEcccc
Coil and Loop (DISEMBL)
MLEVIVTLVLELVKwlappterQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEAKEKGEEIEEKVEKWLTRYQLSKKAKTEVKALIELGEevkkfdivshctipeeiwlKSNKVYEAFESRVSNLKSTQNALtnanggigkTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLDletvkipfrndsrdnNVVLLSMGSKDNFLIANITEEEAWRLFKimngddvenckfkSTAINVAKACGAGLfctlttnasksssIYSHvsndyqsiykpkpylavfqdleptivktafvdpkwYLALKEEFEALQRNQTWSLVHTTAA
Flexible Loop (DISEMBL)
MLEVIVTLVLelvkwlappterqlvYLRKRNYNANLENLKAEleklkvertsiqlrvseakekgeeieekVEKWltryqlskkaKTEVKALIElgeevkkfdivshctipeeiwlksNKVYEAFESRVSNLKSTqnaltnanggigKTTLAKEFAKQAredklfdrvvfsevsqtsdikkiqGDIAeklglelseeaEYRRASRLYERLKNENKILVILANIWKLLDLETVkipfrndsrdnNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLVHTTAA
Low Complexity Region (SEG)
MlevivtlvlelvKWLAPPTERQLVYLRKRNYnanlenlkaeleklkVERTSIQLRVSeakekgeeieekvekWLTRYQLSKKAKTEVKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLVHTTAA
Disordered region (IsUnstruct)
**EVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKL************************VEKWLTRYQLSKKAKTEVKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVS*************GGIGKTTLAKEFAK*AREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS**AEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLV*****
Disordered Region (DISOPRED)
MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSE******EI*EKVEKWLTRYQLSKK******************************************SRVSNLKSTQNALTNANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL*************LYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEP**VKTAFVDPKWYLALKEEFEALQRNQTWSLVHTTAA
Disordered Region (DISEMBL)
MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSE********EEKVEKWLTRYQLSKKAKTEVKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLVHTTAA
Disordered Region (DISPRO)
MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEAKEKGEEIEEKVEKWLTRYQLSKKAKTEVKALIELG*********************SNKVYEAFESRVSNLKSTQNALTNANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLVHTT**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLEVIVTLVLELVKWLAPPTExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxYQLSKKAKTEVKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLxxxxxxxxxxxxxxxxxxxxxNKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLVHTTAA
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	374	2.2.26 [Sep-21-2011]
Q9T048	985	Disease resistance protei	yes	no	0.462	0.175	0.312	6e-17
O81825	919	Probable disease resistan	no	no	0.425	0.173	0.321	5e-13
O23317	719	Probable disease resistan	no	no	0.350	0.182	0.344	6e-13
O22727	967	Probable disease resistan	no	no	0.732	0.283	0.273	1e-12
O64973	889	Disease resistance protei	no	no	0.395	0.166	0.323	4e-12
O64789	925	Probable disease resistan	no	no	0.649	0.262	0.264	1e-10
O64790	762	Probable disease resistan	no	no	0.360	0.177	0.326	5e-10
Q9FG90	862	Probable disease resistan	no	no	0.692	0.300	0.238	6e-10
Q9LVT3	948	Probable disease resistan	no	no	0.644	0.254	0.258	6e-10
Q940K0	889	Probable disease resistan	no	no	0.363	0.152	0.328	2e-09

>sp|Q9T048|DRL27_ARATH Disease resistance protein At4g27190 OS=Arabidopsis thaliana GN=At4g27190 PE=2 SV=1

 Score = 89.0 bits (219), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 59/189 (31%), Positives = 101/189 (53%), Gaps = 16/189 (8%)

Query: 143 GGIGKTTLAKEFAKQARED---KLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS-EEAE 198
           GG+GKTTL +    + RE+   + F  V+F  VS+  D +++Q  IAE+L ++   EE+E
Sbjct: 173 GGVGKTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDPREVQKQIAERLDIDTQMEESE 232

Query: 199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLL--------SMG 250
            + A R+Y  L  E K L+IL ++WK +DL+ + IP   +++ + V+L         SM 
Sbjct: 233 EKLARRIYVGLMKERKFLLILDDVWKPIDLDLLGIPRTEENKGSKVILTSRFLEVCRSMK 292

Query: 251 SKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS---- 306
           +  +  +  + EE+AW LF    GD V +   +  A  V++ CG      +T   +    
Sbjct: 293 TDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAMRGK 352

Query: 307 KSSSIYSHV 315
           K+  +++HV
Sbjct: 353 KNVKLWNHV 361

Disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|O81825|DRL28_ARATH Probable disease resistance protein At4g27220 OS=Arabidopsis thaliana GN=At4g27220 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 56/174 (32%), Positives = 91/174 (52%), Gaps = 15/174 (8%)

Query: 143 GGIGKTTLAK----EFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAE 198
           GG+GKTTL +    +  K A   + F  V++  VS+  D+K++Q DIA++LG   + E  
Sbjct: 143 GGVGKTTLVRTLNNDLLKYAATQQ-FALVIWVTVSKDFDLKRVQMDIAKRLGKRFTREQM 201

Query: 199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND-SRDNNVVLLS--------M 249
            +    + ERL +    L+IL ++W  +DL+ + IP   + S+D+ VVL S        M
Sbjct: 202 NQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLALERSKDSKVVLTSRRLEVCQQM 261

Query: 250 GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTT 303
            + +N  +A + E+EAW LF    G+   +   K  A +V+  C  GL   + T
Sbjct: 262 MTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVSHEC-CGLPLAIIT 314

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O23317|DRL24_ARATH Probable disease resistance protein At4g14610 OS=Arabidopsis thaliana GN=At4g14610 PE=3 SV=1

 Score = 75.5 bits (184), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 51/148 (34%), Positives = 87/148 (58%), Gaps = 17/148 (11%)

Query: 143 GGIGKTTLAKEFAKQARE-DKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL---ELSEEAE 198
           GG+GKTTL  +  K+  E D  FD V++  VS+TS+I +IQ DIA++LGL   E  ++ E
Sbjct: 158 GGVGKTTLLTQINKKFSETDGGFDIVMWVVVSKTSEIYRIQEDIAKRLGLTGEEWDKKNE 217

Query: 199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLL----------S 248
            +RA  ++  L+  +K +++L +IW+ ++LE V +P+   SR+N  ++            
Sbjct: 218 NKRAVDIHNVLRR-HKFVLLLDDIWEKVNLELVGVPY--PSRENGSIVAFTTRSRDVCGR 274

Query: 249 MGSKDNFLIANITEEEAWRLFKIMNGDD 276
           MG  D   ++ +  E+AW LF+   G++
Sbjct: 275 MGVDDPMQVSCLEPEDAWDLFQNKVGEN 302

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O22727|DRL16_ARATH Probable disease resistance protein At1g61190 OS=Arabidopsis thaliana GN=At1g61190 PE=3 SV=1

 Score = 74.3 bits (181), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 150/340 (44%), Gaps = 66/340 (19%)

Query: 30  RNYNANLENLKAELEKLKVERTSIQLRVSEAKEKGEEIEEKVEKWLTRYQLSKKAKTEVK 89
           RN   NL  L+ E+E L+  +  +Q +V+  + + ++  E V+ WL R         E K
Sbjct: 29  RNLEKNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVN---SIDIECK 85

Query: 90  ALIELGE-EVKKFDIVSHCT---------------IPEEIW-LKSNKVYEAF-------- 124
            L+ +   E++K  +   C+               + EE+  LKS   ++          
Sbjct: 86  DLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVFLLLEEVTKLKSEGNFDEVSQPPPRSE 145

Query: 125 -ESRVSN--------LKSTQNALT---------NANGGIGKTTLAKEFA-KQAREDKLFD 165
            E R +         LK   N L          +  GG+GKTTL K+   K A     FD
Sbjct: 146 VEERPTQPTIGQEEMLKKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAETGGTFD 205

Query: 166 RVVFSEVSQTSDIKKIQGDIAEKLGL--EL-SEEAEYRRASRLYERLKNENKILVILANI 222
            V++  VSQ + + K+Q DIAEKL L  +L   + E  +A+ ++  LK + + +++L +I
Sbjct: 206 IVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATDIHRVLKGK-RFVLMLDDI 264

Query: 223 WKLLDLETVKIPFRND---------SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMN 273
           W+ +DLE + IP+ ++         +RD  V    MG      +  +  E+AW LFK   
Sbjct: 265 WEKVDLEAIGIPYPSEVNKCKVAFTTRDQKVC-GQMGDHKPMQVKCLEPEDAWELFKNKV 323

Query: 274 GDDV--ENCKFKSTAINVAKACGA---GLFCTLTTNASKS 308
           GD+    +      A  VA+ C      L C   T ASK+
Sbjct: 324 GDNTLRSDPVIVGLAREVAQKCRGLPLALSCIGETMASKT 363

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O64973|RPS5_ARATH Disease resistance protein RPS5 OS=Arabidopsis thaliana GN=RPS5 PE=1 SV=2

 Score = 72.8 bits (177), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/167 (32%), Positives = 91/167 (54%), Gaps = 19/167 (11%)

Query: 143 GGIGKTTLAKEFA-KQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL---ELSEEAE 198
           GG+GKTTL  +   K ++ D  FD V++  VS++S ++KIQ DIAEK+GL   E SE+ +
Sbjct: 185 GGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWSEKND 244

Query: 199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNV----------VLLS 248
            + A  ++  L+   K +++L +IW+ ++L+ V +P+   S+DN            V   
Sbjct: 245 NQIAVDIHNVLR-RRKFVLLLDDIWEKVNLKAVGVPY--PSKDNGCKVAFTTRSRDVCGR 301

Query: 249 MGSKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKAC 293
           MG  D   ++ +  EE+W LF++  G +    +      A  VA+ C
Sbjct: 302 MGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKC 348

Disease resistance (R) protein that specifically recognizes the avrPphB type III effector avirulence protein from Pseudomonas syringae. Also confers resistance against Hyaloperonospora parasitica (downy mildew). Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Requires PBS1 to trigger the defense reaction against avrPphB. Probably triggers the defense mechanism when PBS1 is cleaved by avrPphB, suggesting that it detects indirectly the protease activity of avrPphB, and possibly binds to the cleaved RPS5.

Arabidopsis thaliana (taxid: 3702)

>sp|O64789|DRL18_ARATH Probable disease resistance protein At1g61310 OS=Arabidopsis thaliana GN=At1g61310 PE=2 SV=1

 Score = 67.8 bits (164), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 134/302 (44%), Gaps = 59/302 (19%)

Query: 30  RNYNANLENLKAELEKLKVERTSIQLRVSEAKEKGEEIEEKVEKWLTRYQLSKKAKTEVK 89
           R    NL  L+ E+E L+  +  +Q +V+  + + ++  E V+ WL R         E K
Sbjct: 30  RTLEKNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVN---SIDIECK 86

Query: 90  ALIELGE-EVKKFDIVSHCT---------------IPEEI-WLKSNKVYEAF-------- 124
            L+ +   E++K  +   CT               + EE+  LKS   ++          
Sbjct: 87  DLLSVSPVELQKLCLCGLCTKYVCSSYKYGKKVFLLLEEVKILKSEGNFDEVSQPPPRSE 146

Query: 125 -ESRVSN--------LKSTQNALT---------NANGGIGKTTLAKEFA-KQAREDKLFD 165
            E R +         L+   N L          +  GG+GKTTL K+   K A     FD
Sbjct: 147 VEERPTQPTIGQEEMLEKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEIGGTFD 206

Query: 166 RVVFSEVSQTSDIKKIQGDIAEKLGL--EL-SEEAEYRRASRLYERLKNENKILVILANI 222
            V++  VSQ + + K+Q DIAEKL L  +L   + E  +A+ ++  LK + + +++L +I
Sbjct: 207 IVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATDIHRVLKGK-RFVLMLDDI 265

Query: 223 WKLLDLETVKIPFRNDSRDNNVVLLS--------MGSKDNFLIANITEEEAWRLFKIMNG 274
           W+ +DLE + IP+ ++     V   +        MG      +  +  E+AW LFK   G
Sbjct: 266 WEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCGEMGDHKPMQVNCLEPEDAWELFKNKVG 325

Query: 275 DD 276
           D+
Sbjct: 326 DN 327

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O64790|DRL17_ARATH Probable disease resistance protein At1g61300 OS=Arabidopsis thaliana GN=At1g61300 PE=2 SV=2

 Score = 65.9 bits (159), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 49/150 (32%), Positives = 83/150 (55%), Gaps = 15/150 (10%)

Query: 140 NANGGIGKTTLAKEFA-KQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL--EL-SE 195
           +  GG+GKTTL K+   K A+    FD V++  VS+ + + K+Q DIAEKL L  +L   
Sbjct: 67  HGMGGVGKTTLFKKIHNKFAKMSSRFDIVIWIVVSKGAKLSKLQEDIAEKLHLCDDLWKN 126

Query: 196 EAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVL 246
           + E  +A+ ++  LK + + +++L +IW+ +DLE + +P+ ++         +RD  V  
Sbjct: 127 KNESDKATDIHRVLKGK-RFVLMLDDIWEKVDLEAIGVPYPSEVNKCKVAFTTRDQKVC- 184

Query: 247 LSMGSKDNFLIANITEEEAWRLFKIMNGDD 276
             MG      +  +  E+AW LFK   GD+
Sbjct: 185 GEMGDHKPMQVKCLEPEDAWELFKNKVGDN 214

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FG90|DRL33_ARATH Probable disease resistance protein At5g43740 OS=Arabidopsis thaliana GN=At5g43740 PE=2 SV=1

 Score = 65.9 bits (159), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 78/327 (23%), Positives = 141/327 (43%), Gaps = 68/327 (20%)

Query: 12  LVKWLAPP-----TERQLVYLRKRNY----NANLENLKAELEKLKVERTSIQLRVSEAKE 62
           ++ WL  P     T     +L  RNY     +NL+ L+  +E+LK  R  +  RVS  ++
Sbjct: 1   MLGWLVIPWNQIFTAACGCFLSDRNYIHMMESNLDALQKTMEELKNGRDDLLGRVSIEED 60

Query: 63  KGEEIEEKVEKWLTRYQLSKKAKTEVKALIE-LGEEVKKFDIVSHCT------------- 108
           KG +   +V  WL+R Q+    ++E K L+E +  E  +  ++ +C+             
Sbjct: 61  KGLQRLAQVNGWLSRVQI---VESEFKDLLEAMSIETGRLCLLGYCSEDCISSYNYGEKV 117

Query: 109 ------------------IPEEIWLKS-----------NKVYEAFESRVSNLKSTQNALT 139
                             + +EI  K            +K+ E   S + N +     L 
Sbjct: 118 SKMLEEVKELLSKKDFRMVAQEIIHKVEKKLIQTTVGLDKLVEMAWSSLMNDEIGTLGLY 177

Query: 140 NANGGIGKTTLAKEFAKQARE-DKLFDRVVFSEVSQTSDIKKIQGDIAEKL--GLELSEE 196
              GG+GKTTL +    +  E +  FD V++  VS+    + IQ  I  +L    E   E
Sbjct: 178 GM-GGVGKTTLLESLNNKFVELESEFDVVIWVVVSKDFQFEGIQDQILGRLRSDKEWERE 236

Query: 197 AEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS-------- 248
            E ++AS +Y  L+ + K +++L ++W  +D+  + +P       + +V  +        
Sbjct: 237 TESKKASLIYNNLERK-KFVLLLDDLWSEVDMTKIGVPPPTRENGSKIVFTTRSTEVCKH 295

Query: 249 MGSKDNFLIANITEEEAWRLFKIMNGD 275
           M +     +A ++ +EAW LF++  GD
Sbjct: 296 MKADKQIKVACLSPDEAWELFRLTVGD 322

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LVT3|DRL38_ARATH Probable disease resistance protein At5g47260 OS=Arabidopsis thaliana GN=At5g47260 PE=3 SV=2

 Score = 65.5 bits (158), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 79/306 (25%), Positives = 137/306 (44%), Gaps = 65/306 (21%)

Query: 28  RKRNYNA--NLENLKAELEKLKVERTSIQLRVSEAKEKGEEIEEKVEKWLTRYQ-LSKKA 84
           RK  YN   NLE L   ++ L   R  +  R+S+ +E G +  ++V++W++  + +  KA
Sbjct: 20  RKYLYNLERNLEALHKVMQDLNAMRNDLLKRLSKEEEIGLQGLQEVKEWISMVEEIEPKA 79

Query: 85  KTEVKALIELGEEVKKFDIVSHCT-IPEEIW---------------LKSNKVYEAFESR- 127
               + L E   E+++     +C+ IP   +               L+S  V+EA   R 
Sbjct: 80  N---RLLDESVSEIQRLSRYGYCSLIPASTYRYSEKVLTTMEGVETLRSKGVFEAVVHRA 136

Query: 128 ----VSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQARED 161
               V  +   Q  ++ A                       GG+GKTTL  +   +   D
Sbjct: 137 LPPLVIKMPPIQLTVSQAKLLDTAWARLMDINVGTLGIYGRGGVGKTTLLTKLRNKLLVD 196

Query: 162 KLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN 221
             F  V+F  V    +++ IQ +I ++LGL+   E + R+A+ +   LK E + +++L  
Sbjct: 197 A-FGLVIFVVVG-FEEVESIQDEIGKRLGLQWRRETKERKAAEILAVLK-EKRFVLLLDG 253

Query: 222 IWKLLDLETVKIPFRNDSRDNNVVLL----SMGSKD-------NFLIANITEEEAWRLFK 270
           I + LDLE + +PF   SRDN   ++    S+ + D          I  ++ EEAW LF+
Sbjct: 254 IQRELDLEEIGVPF--PSRDNGCKIVFTTQSLEACDESKWVDAKVEITCLSPEEAWDLFQ 311

Query: 271 IMNGDD 276
              G++
Sbjct: 312 ETVGEN 317

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q940K0|DRL15_ARATH Probable disease resistance protein At1g61180 OS=Arabidopsis thaliana GN=At1g61180 PE=2 SV=2

 Score = 64.3 bits (155), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 49/149 (32%), Positives = 79/149 (53%), Gaps = 13/149 (8%)

Query: 140 NANGGIGKTTLAKEFA-KQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL--EL-SE 195
           +  GG+GKTTL K+   K A     FD V++  VS+   I K+Q DIAEKL L  +L   
Sbjct: 178 HGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDLWKN 237

Query: 196 EAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS------- 248
           + E  +A+ ++  LK + + +++L +IW+ +DLE + IP+ ++     V   +       
Sbjct: 238 KNESDKATDIHRVLKGK-RFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCG 296

Query: 249 -MGSKDNFLIANITEEEAWRLFKIMNGDD 276
            MG      +  +  E+AW LFK   GD+
Sbjct: 297 EMGDHKPMQVNCLEPEDAWELFKNKVGDN 325

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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	374
224083434	1144	cc-nbs-lrr resistance protein [Populus t	0.807	0.263	0.400	9e-52
359488027	1520	PREDICTED: disease resistance protein At	0.804	0.198	0.382	3e-51
147802546	1409	hypothetical protein VITISV_007222 [Viti	0.804	0.213	0.379	7e-51
224111296	1315	cc-nbs-lrr resistance protein [Populus t	0.818	0.232	0.377	3e-47
147782989	1351	hypothetical protein VITISV_012099 [Viti	0.826	0.228	0.369	6e-47
224147195	554	cc-nbs resistance protein [Populus trich	0.820	0.554	0.361	8e-46
147865073	1694	hypothetical protein VITISV_021876 [Viti	0.935	0.206	0.334	9e-46
147866716	454	hypothetical protein VITISV_025268 [Viti	0.933	0.768	0.328	3e-45
147772601	1392	hypothetical protein VITISV_013427 [Viti	0.810	0.217	0.357	3e-45
296087869	1711	unnamed protein product [Vitis vinifera]	0.812	0.177	0.351	5e-45

>gi|224083434|ref|XP_002307025.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222856474|gb|EEE94021.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  210 bits (535), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 143/357 (40%), Positives = 196/357 (54%), Gaps = 55/357 (15%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           +LE I++ +  + +    P  R++ +  K  YN N ENLK E++KLK  +  +Q  V +A
Sbjct: 2   VLESIISTIGVVSQHTVVPIAREINHCLK--YNHNFENLKREVKKLKSAQLRVQHLVDDA 59

Query: 61  KEKGEEIEEKVEKWLT----------------------------------RYQLSKKAKT 86
           +  GE I E V KWL+                                  RYQ SKKAK 
Sbjct: 60  RNNGEAILEDVIKWLSLVEEASEKVEREILEDEDRARKKCFIGLCPDLKARYQCSKKAKA 119

Query: 87  EVKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN---- 142
           E + +  L +E   F  VSH   P+ +   S + Y+A  SR   LK   NALT A+    
Sbjct: 120 ETRFVASLLDERDGFSTVSHRAAPKGMEAISIRSYDAMPSRTPVLKEIMNALTTADVNMV 179

Query: 143 -----GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEA 197
                GG+GKTTL KE A+QA ++KLF++VVF+ ++QT DIKKIQG IA++L L+  EE+
Sbjct: 180 GVYGMGGMGKTTLVKEAARQAIQEKLFNQVVFATITQTQDIKKIQGQIADQLSLKFDEES 239

Query: 198 EYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVLLS 248
           E  RA RL +RLK E KIL+IL ++WK LDLE V IP +++         SR+ +V+   
Sbjct: 240 ECGRAGRLRQRLKQEQKILIILDDLWKSLDLEAVGIPLKDEHEGCKMLVTSREFDVLSCG 299

Query: 249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA 305
           M  + NF I  ++EEE W LFK M GD VE+   +S AI VAK C AGL   + T A
Sbjct: 300 MDIQKNFPINALSEEETWELFKKMAGDHVEHPDLQSLAIEVAKMC-AGLPVAIVTVA 355

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488027|ref|XP_002269288.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 136/356 (38%), Positives = 196/356 (55%), Gaps = 55/356 (15%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           M E++VT+  ++ ++L  P  R   YL   NY +N+++L+ ++EKL   R  ++  V EA
Sbjct: 1   MEEIVVTIAAKVAEYLVAPIGRSFGYLF--NYRSNIDDLRQQVEKLGDARARLERSVDEA 58

Query: 61  KEKGEEIEEKVEKWLTR---------------------------------YQLSKKAKTE 87
              G+EIE  V+KWL R                                 YQLS++AK  
Sbjct: 59  IRNGDEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKR 118

Query: 88  VKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN----- 142
            + + E+  +  KF+ VS+      I     K +EA ESR++ L     AL +A+     
Sbjct: 119 ARVVAEIQGD-GKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIG 177

Query: 143 ----GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAE 198
                G+GKTTL K+ AKQA E+KLFD+VV + +S T ++KKIQG++A+ LGL+  EE+E
Sbjct: 178 VWGMAGVGKTTLMKQVAKQAEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESE 237

Query: 199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS---------M 249
             RA+RL ERLK   KIL+IL +IW  LDLE V IPF +D +   +VL S         M
Sbjct: 238 MGRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHILSNEM 297

Query: 250 GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA 305
           G++ +F + ++ EEEA  LFK M GD +E    +S AI+VAK C AGL   + T A
Sbjct: 298 GTQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKEC-AGLPIAIVTVA 352

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147802546|emb|CAN77665.1| hypothetical protein VITISV_007222 [Vitis vinifera]

 Score =  207 bits (527), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 135/356 (37%), Positives = 195/356 (54%), Gaps = 55/356 (15%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           M E++VT+  ++ ++L  P  R   YL   NY +N+++L+ ++EKL   R  ++  V EA
Sbjct: 1   MEEIVVTIAAKVAEYLVAPIGRSFGYLF--NYRSNIDDLRQQVEKLGDARARLERSVDEA 58

Query: 61  KEKGEEIEEKVEKWLTR---------------------------------YQLSKKAKTE 87
              G+EIE  V+KWL R                                 YQLS++AK  
Sbjct: 59  IRNGDEIEADVDKWLLRVSGFMEEAGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKR 118

Query: 88  VKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN----- 142
            + + E+  +  KF+ VS+      I     K +EA ESR++ L     AL +A+     
Sbjct: 119 ARVVAEIQGD-GKFERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIG 177

Query: 143 ----GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAE 198
                G+GKTTL K+ AKQ  E+KLFD+VV + +S T ++KKIQG++A+ LGL+  EE+E
Sbjct: 178 VWGMAGVGKTTLMKQVAKQVEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESE 237

Query: 199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS---------M 249
             RA+RL ERLK   KIL+IL +IW  LDLE V IPF +D +   +VL S         M
Sbjct: 238 MGRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHVLSNEM 297

Query: 250 GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA 305
           G++ +F + ++ EEEA  LFK M GD +E    +S AI+VAK C AGL   + T A
Sbjct: 298 GTQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKEC-AGLPIAIVTVA 352

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111296|ref|XP_002332952.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222834264|gb|EEE72741.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  195 bits (496), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 137/363 (37%), Positives = 195/363 (53%), Gaps = 57/363 (15%)

Query: 2   LEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEAK 61
           +E+++++V ++ + L  P +RQ+ Y+   N N N++NLK E+EKL   RT +   + EA+
Sbjct: 1   MEIVISIVAKVAELLVVPIKRQIGYVL--NCNTNIQNLKNEVEKLTDARTRVNHSIEEAR 58

Query: 62  EKGEEIEEKVEKWL-------------------------------TRYQLSKKAKTEVKA 90
             GEEIE +V  WL                                RY+L K AK E+  
Sbjct: 59  RNGEEIEVEVFNWLGSVDGVIDGGGGGVADESSKKCFMGLCPDLKIRYRLGKAAKKELTV 118

Query: 91  LIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN-------- 142
           +++L +E  +FD VS+   P  I     K YEAFESR S L +  +AL +          
Sbjct: 119 VVDL-QEKGRFDRVSYRAAPSGI--GPVKDYEAFESRDSVLNAIVDALKDGGVNMVGVYG 175

Query: 143 -GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRR 201
             G+GKTTL K+ A+Q +E +LFD+ V + VS T DI++IQG+IA+ LGL+L  E +  R
Sbjct: 176 MPGVGKTTLVKKVAEQVKEGRLFDKEVLAVVSHTPDIRRIQGEIADGLGLKLDAETDKGR 235

Query: 202 ASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVLLSMGSK 252
           AS+LYERLK   ++LVIL +IWK L LE V IP  +D         SR+  V+   MGS 
Sbjct: 236 ASQLYERLKKVTRVLVILDDIWKELKLEDVGIPSGSDHEGCKILMSSRNEYVLSREMGSN 295

Query: 253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTT--NASKSSS 310
            NF I  +   EAW LF+ M G  V+    +  A  VA+ C AGL   L T   A K+  
Sbjct: 296 RNFPIQVLPASEAWNLFEKMVGVAVKKHSVRLVAAEVARRC-AGLPILLATVARALKNKD 354

Query: 311 IYS 313
           +Y+
Sbjct: 355 LYA 357

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147782989|emb|CAN68563.1| hypothetical protein VITISV_012099 [Vitis vinifera]

 Score =  194 bits (493), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 134/363 (36%), Positives = 195/363 (53%), Gaps = 54/363 (14%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           M+++++++ +E+ K L  P +RQL YL   NY  N+ +L  ++E L+ ER  +Q+ V+EA
Sbjct: 1   MVDIVISVAVEVAKCLVDPIKRQLGYLL--NYRRNITDLNQQIENLRRERDELQIPVNEA 58

Query: 61  KEKGEEIEEKVEKWLT----------------------------RYQLSKKAKTEVKALI 92
             +G+EI  +V++WLT                            RYQLSK+A+ +   ++
Sbjct: 59  YRQGDEIFPRVQEWLTYAEGIILESNDFNEHERKASKSCFYLKSRYQLSKQAEKQAAKIV 118

Query: 93  ELGEEVKKFDI-VSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN--------- 142
           +  +E + F   VSH   P      S K YEAF+SR S       AL N +         
Sbjct: 119 DKIQEARNFGGRVSHRPPPFSSS-ASFKDYEAFQSRESTFNQIMEALRNEDMRMLGVWGM 177

Query: 143 GGIGKTTLAKEFAKQAREDKLFDRVVFS-EVSQTSDIKKIQGDIAEKLGLELSEEAEYRR 201
           GG+GKTTL K+ A+QA EDKLF +VV    +SQT +I +IQ  IA  LGL+   EA   R
Sbjct: 178 GGVGKTTLVKQVAQQAEEDKLFHKVVMVLHISQTPNITEIQEKIARMLGLKF--EAGEDR 235

Query: 202 ASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS---------MGSK 252
           A RL +RLK E KILVIL +IW  LDL  + IP+ +D +   V+L S         M ++
Sbjct: 236 AGRLKQRLKGEEKILVILDDIWGKLDLGEIGIPYGDDHKGCKVLLTSRERQVLSKDMRTQ 295

Query: 253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSSSIY 312
             F + +++E+EAW LFK   GD VE  + +  A++VAK C  GL   + T A+      
Sbjct: 296 KEFHLQHLSEDEAWNLFKKTAGDSVEKPELRPIAVDVAKKCD-GLPVAIVTIANTLRGES 354

Query: 313 SHV 315
            HV
Sbjct: 355 VHV 357

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224147195|ref|XP_002336426.1| cc-nbs resistance protein [Populus trichocarpa] gi|222834979|gb|EEE73428.1| cc-nbs resistance protein [Populus trichocarpa]

 Score =  190 bits (483), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 131/362 (36%), Positives = 192/362 (53%), Gaps = 55/362 (15%)

Query: 2   LEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEAK 61
           +E+++++V ++ + L  P +RQ+ Y+   + N+N++NLK E+EKL   +T +   + EA+
Sbjct: 1   MEIVISIVAKVAELLVVPIKRQIGYVL--DCNSNIQNLKNEVEKLTDAKTRVIHSIEEAQ 58

Query: 62  EKGEEIEEKVEKWL-------------------------------TRYQLSKKAKTEVKA 90
             GEEIE +V  WL                                RY+L K AK E+  
Sbjct: 59  WNGEEIEVEVLNWLGSVDGVIEGAGGVVADESSKKCFMGLCPDLKIRYRLGKAAKKELTV 118

Query: 91  LIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN-------- 142
           +++L +   KFD VS+   P  I     K YEAFESR S L     AL + +        
Sbjct: 119 VVDL-QGKGKFDRVSYRAAPSGI--GPVKDYEAFESRNSVLNDIVGALKDGDENMVGVFG 175

Query: 143 -GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRR 201
             G+GKTTL K+ A+Q +E +LF+ VV + VSQT DI++IQG+IA+ LGL+L  E +  R
Sbjct: 176 MAGVGKTTLVKKVAEQVKEGRLFNEVVLAVVSQTPDIRRIQGEIADGLGLKLDAETDKGR 235

Query: 202 ASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVLLSMGSK 252
           AS+L + LK   ++LVIL +IWK L LE V IP  +D         SRD NV+   MG+ 
Sbjct: 236 ASQLCKGLKKVTRVLVILDDIWKELKLEDVGIPSGSDHDGCKILMTSRDKNVLSCEMGAN 295

Query: 253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKAC-GAGLFCTLTTNASKSSSI 311
            NF I  + E EAW LF+   G  V+N   +  A  VAK C G  +       A ++  +
Sbjct: 296 KNFQIQVLPESEAWDLFEKTVGVTVKNPSVQPVAAKVAKRCAGLPILLAAVARALRNEEV 355

Query: 312 YS 313
           Y+
Sbjct: 356 YA 357

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865073|emb|CAN83232.1| hypothetical protein VITISV_021876 [Vitis vinifera]

 Score =  190 bits (483), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 140/419 (33%), Positives = 216/419 (51%), Gaps = 69/419 (16%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           M+E+++++  ++ ++L  P  RQL YL   NY AN+E+L  ++EKL+  R  +Q  V EA
Sbjct: 1   MVEIVLSVAAKVSEYLVDPAIRQLGYLF--NYRANIEDLSQQVEKLRDARARLQHSVDEA 58

Query: 61  KEKGEEIEEKVEKWL---------------------------------TRYQLSKKAKTE 87
              G  IE+ V KW+                                 +RYQLS++A+ +
Sbjct: 59  IGNGHIIEDDVRKWMKRADGFIQNACKFLEDEKEARKSCFNGLCPNLKSRYQLSREARKK 118

Query: 88  VKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN----- 142
               +E+     +F+ VS+    +EI    +   EA ESR+  L     AL +AN     
Sbjct: 119 AGVAVEI-HGAGQFERVSYRAPLQEIRTAPS---EALESRMLTLNEVMEALRDANINRIG 174

Query: 143 ----GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAE 198
               GG+GK+TL K+ A+QA ++KLF +VV   V QT D K IQ  IA+KLG++  E +E
Sbjct: 175 VWGMGGVGKSTLVKQVAEQAEQEKLFRKVVMVPVIQTPDFKGIQQQIADKLGMKFEEVSE 234

Query: 199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS---------M 249
             RA RL++R+K EN IL+IL ++W  L+LE V IP  +D +   +VL S         M
Sbjct: 235 QGRADRLHQRIKQENTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEM 294

Query: 250 GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKSS 309
            ++ +F + ++ E+E W LFK   GD +EN + +  A++VAK C AGL   + T A    
Sbjct: 295 STQKDFRVQHLQEDETWILFKNTAGDSIENPELQPIAVDVAKEC-AGLPIAIVTVAKA-- 351

Query: 310 SIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSL 368
                + N   SI+K     A+ Q    T      ++ K Y +LK  +E L+ ++  SL
Sbjct: 352 -----LKNKNVSIWKD----ALQQLNSQTSTNITGMETKVYSSLKLSYEHLEGDEVKSL 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147866716|emb|CAN80506.1| hypothetical protein VITISV_025268 [Vitis vinifera]

 Score =  188 bits (478), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 138/420 (32%), Positives = 220/420 (52%), Gaps = 71/420 (16%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           M+E++V++  ++ ++L  P  RQL YL   NY AN+E+L  ++EKL+  R  +Q  V EA
Sbjct: 1   MVEIVVSVAAKVSEYLVDPAVRQLGYLF--NYRANIEHLSLQVEKLRDARARLQHSVDEA 58

Query: 61  KEKGEEIEEKVEKWL---------------------------------TRYQLSKKAKTE 87
              G  I++ V KW+                                 +RYQLS++A+ +
Sbjct: 59  IGNGHIIKDDVCKWMKRADEFIQNACKFLEDEKEARKSCFNGLCPNLKSRYQLSREARKK 118

Query: 88  VKALIE-LGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN---- 142
               ++ LG+  ++F+ VS+    +EI    +   EA +SR+  L     AL +A+    
Sbjct: 119 AGVAVQILGD--RQFEKVSYRAPLQEI---RSAPSEALQSRMLTLNEVMEALRDADINRI 173

Query: 143 -----GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEA 197
                GG+GK+TL K+ A+ A ++KLF +VV   V QT D K IQ  IA+KLG++  E +
Sbjct: 174 GVWGLGGVGKSTLVKQVAELAEQEKLFRKVVMVPVFQTPDFKGIQQQIADKLGMKFEEVS 233

Query: 198 EYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS--------- 248
           E  RA RL++R+K EN IL+IL ++W  L+LE V IP  +D +   +VL S         
Sbjct: 234 EQGRADRLHQRIKQENTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNE 293

Query: 249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNASKS 308
           M ++ +F + ++ E+E W LFK   GD ++N + +  A++VAK C AGL   + T A+  
Sbjct: 294 MSTQKDFRVQHLQEDETWILFKNTAGDSIKNPELQPIAVDVAKEC-AGLPIAIVTVATA- 351

Query: 309 SSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIVKTAFVDPKWYLALKEEFEALQRNQTWSL 368
                 + N   SI+K     A+ Q   PT      ++ K Y +LK  +E L+ ++  SL
Sbjct: 352 ------LKNKSLSIWKD----ALQQLKRPTSTNIRGMEAKVYSSLKLSYEHLEGDEVKSL 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772601|emb|CAN62857.1| hypothetical protein VITISV_013427 [Vitis vinifera]

 Score =  188 bits (478), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 132/369 (35%), Positives = 199/369 (53%), Gaps = 66/369 (17%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           M+E++ ++  ++++ L  P +RQL YL   NY  N+E+L  E+EKL+  R   Q  V+EA
Sbjct: 1   MVEIVASVAAKVLECLVVPVKRQLGYLF--NYRTNIEDLSQEVEKLRHARDGHQHSVNEA 58

Query: 61  KEKGEEIEEKVEKWLT---------------------------------RYQLSKKAKTE 87
              G +IE+ V KWLT                                 RYQLS++A+ +
Sbjct: 59  SGNGHKIEDYVCKWLTRADGFIQDACKFLEDEKEAQKSCFNGLCPNLKSRYQLSREARKK 118

Query: 88  VKALIE-LGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN---- 142
            +  ++ LG+   +F+ VS+    +EI    +   EA  SRV  L     AL +A     
Sbjct: 119 ARVAVQMLGD--GQFERVSYRAPLQEI---RSAPSEALRSRVLTLDEVMEALRDAKINKI 173

Query: 143 -----GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEA 197
                GG+GKTTL K+ A+ A ++KLFD+VV + V QT D+KKIQG++A+ LG++  EE+
Sbjct: 174 GVWGLGGVGKTTLVKQVAEHAAQEKLFDKVVTAAVLQTPDLKKIQGELADLLGMKFEEES 233

Query: 198 EYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS--------- 248
           E  RA+RLY+R+  E  IL+IL +IW  LDLE + IP  +  +   +VL S         
Sbjct: 234 EQGRAARLYQRMNEEKTILIILDDIWATLDLEKIGIPSPDHHKGCKLVLTSRNEHILSNE 293

Query: 249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS-- 306
           M ++ +F +  + E+E W LFK   G  +EN + K  A++VAK C AGL   + T A+  
Sbjct: 294 MDTQKDFRVQPLQEDETWILFKNTAG-SIENPELKHIAVDVAKEC-AGLPLAMVTVATAL 351

Query: 307 ---KSSSIY 312
              KS SI+
Sbjct: 352 KGEKSVSIW 360

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087869|emb|CBI35152.3| unnamed protein product [Vitis vinifera]

 Score =  187 bits (476), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 129/367 (35%), Positives = 198/367 (53%), Gaps = 63/367 (17%)

Query: 1   MLEVIVTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEA 60
           M+E++V++  ++ ++L  P  RQL YL   NY  N+E+L  ++EKL+  R  +Q  V EA
Sbjct: 1   MVEIVVSVAAKVSEYLVGPVVRQLGYLF--NYRTNIEDLSQKVEKLRGARARLQHSVDEA 58

Query: 61  KEKGEEIEEKVEKWLT--------------------------------RYQLSKKAKTEV 88
              G +IE+ V KW+T                                RYQLS++A+ + 
Sbjct: 59  IRNGHKIEDDVCKWMTRADGFIQKDCKFLEDEEARKSCFNGLCPNLKSRYQLSREARKKA 118

Query: 89  KALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN------ 142
              +E+  E  +F+  S+    +EI    +   EA ESR+  L     AL +A       
Sbjct: 119 GVAVEI-HEAGQFERASYRAPLQEI---RSAPSEALESRMLTLNEVMKALRDAKINKIGV 174

Query: 143 ---GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEY 199
              GG+GKTTL K+ A+QA ++KLFD+VV + V +T D+KKIQG++A+ LG++  EE+E 
Sbjct: 175 WGLGGVGKTTLVKQVAEQAAQEKLFDKVVTAAVLETPDLKKIQGELADLLGMKFEEESEQ 234

Query: 200 RRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS---------MG 250
            RA+RLY+R+  E  IL+IL +IW  LDLE + IP  +  +   +VL S         M 
Sbjct: 235 GRAARLYQRMNEEKTILIILDDIWAKLDLEKIGIPSPDHHKGCKLVLTSRNEHILSNEMD 294

Query: 251 SKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS---- 306
           ++ +F +  + E+E W LFK   G  +EN + +  A++VAK C AGL   + T A+    
Sbjct: 295 TQKDFRVQPLQEDETWILFKNTAG-SIENPELQPIAVDVAKEC-AGLPLAVVTVATALKG 352

Query: 307 -KSSSIY 312
            KS SI+
Sbjct: 353 EKSVSIW 359

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	374
TAIR|locus:2136447	985	AT4G27190 [Arabidopsis thalian	0.542	0.206	0.285	1.4e-15
TAIR|locus:2131689	919	AT4G27220 [Arabidopsis thalian	0.465	0.189	0.307	4.7e-12
TAIR|locus:2008510	967	AT1G61190 "AT1G61190" [Arabido	0.438	0.169	0.336	2e-10
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.395	0.166	0.323	3e-10
TAIR|locus:2197739	762	AT1G61300 [Arabidopsis thalian	0.435	0.213	0.329	8.9e-10
TAIR|locus:2008440	899	AT1G61180 [Arabidopsis thalian	0.521	0.216	0.301	6.8e-09
TAIR|locus:2093192	375	AT3G15700 [Arabidopsis thalian	0.422	0.421	0.274	6.2e-08
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.462	0.194	0.292	8.9e-08
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.411	0.172	0.3	1.5e-07
TAIR|locus:2171589	948	AT5G47260 [Arabidopsis thalian	0.513	0.202	0.261	1.6e-07

TAIR|locus:2136447 AT4G27190 [Arabidopsis thaliana (taxid:3702)]

 Score = 222 (83.2 bits), Expect = 1.4e-15, P = 1.4e-15
 Identities = 64/224 (28%), Positives = 116/224 (51%)

Query:   143 GGIGKTTLAKEFAKQARED---KLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS-EEAE 198
             GG+GKTTL +    + RE+   + F  V+F  VS+  D +++Q  IAE+L ++   EE+E
Sbjct:   173 GGVGKTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDPREVQKQIAERLDIDTQMEESE 232

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS--------MG 250
              + A R+Y  L  E K L+IL ++WK +DL+ + IP   +++ + V+L S        M 
Sbjct:   233 EKLARRIYVGLMKERKFLLILDDVWKPIDLDLLGIPRTEENKGSKVILTSRFLEVCRSMK 292

Query:   251 SKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS---- 306
             +  +  +  + EE+AW LF    GD V +   +  A  V++ CG      +T   +    
Sbjct:   293 TDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAMRGK 352

Query:   307 KSSSIYSHVSNDYQSIYKPKPYLAVFQD--LEPTIVKTAFVDPK 348
             K+  +++HV +    + K  P++   ++   +P  +   F++ K
Sbjct:   353 KNVKLWNHVLS---KLSKSVPWIKSIEEKIFQPLKLSYDFLEDK 393

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2131689 AT4G27220 [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 4.7e-12, P = 4.7e-12
 Identities = 59/192 (30%), Positives = 97/192 (50%)

Query:   143 GGIGKTTLAK----EFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAE 198
             GG+GKTTL +    +  K A   + F  V++  VS+  D+K++Q DIA++LG   + E  
Sbjct:   143 GGVGKTTLVRTLNNDLLKYAATQQ-FALVIWVTVSKDFDLKRVQMDIAKRLGKRFTREQM 201

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND-SRDNNVVLLS--------M 249
              +    + ERL +    L+IL ++W  +DL+ + IP   + S+D+ VVL S        M
Sbjct:   202 NQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLALERSKDSKVVLTSRRLEVCQQM 261

Query:   250 GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVA-KACGAGL-FCTL--TTNA 305
              + +N  +A + E+EAW LF    G+   +   K  A +V+ + CG  L   T+  T   
Sbjct:   262 MTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVSHECCGLPLAIITIGRTLRG 321

Query:   306 SKSSSIYSHVSN 317
                  ++ H  N
Sbjct:   322 KPQVEVWKHTLN 333

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2008510 AT1G61190 "AT1G61190" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 2.0e-10, P = 2.0e-10
 Identities = 62/184 (33%), Positives = 93/184 (50%)

Query:   143 GGIGKTTLAKEFA-KQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL--EL-SEEAE 198
             GG+GKTTL K+   K A     FD V++  VSQ + + K+Q DIAEKL L  +L   + E
Sbjct:   182 GGVGKTTLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNE 241

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVLLSM 249
               +A+ ++  LK +  +L+ L +IW+ +DLE + IP+ ++         +RD  V    M
Sbjct:   242 SDKATDIHRVLKGKRFVLM-LDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRDQKVCG-QM 299

Query:   250 GSKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKACGA---GLFCTLTTN 304
             G      +  +  E+AW LFK   GD+    +      A  VA+ C      L C   T 
Sbjct:   300 GDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSCIGETM 359

Query:   305 ASKS 308
             ASK+
Sbjct:   360 ASKT 363

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2201996 RPS5 "AT1G12220" [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 3.0e-10, P = 3.0e-10
 Identities = 54/167 (32%), Positives = 91/167 (54%)

Query:   143 GGIGKTTLAKEFA-KQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL---ELSEEAE 198
             GG+GKTTL  +   K ++ D  FD V++  VS++S ++KIQ DIAEK+GL   E SE+ +
Sbjct:   185 GGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWSEKND 244

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNV----------VLLS 248
              + A  ++  L+   K +++L +IW+ ++L+ V +P+   S+DN            V   
Sbjct:   245 NQIAVDIHNVLRRR-KFVLLLDDIWEKVNLKAVGVPY--PSKDNGCKVAFTTRSRDVCGR 301

Query:   249 MGSKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKAC 293
             MG  D   ++ +  EE+W LF++  G +    +      A  VA+ C
Sbjct:   302 MGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKC 348

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0006952 "defense response" evidence=IMP;TAS

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008219 "cell death" evidence=IMP

GO:0038023 "signaling receptor activity" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IMP

GO:0005622 "intracellular" evidence=ISS

TAIR|locus:2197739 AT1G61300 [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 8.9e-10, P = 8.9e-10
 Identities = 61/185 (32%), Positives = 96/185 (51%)

Query:   143 GGIGKTTLAKEFA-KQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL--EL-SEEAE 198
             GG+GKTTL K+   K A+    FD V++  VS+ + + K+Q DIAEKL L  +L   + E
Sbjct:    70 GGVGKTTLFKKIHNKFAKMSSRFDIVIWIVVSKGAKLSKLQEDIAEKLHLCDDLWKNKNE 129

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVLLSM 249
               +A+ ++  LK +  +L+ L +IW+ +DLE + +P+ ++         +RD  V    M
Sbjct:   130 SDKATDIHRVLKGKRFVLM-LDDIWEKVDLEAIGVPYPSEVNKCKVAFTTRDQKVCG-EM 187

Query:   250 GSKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKACGAGLFCTLT----T 303
             G      +  +  E+AW LFK   GD+    +      A  VA+ C  GL   L+    T
Sbjct:   188 GDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVELAREVAQKC-RGLPLALSVIGET 246

Query:   304 NASKS 308
              ASK+
Sbjct:   247 MASKT 251

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2008440 AT1G61180 [Arabidopsis thaliana (taxid:3702)]

 Score = 164 (62.8 bits), Expect = 6.8e-09, P = 6.8e-09
 Identities = 64/212 (30%), Positives = 100/212 (47%)

Query:   143 GGIGKTTLAKEFAKQARE-DKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL--EL-SEEAE 198
             GG+GKTTL K+   +  E    FD V++  VS+   I K+Q DIAEKL L  +L   + E
Sbjct:   181 GGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDLWKNKNE 240

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS--------MG 250
               +A+ ++  LK +  +L+ L +IW+ +DLE + IP+ ++     V   +        MG
Sbjct:   241 SDKATDIHRVLKGKRFVLM-LDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCGEMG 299

Query:   251 SKDNFLIANITEEEAWRLFKIMNGDDVENCK--FKSTAINVAKACGAGLFCTLTTNASKS 308
                   +  +  E+AW LFK   GD+  +        A  VA+ C  GL   L       
Sbjct:   300 DHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVELAREVAQKC-RGLPLALNVIGETM 358

Query:   309 SSIYSHVSNDYQSIYKPKPYLAVFQDLEPTIV 340
             SS  + V     +I+      A F D++  I+
Sbjct:   359 SS-KTMVQEWEHAIHVFNTSAAEFSDMQNKIL 389

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

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2093192 AT3G15700 [Arabidopsis thaliana (taxid:3702)]

 Score = 150 (57.9 bits), Expect = 6.2e-08, P = 6.2e-08
 Identities = 48/175 (27%), Positives = 88/175 (50%)

Query:   144 GIGKTTLAKEFAKQAREDKL--FDRVVFSEVSQTSDIKKIQGDIAEKLG-LELS--EEAE 198
             G+GKTT+  +   +  + KL  FD V++  VS+  +++KIQ  I EK+G L+ S   + E
Sbjct:   170 GVGKTTVLTQVNNRLLQHKLNGFDFVIWVFVSKNVNLEKIQDTIREKIGFLDRSWMSKTE 229

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS--------MG 250
               +A +++E L ++ +  + L ++W+ +DL    +P  +    + +V  +        MG
Sbjct:   230 EEKAGKIFEIL-SKRRFALFLDDVWEKVDLVKAGVPPPDGLNRSKIVFTTCSDEVCQEMG 288

Query:   251 SKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKACGAGLFCTLTT 303
             ++    +  +  E AW LFK+  G+++   +      A  VA  C  GL   L T
Sbjct:   289 AQTKIKMEKLPWERAWDLFKMNAGEEIVKSHPDITKVAQEVAAKCD-GLPLALVT 342

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2166320 AT5G63020 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 8.9e-08, P = 8.9e-08
 Identities = 57/195 (29%), Positives = 94/195 (48%)

Query:   143 GGIGKTTLAKEFAKQ-AREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLE---LSEEAE 198
             GG+GKTTL      + +R    FD V++  VS+   I++IQ +I EKL  +     ++ E
Sbjct:   183 GGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDNEKWKQKTE 242

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNN--VVLLS-------- 248
               +AS +Y  LK++  +L +L +IW  +DL  V +PF   SR+N   +V  +        
Sbjct:   243 DIKASNIYNVLKHKRFVL-LLDDIWSKVDLTEVGVPF--PSRENGCKIVFTTRLKEICGR 299

Query:   249 MGSKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKACGAGLFCTLTTNAS 306
             MG   +  +  +  ++AW LF    G+     + +  + A  VAK C  GL   L  N  
Sbjct:   300 MGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKC-RGL--PLALNVI 356

Query:   307 KSSSIYSHVSNDYQS 321
               +  Y     +++S
Sbjct:   357 GETMAYKRTVQEWRS 371

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2034770 SUMM2 "AT1G12280" [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 1.5e-07, P = 1.5e-07
 Identities = 51/170 (30%), Positives = 83/170 (48%)

Query:   143 GGIGKTTLAKEFAKQARED-KLFDRVVFSEVSQTSDIKKIQGDIAEKLGL---ELSEEAE 198
             GG+GKTTL      +  E    F  V++  VS++ DI +IQGDI ++L L   E     E
Sbjct:   185 GGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEEWDNVNE 244

Query:   199 YRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLLS--------MG 250
              +RA  +Y  L  + K +++L +IW+ ++LE + +P+ +      VV  +        M 
Sbjct:   245 NQRALDIYNVL-GKQKFVLLLDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCGRMR 303

Query:   251 SKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVA-KACGAGL 297
               D   ++ +   EAW LF++  G++    +      A  VA K CG  L
Sbjct:   304 VDDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPELARKVAGKCCGLPL 353

GO:0006952 "defense response" evidence=IGI;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2171589 AT5G47260 [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 1.6e-07, P = 1.6e-07
 Identities = 57/218 (26%), Positives = 105/218 (48%)

Query:    78 YQLSKKAKTEVKALIELGEEVKKFDIVSHCTIPE--------EIWLKSNKVYEAFESRVS 129
             Y+ S+K  T ++  +E       F+ V H  +P         ++ +   K+ +   +R+ 
Sbjct:   107 YRYSEKVLTTMEG-VETLRSKGVFEAVVHRALPPLVIKMPPIQLTVSQAKLLDTAWARLM 165

Query:   130 NLKSTQNALTNANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL 189
             ++      +    GG+GKTTL  +   +   D  F  V+F  V    +++ IQ +I ++L
Sbjct:   166 DINVGTLGIYG-RGGVGKTTLLTKLRNKLLVDA-FGLVIFVVVG-FEEVESIQDEIGKRL 222

Query:   190 GLELSEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRNDSRDNNVVLL-- 247
             GL+   E + R+A+ +   LK E + +++L  I + LDLE + +PF   SRDN   ++  
Sbjct:   223 GLQWRRETKERKAAEILAVLK-EKRFVLLLDGIQRELDLEEIGVPF--PSRDNGCKIVFT 279

Query:   248 --SMGSKDNFL-------IANITEEEAWRLFKIMNGDD 276
               S+ + D          I  ++ EEAW LF+   G++
Sbjct:   280 TQSLEACDESKWVDAKVEITCLSPEEAWDLFQETVGEN 317

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0006952 "defense response" evidence=IEA;ISS

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

GO:0043531 "ADP binding" evidence=IEA

GO:0045036 "protein targeting to chloroplast" 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	374
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	9e-16
pfam13401	124	pfam13401, AAA_22, AAA domain	2e-06

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 76.6 bits (189), Expect = 9e-16
 Identities = 40/140 (28%), Positives = 69/140 (49%), Gaps = 13/140 (9%)

Query: 143 GGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLE---LSEEAEY 199
           GG+GKTTLAK+          FD V +  VS+T    ++Q DI ++LGL+     E+ E 
Sbjct: 28  GGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLDDSDWVEKNES 87

Query: 200 RRASRLYERLKNENKILVILANIWKLLDLETVKIPFRN---------DSRDNNVVLLSMG 250
             A ++ E L    + L++L ++W+  D + + +PF +          +R  +V     G
Sbjct: 88  ELAVKIKEALL-RKRFLLVLDDVWEKNDWDKIGVPFPDGENGSRVIVTTRSESVAGRMGG 146

Query: 251 SKDNFLIANITEEEAWRLFK 270
           +     + ++  EE+W LF 
Sbjct: 147 TSKPHEVESLEPEESWELFS 166

Length = 285

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

 Score = 46.5 bits (111), Expect = 2e-06
 Identities = 28/103 (27%), Positives = 37/103 (35%), Gaps = 15/103 (14%)

Query: 144 GIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRAS 203
           G GKTTL +  A+Q        RVV+ E       K +   I   LGL LS         
Sbjct: 14  GSGKTTLLRRLARQLPNR----RVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAELLE 69

Query: 204 RLYERLKNENKILVI-----------LANIWKLLDLETVKIPF 235
            + + LK   + L+I           L  +  L DL    I  
Sbjct: 70  AILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQV 112

Length = 124

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	374
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.96
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.93
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.9
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.85
PRK04841	903	transcriptional regulator MalT; Provisional	98.68
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.63
PF05729	166	NACHT: NACHT domain	98.49
cd01128	249	rho_factor Transcription termination factor rho is	98.48
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.4
PRK09376	416	rho transcription termination factor Rho; Provisio	98.39
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.33
PRK13342	413	recombination factor protein RarA; Reviewed	98.28
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.26
PTZ00202	550	tuzin; Provisional	98.1
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.06
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.0
TIGR00767	415	rho transcription termination factor Rho. Members	98.0
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.93
PRK06893	229	DNA replication initiation factor; Validated	97.92
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.91
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.85
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.84
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.83
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.79
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.78
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.76
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.76
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.74
PTZ00112	1164	origin recognition complex 1 protein; Provisional	97.73
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.72
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.72
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.69
PRK13341	725	recombination factor protein RarA/unknown domain f	97.68
PF14516	331	AAA_35: AAA-like domain	97.67
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.64
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.64
PLN03025	319	replication factor C subunit; Provisional	97.61
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.6
PRK04195	482	replication factor C large subunit; Provisional	97.56
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	97.56
PRK12402	337	replication factor C small subunit 2; Reviewed	97.55
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.54
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.49
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.48
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.48
COG3903	414	Predicted ATPase [General function prediction only	97.48
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.46
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.44
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.43
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.43
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.43
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.43
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.42
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.34
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.32
KOG2028	554	consensus ATPase related to the helicase subunit o	97.3
PF13173	128	AAA_14: AAA domain	97.29
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.29
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.25
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.23
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.23
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.21
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.21
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.18
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.17
COG3899	849	Predicted ATPase [General function prediction only	97.15
PRK08727	233	hypothetical protein; Validated	97.13
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.13
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.06
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.98
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.98
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	96.97
CHL00095	821	clpC Clp protease ATP binding subunit	96.97
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.95
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.92
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.88
PRK03992	389	proteasome-activating nucleotidase; Provisional	96.87
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	96.82
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.78
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.77
PRK09087	226	hypothetical protein; Validated	96.74
PRK12608	380	transcription termination factor Rho; Provisional	96.71
smart00382	148	AAA ATPases associated with a variety of cellular	96.67
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.63
PRK08118	167	topology modulation protein; Reviewed	96.63
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.63
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.62
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.57
PHA02544	316	44 clamp loader, small subunit; Provisional	96.57
PRK08084	235	DNA replication initiation factor; Provisional	96.56
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.55
PRK08181	269	transposase; Validated	96.53
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.48
PRK10865	857	protein disaggregation chaperone; Provisional	96.45
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.44
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.43
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.41
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.38
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.35
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.34
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.32
PF00004	132	AAA: ATPase family associated with various cellula	96.32
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.31
CHL00181	287	cbbX CbbX; Provisional	96.31
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.29
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	96.27
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.26
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.21
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.16
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.08
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.06
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.98
PRK08116	268	hypothetical protein; Validated	95.92
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.92
PHA00729	226	NTP-binding motif containing protein	95.86
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	95.79
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.77
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	95.76
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.72
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	95.68
PRK04132	846	replication factor C small subunit; Provisional	95.67
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.63
PRK07399	314	DNA polymerase III subunit delta'; Validated	95.61
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.57
PRK00149	450	dnaA chromosomal replication initiation protein; R	95.55
PRK07952	244	DNA replication protein DnaC; Validated	95.55
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.54
PRK06526	254	transposase; Provisional	95.52
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.52
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.5
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.49
PRK07261	171	topology modulation protein; Provisional	95.48
PRK09354	349	recA recombinase A; Provisional	95.45
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	95.44
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.29
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.27
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	95.26
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	95.21
PRK12377	248	putative replication protein; Provisional	95.18
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.1
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	95.05
PRK12422	445	chromosomal replication initiation protein; Provis	95.03
PRK05642	234	DNA replication initiation factor; Validated	95.01
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.95
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	94.95
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	94.94
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	94.93
cd01394	218	radB RadB. The archaeal protein radB shares simila	94.91
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	94.89
PRK04301	317	radA DNA repair and recombination protein RadA; Va	94.84
PRK13531	498	regulatory ATPase RavA; Provisional	94.84
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	94.82
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	94.8
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.79
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.79
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	94.74
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	94.73
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.6
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.6
PRK06921	266	hypothetical protein; Provisional	94.58
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.58
PRK08939	306	primosomal protein DnaI; Reviewed	94.58
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	94.54
PRK06871	325	DNA polymerase III subunit delta'; Validated	94.52
PRK08058	329	DNA polymerase III subunit delta'; Validated	94.48
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	94.48
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	94.46
TIGR02236	310	recomb_radA DNA repair and recombination protein R	94.45
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	94.42
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	94.37
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.27
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	94.26
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.25
KOG1969	877	consensus DNA replication checkpoint protein CHL12	94.25
PTZ00035	337	Rad51 protein; Provisional	94.25
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.21
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	94.16
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	94.14
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	94.07
CHL00176	638	ftsH cell division protein; Validated	94.05
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	94.04
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	94.01
PF00154	322	RecA: recA bacterial DNA recombination protein; In	93.98
PRK06090	319	DNA polymerase III subunit delta'; Validated	93.97
PTZ00185	574	ATPase alpha subunit; Provisional	93.9
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	93.88
PRK09183	259	transposase/IS protein; Provisional	93.87
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	93.6
PRK04328	249	hypothetical protein; Provisional	93.57
PRK07993	334	DNA polymerase III subunit delta'; Validated	93.55
PRK06620	214	hypothetical protein; Validated	93.53
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	93.52
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	93.5
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	93.38
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	93.37
PRK05541	176	adenylylsulfate kinase; Provisional	93.36
TIGR00959	428	ffh signal recognition particle protein. This mode	93.22
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	93.19
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	93.17
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	93.08
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	93.02
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	93.01
PRK09519	790	recA DNA recombination protein RecA; Reviewed	92.98
CHL00060	494	atpB ATP synthase CF1 beta subunit	92.83
PRK04196	460	V-type ATP synthase subunit B; Provisional	92.8
PRK08533	230	flagellar accessory protein FlaH; Reviewed	92.78
KOG0736	953	consensus Peroxisome assembly factor 2 containing	92.74
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	92.61
PRK06851	367	hypothetical protein; Provisional	92.61
PRK06936	439	type III secretion system ATPase; Provisional	92.55
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	92.48
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	92.45
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	92.43
PRK06696	223	uridine kinase; Validated	92.37
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	92.21
PRK08149	428	ATP synthase SpaL; Validated	92.19
PRK13765	637	ATP-dependent protease Lon; Provisional	92.17
cd03115	173	SRP The signal recognition particle (SRP) mediates	92.16
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	92.04
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	92.03
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	92.03
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	91.95
PRK06835	329	DNA replication protein DnaC; Validated	91.9
PRK15455	644	PrkA family serine protein kinase; Provisional	91.89
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	91.86
PRK06067	234	flagellar accessory protein FlaH; Validated	91.84
PRK10536	262	hypothetical protein; Provisional	91.84
PRK10867	433	signal recognition particle protein; Provisional	91.82
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	91.62
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	91.58
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	91.58
PRK12678	672	transcription termination factor Rho; Provisional	91.46
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	91.39
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	91.34
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	91.34
CHL00195	489	ycf46 Ycf46; Provisional	91.34
COG0714	329	MoxR-like ATPases [General function prediction onl	91.31
PRK04296	190	thymidine kinase; Provisional	91.15
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	91.09
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	91.03
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	91.0
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	90.99
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	90.93
PRK10865	857	protein disaggregation chaperone; Provisional	90.89
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	90.84
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	90.79
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	90.78
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	90.77
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	90.72
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	90.64
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	90.64
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	90.55
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	90.49
CHL00059	485	atpA ATP synthase CF1 alpha subunit	90.48
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	90.37
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	90.33
TIGR00962	501	atpA proton translocating ATP synthase, F1 alpha s	90.3
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	90.29
PRK05922	434	type III secretion system ATPase; Validated	90.26
COG1157	441	FliI Flagellar biosynthesis/type III secretory pat	90.22
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	90.2
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	90.18
CHL00095	821	clpC Clp protease ATP binding subunit	90.18
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	90.13
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	90.06
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	90.04
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	90.03
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	89.99
PRK07594	433	type III secretion system ATPase SsaN; Validated	89.87
PRK11823	446	DNA repair protein RadA; Provisional	89.85
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	89.83
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	89.83
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	89.79
PRK13849	231	putative crown gall tumor protein VirC1; Provision	89.76
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	89.69
PRK06964	342	DNA polymerase III subunit delta'; Validated	89.55
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	89.36
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	89.25
PRK13343	502	F0F1 ATP synthase subunit alpha; Provisional	89.21
PRK09099	441	type III secretion system ATPase; Provisional	89.21
COG1192	259	Soj ATPases involved in chromosome partitioning [C	89.18
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	89.18
PRK08233	182	hypothetical protein; Provisional	89.17
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	89.12
PRK00771	437	signal recognition particle protein Srp54; Provisi	89.02
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	88.96
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	88.95
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	88.93
PRK07667	193	uridine kinase; Provisional	88.82
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	88.64
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	88.62
PTZ00088	229	adenylate kinase 1; Provisional	88.59
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	88.58
PRK02118	436	V-type ATP synthase subunit B; Provisional	88.57
PF07726	131	AAA_3: ATPase family associated with various cellu	88.49
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	88.43
PRK06820	440	type III secretion system ATPase; Validated	88.28
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	88.26
PRK03839	180	putative kinase; Provisional	88.21
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	88.14
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	88.13
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	88.07
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	88.05
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	87.95
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	87.8
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	87.78
PF01656	195	CbiA: CobQ/CobB/MinD/ParA nucleotide binding domai	87.73
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	87.71
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	87.7
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	87.7
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	87.6
PRK04192	586	V-type ATP synthase subunit A; Provisional	87.47
PRK09302	509	circadian clock protein KaiC; Reviewed	87.47
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	87.46
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	87.43
PRK06762	166	hypothetical protein; Provisional	87.43
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	87.34
PHA02518	211	ParA-like protein; Provisional	87.29
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	87.25
cd02042	104	ParA ParA and ParB of Caulobacter crescentus belon	87.2
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	87.19
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	86.99
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	86.99
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	86.91
COG1158	422	Rho Transcription termination factor [Transcriptio	86.88
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	86.86
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	86.85
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	86.72
KOG1514	767	consensus Origin recognition complex, subunit 1, a	86.7
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	86.69
cd02040	270	NifH NifH gene encodes component II (iron protein)	86.63
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	86.58
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	86.53
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	86.35
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	86.22
PRK05480	209	uridine/cytidine kinase; Provisional	86.16
PRK06547	172	hypothetical protein; Provisional	86.15
PLN02924	220	thymidylate kinase	86.15
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	86.14
PF08303	168	tRNA_lig_kinase: tRNA ligase kinase domain; InterP	86.08
PTZ00301	210	uridine kinase; Provisional	86.06
COG0593	408	DnaA ATPase involved in DNA replication initiation	86.05
TIGR00235	207	udk uridine kinase. Model contains a number of lon	86.05
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	85.98
PRK08760	476	replicative DNA helicase; Provisional	85.9
PRK05748	448	replicative DNA helicase; Provisional	85.89
PRK00625	173	shikimate kinase; Provisional	85.88
PRK06217	183	hypothetical protein; Validated	85.86
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	85.82
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	85.81
PRK09302	509	circadian clock protein KaiC; Reviewed	85.8
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	85.79
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	85.75
PRK00279	215	adk adenylate kinase; Reviewed	85.74
PF07015	231	VirC1: VirC1 protein; InterPro: IPR009744 This fam	85.74
cd02036	179	MinD Bacterial cell division requires the formatio	85.73
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	85.69
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	85.67
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	85.64
TIGR01042	591	V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit. Th	85.56
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	85.54
cd02037	169	MRP-like MRP (Multiple Resistance and pH adaptatio	85.54
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	85.47
PHA02244	383	ATPase-like protein	85.33
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	85.28
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	85.23
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	85.22
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	85.2
PRK13695	174	putative NTPase; Provisional	85.14
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	85.14
PRK00131	175	aroK shikimate kinase; Reviewed	85.13
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	85.09
PRK07773	886	replicative DNA helicase; Validated	85.0
COG4167	267	SapF ABC-type antimicrobial peptide transport syst	84.93
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	84.76
PRK10037	250	cell division protein; Provisional	84.7
TIGR01281	268	DPOR_bchL light-independent protochlorophyllide re	84.44
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	84.33
PRK07165	507	F0F1 ATP synthase subunit alpha; Validated	84.31
PRK05636	505	replicative DNA helicase; Provisional	84.28
KOG2859	293	consensus DNA repair protein, member of the recA/R	84.26
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	84.2
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	84.19
PF13245	76	AAA_19: Part of AAA domain	84.12
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	84.1
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	83.99
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	83.95
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	83.94
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	83.92
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	83.89
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	83.86
COG0125	208	Tmk Thymidylate kinase [Nucleotide transport and m	83.74
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	83.73
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	83.73
TIGR00665	434	DnaB replicative DNA helicase. This model describe	83.71
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	83.7
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	83.67
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	83.64
PRK14529	223	adenylate kinase; Provisional	83.63
PRK14531	183	adenylate kinase; Provisional	83.6
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	83.53
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	83.52
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	83.45
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	83.2
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	83.16
PRK13947	171	shikimate kinase; Provisional	83.15
PRK10646	153	ADP-binding protein; Provisional	83.14
PRK13231	264	nitrogenase reductase-like protein; Reviewed	83.02
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	83.01
PRK11545	163	gntK gluconate kinase 1; Provisional	82.97
PRK13185	270	chlL protochlorophyllide reductase iron-sulfur ATP	82.97
PRK13230	279	nitrogenase reductase-like protein; Reviewed	82.94
TIGR01969	251	minD_arch cell division ATPase MinD, archaeal. Thi	82.9
) 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	82.87
PRK06321	472	replicative DNA helicase; Provisional	82.63
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	82.58
PRK14974	336	cell division protein FtsY; Provisional	82.58
TIGR00064	272	ftsY signal recognition particle-docking protein F	82.49
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	82.49
PF02223	186	Thymidylate_kin: Thymidylate kinase; InterPro: IPR	82.43
TIGR01287	275	nifH nitrogenase iron protein. This model describe	82.37
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	82.31
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	82.28
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	82.16
PRK13233	275	nifH nitrogenase reductase; Reviewed	82.05
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	81.99
cd02032	267	Bchl_like This family of proteins contains bchL an	81.82
PRK05595	444	replicative DNA helicase; Provisional	81.76
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	81.66
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	81.56
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	81.55
PRK13235	274	nifH nitrogenase reductase; Reviewed	81.46
PRK13975	196	thymidylate kinase; Provisional	81.44
PRK13232	273	nifH nitrogenase reductase; Reviewed	81.42
PRK04040	188	adenylate kinase; Provisional	81.29
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	81.26
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	81.18
cd03110	179	Fer4_NifH_child This protein family's function is	81.14
PRK00889	175	adenylylsulfate kinase; Provisional	81.09
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	81.02
TIGR03371	246	cellulose_yhjQ cellulose synthase operon protein Y	80.79
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	80.78
PRK13949	169	shikimate kinase; Provisional	80.77
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	80.71
COG1149	284	MinD superfamily P-loop ATPase containing an inser	80.41
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	80.28
COG4778	235	PhnL ABC-type phosphonate transport system, ATPase	80.15
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	80.15
TIGR01043	578	ATP_syn_A_arch ATP synthase archaeal, A subunit. A	80.07
KOG1547	336	consensus Septin CDC10 and related P-loop GTPases	80.04

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=7.4e-51  Score=419.91  Aligned_cols=347  Identities=23%  Similarity=0.298  Sum_probs=261.2

Q ss_pred             HhhhhHHHhhhhhhhccchHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHhchhhHHHHHHHH---------
Q 045120           15 WLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTSIQ----------LRVSEAKEKGEEIEEKVEKWL---------   75 (374)
Q Consensus        15 ~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~l~~v~----------~~i~~a~~~~~~~~~~v~~wl---------   75 (374)
                      ++.+.+.+....+  .+....+..+++++..|+..+.++.          .|.++.++.+++.++.+..+.         
T Consensus        11 ~~~~~l~~~~~~~--~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~   88 (889)
T KOG4658|consen   11 KLDQLLNRESECL--DGKDNYILELKENLKALQSALEDLDAKRDDLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKAN   88 (889)
T ss_pred             hHHHHHHHHHHHH--hchHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445555555556  6666666777777777777666533          356666666665555544333         


Q ss_pred             -----------------Hhhhh-------HHHHHHHHHHHHHHHHhccCCccccccC-CCcccccccccccccccccHHH
Q 045120           76 -----------------TRYQL-------SKKAKTEVKALIELGEEVKKFDIVSHCT-IPEEIWLKSNKVYEAFESRVSN  130 (374)
Q Consensus        76 -----------------~r~~~-------~~~i~~~~~~l~~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~vGr~~~  130 (374)
                                       ++++.       ++++-++.+.++.+ .....|....... +.......|...... ||.+..
T Consensus        89 ~~l~~~~~~~~~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l-~~~~~~~~~~~~~~~~~~~e~~~~~~~~~-VG~e~~  166 (889)
T KOG4658|consen   89 DLLSTRSVERQRLCLCGFCSKNVSDSYKYGKRVSKVLREVESL-GSKGVFEVVGESLDPREKVETRPIQSESD-VGLETM  166 (889)
T ss_pred             HHhhhhHHHHHHHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHh-ccccceecccccccchhhcccCCCCcccc-ccHHHH
Confidence                             12222       33333333333433 2233344433321 112223333333334 999999


Q ss_pred             HHHHHHHhhcC---------CCCccHHHHHHHHHHHhh-hcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch---hh
Q 045120          131 LKSTQNALTNA---------NGGIGKTTLAKEFAKQAR-EDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE---EA  197 (374)
Q Consensus       131 ~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~-~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~---~~  197 (374)
                      ++++++.|.++         |||+||||||++++|+.. +.++||.++||+||+.++...++++|++.++.....   .+
T Consensus       167 ~~kl~~~L~~d~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~  246 (889)
T KOG4658|consen  167 LEKLWNRLMEDDVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKE  246 (889)
T ss_pred             HHHHHHHhccCCCCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhh
Confidence            99999999876         999999999999999988 999999999999999999999999999999874333   33


Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcCCCC---------CcchhHhhhhcCCCCceecCCCCHHHHHHH
Q 045120          198 EYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVLLSMGSKDNFLIANITEEEAWRL  268 (374)
Q Consensus       198 ~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~~~~---------TR~~~va~~~~~~~~~~~l~~L~~~~s~~L  268 (374)
                      ..+.+..|.+.|.+ |||||||||||+..+|+.++.|+|..         ||+..|+...|+....+++++|+.+|||+|
T Consensus       247 ~~~~~~~i~~~L~~-krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~L  325 (889)
T KOG4658|consen  247 EDELASKLLNLLEG-KRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDL  325 (889)
T ss_pred             HHHHHHHHHHHhcc-CceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHH
Confidence            46788999999998 99999999999999999999999876         999999765588888999999999999999


Q ss_pred             HHHhcCCC--CCCcchHHHHHHHHHHccCCchHHHHHHhc--CCC-cccccccccc----------cCCC-Ccccchhh-
Q 045120          269 FKIMNGDD--VENCKFKSTAINVAKACGAGLFCTLTTNAS--KSS-SIYSHVSNDY----------QSIY-KPKPYLAV-  331 (374)
Q Consensus       269 f~~~a~~~--~~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~-~~~~W~~~~~----------~~~~-~~~~~~~l-  331 (374)
                      |++.+|..  ...+.++.+|++|+++| +|+|||++++|+  +.| +.++|++...          +++. .+.+.+.+ 
T Consensus       326 F~~~v~~~~~~~~~~i~~lak~v~~kC-~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklS  404 (889)
T KOG4658|consen  326 FQKKVGPNTLGSHPDIEELAKEVAEKC-GGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILKLS  404 (889)
T ss_pred             HHHhhccccccccccHHHHHHHHHHHh-CChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhhcc
Confidence            99999844  33456899999999999 999999999999  555 8889944322          1222 33356666 


Q ss_pred             cccCCchhhhhhhc----CchhhhhcHHHHHHHHHhCCcce
Q 045120          332 FQDLEPTIVKTAFV----DPKWYLALKEEFEALQRNQTWSL  368 (374)
Q Consensus       332 y~~Lp~~~lk~cfL----fp~~~~i~~~~Li~~W~~~~~~~  368 (374)
                      |++||+ ++|+|||    ||+||.|++++||..|+|+||.-
T Consensus       405 yd~L~~-~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~  444 (889)
T KOG4658|consen  405 YDNLPE-ELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFID  444 (889)
T ss_pred             HhhhhH-HHHHHHHhhccCCcccccchHHHHHHHHhccCcC
Confidence            999995 5999996    99999999999999999999753

>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=100.00  E-value=1.9e-38  Score=294.45  Aligned_cols=239  Identities=24%  Similarity=0.342  Sum_probs=183.2

Q ss_pred             cHHHHHHHHHHhhc--C---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc-
Q 045120          127 RVSNLKSTQNALTN--A---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS-  194 (374)
Q Consensus       127 r~~~~~~i~~~L~~--~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-  194 (374)
                      ||.++++|.+.|..  +         |||+||||||..++++..++++|+.++|+++++..+...++..|+.+++.... 
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            78999999999988  3         99999999999999987788999999999999999999999999999987732 


Q ss_pred             ---hhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcCCCC---------CcchhHhhhhcCCCCceecCCCCH
Q 045120          195 ---EEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---------SRDNNVVLLSMGSKDNFLIANITE  262 (374)
Q Consensus       195 ---~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~~~~---------TR~~~va~~~~~~~~~~~l~~L~~  262 (374)
                         ..+.......+.+.|.+ +++||||||||+...|+.+...++..         ||+..++....+....|+|++|+.
T Consensus        81 ~~~~~~~~~~~~~l~~~L~~-~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~  159 (287)
T PF00931_consen   81 ISDPKDIEELQDQLRELLKD-KRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSE  159 (287)
T ss_dssp             SSCCSSHHHHHHHHHHHHCC-TSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--H
T ss_pred             cccccccccccccchhhhcc-ccceeeeeeeccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence               34666788999999998 79999999999999998876655432         999888743333367899999999


Q ss_pred             HHHHHHHHHhcCCCC--CCcchHHHHHHHHHHccCCchHHHHHHhc--CCC-ccccccccccc------CC----CCccc
Q 045120          263 EEAWRLFKIMNGDDV--ENCKFKSTAINVAKACGAGLFCTLTTNAS--KSS-SIYSHVSNDYQ------SI----YKPKP  327 (374)
Q Consensus       263 ~~s~~Lf~~~a~~~~--~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~-~~~~W~~~~~~------~~----~~~~~  327 (374)
                      ++|++||++.++...  .++.+.+++++|+++| +|+||||+++|+  +.+ +..+|......      +.    ....+
T Consensus       160 ~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c-~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~~  238 (287)
T PF00931_consen  160 EEALELFKKRAGRKESESPEDLEDLAKEIVEKC-GGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVFS  238 (287)
T ss_dssp             HHHHHHHHHHHTSHS----TTSCTHHHHHHHHT-TT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccc-cccccccccccccccccccccccccccccccccccccccccccccc
Confidence            999999999998443  4566678899999999 999999999999  333 78889443211      11    11112


Q ss_pred             chhh-cccCCchhhhhhhc----CchhhhhcHHHHHHHHHhCCcce
Q 045120          328 YLAV-FQDLEPTIVKTAFV----DPKWYLALKEEFEALQRNQTWSL  368 (374)
Q Consensus       328 ~~~l-y~~Lp~~~lk~cfL----fp~~~~i~~~~Li~~W~~~~~~~  368 (374)
                      .+.+ |+.||++ +|+||+    ||.++.|+++.||++|+++||.-
T Consensus       239 ~l~~s~~~L~~~-~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~  283 (287)
T PF00931_consen  239 ALELSYDSLPDE-LRRCFLYLSIFPEGVPIPRERLIRLWVAEGFIS  283 (287)
T ss_dssp             HHHHHHHSSHTC-CHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC
T ss_pred             cceechhcCCcc-HHHHHhhCcCCCCCceECHHHHHHHHHHCCCCc
Confidence            3334 9999885 999994    99999999999999999999963

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.

>PLN03210 Resistant to P

Probab=99.96  E-value=6.9e-28  Score=260.52  Aligned_cols=237  Identities=17%  Similarity=0.129  Sum_probs=172.4

Q ss_pred             ccccccccHHHHHHHHHHhhcC-----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe---CCC----------
Q 045120          120 VYEAFESRVSNLKSTQNALTNA-----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV---SQT----------  175 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~-----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v---s~~----------  175 (374)
                      ....+|||+..++++..+|.-+           |||+||||||+++|+..  ..+|+..+|+..   +..          
T Consensus       182 ~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l--~~~F~g~vfv~~~~v~~~~~~~~~~~~~  259 (1153)
T PLN03210        182 DFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRL--SRQFQSSVFIDRAFISKSMEIYSSANPD  259 (1153)
T ss_pred             ccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHH--hhcCCeEEEeeccccccchhhccccccc
Confidence            3567999999999999988633           99999999999999954  477999888742   111          


Q ss_pred             -CC-HHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcC---CCC------CcchhH
Q 045120          176 -SD-IKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPF---RND------SRDNNV  244 (374)
Q Consensus       176 -~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~---~~~------TR~~~v  244 (374)
                       ++ ...++..++..+....... . .....+++.|.+ ||+||||||||+..+|+.+....   ..+      ||+..+
T Consensus       260 ~~~~~~~l~~~~l~~il~~~~~~-~-~~~~~~~~~L~~-krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~~v  336 (1153)
T PLN03210        260 DYNMKLHLQRAFLSEILDKKDIK-I-YHLGAMEERLKH-RKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHF  336 (1153)
T ss_pred             ccchhHHHHHHHHHHHhCCCCcc-c-CCHHHHHHHHhC-CeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcHHH
Confidence             01 1234445555442221110 0 012456777888 99999999999998888875432   233      999999


Q ss_pred             hhhhcCCCCceecCCCCHHHHHHHHHHhcCCCC-CCcchHHHHHHHHHHccCCchHHHHHHhc--CCCccccccccccc-
Q 045120          245 VLLSMGSKDNFLIANITEEEAWRLFKIMNGDDV-ENCKFKSTAINVAKACGAGLFCTLTTNAS--KSSSIYSHVSNDYQ-  320 (374)
Q Consensus       245 a~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~-~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~~~~~W~~~~~~-  320 (374)
                      +. .++..++|+++.|++++||+||+++||... .++++.+++++|+++| +|+||||+++|+  ++++.++|...... 
T Consensus       337 l~-~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c-~GLPLAl~vlgs~L~~k~~~~W~~~l~~L  414 (1153)
T PLN03210        337 LR-AHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRA-GNLPLGLNVLGSYLRGRDKEDWMDMLPRL  414 (1153)
T ss_pred             HH-hcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHh-CCCcHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            74 566678999999999999999999999544 3457889999999999 999999999999  78889999554321 


Q ss_pred             --CCC-Ccccchhh-cccCCchhhhhhhc----CchhhhhcHHHHHHHHHhCCc
Q 045120          321 --SIY-KPKPYLAV-FQDLEPTIVKTAFV----DPKWYLALKEEFEALQRNQTW  366 (374)
Q Consensus       321 --~~~-~~~~~~~l-y~~Lp~~~lk~cfL----fp~~~~i~~~~Li~~W~~~~~  366 (374)
                        ... ++...+.+ |+.|+++..|.||+    ||.++.++   .|..|++.+.
T Consensus       415 ~~~~~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~  465 (1153)
T PLN03210        415 RNGLDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSD  465 (1153)
T ss_pred             HhCccHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHH---HHHHHHHhcC
Confidence              111 22235566 99998755999997    67666443   4777887654

syringae 6; Provisional

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.93  E-value=3.6e-08  Score=95.71  Aligned_cols=183  Identities=18%  Similarity=0.129  Sum_probs=116.3

Q ss_pred             cccccccHHHHHHHHHHhhcC-------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA-------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~-------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      +..++||++++++|...|...             ++|+|||++++.++++.......-..++++.....+...++..|+.
T Consensus        29 P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~  108 (394)
T PRK00411         29 PENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIAR  108 (394)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHH
Confidence            456999999999998887321             8899999999999997654332234577777777788899999999


Q ss_pred             HhCcC-C--chhhHHHHHHHHHHHHhc-CCeEEEEEeCCCCcc------ccccccCc---CCC-C------CcchhHh--
Q 045120          188 KLGLE-L--SEEAEYRRASRLYERLKN-ENKILVILANIWKLL------DLETVKIP---FRN-D------SRDNNVV--  245 (374)
Q Consensus       188 ~l~~~-~--~~~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~------~~~~l~~~---~~~-~------TR~~~va--  245 (374)
                      ++... .  ...+..+....+.+.+.. ++..+||||+++...      .+..+...   .+. .      +....+.  
T Consensus       109 ~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~  188 (394)
T PRK00411        109 QLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYI  188 (394)
T ss_pred             HhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhh
Confidence            98652 2  122445666777777764 356899999998532      22232211   111 1      2211111  


Q ss_pred             -----hhhcCCCCceecCCCCHHHHHHHHHHhcCC---C--CCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          246 -----LLSMGSKDNFLIANITEEEAWRLFKIMNGD---D--VENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       246 -----~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~---~--~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                           .... ....+.+++++.++..+++...+..   .  ..+..+..+++...... |..+.|+.++-
T Consensus       189 l~~~~~s~~-~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~-Gd~r~a~~ll~  256 (394)
T PRK00411        189 LDPRVKSVF-RPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREH-GDARVAIDLLR  256 (394)
T ss_pred             cCHHHHhcC-CcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhc-CcHHHHHHHHH
Confidence                 1111 1246789999999999999987631   1  12223333443333335 77888887764

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.90  E-value=8e-08  Score=88.16  Aligned_cols=161  Identities=15%  Similarity=0.158  Sum_probs=98.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHH----HHhcCCeEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYE----RLKNENKILV  217 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~----~L~~~kr~Ll  217 (374)
                      +.|+|||||++.+++..... .+ ..+|+ +....+..+++..|+..++.+....+.......+..    .+..+++.+|
T Consensus        51 ~~G~GKTtl~~~l~~~l~~~-~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~~~~vl  127 (269)
T TIGR03015        51 EVGAGKTTLIRNLLKRLDQE-RV-VAAKL-VNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAGKRALL  127 (269)
T ss_pred             CCCCCHHHHHHHHHHhcCCC-Ce-EEeee-eCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCCCCeEE
Confidence            88999999999999875422 11 12233 333457788999999999876544333333334433    3334478999


Q ss_pred             EEeCCCCcc--ccccccC--cCC--CC-------CcchhHh---------hhhcCCCCceecCCCCHHHHHHHHHHhcCC
Q 045120          218 ILANIWKLL--DLETVKI--PFR--ND-------SRDNNVV---------LLSMGSKDNFLIANITEEEAWRLFKIMNGD  275 (374)
Q Consensus       218 VlDdv~~~~--~~~~l~~--~~~--~~-------TR~~~va---------~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~  275 (374)
                      |+||++...  .++.+..  .+.  +.       +-.....         .........+.+++|+.++..+++...+..
T Consensus       128 iiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~~~l~~~l~~  207 (269)
T TIGR03015       128 VVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPLDREETREYIEHRLER  207 (269)
T ss_pred             EEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCCCHHHHHHHHHHHHHH
Confidence            999998753  2333211  000  00       1111110         000111346789999999999998877641


Q ss_pred             C---CCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          276 D---VENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       276 ~---~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      .   ....--.+..+.|++.| +|.|..|..++.
T Consensus       208 ~g~~~~~~~~~~~~~~i~~~s-~G~p~~i~~l~~  240 (269)
T TIGR03015       208 AGNRDAPVFSEGAFDAIHRFS-RGIPRLINILCD  240 (269)
T ss_pred             cCCCCCCCcCHHHHHHHHHHc-CCcccHHHHHHH
Confidence            1   11122347788999999 999999999886

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.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.85  E-value=1.1e-08  Score=91.33  Aligned_cols=175  Identities=21%  Similarity=0.295  Sum_probs=90.0

Q ss_pred             ccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH---------
Q 045120          124 FESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDI---------  185 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i---------  185 (374)
                      |+||+.++++|.+++..+         +.|+|||+|++.+.+..... .+ .++|+......+... ...+         
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~-~~-~~~y~~~~~~~~~~~-~~~~~~~~~~~~~   77 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEK-GY-KVVYIDFLEESNESS-LRSFIEETSLADE   77 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT---EE-CCCHHCCTTBSHHHH-HHHHHHHHHHHCH
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhc-CC-cEEEEecccchhhhH-HHHHHHHHHHHHH
Confidence            789999999999999864         88999999999999865321 11 344554444432222 2222         


Q ss_pred             -HHHhCcCC-----------chhhHHHHHHHHHHHHhc-CCeEEEEEeCCCCcc-ccc-------cc---cCcCCCC---
Q 045120          186 -AEKLGLEL-----------SEEAEYRRASRLYERLKN-ENKILVILANIWKLL-DLE-------TV---KIPFRND---  238 (374)
Q Consensus       186 -~~~l~~~~-----------~~~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~-~~~-------~l---~~~~~~~---  238 (374)
                       ...+....           ...........+.+.+.. +++.+||+||+.... ...       .+   .......   
T Consensus        78 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  157 (234)
T PF01637_consen   78 LSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNV  157 (234)
T ss_dssp             CHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTE
T ss_pred             HHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCc
Confidence             12221111           011223344555555553 356999999987554 111       11   1111111   


Q ss_pred             ------CcchhHhhh-------hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHH
Q 045120          239 ------SRDNNVVLL-------SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTT  303 (374)
Q Consensus       239 ------TR~~~va~~-------~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~  303 (374)
                            |. ..+...       ..+....+.|++|+.+++++++...+.....-+.-....++|...+ ||.|..|.-
T Consensus       158 ~~v~~~S~-~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~-gG~P~~l~~  233 (234)
T PF01637_consen  158 SIVITGSS-DSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLT-GGNPRYLQE  233 (234)
T ss_dssp             EEEEEESS-HHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC------HHHHHHHHHHH-TT-HHHHHH
T ss_pred             eEEEECCc-hHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHh-CCCHHHHhc
Confidence                  22 212111       1233345999999999999999987643211011234457999999 999998864

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.68  E-value=4.3e-07  Score=97.47  Aligned_cols=178  Identities=13%  Similarity=0.126  Sum_probs=109.4

Q ss_pred             ccccccccccHHHHHHHHHHhhcC------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhC
Q 045120          118 NKVYEAFESRVSNLKSTQNALTNA------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-TSDIKKIQGDIAEKLG  190 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~~~------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~  190 (374)
                      |.....++-|..-.+.+-+.....      ++|.|||||+.+....      ++.++|+++.. ..++..+...++..++
T Consensus        10 p~~~~~~~~R~rl~~~l~~~~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~~l~   83 (903)
T PRK04841         10 PVRLHNTVVRERLLAKLSGANNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIAALQ   83 (903)
T ss_pred             CCCccccCcchHHHHHHhcccCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHHHHH
Confidence            333455777776666554332222      9999999999998752      33689999964 4577777788877774


Q ss_pred             cCCch--------------hhHHHHHHHHHHHHhc-CCeEEEEEeCCCCcc------ccccccCcCCCC------Ccchh
Q 045120          191 LELSE--------------EAEYRRASRLYERLKN-ENKILVILANIWKLL------DLETVKIPFRND------SRDNN  243 (374)
Q Consensus       191 ~~~~~--------------~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~------~~~~l~~~~~~~------TR~~~  243 (374)
                      .....              .+.......+...|.. +.+++|||||+....      .+..+....|.+      ||...
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841         84 QATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             HhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            21111              1112233444444443 478999999997542      233333334444      66531


Q ss_pred             Hhh-hhc-CCCCceecC----CCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          244 VVL-LSM-GSKDNFLIA----NITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       244 va~-~~~-~~~~~~~l~----~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      -.. ... -......+.    +|+.+|+.+||....+..-.    .....+|.+.| +|.|+++..++.
T Consensus       164 ~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~----~~~~~~l~~~t-~Gwp~~l~l~~~  227 (903)
T PRK04841        164 PLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPIE----AAESSRLCDDV-EGWATALQLIAL  227 (903)
T ss_pred             CCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCCC----HHHHHHHHHHh-CChHHHHHHHHH
Confidence            110 000 012244555    99999999999887664322    24456899999 999999998886

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.63  E-value=1.5e-06  Score=83.40  Aligned_cols=179  Identities=17%  Similarity=0.174  Sum_probs=111.7

Q ss_pred             cccccccHHHHHHHHHHhhc----C---------CCCccHHHHHHHHHHHhhhc-CCC---CeEEEEEeCCCCCHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTN----A---------NGGIGKTTLAKEFAKQARED-KLF---DRVVFSEVSQTSDIKKIQG  183 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~----~---------~gGiGKTtLA~~v~~~~~~~-~~F---~~~~wv~vs~~~~~~~~~~  183 (374)
                      +..++||+.++++|...|..    .         ++|+|||++++.++++.... ...   -..+|++.....+...++.
T Consensus        14 p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~   93 (365)
T TIGR02928        14 PDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLV   93 (365)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHH
Confidence            34699999999999999863    1         88999999999999865321 111   1356777777777888999


Q ss_pred             HHHHHhC---cCCch--hhHHHHHHHHHHHHh-cCCeEEEEEeCCCCcc-----ccccccCc-----CCCC-------Cc
Q 045120          184 DIAEKLG---LELSE--EAEYRRASRLYERLK-NENKILVILANIWKLL-----DLETVKIP-----FRND-------SR  240 (374)
Q Consensus       184 ~i~~~l~---~~~~~--~~~~~~~~~l~~~L~-~~kr~LlVlDdv~~~~-----~~~~l~~~-----~~~~-------TR  240 (374)
                      .|+.++.   ...+.  .+..+....+.+.+. .+++++||||+++...     .+..+...     .+..       +.
T Consensus        94 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n  173 (365)
T TIGR02928        94 ELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISN  173 (365)
T ss_pred             HHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEEC
Confidence            9999983   32221  234455566667665 2368899999998651     12222111     1111       22


Q ss_pred             chhHh-------hhhcCCCCceecCCCCHHHHHHHHHHhcC---C-CCCCcchHHHHHHHHHHccCCchHHH
Q 045120          241 DNNVV-------LLSMGSKDNFLIANITEEEAWRLFKIMNG---D-DVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       241 ~~~va-------~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~---~-~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      .....       ..... ...+.+++++.++..+++...+.   . ....++..+....++..+ +|-|-.+
T Consensus       174 ~~~~~~~l~~~~~s~~~-~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~-~Gd~R~a  243 (365)
T TIGR02928       174 DLKFRENLDPRVKSSLC-EEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQE-HGDARKA  243 (365)
T ss_pred             CcchHhhcCHHHhccCC-cceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHh-cCCHHHH
Confidence            11110       01111 24688999999999999998763   1 112233334445677777 7887443

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.

>PF05729 NACHT: NACHT domain

Probab=98.49  E-value=1.3e-06  Score=73.57  Aligned_cols=127  Identities=20%  Similarity=0.269  Sum_probs=75.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHH---HHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKL----FDRVVFSEVSQTSDIK---KIQGDIAEKLGLELSEEAEYRRASRLYERLKNENK  214 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~vs~~~~~~---~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr  214 (374)
                      .+|+||||+++.++.+......    +...+|.+.+......   .+...|..+.........     ..+...+...++
T Consensus         8 ~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~   82 (166)
T PF05729_consen    8 EPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIE-----ELLQELLEKNKR   82 (166)
T ss_pred             CCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhH-----HHHHHHHHcCCc
Confidence            7899999999999987665543    3456677766554332   344444444432211111     133344444589


Q ss_pred             EEEEEeCCCCccc-------------cccccCc-CCCC------CcchhH--hhhhcCCCCceecCCCCHHHHHHHHHHh
Q 045120          215 ILVILANIWKLLD-------------LETVKIP-FRND------SRDNNV--VLLSMGSKDNFLIANITEEEAWRLFKIM  272 (374)
Q Consensus       215 ~LlVlDdv~~~~~-------------~~~l~~~-~~~~------TR~~~v--a~~~~~~~~~~~l~~L~~~~s~~Lf~~~  272 (374)
                      ++||||++.+...             +..+... .+.+      +|....  ..........+.|++|++++..+++.++
T Consensus        83 ~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  162 (166)
T PF05729_consen   83 VLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYLRKY  162 (166)
T ss_pred             eEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHHHHH
Confidence            9999999975432             2222222 2222      555444  2223344468999999999999999876


Q ss_pred             c
Q 045120          273 N  273 (374)
Q Consensus       273 a  273 (374)
                      .
T Consensus       163 f  163 (166)
T PF05729_consen  163 F  163 (166)
T ss_pred             h
Confidence            5

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.48  E-value=4.3e-07  Score=81.92  Aligned_cols=83  Identities=13%  Similarity=0.192  Sum_probs=58.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC--CCHHHHHHHH-----HHHhCcCCchh--hHHHHHHHHHHHHhcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT--SDIKKIQGDI-----AEKLGLELSEE--AEYRRASRLYERLKNE  212 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i-----~~~l~~~~~~~--~~~~~~~~l~~~L~~~  212 (374)
                      ++|+|||||++.+|++.... +|+.++|+.++.+  .++.++++.+     +..++.+....  -..........+...+
T Consensus        24 ~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a~~~~~~G  102 (249)
T cd01128          24 PPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKRLVEHG  102 (249)
T ss_pred             CCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence            88999999999999987654 8999999998877  7999999999     44444321110  1112223333333345


Q ss_pred             CeEEEEEeCCCCc
Q 045120          213 NKILVILANIWKL  225 (374)
Q Consensus       213 kr~LlVlDdv~~~  225 (374)
                      ++.+|++|++...
T Consensus       103 ~~vll~iDei~r~  115 (249)
T cd01128         103 KDVVILLDSITRL  115 (249)
T ss_pred             CCEEEEEECHHHh
Confidence            8999999999743

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.40  E-value=5.1e-06  Score=77.75  Aligned_cols=173  Identities=14%  Similarity=0.025  Sum_probs=102.3

Q ss_pred             ccccccHHHHHHHHHHhhc-----C---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTN-----A---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~-----~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      ..|+|++..+++|..++..     .         +.|+|||+||+.+.+....  .|   ..+..+....... +...+.
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~--~~---~~~~~~~~~~~~~-l~~~l~   77 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGV--NL---KITSGPALEKPGD-LAAILT   77 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCC--CE---EEeccchhcCchh-HHHHHH
Confidence            4699999999999888862     1         8999999999999986542  12   1222211112222 223333


Q ss_pred             HhCcCC-------chhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcCCCC---CcchhHhh---hhcCCCCc
Q 045120          188 KLGLEL-------SEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---SRDNNVVL---LSMGSKDN  254 (374)
Q Consensus       188 ~l~~~~-------~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~~~~---TR~~~va~---~~~~~~~~  254 (374)
                      .++...       ...+ ....+.+...+.+ .+..+|+++..+...+.....++.-.   |+...+..   ..+  ...
T Consensus        78 ~~~~~~vl~iDEi~~l~-~~~~e~l~~~~~~-~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~sR~--~~~  153 (305)
T TIGR00635        78 NLEEGDVLFIDEIHRLS-PAVEELLYPAMED-FRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRF--GII  153 (305)
T ss_pred             hcccCCEEEEehHhhhC-HHHHHHhhHHHhh-hheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHhhc--ceE
Confidence            333221       1011 1233456667776 67788888877665554332221100   33322211   112  246


Q ss_pred             eecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          255 FLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       255 ~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      +.+++++.++..+++.+.+..... .--.+....|++.| +|.|-.+.-++.
T Consensus       154 ~~l~~l~~~e~~~il~~~~~~~~~-~~~~~al~~ia~~~-~G~pR~~~~ll~  203 (305)
T TIGR00635       154 LRLEFYTVEELAEIVSRSAGLLNV-EIEPEAALEIARRS-RGTPRIANRLLR  203 (305)
T ss_pred             EEeCCCCHHHHHHHHHHHHHHhCC-CcCHHHHHHHHHHh-CCCcchHHHHHH
Confidence            899999999999999988863221 11235667899999 999976655553

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.39  E-value=9.1e-07  Score=83.61  Aligned_cols=82  Identities=11%  Similarity=0.162  Sum_probs=56.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC--CHHHHHHHHHHHhCcCCchhhHH-------HHHHHHHHHHhcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS--DIKKIQGDIAEKLGLELSEEAEY-------RRASRLYERLKNE  212 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~l~~~~~~~~~~-------~~~~~l~~~L~~~  212 (374)
                      ++|+||||||+.||++.... +|+.++||.+++..  ++.++++.|...+-....+.+..       .....-......+
T Consensus       177 ppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~~e~G  255 (416)
T PRK09376        177 PPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRLVEHG  255 (416)
T ss_pred             CCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence            89999999999999988765 89999999999987  78888888863222122121111       1122222222345


Q ss_pred             CeEEEEEeCCCC
Q 045120          213 NKILVILANIWK  224 (374)
Q Consensus       213 kr~LlVlDdv~~  224 (374)
                      ++.+|++|++..
T Consensus       256 ~dVlL~iDsItR  267 (416)
T PRK09376        256 KDVVILLDSITR  267 (416)
T ss_pred             CCEEEEEEChHH
Confidence            899999999863

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.33  E-value=1.3e-05  Score=75.87  Aligned_cols=176  Identities=14%  Similarity=0.038  Sum_probs=101.5

Q ss_pred             ccccccccHHHHHHHHHHhhc----C----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 045120          120 VYEAFESRVSNLKSTQNALTN----A----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDI  185 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~----~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  185 (374)
                      ....|+|++..++.+...+..    +          +.|+||||||+.+.+.....  +   .++..+ .......+..+
T Consensus        23 ~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~--~---~~~~~~-~~~~~~~l~~~   96 (328)
T PRK00080         23 SLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVN--I---RITSGP-ALEKPGDLAAI   96 (328)
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCC--e---EEEecc-cccChHHHHHH
Confidence            456799999999998777752    1          89999999999999965421  1   122221 11222233444


Q ss_pred             HHHhCcCC----ch-hh-HHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcC---CCCCcchhHhh---hhcCCCC
Q 045120          186 AEKLGLEL----SE-EA-EYRRASRLYERLKNENKILVILANIWKLLDLETVKIPF---RNDSRDNNVVL---LSMGSKD  253 (374)
Q Consensus       186 ~~~l~~~~----~~-~~-~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~---~~~TR~~~va~---~~~~~~~  253 (374)
                      +..+....    ++ .. .....+.+...+.. .+..+|+|+..+...+.....++   ...|+...+..   ..+  ..
T Consensus        97 l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~-~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~sRf--~~  173 (328)
T PRK00080         97 LTNLEEGDVLFIDEIHRLSPVVEEILYPAMED-FRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRF--GI  173 (328)
T ss_pred             HHhcccCCEEEEecHhhcchHHHHHHHHHHHh-cceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHHhc--Ce
Confidence            44443221    00 00 01123345556665 67778888866554433211111   00133222211   112  24


Q ss_pred             ceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          254 NFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       254 ~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      .+.+++++.++..+++.+.+...... --.+....|++.| +|.|-.+..+..
T Consensus       174 ~~~l~~~~~~e~~~il~~~~~~~~~~-~~~~~~~~ia~~~-~G~pR~a~~~l~  224 (328)
T PRK00080        174 VQRLEFYTVEELEKIVKRSARILGVE-IDEEGALEIARRS-RGTPRIANRLLR  224 (328)
T ss_pred             eeecCCCCHHHHHHHHHHHHHHcCCC-cCHHHHHHHHHHc-CCCchHHHHHHH
Confidence            68999999999999999888632211 1235678999999 999976655553

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.28  E-value=6.3e-06  Score=80.44  Aligned_cols=160  Identities=14%  Similarity=0.126  Sum_probs=90.7

Q ss_pred             cccccccHHHHHH---HHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          121 YEAFESRVSNLKS---TQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       121 ~~~~vGr~~~~~~---i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      ...++|.+..+..   +.+++...         ++|+||||||+.+++...  ..     |+.++....-..-.+.++  
T Consensus        11 l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~--~~-----~~~l~a~~~~~~~ir~ii--   81 (413)
T PRK13342         11 LDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATD--AP-----FEALSAVTSGVKDLREVI--   81 (413)
T ss_pred             HHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhC--CC-----EEEEecccccHHHHHHHH--
Confidence            4568888877655   66666554         889999999999998543  22     232222211111111111  


Q ss_pred             hCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccccCcCCCC--------Ccchh--HhhhhcCCCCcee
Q 045120          189 LGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVKIPFRND--------SRDNN--VVLLSMGSKDNFL  256 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~--------TR~~~--va~~~~~~~~~~~  256 (374)
                                    +........+++.+|+||+++...  ..+.|...+..+        |.+..  +..........+.
T Consensus        82 --------------~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~~~iilI~att~n~~~~l~~aL~SR~~~~~  147 (413)
T PRK13342         82 --------------EEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVFE  147 (413)
T ss_pred             --------------HHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhcCcEEEEEeCCCChhhhccHHHhccceeeE
Confidence                          222222222378899999998542  333333333222        22221  1011112225789


Q ss_pred             cCCCCHHHHHHHHHHhcCCCC-CC-cchHHHHHHHHHHccCCchHHHHHH
Q 045120          257 IANITEEEAWRLFKIMNGDDV-EN-CKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       257 l~~L~~~~s~~Lf~~~a~~~~-~~-~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                      +.+|+.++..+++.+.+.... .. .--.+....|++.| +|-|..+.-+
T Consensus       148 ~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s-~Gd~R~aln~  196 (413)
T PRK13342        148 LKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLA-NGDARRALNL  196 (413)
T ss_pred             eCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhC-CCCHHHHHHH
Confidence            999999999999998764211 01 12245667899999 9988766443

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.26  E-value=3.3e-06  Score=68.36  Aligned_cols=84  Identities=26%  Similarity=0.382  Sum_probs=64.7

Q ss_pred             CCCccHHHHHHHHHHHhhhc---CCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch-hhHHHHHHHHHHHHhcCCeEEE
Q 045120          142 NGGIGKTTLAKEFAKQARED---KLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE-EAEYRRASRLYERLKNENKILV  217 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~---~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~~kr~Ll  217 (374)
                      ..|+|||++++.+.++....   ..-..++|+.++...+...+...|+..++..... .+..++.+.+.+.+...+..+|
T Consensus        12 ~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~~~~~l   91 (131)
T PF13401_consen   12 PPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDRRRVVLL   91 (131)
T ss_dssp             -TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHCTEEEE
T ss_pred             CCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHhcCCeEE
Confidence            78999999999998865321   1124567999988889999999999999987666 5667777889999987556799


Q ss_pred             EEeCCCCc
Q 045120          218 ILANIWKL  225 (374)
Q Consensus       218 VlDdv~~~  225 (374)
                      |+|++...
T Consensus        92 viDe~~~l   99 (131)
T PF13401_consen   92 VIDEADHL   99 (131)
T ss_dssp             EEETTHHH
T ss_pred             EEeChHhc
Confidence            99998653

>PTZ00202 tuzin; Provisional

Probab=98.10  E-value=0.00049  Score=66.08  Aligned_cols=95  Identities=20%  Similarity=0.243  Sum_probs=65.5

Q ss_pred             cccccccccccHHHHHHHHHHhhcC------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          117 SNKVYEAFESRVSNLKSTQNALTNA------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       117 ~~~~~~~~vGr~~~~~~i~~~L~~~------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      .|.....|+||+.++..+...|.+.            ++|+|||||++.+.....    + ..++++..   +..+++..
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~----~-~qL~vNpr---g~eElLr~  328 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----M-PAVFVDVR---GTEDTLRS  328 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC----c-eEEEECCC---CHHHHHHH
Confidence            3455668999999999999988642            889999999999986432    2 23444333   67999999


Q ss_pred             HHHHhCcCCchhhHHHHHHHHHHHHh----c-CCeEEEEEe
Q 045120          185 IAEKLGLELSEEAEYRRASRLYERLK----N-ENKILVILA  220 (374)
Q Consensus       185 i~~~l~~~~~~~~~~~~~~~l~~~L~----~-~kr~LlVlD  220 (374)
                      |+..||.+.. ....++...|.+.|.    . +++-+||+-
T Consensus       329 LL~ALGV~p~-~~k~dLLrqIqeaLl~~~~e~GrtPVLII~  368 (550)
T PTZ00202        329 VVKALGVPNV-EACGDLLDFISEACRRAKKMNGETPLLVLK  368 (550)
T ss_pred             HHHHcCCCCc-ccHHHHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            9999997432 223444455555443    2 466666664

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.06  E-value=0.00053  Score=70.13  Aligned_cols=184  Identities=15%  Similarity=0.086  Sum_probs=103.6

Q ss_pred             ccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCC---eEEEEEeCCC---CCHHHHHHH
Q 045120          120 VYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFD---RVVFSEVSQT---SDIKKIQGD  184 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~---~~~wv~vs~~---~~~~~~~~~  184 (374)
                      ....++|++..+..+.+.+...         +.|+||||||+.+++.......++   ..-|+.+...   .+...+...
T Consensus       152 ~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~  231 (615)
T TIGR02903       152 AFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNP  231 (615)
T ss_pred             cHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHH
Confidence            3456899999999988877543         889999999999998765433332   2345544321   122222111


Q ss_pred             H---------------HHHhCcCC----------------ch--hhHHHHHHHHHHHHhcCCeEEEEEeCCCCc--cccc
Q 045120          185 I---------------AEKLGLEL----------------SE--EAEYRRASRLYERLKNENKILVILANIWKL--LDLE  229 (374)
Q Consensus       185 i---------------~~~l~~~~----------------~~--~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~--~~~~  229 (374)
                      +               +...+...                ++  .=+......|.+.|.+ ++++++.|+.|..  ..|+
T Consensus       232 llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~-~~v~~~~~~~~~~~~~~~~  310 (615)
T TIGR02903       232 LLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLED-KRVEFSSSYYDPDDPNVPK  310 (615)
T ss_pred             hcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhh-CeEEeecceeccCCcccch
Confidence            1               11111100                00  0112356788888888 7899997777654  2355


Q ss_pred             cccCcCCCC-----------CcchhH-hhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCc
Q 045120          230 TVKIPFRND-----------SRDNNV-VLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL  297 (374)
Q Consensus       230 ~l~~~~~~~-----------TR~~~v-a~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~Gl  297 (374)
                      .+...+..+           |++... ..........+.+.+++.++.+.++.+.+......- -.++...|...+ ..-
T Consensus       311 ~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~l-s~eal~~L~~ys-~~g  388 (615)
T TIGR02903       311 YIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHL-AAGVEELIARYT-IEG  388 (615)
T ss_pred             hhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHCC-CcH
Confidence            554333322           332221 110011123678899999999999999875321111 134455566666 555


Q ss_pred             hHHHHHHhc
Q 045120          298 FCTLTTNAS  306 (374)
Q Consensus       298 PLai~~ig~  306 (374)
                      +-|+..++.
T Consensus       389 Rraln~L~~  397 (615)
T TIGR02903       389 RKAVNILAD  397 (615)
T ss_pred             HHHHHHHHH
Confidence            777776654

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.

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

Probab=98.00  E-value=8.8e-05  Score=69.73  Aligned_cols=109  Identities=17%  Similarity=0.185  Sum_probs=65.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ++|+||||||+.+.....  ..|     ..+|-..+-.+-++.++                +.-++.+..+++.+|.+|.
T Consensus        56 PPG~GKTTlA~liA~~~~--~~f-----~~~sAv~~gvkdlr~i~----------------e~a~~~~~~gr~tiLflDE  112 (436)
T COG2256          56 PPGTGKTTLARLIAGTTN--AAF-----EALSAVTSGVKDLREII----------------EEARKNRLLGRRTILFLDE  112 (436)
T ss_pred             CCCCCHHHHHHHHHHhhC--Cce-----EEeccccccHHHHHHHH----------------HHHHHHHhcCCceEEEEeh
Confidence            999999999999998443  333     33343332222222222                2222222224899999999


Q ss_pred             CCC--ccccccccCcCCCC--------CcchhHh--hhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          222 IWK--LLDLETVKIPFRND--------SRDNNVV--LLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       222 v~~--~~~~~~l~~~~~~~--------TR~~~va--~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                      |..  ..+-+.|.+..-++        |-+..-.  .....-..++.+++|+.++-.+++.+.+
T Consensus       113 IHRfnK~QQD~lLp~vE~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~  176 (436)
T COG2256         113 IHRFNKAQQDALLPHVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRAL  176 (436)
T ss_pred             hhhcChhhhhhhhhhhcCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHH
Confidence            974  34555566655555        3333211  0012334589999999999999999844

>TIGR00767 rho transcription termination factor Rho

Probab=98.00  E-value=2.4e-05  Score=74.45  Aligned_cols=83  Identities=12%  Similarity=0.190  Sum_probs=57.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC--CCHHHHHHHHHHHhCcCCchhhH-------HHHHHHHHHHHhcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT--SDIKKIQGDIAEKLGLELSEEAE-------YRRASRLYERLKNE  212 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i~~~l~~~~~~~~~-------~~~~~~l~~~L~~~  212 (374)
                      .+|+|||||++.+++..... +|+..+||.+.+.  .++.++++.|...+-....+.+.       ....+........+
T Consensus       176 ~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~Ae~~~~~G  254 (415)
T TIGR00767       176 PPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHK  254 (415)
T ss_pred             CCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHHHHHHHcC
Confidence            77999999999999987644 7999999999977  78999999985433222111111       11222333333346


Q ss_pred             CeEEEEEeCCCCc
Q 045120          213 NKILVILANIWKL  225 (374)
Q Consensus       213 kr~LlVlDdv~~~  225 (374)
                      ++.+|++|.+...
T Consensus       255 kdVVLlIDEitR~  267 (415)
T TIGR00767       255 KDVVILLDSITRL  267 (415)
T ss_pred             CCeEEEEEChhHH
Confidence            8999999998643

Members of this family differ in the specificity of RNA binding.

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

Probab=97.93  E-value=9.8e-05  Score=70.49  Aligned_cols=182  Identities=22%  Similarity=0.269  Sum_probs=116.3

Q ss_pred             ccccccHHHHHHHHHHhhcC-------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA-------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~-------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      ..+.+||.+++++...|..-             ..|+|||+.++.|....+....=..+++|+.-...+..+++..|+.+
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~   96 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNK   96 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHH
Confidence            34889999999999887643             78999999999999976533211127899999999999999999999


Q ss_pred             hCc-CCchhhHHHHHHHHHHHHhc-CCeEEEEEeCCCCccc-----cccccCcCCC-C--------Ccch--------hH
Q 045120          189 LGL-ELSEEAEYRRASRLYERLKN-ENKILVILANIWKLLD-----LETVKIPFRN-D--------SRDN--------NV  244 (374)
Q Consensus       189 l~~-~~~~~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~~-----~~~l~~~~~~-~--------TR~~--------~v  244 (374)
                      ++. +....+..+....+.+.+.. ++.+++|||++.....     +-.|...... .        +-+.        .|
T Consensus        97 ~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv  176 (366)
T COG1474          97 LGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRV  176 (366)
T ss_pred             cCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhh
Confidence            962 22334556667777777764 5799999999975321     2222111111 1        1111        11


Q ss_pred             hhhhcCCCCceecCCCCHHHHHHHHHHhcC---C-CC-CCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          245 VLLSMGSKDNFLIANITEEEAWRLFKIMNG---D-DV-ENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       245 a~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~---~-~~-~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                       ....+.. .+..+|-+.++-.+++...+.   . .. .+.-++-++...+... |-.=.||.++-.
T Consensus       177 -~s~l~~~-~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~-GDAR~aidilr~  240 (366)
T COG1474         177 -KSSLGPS-EIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAES-GDARKAIDILRR  240 (366)
T ss_pred             -hhccCcc-eeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcC-ccHHHHHHHHHH
Confidence             1123333 377888899999999888774   2 22 2333334444444444 555666665554

>PRK06893 DNA replication initiation factor; Validated

Probab=97.92  E-value=7.9e-05  Score=66.70  Aligned_cols=130  Identities=14%  Similarity=0.125  Sum_probs=74.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+|||+|++.+++.....  ...+.|+++....   ...                    ..+.+.+.  +.-+|||||
T Consensus        47 ~~G~GKThL~~ai~~~~~~~--~~~~~y~~~~~~~---~~~--------------------~~~~~~~~--~~dlLilDD   99 (229)
T PRK06893         47 GKSSGKSHLLKAVSNHYLLN--QRTAIYIPLSKSQ---YFS--------------------PAVLENLE--QQDLVCLDD   99 (229)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCCeEEeeHHHhh---hhh--------------------HHHHhhcc--cCCEEEEeC
Confidence            88999999999999975433  3355677653110   000                    01122222  245899999


Q ss_pred             CCCc---ccccc-ccC---cC-CCC------C----------cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCC
Q 045120          222 IWKL---LDLET-VKI---PF-RND------S----------RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDV  277 (374)
Q Consensus       222 v~~~---~~~~~-l~~---~~-~~~------T----------R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~  277 (374)
                      ++..   ..|+. +..   .. ..+      |          ....+. ..+.....++++++++++.++++++.+....
T Consensus       100 i~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~-sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~  178 (229)
T PRK06893        100 LQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLA-SRLTWGEIYQLNDLTDEQKIIVLQRNAYQRG  178 (229)
T ss_pred             hhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHH-HHHhcCCeeeCCCCCHHHHHHHHHHHHHHcC
Confidence            9853   22321 100   00 000      1          123443 2445556899999999999999999886332


Q ss_pred             CCcchHHHHHHHHHHccCCchHHH
Q 045120          278 ENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       278 ~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      ..- -.++..-|++.+ +|-.-++
T Consensus       179 l~l-~~~v~~~L~~~~-~~d~r~l  200 (229)
T PRK06893        179 IEL-SDEVANFLLKRL-DRDMHTL  200 (229)
T ss_pred             CCC-CHHHHHHHHHhc-cCCHHHH
Confidence            111 135667888888 6554443

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.91  E-value=4.3e-05  Score=65.57  Aligned_cols=39  Identities=23%  Similarity=0.426  Sum_probs=30.1

Q ss_pred             cccccHHHHHHHHHHhh--cC----------CCCccHHHHHHHHHHHhhhc
Q 045120          123 AFESRVSNLKSTQNALT--NA----------NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~--~~----------~gGiGKTtLA~~v~~~~~~~  161 (374)
                      .|+||+++++++.+.|.  ..          .+|+|||+|.+.++......
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            38999999999999993  11          88999999999999877655

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.85  E-value=0.00029  Score=70.99  Aligned_cols=179  Identities=12%  Similarity=0.111  Sum_probs=92.7

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ...++||-+..++.|.+++..+          ..|+||||+|+.+.+..-..+. +..--+ .+..+........|...-
T Consensus        14 tFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p-~~~~g~-~~~PCG~C~sC~~I~aG~   91 (700)
T PRK12323         14 DFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGA-DGEGGI-TAQPCGQCRACTEIDAGR   91 (700)
T ss_pred             cHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCc-cccccC-CCCCCcccHHHHHHHcCC
Confidence            3567999999999999998876          7899999999999875432110 000000 000111111111111100


Q ss_pred             CcC-----C-chhhHHHHHHHHHHHH----hcCCeEEEEEeCCCCcc--ccccccCcC----CCC------CcchhHhhh
Q 045120          190 GLE-----L-SEEAEYRRASRLYERL----KNENKILVILANIWKLL--DLETVKIPF----RND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~-----~-~~~~~~~~~~~l~~~L----~~~kr~LlVlDdv~~~~--~~~~l~~~~----~~~------TR~~~va~~  247 (374)
                      ...     . .....++.. .+.+.+    ..++.-++|||++....  ..+.|...+    +..      |....+...
T Consensus        92 hpDviEIdAas~~gVDdIR-eLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpT  170 (700)
T PRK12323         92 FVDYIEMDAASNRGVDEMA-QLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVT  170 (700)
T ss_pred             CCcceEecccccCCHHHHH-HHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhH
Confidence            000     0 001112111 122221    12356799999998542  233332222    222      333333321


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTT  303 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~  303 (374)
                      ...-...+.+..++.++..+.+.+.+....... -.+..+.|++.+ +|.|.....
T Consensus       171 IrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~-d~eAL~~IA~~A-~Gs~RdALs  224 (700)
T PRK12323        171 VLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAH-EVNALRLLAQAA-QGSMRDALS  224 (700)
T ss_pred             HHHHHHhcccCCCChHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHHHH
Confidence            122224789999999999998887764221111 134456889999 888864433

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.84  E-value=0.00037  Score=69.23  Aligned_cols=174  Identities=13%  Similarity=0.123  Sum_probs=91.5

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCe-EEEEEeCCCCCHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDR-VVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ...++|-+..+..|.+.+..+          +.|+||||+|+.+++..-....+.. ..+    ..+........|....
T Consensus        20 f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~----~~C~~C~~C~~i~~~~   95 (507)
T PRK06645         20 FAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTI----KTCEQCTNCISFNNHN   95 (507)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCc----CCCCCChHHHHHhcCC
Confidence            456889999999988877665          8899999999999885432211100 000    0001111111111110


Q ss_pred             CcC------CchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cccccccC----cCCCC------CcchhHhhh
Q 045120          190 GLE------LSEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVKI----PFRND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~------~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~~----~~~~~------TR~~~va~~  247 (374)
                      ...      ......++... +.+...    .+++-++|+|+++..  ..++.|..    +-+..      |+...+...
T Consensus        96 h~Dv~eidaas~~~vd~Ir~-iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~t  174 (507)
T PRK06645         96 HPDIIEIDAASKTSVDDIRR-IIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPAT  174 (507)
T ss_pred             CCcEEEeeccCCCCHHHHHH-HHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHH
Confidence            000      00011111111 111111    126778999999854  23444332    22221      444444322


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      .......+++.+++.++....+.+.+......-+ .+....|++.+ +|.+--+
T Consensus       175 I~SRc~~~ef~~ls~~el~~~L~~i~~~egi~ie-~eAL~~Ia~~s-~GslR~a  226 (507)
T PRK06645        175 IISRCQRYDLRRLSFEEIFKLLEYITKQENLKTD-IEALRIIAYKS-EGSARDA  226 (507)
T ss_pred             HHhcceEEEccCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHc-CCCHHHH
Confidence            2222347899999999999999988753221111 34556788999 8876433

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.83  E-value=9.3e-05  Score=71.62  Aligned_cols=102  Identities=17%  Similarity=0.168  Sum_probs=67.7

Q ss_pred             ccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc
Q 045120          122 EAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS  194 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~  194 (374)
                      ..+++.+..++.+...|...       ++|+|||++|+.+++.......|+.+.||.+++..+..++...+.-. +....
T Consensus       175 ~d~~i~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~-~vgy~  253 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPN-GVGFR  253 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCC-CCCeE
Confidence            45778899999999998765       99999999999999877655678889999999998877765432110 00000


Q ss_pred             hhhHHHHHHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          195 EEAEYRRASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       195 ~~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                       ....-..+.+...-.. +++++||+|++...
T Consensus       254 -~~~G~f~~~~~~A~~~p~~~~vliIDEINRa  284 (459)
T PRK11331        254 -RKDGIFYNFCQQAKEQPEKKYVFIIDEINRA  284 (459)
T ss_pred             -ecCchHHHHHHHHHhcccCCcEEEEehhhcc
Confidence             0001111222222221 36899999999744

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.79  E-value=0.00049  Score=70.42  Aligned_cols=174  Identities=16%  Similarity=0.176  Sum_probs=91.9

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ...+++|.+..++.|.+++..+          ..|+||||+|+.+.+.......++       +..+........|...-
T Consensus        14 tFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~-------~~PCG~C~sCr~I~~G~   86 (830)
T PRK07003         14 DFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVT-------SQPCGVCRACREIDEGR   86 (830)
T ss_pred             cHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCC-------CCCCcccHHHHHHhcCC
Confidence            3567999999999999998875          779999999998887543221111       01112122222221110


Q ss_pred             CcC-----C-chhhHHHHHHHHHHHH----hcCCeEEEEEeCCCCcc--ccccccCcC---CCC-------CcchhHhhh
Q 045120          190 GLE-----L-SEEAEYRRASRLYERL----KNENKILVILANIWKLL--DLETVKIPF---RND-------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~-----~-~~~~~~~~~~~l~~~L----~~~kr~LlVlDdv~~~~--~~~~l~~~~---~~~-------TR~~~va~~  247 (374)
                      ...     . .....++.. .+.+.+    ..++.-++|||++....  .++.|...+   +..       |....+...
T Consensus        87 h~DviEIDAas~rgVDdIR-eLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~T  165 (830)
T PRK07003         87 FVDYVEMDAASNRGVDEMA-ALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVT  165 (830)
T ss_pred             CceEEEecccccccHHHHH-HHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccch
Confidence            000     0 000111111 111211    12245588899998553  233332221   222       222233211


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch-HHHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF-CTLTT  303 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP-Lai~~  303 (374)
                      ...-...++++.|+.++..+.+.+........ --.+..+.|++.| +|.. -|+..
T Consensus       166 IrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~-id~eAL~lIA~~A-~GsmRdALsL  220 (830)
T PRK07003        166 VLSRCLQFNLKQMPAGHIVSHLERILGEERIA-FEPQALRLLARAA-QGSMRDALSL  220 (830)
T ss_pred             hhhheEEEecCCcCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHHHHH
Confidence            11222479999999999999998877532211 1235566889999 6644 56555

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.78  E-value=0.00056  Score=65.63  Aligned_cols=171  Identities=15%  Similarity=0.164  Sum_probs=88.8

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|-+..++.+.+.+..+          +.|+||||+|+.+.+.......+.       +..+........+.....
T Consensus        15 ~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~-------~~pc~~c~~c~~~~~~~~   87 (363)
T PRK14961         15 FRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGIT-------SNPCRKCIICKEIEKGLC   87 (363)
T ss_pred             hhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCCCHHHHHHhcCCC
Confidence            456899999999999888765          889999999999988543211110       000111111111111100


Q ss_pred             cCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccccCcC---CCC-------CcchhHhhhh
Q 045120          191 LEL------SEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETVKIPF---RND-------SRDNNVVLLS  248 (374)
Q Consensus       191 ~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l~~~~---~~~-------TR~~~va~~~  248 (374)
                      ...      .....+ ....+.+.+.    .+++-++|+|++....  .++.+...+   |..       |....+....
T Consensus        88 ~d~~~~~~~~~~~v~-~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI  166 (363)
T PRK14961         88 LDLIEIDAASRTKVE-EMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTI  166 (363)
T ss_pred             CceEEecccccCCHH-HHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHH
Confidence            000      000111 1122222221    1245689999987543  233322211   111       2222232111


Q ss_pred             cCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       249 ~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      .+....+++.+++.++..+.+...+...... --.+....|+..+ +|.|-.+
T Consensus       167 ~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~-i~~~al~~ia~~s-~G~~R~a  217 (363)
T PRK14961        167 LSRCLQFKLKIISEEKIFNFLKYILIKESID-TDEYALKLIAYHA-HGSMRDA  217 (363)
T ss_pred             HhhceEEeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHH
Confidence            2223479999999999998888766422111 1134566889999 9988643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.76  E-value=0.00039  Score=68.67  Aligned_cols=165  Identities=17%  Similarity=0.166  Sum_probs=91.7

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCC-------------------CCeEEEE
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKL-------------------FDRVVFS  170 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~-------------------F~~~~wv  170 (374)
                      ....++|.+.....|.+.+..+          +.|+||||+|+.+.+.......                   +...+.+
T Consensus        12 ~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el   91 (472)
T PRK14962         12 TFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIEL   91 (472)
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEE
Confidence            3456899988888888877655          8899999999999875432110                   0011222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cccccccCcC---CCC---
Q 045120          171 EVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVKIPF---RND---  238 (374)
Q Consensus       171 ~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~~~~---~~~---  238 (374)
                      +.+...+...+                     ..+.+...    .+++-++|+|++...  ...+.|...+   +..   
T Consensus        92 ~aa~~~gid~i---------------------R~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~  150 (472)
T PRK14962         92 DAASNRGIDEI---------------------RKIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVF  150 (472)
T ss_pred             eCcccCCHHHH---------------------HHHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEE
Confidence            22211111111                     12222221    125678999998643  2222222221   111   


Q ss_pred             ----CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          239 ----SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       239 ----TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                          |....+..........+.+.+++.++....+.+.+...... --.+....|++.++|+++.++..+-.
T Consensus       151 Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~-i~~eal~~Ia~~s~GdlR~aln~Le~  221 (472)
T PRK14962        151 VLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIE-IDREALSFIAKRASGGLRDALTMLEQ  221 (472)
T ss_pred             EEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence                22223322122223478999999999988888877422111 11345667888885777888877765

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.76  E-value=0.00038  Score=71.18  Aligned_cols=239  Identities=14%  Similarity=0.113  Sum_probs=134.7

Q ss_pred             cccccccHHHHHHHHHHhhcC------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcCC
Q 045120          121 YEAFESRVSNLKSTQNALTNA------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLEL  193 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~~  193 (374)
                      +.+.+-|..-.+.+-+.....      ++|.|||||+-+......   .=..+.|.++... .++..+.+.++..++.-.
T Consensus        18 ~~~~v~R~rL~~~L~~~~~~RL~li~APAGfGKttl~aq~~~~~~---~~~~v~Wlslde~dndp~rF~~yLi~al~~~~   94 (894)
T COG2909          18 PDNYVVRPRLLDRLRRANDYRLILISAPAGFGKTTLLAQWRELAA---DGAAVAWLSLDESDNDPARFLSYLIAALQQAT   94 (894)
T ss_pred             cccccccHHHHHHHhcCCCceEEEEeCCCCCcHHHHHHHHHHhcC---cccceeEeecCCccCCHHHHHHHHHHHHHHhC
Confidence            445666654444443322211      999999999999876221   2346899998765 678999999998887332


Q ss_pred             chh--------------hHHHHHHHHHHHHhc-CCeEEEEEeCCC---Cc---cccccccCcCCCC------CcchhHhh
Q 045120          194 SEE--------------AEYRRASRLYERLKN-ENKILVILANIW---KL---LDLETVKIPFRND------SRDNNVVL  246 (374)
Q Consensus       194 ~~~--------------~~~~~~~~l~~~L~~-~kr~LlVlDdv~---~~---~~~~~l~~~~~~~------TR~~~va~  246 (374)
                      +..              +.....+.+...|.. .++.++||||--   +.   .-++-+....|++      ||+..-. 
T Consensus        95 p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l-  173 (894)
T COG2909          95 PTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQL-  173 (894)
T ss_pred             ccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCC-
Confidence            221              223344455555543 368999999964   22   1245555666766      6655321 


Q ss_pred             hhcCC----CCceecC----CCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc--C-CCcccccc
Q 045120          247 LSMGS----KDNFLIA----NITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS--K-SSSIYSHV  315 (374)
Q Consensus       247 ~~~~~----~~~~~l~----~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~-~~~~~~W~  315 (374)
                       ..+.    ....+++    .|+.+|+-++|....+..-+    ..-.+.+.+.. +|-+-|+..++=  + +.+.+.--
T Consensus       174 -~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld----~~~~~~L~~~t-eGW~~al~L~aLa~~~~~~~~q~~  247 (894)
T COG2909         174 -GLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPLD----AADLKALYDRT-EGWAAALQLIALALRNNTSAEQSL  247 (894)
T ss_pred             -cccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCCC----hHHHHHHHhhc-ccHHHHHHHHHHHccCCCcHHHHh
Confidence             1111    1122332    37899999999877643222    23345788888 999999887775  4 22322221


Q ss_pred             cccccCCCCccc-chhh--cccCCchhhhhhhc-------Cchhh-----hh-cHHHHHHHHHhCCcceecC
Q 045120          316 SNDYQSIYKPKP-YLAV--FQDLEPTIVKTAFV-------DPKWY-----LA-LKEEFEALQRNQTWSLVHT  371 (374)
Q Consensus       316 ~~~~~~~~~~~~-~~~l--y~~Lp~~~lk~cfL-------fp~~~-----~i-~~~~Li~~W~~~~~~~~~~  371 (374)
                      .. .++....+. ++.=  ++.||++ +|..++       |...-     .+ +-..++..=.+.|+.+++-
T Consensus       248 ~~-LsG~~~~l~dYL~eeVld~Lp~~-l~~FLl~~svl~~f~~eL~~~Ltg~~ng~amLe~L~~~gLFl~~L  317 (894)
T COG2909         248 RG-LSGAASHLSDYLVEEVLDRLPPE-LRDFLLQTSVLSRFNDELCNALTGEENGQAMLEELERRGLFLQRL  317 (894)
T ss_pred             hh-ccchHHHHHHHHHHHHHhcCCHH-HHHHHHHHHhHHHhhHHHHHHHhcCCcHHHHHHHHHhCCCceeee
Confidence            11 112112110 1111  8999986 888774       22111     11 2334455556666666553

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.74  E-value=0.00068  Score=63.69  Aligned_cols=161  Identities=14%  Similarity=0.165  Sum_probs=92.3

Q ss_pred             ccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhh----hcCCCCeEEEEE-eCCCCCHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAR----EDKLFDRVVFSE-VSQTSDIKKIQGDIA  186 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~----~~~~F~~~~wv~-vs~~~~~~~~~~~i~  186 (374)
                      ..++|-+..++.+.+++..+          +.|+||||+|+.++...-    ...|+|...|.. -+......++ +++.
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~i-r~~~   82 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDI-RNII   82 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHH-HHHH
Confidence            45789888899999998765          789999999999988532    235667766654 2333344342 2333


Q ss_pred             HHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC--CccccccccCcC---CCC------Ccchh-HhhhhcCCCCc
Q 045120          187 EKLGLELSEEAEYRRASRLYERLKNENKILVILANIW--KLLDLETVKIPF---RND------SRDNN-VVLLSMGSKDN  254 (374)
Q Consensus       187 ~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~--~~~~~~~l~~~~---~~~------TR~~~-va~~~~~~~~~  254 (374)
                      +.+....               ..+ ++-++|+|++.  +...++.+...+   |.+      |.+.+ +..........
T Consensus        83 ~~~~~~p---------------~~~-~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~  146 (313)
T PRK05564         83 EEVNKKP---------------YEG-DKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQI  146 (313)
T ss_pred             HHHhcCc---------------ccC-CceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhcee
Confidence            3332110               012 44555666554  333333332222   222      33222 21111122247


Q ss_pred             eecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          255 FLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       255 ~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      +++.+++.++....+.+.....  +   ...+..++..| +|.|..+....
T Consensus       147 ~~~~~~~~~~~~~~l~~~~~~~--~---~~~~~~l~~~~-~g~~~~a~~~~  191 (313)
T PRK05564        147 YKLNRLSKEEIEKFISYKYNDI--K---EEEKKSAIAFS-DGIPGKVEKFI  191 (313)
T ss_pred             eeCCCcCHHHHHHHHHHHhcCC--C---HHHHHHHHHHc-CCCHHHHHHHh
Confidence            8999999999988776654211  1   23356788999 99997665444

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=97.73  E-value=0.00041  Score=71.72  Aligned_cols=183  Identities=16%  Similarity=0.136  Sum_probs=110.1

Q ss_pred             cccccccHHHHHHHHHHhhcC--------------CCCccHHHHHHHHHHHhhh---cCCCC--eEEEEEeCCCCCHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA--------------NGGIGKTTLAKEFAKQARE---DKLFD--RVVFSEVSQTSDIKKI  181 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~--------------~gGiGKTtLA~~v~~~~~~---~~~F~--~~~wv~vs~~~~~~~~  181 (374)
                      +..+.|||.++++|...|...              +.|+|||+.++.|.+....   +...+  .+++|+...-.+...+
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sI  833 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAA  833 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHH
Confidence            456889999999998887542              7899999999999876432   12222  2567776666788899


Q ss_pred             HHHHHHHhCcCCchh--hHHHHHHHHHHHHhc--CCeEEEEEeCCCCcc-----ccccccC-cC-CCC-------Ccc--
Q 045120          182 QGDIAEKLGLELSEE--AEYRRASRLYERLKN--ENKILVILANIWKLL-----DLETVKI-PF-RND-------SRD--  241 (374)
Q Consensus       182 ~~~i~~~l~~~~~~~--~~~~~~~~l~~~L~~--~kr~LlVlDdv~~~~-----~~~~l~~-~~-~~~-------TR~--  241 (374)
                      +..|..++....+..  +..+....+...+..  ....+||||++....     .+-.|.. +. ...       +..  
T Consensus       834 YqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlD  913 (1164)
T PTZ00112        834 YQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMD  913 (1164)
T ss_pred             HHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchh
Confidence            999999985443321  233455666666532  134699999997432     1221111 11 111       111  


Q ss_pred             ------hhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCC---CCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          242 ------NNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDD---VENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       242 ------~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~---~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                            ..+ ...++ ...+..+|++.++-.+++...+...   ..+..+.-+|..++..- |-.=.||.++-.
T Consensus       914 LperLdPRL-RSRLg-~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~S-GDARKALDILRr  984 (1164)
T PTZ00112        914 LPERLIPRC-RSRLA-FGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVS-GDIRKALQICRK  984 (1164)
T ss_pred             cchhhhhhh-hhccc-cccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcC-CHHHHHHHHHHH
Confidence                  111 11222 2246679999999999999987632   12333444444444444 666677766654

>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=97.72  E-value=0.00012  Score=64.13  Aligned_cols=171  Identities=16%  Similarity=0.109  Sum_probs=78.2

Q ss_pred             cccccccccHHHHHHHHHHhh---c--C---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          119 KVYEAFESRVSNLKSTQNALT---N--A---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~---~--~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      ....+|+|-+.-++++.-++.   .  +         ++|+||||||..+.+.....  |.   +.+.+.-....+ +..
T Consensus        21 ~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~--~~---~~sg~~i~k~~d-l~~   94 (233)
T PF05496_consen   21 KSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVN--FK---ITSGPAIEKAGD-LAA   94 (233)
T ss_dssp             SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT----EE---EEECCC--SCHH-HHH
T ss_pred             CCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCC--eE---eccchhhhhHHH-HHH
Confidence            445679999988877644432   1  1         99999999999999966532  31   222211111111 122


Q ss_pred             HHHHhCcCC----chh--hHHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcCCCC------CcchhHhhhhcCCC
Q 045120          185 IAEKLGLEL----SEE--AEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND------SRDNNVVLLSMGSK  252 (374)
Q Consensus       185 i~~~l~~~~----~~~--~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~~~~------TR~~~va~~~~~~~  252 (374)
                      ++..+....    ++-  =.....+.|.-.+.+ .+.-||+.-=-+..   .+...+|.-      ||...+.. ..-.-
T Consensus        95 il~~l~~~~ILFIDEIHRlnk~~qe~LlpamEd-~~idiiiG~g~~ar---~~~~~l~~FTligATTr~g~ls~-pLrdR  169 (233)
T PF05496_consen   95 ILTNLKEGDILFIDEIHRLNKAQQEILLPAMED-GKIDIIIGKGPNAR---SIRINLPPFTLIGATTRAGLLSS-PLRDR  169 (233)
T ss_dssp             HHHT--TT-EEEECTCCC--HHHHHHHHHHHHC-SEEEEEBSSSSS-B---EEEEE----EEEEEESSGCCTSH-CCCTT
T ss_pred             HHHhcCCCcEEEEechhhccHHHHHHHHHHhcc-CeEEEEeccccccc---eeeccCCCceEeeeeccccccch-hHHhh
Confidence            233332110    000  011122333333333 23323333211110   011111111      66655431 11111


Q ss_pred             --CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHH
Q 045120          253 --DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLT  302 (374)
Q Consensus       253 --~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~  302 (374)
                        -..+++..+.+|-.++..+.+..-... --.+.+.+|++.| .|-|--+.
T Consensus       170 Fgi~~~l~~Y~~~el~~Iv~r~a~~l~i~-i~~~~~~~Ia~rs-rGtPRiAn  219 (233)
T PF05496_consen  170 FGIVLRLEFYSEEELAKIVKRSARILNIE-IDEDAAEEIARRS-RGTPRIAN  219 (233)
T ss_dssp             SSEEEE----THHHHHHHHHHCCHCTT-E-E-HHHHHHHHHCT-TTSHHHHH
T ss_pred             cceecchhcCCHHHHHHHHHHHHHHhCCC-cCHHHHHHHHHhc-CCChHHHH
Confidence              145899999999999999887532211 1246788999999 99996543

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.72  E-value=0.00062  Score=67.83  Aligned_cols=176  Identities=13%  Similarity=0.087  Sum_probs=92.8

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|-+..++.|.+++..+          +.|+||||+|+.+.+.....+.++..+|.|.+-. .+......-+..++
T Consensus        13 ~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~-~i~~~~h~dv~el~   91 (504)
T PRK14963         13 FDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCL-AVRRGAHPDVLEID   91 (504)
T ss_pred             HHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhH-HHhcCCCCceEEec
Confidence            456899999888888887765          8899999999999886543333332333322100 00000000000000


Q ss_pred             cCCchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccccCcC----CCC------CcchhHhhhhcCCCCc
Q 045120          191 LELSEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETVKIPF----RND------SRDNNVVLLSMGSKDN  254 (374)
Q Consensus       191 ~~~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l~~~~----~~~------TR~~~va~~~~~~~~~  254 (374)
                      .. .....+ ....+.+.+.    .+++-++|+|+++...  .++.|...+    +..      +....+..........
T Consensus        92 ~~-~~~~vd-~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~  169 (504)
T PRK14963         92 AA-SNNSVE-DVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQH  169 (504)
T ss_pred             cc-ccCCHH-HHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEE
Confidence            00 000111 1122233222    1256789999987542  233332222    111      2222332111222347


Q ss_pred             eecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          255 FLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       255 ~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      +++.+++.++..+.+.+.+......- -.+....|++.+ +|.+--+
T Consensus       170 ~~f~~ls~~el~~~L~~i~~~egi~i-~~~Al~~ia~~s-~GdlR~a  214 (504)
T PRK14963        170 FRFRRLTEEEIAGKLRRLLEAEGREA-EPEALQLVARLA-DGAMRDA  214 (504)
T ss_pred             EEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHH
Confidence            99999999999999998775222111 135567899999 8877554

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.69  E-value=0.00076  Score=70.32  Aligned_cols=164  Identities=15%  Similarity=0.183  Sum_probs=90.3

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCC-------------------CeEEEEE
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLF-------------------DRVVFSE  171 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F-------------------~~~~wv~  171 (374)
                      ...++|-+..++.|.+++..+          ..|+||||+|+.+.+..-.....                   .-.+++.
T Consensus        15 FddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEid   94 (944)
T PRK14949         15 FEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVD   94 (944)
T ss_pred             HHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEec
Confidence            456999999999999888775          78999999999999864322111                   0111111


Q ss_pred             eCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc--cccccccCcC---CCC-------C
Q 045120          172 VSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL--LDLETVKIPF---RND-------S  239 (374)
Q Consensus       172 vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~--~~~~~l~~~~---~~~-------T  239 (374)
                      .+....+.. .++|.                ..+...-..+++-++|||++...  ...+.|...+   |..       |
T Consensus        95 Aas~~kVDd-IReLi----------------e~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTT  157 (944)
T PRK14949         95 AASRTKVDD-TRELL----------------DNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATT  157 (944)
T ss_pred             cccccCHHH-HHHHH----------------HHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECC
Confidence            110011111 11111                11111111236779999998754  2233322211   111       3


Q ss_pred             cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHH
Q 045120          240 RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTT  303 (374)
Q Consensus       240 R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~  303 (374)
                      ....+..........|++++|+.++..+.+.+.+..... .--.+....|++.+ +|.|--+..
T Consensus       158 e~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI-~~edeAL~lIA~~S-~Gd~R~ALn  219 (944)
T PRK14949        158 DPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQL-PFEAEALTLLAKAA-NGSMRDALS  219 (944)
T ss_pred             CchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHc-CCCHHHHHH
Confidence            333332111122257999999999999998887642211 11235567899999 998754433

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

Probab=97.68  E-value=0.00028  Score=73.11  Aligned_cols=155  Identities=18%  Similarity=0.234  Sum_probs=83.2

Q ss_pred             cccccccccHHHHH---HHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          119 KVYEAFESRVSNLK---STQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       119 ~~~~~~vGr~~~~~---~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      .....|+|.+..+.   .+.+.+..+         ++|+||||||+.+++...  .+|.   .++.+. ....+      
T Consensus        25 ~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~--~~f~---~lna~~-~~i~d------   92 (725)
T PRK13341         25 RTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTR--AHFS---SLNAVL-AGVKD------   92 (725)
T ss_pred             CcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhc--Ccce---eehhhh-hhhHH------
Confidence            33456899988774   455555544         899999999999998543  3341   111110 00000      


Q ss_pred             HHhCcCCchhhHHHHHHHHHHHHh-cCCeEEEEEeCCCCc--cccccccCcCCCC--------Ccchh--HhhhhcCCCC
Q 045120          187 EKLGLELSEEAEYRRASRLYERLK-NENKILVILANIWKL--LDLETVKIPFRND--------SRDNN--VVLLSMGSKD  253 (374)
Q Consensus       187 ~~l~~~~~~~~~~~~~~~l~~~L~-~~kr~LlVlDdv~~~--~~~~~l~~~~~~~--------TR~~~--va~~~~~~~~  253 (374)
                                 ..+......+.+. .+++.+|+|||++..  ...+.+...+..+        |.+..  +.........
T Consensus        93 -----------ir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~g~IiLI~aTTenp~~~l~~aL~SR~~  161 (725)
T PRK13341         93 -----------LRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYFEVNKALVSRSR  161 (725)
T ss_pred             -----------HHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhcCceEEEEEecCCChHhhhhhHhhcccc
Confidence                       0111122222222 125789999999743  3333343333222        23221  1111111234


Q ss_pred             ceecCCCCHHHHHHHHHHhcCC------CCCCcchHHHHHHHHHHccCCc
Q 045120          254 NFLIANITEEEAWRLFKIMNGD------DVENCKFKSTAINVAKACGAGL  297 (374)
Q Consensus       254 ~~~l~~L~~~~s~~Lf~~~a~~------~~~~~~l~~~~~~I~~~c~~Gl  297 (374)
                      .+.+++|+.++...++.+.+..      .....--.+....|++.+ +|-
T Consensus       162 v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s-~GD  210 (725)
T PRK13341        162 LFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVA-NGD  210 (725)
T ss_pred             ceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhC-CCC
Confidence            7999999999999999887641      111111235567888888 654

>PF14516 AAA_35: AAA-like domain

Probab=97.67  E-value=0.0011  Score=62.68  Aligned_cols=178  Identities=13%  Similarity=0.171  Sum_probs=106.7

Q ss_pred             cccccccHHHHHHHHHHhhc-C-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-----CCHHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTN-A-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-----SDIKKIQGDIAE  187 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~-~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~~~~~i~~  187 (374)
                      ....|.|...-+++.+.|.+ +       +-.+|||+|...+.+..... .| .++++++..-     .+...+++.++.
T Consensus        10 ~~~Yi~R~~~e~~~~~~i~~~G~~~~I~apRq~GKTSll~~l~~~l~~~-~~-~~v~id~~~~~~~~~~~~~~f~~~~~~   87 (331)
T PF14516_consen   10 SPFYIERPPAEQECYQEIVQPGSYIRIKAPRQMGKTSLLLRLLERLQQQ-GY-RCVYIDLQQLGSAIFSDLEQFLRWFCE   87 (331)
T ss_pred             CCcccCchHHHHHHHHHHhcCCCEEEEECcccCCHHHHHHHHHHHHHHC-CC-EEEEEEeecCCCcccCCHHHHHHHHHH
Confidence            34577898777778877776 3       78999999999998876644 33 3457766542     245555555554


Q ss_pred             ----HhCcCCchh--------hHHHHHHHHHHHH-hc-CCeEEEEEeCCCCcccc----ccccCcC------------CC
Q 045120          188 ----KLGLELSEE--------AEYRRASRLYERL-KN-ENKILVILANIWKLLDL----ETVKIPF------------RN  237 (374)
Q Consensus       188 ----~l~~~~~~~--------~~~~~~~~l~~~L-~~-~kr~LlVlDdv~~~~~~----~~l~~~~------------~~  237 (374)
                          +++....-.        +.......+.+.+ .. +++.+|+||++......    ..+...+            ..
T Consensus        88 ~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~  167 (331)
T PF14516_consen   88 EISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQ  167 (331)
T ss_pred             HHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccc
Confidence                444332110        1122333444443 22 48999999999743211    1111100            00


Q ss_pred             C--------CcchhHh---hhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          238 D--------SRDNNVV---LLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       238 ~--------TR~~~va---~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      .        |......   ....+....+.|++++.+|...|...+-....     ....++|...+ ||+|.-+..++.
T Consensus       168 ~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~~-----~~~~~~l~~~t-gGhP~Lv~~~~~  241 (331)
T PF14516_consen  168 KLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLEFS-----QEQLEQLMDWT-GGHPYLVQKACY  241 (331)
T ss_pred             eEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhccCC-----HHHHHHHHHHH-CCCHHHHHHHHH
Confidence            0        2221111   11123334799999999999999988743311     12267899999 999999998888

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.64  E-value=0.0033  Score=57.77  Aligned_cols=156  Identities=18%  Similarity=0.244  Sum_probs=96.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCC----eEEEEEeCCCCCHHHHHHHHHHHhCcCCch-hhHHHHHHHHHHHHhcCCeEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFD----RVVFSEVSQTSDIKKIQGDIAEKLGLELSE-EAEYRRASRLYERLKNENKIL  216 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~----~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~~kr~L  216 (374)
                      ..|+|||++++.+...+-....=+    .++.|.+...++...+...|+..++.+... .+.........+.|+.-+--+
T Consensus        69 ~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrm  148 (302)
T PF05621_consen   69 DSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRM  148 (302)
T ss_pred             CCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcE
Confidence            679999999999987653221111    467888899999999999999999988654 344455556666776545679


Q ss_pred             EEEeCCCCcc------------ccccccCcCCC-----C--------CcchhHhhhhcCCCCceecCCCCH-HHHHHHHH
Q 045120          217 VILANIWKLL------------DLETVKIPFRN-----D--------SRDNNVVLLSMGSKDNFLIANITE-EEAWRLFK  270 (374)
Q Consensus       217 lVlDdv~~~~------------~~~~l~~~~~~-----~--------TR~~~va~~~~~~~~~~~l~~L~~-~~s~~Lf~  270 (374)
                      ||+|.+.+.-            .+..|...+.-     |        ..+.+.+. .+   .++.|+.-.. ++...|+.
T Consensus       149 LIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa~-RF---~~~~Lp~W~~d~ef~~LL~  224 (302)
T PF05621_consen  149 LIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLAS-RF---EPFELPRWELDEEFRRLLA  224 (302)
T ss_pred             EEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHHh-cc---CCccCCCCCCCcHHHHHHH
Confidence            9999997531            12222222211     1        34444432 22   2455555433 34555554


Q ss_pred             HhcC----CCCCCcchHHHHHHHHHHccCCchHHHH
Q 045120          271 IMNG----DDVENCKFKSTAINVAKACGAGLFCTLT  302 (374)
Q Consensus       271 ~~a~----~~~~~~~l~~~~~~I~~~c~~GlPLai~  302 (374)
                      ....    ....+-...++++.|...+ +|+.=-+.
T Consensus       225 s~e~~LPLr~~S~l~~~~la~~i~~~s-~G~iG~l~  259 (302)
T PF05621_consen  225 SFERALPLRKPSNLASPELARRIHERS-EGLIGELS  259 (302)
T ss_pred             HHHHhCCCCCCCCCCCHHHHHHHHHHc-CCchHHHH
Confidence            4332    2222234468899999999 99875443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.64  E-value=0.0025  Score=60.69  Aligned_cols=181  Identities=12%  Similarity=0.048  Sum_probs=100.1

Q ss_pred             ccccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCC--CCeEEEEEeCCCCCHHHHHHHH
Q 045120          118 NKVYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKL--FDRVVFSEVSQTSDIKKIQGDI  185 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~--F~~~~wv~vs~~~~~~~~~~~i  185 (374)
                      |.....++|-+.....+...+..+          ..|+||||||..+.+..-....  +...   .....+.-....+.|
T Consensus        19 P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~---~~~~~~~~c~~c~~i   95 (351)
T PRK09112         19 PSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPE---TLADPDPASPVWRQI   95 (351)
T ss_pred             CCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcc---ccCCCCCCCHHHHHH
Confidence            344567999999999999998876          7899999999998886532110  1111   011111112223333


Q ss_pred             HHHhC-------cCCc--------hhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--c----cccccCcCCCC--
Q 045120          186 AEKLG-------LELS--------EEAEYRRASRLYERLK----NENKILVILANIWKLL--D----LETVKIPFRND--  238 (374)
Q Consensus       186 ~~~l~-------~~~~--------~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~----~~~l~~~~~~~--  238 (374)
                      ...-.       .+..        .-+. +....+.+++.    .+++-++|+|++....  .    +..+..+-+..  
T Consensus        96 ~~~~hPdl~~l~~~~~~~~~~~~~~I~v-d~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~f  174 (351)
T PRK09112         96 AQGAHPNLLHITRPFDEKTGKFKTAITV-DEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALF  174 (351)
T ss_pred             HcCCCCCEEEeecccccccccccccCCH-HHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceE
Confidence            22211       0000        0111 22334555554    2467799999998542  1    22232221112  


Q ss_pred             ---C-cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          239 ---S-RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       239 ---T-R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                         | +...+..........+++.+++.++..+++........   --......|+..+ +|.|.....+..
T Consensus       175 iLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~---~~~~~~~~i~~~s-~G~pr~Al~ll~  242 (351)
T PRK09112        175 ILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG---SDGEITEALLQRS-KGSVRKALLLLN  242 (351)
T ss_pred             EEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC---CCHHHHHHHHHHc-CCCHHHHHHHHh
Confidence               2 22122111112224899999999999999987432211   1134466889999 999987766654

>PLN03025 replication factor C subunit; Provisional

Probab=97.61  E-value=0.0012  Score=62.09  Aligned_cols=168  Identities=11%  Similarity=0.079  Sum_probs=87.8

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFD-RVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|.+..++.|..++..+         +.|+||||+|+.+.+...- ..|. .++-++.+...+.. ..++++..+.
T Consensus        12 l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~-~~~~~~~~eln~sd~~~~~-~vr~~i~~~~   89 (319)
T PLN03025         12 LDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLG-PNYKEAVLELNASDDRGID-VVRNKIKMFA   89 (319)
T ss_pred             HHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhc-ccCccceeeecccccccHH-HHHHHHHHHH
Confidence            456889888888888777654         8899999999999886431 1232 22223333322222 1222222111


Q ss_pred             cCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--c---cccccCcCCCCCc-------chhHhhhhcCCCCceecC
Q 045120          191 LELSEEAEYRRASRLYERLKNENKILVILANIWKLL--D---LETVKIPFRNDSR-------DNNVVLLSMGSKDNFLIA  258 (374)
Q Consensus       191 ~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~---~~~l~~~~~~~TR-------~~~va~~~~~~~~~~~l~  258 (374)
                      ....             .+..++.-+++||++....  .   +..+....+..||       ...+..........++++
T Consensus        90 ~~~~-------------~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~  156 (319)
T PLN03025         90 QKKV-------------TLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFS  156 (319)
T ss_pred             hccc-------------cCCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCC
Confidence            0000             0011246688999987542  1   2111111122221       111100001112478999


Q ss_pred             CCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHH
Q 045120          259 NITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       259 ~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                      +++.++....+...+......-. .+....|++.|+|.+.-++..+
T Consensus       157 ~l~~~~l~~~L~~i~~~egi~i~-~~~l~~i~~~~~gDlR~aln~L  201 (319)
T PLN03025        157 RLSDQEILGRLMKVVEAEKVPYV-PEGLEAIIFTADGDMRQALNNL  201 (319)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHHH
Confidence            99999999998887753221111 3456789999944444555444

>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=97.60  E-value=0.00046  Score=56.11  Aligned_cols=49  Identities=22%  Similarity=0.263  Sum_probs=35.4

Q ss_pred             cccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          125 ESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       125 vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      +|++..+..+...+...         ..|+|||||++.+++...  ..-..++++..+..
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~--~~~~~v~~~~~~~~   58 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDL   58 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhh--cCCCCeEEEehhhh
Confidence            37788888888888762         889999999999999654  11234566655443

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.

>PRK04195 replication factor C large subunit; Provisional

Probab=97.56  E-value=0.00094  Score=66.60  Aligned_cols=159  Identities=12%  Similarity=0.147  Sum_probs=86.9

Q ss_pred             ccccccccHHHHHHHHHHhhc------C-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          120 VYEAFESRVSNLKSTQNALTN------A-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~------~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      ....++|.+..++.+.+|+..      .       +.|+||||+|+.++++..    |+ .+-++.+...+.. ....++
T Consensus        12 ~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~----~~-~ielnasd~r~~~-~i~~~i   85 (482)
T PRK04195         12 TLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG----WE-VIELNASDQRTAD-VIERVA   85 (482)
T ss_pred             CHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC----CC-EEEEcccccccHH-HHHHHH
Confidence            355699999999999998862      1       889999999999999653    33 3334444433322 222222


Q ss_pred             HHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc------cccccCcCCCC-------Ccc-hhHhh-hhcCC
Q 045120          187 EKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD------LETVKIPFRND-------SRD-NNVVL-LSMGS  251 (374)
Q Consensus       187 ~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~------~~~l~~~~~~~-------TR~-~~va~-~~~~~  251 (374)
                      ........             .... ++-+||||++.....      +..+...+...       +.. ..+.. .....
T Consensus        86 ~~~~~~~s-------------l~~~-~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~~~~~iIli~n~~~~~~~k~Lrsr  151 (482)
T PRK04195         86 GEAATSGS-------------LFGA-RRKLILLDEVDGIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNA  151 (482)
T ss_pred             HHhhccCc-------------ccCC-CCeEEEEecCcccccccchhHHHHHHHHHHcCCCCEEEeccCccccchhhHhcc
Confidence            22211000             0012 578999999975421      22221111110       100 00000 01112


Q ss_pred             CCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH
Q 045120          252 KDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       252 ~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      ...+.+.+++.++....+.+.+......-. .++...|++.| +|-.-.
T Consensus       152 ~~~I~f~~~~~~~i~~~L~~i~~~egi~i~-~eaL~~Ia~~s-~GDlR~  198 (482)
T PRK04195        152 CLMIEFKRLSTRSIVPVLKRICRKEGIECD-DEALKEIAERS-GGDLRS  198 (482)
T ss_pred             ceEEEecCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHc-CCCHHH
Confidence            346889999999998888877642211111 35567888888 664443

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=97.56  E-value=0.005  Score=59.25  Aligned_cols=186  Identities=14%  Similarity=0.100  Sum_probs=108.6

Q ss_pred             cccccccccHHHHHHHHHHhhcC-------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA-------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDI  185 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~-------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  185 (374)
                      ..+..++||+.+++.+.+++...             -+|.|||.+...++.+......=.++++++...-....+++..|
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI  226 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKI  226 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHH
Confidence            33456899999999999998765             77999999999999876432221345777666555667777777


Q ss_pred             HHHhC-cCCchhhHHHHHHHHHHHHhcCC-eEEEEEeCCCCc-----cccccc--cCcCCCC-------------Ccchh
Q 045120          186 AEKLG-LELSEEAEYRRASRLYERLKNEN-KILVILANIWKL-----LDLETV--KIPFRND-------------SRDNN  243 (374)
Q Consensus       186 ~~~l~-~~~~~~~~~~~~~~l~~~L~~~k-r~LlVlDdv~~~-----~~~~~l--~~~~~~~-------------TR~~~  243 (374)
                      ...+- .........+....+.+...+.+ -+|+|||..+..     ..+..+  ...+|..             |++--
T Consensus       227 ~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~L  306 (529)
T KOG2227|consen  227 FSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFL  306 (529)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHh
Confidence            77762 11111222344455555555433 789999998642     112221  1112222             22221


Q ss_pred             Hh-hh-hcCCCCceecCCCCHHHHHHHHHHhcCCCCC----CcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          244 VV-LL-SMGSKDNFLIANITEEEAWRLFKIMNGDDVE----NCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       244 va-~~-~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~----~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      .- .. ..-....+..+|-+.++-.++|.........    +..++-.|++++.-. |.+--|+.+.-
T Consensus       307 prL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~S-GDlRkaLdv~R  373 (529)
T KOG2227|consen  307 PRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPS-GDLRKALDVCR  373 (529)
T ss_pred             hhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCc-hhHHHHHHHHH
Confidence            10 00 1122347788999999999999988753322    223333444444444 55555555444

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.55  E-value=0.0017  Score=61.47  Aligned_cols=178  Identities=12%  Similarity=0.099  Sum_probs=88.6

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCH-HHHHH---HHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFD-RVVFSEVSQTSDI-KKIQG---DIA  186 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~vs~~~~~-~~~~~---~i~  186 (374)
                      ...++|++..++.+.+++..+         +.|+||||+|+.+.+.... ..++ ..+.++++...+. ...+.   ...
T Consensus        14 ~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   92 (337)
T PRK12402         14 LEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYG-DPWENNFTEFNVADFFDQGKKYLVEDPRFA   92 (337)
T ss_pred             HHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcC-cccccceEEechhhhhhcchhhhhcCcchh
Confidence            456889999999999988765         8899999999999885432 1222 2344444321100 00000   000


Q ss_pred             HHhCcC-CchhhHHHHHHHHHHHHh-----cCCeEEEEEeCCCCcc--cccccc---CcCCCC-------CcchhHhhhh
Q 045120          187 EKLGLE-LSEEAEYRRASRLYERLK-----NENKILVILANIWKLL--DLETVK---IPFRND-------SRDNNVVLLS  248 (374)
Q Consensus       187 ~~l~~~-~~~~~~~~~~~~l~~~L~-----~~kr~LlVlDdv~~~~--~~~~l~---~~~~~~-------TR~~~va~~~  248 (374)
                      ..++.. ....+..+....+.+...     ...+-+||+||+....  ....+.   ...+..       +....+....
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L  172 (337)
T PRK12402         93 HFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPI  172 (337)
T ss_pred             hhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhh
Confidence            000000 000011111222211111     0134589999996442  111121   112221       2222221111


Q ss_pred             cCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       249 ~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      ......+.+.+++.++...++.+.+...... --.+....+++.+ +|.+-.+
T Consensus       173 ~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~-~~~~al~~l~~~~-~gdlr~l  223 (337)
T PRK12402        173 RSRCLPLFFRAPTDDELVDVLESIAEAEGVD-YDDDGLELIAYYA-GGDLRKA  223 (337)
T ss_pred             cCCceEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHH
Confidence            1122468889999999999988876422211 1145667888999 6655444

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.54  E-value=0.0021  Score=65.13  Aligned_cols=172  Identities=13%  Similarity=0.165  Sum_probs=89.5

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|.+..++.|.+++..+          +.|+||||+|+.+.+..-...      ++. +..++.....+.|...-
T Consensus        13 tFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~------~~~-~~pCg~C~sC~~I~~g~   85 (702)
T PRK14960         13 NFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCET------GVT-STPCEVCATCKAVNEGR   85 (702)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCc------CCC-CCCCccCHHHHHHhcCC
Confidence            3567999999999999998866          779999999999987543211      110 01111111111111110


Q ss_pred             CcCC------chhhHHHHHHHHHHHH----hcCCeEEEEEeCCCCcc--ccccc----cCcCCCC-----Ccc-hhHhhh
Q 045120          190 GLEL------SEEAEYRRASRLYERL----KNENKILVILANIWKLL--DLETV----KIPFRND-----SRD-NNVVLL  247 (374)
Q Consensus       190 ~~~~------~~~~~~~~~~~l~~~L----~~~kr~LlVlDdv~~~~--~~~~l----~~~~~~~-----TR~-~~va~~  247 (374)
                      ....      .....++ .+.+....    ..+++-++|+|++....  ....|    ..+-+..     |.+ ..+...
T Consensus        86 hpDviEIDAAs~~~Vdd-IReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~T  164 (702)
T PRK14960         86 FIDLIEIDAASRTKVED-TRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPIT  164 (702)
T ss_pred             CCceEEecccccCCHHH-HHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHH
Confidence            0000      0001111 11122211    12356689999997542  22222    2221111     222 222111


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      .......+++.+|+.++..+.+.+.+......- -.+....|++.+ +|.+-.+
T Consensus       165 IlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~i-d~eAL~~IA~~S-~GdLRdA  216 (702)
T PRK14960        165 VISRCLQFTLRPLAVDEITKHLGAILEKEQIAA-DQDAIWQIAESA-QGSLRDA  216 (702)
T ss_pred             HHHhhheeeccCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHH
Confidence            122235799999999999998887765322111 134556888999 7766443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.49  E-value=0.0023  Score=63.95  Aligned_cols=163  Identities=11%  Similarity=0.156  Sum_probs=86.8

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCC-------------------CeEEEE
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLF-------------------DRVVFS  170 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F-------------------~~~~wv  170 (374)
                      ...+++|-+..++.|.+++..+          +.|+||||+|+.+.+..-....+                   .-++.+
T Consensus        14 ~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~ei   93 (509)
T PRK14958         14 CFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEV   93 (509)
T ss_pred             CHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEE
Confidence            3567999999999999999765          88999999999998754322111                   112222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc--ccccc----ccCcCCCC------
Q 045120          171 EVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL--LDLET----VKIPFRND------  238 (374)
Q Consensus       171 ~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~--~~~~~----l~~~~~~~------  238 (374)
                      ..+....+.++ +++++.+.                ..-..++.-++|+|+|...  ...+.    +..+-+..      
T Consensus        94 daas~~~v~~i-R~l~~~~~----------------~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958         94 DAASRTKVEDT-RELLDNIP----------------YAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             cccccCCHHHH-HHHHHHHh----------------hccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEE
Confidence            22211122211 11111111                0001235668889998753  22222    22221111      


Q ss_pred             CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          239 SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       239 TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      |....+..........+++.+++.++-...+.+.+......- -......|++.+ +|.|--+
T Consensus       157 td~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~-~~~al~~ia~~s-~GslR~a  217 (509)
T PRK14958        157 TDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEF-ENAALDLLARAA-NGSVRDA  217 (509)
T ss_pred             CChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCcHHHH
Confidence            222222211112224688999999887777666654221111 124456788899 8877544

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.48  E-value=0.0021  Score=65.28  Aligned_cols=175  Identities=13%  Similarity=0.130  Sum_probs=90.1

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCC--CeEEEEEeCCCCCHHHHHHHHHH
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLF--DRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      ...+++|-+..+..|.+++..+          ..|+||||+|+.+.+..-..+..  ....    ...++.....+.|..
T Consensus        14 ~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~----~~pCg~C~~C~~i~~   89 (618)
T PRK14951         14 SFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGIT----ATPCGVCQACRDIDS   89 (618)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCC----CCCCCccHHHHHHHc
Confidence            3556899999999999988776          88999999999997643221110  0000    011122222222211


Q ss_pred             HhCcCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccccCcC---CCC-------CcchhHh
Q 045120          188 KLGLEL------SEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETVKIPF---RND-------SRDNNVV  245 (374)
Q Consensus       188 ~l~~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l~~~~---~~~-------TR~~~va  245 (374)
                      .-....      .....++. ..+.+.+.    .++.-++|||+|....  ..+.+...+   |..       |....+.
T Consensus        90 g~h~D~~eldaas~~~Vd~i-Reli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil  168 (618)
T PRK14951         90 GRFVDYTELDAASNRGVDEV-QQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVP  168 (618)
T ss_pred             CCCCceeecCcccccCHHHH-HHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhh
Confidence            000000      00111111 12222221    1245589999998542  233332222   121       2222332


Q ss_pred             hhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          246 LLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       246 ~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      .........+++++|+.++..+.+.+.+......- -.+....|++.+ +|.+--+
T Consensus       169 ~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~i-e~~AL~~La~~s-~GslR~a  222 (618)
T PRK14951        169 VTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPA-EPQALRLLARAA-RGSMRDA  222 (618)
T ss_pred             HHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHH
Confidence            22222335799999999999888887764222111 134566888899 7766444

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.48  E-value=0.0034  Score=62.07  Aligned_cols=163  Identities=12%  Similarity=0.113  Sum_probs=89.9

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhc-------------------CCCCeEEEE
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQARED-------------------KLFDRVVFS  170 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~-------------------~~F~~~~wv  170 (374)
                      ....++|-+..++.+.+.+..+          +.|+||||+|+.+....-..                   +.+.-++.+
T Consensus        11 ~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~ei   90 (491)
T PRK14964         11 SFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEI   90 (491)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEE
Confidence            3567899999999888888765          88999999999987632111                   011122333


Q ss_pred             EeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--cccc----ccCcCCCC------
Q 045120          171 EVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLET----VKIPFRND------  238 (374)
Q Consensus       171 ~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~----l~~~~~~~------  238 (374)
                      +.+...++.++ ++|++...                ..=..+++-++|+|++....  ..+.    +..+-+..      
T Consensus        91 daas~~~vddI-R~Iie~~~----------------~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964         91 DAASNTSVDDI-KVILENSC----------------YLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             ecccCCCHHHH-HHHHHHHH----------------hccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEe
Confidence            33322222221 11111110                00001256689999986432  2222    22222222      


Q ss_pred             CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          239 SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       239 TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      |....+..........+++.+++.++....+.+.+......- -.+....|++.+ +|.+-.+
T Consensus       154 te~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i-~~eAL~lIa~~s-~GslR~a  214 (491)
T PRK14964        154 TEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEH-DEESLKLIAENS-SGSMRNA  214 (491)
T ss_pred             CChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHH
Confidence            444444322223335789999999999999888775322111 134556888999 8877543

>COG3903 Predicted ATPase [General function prediction only]

Probab=97.48  E-value=0.00014  Score=68.61  Aligned_cols=155  Identities=21%  Similarity=0.242  Sum_probs=101.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC-CeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF-DRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILA  220 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlD  220 (374)
                      .|||||||++-++.+ ..  .-| +.+.++....-.+...+.-.+...++.+....  +.....+...+.. +|.++|+|
T Consensus        22 ~ggvgkttl~~~~a~-~~--~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~g--~~~~~~~~~~~~~-rr~llvld   95 (414)
T COG3903          22 AGGVGKTTLALQAAH-AA--SEYADGVAFVDLAPITDPALVFPTLAGALGLHVQPG--DSAVDTLVRRIGD-RRALLVLD   95 (414)
T ss_pred             cCccceehhhhhhHh-Hh--hhcccceeeeeccccCchhHhHHHHHhhcccccccc--hHHHHHHHHHHhh-hhHHHHhc
Confidence            999999999999988 33  447 56777877777777777777777677665431  2233455666666 89999999


Q ss_pred             CCCCccc-----cccccCcCCCC----CcchhHhhhhcCCCCceecCCCCHH-HHHHHHHHhcCCC----CCCcchHHHH
Q 045120          221 NIWKLLD-----LETVKIPFRND----SRDNNVVLLSMGSKDNFLIANITEE-EAWRLFKIMNGDD----VENCKFKSTA  286 (374)
Q Consensus       221 dv~~~~~-----~~~l~~~~~~~----TR~~~va~~~~~~~~~~~l~~L~~~-~s~~Lf~~~a~~~----~~~~~l~~~~  286 (374)
                      |..+..+     ...+....+..    |-.+.+   .......+.+++|+.. ++.++|...+...    .....-....
T Consensus        96 ncehl~~~~a~~i~all~~~~~~~~~atsre~~---l~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~~~~~a~v  172 (414)
T COG3903          96 NCEHLLDACAALIVALLGACPRLAILATSREAI---LVAGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWLTDDNAAAV  172 (414)
T ss_pred             CcHHHHHHHHHHHHHHHccchhhhhHHHhHhhh---cccccccccCCccccCCchhHHHHHHHHHhccceeecCCchHHH
Confidence            9875522     11222222222    222222   2334457788888765 7889988776411    1122224566


Q ss_pred             HHHHHHccCCchHHHHHHhc
Q 045120          287 INVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       287 ~~I~~~c~~GlPLai~~ig~  306 (374)
                      .+|.++. .|.||+|...++
T Consensus       173 ~~icr~l-dg~~laielaaa  191 (414)
T COG3903         173 AEICRRL-DGIPLAIELAAA  191 (414)
T ss_pred             HHHHHHh-hcchHHHHHHHH
Confidence            7999999 999999999887

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.46  E-value=0.0034  Score=62.96  Aligned_cols=166  Identities=13%  Similarity=0.133  Sum_probs=89.7

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcC-------------------CCCeEEEE
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDK-------------------LFDRVVFS  170 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~-------------------~F~~~~wv  170 (374)
                      ....++|-+..++.|.+.+..+          +.|+||||+|+.+.+......                   .|...+++
T Consensus        14 ~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dliei   93 (546)
T PRK14957         14 SFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEI   93 (546)
T ss_pred             cHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEe
Confidence            3456899999999999988765          889999999999987432111                   11122222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccccCc---CCCC-------
Q 045120          171 EVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVKIP---FRND-------  238 (374)
Q Consensus       171 ~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~~~---~~~~-------  238 (374)
                      .......+.+                 ..+..+.+...-..+++-++|+|++....  ..+.|...   .|..       
T Consensus        94 daas~~gvd~-----------------ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957         94 DAASRTGVEE-----------------TKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             ecccccCHHH-----------------HHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEE
Confidence            2211111111                 11112222211112356799999987432  22222221   1222       


Q ss_pred             CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch-HHHHHH
Q 045120          239 SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF-CTLTTN  304 (374)
Q Consensus       239 TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP-Lai~~i  304 (374)
                      |....+..........+++.+++.++-...+.+.+...... --......|++.+ +|.+ -|+..+
T Consensus       157 td~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~-~e~~Al~~Ia~~s-~GdlR~alnlL  221 (546)
T PRK14957        157 TDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENIN-SDEQSLEYIAYHA-KGSLRDALSLL  221 (546)
T ss_pred             CChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            32222321112223579999999999887877755422111 1234456788899 8865 444444

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.44  E-value=0.001  Score=65.24  Aligned_cols=170  Identities=12%  Similarity=0.138  Sum_probs=90.8

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|-+..+..|..++..+          +.|+||||+|+.+.+..........   .......+    ...|....
T Consensus        16 ~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~---~pCg~C~s----C~~i~~g~   88 (484)
T PRK14956         16 FFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGN---EPCNECTS----CLEITKGI   88 (484)
T ss_pred             CHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCc---cccCCCcH----HHHHHccC
Confidence            3456899999999999988765          7899999999999885432111000   00000111    11222111


Q ss_pred             CcCC---c---hhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cccccccCcC----CCC------CcchhHhhh
Q 045120          190 GLEL---S---EEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVKIPF----RND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~~---~---~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~~~~----~~~------TR~~~va~~  247 (374)
                      ....   .   ....+ ....+.+.+.    .++.-++|+|++...  ..++.|...+    ...      |....+...
T Consensus        89 ~~dviEIdaas~~gVd-~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~T  167 (484)
T PRK14956         89 SSDVLEIDAASNRGIE-NIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPET  167 (484)
T ss_pred             CccceeechhhcccHH-HHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHH
Confidence            1110   0   00111 1222222222    235669999999854  2344433222    111      333333221


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL  299 (374)
                      .......|.+.+++.++-.+.+.+.+...... --.+....|++.+ +|.|-
T Consensus       168 I~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~-~e~eAL~~Ia~~S-~Gd~R  217 (484)
T PRK14956        168 ILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQ-YDQEGLFWIAKKG-DGSVR  217 (484)
T ss_pred             HHhhhheeeecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CChHH
Confidence            22223469999999999888888776422111 1135567899999 88773

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.43  E-value=0.0023  Score=65.26  Aligned_cols=163  Identities=15%  Similarity=0.192  Sum_probs=86.5

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCC-------------------CCeEEEE
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKL-------------------FDRVVFS  170 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~-------------------F~~~~wv  170 (374)
                      ....++|.+..++.|.+++..+          ..|+||||+|+.+.+..-....                   |.-.+.+
T Consensus        14 tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEi   93 (709)
T PRK08691         14 TFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEI   93 (709)
T ss_pred             CHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEE
Confidence            3567999999999999998876          7799999999998775322111                   1011112


Q ss_pred             EeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc--cc----cccCcCCCC-----C
Q 045120          171 EVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD--LE----TVKIPFRND-----S  239 (374)
Q Consensus       171 ~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~--~~----~l~~~~~~~-----T  239 (374)
                      +.+....+.. .+++                .......-..+++-++|+|++.....  ..    .+..+-+..     |
T Consensus        94 daAs~~gVd~-IRel----------------le~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691         94 DAASNTGIDN-IREV----------------LENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             eccccCCHHH-HHHH----------------HHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEe
Confidence            1111111110 1111                11110000112567899999875421  22    222211111     2


Q ss_pred             -cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          240 -RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       240 -R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                       ....+.....+....+.+.+++.++....+.+.+...... --......|++.+ +|.+--+
T Consensus       157 td~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~-id~eAL~~Ia~~A-~GslRdA  217 (709)
T PRK08691        157 TDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIA-YEPPALQLLGRAA-AGSMRDA  217 (709)
T ss_pred             CCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCC-cCHHHHHHHHHHh-CCCHHHH
Confidence             1222211111222367888999999988888776522211 1134567899999 8877444

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.43  E-value=0.0044  Score=58.15  Aligned_cols=162  Identities=10%  Similarity=0.133  Sum_probs=84.1

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe--CCCCCHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV--SQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v--s~~~~~~~~~~~i~~~l  189 (374)
                      ...++|++..++.+..++..+         ..|+||||+|+.+.+...... +.. .++.+  +.......+. ..+..+
T Consensus        16 ~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~-~~~-~~i~~~~~~~~~~~~~~-~~i~~~   92 (319)
T PRK00440         16 LDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGED-WRE-NFLELNASDERGIDVIR-NKIKEF   92 (319)
T ss_pred             HHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCc-ccc-ceEEeccccccchHHHH-HHHHHH
Confidence            456889999999999998765         789999999999988653221 211 22222  2222211111 111111


Q ss_pred             CcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--cccccc---CcCCCC------C-cchhHhhhhcCCCCceec
Q 045120          190 GLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVK---IPFRND------S-RDNNVVLLSMGSKDNFLI  257 (374)
Q Consensus       190 ~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~---~~~~~~------T-R~~~va~~~~~~~~~~~l  257 (374)
                      ....+              .....+-++++|++....  ....+.   ...+..      + ....+..........+++
T Consensus        93 ~~~~~--------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~  158 (319)
T PRK00440         93 ARTAP--------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRF  158 (319)
T ss_pred             HhcCC--------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeee
Confidence            00000              000135578888875431  111121   111111      1 111111000111236889


Q ss_pred             CCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          258 ANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       258 ~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      ++++.++....+...+...... --.+....+++.+ +|.+--+
T Consensus       159 ~~l~~~ei~~~l~~~~~~~~~~-i~~~al~~l~~~~-~gd~r~~  200 (319)
T PRK00440        159 SPLKKEAVAERLRYIAENEGIE-ITDDALEAIYYVS-EGDMRKA  200 (319)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHH
Confidence            9999999988888877522211 1134567889999 7776553

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.43  E-value=0.00064  Score=65.02  Aligned_cols=181  Identities=13%  Similarity=0.060  Sum_probs=95.4

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEE----EEeCCCCCHHHHHHH
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVF----SEVSQTSDIKKIQGD  184 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~w----v~vs~~~~~~~~~~~  184 (374)
                      .....++|-+...+.+.+.+..+          +.|+||||||..+.+..-..........    .++. ........+.
T Consensus        16 ~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~-~~~~c~~c~~   94 (365)
T PRK07471         16 RETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLA-IDPDHPVARR   94 (365)
T ss_pred             CchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCcccccccccc-CCCCChHHHH
Confidence            34567999999999999998876          8899999999888775432221110000    0000 0000111111


Q ss_pred             HHHHhCcC-------Cchhh-------HHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--c----cccccCcCCCC--
Q 045120          185 IAEKLGLE-------LSEEA-------EYRRASRLYERLK----NENKILVILANIWKLL--D----LETVKIPFRND--  238 (374)
Q Consensus       185 i~~~l~~~-------~~~~~-------~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~----~~~l~~~~~~~--  238 (374)
                      |...-...       ..+..       .-+.+..+.+.+.    .+++-++|+|++...+  .    +..+..+-+..  
T Consensus        95 i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~  174 (365)
T PRK07471         95 IAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEPPARSLF  174 (365)
T ss_pred             HHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEE
Confidence            11111000       00000       0122344444443    2356799999987542  2    22222222222  


Q ss_pred             ---Ccch-hHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          239 ---SRDN-NVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       239 ---TR~~-~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                         |.+. .+..........+.+.+++.++..+++........     ......++..+ +|.|+.+..+..
T Consensus       175 IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~~~-----~~~~~~l~~~s-~Gsp~~Al~ll~  240 (365)
T PRK07471        175 LLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPDLP-----DDPRAALAALA-EGSVGRALRLAG  240 (365)
T ss_pred             EEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcccCC-----HHHHHHHHHHc-CCCHHHHHHHhc
Confidence               2222 22221223335899999999999999987653211     11125788999 999987666654

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.43  E-value=0.0035  Score=63.98  Aligned_cols=175  Identities=12%  Similarity=0.109  Sum_probs=92.3

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|-+..++.|.+.+..+          ..|+||||+|+.+.+..-....+.       +..+........|...-
T Consensus        14 ~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~-------~~pCg~C~~C~~i~~g~   86 (647)
T PRK07994         14 TFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGIT-------ATPCGECDNCREIEQGR   86 (647)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCC-------CCCCCCCHHHHHHHcCC
Confidence            3567999999999999988775          789999999999987543211110       01111122222222110


Q ss_pred             CcC-----Cc-hhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccc----cCcCCCC------CcchhHhhh
Q 045120          190 GLE-----LS-EEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETV----KIPFRND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~-----~~-~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l----~~~~~~~------TR~~~va~~  247 (374)
                      ...     .. ....++ ...+.+.+.    .+++-++|||++....  ..+.|    ..+-+..      |....+...
T Consensus        87 ~~D~ieidaas~~~Vdd-iR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~T  165 (647)
T PRK07994         87 FVDLIEIDAASRTKVED-TRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVT  165 (647)
T ss_pred             CCCceeecccccCCHHH-HHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchH
Confidence            000     00 011111 122222221    2366789999997432  22222    2222222      333333211


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                      ...-...+++.+|+.++....+.+........ .-......|++.+ +|.|-.+..+
T Consensus       166 I~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~-~e~~aL~~Ia~~s-~Gs~R~Al~l  220 (647)
T PRK07994        166 ILSRCLQFHLKALDVEQIRQQLEHILQAEQIP-FEPRALQLLARAA-DGSMRDALSL  220 (647)
T ss_pred             HHhhheEeeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHHHHH
Confidence            12223479999999999999888766321111 1134456888999 8877644333

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.42  E-value=0.00095  Score=62.49  Aligned_cols=179  Identities=17%  Similarity=0.162  Sum_probs=106.2

Q ss_pred             cccccccHHHHHHHHHHhhcC------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      ...|.+|+..+..+...+.+.            -.|.|||.+.+++++....     ..+|+++-..++..-++..|+.+
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~IL~~   79 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKILNK   79 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHHHHH
Confidence            345789999999999988765            5699999999999997642     25899999999999999999999


Q ss_pred             hCcCC-chh-hH--HH----HHHHHHH--HHhc-CCeEEEEEeCCCCccccccccCc----------CCCC------Ccc
Q 045120          189 LGLEL-SEE-AE--YR----RASRLYE--RLKN-ENKILVILANIWKLLDLETVKIP----------FRND------SRD  241 (374)
Q Consensus       189 l~~~~-~~~-~~--~~----~~~~l~~--~L~~-~kr~LlVlDdv~~~~~~~~l~~~----------~~~~------TR~  241 (374)
                      .+... +.. ..  .+    ....+.+  ...+ ++.++||||++....+.+.+..+          .+..      +--
T Consensus        80 ~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~  159 (438)
T KOG2543|consen   80 SQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSC  159 (438)
T ss_pred             hccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEecccc
Confidence            96322 221 11  11    2222322  1112 25899999999876554442111          1110      111


Q ss_pred             hhHhhhhcCCCC--ceecCCCCHHHHHHHHHHhcCCCCC----CcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          242 NNVVLLSMGSKD--NFLIANITEEEAWRLFKIMNGDDVE----NCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       242 ~~va~~~~~~~~--~~~l~~L~~~~s~~Lf~~~a~~~~~----~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      +..-...+|...  ++..+.-+.+|-.++|.+.-.+...    ..-+.-+..-....| + -|-++..+.+
T Consensus       160 e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~r~~~~ya~fl~v~l~vF~~~c-r-d~~eL~~~~~  228 (438)
T KOG2543|consen  160 EKQYLINTGTLEIVVLHFPQYSVEETQVILSRDNPGKRKLDVYAQFLHVLLQVFYMAC-R-DVNELRSLIS  228 (438)
T ss_pred             HHHhhcccCCCCceEEecCCCCHHHHHHHHhcCCccccchHHHHHHHHHHHHHHHHHh-C-CHHHHHHHHH
Confidence            111111234333  4566777888888887764431110    111222333444566 5 5555555554

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.34  E-value=0.0016  Score=62.50  Aligned_cols=157  Identities=17%  Similarity=0.171  Sum_probs=84.3

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      .....+.|++..+++|.+.+...                      ++|+|||+||+.+++...  ..|     +.+.   
T Consensus       119 ~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~--~~~-----~~v~---  188 (364)
T TIGR01242       119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN--ATF-----IRVV---  188 (364)
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCC--CCE-----Eecc---
Confidence            33456889999999998876321                      889999999999998553  223     2221   


Q ss_pred             CHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------------ccccccCc---CC-
Q 045120          177 DIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL----------------DLETVKIP---FR-  236 (374)
Q Consensus       177 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~----------------~~~~l~~~---~~-  236 (374)
                       ...+...   .++      ........+.+........+|+||+++...                .+..+...   +. 
T Consensus       189 -~~~l~~~---~~g------~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~  258 (364)
T TIGR01242       189 -GSELVRK---YIG------EGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDP  258 (364)
T ss_pred             -hHHHHHH---hhh------HHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCC
Confidence             1111111   011      111222333333333357899999986431                01111111   11 


Q ss_pred             -CC------Ccchh-Hhhhhc---CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch
Q 045120          237 -ND------SRDNN-VVLLSM---GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF  298 (374)
Q Consensus       237 -~~------TR~~~-va~~~~---~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP  298 (374)
                       .+      |.... +.....   .-...+.++..+.++..++|..++......++..  ...+++.+ .|..
T Consensus       259 ~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~--~~~la~~t-~g~s  328 (364)
T TIGR01242       259 RGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVD--LEAIAKMT-EGAS  328 (364)
T ss_pred             CCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCC--HHHHHHHc-CCCC
Confidence             11      22211 111011   1234788999999999999998876433222111  24677777 6654

Many proteins may score above the trusted cutoff because an internal

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.32  E-value=0.0016  Score=57.92  Aligned_cols=149  Identities=13%  Similarity=0.114  Sum_probs=81.7

Q ss_pred             cHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhh
Q 045120          127 RVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEA  197 (374)
Q Consensus       127 r~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~  197 (374)
                      .+..++.+.+++...         ..|+|||+||+.+++....  .....++++++.-.+      ..            
T Consensus        22 ~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~--~~~~~~~i~~~~~~~------~~------------   81 (226)
T TIGR03420        22 NAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEE--RGKSAIYLPLAELAQ------AD------------   81 (226)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHh--cCCcEEEEeHHHHHH------hH------------
Confidence            445666777765332         8899999999999986542  233456665432211      00            


Q ss_pred             HHHHHHHHHHHHhcCCeEEEEEeCCCCcc---cc-ccccCcC----C--CC----Ccc---------hhHhhhhcCCCCc
Q 045120          198 EYRRASRLYERLKNENKILVILANIWKLL---DL-ETVKIPF----R--ND----SRD---------NNVVLLSMGSKDN  254 (374)
Q Consensus       198 ~~~~~~~l~~~L~~~kr~LlVlDdv~~~~---~~-~~l~~~~----~--~~----TR~---------~~va~~~~~~~~~  254 (374)
                           ..+...+.+  .-+|||||+....   .| +.+...+    .  ..    |+.         ..+ .........
T Consensus        82 -----~~~~~~~~~--~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L-~~r~~~~~~  153 (226)
T TIGR03420        82 -----PEVLEGLEQ--ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDL-RTRLAWGLV  153 (226)
T ss_pred             -----HHHHhhccc--CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHH-HHHHhcCee
Confidence                 011112222  3488899987432   11 1121110    0  01    111         112 112222457


Q ss_pred             eecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          255 FLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       255 ~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      +.+++++.++-..++...+...... --.+....|++.+ +|.|..+.-+-
T Consensus       154 i~l~~l~~~e~~~~l~~~~~~~~~~-~~~~~l~~L~~~~-~gn~r~L~~~l  202 (226)
T TIGR03420       154 FQLPPLSDEEKIAALQSRAARRGLQ-LPDEVADYLLRHG-SRDMGSLMALL  202 (226)
T ss_pred             EecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhc-cCCHHHHHHHH
Confidence            9999999999999998765311111 1134556788889 99888776553

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.

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

Probab=97.30  E-value=0.0019  Score=60.18  Aligned_cols=113  Identities=19%  Similarity=0.222  Sum_probs=71.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ++|+||||||+.+.+..+...    ..||..|-...-..-.+.|.++-.             . ...|. ++|..|.+|.
T Consensus       170 ppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq-------------~-~~~l~-krkTilFiDE  230 (554)
T KOG2028|consen  170 PPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQ-------------N-EKSLT-KRKTILFIDE  230 (554)
T ss_pred             CCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHH-------------H-HHhhh-cceeEEEeHH
Confidence            899999999999998665333    568888876554444445544431             1 11122 3789999999


Q ss_pred             CCC--ccccccccCcCCCC--------CcchhHh--hhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          222 IWK--LLDLETVKIPFRND--------SRDNNVV--LLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       222 v~~--~~~~~~l~~~~~~~--------TR~~~va--~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                      |..  ..+-+.|.+..-+|        |-+...-  ......-.++-|++|+.++-..++.+..
T Consensus       231 iHRFNksQQD~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~rai  294 (554)
T KOG2028|consen  231 IHRFNKSQQDTFLPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAI  294 (554)
T ss_pred             hhhhhhhhhhcccceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHH
Confidence            963  34455555554444        3222210  0122334588899999999999988844

>PF13173 AAA_14: AAA domain

Probab=97.29  E-value=0.00022  Score=57.61  Aligned_cols=104  Identities=19%  Similarity=0.184  Sum_probs=57.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+|||||+++++.+..   ....+++++...........                .+..+.+.+.... ++.+|+||+
T Consensus        10 ~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~----------------~~~~~~~~~~~~~-~~~~i~iDE   69 (128)
T PF13173_consen   10 PRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLAD----------------PDLLEYFLELIKP-GKKYIFIDE   69 (128)
T ss_pred             CCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhh----------------hhhHHHHHHhhcc-CCcEEEEeh
Confidence            779999999999998654   23456777655432211000                0022233333333 578999999


Q ss_pred             CCCccccccccCcC----CCC-----CcchhHh-----hhhcCCCCceecCCCCHHHH
Q 045120          222 IWKLLDLETVKIPF----RND-----SRDNNVV-----LLSMGSKDNFLIANITEEEA  265 (374)
Q Consensus       222 v~~~~~~~~l~~~~----~~~-----TR~~~va-----~~~~~~~~~~~l~~L~~~~s  265 (374)
                      +....+|......+    ++.     +......     ....|....++|.||+-.|-
T Consensus        70 iq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   70 IQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             hhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            98877666543221    121     1111111     11223334688999987763

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.29  E-value=0.0069  Score=57.81  Aligned_cols=165  Identities=14%  Similarity=0.179  Sum_probs=88.2

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhc--------------------CCCCeEEE
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQARED--------------------KLFDRVVF  169 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~--------------------~~F~~~~w  169 (374)
                      ....++|.+..++.+.+++..+          +.|+||||+|+.+.......                    .+|+. ++
T Consensus        12 ~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~-~~   90 (355)
T TIGR02397        12 TFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDV-IE   90 (355)
T ss_pred             cHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EE
Confidence            3456899999999999988765          88999999999887754211                    12222 22


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc--cccccccCcC---CCC------
Q 045120          170 SEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL--LDLETVKIPF---RND------  238 (374)
Q Consensus       170 v~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~--~~~~~l~~~~---~~~------  238 (374)
                      ++-+....... .+.+...+...               -..+ ++-++|+|++...  .....+...+   |..      
T Consensus        91 ~~~~~~~~~~~-~~~l~~~~~~~---------------p~~~-~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~  153 (355)
T TIGR02397        91 IDAASNNGVDD-IREILDNVKYA---------------PSSG-KYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILA  153 (355)
T ss_pred             eeccccCCHHH-HHHHHHHHhcC---------------cccC-CceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEE
Confidence            22211111111 11122211100               0112 4558889987543  2222221111   111      


Q ss_pred             C-cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHH
Q 045120          239 S-RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       239 T-R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                      | ....+..........+++.+++.++..+.+...+......- -.+....+++.+ +|.|..+...
T Consensus       154 ~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i-~~~a~~~l~~~~-~g~~~~a~~~  218 (355)
T TIGR02397       154 TTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKI-EDEALELIARAA-DGSLRDALSL  218 (355)
T ss_pred             eCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCChHHHHHH
Confidence            2 22222111111224788899999999888887664222111 135667889999 9988655433

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.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.25  E-value=0.012  Score=57.00  Aligned_cols=86  Identities=16%  Similarity=0.134  Sum_probs=50.4

Q ss_pred             CeEEEEEeCCCCcc--c----cccccCcCCCC------CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCc
Q 045120          213 NKILVILANIWKLL--D----LETVKIPFRND------SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENC  280 (374)
Q Consensus       213 kr~LlVlDdv~~~~--~----~~~l~~~~~~~------TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~  280 (374)
                      ++-++|+|++....  .    +..+..|-+..      |....+..........+.+.+++.++..+.+.+..+.   + 
T Consensus       117 ~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~~---~-  192 (394)
T PRK07940        117 RWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDGV---D-  192 (394)
T ss_pred             CcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcCC---C-
Confidence            45588889987542  2    22233332222      3333332211222348999999999999888754321   1 


Q ss_pred             chHHHHHHHHHHccCCchHHHHHHh
Q 045120          281 KFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       281 ~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                        .+.+..++..+ +|.|.....+.
T Consensus       193 --~~~a~~la~~s-~G~~~~A~~l~  214 (394)
T PRK07940        193 --PETARRAARAS-QGHIGRARRLA  214 (394)
T ss_pred             --HHHHHHHHHHc-CCCHHHHHHHh
Confidence              24466889999 99997664443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.23  E-value=0.0079  Score=61.21  Aligned_cols=177  Identities=12%  Similarity=0.138  Sum_probs=92.9

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCe--EEEEEeCCCCCHHHHHHHHH
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDR--VVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~--~~wv~vs~~~~~~~~~~~i~  186 (374)
                      .....++|.+..++.|.+.+..+          +.|+||||+|+.+.+..-.......  ..+    ..+......+.|.
T Consensus        21 ~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~----~~cg~c~~C~~i~   96 (598)
T PRK09111         21 QTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTI----DLCGVGEHCQAIM   96 (598)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCcc----ccCcccHHHHHHh
Confidence            33567999999999999988766          8899999999999885432211100  000    0111111112222


Q ss_pred             HHhCcCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccc----cCcCCCC------CcchhH
Q 045120          187 EKLGLEL------SEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETV----KIPFRND------SRDNNV  244 (374)
Q Consensus       187 ~~l~~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l----~~~~~~~------TR~~~v  244 (374)
                      .......      .....++ +..+.+.+.    ..++-++|+|++....  ..+.|    ..+.+..      |....+
T Consensus        97 ~g~h~Dv~e~~a~s~~gvd~-IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kl  175 (598)
T PRK09111         97 EGRHVDVLEMDAASHTGVDD-IREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKV  175 (598)
T ss_pred             cCCCCceEEecccccCCHHH-HHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhh
Confidence            2111110      0011111 122222222    1245678999986442  22222    2222222      333333


Q ss_pred             hhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHH
Q 045120          245 VLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLT  302 (374)
Q Consensus       245 a~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~  302 (374)
                      ..........+++.+++.++....+.+.+......- -.+....|+..+ +|.+.-+.
T Consensus       176 l~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i-~~eAl~lIa~~a-~Gdlr~al  231 (598)
T PRK09111        176 PVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEV-EDEALALIARAA-EGSVRDGL  231 (598)
T ss_pred             hHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHHH
Confidence            221122224789999999999988888764221111 125566888999 88876553

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.23  E-value=0.0061  Score=64.74  Aligned_cols=140  Identities=13%  Similarity=0.181  Sum_probs=76.7

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcC----CCCeEEE-EEeCCCCCHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDK----LFDRVVF-SEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~----~F~~~~w-v~vs~~~~~~~~~~~i~  186 (374)
                      ..+++||+.++.+++..|...         .+|+||||||..+........    -.+..+| +.++.-..         
T Consensus       186 ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~a---------  256 (852)
T TIGR03345       186 IDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQA---------  256 (852)
T ss_pred             CCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhc---------
Confidence            356999999999999988765         889999999999988643211    1123333 22221000         


Q ss_pred             HHhCcCCchhhHHHHHHHHHHHHh-cCCeEEEEEeCCCCcc-------ccc---cccCcCCCC-------CcchhH----
Q 045120          187 EKLGLELSEEAEYRRASRLYERLK-NENKILVILANIWKLL-------DLE---TVKIPFRND-------SRDNNV----  244 (374)
Q Consensus       187 ~~l~~~~~~~~~~~~~~~l~~~L~-~~kr~LlVlDdv~~~~-------~~~---~l~~~~~~~-------TR~~~v----  244 (374)
                         +.... ..-+.....+.+.+. .+++.+|++|++....       ..+   .|.+.+..+       |.....    
T Consensus       257 ---g~~~~-ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~G~l~~IgaTT~~e~~~~~  332 (852)
T TIGR03345       257 ---GASVK-GEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALARGELRTIAATTWAEYKKYF  332 (852)
T ss_pred             ---ccccc-hHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHhhCCCeEEEEecCHHHHhhhh
Confidence               00011 111122223333332 2368999999986431       111   133344444       332211    


Q ss_pred             h--hhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          245 V--LLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       245 a--~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                      .  ......-..+.+++++.++..+++....
T Consensus       333 ~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~  363 (852)
T TIGR03345       333 EKDPALTRRFQVVKVEEPDEETAIRMLRGLA  363 (852)
T ss_pred             hccHHHHHhCeEEEeCCCCHHHHHHHHHHHH
Confidence            0  0001112379999999999999975444

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.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.21  E-value=0.0085  Score=60.48  Aligned_cols=177  Identities=15%  Similarity=0.144  Sum_probs=91.3

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|.+..++.+.+++..+          +.|+||||+|+.+.+.....+      |... ..++.....+.+....
T Consensus        14 ~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~------~~~~-~~Cg~C~sCr~i~~~~   86 (605)
T PRK05896         14 NFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLN------PKDG-DCCNSCSVCESINTNQ   86 (605)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCC------CCCC-CCCcccHHHHHHHcCC
Confidence            3457899999999999988664          889999999999987543211      1111 1112222222222111


Q ss_pred             CcCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cccccccC----cCCCC------CcchhHhhh
Q 045120          190 GLEL------SEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVKI----PFRND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~~----~~~~~------TR~~~va~~  247 (374)
                      ....      .....++ .+.+.+.+.    .+++-++|+|++...  ..+..|..    |.+..      +....+...
T Consensus        87 h~DiieIdaas~igVd~-IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~T  165 (605)
T PRK05896         87 SVDIVELDAASNNGVDE-IRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLT  165 (605)
T ss_pred             CCceEEeccccccCHHH-HHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHH
Confidence            1000      0001111 112222111    113446999998743  22222222    21121      333333211


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch-HHHHHHhc
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF-CTLTTNAS  306 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP-Lai~~ig~  306 (374)
                      .......+++.+++.++....+...+......- -.+.+..+++.+ +|.| .|+..+-.
T Consensus       166 I~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~I-s~eal~~La~lS-~GdlR~AlnlLek  223 (605)
T PRK05896        166 IISRCQRYNFKKLNNSELQELLKSIAKKEKIKI-EDNAIDKIADLA-DGSLRDGLSILDQ  223 (605)
T ss_pred             HHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCcHHHHHHHHHH
Confidence            122234789999999999988887664221111 134566888999 7755 45555443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.21  E-value=0.0059  Score=61.40  Aligned_cols=156  Identities=15%  Similarity=0.170  Sum_probs=84.6

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCC-------------------CCeEEEEE
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKL-------------------FDRVVFSE  171 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~-------------------F~~~~wv~  171 (374)
                      ...++|-+..++.+.+++..+          +.|+||||+|+.+.+..-....                   |.-.+++.
T Consensus        15 f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~   94 (527)
T PRK14969         15 FSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVD   94 (527)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEee
Confidence            456899999999999988765          8899999999999875432111                   11112222


Q ss_pred             eCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCccc--cc----cccCcCCCC---
Q 045120          172 VSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLK----NENKILVILANIWKLLD--LE----TVKIPFRND---  238 (374)
Q Consensus       172 vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~~--~~----~l~~~~~~~---  238 (374)
                      .+....                    .++ ...+.+...    .+++-++|+|++.....  .+    .+..+-+..   
T Consensus        95 ~~~~~~--------------------vd~-ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fI  153 (527)
T PRK14969         95 AASNTQ--------------------VDA-MRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFI  153 (527)
T ss_pred             ccccCC--------------------HHH-HHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEE
Confidence            111111                    111 111222221    13567899999875422  22    222221111   


Q ss_pred             --C-cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH
Q 045120          239 --S-RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       239 --T-R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL  299 (374)
                        | ....+..........+++.+++.++..+.+.+.+...... .-......|++.+ +|.+-
T Consensus       154 L~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~-~~~~al~~la~~s-~Gslr  215 (527)
T PRK14969        154 LATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIP-FDATALQLLARAA-AGSMR  215 (527)
T ss_pred             EEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHH
Confidence              2 2222211011112378899999999888887766422111 1134456788899 88775

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.18  E-value=0.0046  Score=60.09  Aligned_cols=177  Identities=15%  Similarity=0.168  Sum_probs=90.4

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEE-eCCCCCHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSE-VSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~~~~~i~~~l  189 (374)
                      ..+++|-+..++.|.+++..+          +.|+||||+|..+.+.......++...|.. ....+......+.+....
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~   94 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAGT   94 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcCC
Confidence            456899999999999888875          889999999999988654322111111110 011111111222222111


Q ss_pred             CcCC---c--hhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccc----cCcCCCC------CcchhHhhhh
Q 045120          190 GLEL---S--EEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETV----KIPFRND------SRDNNVVLLS  248 (374)
Q Consensus       190 ~~~~---~--~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l----~~~~~~~------TR~~~va~~~  248 (374)
                      ....   .  .....+.+..+.+.+.    .+++-++|+|++....  .++.+    ..+.+..      ++...+....
T Consensus        95 ~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl  174 (397)
T PRK14955         95 SLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATI  174 (397)
T ss_pred             CCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHH
Confidence            1110   0  0000111222333332    1256688999987542  23332    2222222      3333332111


Q ss_pred             cCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH
Q 045120          249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       249 ~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL  299 (374)
                      ......+++.+++.++..+.+...+..... .--.+.+..|+..+ +|.+-
T Consensus       175 ~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~-~i~~~al~~l~~~s-~g~lr  223 (397)
T PRK14955        175 ASRCQRFNFKRIPLEEIQQQLQGICEAEGI-SVDADALQLIGRKA-QGSMR  223 (397)
T ss_pred             HHHHHHhhcCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHc-CCCHH
Confidence            111236889999999988888776632111 11135667889999 88664

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.17  E-value=0.008  Score=61.37  Aligned_cols=172  Identities=15%  Similarity=0.157  Sum_probs=92.2

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|-+..++.|.+++..+          ..|+||||+|+.+.+.......+.      -...++.....+.|....+
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~------~~~~c~~c~~c~~i~~~~~   88 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP------KGRPCGTCEMCRAIAEGSA   88 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCCCCccCHHHHHHhcCCC
Confidence            457899999999999888765          789999999999987543211100      0112222333333333222


Q ss_pred             cCC------chhhHHHHHHHHHHHHhc----CCeEEEEEeCCCCc--ccccccc----CcCCCC------CcchhHhhhh
Q 045120          191 LEL------SEEAEYRRASRLYERLKN----ENKILVILANIWKL--LDLETVK----IPFRND------SRDNNVVLLS  248 (374)
Q Consensus       191 ~~~------~~~~~~~~~~~l~~~L~~----~kr~LlVlDdv~~~--~~~~~l~----~~~~~~------TR~~~va~~~  248 (374)
                      ...      .....++ ...+.+.+..    .++-++|+|++...  ...+.|.    .+-+..      +....+....
T Consensus        89 ~d~~~i~~~~~~~vd~-ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI  167 (585)
T PRK14950         89 VDVIEMDAASHTSVDD-AREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATI  167 (585)
T ss_pred             CeEEEEeccccCCHHH-HHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHH
Confidence            110      0011111 1222222221    25678999998643  2233332    221111      2222222111


Q ss_pred             cCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       249 ~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      ......+.+..++.++....+.+.+......- -.+....|+..| +|.+..+
T Consensus       168 ~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i-~~eal~~La~~s-~Gdlr~a  218 (585)
T PRK14950        168 LSRCQRFDFHRHSVADMAAHLRKIAAAEGINL-EPGALEAIARAA-TGSMRDA  218 (585)
T ss_pred             HhccceeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHH
Confidence            12224688889999998888887765322111 135567889999 8888644

>COG3899 Predicted ATPase [General function prediction only]

Probab=97.15  E-value=0.0062  Score=64.70  Aligned_cols=217  Identities=14%  Similarity=0.106  Sum_probs=117.5

Q ss_pred             cccccHHHHHHHHHHhhcC------------CCCccHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCC---CHHHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTNA------------NGGIGKTTLAKEFAKQARED-KLFDRVVFSEVSQTS---DIKKIQGDIA  186 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~~------------~gGiGKTtLA~~v~~~~~~~-~~F~~~~wv~vs~~~---~~~~~~~~i~  186 (374)
                      +++||+.+++.|...+..-            ..|||||+|++.|.....-+ +.|=...|-....+.   .....+++++
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~~~~i~~~f~q~~~~ipl~~lvq~~r~l~   80 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRGYFIKGKFDQFERNIPLSPLVQAFRDLM   80 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhccceeeeHhhcccccCCCchHHHHHHHHHHH
Confidence            3789999999999888643            77999999999998854322 222111111122221   2233334444


Q ss_pred             HHh-------------------CcCCc-----------------------hhhHHH-----HHHHHHHHHhcCCeEEEEE
Q 045120          187 EKL-------------------GLELS-----------------------EEAEYR-----RASRLYERLKNENKILVIL  219 (374)
Q Consensus       187 ~~l-------------------~~~~~-----------------------~~~~~~-----~~~~l~~~L~~~kr~LlVl  219 (374)
                      .++                   +....                       +.....     ....+......+++..+|+
T Consensus        81 ~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi~l  160 (849)
T COG3899          81 GQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVIVL  160 (849)
T ss_pred             HHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEEEE
Confidence            433                   11100                       000001     1223333444557999999


Q ss_pred             eCCCCcc-----ccccccCcCC-----CC---------CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCc
Q 045120          220 ANIWKLL-----DLETVKIPFR-----ND---------SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENC  280 (374)
Q Consensus       220 Ddv~~~~-----~~~~l~~~~~-----~~---------TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~  280 (374)
                      ||+.-.+     -++.+....+     .+         .+...+ .....+...+.|.||+..+...|.....+..... 
T Consensus       161 eDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~-~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~~~~-  238 (849)
T COG3899         161 EDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEI-LKSATNITTITLAPLSRADTNQLVAATLGCTKLL-  238 (849)
T ss_pred             ecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHH-hhcCCceeEEecCcCchhhHHHHHHHHhCCcccc-
Confidence            9995221     1111111111     11         121222 2233444689999999999999998888753322 


Q ss_pred             chHHHHHHHHHHccCCchHHHHHHhc---------CCCcccccccc----cccC-CCCcccchhh-cccCCchhhhhhh
Q 045120          281 KFKSTAINVAKACGAGLFCTLTTNAS---------KSSSIYSHVSN----DYQS-IYKPKPYLAV-FQDLEPTIVKTAF  344 (374)
Q Consensus       281 ~l~~~~~~I~~~c~~GlPLai~~ig~---------~~~~~~~W~~~----~~~~-~~~~~~~~~l-y~~Lp~~~lk~cf  344 (374)
                       ..+..+.|.++- .|.|+-+.-+-.         .+.+...|.-.    .... .+.++.++.. -+.||+. .|...
T Consensus       239 -~~p~~~~i~~kt-~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~~~~~~vv~~l~~rl~kL~~~-t~~Vl  314 (849)
T COG3899         239 -PAPLLELIFEKT-KGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGILATTDAVVEFLAARLQKLPGT-TREVL  314 (849)
T ss_pred             -cchHHHHHHHHh-cCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCchhhHHHHHHHHHHHhcCCHH-HHHHH
Confidence             235677899999 999999876655         23455566221    1111 2221112333 8888775 55544

>PRK08727 hypothetical protein; Validated

Probab=97.13  E-value=0.0052  Score=55.09  Aligned_cols=129  Identities=11%  Similarity=0.022  Sum_probs=70.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||+|++.+++...-.  ...+.|+++.+      ....+.                 ...+.+.  +.-+|||||
T Consensus        49 ~~G~GKThL~~a~~~~~~~~--~~~~~y~~~~~------~~~~~~-----------------~~~~~l~--~~dlLiIDD  101 (233)
T PRK08727         49 PAGTGKTHLALALCAAAEQA--GRSSAYLPLQA------AAGRLR-----------------DALEALE--GRSLVALDG  101 (233)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCcEEEEeHHH------hhhhHH-----------------HHHHHHh--cCCEEEEeC
Confidence            88999999999998865422  33556765432      111100                 1112222  345888888


Q ss_pred             CCCcc---cccc-ccCcCC----CC---------------CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCC
Q 045120          222 IWKLL---DLET-VKIPFR----ND---------------SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVE  278 (374)
Q Consensus       222 v~~~~---~~~~-l~~~~~----~~---------------TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~  278 (374)
                      +....   .+.. +...+.    .+               .....+. ..+.....+++++++.++-.+++.+.+.....
T Consensus       102 i~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~-SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l  180 (233)
T PRK08727        102 LESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLR-SRLAQCIRIGLPVLDDVARAAVLRERAQRRGL  180 (233)
T ss_pred             cccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHH-HHHhcCceEEecCCCHHHHHHHHHHHHHHcCC
Confidence            76321   1111 100000    00               2233332 24444568999999999999999987752211


Q ss_pred             CcchHHHHHHHHHHccCCchHH
Q 045120          279 NCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       279 ~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      .- -.+...-|++.| +|-.-.
T Consensus       181 ~l-~~e~~~~La~~~-~rd~r~  200 (233)
T PRK08727        181 AL-DEAAIDWLLTHG-ERELAG  200 (233)
T ss_pred             CC-CHHHHHHHHHhC-CCCHHH
Confidence            11 135566788888 654433

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.13  E-value=0.01  Score=62.48  Aligned_cols=170  Identities=12%  Similarity=0.016  Sum_probs=86.5

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...+||.+..++.|.+++..+          ..|+||||+|+.+.+..........       ..++.+...+.|...-.
T Consensus        14 f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~-------~pCg~C~sC~~~~~g~~   86 (824)
T PRK07764         14 FAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTS-------TPCGECDSCVALAPGGP   86 (824)
T ss_pred             HHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCC-------CCCcccHHHHHHHcCCC
Confidence            456899999999999998875          7899999999999876532211100       00111111111111100


Q ss_pred             c-------CC-chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccccCc---CCCC-------CcchhHhh
Q 045120          191 L-------EL-SEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETVKIP---FRND-------SRDNNVVL  246 (374)
Q Consensus       191 ~-------~~-~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l~~~---~~~~-------TR~~~va~  246 (374)
                      .       .. .....++ +..+.+.+.    .+++-++|||++....  ..+.|...   .+..       |....+..
T Consensus        87 ~~~dv~eidaas~~~Vd~-iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~  165 (824)
T PRK07764         87 GSLDVTEIDAASHGGVDD-ARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIG  165 (824)
T ss_pred             CCCcEEEecccccCCHHH-HHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhH
Confidence            0       00 0001111 111222211    1245578899887442  22222221   2222       33333322


Q ss_pred             hhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH
Q 045120          247 LSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       247 ~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      ........|++..++.++..+.+.+........ --......|++.+ +|.+..
T Consensus       166 TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~-id~eal~lLa~~s-gGdlR~  217 (824)
T PRK07764        166 TIRSRTHHYPFRLVPPEVMRGYLERICAQEGVP-VEPGVLPLVIRAG-GGSVRD  217 (824)
T ss_pred             HHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHH
Confidence            122233578999999999888887765322111 1134456788889 887743

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.06  E-value=0.011  Score=60.44  Aligned_cols=179  Identities=16%  Similarity=0.175  Sum_probs=91.4

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEE-eCCCCCHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSE-VSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~~~~~i~~~l  189 (374)
                      ...++|-+..++.|.+.+..+          +.|+||||+|+.+.+..-....++.-.|.. +...++.....+.+...-
T Consensus        15 f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~   94 (620)
T PRK14954         15 FADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFDAGT   94 (620)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHhccC
Confidence            466899999999999988765          889999999999987653322111111110 011111122222221111


Q ss_pred             CcCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccc----cCcCCCC------CcchhHhhh
Q 045120          190 GLEL------SEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETV----KIPFRND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l----~~~~~~~------TR~~~va~~  247 (374)
                      ..+.      .....++. ..+.+.+.    .+.+-++|+|++....  ..+.|    ..+-+..      ++...+...
T Consensus        95 ~~n~~~~d~~s~~~vd~I-r~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~T  173 (620)
T PRK14954         95 SLNISEFDAASNNSVDDI-RQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPAT  173 (620)
T ss_pred             CCCeEEecccccCCHHHH-HHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHH
Confidence            1100      00011221 22222221    1245688999987542  22222    2222222      333344322


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCc-hHHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL-FCTLT  302 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~Gl-PLai~  302 (374)
                      .......+++.+++.++....+.+.+...... --.+.+..|+..+ +|. -.|+.
T Consensus       174 I~SRc~~vef~~l~~~ei~~~L~~i~~~egi~-I~~eal~~La~~s-~Gdlr~al~  227 (620)
T PRK14954        174 IASRCQRFNFKRIPLDEIQSQLQMICRAEGIQ-IDADALQLIARKA-QGSMRDAQS  227 (620)
T ss_pred             HHhhceEEecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHh-CCCHHHHHH
Confidence            22334579999999999887777765421111 1135567889999 774 44444

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.98  E-value=0.01  Score=60.20  Aligned_cols=175  Identities=13%  Similarity=0.138  Sum_probs=91.7

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ..+++|-+..++.|.+.+..+          +.|+||||+|+.+.+..-.....+       ...++.....+.|.....
T Consensus        15 f~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~-------~~pCg~C~sC~~i~~g~h   87 (624)
T PRK14959         15 FAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPT-------GEPCNTCEQCRKVTQGMH   87 (624)
T ss_pred             HHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCC-------CCCCcccHHHHHHhcCCC
Confidence            456889888888888888765          889999999999987543211110       011122222222221111


Q ss_pred             cCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cccccccCcC----CCC-----Ccc-hhHhhhh
Q 045120          191 LEL------SEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVKIPF----RND-----SRD-NNVVLLS  248 (374)
Q Consensus       191 ~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~~~~----~~~-----TR~-~~va~~~  248 (374)
                      ...      .....+ .++.+.+.+.    .+++-+||+|++...  ...+.|...+    +..     |.. ..+....
T Consensus        88 pDv~eId~a~~~~Id-~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI  166 (624)
T PRK14959         88 VDVVEIDGASNRGID-DAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTI  166 (624)
T ss_pred             CceEEEecccccCHH-HHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHH
Confidence            000      000111 1122222222    235679999999754  2233332222    111     322 2332111


Q ss_pred             cCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCc-hHHHHHHh
Q 045120          249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL-FCTLTTNA  305 (374)
Q Consensus       249 ~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~Gl-PLai~~ig  305 (374)
                      ......+++.+++.++....+...+..... .--.+....|++.+ +|. -.|+..+.
T Consensus       167 ~SRcq~i~F~pLs~~eL~~~L~~il~~egi-~id~eal~lIA~~s-~GdlR~Al~lLe  222 (624)
T PRK14959        167 VSRCQHFTFTRLSEAGLEAHLTKVLGREGV-DYDPAAVRLIARRA-AGSVRDSMSLLG  222 (624)
T ss_pred             HhhhhccccCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHc-CCCHHHHHHHHH
Confidence            112237899999999999888876642211 11135567888899 774 46776664

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

Probab=96.98  E-value=0.0038  Score=65.51  Aligned_cols=138  Identities=17%  Similarity=0.268  Sum_probs=78.6

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcC---CC-CeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDK---LF-DRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~---~F-~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .+++||+.++.++++.|...         .+|+|||+||+.+.+......   .+ +..+|..     ++..+...    
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~-----~~~~l~a~----  252 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSL-----DMGSLLAG----  252 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEe-----cHHHHhhh----
Confidence            46999999999999988754         889999999999988653211   11 3344421     22222110    


Q ss_pred             hCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc----------cccc-ccCcCCCC-------Ccchh-------
Q 045120          189 LGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL----------DLET-VKIPFRND-------SRDNN-------  243 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~----------~~~~-l~~~~~~~-------TR~~~-------  243 (374)
                        ... ...-++....+.+.+...++.+|++|++....          +... +...+..+       |....       
T Consensus       253 --~~~-~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~g~i~~IgaTt~~e~~~~~~~  329 (731)
T TIGR02639       253 --TKY-RGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSSGKLRCIGSTTYEEYKNHFEK  329 (731)
T ss_pred             --ccc-cchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhCCCeEEEEecCHHHHHHHhhh
Confidence              000 01122334444444443357899999986221          1112 33333333       33211       


Q ss_pred             -HhhhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          244 -VVLLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       244 -va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                       -|-..  --..+.+++++.++..+++....
T Consensus       330 d~al~r--Rf~~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       330 DRALSR--RFQKIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             hHHHHH--hCceEEeCCCCHHHHHHHHHHHH
Confidence             11111  12368999999999999999654

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.97  E-value=0.014  Score=56.13  Aligned_cols=166  Identities=12%  Similarity=0.156  Sum_probs=86.6

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhc------CCCCeEE-EEEeCCCCCHHHHH
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQARED------KLFDRVV-FSEVSQTSDIKKIQ  182 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~------~~F~~~~-wv~vs~~~~~~~~~  182 (374)
                      ....++|.+..++.+.+.+..+          +.|+||||+|+.+.+.....      ..|+..+ -++.....+... .
T Consensus        15 ~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-i   93 (367)
T PRK14970         15 TFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD-I   93 (367)
T ss_pred             cHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHH-H
Confidence            3566899999999999998765          88999999999997754321      1122111 111111111111 1


Q ss_pred             HHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--cccccc----CcCCCC------CcchhHhhhhcC
Q 045120          183 GDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVK----IPFRND------SRDNNVVLLSMG  250 (374)
Q Consensus       183 ~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~----~~~~~~------TR~~~va~~~~~  250 (374)
                      ..+++.+...               -..+ ++-++++|++....  .+..+.    .+.+..      +....+......
T Consensus        94 ~~l~~~~~~~---------------p~~~-~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~s  157 (367)
T PRK14970         94 RNLIDQVRIP---------------PQTG-KYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILS  157 (367)
T ss_pred             HHHHHHHhhc---------------cccC-CcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHh
Confidence            1222211100               0012 45679999886432  233321    111111      222222111122


Q ss_pred             CCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH-HHHHH
Q 045120          251 SKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC-TLTTN  304 (374)
Q Consensus       251 ~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL-ai~~i  304 (374)
                      ....+++.+++.++....+...+...... --.+....|+..+ +|-+- ++..+
T Consensus       158 r~~~v~~~~~~~~~l~~~l~~~~~~~g~~-i~~~al~~l~~~~-~gdlr~~~~~l  210 (367)
T PRK14970        158 RCQIFDFKRITIKDIKEHLAGIAVKEGIK-FEDDALHIIAQKA-DGALRDALSIF  210 (367)
T ss_pred             cceeEecCCccHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhC-CCCHHHHHHHH
Confidence            23478999999999888888766422211 1135666788888 77544 43333

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.97  E-value=0.0045  Score=65.80  Aligned_cols=139  Identities=16%  Similarity=0.295  Sum_probs=76.7

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcC---CC-CeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDK---LF-DRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~---~F-~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .+++||+.+++++++.|...         .+|+|||++|..+........   .. +..+|.     .+...++.     
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~-----l~~~~l~a-----  248 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT-----LDIGLLLA-----  248 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE-----eeHHHHhc-----
Confidence            46899999999999999754         899999999999988653211   11 234553     12222211     


Q ss_pred             hCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc---------ccccc-ccCcCCCC-------CcchhHhh-----
Q 045120          189 LGLELSEEAEYRRASRLYERLKNENKILVILANIWKL---------LDLET-VKIPFRND-------SRDNNVVL-----  246 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~---------~~~~~-l~~~~~~~-------TR~~~va~-----  246 (374)
                       +..... .-++....+.+.+...++.+|++|++...         .+... |.+.+..+       |.......     
T Consensus       249 -g~~~~g-e~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~rg~l~~IgaTt~~ey~~~ie~D  326 (821)
T CHL00095        249 -GTKYRG-EFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALARGELQCIGATTLDEYRKHIEKD  326 (821)
T ss_pred             -cCCCcc-HHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhCCCcEEEEeCCHHHHHHHHhcC
Confidence             111111 22233344444444336899999998521         11222 22223333       33332210     


Q ss_pred             -hhcCCCCceecCCCCHHHHHHHHHHh
Q 045120          247 -LSMGSKDNFLIANITEEEAWRLFKIM  272 (374)
Q Consensus       247 -~~~~~~~~~~l~~L~~~~s~~Lf~~~  272 (374)
                       .......++.+...+.++...++...
T Consensus       327 ~aL~rRf~~I~v~ep~~~e~~aILr~l  353 (821)
T CHL00095        327 PALERRFQPVYVGEPSVEETIEILFGL  353 (821)
T ss_pred             HHHHhcceEEecCCCCHHHHHHHHHHH
Confidence             01112236788888888888887643

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.95  E-value=0.017  Score=58.51  Aligned_cols=169  Identities=11%  Similarity=0.018  Sum_probs=87.0

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ..+++|.+..++.|.+++..+          +.|+||||+|+.+.+........+       ...++.......|...-+
T Consensus        12 f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~-------~~pCg~C~~C~~i~~~~~   84 (584)
T PRK14952         12 FAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPT-------ATPCGVCESCVALAPNGP   84 (584)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCC-------CCcccccHHHHHhhcccC
Confidence            457899999999999998875          889999999999987543211110       001111111111111000


Q ss_pred             cC-------C-chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cccccccCc---CCCC-------CcchhHhh
Q 045120          191 LE-------L-SEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVKIP---FRND-------SRDNNVVL  246 (374)
Q Consensus       191 ~~-------~-~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~~~---~~~~-------TR~~~va~  246 (374)
                      ..       . .....++ ...+.+.+.    .+++-++|+|++...  ...+.|...   .|..       |....+..
T Consensus        85 ~~~dvieidaas~~gvd~-iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~  163 (584)
T PRK14952         85 GSIDVVELDAASHGGVDD-TRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLP  163 (584)
T ss_pred             CCceEEEeccccccCHHH-HHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHH
Confidence            00       0 0001111 112222221    125568899998643  222222221   1222       33333322


Q ss_pred             hhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH
Q 045120          247 LSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       247 ~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL  299 (374)
                      ........+++.+++.++..+.+.+.+......- -......|++.+ +|.+-
T Consensus       164 TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i-~~~al~~Ia~~s-~GdlR  214 (584)
T PRK14952        164 TIRSRTHHYPFRLLPPRTMRALIARICEQEGVVV-DDAVYPLVIRAG-GGSPR  214 (584)
T ss_pred             HHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHH
Confidence            1122235799999999998888877664221111 134556788888 88663

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.92  E-value=0.031  Score=48.22  Aligned_cols=40  Identities=13%  Similarity=0.121  Sum_probs=31.4

Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      ..+.+.+++.++..+.+.+. +  . +   .+.+..|+..+ +|.|..
T Consensus       148 ~~~~~~~~~~~~~~~~l~~~-g--i-~---~~~~~~i~~~~-~g~~r~  187 (188)
T TIGR00678       148 QVLPFPPLSEEALLQWLIRQ-G--I-S---EEAAELLLALA-GGSPGA  187 (188)
T ss_pred             EEeeCCCCCHHHHHHHHHHc-C--C-C---HHHHHHHHHHc-CCCccc
Confidence            48999999999998888876 2  1 1   35677999999 998853

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.88  E-value=0.035  Score=56.90  Aligned_cols=159  Identities=13%  Similarity=0.168  Sum_probs=87.4

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhh---------------------cCCCCeEEE
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQARE---------------------DKLFDRVVF  169 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~---------------------~~~F~~~~w  169 (374)
                      ...++|-+..++.|.+++..+          ..|+||||+|+.+....-.                     ..+|+.. .
T Consensus        16 f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~-~   94 (614)
T PRK14971         16 FESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIH-E   94 (614)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceE-E
Confidence            456899999999999998776          7899999999888775421                     1133322 1


Q ss_pred             EEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccccCc---CCCC------
Q 045120          170 SEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVKIP---FRND------  238 (374)
Q Consensus       170 v~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~~~---~~~~------  238 (374)
                      +..+...+...+. .++.++....                ..+++-++|+|++....  ..+.|...   .|..      
T Consensus        95 ld~~~~~~vd~Ir-~li~~~~~~P----------------~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~  157 (614)
T PRK14971         95 LDAASNNSVDDIR-NLIEQVRIPP----------------QIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILA  157 (614)
T ss_pred             ecccccCCHHHHH-HHHHHHhhCc----------------ccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEE
Confidence            2222111222211 1222211000                01245578899887542  23332221   2222      


Q ss_pred             -CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH
Q 045120          239 -SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       239 -TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL  299 (374)
                       |....+.........++++.+++.++....+.+.+......- -.+....|+..+ ||-+-
T Consensus       158 tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i-~~~al~~La~~s-~gdlr  217 (614)
T PRK14971        158 TTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITA-EPEALNVIAQKA-DGGMR  217 (614)
T ss_pred             eCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHH
Confidence             333333321222234799999999999988887664222111 124566888999 77554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=96.87  E-value=0.011  Score=57.40  Aligned_cols=162  Identities=17%  Similarity=0.190  Sum_probs=84.5

Q ss_pred             cccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ...+.|++..+++|.+.+..+                      ++|+|||+||+.+++...  ..     |+.++.    
T Consensus       130 ~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~--~~-----~i~v~~----  198 (389)
T PRK03992        130 YEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN--AT-----FIRVVG----  198 (389)
T ss_pred             HHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhC--CC-----EEEeeh----
Confidence            446889999999988866321                      889999999999998543  22     232221    


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc------------c----cccccC---cCCC--
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL------------D----LETVKI---PFRN--  237 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~------------~----~~~l~~---~~~~--  237 (374)
                      ..+.    ...-    . ........+.+........+|+||++....            .    +..+..   .+..  
T Consensus       199 ~~l~----~~~~----g-~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~  269 (389)
T PRK03992        199 SELV----QKFI----G-EGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRG  269 (389)
T ss_pred             HHHh----Hhhc----c-chHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCC
Confidence            1111    1110    0 111223334443333357899999987420            0    111111   1111  


Q ss_pred             C------CcchhHhhhh-c---CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCc-hHHHHHHh
Q 045120          238 D------SRDNNVVLLS-M---GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL-FCTLTTNA  305 (374)
Q Consensus       238 ~------TR~~~va~~~-~---~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~Gl-PLai~~ig  305 (374)
                      +      |......... .   .-...+.+++.+.++-.++|+.+...........  ...+++.+ .|+ +--|..+.
T Consensus       270 ~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~--~~~la~~t-~g~sgadl~~l~  345 (389)
T PRK03992        270 NVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVD--LEELAELT-EGASGADLKAIC  345 (389)
T ss_pred             CEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCC--HHHHHHHc-CCCCHHHHHHHH
Confidence            1      2222111101 1   1134689999999999999998876332222111  23566666 553 34444433

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.054  Score=53.94  Aligned_cols=158  Identities=15%  Similarity=0.157  Sum_probs=86.2

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcC-------------------CCCeEEEEE
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDK-------------------LFDRVVFSE  171 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~-------------------~F~~~~wv~  171 (374)
                      ...++|-+..+..+.+++..+          +.|+||||+|+.+....-...                   .|...+.+.
T Consensus        15 f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eid   94 (486)
T PRK14953         15 FKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEID   94 (486)
T ss_pred             HHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEEe
Confidence            456889999999999998765          889999999999877432100                   011112221


Q ss_pred             eCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccc----cccCcCCCC---
Q 045120          172 VSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLE----TVKIPFRND---  238 (374)
Q Consensus       172 vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~----~l~~~~~~~---  238 (374)
                      .+.....                    + ..+.+.+.+.    .+++-++|+|++....  ..+    .+..+.+..   
T Consensus        95 aas~~gv--------------------d-~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~I  153 (486)
T PRK14953         95 AASNRGI--------------------D-DIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFI  153 (486)
T ss_pred             CccCCCH--------------------H-HHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEE
Confidence            1111111                    1 1112222222    1356799999987432  222    222222222   


Q ss_pred             ---CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          239 ---SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       239 ---TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                         |+...+..........+.+.+++.++-...+...+...... --.+....|+..+ +|.+-.+
T Consensus       154 l~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~-id~~al~~La~~s-~G~lr~a  217 (486)
T PRK14953        154 LCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIE-YEEKALDLLAQAS-EGGMRDA  217 (486)
T ss_pred             EEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHH
Confidence               33333321111222478899999999888888766422111 1134556788888 7866544

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.78  E-value=0.014  Score=57.59  Aligned_cols=148  Identities=14%  Similarity=0.122  Sum_probs=85.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||+|++.+.+.......--.+++++      ..++...+...++...      .....+.+.+..  .-+|||||
T Consensus       149 ~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~------~~~f~~~~~~~l~~~~------~~~~~~~~~~~~--~dvLiIDD  214 (450)
T PRK14087        149 ESGMGKTHLLKAAKNYIESNFSDLKVSYMS------GDEFARKAVDILQKTH------KEIEQFKNEICQ--NDVLIIDD  214 (450)
T ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCeEEEEE------HHHHHHHHHHHHHHhh------hHHHHHHHHhcc--CCEEEEec
Confidence            779999999999998554222112344543      3456666666664210      122334444443  45899999


Q ss_pred             CCCcc---cc-ccccC---cC-CCC-----C--c--------chhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCC
Q 045120          222 IWKLL---DL-ETVKI---PF-RND-----S--R--------DNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVE  278 (374)
Q Consensus       222 v~~~~---~~-~~l~~---~~-~~~-----T--R--------~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~  278 (374)
                      +....   .+ +.+..   .+ ..+     |  +        ...+. ..+...-++.+++++.++-.+++.+.+.....
T Consensus       215 iq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~-SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl  293 (450)
T PRK14087        215 VQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLI-TRFNMGLSIAIQKLDNKTATAIIKKEIKNQNI  293 (450)
T ss_pred             cccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHH-HHHhCCceeccCCcCHHHHHHHHHHHHHhcCC
Confidence            96431   11 11111   10 111     1  1        12222 24445568899999999999999998853211


Q ss_pred             -CcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          279 -NCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       279 -~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                       ..--.++..-|+..+ +|.|-.+.-+-
T Consensus       294 ~~~l~~evl~~Ia~~~-~gd~R~L~gaL  320 (450)
T PRK14087        294 KQEVTEEAINFISNYY-SDDVRKIKGSV  320 (450)
T ss_pred             CCCCCHHHHHHHHHcc-CCCHHHHHHHH
Confidence             112246777899999 88887765444

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.77  E-value=0.005  Score=61.19  Aligned_cols=147  Identities=17%  Similarity=0.203  Sum_probs=77.3

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcC---CCCeEEEEEeC
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDK---LFDRVVFSEVS  173 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~---~F~~~~wv~vs  173 (374)
                      .....+.|.+..+++|.+.+..+                      ++|+|||++|+.+++......   .+....|+++.
T Consensus       179 v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~  258 (512)
T TIGR03689       179 VTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIK  258 (512)
T ss_pred             CCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEecc
Confidence            34456888999999988876421                      889999999999999654221   12234555544


Q ss_pred             CCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc---------c-----cccccCcC---C
Q 045120          174 QTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL---------D-----LETVKIPF---R  236 (374)
Q Consensus       174 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~---------~-----~~~l~~~~---~  236 (374)
                      ..    .+    +...... ............++....+++++|+||++....         +     +..+...+   .
T Consensus       259 ~~----eL----l~kyvGe-te~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~  329 (512)
T TIGR03689       259 GP----EL----LNKYVGE-TERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVE  329 (512)
T ss_pred             ch----hh----cccccch-HHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccc
Confidence            32    11    1111000 000011112222222223368999999997420         1     11121111   1


Q ss_pred             C--C------CcchhHhhhh-c--C-CCCceecCCCCHHHHHHHHHHhcC
Q 045120          237 N--D------SRDNNVVLLS-M--G-SKDNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       237 ~--~------TR~~~va~~~-~--~-~~~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      .  +      |......... .  + -...+.++..+.++..++|..+..
T Consensus       330 ~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~  379 (512)
T TIGR03689       330 SLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLT  379 (512)
T ss_pred             cCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhh
Confidence            1  1      2222211101 1  1 123689999999999999999875

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.

>PRK09087 hypothetical protein; Validated

Probab=96.74  E-value=0.0052  Score=54.81  Aligned_cols=53  Identities=4%  Similarity=-0.108  Sum_probs=37.3

Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLT  302 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~  302 (374)
                      .+....++++++++.++-.+++.+.+...... --+++..-|++.+ .|..-++.
T Consensus       141 Rl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~-l~~ev~~~La~~~-~r~~~~l~  193 (226)
T PRK09087        141 RLKAATVVEIGEPDDALLSQVIFKLFADRQLY-VDPHVVYYLVSRM-ERSLFAAQ  193 (226)
T ss_pred             HHhCCceeecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHh-hhhHHHHH
Confidence            44555689999999999999999988532111 1145667788888 66666554

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.71  E-value=0.012  Score=55.82  Aligned_cols=92  Identities=9%  Similarity=0.160  Sum_probs=59.6

Q ss_pred             HHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCe-EEEEEeCCC-CCHHHHHHHHHHHhCcCCchhhHH
Q 045120          132 KSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDR-VVFSEVSQT-SDIKKIQGDIAEKLGLELSEEAEY  199 (374)
Q Consensus       132 ~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~vs~~-~~~~~~~~~i~~~l~~~~~~~~~~  199 (374)
                      .++++.+..-          ..|+|||||++.+.+..... +-+. ++|+.+.+. .++.++++.+...+..+..+.+..
T Consensus       121 ~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~-~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~  199 (380)
T PRK12608        121 MRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAAN-HPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPD  199 (380)
T ss_pred             HhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHH
Confidence            4467766532          78999999999998865432 3344 367777766 468888888888776554322111


Q ss_pred             ------HHHHHHHHHH-hcCCeEEEEEeCCCC
Q 045120          200 ------RRASRLYERL-KNENKILVILANIWK  224 (374)
Q Consensus       200 ------~~~~~l~~~L-~~~kr~LlVlDdv~~  224 (374)
                            .....+.+++ ..+++.+||+|++..
T Consensus       200 ~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr  231 (380)
T PRK12608        200 EHIRVAELVLERAKRLVEQGKDVVILLDSLTR  231 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHH
Confidence                  1222333333 346999999999853

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.67  E-value=0.006  Score=48.88  Aligned_cols=82  Identities=21%  Similarity=0.113  Sum_probs=43.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+||||+|+.+.+.....  ...+++++.+........... ...................+.+.....+..+|++|+
T Consensus        10 ~~G~GKTtl~~~l~~~~~~~--~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe   86 (148)
T smart00382       10 PPGSGKTTLARALARELGPP--GGGVIYIDGEDILEEVLDQLL-LIIVGGKKASGSGELRLRLALALARKLKPDVLILDE   86 (148)
T ss_pred             CCCCcHHHHHHHHHhccCCC--CCCEEEECCEEccccCHHHHH-hhhhhccCCCCCHHHHHHHHHHHHHhcCCCEEEEEC
Confidence            78999999999998855422  123566655544322222111 111111111122233334555555542349999999


Q ss_pred             CCCcc
Q 045120          222 IWKLL  226 (374)
Q Consensus       222 v~~~~  226 (374)
                      +....
T Consensus        87 i~~~~   91 (148)
T smart00382       87 ITSLL   91 (148)
T ss_pred             CcccC
Confidence            98653

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.63  E-value=0.079  Score=53.78  Aligned_cols=171  Identities=16%  Similarity=0.175  Sum_probs=88.3

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|.+..++.+.+++..+          +.|+||||+|+.+....-....-+       +..++.......|....
T Consensus        14 ~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~-------~~pC~~C~~C~~i~~g~   86 (559)
T PRK05563         14 TFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPD-------GEPCNECEICKAITNGS   86 (559)
T ss_pred             cHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC-------CCCCCccHHHHHHhcCC
Confidence            3567999999999999998765          889999999999876432111000       11122222222222111


Q ss_pred             CcCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--ccccccc----CcCCCC------CcchhHhhh
Q 045120          190 GLEL------SEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVK----IPFRND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~----~~~~~~------TR~~~va~~  247 (374)
                      ....      ..... +....+.+...    .+++-++|+|++...  ..+..|.    .+.+..      |....+...
T Consensus        87 ~~dv~eidaas~~~v-d~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~t  165 (559)
T PRK05563         87 LMDVIEIDAASNNGV-DEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPAT  165 (559)
T ss_pred             CCCeEEeeccccCCH-HHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHH
Confidence            1100      00111 11222223222    235678899998743  2233322    221111      333322211


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      .......+.+.+++.++....+...+......-+ .+....|++.+ +|-+..
T Consensus       166 I~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i~-~~al~~ia~~s-~G~~R~  216 (559)
T PRK05563        166 ILSRCQRFDFKRISVEDIVERLKYILDKEGIEYE-DEALRLIARAA-EGGMRD  216 (559)
T ss_pred             HHhHheEEecCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHc-CCCHHH
Confidence            1122246888999999988888877642221111 34566788888 666543

>PRK08118 topology modulation protein; Reviewed

Probab=96.63  E-value=0.00089  Score=56.79  Aligned_cols=28  Identities=29%  Similarity=0.573  Sum_probs=22.8

Q ss_pred             CCCccHHHHHHHHHHHhhhc-CCCCeEEE
Q 045120          142 NGGIGKTTLAKEFAKQARED-KLFDRVVF  169 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~-~~F~~~~w  169 (374)
                      ++|+||||||+.+++..... -+||..+|
T Consensus         9 ~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          9 SGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             CCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            78999999999999976544 45777775

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=96.63  E-value=0.0061  Score=54.50  Aligned_cols=29  Identities=34%  Similarity=0.463  Sum_probs=22.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV  172 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v  172 (374)
                      ..|+|||||+..+..+..  +.|+.++.++-
T Consensus        21 ~sGSGKT~li~~lL~~~~--~~f~~I~l~t~   49 (241)
T PF04665_consen   21 KSGSGKTTLIKSLLYYLR--HKFDHIFLITP   49 (241)
T ss_pred             CCCCCHHHHHHHHHHhhc--ccCCEEEEEec
Confidence            789999999999987644  67877766643

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.62  E-value=0.043  Score=56.73  Aligned_cols=170  Identities=16%  Similarity=0.184  Sum_probs=88.7

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|-+..++.|.+++..+          +.|+||||+|+.+....-.....+         ...+.......   .
T Consensus        16 ~f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~---------~~~pC~~C~~~---~   83 (725)
T PRK07133         16 TFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTD---------LLEPCQECIEN---V   83 (725)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCC---------CCCchhHHHHh---h
Confidence            3556899999999999998775          889999999999877432111000         00000000000   0


Q ss_pred             CcCC--------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--ccccccc----CcCCCC------CcchhHh
Q 045120          190 GLEL--------SEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVK----IPFRND------SRDNNVV  245 (374)
Q Consensus       190 ~~~~--------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~----~~~~~~------TR~~~va  245 (374)
                      +...        .....+ ..+.+.+.+.    .+++-++|+|++...  ..+..|.    .|-+..      |....+.
T Consensus        84 ~~~~Dvieidaasn~~vd-~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl  162 (725)
T PRK07133         84 NNSLDIIEMDAASNNGVD-EIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIP  162 (725)
T ss_pred             cCCCcEEEEeccccCCHH-HHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhh
Confidence            0000        000111 1222333332    135668999998643  2233322    222221      3333443


Q ss_pred             hhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch-HHHHHH
Q 045120          246 LLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF-CTLTTN  304 (374)
Q Consensus       246 ~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP-Lai~~i  304 (374)
                      .........+++.+++.++....+...+......- -.+.+..|++.+ +|.+ .|+..+
T Consensus       163 ~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~i-d~eAl~~LA~lS-~GslR~AlslL  220 (725)
T PRK07133        163 LTILSRVQRFNFRRISEDEIVSRLEFILEKENISY-EKNALKLIAKLS-SGSLRDALSIA  220 (725)
T ss_pred             HHHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHHHHHH
Confidence            21222234899999999999888887653211111 134566888999 7765 444443

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.57  E-value=0.035  Score=50.51  Aligned_cols=81  Identities=26%  Similarity=0.375  Sum_probs=52.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC----CeEEEEEeCCCCCHHHHHHHHHHHhCcCCch-------------hhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF----DRVVFSEVSQTSDIKKIQGDIAEKLGLELSE-------------EAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~-------------~~~~~~~~~  204 (374)
                      .+|+|||.|+.+++-+.......    ..++|++-...|+..++. +|++..+.....             .........
T Consensus        46 ~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~~~l~~~L~~  124 (256)
T PF08423_consen   46 ESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDLEELLELLEQ  124 (256)
T ss_dssp             STTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSHHHHHHHHHH
T ss_pred             ecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCHHHHHHHHHH
Confidence            89999999999887654432211    358999999999988875 466665533111             122233445


Q ss_pred             HHHHHhcCCeEEEEEeCCC
Q 045120          205 LYERLKNENKILVILANIW  223 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~  223 (374)
                      +...+.+.+=-|||+|.+-
T Consensus       125 l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  125 LPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHSCEEEEEEETSS
T ss_pred             HHhhccccceEEEEecchH
Confidence            5555555466799999875

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.57  E-value=0.027  Score=52.80  Aligned_cols=40  Identities=18%  Similarity=0.292  Sum_probs=33.7

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~  158 (374)
                      .....++|.+...+.+..++..+          +.|+||||+|+.+++..
T Consensus        18 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~   67 (316)
T PHA02544         18 STIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV   67 (316)
T ss_pred             CcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            34567899999999999988765          78999999999998854

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.56  E-value=0.12  Score=46.41  Aligned_cols=51  Identities=8%  Similarity=-0.039  Sum_probs=34.4

Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      .+....+++++++++++-.+++.+.+..... .--+++..-|++.| .|-.-+
T Consensus       155 Rl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~-~l~~~v~~~L~~~~-~~d~r~  205 (235)
T PRK08084        155 RLDWGQIYKLQPLSDEEKLQALQLRARLRGF-ELPEDVGRFLLKRL-DREMRT  205 (235)
T ss_pred             HHhCCceeeecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhh-cCCHHH
Confidence            4555668999999999999999886643211 11145667788888 554433

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.55  E-value=0.059  Score=54.61  Aligned_cols=172  Identities=12%  Similarity=0.091  Sum_probs=88.2

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|-+..++.|.+++..+          +.|+||||+|+.+.+..-.......       ..++.....+.|...-
T Consensus        14 ~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~-------~pC~~C~~C~~i~~~~   86 (563)
T PRK06647         14 DFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP-------MPCGECSSCKSIDNDN   86 (563)
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCC-------CCCccchHHHHHHcCC
Confidence            3457899999999999999776          8899999999999875432111100       0000001111111110


Q ss_pred             CcC------CchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccccCcC---CCC-------CcchhHhhh
Q 045120          190 GLE------LSEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETVKIPF---RND-------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~------~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l~~~~---~~~-------TR~~~va~~  247 (374)
                      ...      ......++. ..+.+.+.    .+++-++|+|++....  .++.|...+   |..       |....+...
T Consensus        87 ~~dv~~idgas~~~vddI-r~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~t  165 (563)
T PRK06647         87 SLDVIEIDGASNTSVQDV-RQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPAT  165 (563)
T ss_pred             CCCeEEecCcccCCHHHH-HHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHH
Confidence            000      000111111 12221111    1256689999987542  233332222   122       333333221


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      .......+++.+++.++-...+...+...... --.+....|++.+ +|.+-.+
T Consensus       166 I~SRc~~~~f~~l~~~el~~~L~~i~~~egi~-id~eAl~lLa~~s-~GdlR~a  217 (563)
T PRK06647        166 IKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIK-YEDEALKWIAYKS-TGSVRDA  217 (563)
T ss_pred             HHHhceEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHH
Confidence            12223368899999999888888776422211 1135566788888 8877533

>PRK08181 transposase; Validated

Probab=96.53  E-value=0.077  Score=48.56  Aligned_cols=64  Identities=22%  Similarity=0.166  Sum_probs=36.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.||..+.+...-  ..-.++|+++      .+++..+.....    ..+.    ..+.+.+.  +-=||||||
T Consensus       114 p~GtGKTHLa~Aia~~a~~--~g~~v~f~~~------~~L~~~l~~a~~----~~~~----~~~l~~l~--~~dLLIIDD  175 (269)
T PRK08181        114 PPGGGKSHLAAAIGLALIE--NGWRVLFTRT------TDLVQKLQVARR----ELQL----ESAIAKLD--KFDLLILDD  175 (269)
T ss_pred             cCCCcHHHHHHHHHHHHHH--cCCceeeeeH------HHHHHHHHHHHh----CCcH----HHHHHHHh--cCCEEEEec
Confidence            8899999999999886532  2234566643      445554433211    1111    12233333  346999999


Q ss_pred             CC
Q 045120          222 IW  223 (374)
Q Consensus       222 v~  223 (374)
                      +-
T Consensus       176 lg  177 (269)
T PRK08181        176 LA  177 (269)
T ss_pred             cc
Confidence            85

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.48  E-value=0.11  Score=52.11  Aligned_cols=163  Identities=15%  Similarity=0.167  Sum_probs=85.9

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCC-------------------eEEEEE
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFD-------------------RVVFSE  171 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~-------------------~~~wv~  171 (374)
                      ...++|-+..++.+...+..+          ..|+||||+|+.+.+..-....-+                   .++.+.
T Consensus        13 fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eld   92 (535)
T PRK08451         13 FDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMD   92 (535)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEec
Confidence            456899999999999988766          779999999998877532111000                   111221


Q ss_pred             eCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--cccc----ccCcCCCC------C
Q 045120          172 VSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLET----VKIPFRND------S  239 (374)
Q Consensus       172 vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~----l~~~~~~~------T  239 (374)
                      .+....+..+. +++....                ..-..+++-++|+|++....  ..+.    +..+ |..      |
T Consensus        93 aas~~gId~IR-elie~~~----------------~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEp-p~~t~FIL~t  154 (535)
T PRK08451         93 AASNRGIDDIR-ELIEQTK----------------YKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEP-PSYVKFILAT  154 (535)
T ss_pred             cccccCHHHHH-HHHHHHh----------------hCcccCCeEEEEEECcccCCHHHHHHHHHHHhhc-CCceEEEEEE
Confidence            11111111111 1111110                00001245688899886432  1222    2222 222      2


Q ss_pred             cc-hhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHH
Q 045120          240 RD-NNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTT  303 (374)
Q Consensus       240 R~-~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~  303 (374)
                      .+ ..+..........+++.+++.++....+.+.+...... --.+....|++.+ +|.+--+..
T Consensus       155 td~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~-i~~~Al~~Ia~~s-~GdlR~aln  217 (535)
T PRK08451        155 TDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVS-YEPEALEILARSG-NGSLRDTLT  217 (535)
T ss_pred             CChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCcHHHHHH
Confidence            22 22211111123478999999999988887766422211 1135667899999 888854433

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.45  E-value=0.013  Score=62.32  Aligned_cols=38  Identities=21%  Similarity=0.404  Sum_probs=33.0

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      ..+++||+.++.++++.|+..         .+|+|||+||..+....
T Consensus       177 l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i  223 (857)
T PRK10865        177 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRI  223 (857)
T ss_pred             CCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHh
Confidence            356999999999999988764         88999999999998864

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.44  E-value=0.023  Score=52.59  Aligned_cols=22  Identities=14%  Similarity=0.119  Sum_probs=18.6

Q ss_pred             CceecCCCCHHHHHHHHHHhcC
Q 045120          253 DNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      ..+++++++.+|-.+++...+.
T Consensus       188 ~~i~fp~l~~edl~~I~~~~l~  209 (284)
T TIGR02880       188 HHVDFPDYSEAELLVIAGLMLK  209 (284)
T ss_pred             cEEEeCCcCHHHHHHHHHHHHH
Confidence            4688999999999999888764

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.43  E-value=0.07  Score=54.41  Aligned_cols=175  Identities=15%  Similarity=0.196  Sum_probs=87.5

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|-+..++.|.+.+..+          ..|+||||+|+.+.+..-.....+       ...++.......|...-
T Consensus        14 ~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~-------~~~c~~c~~c~~i~~g~   86 (576)
T PRK14965         14 TFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLT-------AEPCNVCPPCVEITEGR   86 (576)
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCC-------CCCCCccHHHHHHhcCC
Confidence            3567999999999999998775          889999999999887532211110       00111111111111100


Q ss_pred             CcCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--cccc----ccCcCCCC------CcchhHhhh
Q 045120          190 GLEL------SEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLET----VKIPFRND------SRDNNVVLL  247 (374)
Q Consensus       190 ~~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~----l~~~~~~~------TR~~~va~~  247 (374)
                      ....      .....+ .+..+.+.+.    .+++-++|+|++....  ..+.    +..+.+..      |....+...
T Consensus        87 ~~d~~eid~~s~~~v~-~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~t  165 (576)
T PRK14965         87 SVDVFEIDGASNTGVD-DIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPIT  165 (576)
T ss_pred             CCCeeeeeccCccCHH-HHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHH
Confidence            0000      000011 1222223222    1245578899986432  2222    22222222      333334321


Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch-HHHHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF-CTLTTN  304 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP-Lai~~i  304 (374)
                      .......+++.+++.++....+...+......- -.+....|++.+ +|.. .|+..+
T Consensus       166 I~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i-~~~al~~la~~a-~G~lr~al~~L  221 (576)
T PRK14965        166 ILSRCQRFDFRRIPLQKIVDRLRYIADQEGISI-SDAALALVARKG-DGSMRDSLSTL  221 (576)
T ss_pred             HHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHc-CCCHHHHHHHH
Confidence            222234688889999888877776654221111 134456788888 6644 455444

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.41  E-value=0.086  Score=52.08  Aligned_cols=38  Identities=34%  Similarity=0.380  Sum_probs=32.5

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~  158 (374)
                      ...++|.+..++.+.+++..+          ..|+||||+|+.+.+..
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l   63 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKAL   63 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            456899999999999998765          88999999999987754

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.38  E-value=0.025  Score=50.59  Aligned_cols=82  Identities=22%  Similarity=0.270  Sum_probs=50.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCcCC-------------chhhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKL----FDRVVFSEVSQTSDIKKIQGDIAEKLGLEL-------------SEEAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~-------------~~~~~~~~~~~  204 (374)
                      .+|+|||+||.++.-.......    -..++|++....++...+. ++++.++...             ...........
T Consensus        27 ~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~l~~  105 (235)
T cd01123          27 EFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLV-QIAERFGLDPEEVLDNIYVARAYNSDHQLQLLEE  105 (235)
T ss_pred             CCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHH-HHHHHhccChHhHhcCEEEEecCCHHHHHHHHHH
Confidence            8899999999998754332221    2578999988877765543 3344433211             11122234456


Q ss_pred             HHHHHhcC-CeEEEEEeCCCC
Q 045120          205 LYERLKNE-NKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~~-kr~LlVlDdv~~  224 (374)
                      +.+.+... +--|||+|.+..
T Consensus       106 l~~~l~~~~~~~liVIDSis~  126 (235)
T cd01123         106 LEAILIESSRIKLVIVDSVTA  126 (235)
T ss_pred             HHHHHhhcCCeeEEEEeCcHH
Confidence            66666664 678999998853

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 .

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

Probab=96.35  E-value=0.089  Score=51.04  Aligned_cols=41  Identities=24%  Similarity=0.268  Sum_probs=31.4

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      .....+.|.+..+++|.+.+..+                      +.|+|||+||+.+.+...
T Consensus       142 v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~  204 (398)
T PTZ00454        142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTT  204 (398)
T ss_pred             CCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcC
Confidence            33456889998888887766421                      889999999999998543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.34  E-value=0.14  Score=52.63  Aligned_cols=173  Identities=15%  Similarity=0.112  Sum_probs=89.0

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|.+..+..|.+++..+          ..|+||||+|+.+.+..-.......     ....+......+.+.....
T Consensus        15 f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~-----~~~~Cg~C~~C~~i~~g~h   89 (620)
T PRK14948         15 FDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKP-----TPEPCGKCELCRAIAAGNA   89 (620)
T ss_pred             HhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCC-----CCCCCcccHHHHHHhcCCC
Confidence            456889999999999888765          7899999999999886532211100     0112222333333332222


Q ss_pred             cCC------chhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccccC----cCCCC-----C-cchhHhhhh
Q 045120          191 LEL------SEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETVKI----PFRND-----S-RDNNVVLLS  248 (374)
Q Consensus       191 ~~~------~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l~~----~~~~~-----T-R~~~va~~~  248 (374)
                      ...      .....+ .++.+.+.+.    .+++-++|+|++....  ..+.|..    +.+..     | ....+....
T Consensus        90 ~D~~ei~~~~~~~vd-~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTI  168 (620)
T PRK14948         90 LDVIEIDAASNTGVD-NIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTI  168 (620)
T ss_pred             ccEEEEeccccCCHH-HHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHH
Confidence            110      001111 1122222222    1245688999987542  2333222    11111     2 222222111


Q ss_pred             cCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       249 ~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      ......+.+..++.++....+.+.+......- -.+....|++.+ +|.+..+
T Consensus       169 rSRc~~~~f~~l~~~ei~~~L~~ia~kegi~i-s~~al~~La~~s-~G~lr~A  219 (620)
T PRK14948        169 ISRCQRFDFRRIPLEAMVQHLSEIAEKESIEI-EPEALTLVAQRS-QGGLRDA  219 (620)
T ss_pred             HhheeEEEecCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHc-CCCHHHH
Confidence            12224678889999988887777664321111 124567888999 7766543

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.32  E-value=0.024  Score=51.75  Aligned_cols=81  Identities=20%  Similarity=0.316  Sum_probs=50.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC-CeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF-DRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLY  206 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F-~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~  206 (374)
                      ..|+|||||++.++++.+.  +| +.++++-++... ...++.+++...=...       ..+++..      ...-.+.
T Consensus        77 ~~G~GKTtLa~~i~~~i~~--~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~~~a~~~A  154 (274)
T cd01133          77 GAGVGKTVLIMELINNIAK--AHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVALTGLTMA  154 (274)
T ss_pred             CCCCChhHHHHHHHHHHHh--cCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            7799999999999997663  35 556777777765 3455655555421111       1111111      1233566


Q ss_pred             HHHh-c-CCeEEEEEeCCCC
Q 045120          207 ERLK-N-ENKILVILANIWK  224 (374)
Q Consensus       207 ~~L~-~-~kr~LlVlDdv~~  224 (374)
                      ++++ . ++..||++||+..
T Consensus       155 Eyfr~~~g~~Vl~~~Dsltr  174 (274)
T cd01133         155 EYFRDEEGQDVLLFIDNIFR  174 (274)
T ss_pred             HHHHHhcCCeEEEEEeChhH
Confidence            6664 2 4899999999854

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>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=96.32  E-value=0.0093  Score=47.77  Aligned_cols=18  Identities=44%  Similarity=0.545  Sum_probs=16.0

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.+...
T Consensus         6 ~~G~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    6 PPGTGKTTLARALAQYLG   23 (132)
T ss_dssp             STTSSHHHHHHHHHHHTT
T ss_pred             cCCCCeeHHHHHHHhhcc
Confidence            689999999999999753

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 ....

>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=96.31  E-value=0.015  Score=51.61  Aligned_cols=141  Identities=16%  Similarity=0.136  Sum_probs=69.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.|.+++++.......=..+++++      ..++...+...+...        ....+++.+..  -=+|+|||
T Consensus        42 ~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~------~~~f~~~~~~~~~~~--------~~~~~~~~~~~--~DlL~iDD  105 (219)
T PF00308_consen   42 PSGLGKTHLLQAIANEAQKQHPGKRVVYLS------AEEFIREFADALRDG--------EIEEFKDRLRS--ADLLIIDD  105 (219)
T ss_dssp             STTSSHHHHHHHHHHHHHHHCTTS-EEEEE------HHHHHHHHHHHHHTT--------SHHHHHHHHCT--SSEEEEET
T ss_pred             CCCCCHHHHHHHHHHHHHhccccccceeec------HHHHHHHHHHHHHcc--------cchhhhhhhhc--CCEEEEec
Confidence            789999999999999765322112355654      344444444444221        11223333332  34566666


Q ss_pred             CCCccc---ccc-cc---C--------------cCCCC--CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCC
Q 045120          222 IWKLLD---LET-VK---I--------------PFRND--SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVE  278 (374)
Q Consensus       222 v~~~~~---~~~-l~---~--------------~~~~~--TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~  278 (374)
                      +.....   |.. +.   .              ..|..  .-...+. ..+...-++++++++.++-.+++.+.+.....
T Consensus       106 i~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~-SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~  184 (219)
T PF00308_consen  106 IQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLR-SRLSWGLVVELQPPDDEDRRRILQKKAKERGI  184 (219)
T ss_dssp             GGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHH-HHHHCSEEEEE----HHHHHHHHHHHHHHTT-
T ss_pred             chhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhh-hhHhhcchhhcCCCCHHHHHHHHHHHHHHhCC
Confidence            643211   111 00   0              00111  2223332 24555568999999999999999998862221


Q ss_pred             CcchHHHHHHHHHHccCCchHHH
Q 045120          279 NCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       279 ~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      . --.++..-|++.+ .+..-.+
T Consensus       185 ~-l~~~v~~~l~~~~-~~~~r~L  205 (219)
T PF00308_consen  185 E-LPEEVIEYLARRF-RRDVREL  205 (219)
T ss_dssp             --S-HHHHHHHHHHT-TSSHHHH
T ss_pred             C-CcHHHHHHHHHhh-cCCHHHH
Confidence            1 1135666777777 5544433

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.

>CHL00181 cbbX CbbX; Provisional

Probab=96.31  E-value=0.073  Score=49.30  Aligned_cols=22  Identities=27%  Similarity=0.294  Sum_probs=17.6

Q ss_pred             CceecCCCCHHHHHHHHHHhcC
Q 045120          253 DNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      ..+.+++++.++..+++...+.
T Consensus       189 ~~i~F~~~t~~el~~I~~~~l~  210 (287)
T CHL00181        189 NHVDFPDYTPEELLQIAKIMLE  210 (287)
T ss_pred             ceEEcCCcCHHHHHHHHHHHHH
Confidence            3688888888888888887764

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

Probab=96.29  E-value=0.016  Score=60.60  Aligned_cols=137  Identities=17%  Similarity=0.275  Sum_probs=77.0

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcC-C---CCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDK-L---FDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~-~---F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .+++||+.++.++++.|...         ..|+|||+||+.+........ .   .++.+|..     ++..++    . 
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l-----~~~~ll----a-  255 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL-----DIGSLL----A-  255 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEec-----cHHHHh----c-
Confidence            46999999999999988764         889999999999987542111 1   24445421     222111    0 


Q ss_pred             hCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc----------ccccc-ccCcCCCC-------CcchhH------
Q 045120          189 LGLELSEEAEYRRASRLYERLKNENKILVILANIWKL----------LDLET-VKIPFRND-------SRDNNV------  244 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~----------~~~~~-l~~~~~~~-------TR~~~v------  244 (374)
                       +.... ..-+.....+.+.+...+..+|++|++...          .+... +...+..+       |.....      
T Consensus       256 -G~~~~-Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~g~i~vIgATt~~E~~~~~~~  333 (758)
T PRK11034        256 -GTKYR-GDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEK  333 (758)
T ss_pred             -ccchh-hhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhCCCeEEEecCChHHHHHHhhc
Confidence             11111 122233344444444335789999998632          11222 22222222       322221      


Q ss_pred             --h-hhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          245 --V-LLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       245 --a-~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                        + ...+   ..+.+++.+.++..+++....
T Consensus       334 D~AL~rRF---q~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        334 DRALARRF---QKIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             cHHHHhhC---cEEEeCCCCHHHHHHHHHHHH
Confidence              1 1122   368999999999999988653

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

Probab=96.27  E-value=0.056  Score=48.26  Aligned_cols=44  Identities=11%  Similarity=0.142  Sum_probs=32.7

Q ss_pred             ccccccccccHHHHHHHHHHh---hcC----------CCCccHHHHHHHHHHHhhhc
Q 045120          118 NKVYEAFESRVSNLKSTQNAL---TNA----------NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L---~~~----------~gGiGKTtLA~~v~~~~~~~  161 (374)
                      +.....++|.|..++.|++-.   ..+          ..|+|||+|++.+.+...-+
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc
Confidence            344567999999988876533   222          88999999999999866543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.26  E-value=0.03  Score=49.82  Aligned_cols=52  Identities=4%  Similarity=-0.075  Sum_probs=34.9

Q ss_pred             CCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          252 KDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       252 ~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      ...+.+++|++++-..++.+.+...... --.+....+++.+ .|.|..+..+-
T Consensus       149 ~~~i~l~pl~~~~~~~~l~~~~~~~~v~-l~~~al~~L~~~~-~gn~~~l~~~l  200 (227)
T PRK08903        149 GLVYELKPLSDADKIAALKAAAAERGLQ-LADEVPDYLLTHF-RRDMPSLMALL  200 (227)
T ss_pred             CeEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhc-cCCHHHHHHHH
Confidence            3588999999988777777654321111 1135666788888 99988876554

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.21  E-value=0.032  Score=48.92  Aligned_cols=78  Identities=15%  Similarity=0.153  Sum_probs=47.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh----CcC------CchhhHHHHHHHHHHHHhc
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL----GLE------LSEEAEYRRASRLYERLKN  211 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l----~~~------~~~~~~~~~~~~l~~~L~~  211 (374)
                      .+|+|||+||.++..+..  ..-..++|++... ++...+.+. ++..    ...      ............+.+.+..
T Consensus        20 ~~GsGKT~l~~~~~~~~~--~~g~~v~yi~~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~   95 (209)
T TIGR02237        20 PPGSGKTNICMILAVNAA--RQGKKVVYIDTEG-LSPERFKQI-AEDRPERALSNFIVFEVFDFDEQGVAIQKTSKFIDR   95 (209)
T ss_pred             CCCCCHHHHHHHHHHHHH--hCCCeEEEEECCC-CCHHHHHHH-HHhChHHHhcCEEEEECCCHHHHHHHHHHHHHHHhh
Confidence            889999999999877543  2346789998875 666555443 2221    011      0111222335556666654


Q ss_pred             CCeEEEEEeCCC
Q 045120          212 ENKILVILANIW  223 (374)
Q Consensus       212 ~kr~LlVlDdv~  223 (374)
                      .+.-+||+|.+.
T Consensus        96 ~~~~lvVIDSis  107 (209)
T TIGR02237        96 DSASLVVVDSFT  107 (209)
T ss_pred             cCccEEEEeCcH
Confidence            356689999874

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.16  E-value=0.03  Score=59.79  Aligned_cols=37  Identities=22%  Similarity=0.428  Sum_probs=32.5

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      .+++||+.++.+++..|...         .+|+|||+||..+....
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i  218 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRI  218 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            46999999999999988764         88999999999988864

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.08  E-value=0.13  Score=51.18  Aligned_cols=78  Identities=22%  Similarity=0.285  Sum_probs=38.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCcCCchh-hHHHHHHHHHHHHhcCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI--KKIQGDIAEKLGLELSEE-AEYRRASRLYERLKNENKILVI  218 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~~~~-~~~~~~~~l~~~L~~~kr~LlV  218 (374)
                      .+|+||||++..+......+.....+..++.. .+..  ..-+......++...... +...+...+ +.+.  ..-+|+
T Consensus       358 PtGvGKTTtaakLAa~la~~~~gkkVaLIdtD-tyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL-~~l~--~~DLVL  433 (559)
T PRK12727        358 PTGAGKTTTIAKLAQRFAAQHAPRDVALVTTD-TQRVGGREQLHSYGRQLGIAVHEADSAESLLDLL-ERLR--DYKLVL  433 (559)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCCceEEEecc-cccccHHHHHHHhhcccCceeEecCcHHHHHHHH-HHhc--cCCEEE
Confidence            78999999998887754432222345555432 2222  222333333444332221 222233333 3333  356888


Q ss_pred             EeCCC
Q 045120          219 LANIW  223 (374)
Q Consensus       219 lDdv~  223 (374)
                      +|..-
T Consensus       434 IDTaG  438 (559)
T PRK12727        434 IDTAG  438 (559)
T ss_pred             ecCCC
Confidence            88763

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.06  E-value=0.013  Score=53.49  Aligned_cols=22  Identities=18%  Similarity=0.051  Sum_probs=18.0

Q ss_pred             CceecCCCCHHHHHHHHHHhcC
Q 045120          253 DNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      ..+.+++++.++-.+++.+.+.
T Consensus       171 ~~i~f~~~~~~el~~Il~~~~~  192 (261)
T TIGR02881       171 ISIDFPDYTVEELMEIAERMVK  192 (261)
T ss_pred             eEEEECCCCHHHHHHHHHHHHH
Confidence            3578889999999999887775

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.98  E-value=0.049  Score=53.66  Aligned_cols=138  Identities=14%  Similarity=0.140  Sum_probs=74.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFD-RVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILA  220 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlD  220 (374)
                      ..|+|||+|++.+.+.... .+.+ .++|++.      .++...+...+...    +    ...+.+.+.. +.-+|+||
T Consensus       138 ~~G~GKTHLl~ai~~~l~~-~~~~~~v~yi~~------~~f~~~~~~~~~~~----~----~~~f~~~~~~-~~dvLlID  201 (440)
T PRK14088        138 GVGLGKTHLLQSIGNYVVQ-NEPDLRVMYITS------EKFLNDLVDSMKEG----K----LNEFREKYRK-KVDVLLID  201 (440)
T ss_pred             CCCCcHHHHHHHHHHHHHH-hCCCCeEEEEEH------HHHHHHHHHHHhcc----c----HHHHHHHHHh-cCCEEEEe
Confidence            8899999999999997542 2233 4566653      44555665555321    1    1233334433 45689999


Q ss_pred             CCCCcc---cc-ccccCc----CCCC------C-cch----hHh---hhhcCCCCceecCCCCHHHHHHHHHHhcCCCCC
Q 045120          221 NIWKLL---DL-ETVKIP----FRND------S-RDN----NVV---LLSMGSKDNFLIANITEEEAWRLFKIMNGDDVE  278 (374)
Q Consensus       221 dv~~~~---~~-~~l~~~----~~~~------T-R~~----~va---~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~  278 (374)
                      |+....   .. +.+...    ...+      | +..    .+.   ...+....++.+++.+.+.-..++.+.+.....
T Consensus       202 Di~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~  281 (440)
T PRK14088        202 DVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIEHG  281 (440)
T ss_pred             chhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHHhcCC
Confidence            997421   01 111110    0111      1 111    110   112334457899999999999999988752211


Q ss_pred             CcchHHHHHHHHHHccCCc
Q 045120          279 NCKFKSTAINVAKACGAGL  297 (374)
Q Consensus       279 ~~~l~~~~~~I~~~c~~Gl  297 (374)
                      .- -.++..-|++.+ .|.
T Consensus       282 ~l-~~ev~~~Ia~~~-~~~  298 (440)
T PRK14088        282 EL-PEEVLNFVAENV-DDN  298 (440)
T ss_pred             CC-CHHHHHHHHhcc-ccC
Confidence            10 134566677766 553

>PRK08116 hypothetical protein; Validated

Probab=95.92  E-value=0.042  Score=50.38  Aligned_cols=67  Identities=25%  Similarity=0.255  Sum_probs=40.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.||.++++.....  -..+++++      ..+++..|...+..... .+    ...+.+.+.+  -=||||||
T Consensus       122 ~~GtGKThLa~aia~~l~~~--~~~v~~~~------~~~ll~~i~~~~~~~~~-~~----~~~~~~~l~~--~dlLviDD  186 (268)
T PRK08116        122 SVGTGKTYLAACIANELIEK--GVPVIFVN------FPQLLNRIKSTYKSSGK-ED----ENEIIRSLVN--ADLLILDD  186 (268)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCeEEEEE------HHHHHHHHHHHHhcccc-cc----HHHHHHHhcC--CCEEEEec
Confidence            78999999999999976533  23456664      34455555555432211 11    1233444444  23899999


Q ss_pred             CC
Q 045120          222 IW  223 (374)
Q Consensus       222 v~  223 (374)
                      +-
T Consensus       187 lg  188 (268)
T PRK08116        187 LG  188 (268)
T ss_pred             cc
Confidence            94

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

Probab=95.92  E-value=0.012  Score=57.50  Aligned_cols=125  Identities=20%  Similarity=0.253  Sum_probs=74.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHH----HHhcCCeEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYE----RLKNENKILV  217 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~----~L~~~kr~Ll  217 (374)
                      ++|+|||+||..+...    ..|+.+--++-..-..                  .++......+.+    ..+. .--.|
T Consensus       546 p~~sGKTaLAA~iA~~----S~FPFvKiiSpe~miG------------------~sEsaKc~~i~k~F~DAYkS-~lsii  602 (744)
T KOG0741|consen  546 PPGSGKTALAAKIALS----SDFPFVKIISPEDMIG------------------LSESAKCAHIKKIFEDAYKS-PLSII  602 (744)
T ss_pred             CCCCChHHHHHHHHhh----cCCCeEEEeChHHccC------------------ccHHHHHHHHHHHHHHhhcC-cceEE
Confidence            8899999999999863    4477654443211111                  122222233333    3334 56789


Q ss_pred             EEeCCCCccccccccCcCCCC------------------------CcchhHhhhhcCC----CCceecCCCCH-HHHHHH
Q 045120          218 ILANIWKLLDLETVKIPFRND------------------------SRDNNVVLLSMGS----KDNFLIANITE-EEAWRL  268 (374)
Q Consensus       218 VlDdv~~~~~~~~l~~~~~~~------------------------TR~~~va~~~~~~----~~~~~l~~L~~-~~s~~L  268 (374)
                      |+||+...-+|-.+++.+.+.                        |....+.. .|+-    ...|+++.|+. ++..+.
T Consensus       603 vvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~-~m~i~~~F~~~i~Vpnl~~~~~~~~v  681 (744)
T KOG0741|consen  603 VVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQ-EMGILDCFSSTIHVPNLTTGEQLLEV  681 (744)
T ss_pred             EEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHH-HcCHHHhhhheeecCccCchHHHHHH
Confidence            999999888888887765443                        44455542 3332    24788888887 777777


Q ss_pred             HHHhc-CCCCCCcchHHHHHHHHHHc
Q 045120          269 FKIMN-GDDVENCKFKSTAINVAKAC  293 (374)
Q Consensus       269 f~~~a-~~~~~~~~l~~~~~~I~~~c  293 (374)
                      ++..- |.   +.+...++++...+|
T Consensus       682 l~~~n~fs---d~~~~~~~~~~~~~~  704 (744)
T KOG0741|consen  682 LEELNIFS---DDEVRAIAEQLLSKK  704 (744)
T ss_pred             HHHccCCC---cchhHHHHHHHhccc
Confidence            77654 32   233345555555554

>PHA00729 NTP-binding motif containing protein

Probab=95.86  E-value=0.049  Score=48.25  Aligned_cols=23  Identities=4%  Similarity=-0.038  Sum_probs=18.5

Q ss_pred             CCceecCCCCHHHHHHHHHHhcC
Q 045120          252 KDNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       252 ~~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      ...+.+.++++++..+++.....
T Consensus       119 ~~l~il~~ls~edL~~~Lr~Rg~  141 (226)
T PHA00729        119 VSAVIFTTPSPEDLAFYLREKGW  141 (226)
T ss_pred             CcEEEEecCCHHHHHHHHHhCCC
Confidence            34688999999999999987553

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=95.79  E-value=0.088  Score=51.32  Aligned_cols=139  Identities=16%  Similarity=0.132  Sum_probs=75.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||+|++.+++.......=-.++|++      ..++...+...+...        ....+.+.+.+  .-+|||||
T Consensus       144 ~~G~GKThL~~ai~~~l~~~~~~~~v~yi~------~~~~~~~~~~~~~~~--------~~~~~~~~~~~--~dlLiiDD  207 (405)
T TIGR00362       144 GVGLGKTHLLHAIGNEILENNPNAKVVYVS------SEKFTNDFVNALRNN--------KMEEFKEKYRS--VDLLLIDD  207 (405)
T ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCcEEEEE------HHHHHHHHHHHHHcC--------CHHHHHHHHHh--CCEEEEeh
Confidence            889999999999999765321112345654      334444555544321        12233444443  34888999


Q ss_pred             CCCccc---c-ccccC---cC-CCC-------Ccc--------hhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCC
Q 045120          222 IWKLLD---L-ETVKI---PF-RND-------SRD--------NNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVE  278 (374)
Q Consensus       222 v~~~~~---~-~~l~~---~~-~~~-------TR~--------~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~  278 (374)
                      +.....   + +.+..   .+ ..+       ++.        ..+ ...+.....+.+++.+.++-..++.+.+.....
T Consensus       208 i~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l-~SRl~~g~~v~i~~pd~~~r~~il~~~~~~~~~  286 (405)
T TIGR00362       208 IQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERL-RSRFEWGLVVDIEPPDLETRLAILQKKAEEEGL  286 (405)
T ss_pred             hhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhh-hhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCC
Confidence            974311   1 11110   00 111       111        111 123333457899999999999999998863221


Q ss_pred             CcchHHHHHHHHHHccCCchH
Q 045120          279 NCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       279 ~~~l~~~~~~I~~~c~~GlPL  299 (374)
                      .- -.++..-|++.+ .|.+-
T Consensus       287 ~l-~~e~l~~ia~~~-~~~~r  305 (405)
T TIGR00362       287 EL-PDEVLEFIAKNI-RSNVR  305 (405)
T ss_pred             CC-CHHHHHHHHHhc-CCCHH
Confidence            11 135666778888 66544

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).

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

Probab=95.77  E-value=0.062  Score=48.82  Aligned_cols=66  Identities=23%  Similarity=0.277  Sum_probs=41.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.||.++.+... +..+ .+.|++      ..++.+++......       .....+|.+.+.  +-=||||||
T Consensus       113 ~~G~GKThLa~Ai~~~l~-~~g~-sv~f~~------~~el~~~Lk~~~~~-------~~~~~~l~~~l~--~~dlLIiDD  175 (254)
T COG1484         113 PPGVGKTHLAIAIGNELL-KAGI-SVLFIT------APDLLSKLKAAFDE-------GRLEEKLLRELK--KVDLLIIDD  175 (254)
T ss_pred             CCCCcHHHHHHHHHHHHH-HcCC-eEEEEE------HHHHHHHHHHHHhc-------CchHHHHHHHhh--cCCEEEEec
Confidence            889999999999999876 4333 345553      45566666555532       112234444343  346999999


Q ss_pred             CCC
Q 045120          222 IWK  224 (374)
Q Consensus       222 v~~  224 (374)
                      +--
T Consensus       176 lG~  178 (254)
T COG1484         176 IGY  178 (254)
T ss_pred             ccC
Confidence            854

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=95.76  E-value=0.075  Score=49.79  Aligned_cols=82  Identities=21%  Similarity=0.245  Sum_probs=51.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch----------hhHH---HHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDK----LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE----------EAEY---RRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~----------~~~~---~~~~~  204 (374)
                      ..|+|||+|+.+++-......    .=..++||+....|++.++.+ +++.++.....          .+.+   +....
T Consensus       104 ~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~-~a~~~g~d~~~~l~~i~~~~~~~~e~~~~~l~~  182 (313)
T TIGR02238       104 EFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA-IAERFGVDPDAVLDNILYARAYTSEHQMELLDY  182 (313)
T ss_pred             CCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH-HHHHcCCChHHhcCcEEEecCCCHHHHHHHHHH
Confidence            889999999988764332211    114689999999899888754 56766543211          1222   23344


Q ss_pred             HHHHHhcCCeEEEEEeCCCC
Q 045120          205 LYERLKNENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~~  224 (374)
                      +...+..++--|||+|.+..
T Consensus       183 l~~~i~~~~~~LvVIDSisa  202 (313)
T TIGR02238       183 LAAKFSEEPFRLLIVDSIMA  202 (313)
T ss_pred             HHHHhhccCCCEEEEEcchH
Confidence            45455543566899998753

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

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

Probab=95.72  E-value=0.11  Score=51.70  Aligned_cols=169  Identities=15%  Similarity=0.184  Sum_probs=91.7

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ..+++|-+.-+..|.+.+..+          +-|+||||+|+-+..-.-..+      + .....++.....+.|...-.
T Consensus        15 F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~------~-~~~ePC~~C~~Ck~I~~g~~   87 (515)
T COG2812          15 FDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCEN------G-PTAEPCGKCISCKEINEGSL   87 (515)
T ss_pred             HHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCC------C-CCCCcchhhhhhHhhhcCCc
Confidence            456899999999999998876          779999999998877432211      1 11223333333344433311


Q ss_pred             cCCchh-----hHHHHHHHHHHHHh----cCCeEEEEEeCCCC--ccccccc----cCcCCCC-----Ccc-hhHhhhhc
Q 045120          191 LELSEE-----AEYRRASRLYERLK----NENKILVILANIWK--LLDLETV----KIPFRND-----SRD-NNVVLLSM  249 (374)
Q Consensus       191 ~~~~~~-----~~~~~~~~l~~~L~----~~kr~LlVlDdv~~--~~~~~~l----~~~~~~~-----TR~-~~va~~~~  249 (374)
                      ...-+.     +.-+-.+.|.+...    .++-=..|+|.|.-  ...|..+    ..|.+.-     |++ ..+.....
T Consensus        88 ~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIl  167 (515)
T COG2812          88 IDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTIL  167 (515)
T ss_pred             ccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhh
Confidence            111010     11122333444433    23445788999863  3334443    3333332     333 33433333


Q ss_pred             CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch
Q 045120          250 GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF  298 (374)
Q Consensus       250 ~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP  298 (374)
                      .....|.++.|+.++-...+...+....-.-+ .+...-|++.. +|..
T Consensus       168 SRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e-~~aL~~ia~~a-~Gs~  214 (515)
T COG2812         168 SRCQRFDFKRLDLEEIAKHLAAILDKEGINIE-EDALSLIARAA-EGSL  214 (515)
T ss_pred             hccccccccCCCHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHc-CCCh
Confidence            44457899999999888888777753221111 23334566666 6643

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=95.68  E-value=0.098  Score=49.57  Aligned_cols=82  Identities=20%  Similarity=0.189  Sum_probs=51.5

Q ss_pred             CCCccHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch----------hhHHH---HHHH
Q 045120          142 NGGIGKTTLAKEFAKQARED---K-LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE----------EAEYR---RASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~----------~~~~~---~~~~  204 (374)
                      ..|+|||+|+.+++-.....   + .-..++||+....|++.++.+ +++.++.....          .+.++   ....
T Consensus       134 ~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~~~~~~~e~~~~~l~~  212 (344)
T PLN03187        134 EFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIYARAYTYEHQYNLLLG  212 (344)
T ss_pred             CCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEEecCCCHHHHHHHHHH
Confidence            88999999998886433221   1 124689999999999888765 56666554211          12222   3334


Q ss_pred             HHHHHhcCCeEEEEEeCCCC
Q 045120          205 LYERLKNENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~~  224 (374)
                      +...+...+--|||+|.+..
T Consensus       213 l~~~i~~~~~~LvVIDSita  232 (344)
T PLN03187        213 LAAKMAEEPFRLLIVDSVIA  232 (344)
T ss_pred             HHHHHHhcCCCEEEEeCcHH
Confidence            44445443556899998753

>PRK04132 replication factor C small subunit; Provisional

Probab=95.67  E-value=0.33  Score=51.37  Aligned_cols=142  Identities=9%  Similarity=0.098  Sum_probs=77.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC-CeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF-DRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILA  220 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlD  220 (374)
                      +-++||||+|..+.++.--. .+ ..++-++.|...+...+. +++..+....+              +.+.+.-++|||
T Consensus       574 Ph~lGKTT~A~ala~~l~g~-~~~~~~lElNASd~rgid~IR-~iIk~~a~~~~--------------~~~~~~KVvIID  637 (846)
T PRK04132        574 PTVLHNTTAALALARELFGE-NWRHNFLELNASDERGINVIR-EKVKEFARTKP--------------IGGASFKIIFLD  637 (846)
T ss_pred             CCcccHHHHHHHHHHhhhcc-cccCeEEEEeCCCcccHHHHH-HHHHHHHhcCC--------------cCCCCCEEEEEE
Confidence            66899999999999864221 22 246777777665555433 33333211100              001145788899


Q ss_pred             CCCCcc--ccccccCc---CCCC-------CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 045120          221 NIWKLL--DLETVKIP---FRND-------SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAIN  288 (374)
Q Consensus       221 dv~~~~--~~~~l~~~---~~~~-------TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~  288 (374)
                      ++....  ....|...   .+..       +....+..........+.+.+++.++-.+.+...+......- -.+....
T Consensus       638 EaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i-~~e~L~~  716 (846)
T PRK04132        638 EADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLEL-TEEGLQA  716 (846)
T ss_pred             CcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCC-CHHHHHH
Confidence            887542  22222211   1122       222222111112224789999999998888887664221111 1346678


Q ss_pred             HHHHccCCchHHH
Q 045120          289 VAKACGAGLFCTL  301 (374)
Q Consensus       289 I~~~c~~GlPLai  301 (374)
                      |++.| +|-+-.+
T Consensus       717 Ia~~s-~GDlR~A  728 (846)
T PRK04132        717 ILYIA-EGDMRRA  728 (846)
T ss_pred             HHHHc-CCCHHHH
Confidence            99999 8877433

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.63  E-value=0.095  Score=46.54  Aligned_cols=77  Identities=21%  Similarity=0.199  Sum_probs=44.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH----hCcC------CchhhHHHHHHHHHHHHhc
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEK----LGLE------LSEEAEYRRASRLYERLKN  211 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~----l~~~------~~~~~~~~~~~~l~~~L~~  211 (374)
                      .+|+|||+||.++..+...  .-..++|++.. .++...+.+ +...    +..+      .......+..+.+...+..
T Consensus        31 ~~GsGKT~l~~~la~~~~~--~~~~v~yi~~e-~~~~~r~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  106 (225)
T PRK09361         31 PPGSGKTNICLQLAVEAAK--NGKKVIYIDTE-GLSPERFKQ-IAGEDFEELLSNIIIFEPSSFEEQSEAIRKAEKLAKE  106 (225)
T ss_pred             CCCCCHHHHHHHHHHHHHH--CCCeEEEEECC-CCCHHHHHH-HHhhChHhHhhCeEEEeCCCHHHHHHHHHHHHHHHHh
Confidence            8899999999998876542  24578899877 555554432 2222    1000      0001122233444445544


Q ss_pred             CCeEEEEEeCCC
Q 045120          212 ENKILVILANIW  223 (374)
Q Consensus       212 ~kr~LlVlDdv~  223 (374)
                       +--++|+|.+.
T Consensus       107 -~~~lvVIDsi~  117 (225)
T PRK09361        107 -NVGLIVLDSAT  117 (225)
T ss_pred             -cccEEEEeCcH
Confidence             67799999874

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=95.61  E-value=0.41  Score=44.90  Aligned_cols=178  Identities=13%  Similarity=0.159  Sum_probs=92.2

Q ss_pred             ccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcC-------------CCCeEEEEEeCCCCCH
Q 045120          122 EAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDK-------------LFDRVVFSEVSQTSDI  178 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~-------------~F~~~~wv~vs~~~~~  178 (374)
                      ..++|-+..++.+.+.+..+          ..|+||+++|..+.+..-...             .++-..|+.-....+-
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~g   83 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQG   83 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccccc
Confidence            45889999999999998766          779999999988876532111             1222344421100000


Q ss_pred             HHHHHHHHHHhCc--CCchhhHHHHHHHHHHHHhc----CCeEEEEEeCCCCcc--c----cccccCcCCCC------Cc
Q 045120          179 KKIQGDIAEKLGL--ELSEEAEYRRASRLYERLKN----ENKILVILANIWKLL--D----LETVKIPFRND------SR  240 (374)
Q Consensus       179 ~~~~~~i~~~l~~--~~~~~~~~~~~~~l~~~L~~----~kr~LlVlDdv~~~~--~----~~~l~~~~~~~------TR  240 (374)
                      ..+-..-+...+.  .....-.-+..+.+.+.+..    +++-++|+|++..-.  .    +..+..| |..      +.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEP-p~~~fILi~~~  162 (314)
T PRK07399         84 KLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEP-GNGTLILIAPS  162 (314)
T ss_pred             cccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCC-CCCeEEEEECC
Confidence            0000001111110  00000001123345555541    356788899886432  1    2233333 233      22


Q ss_pred             chhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          241 DNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       241 ~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      ...+..........+++.+++.++..+.+.+........    .....++..+ +|.|..+...-
T Consensus       163 ~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~~~----~~~~~l~~~a-~Gs~~~al~~l  222 (314)
T PRK07399        163 PESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEILN----INFPELLALA-QGSPGAAIANI  222 (314)
T ss_pred             hHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhccccch----hHHHHHHHHc-CCCHHHHHHHH
Confidence            222222222233478999999999999999865321111    1124788889 99997654433

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.57  E-value=0.044  Score=51.36  Aligned_cols=76  Identities=22%  Similarity=0.251  Sum_probs=49.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCC------chhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLEL------SEEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~------~~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ++|+||||||.+++.....  .-..++|++....+++.     .+++++...      ...+.++....+...++.+.--
T Consensus        63 p~GsGKTtLal~~~~~~~~--~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~s~~~~  135 (325)
T cd00983          63 PESSGKTTLALHAIAEAQK--LGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIADSLVRSGAVD  135 (325)
T ss_pred             CCCCCHHHHHHHHHHHHHH--cCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHHHHHhccCCC
Confidence            8899999999998765432  23568899887777653     345555431      1123444555555555554677


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      +||+|-|..
T Consensus       136 lIVIDSvaa  144 (325)
T cd00983         136 LIVVDSVAA  144 (325)
T ss_pred             EEEEcchHh
Confidence            999998753

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=95.55  E-value=0.091  Score=52.00  Aligned_cols=139  Identities=15%  Similarity=0.094  Sum_probs=74.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||+|++.+.+.......--.++|++.      .++...+...+...        ....+.+.++.  .-+|||||
T Consensus       156 ~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~------~~~~~~~~~~~~~~--------~~~~~~~~~~~--~dlLiiDD  219 (450)
T PRK00149        156 GVGLGKTHLLHAIGNYILEKNPNAKVVYVTS------EKFTNDFVNALRNN--------TMEEFKEKYRS--VDVLLIDD  219 (450)
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHHcC--------cHHHHHHHHhc--CCEEEEeh
Confidence            8899999999999997652211123456543      33344444444211        11234444443  45889999


Q ss_pred             CCCccc---c-ccccC---c-CCCC-------Ccc--------hhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCC
Q 045120          222 IWKLLD---L-ETVKI---P-FRND-------SRD--------NNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVE  278 (374)
Q Consensus       222 v~~~~~---~-~~l~~---~-~~~~-------TR~--------~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~  278 (374)
                      +.....   . +.+..   . ...+       ++.        ..+ ...+....++++++.+.++-..++.+.+.....
T Consensus       220 i~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l-~SRl~~gl~v~i~~pd~~~r~~il~~~~~~~~~  298 (450)
T PRK00149        220 IQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERL-RSRFEWGLTVDIEPPDLETRIAILKKKAEEEGI  298 (450)
T ss_pred             hhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHH-HhHhcCCeeEEecCCCHHHHHHHHHHHHHHcCC
Confidence            963210   1 11111   1 1111       111        111 123444458999999999999999998853211


Q ss_pred             CcchHHHHHHHHHHccCCchH
Q 045120          279 NCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       279 ~~~l~~~~~~I~~~c~~GlPL  299 (374)
                       .--.++..-|++.+ +|..-
T Consensus       299 -~l~~e~l~~ia~~~-~~~~R  317 (450)
T PRK00149        299 -DLPDEVLEFIAKNI-TSNVR  317 (450)
T ss_pred             -CCCHHHHHHHHcCc-CCCHH
Confidence             11135566777777 65543

>PRK07952 DNA replication protein DnaC; Validated

Probab=95.55  E-value=0.052  Score=48.94  Aligned_cols=68  Identities=22%  Similarity=0.280  Sum_probs=39.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      .+|+|||+||..+.+.....  -..+++++      ..+++..+-..+..  ...+.    ..+.+.+..  .=||||||
T Consensus       107 ~~GtGKThLa~aia~~l~~~--g~~v~~it------~~~l~~~l~~~~~~--~~~~~----~~~l~~l~~--~dlLvIDD  170 (244)
T PRK07952        107 KPGTGKNHLAAAICNELLLR--GKSVLIIT------VADIMSAMKDTFSN--SETSE----EQLLNDLSN--VDLLVIDE  170 (244)
T ss_pred             CCCCCHHHHHHHHHHHHHhc--CCeEEEEE------HHHHHHHHHHHHhh--ccccH----HHHHHHhcc--CCEEEEeC
Confidence            78999999999999976533  23556664      34455444443321  11111    223344443  45889999


Q ss_pred             CCCc
Q 045120          222 IWKL  225 (374)
Q Consensus       222 v~~~  225 (374)
                      +-..
T Consensus       171 ig~~  174 (244)
T PRK07952        171 IGVQ  174 (244)
T ss_pred             CCCC
Confidence            8643

>TIGR02012 tigrfam_recA protein RecA

Probab=95.54  E-value=0.048  Score=51.06  Aligned_cols=76  Identities=17%  Similarity=0.201  Sum_probs=49.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc------hhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS------EEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.++......  .=..++|++....++..     .+++++....      ..+.++....+...++.+.--
T Consensus        63 ~~GsGKTtLaL~~~~~~~~--~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~~~~~~  135 (321)
T TIGR02012        63 PESSGKTTLALHAIAEAQK--AGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVD  135 (321)
T ss_pred             CCCCCHHHHHHHHHHHHHH--cCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhccCCc
Confidence            8899999999988775542  23567899877766653     3555554321      123444555555555554677


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      +||+|.|..
T Consensus       136 lIVIDSv~a  144 (321)
T TIGR02012       136 IIVVDSVAA  144 (321)
T ss_pred             EEEEcchhh
Confidence            999999864

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.

>PRK06526 transposase; Provisional

Probab=95.52  E-value=0.17  Score=45.89  Aligned_cols=18  Identities=39%  Similarity=0.392  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+|||+||..+.+...
T Consensus       106 p~GtGKThLa~al~~~a~  123 (254)
T PRK06526        106 PPGTGKTHLAIGLGIRAC  123 (254)
T ss_pred             CCCCchHHHHHHHHHHHH
Confidence            899999999999988654

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.52  E-value=0.34  Score=45.80  Aligned_cols=87  Identities=9%  Similarity=0.069  Sum_probs=49.7

Q ss_pred             CeEEEEEeCCCCcc--c----cccccCcCCCC-----Ccch-hHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCc
Q 045120          213 NKILVILANIWKLL--D----LETVKIPFRND-----SRDN-NVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENC  280 (374)
Q Consensus       213 kr~LlVlDdv~~~~--~----~~~l~~~~~~~-----TR~~-~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~  280 (374)
                      ++-.+|+|++..-.  .    +..+..|-+..     |.+. .+......--..+.+.+++.+++.+.+.......  . 
T Consensus       106 ~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~~~--~-  182 (328)
T PRK05707        106 GRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALPES--D-  182 (328)
T ss_pred             CCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhcccC--C-
Confidence            34455779987532  2    33343333333     3322 2222122223468999999999998888754211  1 


Q ss_pred             chHHHHHHHHHHccCCchHHHHHHh
Q 045120          281 KFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       281 ~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                        .+.+..++..+ +|.|+.+..+.
T Consensus       183 --~~~~~~~l~la-~Gsp~~A~~l~  204 (328)
T PRK05707        183 --ERERIELLTLA-GGSPLRALQLH  204 (328)
T ss_pred             --hHHHHHHHHHc-CCCHHHHHHHH
Confidence              23345678899 99998665554

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

Probab=95.50  E-value=0.024  Score=48.53  Aligned_cols=65  Identities=28%  Similarity=0.351  Sum_probs=36.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.||..+.+..... .+ .+.|++      ..+++..+-.    ........    .+.+.+.+  -=||||||
T Consensus        55 ~~G~GKThLa~ai~~~~~~~-g~-~v~f~~------~~~L~~~l~~----~~~~~~~~----~~~~~l~~--~dlLilDD  116 (178)
T PF01695_consen   55 PPGTGKTHLAVAIANEAIRK-GY-SVLFIT------ASDLLDELKQ----SRSDGSYE----ELLKRLKR--VDLLILDD  116 (178)
T ss_dssp             STTSSHHHHHHHHHHHHHHT-T---EEEEE------HHHHHHHHHC----CHCCTTHC----HHHHHHHT--SSCEEEET
T ss_pred             hHhHHHHHHHHHHHHHhccC-Cc-ceeEee------cCceeccccc----cccccchh----hhcCcccc--ccEecccc
Confidence            88999999999998865432 23 356664      3444444432    21111111    22333433  46888999


Q ss_pred             CCC
Q 045120          222 IWK  224 (374)
Q Consensus       222 v~~  224 (374)
                      +-.
T Consensus       117 lG~  119 (178)
T PF01695_consen  117 LGY  119 (178)
T ss_dssp             CTS
T ss_pred             cce
Confidence            864

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.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.49  E-value=0.13  Score=45.60  Aligned_cols=82  Identities=20%  Similarity=0.226  Sum_probs=47.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCC----------chhhHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDK----LFDRVVFSEVSQTSDIKKIQGDIAEKLGLEL----------SEEAEYRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~----------~~~~~~~~~~~l~~  207 (374)
                      .+|+|||+||.++.......+    .=..++|++....++...+. .+.+..+...          ...+.++....+.+
T Consensus        27 ~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~  105 (226)
T cd01393          27 EFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVARPYNGEQQLEIVEE  105 (226)
T ss_pred             CCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEeCCCHHHHHHHHHH
Confidence            889999999999876543221    01467899887777765544 3333332210          01133344444444


Q ss_pred             HHh---cCCeEEEEEeCCCC
Q 045120          208 RLK---NENKILVILANIWK  224 (374)
Q Consensus       208 ~L~---~~kr~LlVlDdv~~  224 (374)
                      .+.   ..+--|+|+|.+..
T Consensus       106 ~~~~~~~~~~~lvVIDsis~  125 (226)
T cd01393         106 LERIMSSGRVDLVVVDSVAA  125 (226)
T ss_pred             HHHHhhcCCeeEEEEcCcch
Confidence            433   43556999998753

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.

>PRK07261 topology modulation protein; Provisional

Probab=95.48  E-value=0.052  Score=46.12  Aligned_cols=28  Identities=29%  Similarity=0.446  Sum_probs=19.4

Q ss_pred             CCCccHHHHHHHHHHHhhhc-CCCCeEEE
Q 045120          142 NGGIGKTTLAKEFAKQARED-KLFDRVVF  169 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~-~~F~~~~w  169 (374)
                      ++|+||||||+.+....... -+.|...|
T Consensus         8 ~~GsGKSTla~~l~~~~~~~~i~~D~~~~   36 (171)
T PRK07261          8 YSGSGKSTLARKLSQHYNCPVLHLDTLHF   36 (171)
T ss_pred             CCCCCHHHHHHHHHHHhCCCeEecCCEEe
Confidence            78999999999998754321 13455555

>PRK09354 recA recombinase A; Provisional

Probab=95.45  E-value=0.057  Score=51.07  Aligned_cols=76  Identities=18%  Similarity=0.208  Sum_probs=50.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCC------chhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLEL------SEEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~------~~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      +.|+||||||.++......  .=..++|++....++..     .++.++...      ...+.++....+...++.++--
T Consensus        68 ~~GsGKTtLal~~~~~~~~--~G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~s~~~~  140 (349)
T PRK09354         68 PESSGKTTLALHAIAEAQK--AGGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVD  140 (349)
T ss_pred             CCCCCHHHHHHHHHHHHHH--cCCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhcCCCC
Confidence            8899999999998765442  23568899888877753     455555431      1123444555555555555677


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      +||+|-|..
T Consensus       141 lIVIDSvaa  149 (349)
T PRK09354        141 LIVVDSVAA  149 (349)
T ss_pred             EEEEeChhh
Confidence            999999864

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

Probab=95.44  E-value=0.079  Score=48.60  Aligned_cols=173  Identities=17%  Similarity=0.188  Sum_probs=97.1

Q ss_pred             cccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEE-EEEeCCCCCHHHHHHHHHHH
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVV-FSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~-wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .....++|-+..+.-+.+.+...         +.|.|||+-|..+....--.+.|.+.+ =.++|..-.+.-+-..+ . 
T Consensus        33 kt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Ki-k-  110 (346)
T KOG0989|consen   33 KTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKI-K-  110 (346)
T ss_pred             CcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhh-c-
Confidence            34566889999999988888763         999999998888776544445665543 34555443322110000 0 


Q ss_pred             hCcCCchhhHHHHHHHHHHHH----h-cCCe-EEEEEeCCCCc--cccccccCcCCC---CCcchhHhhh-------hcC
Q 045120          189 LGLELSEEAEYRRASRLYERL----K-NENK-ILVILANIWKL--LDLETVKIPFRN---DSRDNNVVLL-------SMG  250 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L----~-~~kr-~LlVlDdv~~~--~~~~~l~~~~~~---~TR~~~va~~-------~~~  250 (374)
                              +    ..++.-..    . ..+. -.+|||++.+.  +.|..+...+.+   .||.--|..+       ...
T Consensus       111 --------~----fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~S  178 (346)
T KOG0989|consen  111 --------N----FAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVS  178 (346)
T ss_pred             --------C----HHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHh
Confidence                    0    00111111    0 0123 36788988754  446666443322   2333222100       001


Q ss_pred             CCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          251 SKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       251 ~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      .-..+..++|.+++...-+..++......-+ .+..+.|++.++|-|--|+.++-+
T Consensus       179 RC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d-~~al~~I~~~S~GdLR~Ait~Lqs  233 (346)
T KOG0989|consen  179 RCQKFRFKKLKDEDIVDRLEKIASKEGVDID-DDALKLIAKISDGDLRRAITTLQS  233 (346)
T ss_pred             hHHHhcCCCcchHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHcCCcHHHHHHHHHH
Confidence            1125788999999999988888863332222 355678999995556666666655

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.29  E-value=0.059  Score=53.99  Aligned_cols=41  Identities=10%  Similarity=0.065  Sum_probs=26.3

Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG  296 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G  296 (374)
                      ..+.++..+.++-.++|..+.......++. . ...+++.+ .|
T Consensus       218 ~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~-~-l~~la~~t-~G  258 (495)
T TIGR01241       218 RQVVVDLPDIKGREEILKVHAKNKKLAPDV-D-LKAVARRT-PG  258 (495)
T ss_pred             EEEEcCCCCHHHHHHHHHHHHhcCCCCcch-h-HHHHHHhC-CC
Confidence            468888889989999998877533221111 1 23667777 65

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.

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

Probab=95.27  E-value=0.082  Score=52.78  Aligned_cols=83  Identities=19%  Similarity=0.305  Sum_probs=52.7

Q ss_pred             cccccccHHHHHHHHHHhhcC---------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      ...+-|.+..++++.+++..-                     ++|+|||.||+.+.++..+-       |++++.+    
T Consensus       189 f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vP-------f~~isAp----  257 (802)
T KOG0733|consen  189 FSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVP-------FLSISAP----  257 (802)
T ss_pred             hhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCc-------eEeecch----
Confidence            345778998888887776421                     88999999999999976643       3443322    


Q ss_pred             HHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          180 KIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       180 ~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                          +|+....    .++ ++.+..+++.-.+.-.+++.+|++.
T Consensus       258 ----eivSGvS----GES-EkkiRelF~~A~~~aPcivFiDeID  292 (802)
T KOG0733|consen  258 ----EIVSGVS----GES-EKKIRELFDQAKSNAPCIVFIDEID  292 (802)
T ss_pred             ----hhhcccC----ccc-HHHHHHHHHHHhccCCeEEEeeccc
Confidence                2222222    122 2334444444444478999999986

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=95.26  E-value=1.2  Score=40.10  Aligned_cols=159  Identities=16%  Similarity=0.112  Sum_probs=91.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCcCCchh---hHHHHHHHHHHHHhcCCe-EE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-TSDIKKIQGDIAEKLGLELSEE---AEYRRASRLYERLKNENK-IL  216 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~~~~---~~~~~~~~l~~~L~~~kr-~L  216 (374)
                      .-|+|||++.+.+.....-    |.++=|.+.. ..+...+...|+..+.......   ........|....++++| ..
T Consensus        59 evGsGKTv~~Ral~~s~~~----d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v~  134 (269)
T COG3267          59 EVGSGKTVLRRALLASLNE----DQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPVV  134 (269)
T ss_pred             cCCCchhHHHHHHHHhcCC----CceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCeE
Confidence            5699999999955442221    2222244443 4677888888888887632111   223344556666666678 99


Q ss_pred             EEEeCCCCc--ccccccc-----------------CcCCCC-C--cchhHhhhhcCCCCc-eecCCCCHHHHHHHHHHhc
Q 045120          217 VILANIWKL--LDLETVK-----------------IPFRND-S--RDNNVVLLSMGSKDN-FLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       217 lVlDdv~~~--~~~~~l~-----------------~~~~~~-T--R~~~va~~~~~~~~~-~~l~~L~~~~s~~Lf~~~a  273 (374)
                      ++.|+....  +.++.++                 ..-|.- -  |...... .-.-..+ |.++|++.++...++....
T Consensus       135 l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e-~~~R~~ir~~l~P~~~~~t~~yl~~~L  213 (269)
T COG3267         135 LMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRE-LEQRIDIRIELPPLTEAETGLYLRHRL  213 (269)
T ss_pred             EeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHh-hhheEEEEEecCCcChHHHHHHHHHHH
Confidence            999998643  1222211                 111111 1  2221111 1111124 9999999998888887776


Q ss_pred             CCCCCCcc--hHHHHHHHHHHccCCchHHHHHHhc
Q 045120          274 GDDVENCK--FKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       274 ~~~~~~~~--l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      .....+..  -.+....|.... .|.|.+|.-++.
T Consensus       214 e~a~~~~~l~~~~a~~~i~~~s-qg~P~lin~~~~  247 (269)
T COG3267         214 EGAGLPEPLFSDDALLLIHEAS-QGIPRLINNLAT  247 (269)
T ss_pred             hccCCCcccCChhHHHHHHHHh-ccchHHHHHHHH
Confidence            52221111  134556788888 999999987765

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=95.21  E-value=0.15  Score=48.33  Aligned_cols=82  Identities=15%  Similarity=0.123  Sum_probs=51.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch----------hhHHH---HHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDK----LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE----------EAEYR---RASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~----------~~~~~---~~~~  204 (374)
                      .+|+|||+|+..++-......    .=..++|++....|++.++. +|++.++.....          .+.++   ....
T Consensus       131 ~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~-qia~~~~~~~~~~l~~i~~~~~~~~e~~~~ll~~  209 (342)
T PLN03186        131 EFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLI-QIAERFGLNGADVLENVAYARAYNTDHQSELLLE  209 (342)
T ss_pred             CCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHH-HHHHHcCCChhhhccceEEEecCCHHHHHHHHHH
Confidence            889999999988775433211    11368999999999988764 556766543211          12222   2333


Q ss_pred             HHHHHhcCCeEEEEEeCCCC
Q 045120          205 LYERLKNENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~~  224 (374)
                      +...+...+--|||+|-+..
T Consensus       210 ~~~~~~~~~~~LIVIDSI~a  229 (342)
T PLN03186        210 AASMMAETRFALMIVDSATA  229 (342)
T ss_pred             HHHHhhccCCCEEEEeCcHH
Confidence            33334443567999998753

>PRK12377 putative replication protein; Provisional

Probab=95.18  E-value=0.07  Score=48.21  Aligned_cols=65  Identities=18%  Similarity=0.255  Sum_probs=39.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||+||.++.+...-.  .-.++++++.      +++..|-......   .+.    ..+.+.+.  +-=||||||
T Consensus       109 ~~GtGKThLa~AIa~~l~~~--g~~v~~i~~~------~l~~~l~~~~~~~---~~~----~~~l~~l~--~~dLLiIDD  171 (248)
T PRK12377        109 KPGTGKNHLAAAIGNRLLAK--GRSVIVVTVP------DVMSRLHESYDNG---QSG----EKFLQELC--KVDLLVLDE  171 (248)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCCeEEEEHH------HHHHHHHHHHhcc---chH----HHHHHHhc--CCCEEEEcC
Confidence            67999999999999976532  3345666543      4444444433211   111    12333333  467999999


Q ss_pred             CC
Q 045120          222 IW  223 (374)
Q Consensus       222 v~  223 (374)
                      +-
T Consensus       172 lg  173 (248)
T PRK12377        172 IG  173 (248)
T ss_pred             CC
Confidence            94

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.10  E-value=0.25  Score=50.23  Aligned_cols=116  Identities=13%  Similarity=0.108  Sum_probs=63.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.|++.+.+.......--.++|++      ..++..++...+...        ....+++.+.+  -=+|||||
T Consensus       322 ~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit------aeef~~el~~al~~~--------~~~~f~~~y~~--~DLLlIDD  385 (617)
T PRK14086        322 ESGLGKTHLLHAIGHYARRLYPGTRVRYVS------SEEFTNEFINSIRDG--------KGDSFRRRYRE--MDILLVDD  385 (617)
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCCCeEEEee------HHHHHHHHHHHHHhc--------cHHHHHHHhhc--CCEEEEeh
Confidence            679999999999999654221112345654      334444444333211        11233344433  35788899


Q ss_pred             CCCcc---ccc----cccCcCCC-C-----C----------cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcC
Q 045120          222 IWKLL---DLE----TVKIPFRN-D-----S----------RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       222 v~~~~---~~~----~l~~~~~~-~-----T----------R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      +....   .+.    .+...+.. +     |          -...+. ..+...-++.|++.+.+.-..++.+.+.
T Consensus       386 Iq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~-SRf~~GLvv~I~~PD~EtR~aIL~kka~  460 (617)
T PRK14086        386 IQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLR-NRFEWGLITDVQPPELETRIAILRKKAV  460 (617)
T ss_pred             hccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHH-hhhhcCceEEcCCCCHHHHHHHHHHHHH
Confidence            86431   111    11111111 1     1          112222 2455556899999999999999998875

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=95.05  E-value=0.15  Score=46.56  Aligned_cols=84  Identities=29%  Similarity=0.347  Sum_probs=53.4

Q ss_pred             CCCccHHHHHHHHHHHhhh--cCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQARE--DKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~--~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l  205 (374)
                      -.|+|||+|+..+.++...  +++-+.++++-+++.. +..++.+++...=...       ..+++..      ...-.+
T Consensus        77 g~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a~~~a~ai  156 (276)
T cd01135          77 GSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIITPRMALTT  156 (276)
T ss_pred             CCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHHHHHHHHH
Confidence            5689999999998876541  1234788999998875 4566666665532211       1112211      123456


Q ss_pred             HHHHhc--CCeEEEEEeCCCCc
Q 045120          206 YERLKN--ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~--~kr~LlVlDdv~~~  225 (374)
                      .++++.  +++.|+++||+...
T Consensus       157 AEyfrd~~g~~VLl~~D~ltr~  178 (276)
T cd01135         157 AEYLAYEKGKHVLVILTDMTNY  178 (276)
T ss_pred             HHHHHhccCCeEEEEEcChhHH
Confidence            777763  48999999998643

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.03  E-value=0.18  Score=49.72  Aligned_cols=114  Identities=11%  Similarity=0.126  Sum_probs=63.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+|||+|++.+.+.....  --.+++++      ...+...+...+...        ....+++.+.  +.-+|++||
T Consensus       149 ~~G~GKTHLl~Ai~~~l~~~--~~~v~yi~------~~~f~~~~~~~l~~~--------~~~~f~~~~~--~~dvLiIDD  210 (445)
T PRK12422        149 PEGSGKTHLMQAAVHALRES--GGKILYVR------SELFTEHLVSAIRSG--------EMQRFRQFYR--NVDALFIED  210 (445)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCCEEEee------HHHHHHHHHHHHhcc--------hHHHHHHHcc--cCCEEEEcc
Confidence            78999999999999975422  23345554      234444554444321        1123333333  345888999


Q ss_pred             CCCccc--c--ccccCc---C-CCC-------Ccc--------hhHhhhhcCCCCceecCCCCHHHHHHHHHHhcC
Q 045120          222 IWKLLD--L--ETVKIP---F-RND-------SRD--------NNVVLLSMGSKDNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       222 v~~~~~--~--~~l~~~---~-~~~-------TR~--------~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      +.....  +  +.+...   + ..+       ++.        ..+. ..+....++.+++++.++-..++.+.+.
T Consensus       211 iq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~-SR~~~Gl~~~l~~pd~e~r~~iL~~k~~  285 (445)
T PRK12422        211 IEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLI-SRFEWGIAIPLHPLTKEGLRSFLERKAE  285 (445)
T ss_pred             hhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHH-hhhcCCeEEecCCCCHHHHHHHHHHHHH
Confidence            864311  1  111111   0 111       111        1221 2344446899999999999999998775

>PRK05642 DNA replication initiation factor; Validated

Probab=95.01  E-value=0.37  Score=43.16  Aligned_cols=52  Identities=8%  Similarity=0.068  Sum_probs=34.2

Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      .+....++++++++.++-.+++...+...... --.++..-|++.+ .|-.-.+
T Consensus       154 Rl~~gl~~~l~~~~~e~~~~il~~ka~~~~~~-l~~ev~~~L~~~~-~~d~r~l  205 (234)
T PRK05642        154 RLTLALVFQMRGLSDEDKLRALQLRASRRGLH-LTDEVGHFILTRG-TRSMSAL  205 (234)
T ss_pred             HHhcCeeeecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhc-CCCHHHH
Confidence            33444578999999999999999666422111 1146677888888 6654433

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.95  E-value=1.8  Score=41.53  Aligned_cols=79  Identities=19%  Similarity=0.163  Sum_probs=43.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCcCCchh-hHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-TSDIKKIQGDIAEKLGLELSEE-AEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      +.|+||||++..+......+.....+.+++... .....+-++...+.++.+.... +..+....+ ..+.+  +-+|++
T Consensus       145 ptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l-~~l~~--~DlVLI  221 (374)
T PRK14722        145 PTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLAL-AELRN--KHMVLI  221 (374)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHH-HHhcC--CCEEEE
Confidence            889999999999987654221123455555322 1234555566666776654332 222222222 33333  466778


Q ss_pred             eCCC
Q 045120          220 ANIW  223 (374)
Q Consensus       220 Ddv~  223 (374)
                      |..-
T Consensus       222 DTaG  225 (374)
T PRK14722        222 DTIG  225 (374)
T ss_pred             cCCC
Confidence            9873

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

Probab=94.95  E-value=0.025  Score=51.21  Aligned_cols=47  Identities=15%  Similarity=-0.005  Sum_probs=33.6

Q ss_pred             ceecCCCCHHHHHHHHHHhcC--CCCCCcchHHHHHHHHHHccCCchHHHHHH
Q 045120          254 NFLIANITEEEAWRLFKIMNG--DDVENCKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       254 ~~~l~~L~~~~s~~Lf~~~a~--~~~~~~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                      +.+++--+.+|-.++..+.+.  +-...   .+-+.+|+++. .|-|--..-+
T Consensus       175 ~~rlefY~~~eL~~Iv~r~a~~l~i~i~---~~~a~eIA~rS-RGTPRIAnRL  223 (332)
T COG2255         175 IQRLEFYTVEELEEIVKRSAKILGIEID---EEAALEIARRS-RGTPRIANRL  223 (332)
T ss_pred             eeeeecCCHHHHHHHHHHHHHHhCCCCC---hHHHHHHHHhc-cCCcHHHHHH
Confidence            678888899999999998885  22111   35567899999 9999644333

>TIGR00763 lon ATP-dependent protease La

Probab=94.94  E-value=1.2  Score=47.20  Aligned_cols=37  Identities=24%  Similarity=0.218  Sum_probs=29.5

Q ss_pred             cccccHHHHHHHHHHhhc--------C-------CCCccHHHHHHHHHHHhh
Q 045120          123 AFESRVSNLKSTQNALTN--------A-------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~--------~-------~gGiGKTtLA~~v~~~~~  159 (374)
                      .++|.+..++.|.+++..        +       +.|+|||+||+.+.+...
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~  372 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALN  372 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            477989888888886531        1       889999999999998653

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.

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

Probab=94.93  E-value=0.043  Score=53.76  Aligned_cols=39  Identities=26%  Similarity=0.361  Sum_probs=30.5

Q ss_pred             cccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhh
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      ...+.|.+..+++|.+.+.-.                      +.|+|||+||+.+++...
T Consensus       182 ~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~  242 (438)
T PTZ00361        182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETS  242 (438)
T ss_pred             HHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhC
Confidence            345778999998887776421                      889999999999999543

>cd01394 radB RadB

Probab=94.91  E-value=0.24  Score=43.73  Aligned_cols=34  Identities=24%  Similarity=0.307  Sum_probs=24.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD  177 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~  177 (374)
                      .+|+||||||.++......  .=..++|++....+.
T Consensus        27 ~~GsGKT~l~~~~a~~~~~--~g~~v~yi~~e~~~~   60 (218)
T cd01394          27 PPGTGKTNIAIQLAVETAG--QGKKVAYIDTEGLSS   60 (218)
T ss_pred             CCCCCHHHHHHHHHHHHHh--cCCeEEEEECCCCCH
Confidence            8899999999998875532  224567887655543

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

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

Probab=94.89  E-value=0.1  Score=48.89  Aligned_cols=87  Identities=21%  Similarity=0.281  Sum_probs=55.1

Q ss_pred             cccccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          117 SNKVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       117 ~~~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      |...+..+=|-++.+++|.+.+.-+                      ++|.|||-||++|+|+..  ..|     +-|..
T Consensus       146 PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~--AtF-----Irvvg  218 (406)
T COG1222         146 PDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTD--ATF-----IRVVG  218 (406)
T ss_pred             CCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccC--ceE-----EEecc
Confidence            3344556778899999888876543                      899999999999999554  223     43332


Q ss_pred             CCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          175 TSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       175 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                      +        ++++..-.     .-..+...+++.-+.+..+.|.+|.+.
T Consensus       219 S--------ElVqKYiG-----EGaRlVRelF~lArekaPsIIFiDEID  254 (406)
T COG1222         219 S--------ELVQKYIG-----EGARLVRELFELAREKAPSIIFIDEID  254 (406)
T ss_pred             H--------HHHHHHhc-----cchHHHHHHHHHHhhcCCeEEEEechh
Confidence            1        22222211     112344556666666678999999885

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=94.84  E-value=0.34  Score=45.58  Aligned_cols=82  Identities=27%  Similarity=0.342  Sum_probs=50.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC----CeEEEEEeCCCCCHHHHHHHHHHHhCcCCch-------------hhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF----DRVVFSEVSQTSDIKKIQGDIAEKLGLELSE-------------EAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~-------------~~~~~~~~~  204 (374)
                      .+|+|||+|+.++.-.......+    ..++||+....+++..+.+ +++.++.....             .........
T Consensus       110 ~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g~~~~~~l~~i~~~~~~~~~~~~~~~~~  188 (317)
T PRK04301        110 EFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALGLDPDEVLDNIHVARAYNSDHQMLLAEK  188 (317)
T ss_pred             CCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcCCChHhhhccEEEEeCCCHHHHHHHHHH
Confidence            88999999999987654322111    3789999988888877654 44555432110             111223445


Q ss_pred             HHHHHhc-CCeEEEEEeCCCC
Q 045120          205 LYERLKN-ENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~-~kr~LlVlDdv~~  224 (374)
                      +.+.+.. .+--|||+|-+..
T Consensus       189 l~~~i~~~~~~~lvVIDSisa  209 (317)
T PRK04301        189 AEELIKEGENIKLVIVDSLTA  209 (317)
T ss_pred             HHHHHhccCceeEEEEECchH
Confidence            5555543 2455999998753

>PRK13531 regulatory ATPase RavA; Provisional

Probab=94.84  E-value=0.077  Score=52.24  Aligned_cols=38  Identities=16%  Similarity=0.191  Sum_probs=32.6

Q ss_pred             ccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhh
Q 045120          122 EAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~  159 (374)
                      ..++||++.++.+...+..+       .+|+|||+||+.+.....
T Consensus        20 ~~i~gre~vI~lll~aalag~hVLL~GpPGTGKT~LAraLa~~~~   64 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAFQ   64 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCCCEEEECCCChhHHHHHHHHHHHhc
Confidence            34899999999998888766       889999999999988543

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=94.82  E-value=0.24  Score=46.57  Aligned_cols=82  Identities=16%  Similarity=0.133  Sum_probs=48.7

Q ss_pred             CCCccHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch----------hhHHH---HHHH
Q 045120          142 NGGIGKTTLAKEFAKQARED---K-LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE----------EAEYR---RASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~----------~~~~~---~~~~  204 (374)
                      ..|+|||||+..++......   + .-..++|++-...++..++ .++++.++.....          .+.++   ....
T Consensus       104 ~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~~~~~~l~~i~~~~~~~~~~~~~~l~~  182 (316)
T TIGR02239       104 EFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGLNPEDVLDNVAYARAYNTDHQLQLLQQ  182 (316)
T ss_pred             CCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCCChHHhhccEEEEecCChHHHHHHHHH
Confidence            78999999999887643221   1 1135799998887887764 4455655443211          12222   2333


Q ss_pred             HHHHHhcCCeEEEEEeCCCC
Q 045120          205 LYERLKNENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~~  224 (374)
                      +...+...+--|||+|-+..
T Consensus       183 ~~~~~~~~~~~LvVIDSI~a  202 (316)
T TIGR02239       183 AAAMMSESRFALLIVDSATA  202 (316)
T ss_pred             HHHhhccCCccEEEEECcHH
Confidence            33444443566899998753

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

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

Probab=94.80  E-value=2.5  Score=38.96  Aligned_cols=82  Identities=20%  Similarity=0.287  Sum_probs=53.4

Q ss_pred             ccccccHHHHHHHHHHhhcC---------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKK  180 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  180 (374)
                      ..+.|.|..++.|.+.+.-+                     ++|.||+.||++|.....  .     -|.+||..    +
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAn--S-----TFFSvSSS----D  201 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEAN--S-----TFFSVSSS----D  201 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcC--C-----ceEEeehH----H
Confidence            45778888888887765433                     899999999999998543  2     23444432    1


Q ss_pred             HHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          181 IQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       181 ~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                      +.   -.++|      ..+.+...|++.-+..|.-+|.+|.+.
T Consensus       202 Lv---SKWmG------ESEkLVknLFemARe~kPSIIFiDEiD  235 (439)
T KOG0739|consen  202 LV---SKWMG------ESEKLVKNLFEMARENKPSIIFIDEID  235 (439)
T ss_pred             HH---HHHhc------cHHHHHHHHHHHHHhcCCcEEEeehhh
Confidence            11   11222      123455667777676689999999885

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

Probab=94.79  E-value=0.35  Score=50.31  Aligned_cols=106  Identities=17%  Similarity=0.248  Sum_probs=59.5

Q ss_pred             ccccccHHHHHHHHHHhhcC------------------CCCccHHHHHHHHHHHhhhcCCC---CeEEEEEeCCCCCHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA------------------NGGIGKTTLAKEFAKQAREDKLF---DRVVFSEVSQTSDIKK  180 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~------------------~gGiGKTtLA~~v~~~~~~~~~F---~~~~wv~vs~~~~~~~  180 (374)
                      ..++|-+..++.+.+.+...                  +-|+|||-||+.+....     |   +..+-+++|.-..-. 
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~L-----fg~e~aliR~DMSEy~EkH-  564 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEAL-----FGDEQALIRIDMSEYMEKH-  564 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHh-----cCCCccceeechHHHHHHH-
Confidence            34778888888877776532                  78999999999998733     5   334444444332211 


Q ss_pred             HHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeE-EEEEeCCCCc--cccccccCcCCCC
Q 045120          181 IQGDIAEKLGLELSEEAEYRRASRLYERLKNENKI-LVILANIWKL--LDLETVKIPFRND  238 (374)
Q Consensus       181 ~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~-LlVlDdv~~~--~~~~~l~~~~~~~  238 (374)
                         .+.+-+|.+..--.-++ -..|-+..+. +.| .|.||.+...  +.++-|...+.+|
T Consensus       565 ---sVSrLIGaPPGYVGyee-GG~LTEaVRr-~PySViLlDEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         565 ---SVSRLIGAPPGYVGYEE-GGQLTEAVRR-KPYSVILLDEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             ---HHHHHhCCCCCCceecc-ccchhHhhhc-CCCeEEEechhhhcCHHHHHHHHHHhcCC
Confidence               22333343311110011 2345555556 666 8889999854  3454454444444

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.79  E-value=1.4  Score=41.38  Aligned_cols=86  Identities=15%  Similarity=0.018  Sum_probs=51.0

Q ss_pred             CeEEEEEeCCCCcc------ccccccCcCCCC-----Cc-chhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCc
Q 045120          213 NKILVILANIWKLL------DLETVKIPFRND-----SR-DNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENC  280 (374)
Q Consensus       213 kr~LlVlDdv~~~~------~~~~l~~~~~~~-----TR-~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~  280 (374)
                      ++-++|+|++..-.      -+..+..|-+..     |. ...+......--..+.+.+++.+++.+.+... +  . + 
T Consensus       113 ~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~-~--~-~-  187 (319)
T PRK08769        113 IAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQ-G--V-S-  187 (319)
T ss_pred             CcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHc-C--C-C-
Confidence            56788999987442      144444444433     22 22222212222236889999999998888753 1  1 1 


Q ss_pred             chHHHHHHHHHHccCCchHHHHHHhc
Q 045120          281 KFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       281 ~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                        ..-+..++..+ +|.|+.+.....
T Consensus       188 --~~~a~~~~~l~-~G~p~~A~~~~~  210 (319)
T PRK08769        188 --ERAAQEALDAA-RGHPGLAAQWLR  210 (319)
T ss_pred             --hHHHHHHHHHc-CCCHHHHHHHhc
Confidence              12255778999 999987766654

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=94.74  E-value=0.12  Score=45.61  Aligned_cols=78  Identities=23%  Similarity=0.397  Sum_probs=47.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||+|+..+.++..    -+..+++.+++.. ...++.+++...-...       ..+++..      ...-.+.+
T Consensus        23 ~~g~GKt~Ll~~i~~~~~----~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~a~t~AE   98 (215)
T PF00006_consen   23 GAGVGKTVLLQEIANNQD----ADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYTALTIAE   98 (215)
T ss_dssp             STTSSHHHHHHHHHHHCT----TTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHHHHHHHH
T ss_pred             CcccccchhhHHHHhccc----ccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhccchhhhH
Confidence            789999999999988764    3456888888764 5566666664431111       1111111      11223444


Q ss_pred             HHh-cCCeEEEEEeCCC
Q 045120          208 RLK-NENKILVILANIW  223 (374)
Q Consensus       208 ~L~-~~kr~LlVlDdv~  223 (374)
                      +++ .++..|+++||+.
T Consensus        99 yfrd~G~dVlli~Dslt  115 (215)
T PF00006_consen   99 YFRDQGKDVLLIIDSLT  115 (215)
T ss_dssp             HHHHTTSEEEEEEETHH
T ss_pred             HHhhcCCceeehhhhhH
Confidence            454 2599999999984

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

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

Probab=94.73  E-value=0.4  Score=49.67  Aligned_cols=158  Identities=15%  Similarity=0.124  Sum_probs=85.7

Q ss_pred             cccccccHHHH---HHHHHHhhcC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          121 YEAFESRVSNL---KSTQNALTNA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       121 ~~~~vGr~~~~---~~i~~~L~~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      ..++.|-|+.+   .++++.|.++                  ++|+|||-||++++....+-       |+++|..    
T Consensus       310 FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVP-------F~svSGS----  378 (774)
T KOG0731|consen  310 FKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVP-------FFSVSGS----  378 (774)
T ss_pred             cccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCc-------eeeechH----
Confidence            44678877555   4556667665                  88999999999999866533       4544432    


Q ss_pred             HHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc-----------------cccccCcC---CCC-
Q 045120          180 KIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD-----------------LETVKIPF---RND-  238 (374)
Q Consensus       180 ~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~-----------------~~~l~~~~---~~~-  238 (374)
                          +.++.+...     ...+...|...-+....++|.+|++....-                 +.++...+   ... 
T Consensus       379 ----EFvE~~~g~-----~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~  449 (774)
T KOG0731|consen  379 ----EFVEMFVGV-----GASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSK  449 (774)
T ss_pred             ----HHHHHhccc-----chHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCC
Confidence                111111111     022334444444444678888888764321                 11111100   000 


Q ss_pred             -------CcchhHhhh---hcC-CCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH
Q 045120          239 -------SRDNNVVLL---SMG-SKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       239 -------TR~~~va~~---~~~-~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                             |++.++.+.   ..| -...+.++.=+.....++|.-++.......+..++++ |+..- -|++=|
T Consensus       450 ~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~-~a~~t-~gf~ga  520 (774)
T KOG0731|consen  450 GVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSK-LASLT-PGFSGA  520 (774)
T ss_pred             cEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHH-HHhcC-CCCcHH
Confidence                   444444321   111 1235677777778888899888864433334445555 66555 665544

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.60  E-value=0.2  Score=46.00  Aligned_cols=81  Identities=20%  Similarity=0.195  Sum_probs=50.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCc---CCch--hhHHHHHHHHHHHHhcCCeEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL---ELSE--EAEYRRASRLYERLKNENKIL  216 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~---~~~~--~~~~~~~~~l~~~L~~~kr~L  216 (374)
                      +.|+||||||.+++-...  ..-..++|++..+.+++..+.+--...+..   ..+.  ......++.+.....+ +--|
T Consensus        68 ~~gsGKT~lal~~~~~aq--~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~v~~~~~~e~q~~i~~~~~~~~~~-~i~L  144 (279)
T COG0468          68 PESSGKTTLALQLVANAQ--KPGGKAAFIDTEHALDPERAKQLGVDLLDNLLVSQPDTGEQQLEIAEKLARSGAE-KIDL  144 (279)
T ss_pred             CCCcchhhHHHHHHHHhh--cCCCeEEEEeCCCCCCHHHHHHHHHhhhcceeEecCCCHHHHHHHHHHHHHhccC-CCCE
Confidence            889999999999877554  334588999999999988765433331221   1111  1222334444444443 4679


Q ss_pred             EEEeCCCCc
Q 045120          217 VILANIWKL  225 (374)
Q Consensus       217 lVlDdv~~~  225 (374)
                      +|+|.|-..
T Consensus       145 vVVDSvaa~  153 (279)
T COG0468         145 LVVDSVAAL  153 (279)
T ss_pred             EEEecCccc
Confidence            999988643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.60  E-value=0.39  Score=50.65  Aligned_cols=160  Identities=14%  Similarity=0.187  Sum_probs=83.1

Q ss_pred             cccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ...+.|.+..++.|.+.+.-.                      +.|+|||+||+.+.+...  ..|     +.++.    
T Consensus       452 ~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~--~~f-----i~v~~----  520 (733)
T TIGR01243       452 WSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESG--ANF-----IAVRG----  520 (733)
T ss_pred             hhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcC--CCE-----EEEeh----
Confidence            345778888877776655321                      889999999999998643  222     22221    


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------------ccccccCcCC-----CC-
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--------------DLETVKIPFR-----ND-  238 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--------------~~~~l~~~~~-----~~-  238 (374)
                      .+    ++..    ....+ +.....+.+..+....++|+||++....              ....+...+.     .+ 
T Consensus       521 ~~----l~~~----~vGes-e~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v  591 (733)
T TIGR01243       521 PE----ILSK----WVGES-EKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNV  591 (733)
T ss_pred             HH----Hhhc----ccCcH-HHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCE
Confidence            11    1111    11111 2233444444444367999999985320              0111111111     11 


Q ss_pred             -----CcchhHhhhh-c---CCCCceecCCCCHHHHHHHHHHhcCCCCC--CcchHHHHHHHHHHccCCc-hHHHHHHh
Q 045120          239 -----SRDNNVVLLS-M---GSKDNFLIANITEEEAWRLFKIMNGDDVE--NCKFKSTAINVAKACGAGL-FCTLTTNA  305 (374)
Q Consensus       239 -----TR~~~va~~~-~---~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~--~~~l~~~~~~I~~~c~~Gl-PLai~~ig  305 (374)
                           |......... .   .-...+.++..+.++-.++|+.+......  ..++    ..+++.| .|. +-.|..+.
T Consensus       592 ~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l----~~la~~t-~g~sgadi~~~~  665 (733)
T TIGR01243       592 VVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDL----EELAEMT-EGYTGADIEAVC  665 (733)
T ss_pred             EEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCH----HHHHHHc-CCCCHHHHHHHH
Confidence                 3333221111 1   12347888888999999999877653222  2223    3566777 554 33344433

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.

>PRK06921 hypothetical protein; Provisional

Probab=94.58  E-value=0.14  Score=46.82  Aligned_cols=30  Identities=27%  Similarity=0.232  Sum_probs=21.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV  172 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v  172 (374)
                      ..|+|||+||.++.+....+. -..++|++.
T Consensus       125 ~~G~GKThLa~aia~~l~~~~-g~~v~y~~~  154 (266)
T PRK06921        125 QPGSGKTHLLTAAANELMRKK-GVPVLYFPF  154 (266)
T ss_pred             CCCCcHHHHHHHHHHHHhhhc-CceEEEEEH
Confidence            789999999999999654221 234566654

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.58  E-value=0.3  Score=43.78  Aligned_cols=39  Identities=10%  Similarity=0.301  Sum_probs=25.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      .+|+|||+||.++.....  ..-..++|++...  ++.++.+.
T Consensus        29 ~pGsGKT~la~~~l~~~~--~~ge~~lyvs~ee--~~~~i~~~   67 (237)
T TIGR03877        29 GPGTGKSIFSQQFLWNGL--QMGEPGIYVALEE--HPVQVRRN   67 (237)
T ss_pred             CCCCCHHHHHHHHHHHHH--HcCCcEEEEEeeC--CHHHHHHH
Confidence            889999999988655432  1235678887654  44455444

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.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=94.58  E-value=0.054  Score=50.59  Aligned_cols=65  Identities=14%  Similarity=0.205  Sum_probs=39.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.||..+++.... ..+ .+.|++++      .++..+...++..    +.    ....+.+.  +-=||||||
T Consensus       164 ~~G~GKThLa~Aia~~l~~-~g~-~v~~~~~~------~l~~~lk~~~~~~----~~----~~~l~~l~--~~dlLiIDD  225 (306)
T PRK08939        164 DFGVGKSYLLAAIANELAK-KGV-SSTLLHFP------EFIRELKNSISDG----SV----KEKIDAVK--EAPVLMLDD  225 (306)
T ss_pred             CCCCCHHHHHHHHHHHHHH-cCC-CEEEEEHH------HHHHHHHHHHhcC----cH----HHHHHHhc--CCCEEEEec
Confidence            7799999999999997652 223 34566543      4555555544211    11    12222333  467999999


Q ss_pred             CCC
Q 045120          222 IWK  224 (374)
Q Consensus       222 v~~  224 (374)
                      +-.
T Consensus       226 iG~  228 (306)
T PRK08939        226 IGA  228 (306)
T ss_pred             CCC
Confidence            853

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=94.54  E-value=0.18  Score=49.35  Aligned_cols=83  Identities=18%  Similarity=0.339  Sum_probs=53.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~------~~~~~~l~~  207 (374)
                      ..|+|||+|+..+..+..- .+-+.++|+-++... ...++.+++...=...       ..+++.      ...+-.+.+
T Consensus       146 ~~G~GKt~l~~~~~~~~~~-~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~~a~tiAE  224 (449)
T TIGR03305       146 GAGVGKTVLLTEMIHNMVG-QHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGHTALTMAE  224 (449)
T ss_pred             CCCCChhHHHHHHHHHHHh-cCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHHHHHHHHH
Confidence            7799999999998776542 234788999888775 3555666655432111       111221      123346777


Q ss_pred             HHhc--CCeEEEEEeCCCCc
Q 045120          208 RLKN--ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~--~kr~LlVlDdv~~~  225 (374)
                      +++.  +++.||++||+...
T Consensus       225 yfrd~~G~~VLl~~DslTR~  244 (449)
T TIGR03305       225 YFRDDEKQDVLLLIDNIFRF  244 (449)
T ss_pred             HHHHhcCCceEEEecChHHH
Confidence            7764  58999999999754

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=94.52  E-value=1.9  Score=40.65  Aligned_cols=86  Identities=15%  Similarity=0.108  Sum_probs=49.8

Q ss_pred             CCeEEEEEeCCCCcc------ccccccCcCCCC-----C-cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCC
Q 045120          212 ENKILVILANIWKLL------DLETVKIPFRND-----S-RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVEN  279 (374)
Q Consensus       212 ~kr~LlVlDdv~~~~------~~~~l~~~~~~~-----T-R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~  279 (374)
                      +++=.+|+|++..-.      -+..+..|-+..     | ....+......--..+.+.+++.++..+.+.......   
T Consensus       106 g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~~~~---  182 (325)
T PRK06871        106 GGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQSSAE---  182 (325)
T ss_pred             CCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHhccC---
Confidence            356688899987542      144444444433     2 2223322222223478999999999998888764211   


Q ss_pred             cchHHHHHHHHHHccCCchHHHHHH
Q 045120          280 CKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       280 ~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                         ...+...+..+ +|.|+.+..+
T Consensus       183 ---~~~~~~~~~l~-~g~p~~A~~~  203 (325)
T PRK06871        183 ---ISEILTALRIN-YGRPLLALTF  203 (325)
T ss_pred             ---hHHHHHHHHHc-CCCHHHHHHH
Confidence               11244667788 9999744333

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=94.48  E-value=1.2  Score=42.22  Aligned_cols=35  Identities=26%  Similarity=0.285  Sum_probs=26.1

Q ss_pred             ccc-cHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHh
Q 045120          124 FES-RVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       124 ~vG-r~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~  158 (374)
                      ++| -+..++.+.+.+..+          +.|+||||+|..+.+..
T Consensus         7 i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l   52 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSL   52 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            455 556667777777655          88999999999987753

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.48  E-value=0.79  Score=44.93  Aligned_cols=77  Identities=18%  Similarity=0.164  Sum_probs=38.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCcCCch-hhHHHHHHHHHHHHhcCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI--KKIQGDIAEKLGLELSE-EAEYRRASRLYERLKNENKILVI  218 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~~kr~LlV  218 (374)
                      ++|+||||++..+.........-..+..|+.. .+..  ..-+....+.++.+... .+..+....+.+ +.  ..=+|+
T Consensus       229 ptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D-~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~-~~--~~DlVl  304 (424)
T PRK05703        229 PTGVGKTTTLAKLAARYALLYGKKKVALITLD-TYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQ-LR--DCDVIL  304 (424)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCCeEEEEECC-ccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHH-hC--CCCEEE
Confidence            89999999888876654311122345566543 2221  22233334445544322 223333333332 22  346788


Q ss_pred             EeCC
Q 045120          219 LANI  222 (374)
Q Consensus       219 lDdv  222 (374)
                      +|..
T Consensus       305 IDt~  308 (424)
T PRK05703        305 IDTA  308 (424)
T ss_pred             EeCC
Confidence            8865

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=94.46  E-value=0.33  Score=39.95  Aligned_cols=34  Identities=29%  Similarity=0.393  Sum_probs=25.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD  177 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~  177 (374)
                      ..|+||||++..+......  .-..++|++.....+
T Consensus         7 ~~G~GKT~l~~~i~~~~~~--~~~~v~~~~~e~~~~   40 (165)
T cd01120           7 PTGSGKTTLALQLALNIAT--KGGKVVYVDIEEEIE   40 (165)
T ss_pred             CCCCCHHHHHHHHHHHHHh--cCCEEEEEECCcchH
Confidence            6799999999999886542  235677887765543

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=94.45  E-value=0.4  Score=44.87  Aligned_cols=82  Identities=21%  Similarity=0.263  Sum_probs=50.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch-------------hhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKL----FDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE-------------EAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~-------------~~~~~~~~~  204 (374)
                      ..|+|||||+.+++-+......    =..++||+....++..++. ++++.++.....             .......+.
T Consensus       103 ~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl~~~~~~~~i~i~~~~~~~~~~~lld~  181 (310)
T TIGR02236       103 EFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGLDPDEVLKNIYVARAYNSNHQMLLVEK  181 (310)
T ss_pred             CCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCCCHHHHhhceEEEecCCHHHHHHHHHH
Confidence            8899999999998765432111    1378999998888887765 445555433110             111123455


Q ss_pred             HHHHHhcCC--eEEEEEeCCCC
Q 045120          205 LYERLKNEN--KILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~~k--r~LlVlDdv~~  224 (374)
                      +.+.+...+  --+||+|.+..
T Consensus       182 l~~~i~~~~~~~~lVVIDSisa  203 (310)
T TIGR02236       182 AEDLIKELNNPVKLLIVDSLTS  203 (310)
T ss_pred             HHHHHHhcCCCceEEEEecchH
Confidence            666665422  45899998864

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.

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=94.42  E-value=0.18  Score=49.62  Aligned_cols=83  Identities=22%  Similarity=0.336  Sum_probs=53.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||+..+.+..... +-+.++++-++... ...++...+...-...       ..+++..      ..+-.+.+
T Consensus       151 ~~G~GKt~Ll~~~~~~~~~~-~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~~a~tiAE  229 (461)
T PRK12597        151 GAGVGKTVLMMELIFNISKQ-HSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVLTGLTIAE  229 (461)
T ss_pred             CCCCChhHHHHHHHHHHHhh-CCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            67999999999888876533 56888898887765 4556666665432211       1122221      23346777


Q ss_pred             HHhc--CCeEEEEEeCCCCc
Q 045120          208 RLKN--ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~--~kr~LlVlDdv~~~  225 (374)
                      +++.  +++.||++||+...
T Consensus       230 yfrd~~G~~VLl~~DslTR~  249 (461)
T PRK12597        230 YLRDEEKEDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHhcCCceEEEeccchHH
Confidence            7753  48999999999643

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=94.37  E-value=0.4  Score=46.59  Aligned_cols=55  Identities=15%  Similarity=0.151  Sum_probs=35.4

Q ss_pred             CeEEEEEeCCCCccccccccCcCCCC----------Cc---chhHhhhhcCCCCceecCCCCHHHHHH
Q 045120          213 NKILVILANIWKLLDLETVKIPFRND----------SR---DNNVVLLSMGSKDNFLIANITEEEAWR  267 (374)
Q Consensus       213 kr~LlVlDdv~~~~~~~~l~~~~~~~----------TR---~~~va~~~~~~~~~~~l~~L~~~~s~~  267 (374)
                      ++.+|+||.|.....|......+.+.          +.   ....+..-.|-...+++-|||-.|-..
T Consensus        94 ~~~yifLDEIq~v~~W~~~lk~l~d~~~~~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~  161 (398)
T COG1373          94 EKSYIFLDEIQNVPDWERALKYLYDRGNLDVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLK  161 (398)
T ss_pred             CCceEEEecccCchhHHHHHHHHHccccceEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHh
Confidence            57899999999998887653332221          10   111222234555689999999998865

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

Probab=94.27  E-value=0.17  Score=52.59  Aligned_cols=90  Identities=14%  Similarity=0.306  Sum_probs=52.7

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKL----FDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .+++||+.++.++++.|+..         -+|+|||++|.-++...--.+-    =+..++.     .++..+       
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~s-----LD~g~L-------  237 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYS-----LDLGSL-------  237 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEE-----ecHHHH-------
Confidence            46999999999999999854         5599999987777664321110    0112221     111111       


Q ss_pred             hCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          189 LGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                      +........-+++...+.+.++..++..|.+|.+.
T Consensus       238 vAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiH  272 (786)
T COG0542         238 VAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIH  272 (786)
T ss_pred             hccccccCcHHHHHHHHHHHHhcCCCeEEEEechh
Confidence            11111112334455555555554358999999875

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

Probab=94.26  E-value=2.5  Score=44.88  Aligned_cols=37  Identities=22%  Similarity=0.198  Sum_probs=30.9

Q ss_pred             ccccccHHHHHHHHHHhhcC---------------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTNA---------------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------------~gGiGKTtLA~~v~~~~  158 (374)
                      ...+|.+..+++|+++|...               +.|+||||+|+.+....
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l  373 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKAT  373 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            34889999999999887631               88999999999999744

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.25  E-value=3.4  Score=39.77  Aligned_cols=78  Identities=18%  Similarity=0.155  Sum_probs=44.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcCCch-hhHHHHHHHHHHHHh-cCCeEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLELSE-EAEYRRASRLYERLK-NENKILV  217 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~-~~kr~Ll  217 (374)
                      +.|+||||++..+......++  ..+.+|+.. ++.  ..+-++...+.++.+... .+..+....+ +.+. .+..=+|
T Consensus       214 ptGvGKTTt~akLA~~l~~~g--~~V~lItaD-tyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al-~~l~~~~~~D~V  289 (407)
T PRK12726        214 QTGVGKTTTLVKLGWQLLKQN--RTVGFITTD-TFRSGAVEQFQGYADKLDVELIVATSPAELEEAV-QYMTYVNCVDHI  289 (407)
T ss_pred             CCCCCHHHHHHHHHHHHHHcC--CeEEEEeCC-ccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHH-HHHHhcCCCCEE
Confidence            779999999988877553332  245566543 333  244556666666655322 2344443333 3333 1145688


Q ss_pred             EEeCCC
Q 045120          218 ILANIW  223 (374)
Q Consensus       218 VlDdv~  223 (374)
                      ++|-.-
T Consensus       290 LIDTAG  295 (407)
T PRK12726        290 LIDTVG  295 (407)
T ss_pred             EEECCC
Confidence            888764

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

Probab=94.25  E-value=0.076  Score=54.07  Aligned_cols=65  Identities=26%  Similarity=0.318  Sum_probs=44.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHH-hcCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERL-KNENKILVILA  220 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L-~~~kr~LlVlD  220 (374)
                      ++|+||||||.-|+++.-    | .++=|++|..-+...+-..|...+..+              ..| .+++..-||+|
T Consensus       334 ppGlGKTTLAHViAkqaG----Y-sVvEINASDeRt~~~v~~kI~~avq~~--------------s~l~adsrP~CLViD  394 (877)
T KOG1969|consen  334 PPGLGKTTLAHVIAKQAG----Y-SVVEINASDERTAPMVKEKIENAVQNH--------------SVLDADSRPVCLVID  394 (877)
T ss_pred             CCCCChhHHHHHHHHhcC----c-eEEEecccccccHHHHHHHHHHHHhhc--------------cccccCCCcceEEEe
Confidence            899999999999998653    3 467788888877777666665554322              122 12367778888


Q ss_pred             CCCCc
Q 045120          221 NIWKL  225 (374)
Q Consensus       221 dv~~~  225 (374)
                      .+...
T Consensus       395 EIDGa  399 (877)
T KOG1969|consen  395 EIDGA  399 (877)
T ss_pred             cccCC
Confidence            88754

>PTZ00035 Rad51 protein; Provisional

Probab=94.25  E-value=0.53  Score=44.66  Aligned_cols=82  Identities=20%  Similarity=0.224  Sum_probs=48.7

Q ss_pred             CCCccHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch----------hhHHHH---HHH
Q 045120          142 NGGIGKTTLAKEFAKQARED---K-LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE----------EAEYRR---ASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~----------~~~~~~---~~~  204 (374)
                      ..|+|||||+..+.-....-   + .=..++|++-...++..++ .++++.++.....          .+.++.   ...
T Consensus       126 ~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g~~~~~~l~nI~~~~~~~~e~~~~~l~~  204 (337)
T PTZ00035        126 EFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFGLDPEDVLDNIAYARAYNHEHQMQLLSQ  204 (337)
T ss_pred             CCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhCCChHhHhhceEEEccCCHHHHHHHHHH
Confidence            88999999999887544321   1 1135679988877887774 4456665543210          122222   233


Q ss_pred             HHHHHhcCCeEEEEEeCCCC
Q 045120          205 LYERLKNENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~~  224 (374)
                      +...+...+--|||+|-+..
T Consensus       205 ~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        205 AAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             HHHHhhccCccEEEEECcHH
Confidence            34444443567999998853

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.21  E-value=0.17  Score=53.30  Aligned_cols=38  Identities=29%  Similarity=0.339  Sum_probs=30.3

Q ss_pred             cccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~  158 (374)
                      ...+.|.+..+++|.+.+...                      +.|+||||||+.+.+..
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~  236 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEA  236 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHh
Confidence            445889999998887776321                      78999999999999854

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.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=94.16  E-value=0.051  Score=51.49  Aligned_cols=37  Identities=19%  Similarity=0.201  Sum_probs=32.4

Q ss_pred             cccccHHHHHHHHHHhhcC---------------CCCccHHHHHHHHHHHhh
Q 045120          123 AFESRVSNLKSTQNALTNA---------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~~---------------~gGiGKTtLA~~v~~~~~  159 (374)
                      .++|.++.++++++++...               +.|+||||||..+.+...
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~  103 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLE  103 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            6999999999999998642               889999999999988764

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=94.14  E-value=0.29  Score=48.13  Aligned_cols=83  Identities=19%  Similarity=0.341  Sum_probs=52.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||+..+..+..... =+.++++-++... ...++.+++...=...       ..+++..      ...-.+.+
T Consensus       152 ~~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~~a~tiAE  230 (463)
T PRK09280        152 GAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVALTGLTMAE  230 (463)
T ss_pred             CCCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            679999999999877655332 2567888887765 4566666666532211       1122221      12345667


Q ss_pred             HHhc--CCeEEEEEeCCCCc
Q 045120          208 RLKN--ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~--~kr~LlVlDdv~~~  225 (374)
                      +++.  +++.||++|++...
T Consensus       231 yfrd~~G~~VLll~DslTR~  250 (463)
T PRK09280        231 YFRDVEGQDVLLFIDNIFRF  250 (463)
T ss_pred             HHHHhcCCceEEEecchHHH
Confidence            7743  59999999999643

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

Probab=94.07  E-value=0.47  Score=48.54  Aligned_cols=53  Identities=23%  Similarity=0.202  Sum_probs=38.0

Q ss_pred             ccccccHHHHHHHHHHhhcC---------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      .+-+|.+..+++|++.|--.               ++|+|||+|++.|+.-..  ..|   +-++++.--|..
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~--Rkf---vR~sLGGvrDEA  390 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALG--RKF---VRISLGGVRDEA  390 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhC--CCE---EEEecCccccHH
Confidence            34679999999999988532               999999999999998443  444   334555444433

>CHL00176 ftsH cell division protein; Validated

Probab=94.05  E-value=0.17  Score=52.08  Aligned_cols=41  Identities=10%  Similarity=0.107  Sum_probs=26.1

Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG  296 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G  296 (374)
                      ..+.++..+.++-.++|+.++......+  ......++..+ .|
T Consensus       346 ~~I~v~lPd~~~R~~IL~~~l~~~~~~~--d~~l~~lA~~t-~G  386 (638)
T CHL00176        346 RQITVSLPDREGRLDILKVHARNKKLSP--DVSLELIARRT-PG  386 (638)
T ss_pred             eEEEECCCCHHHHHHHHHHHHhhcccch--hHHHHHHHhcC-CC
Confidence            4678888899999999988875322111  12234566666 55

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

Probab=94.04  E-value=0.17  Score=49.80  Aligned_cols=83  Identities=23%  Similarity=0.260  Sum_probs=50.5

Q ss_pred             ccccccH---HHHHHHHHHhhcC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH
Q 045120          122 EAFESRV---SNLKSTQNALTNA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKK  180 (374)
Q Consensus       122 ~~~vGr~---~~~~~i~~~L~~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  180 (374)
                      +++-|-|   .++++|++.|.++                  ++|.|||-||++|.....|-  |    |...+..|+.. 
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VP--F----F~~sGSEFdEm-  376 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVP--F----FYASGSEFDEM-  376 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCC--e----Eeccccchhhh-
Confidence            4466766   5667888999876                  88999999999999866543  2    33333333311 


Q ss_pred             HHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 045120          181 IQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWK  224 (374)
Q Consensus       181 ~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~  224 (374)
                           +-..        -..+...|+..-+..-.|.|.+|.+..
T Consensus       377 -----~VGv--------GArRVRdLF~aAk~~APcIIFIDEiDa  407 (752)
T KOG0734|consen  377 -----FVGV--------GARRVRDLFAAAKARAPCIIFIDEIDA  407 (752)
T ss_pred             -----hhcc--------cHHHHHHHHHHHHhcCCeEEEEechhh
Confidence                 0000        012233344444444689999998864

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=94.01  E-value=0.33  Score=41.74  Aligned_cols=34  Identities=32%  Similarity=0.495  Sum_probs=22.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC--------CeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF--------DRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F--------~~~~wv~vs~~  175 (374)
                      .+|+||||++.++..+......|        ..++|++....
T Consensus        40 ~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   40 PPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             CSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             CCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            89999999999988776543333        25678776655

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=93.98  E-value=0.23  Score=46.55  Aligned_cols=77  Identities=23%  Similarity=0.228  Sum_probs=46.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc------hhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS------EEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.++.....  ..-..++||.....++...     ++.+|...+      ..+.++....+...++.+..-
T Consensus        61 ~~ssGKttLaL~~ia~~q--~~g~~~a~ID~e~~ld~~~-----a~~lGvdl~rllv~~P~~~E~al~~~e~lirsg~~~  133 (322)
T PF00154_consen   61 PESSGKTTLALHAIAEAQ--KQGGICAFIDAEHALDPEY-----AESLGVDLDRLLVVQPDTGEQALWIAEQLIRSGAVD  133 (322)
T ss_dssp             STTSSHHHHHHHHHHHHH--HTT-EEEEEESSS---HHH-----HHHTT--GGGEEEEE-SSHHHHHHHHHHHHHTTSES
T ss_pred             CCCCchhhhHHHHHHhhh--cccceeEEecCcccchhhH-----HHhcCccccceEEecCCcHHHHHHHHHHHhhccccc
Confidence            778999999999887543  2345689999988877543     445554422      223445555666666665667


Q ss_pred             EEEEeCCCCc
Q 045120          216 LVILANIWKL  225 (374)
Q Consensus       216 LlVlDdv~~~  225 (374)
                      ++|+|-|-..
T Consensus       134 lVVvDSv~al  143 (322)
T PF00154_consen  134 LVVVDSVAAL  143 (322)
T ss_dssp             EEEEE-CTT-
T ss_pred             EEEEecCccc
Confidence            9999988644

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=93.97  E-value=2.9  Score=39.29  Aligned_cols=84  Identities=11%  Similarity=0.048  Sum_probs=50.6

Q ss_pred             CeEEEEEeCCCCcc--c----cccccCcCCCC-----Cc-chhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCc
Q 045120          213 NKILVILANIWKLL--D----LETVKIPFRND-----SR-DNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENC  280 (374)
Q Consensus       213 kr~LlVlDdv~~~~--~----~~~l~~~~~~~-----TR-~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~  280 (374)
                      ++=.+|+|++..-.  .    +..+..|-+..     |. ...+..+...--..+.+.+++.++..+.+......     
T Consensus       108 ~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~~~-----  182 (319)
T PRK06090        108 GYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQGIT-----  182 (319)
T ss_pred             CceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHcCCc-----
Confidence            45688888887432  1    33444444333     22 22332222222347889999999998888653111     


Q ss_pred             chHHHHHHHHHHccCCchHHHHHHhc
Q 045120          281 KFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       281 ~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                          ....++..+ +|.|+.+.-+..
T Consensus       183 ----~~~~~l~l~-~G~p~~A~~~~~  203 (319)
T PRK06090        183 ----VPAYALKLN-MGSPLKTLAMMK  203 (319)
T ss_pred             ----hHHHHHHHc-CCCHHHHHHHhC
Confidence                134678889 999998876664

>PTZ00185 ATPase alpha subunit; Provisional

Probab=93.90  E-value=0.4  Score=47.59  Aligned_cols=84  Identities=18%  Similarity=0.181  Sum_probs=49.8

Q ss_pred             CCCccHHHHH-HHHHHHhhhc-----CCCCeEEEEEeCCCCCHHHHHHHHHHHhC-cC-------CchhhHHH------H
Q 045120          142 NGGIGKTTLA-KEFAKQARED-----KLFDRVVFSEVSQTSDIKKIQGDIAEKLG-LE-------LSEEAEYR------R  201 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~-----~~F~~~~wv~vs~~~~~~~~~~~i~~~l~-~~-------~~~~~~~~------~  201 (374)
                      -.|+|||+|| -.+.|...+.     ++-+.++++-+++..+-..-+.+.++.-+ ..       ..+++...      .
T Consensus       197 d~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~~r~~Apy~  276 (574)
T PTZ00185        197 DRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGLQYLAPYS  276 (574)
T ss_pred             CCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHHHHHHHHHH
Confidence            6699999997 6667755321     23467899999988654333444444433 11       11111111      2


Q ss_pred             HHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          202 ASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       202 ~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .-.+.+++++ ++..|||+||+...
T Consensus       277 a~tiAEYFrd~GkdVLiv~DDLTr~  301 (574)
T PTZ00185        277 GVTMGEYFMNRGRHCLCVYDDLSKQ  301 (574)
T ss_pred             HHHHHHHHHHcCCCEEEEEcCchHH
Confidence            2345555542 58999999999754

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

Probab=93.88  E-value=0.27  Score=50.14  Aligned_cols=64  Identities=25%  Similarity=0.274  Sum_probs=40.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC--CCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT--SDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      ..|+|||+||+.+++... +++.-.+.+|+.+.-  ..+..+++.+-                ....+.+.. ..-+|||
T Consensus       439 ~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~----------------~vfse~~~~-~PSiIvL  500 (952)
T KOG0735|consen  439 PKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLN----------------NVFSEALWY-APSIIVL  500 (952)
T ss_pred             CCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHH----------------HHHHHHHhh-CCcEEEE
Confidence            789999999999999765 344444556655432  22333333222                233344445 6899999


Q ss_pred             eCCC
Q 045120          220 ANIW  223 (374)
Q Consensus       220 Ddv~  223 (374)
                      ||+.
T Consensus       501 Ddld  504 (952)
T KOG0735|consen  501 DDLD  504 (952)
T ss_pred             cchh
Confidence            9986

>PRK09183 transposase/IS protein; Provisional

Probab=93.87  E-value=3  Score=37.95  Aligned_cols=18  Identities=39%  Similarity=0.519  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+|||+||..+.+...
T Consensus       110 p~GtGKThLa~al~~~a~  127 (259)
T PRK09183        110 PSGVGKTHLAIALGYEAV  127 (259)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            889999999999977543

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

Probab=93.60  E-value=0.21  Score=44.19  Aligned_cols=61  Identities=16%  Similarity=0.149  Sum_probs=39.8

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKI  181 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~  181 (374)
                      ..++||-|+.++.+.-.-.++         |+|+||||=+..+.+..--..+=+.++=.+.|+.-.+.-+
T Consensus        26 l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvV   95 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVV   95 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHH
Confidence            456899999888887766655         9999999977776664432222244555555555444333

>PRK04328 hypothetical protein; Provisional

Probab=93.57  E-value=0.42  Score=43.25  Aligned_cols=32  Identities=16%  Similarity=0.273  Sum_probs=22.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      .+|+|||+||.++......+  -..++|++....
T Consensus        31 ~pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee~   62 (249)
T PRK04328         31 GPGTGKSIFSQQFLWNGLQM--GEPGVYVALEEH   62 (249)
T ss_pred             CCCCCHHHHHHHHHHHHHhc--CCcEEEEEeeCC
Confidence            78999999998866543212  346788877654

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=93.55  E-value=3.7  Score=38.89  Aligned_cols=87  Identities=15%  Similarity=0.050  Sum_probs=50.3

Q ss_pred             CCeEEEEEeCCCCcc------ccccccCcCCCC-----Ccc-hhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCC
Q 045120          212 ENKILVILANIWKLL------DLETVKIPFRND-----SRD-NNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVEN  279 (374)
Q Consensus       212 ~kr~LlVlDdv~~~~------~~~~l~~~~~~~-----TR~-~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~  279 (374)
                      +++=.+|+|++..-.      -+..+..|-+..     |.+ ..+..+...--..+.+.+++.++..+.+....+.   +
T Consensus       107 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~~~---~  183 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREVTM---S  183 (334)
T ss_pred             CCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHccCC---C
Confidence            366788999887432      144444444433     322 3332221222236789999999998887654321   1


Q ss_pred             cchHHHHHHHHHHccCCchHHHHHHh
Q 045120          280 CKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       280 ~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                         .+.+..++..+ +|.|..+.-+.
T Consensus       184 ---~~~a~~~~~la-~G~~~~Al~l~  205 (334)
T PRK07993        184 ---QDALLAALRLS-AGAPGAALALL  205 (334)
T ss_pred             ---HHHHHHHHHHc-CCCHHHHHHHh
Confidence               12355778899 99997544443

>PRK06620 hypothetical protein; Validated

Probab=93.53  E-value=0.53  Score=41.54  Aligned_cols=48  Identities=8%  Similarity=-0.182  Sum_probs=32.5

Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCc
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL  297 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~Gl  297 (374)
                      .+....++++++++.++-..++.+.+..... .--+++..-|++.+ .|-
T Consensus       135 Rl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l-~l~~ev~~~L~~~~-~~d  182 (214)
T PRK06620        135 RIKSVLSILLNSPDDELIKILIFKHFSISSV-TISRQIIDFLLVNL-PRE  182 (214)
T ss_pred             HHhCCceEeeCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHc-cCC
Confidence            4455568999999999988888887752211 11146667788888 543

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=93.52  E-value=0.48  Score=46.52  Aligned_cols=83  Identities=18%  Similarity=0.326  Sum_probs=52.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||+..+..+.... +=+.++++-++... ...++++++...=...       ..+++..      ...-.+.+
T Consensus       151 ~~G~GKt~L~~~~~~~~~~~-~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~~a~tiAE  229 (461)
T TIGR01039       151 GAGVGKTVLIQELINNIAKE-HGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVALTGLTMAE  229 (461)
T ss_pred             CCCCChHHHHHHHHHHHHhc-CCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            67999999999988765432 22477888887765 4566666665432111       1122211      13346777


Q ss_pred             HHhc--CCeEEEEEeCCCCc
Q 045120          208 RLKN--ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~--~kr~LlVlDdv~~~  225 (374)
                      +++.  +++.||++||+...
T Consensus       230 yfrd~~G~~VLll~DslTR~  249 (461)
T TIGR01039       230 YFRDEQGQDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHhcCCeeEEEecchhHH
Confidence            7754  58999999999754

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=93.50  E-value=0.42  Score=46.81  Aligned_cols=84  Identities=25%  Similarity=0.330  Sum_probs=53.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcC--CCC---------eEEEEEeCCCCCHHHHHHHHHHHhC-cC-------CchhhHH---
Q 045120          142 NGGIGKTTLAKEFAKQAREDK--LFD---------RVVFSEVSQTSDIKKIQGDIAEKLG-LE-------LSEEAEY---  199 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~--~F~---------~~~wv~vs~~~~~~~~~~~i~~~l~-~~-------~~~~~~~---  199 (374)
                      -.|+|||||+..+.+......  -.|         .++++.++......+.+...+..-+ ..       ..+.+..   
T Consensus       149 gsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~atsd~p~~~R~  228 (466)
T TIGR01040       149 AAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLANDPTIERI  228 (466)
T ss_pred             CCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHH
Confidence            569999999999988654210  022         6788888888666665665555544 21       1112111   


Q ss_pred             ---HHHHHHHHHHh--cCCeEEEEEeCCCCc
Q 045120          200 ---RRASRLYERLK--NENKILVILANIWKL  225 (374)
Q Consensus       200 ---~~~~~l~~~L~--~~kr~LlVlDdv~~~  225 (374)
                         ...-.+.++++  .+++.||++||+...
T Consensus       229 ~a~~~a~tiAEyfr~~~G~~VLl~~DslTr~  259 (466)
T TIGR01040       229 ITPRLALTTAEYLAYQCEKHVLVILTDMSSY  259 (466)
T ss_pred             HHHhhhHHHHHHHHHhcCCcEEEeccChHHH
Confidence               12345777777  258999999999643

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=93.38  E-value=0.37  Score=46.13  Aligned_cols=77  Identities=23%  Similarity=0.351  Sum_probs=47.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchh--hHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEE--AEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      -+|||||||..++..+..-+.   .++||+-..  ++.++ +--++.++.+...-  -.+-..+.+.+.+...+.-|+|+
T Consensus       101 dPGIGKSTLLLQva~~lA~~~---~vLYVsGEE--S~~Qi-klRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~p~lvVI  174 (456)
T COG1066         101 DPGIGKSTLLLQVAARLAKRG---KVLYVSGEE--SLQQI-KLRADRLGLPTNNLYLLAETNLEDIIAELEQEKPDLVVI  174 (456)
T ss_pred             CCCCCHHHHHHHHHHHHHhcC---cEEEEeCCc--CHHHH-HHHHHHhCCCccceEEehhcCHHHHHHHHHhcCCCEEEE
Confidence            669999999999998776443   677775433  33332 33456666543321  11223345555555558899999


Q ss_pred             eCCCC
Q 045120          220 ANIWK  224 (374)
Q Consensus       220 Ddv~~  224 (374)
                      |-+..
T Consensus       175 DSIQT  179 (456)
T COG1066         175 DSIQT  179 (456)
T ss_pred             eccce
Confidence            99853

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=93.37  E-value=0.42  Score=47.09  Aligned_cols=84  Identities=27%  Similarity=0.331  Sum_probs=52.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCC--eEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFD--RVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~--~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l  205 (374)
                      -.|+|||||+..+.+.....+.+.  .++++-+++.. ...++.+.+...=...       ..+++..      ...-.+
T Consensus       149 g~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a~~~a~ti  228 (458)
T TIGR01041       149 GSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVTPRMALTA  228 (458)
T ss_pred             CCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHHHHHHHHH
Confidence            669999999999988665432121  66788887765 4556666665432211       1112111      123457


Q ss_pred             HHHHh--cCCeEEEEEeCCCCc
Q 045120          206 YERLK--NENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~--~~kr~LlVlDdv~~~  225 (374)
                      .++++  .+++.||++||+...
T Consensus       229 AEyfr~d~G~~VLli~DslTR~  250 (458)
T TIGR01041       229 AEYLAFEKDMHVLVILTDMTNY  250 (458)
T ss_pred             HHHHHHccCCcEEEEEcChhHH
Confidence            78887  368999999999754

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=93.36  E-value=0.22  Score=42.26  Aligned_cols=27  Identities=30%  Similarity=0.503  Sum_probs=21.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFS  170 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  170 (374)
                      +.|+||||+|+.+++...  ..+...+++
T Consensus        15 ~~GsGKst~a~~l~~~l~--~~~~~~~~~   41 (176)
T PRK05541         15 LAGSGKTTIAKALYERLK--LKYSNVIYL   41 (176)
T ss_pred             CCCCCHHHHHHHHHHHHH--HcCCcEEEE
Confidence            789999999999998664  345555665

>TIGR00959 ffh signal recognition particle protein

Probab=93.22  E-value=0.74  Score=45.08  Aligned_cols=17  Identities=35%  Similarity=0.282  Sum_probs=14.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||.|..+....
T Consensus       107 ~~GsGKTTtaakLA~~l  123 (428)
T TIGR00959       107 LQGSGKTTTCGKLAYYL  123 (428)
T ss_pred             CCCCcHHHHHHHHHHHH
Confidence            89999999987777653

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=93.19  E-value=0.49  Score=46.31  Aligned_cols=80  Identities=19%  Similarity=0.327  Sum_probs=48.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    .+.++++-++...+ ..++..+.+..-+..       ..+++..      ...-.+.+
T Consensus       166 ~sG~GKTtLL~~I~~~~~----~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~~~a~tiAE  241 (442)
T PRK08927        166 GSGVGKSVLLSMLARNAD----ADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAAYLTLAIAE  241 (442)
T ss_pred             CCCCCHHHHHHHHHhccC----CCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            679999999999987543    35667777777654 345554444332211       1112111      12335666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.|+++||+-..
T Consensus       242 yfrd~G~~Vll~~DslTr~  260 (442)
T PRK08927        242 YFRDQGKDVLCLMDSVTRF  260 (442)
T ss_pred             HHHHCCCcEEEEEeCcHHH
Confidence            6642 58999999999643

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=93.17  E-value=0.34  Score=47.25  Aligned_cols=80  Identities=16%  Similarity=0.328  Sum_probs=49.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    .+.++++-++...+ ..++.+.++..-+..       ..+++..      ..+-.+.+
T Consensus       170 ~sG~GKSTLL~~I~~~~~----~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~A~tiAE  245 (444)
T PRK08972        170 GSGVGKSVLLGMMTRGTT----ADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCETATTIAE  245 (444)
T ss_pred             CCCCChhHHHHHhccCCC----CCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            779999999999986322    36777777777654 455655554432211       1112211      12334666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       246 yfrd~G~~VLl~~DslTR~  264 (444)
T PRK08972        246 YFRDQGLNVLLLMDSLTRY  264 (444)
T ss_pred             HHHHcCCCEEEEEcChHHH
Confidence            6642 58999999998643

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

Probab=93.08  E-value=1.5  Score=44.97  Aligned_cols=89  Identities=19%  Similarity=0.264  Sum_probs=53.9

Q ss_pred             ccccccHHHHHHHHHHhhcC---------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      +.-+|+++-+++|++++--.               ++|+|||.+|+.|..-.-  ..|   +-++|+.-.|..+|--.  
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALn--RkF---fRfSvGG~tDvAeIkGH--  483 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALN--RKF---FRFSVGGMTDVAEIKGH--  483 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhC--Cce---EEEeccccccHHhhccc--
Confidence            45679999999999987532               899999999999998543  333   23456655554443210  


Q ss_pred             HHhCcCCchhhHHHHHHHHHHHHhc--CCeEEEEEeCCCC
Q 045120          187 EKLGLELSEEAEYRRASRLYERLKN--ENKILVILANIWK  224 (374)
Q Consensus       187 ~~l~~~~~~~~~~~~~~~l~~~L~~--~kr~LlVlDdv~~  224 (374)
                             ...-...+-.++.+.|+.  ..+=|+.||.|..
T Consensus       484 -------RRTYVGAMPGkiIq~LK~v~t~NPliLiDEvDK  516 (906)
T KOG2004|consen  484 -------RRTYVGAMPGKIIQCLKKVKTENPLILIDEVDK  516 (906)
T ss_pred             -------ceeeeccCChHHHHHHHhhCCCCceEEeehhhh
Confidence                   000011122345555542  2456788888763

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=93.02  E-value=0.3  Score=46.91  Aligned_cols=78  Identities=21%  Similarity=0.277  Sum_probs=43.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchh--hHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEE--AEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      .+|+|||||+.++.......  -..++|++....  ...+ ..-+..++......  ......+.+.+.+...+.-+||+
T Consensus        90 ~pG~GKStLllq~a~~~a~~--g~~VlYvs~EEs--~~qi-~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~~~~lVVI  164 (372)
T cd01121          90 DPGIGKSTLLLQVAARLAKR--GGKVLYVSGEES--PEQI-KLRADRLGISTENLYLLAETNLEDILASIEELKPDLVII  164 (372)
T ss_pred             CCCCCHHHHHHHHHHHHHhc--CCeEEEEECCcC--HHHH-HHHHHHcCCCcccEEEEccCcHHHHHHHHHhcCCcEEEE
Confidence            78999999999998765422  246778765433  3332 22244555432211  00111233444444436778999


Q ss_pred             eCCCC
Q 045120          220 ANIWK  224 (374)
Q Consensus       220 Ddv~~  224 (374)
                      |.+..
T Consensus       165 DSIq~  169 (372)
T cd01121         165 DSIQT  169 (372)
T ss_pred             cchHH
Confidence            99853

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.

>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=93.01  E-value=0.07  Score=42.11  Aligned_cols=17  Identities=53%  Similarity=0.690  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+.+..
T Consensus         7 ~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    7 PPGSGKSTLAKELAERL   23 (121)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            68999999999998854

...

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=92.98  E-value=0.38  Score=50.35  Aligned_cols=75  Identities=19%  Similarity=0.202  Sum_probs=50.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.++.......  =..++|++....++.     ..+++++.....      .+.+.....+...+..++--
T Consensus        68 ~~GsGKTtLal~~~~~a~~~--G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~~~~~~  140 (790)
T PRK09519         68 PESSGKTTVALHAVANAQAA--GGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALD  140 (790)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHHHHHhhcCCCe
Confidence            88999999998866543322  256799988877774     367777765321      23344555566666655677


Q ss_pred             EEEEeCCC
Q 045120          216 LVILANIW  223 (374)
Q Consensus       216 LlVlDdv~  223 (374)
                      |||+|-+.
T Consensus       141 LVVIDSI~  148 (790)
T PRK09519        141 IVVIDSVA  148 (790)
T ss_pred             EEEEcchh
Confidence            99999986

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=92.83  E-value=0.44  Score=47.13  Aligned_cols=83  Identities=19%  Similarity=0.298  Sum_probs=52.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC--------------CchhhHH------H
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE--------------LSEEAEY------R  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~--------------~~~~~~~------~  200 (374)
                      -.|+|||||+..+..+... .+=+.++++-++... ...++...++..-...              ..+++..      .
T Consensus       169 g~GvGKs~L~~~~~~~~~~-~~~dv~V~~lIGERgrEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd~p~~~R~~a~~  247 (494)
T CHL00060        169 GAGVGKTVLIMELINNIAK-AHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPGARMRVGL  247 (494)
T ss_pred             CCCCChhHHHHHHHHHHHH-hcCCeEEEEEeccCchHHHHHHHHHHhcCccccCcccccceEEEEECCCCCHHHHHHHHH
Confidence            6699999999988876321 112788999888875 4566666666511100              1111211      2


Q ss_pred             HHHHHHHHHhc-CC-eEEEEEeCCCCc
Q 045120          201 RASRLYERLKN-EN-KILVILANIWKL  225 (374)
Q Consensus       201 ~~~~l~~~L~~-~k-r~LlVlDdv~~~  225 (374)
                      ..-.+.++++. ++ +.||++||+...
T Consensus       248 ~A~tiAEyfrd~g~~~VLll~DslTR~  274 (494)
T CHL00060        248 TALTMAEYFRDVNKQDVLLFIDNIFRF  274 (494)
T ss_pred             HHHHHHHHHHHcCCCCEEEEcccchHH
Confidence            33467788864 34 999999999754

>PRK04196 V-type ATP synthase subunit B; Provisional

Probab=92.80  E-value=0.5  Score=46.65  Aligned_cols=83  Identities=29%  Similarity=0.367  Sum_probs=53.3

Q ss_pred             CCCccHHHHHHHHHHHhhhc---CCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHH
Q 045120          142 NGGIGKTTLAKEFAKQARED---KLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~---~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~  204 (374)
                      -.|+|||||+..+.+.....   ..| .++++-+++.. ...++++.+...=...       ..+++..      ...-.
T Consensus       151 g~G~GKs~L~~~ia~~~~~d~~~~~~-v~V~~~iGeRgrEv~e~~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~~a~t  229 (460)
T PRK04196        151 GSGLPHNELAAQIARQAKVLGEEENF-AVVFAAMGITFEEANFFMEDFEETGALERSVVFLNLADDPAIERILTPRMALT  229 (460)
T ss_pred             CCCCCccHHHHHHHHhhhhccCCCce-EEEEEEeccccHHHHHHHHHHHhcCCcceEEEEEEcCCCCHHHHHHHHHHHHH
Confidence            56999999999998876532   111 67888887765 4566666665542211       1112211      13346


Q ss_pred             HHHHHh--cCCeEEEEEeCCCCc
Q 045120          205 LYERLK--NENKILVILANIWKL  225 (374)
Q Consensus       205 l~~~L~--~~kr~LlVlDdv~~~  225 (374)
                      +.++++  .+++.||++||+...
T Consensus       230 iAEyfr~d~G~~VLli~DslTR~  252 (460)
T PRK04196        230 AAEYLAFEKGMHVLVILTDMTNY  252 (460)
T ss_pred             HHHHHHHhcCCcEEEEEcChHHH
Confidence            778877  368999999999754

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=92.78  E-value=0.87  Score=40.67  Aligned_cols=44  Identities=16%  Similarity=0.200  Sum_probs=25.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ..|+||||||.++...... .. ..+++++  ...+..++++.+ .+++
T Consensus        32 ~~G~GKTtl~~~~~~~~~~-~g-~~~~yi~--~e~~~~~~~~~~-~~~g   75 (230)
T PRK08533         32 DESTGKSILSQRLAYGFLQ-NG-YSVSYVS--TQLTTTEFIKQM-MSLG   75 (230)
T ss_pred             CCCCCHHHHHHHHHHHHHh-CC-CcEEEEe--CCCCHHHHHHHH-HHhC
Confidence            7899999998666554321 22 3456666  333456666665 3444

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

Probab=92.74  E-value=0.45  Score=49.02  Aligned_cols=88  Identities=17%  Similarity=0.246  Sum_probs=55.8

Q ss_pred             ccccccccccHHHHHHHHHHhhcC---------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          118 NKVYEAFESRVSNLKSTQNALTNA---------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~~~---------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      ...-.++=|.++.+.+|.+-+.-+                     ++|.|||-||++|......       -|++|-.. 
T Consensus       668 nV~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL-------~FlSVKGP-  739 (953)
T KOG0736|consen  668 NVSWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSL-------NFLSVKGP-  739 (953)
T ss_pred             ccchhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhcee-------eEEeecCH-
Confidence            333455778888888888876542                     8999999999999986553       35655433 


Q ss_pred             CHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 045120          177 DIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL  225 (374)
Q Consensus       177 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~  225 (374)
                         +++..   .+|     ++ ++..+.+++.-+.-+.|.|.||.+.+.
T Consensus       740 ---ELLNM---YVG-----qS-E~NVR~VFerAR~A~PCVIFFDELDSl  776 (953)
T KOG0736|consen  740 ---ELLNM---YVG-----QS-EENVREVFERARSAAPCVIFFDELDSL  776 (953)
T ss_pred             ---HHHHH---Hhc-----ch-HHHHHHHHHHhhccCCeEEEecccccc
Confidence               11111   111     11 223345555555558999999998753

>TIGR00602 rad24 checkpoint protein rad24

Probab=92.61  E-value=0.16  Score=52.06  Aligned_cols=41  Identities=17%  Similarity=0.247  Sum_probs=33.3

Q ss_pred             ccccccccccHHHHHHHHHHhhcC--------------CCCccHHHHHHHHHHHh
Q 045120          118 NKVYEAFESRVSNLKSTQNALTNA--------------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~~~--------------~gGiGKTtLA~~v~~~~  158 (374)
                      |....+++|-+..++++..+|...              +.|+||||+++.+.+..
T Consensus        80 P~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l  134 (637)
T TIGR00602        80 PETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKEL  134 (637)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            344567999999999999888642              88999999999998754

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK06851 hypothetical protein; Provisional

Probab=92.61  E-value=1.8  Score=41.46  Aligned_cols=33  Identities=36%  Similarity=0.411  Sum_probs=24.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      ..|+|||||++.++.....+ .++..++-|-+.+
T Consensus       222 ~pG~GKstl~~~i~~~a~~~-G~~v~~~hC~~dP  254 (367)
T PRK06851        222 RPGTGKSTMLKKIAKAAEER-GFDVEVYHCGFDP  254 (367)
T ss_pred             CCCCcHHHHHHHHHHHHHhC-CCeEEEEeCCCCC
Confidence            88999999999999977544 4666666554444

>PRK06936 type III secretion system ATPase; Provisional

Probab=92.55  E-value=0.52  Score=46.09  Aligned_cols=80  Identities=18%  Similarity=0.366  Sum_probs=48.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHHH------HHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEYR------RASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~------~~~~l~~  207 (374)
                      ..|+|||||.+.+++...    -+.++++-++... ...++....+..-+..       ..+++...      ..-.+.+
T Consensus       170 ~sG~GKStLl~~Ia~~~~----~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~a~tiAE  245 (439)
T PRK06936        170 AAGGGKSTLLASLIRSAE----VDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAGFVATSIAE  245 (439)
T ss_pred             CCCCChHHHHHHHhcCCC----CCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            679999999999998543    3678888887765 3444444433321111       11122211      2234666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       246 yfrd~G~~Vll~~DslTR~  264 (439)
T PRK06936        246 YFRDQGKRVLLLMDSVTRF  264 (439)
T ss_pred             HHHHcCCCEEEeccchhHH
Confidence            6642 58999999999644

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

Probab=92.48  E-value=0.69  Score=41.73  Aligned_cols=87  Identities=16%  Similarity=0.241  Sum_probs=50.9

Q ss_pred             cccccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          117 SNKVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       117 ~~~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      |-..+..+-|=.+.+++|.+-+..+                      ++|.|||-+|++|.|...  ..|     +-|-.
T Consensus       172 pdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtd--acf-----irvig  244 (435)
T KOG0729|consen  172 PDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTD--ACF-----IRVIG  244 (435)
T ss_pred             CCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccC--ceE-----Eeehh
Confidence            3344455667777777776655433                      889999999999999433  334     32211


Q ss_pred             CCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          175 TSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       175 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                              .++++..-.     ....+...|++.-+.+|-|+|.+|.+.
T Consensus       245 --------selvqkyvg-----egarmvrelf~martkkaciiffdeid  280 (435)
T KOG0729|consen  245 --------SELVQKYVG-----EGARMVRELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             --------HHHHHHHhh-----hhHHHHHHHHHHhcccceEEEEeeccc
Confidence                    122222100     112234455555566678999999875

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

Probab=92.45  E-value=0.36  Score=50.86  Aligned_cols=93  Identities=17%  Similarity=0.198  Sum_probs=52.3

Q ss_pred             cccccHHHHHHHHHHhhc----------C--------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTN----------A--------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~----------~--------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      .++|-+..++.|.+.+..          +        +.|+|||+||+.+....     +...+.++++.-.+..    .
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l-----~~~~~~~d~se~~~~~----~  525 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL-----GVHLERFDMSEYMEKH----T  525 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHh-----cCCeEEEeCchhhhcc----c
Confidence            477888888888777652          1        78999999999998744     2234555554432211    1


Q ss_pred             HHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 045120          185 IAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL  225 (374)
Q Consensus       185 i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~  225 (374)
                      +...++.+.....- +....+.+.++.....+|+||++...
T Consensus       526 ~~~lig~~~gyvg~-~~~~~l~~~~~~~p~~VvllDEieka  565 (731)
T TIGR02639       526 VSRLIGAPPGYVGF-EQGGLLTEAVRKHPHCVLLLDEIEKA  565 (731)
T ss_pred             HHHHhcCCCCCccc-chhhHHHHHHHhCCCeEEEEechhhc
Confidence            12222222111000 01123444554434569999999743

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

Probab=92.43  E-value=0.44  Score=42.40  Aligned_cols=89  Identities=15%  Similarity=0.184  Sum_probs=53.1

Q ss_pred             cccccccHHHHHHHHHHh---hcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNAL---TNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L---~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      -..++|.|...+.+++--   ..+          ..|+||++|++++.+...-+  .-.  -|.|++.            
T Consensus        59 L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~--glr--LVEV~k~------------  122 (287)
T COG2607          59 LADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADE--GLR--LVEVDKE------------  122 (287)
T ss_pred             HHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhc--CCe--EEEEcHH------------
Confidence            445889888877776532   222          77999999999999966522  222  3333321            


Q ss_pred             HhCcCCchhhHHHHHHHHHHHHhc-CCeEEEEEeCCCCc---cccccccCcC
Q 045120          188 KLGLELSEEAEYRRASRLYERLKN-ENKILVILANIWKL---LDLETVKIPF  235 (374)
Q Consensus       188 ~l~~~~~~~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~---~~~~~l~~~~  235 (374)
                                +-.....|.+.|+. ..||.|..||+.=+   .....+...+
T Consensus       123 ----------dl~~Lp~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~L  164 (287)
T COG2607         123 ----------DLATLPDLVELLRARPEKFILFCDDLSFEEGDDAYKALKSAL  164 (287)
T ss_pred             ----------HHhhHHHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHh
Confidence                      11112344555543 37999999999733   2355554444

>PRK06696 uridine kinase; Validated

Probab=92.37  E-value=0.16  Score=45.20  Aligned_cols=34  Identities=29%  Similarity=0.347  Sum_probs=24.9

Q ss_pred             ccHHHHHHHHHHhhcC------------CCCccHHHHHHHHHHHhh
Q 045120          126 SRVSNLKSTQNALTNA------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       126 Gr~~~~~~i~~~L~~~------------~gGiGKTtLA~~v~~~~~  159 (374)
                      .|.+-+++|.+.+...            .+|+||||||+.+.....
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~   47 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIK   47 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3556666676666431            789999999999988654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=92.21  E-value=0.6  Score=43.10  Aligned_cols=76  Identities=21%  Similarity=0.218  Sum_probs=38.7

Q ss_pred             CCCccHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcCCch-hhHHHHHHHHHHHHhcCCeEEE
Q 045120          142 NGGIGKTTLAKEFAKQARED-KLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLELSE-EAEYRRASRLYERLKNENKILV  217 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~-~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~~kr~Ll  217 (374)
                      +.|+||||++..+......+ +.+ .+..|+.. .+.  ....+......++.+... .+..++...+. .+.  ..=+|
T Consensus       202 ptGvGKTTt~~kLa~~~~~~~g~~-~V~li~~D-~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~-~~~--~~d~v  276 (282)
T TIGR03499       202 PTGVGKTTTLAKLAARFVLEHGNK-KVALITTD-TYRIGAVEQLKTYAKILGVPVKVARDPKELRKALD-RLR--DKDLI  276 (282)
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCC-eEEEEECC-ccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHH-Hcc--CCCEE
Confidence            88999999998887765433 222 34555533 222  223333444444544322 12233332332 333  24578


Q ss_pred             EEeCC
Q 045120          218 ILANI  222 (374)
Q Consensus       218 VlDdv  222 (374)
                      ++|..
T Consensus       277 liDt~  281 (282)
T TIGR03499       277 LIDTA  281 (282)
T ss_pred             EEeCC
Confidence            88853

>PRK08149 ATP synthase SpaL; Validated

Probab=92.19  E-value=0.63  Score=45.41  Aligned_cols=80  Identities=14%  Similarity=0.272  Sum_probs=48.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~------~~~~~~l~~  207 (374)
                      ..|+|||||+..+.+...    -+.+++..+.... ++..+...........       ..+++.      ...+..+.+
T Consensus       159 ~sG~GKTTLl~~i~~~~~----~dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~~~a~tiAE  234 (428)
T PRK08149        159 SAGCGKTSLMNMLIEHSE----ADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAALVATTVAE  234 (428)
T ss_pred             CCCCChhHHHHHHhcCCC----CCeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHHHHHHHHHH
Confidence            779999999999987433    3455555565543 5566666666543221       111211      123345566


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      +++. +|+.||++||+-..
T Consensus       235 ~fr~~G~~Vll~~DslTr~  253 (428)
T PRK08149        235 YFRDQGKRVVLFIDSMTRY  253 (428)
T ss_pred             HHHHcCCCEEEEccchHHH
Confidence            6642 58999999999644

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=92.17  E-value=0.28  Score=50.36  Aligned_cols=72  Identities=13%  Similarity=0.167  Sum_probs=53.0

Q ss_pred             cccccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCc
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL  191 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  191 (374)
                      .....++|.+..++.|...+...       ..|+||||+|+.+.+..- ..+|+..+|..- ...+...+++.++..++.
T Consensus        28 ~~~~~vigq~~a~~~L~~~~~~~~~~l~~G~~G~GKttla~~l~~~l~-~~~~~~~~~~~n-p~~~~~~~~~~v~~~~G~  105 (637)
T PRK13765         28 RLIDQVIGQEHAVEVIKKAAKQRRHVMMIGSPGTGKSMLAKAMAELLP-KEELQDILVYPN-PEDPNNPKIRTVPAGKGK  105 (637)
T ss_pred             ccHHHcCChHHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHcC-hHhHHHheEeeC-CCcchHHHHHHHHHhcCH
Confidence            44567999999999888877765       889999999999987542 234577778654 334677778888777764


Q ss_pred             C
Q 045120          192 E  192 (374)
Q Consensus       192 ~  192 (374)
                      .
T Consensus       106 ~  106 (637)
T PRK13765        106 Q  106 (637)
T ss_pred             H
Confidence            3

>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=92.16  E-value=0.77  Score=38.78  Aligned_cols=18  Identities=39%  Similarity=0.455  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+||||++..+.....
T Consensus         8 ~~G~GKTt~~~~la~~~~   25 (173)
T cd03115           8 LQGVGKTTTAAKLALYLK   25 (173)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            789999999999887654

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.

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

Probab=92.04  E-value=0.55  Score=42.30  Aligned_cols=40  Identities=25%  Similarity=0.328  Sum_probs=31.4

Q ss_pred             cccccccHHHHHH---HHHHhhcC---------------CCCccHHHHHHHHHHHhhh
Q 045120          121 YEAFESRVSNLKS---TQNALTNA---------------NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       121 ~~~~vGr~~~~~~---i~~~L~~~---------------~gGiGKTtLA~~v~~~~~~  160 (374)
                      ...++|-+..+.+   |++.|.++               +.|.|||-+|+++.|..++
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kv  177 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKV  177 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCC
Confidence            3458898877654   67777765               8999999999999996653

>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=92.03  E-value=1.1  Score=38.99  Aligned_cols=79  Identities=19%  Similarity=0.207  Sum_probs=45.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcCCch----hhHHHHHHHHHHHHhcCCeEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLELSE----EAEYRRASRLYERLKNENKIL  216 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~~~~----~~~~~~~~~l~~~L~~~kr~L  216 (374)
                      +.|+||||.+-.+......+  =..+..++.... ....+-++..++.++.+...    .++.+......+.+..++.=+
T Consensus         9 ptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~~~~~~D~   86 (196)
T PF00448_consen    9 PTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKFRKKGYDL   86 (196)
T ss_dssp             STTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHHHHTTSSE
T ss_pred             CCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHHhhcCCCE
Confidence            78999999777776655533  234666765322 34556677888888876321    234444444344444423457


Q ss_pred             EEEeCC
Q 045120          217 VILANI  222 (374)
Q Consensus       217 lVlDdv  222 (374)
                      |++|-.
T Consensus        87 vlIDT~   92 (196)
T PF00448_consen   87 VLIDTA   92 (196)
T ss_dssp             EEEEE-
T ss_pred             EEEecC
Confidence            888865

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 ....

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=92.03  E-value=0.57  Score=39.68  Aligned_cols=76  Identities=17%  Similarity=0.157  Sum_probs=43.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcC-CeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNE-NKILVILA  220 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~-kr~LlVlD  220 (374)
                      ..|+|||++|.++...     ....++++.-...++. ++.+.|...-..........+....|.+.+... +.-.+++|
T Consensus         7 ~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLID   80 (169)
T cd00544           7 GARSGKSRFAERLAAE-----LGGPVTYIATAEAFDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLID   80 (169)
T ss_pred             CCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEE
Confidence            5699999999998753     2245677777777764 355555443322222222223333455555331 23479999


Q ss_pred             CCC
Q 045120          221 NIW  223 (374)
Q Consensus       221 dv~  223 (374)
                      .+.
T Consensus        81 clt   83 (169)
T cd00544          81 CLT   83 (169)
T ss_pred             cHh
Confidence            874

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.

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=91.95  E-value=0.85  Score=41.68  Aligned_cols=80  Identities=15%  Similarity=0.230  Sum_probs=46.0

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCeE-EEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHHH------HHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDRV-VFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEYR------RASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~------~~~~l  205 (374)
                      ..|+|||+|| ..+.+..    +-+.+ +++-++... ...++.+++...-...       ..+++...      ..-.+
T Consensus        77 ~~g~GKt~L~l~~i~~~~----~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a~~~a~ai  152 (274)
T cd01132          77 DRQTGKTAIAIDTIINQK----GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAPYTGCAM  152 (274)
T ss_pred             CCCCCccHHHHHHHHHhc----CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHHHHHHHHH
Confidence            5579999996 5666532    23555 777777765 4556666655432111       11121211      12345


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .+++.. ++..||++||+...
T Consensus       153 AE~fr~~G~~Vlvl~DslTr~  173 (274)
T cd01132         153 GEYFMDNGKHALIIYDDLSKQ  173 (274)
T ss_pred             HHHHHHCCCCEEEEEcChHHH
Confidence            555543 48999999998643

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PRK06835 DNA replication protein DnaC; Validated

Probab=91.90  E-value=0.62  Score=44.00  Aligned_cols=29  Identities=31%  Similarity=0.456  Sum_probs=21.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV  172 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v  172 (374)
                      ..|+|||.||..+.+...-++  -.++|+++
T Consensus       191 ~~GtGKThLa~aIa~~l~~~g--~~V~y~t~  219 (329)
T PRK06835        191 NTGTGKTFLSNCIAKELLDRG--KSVIYRTA  219 (329)
T ss_pred             CCCCcHHHHHHHHHHHHHHCC--CeEEEEEH
Confidence            779999999999999764332  25666654

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=91.89  E-value=0.14  Score=51.50  Aligned_cols=37  Identities=22%  Similarity=0.262  Sum_probs=31.4

Q ss_pred             ccccccHHHHHHHHHHhhcC---------------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTNA---------------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|.++.+++|++.|...               +.|+||||||+.+.+-.
T Consensus        76 ~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         76 EEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             hcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHH
Confidence            35889999999999998432               88999999999998844

>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=91.86  E-value=1.1  Score=38.24  Aligned_cols=39  Identities=18%  Similarity=0.297  Sum_probs=24.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      .+|+|||+||.++.......+  ..++|++...  +...+.+.
T Consensus         7 ~~G~GKT~l~~~~~~~~~~~g--~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           7 GPGTGKTTFALQFLYAGLARG--EPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CcEEEEECCC--CHHHHHHH
Confidence            689999999998866543221  3567876544  34444433

A related protein is found in archaea.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=91.84  E-value=1.3  Score=39.50  Aligned_cols=77  Identities=18%  Similarity=0.286  Sum_probs=45.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc---------------------hhhHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS---------------------EEAEYR  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~---------------------~~~~~~  200 (374)
                      ..|+||||||.++.......  =..++|++....  +.++.+.+ .+++....                     ..+...
T Consensus        33 ~~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~~~~~  107 (234)
T PRK06067         33 DHGTGKSVLSQQFVYGALKQ--GKKVYVITTENT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGFEWNSTLANK  107 (234)
T ss_pred             CCCCChHHHHHHHHHHHHhC--CCEEEEEEcCCC--HHHHHHHH-HHCCCChhHHHhCCCceEEeccccccccCcchHHH
Confidence            88999999999985543212  246788887654  34554443 33332111                     112244


Q ss_pred             HHHHHHHHHhcCCeEEEEEeCCC
Q 045120          201 RASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       201 ~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                      ....+.+.+...+.-++|+|.+.
T Consensus       108 ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067        108 LLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             HHHHHHHHHHhcCCCEEEEecHH
Confidence            55666666654345688899764

>PRK10536 hypothetical protein; Provisional

Probab=91.84  E-value=0.39  Score=43.43  Aligned_cols=49  Identities=22%  Similarity=0.230  Sum_probs=35.2

Q ss_pred             cccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEE
Q 045120          121 YEAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVF  169 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~w  169 (374)
                      ...+.+|......++.+|.+.       ..|+|||+||..+..+.-..+.|+..+-
T Consensus        54 ~~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI  109 (262)
T PRK10536         54 TSPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIV  109 (262)
T ss_pred             CccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEE
Confidence            344667888888888888766       8899999999998875432344544433

>PRK10867 signal recognition particle protein; Provisional

Probab=91.82  E-value=1.1  Score=43.81  Aligned_cols=18  Identities=44%  Similarity=0.468  Sum_probs=14.1

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||.+..+.....
T Consensus       108 ~~GsGKTTtaakLA~~l~  125 (433)
T PRK10867        108 LQGAGKTTTAGKLAKYLK  125 (433)
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            899999998777766443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=91.62  E-value=1  Score=42.02  Aligned_cols=36  Identities=25%  Similarity=0.212  Sum_probs=24.0

Q ss_pred             ccccHHHHHHHHHHhhc-----------CCCCccHHHHHHHHHHHhh
Q 045120          124 FESRVSNLKSTQNALTN-----------ANGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~~-----------~~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|-+....++..+...           ++.|+||||+|..+.+..-
T Consensus         3 ~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~   49 (325)
T COG0470           3 LVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELL   49 (325)
T ss_pred             cccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHh
Confidence            34445555555555542           2779999999999988654

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.58  E-value=0.71  Score=44.87  Aligned_cols=75  Identities=16%  Similarity=0.130  Sum_probs=37.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      ++|+||||++..+.........+  .+-+...+.+.  ....+...++.++.+.....  . ...+.+.+.....=+||+
T Consensus       231 ptGvGKTTtaaKLA~~~~~~~G~--~V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~~~~--~-~~~l~~~l~~~~~D~VLI  305 (432)
T PRK12724        231 PTGSGKTTSIAKLAAKYFLHMGK--SVSLYTTDNYRIAAIEQLKRYADTMGMPFYPVK--D-IKKFKETLARDGSELILI  305 (432)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCC--eEEEecccchhhhHHHHHHHHHHhcCCCeeehH--H-HHHHHHHHHhCCCCEEEE
Confidence            89999999999988754322222  23222233332  23334444455554432211  1 223444444323456888


Q ss_pred             eC
Q 045120          220 AN  221 (374)
Q Consensus       220 Dd  221 (374)
                      |-
T Consensus       306 DT  307 (432)
T PRK12724        306 DT  307 (432)
T ss_pred             eC
Confidence            84

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=91.58  E-value=0.95  Score=44.91  Aligned_cols=80  Identities=14%  Similarity=0.266  Sum_probs=49.3

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCe-EEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHHH------HHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDR-VVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEYR------RASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~------~~~~l  205 (374)
                      ..|+|||||| ..+.|..    .-|. ++++-+++.. ...++.+.+...=...       ..+.+...      ..-.+
T Consensus       170 ~~g~GKT~Lal~~I~~q~----~~dv~~V~~~IGeR~rev~e~i~~l~~~~~l~~tvvV~atsd~p~~~r~~ap~~a~ai  245 (497)
T TIGR03324       170 DRQTGKTAIAIDTILNQK----GRNVLCIYCAIGQRASAVAKVVANLREHGAMDYTIVVVTEGNDPPGLQYIAPYAATSI  245 (497)
T ss_pred             CCCCCHHHHHHHHHHHhc----CCCcEEEEEEeccCcHHHHHHHHHhhhcCCcceeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            4499999996 5777743    2465 7889898875 4556666665542221       11111111      22346


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .++++. +++.|||+||+...
T Consensus       246 AEyfrd~G~~VLlv~DdlTr~  266 (497)
T TIGR03324       246 GEHFMEQGRDVLIVYDDLTQH  266 (497)
T ss_pred             HHHHHhCCCCEEEEEcChhHH
Confidence            666643 58999999999754

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.

>PRK12678 transcription termination factor Rho; Provisional

Probab=91.46  E-value=0.72  Score=46.45  Aligned_cols=83  Identities=17%  Similarity=0.174  Sum_probs=44.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEE-EEEeCCCCC-HHHHHHHHHHHhCcCCchhh------HHHHHHHHHHHHh-cC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVV-FSEVSQTSD-IKKIQGDIAEKLGLELSEEA------EYRRASRLYERLK-NE  212 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~-wv~vs~~~~-~~~~~~~i~~~l~~~~~~~~------~~~~~~~l~~~L~-~~  212 (374)
                      ..|+|||||++.|.+.... .+-++.+ .+-|...+. +.++.+.+-..+-....+.+      .....-.+.++|. .+
T Consensus       424 pp~aGKTtLL~~IAn~i~~-n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~~Ae~fre~G  502 (672)
T PRK12678        424 PPKAGKTTILQNIANAITT-NNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIERAKRLVELG  502 (672)
T ss_pred             CCCCCHHHHHHHHHHHHhh-cCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence            7899999999999985532 2334444 445555543 33333332111111111111      1223334555553 35


Q ss_pred             CeEEEEEeCCCCc
Q 045120          213 NKILVILANIWKL  225 (374)
Q Consensus       213 kr~LlVlDdv~~~  225 (374)
                      +.+||++|++...
T Consensus       503 ~dVlillDSlTR~  515 (672)
T PRK12678        503 KDVVVLLDSITRL  515 (672)
T ss_pred             CCEEEEEeCchHH
Confidence            8999999998643

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=91.39  E-value=0.49  Score=48.56  Aligned_cols=69  Identities=13%  Similarity=0.169  Sum_probs=46.5

Q ss_pred             cccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCc
Q 045120          121 YEAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL  191 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~  191 (374)
                      ...++|.+..++.+...+...       +.|+||||||+.+.+.... ..|...+++.-+ ..+...++..++..++.
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~~~ll~G~pG~GKT~la~~la~~l~~-~~~~~~~~~~n~-~~~~~~~~~~v~~~~g~   92 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMAELLPD-EELEDILVYPNP-EDPNMPRIVEVPAGEGR   92 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHcCc-hhheeEEEEeCC-CCCchHHHHHHHHhhch
Confidence            456889998888888777665       8899999999999985432 233333333222 23455667777777764

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=91.34  E-value=0.58  Score=39.84  Aligned_cols=17  Identities=24%  Similarity=0.300  Sum_probs=14.9

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus         7 ~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         7 GPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            78999999999998744

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.

>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=91.34  E-value=0.15  Score=40.48  Aligned_cols=17  Identities=53%  Similarity=0.649  Sum_probs=14.9

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||||+.+....
T Consensus         6 ~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    6 IPGSGKTTIAKELAERL   22 (129)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            67999999999998863

...

>CHL00195 ycf46 Ycf46; Provisional

Probab=91.34  E-value=0.95  Score=45.15  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=17.8

Q ss_pred             CceecCCCCHHHHHHHHHHhcC
Q 045120          253 DNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      ..+.++.-+.++-.++|..+..
T Consensus       385 ~~i~v~lP~~~eR~~Il~~~l~  406 (489)
T CHL00195        385 EIFFLDLPSLEEREKIFKIHLQ  406 (489)
T ss_pred             eEEEeCCcCHHHHHHHHHHHHh
Confidence            4677888888999999988775

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

Probab=91.31  E-value=0.51  Score=44.58  Aligned_cols=55  Identities=20%  Similarity=0.170  Sum_probs=39.1

Q ss_pred             ccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 045120          124 FESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQG  183 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  183 (374)
                      ++|++..+..+...+..+       ..|+|||+||+++.....  .   ....|.........++.-
T Consensus        26 ~~g~~~~~~~~l~a~~~~~~vll~G~PG~gKT~la~~lA~~l~--~---~~~~i~~t~~l~p~d~~G   87 (329)
T COG0714          26 VVGDEEVIELALLALLAGGHVLLEGPPGVGKTLLARALARALG--L---PFVRIQCTPDLLPSDLLG   87 (329)
T ss_pred             eeccHHHHHHHHHHHHcCCCEEEECCCCccHHHHHHHHHHHhC--C---CeEEEecCCCCCHHHhcC
Confidence            788888888877666654       889999999999998544  2   235555566666555543

>PRK04296 thymidine kinase; Provisional

Probab=91.15  E-value=0.29  Score=42.31  Aligned_cols=76  Identities=17%  Similarity=0.122  Sum_probs=40.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch---hhHHHHHHHHHHHHhcCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE---EAEYRRASRLYERLKNENKILVI  218 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~---~~~~~~~~~l~~~L~~~kr~LlV  218 (374)
                      ..|.||||+|..+.......  -..++.+.  ..++.......++++++.....   ....+....+.+  ..++.-+||
T Consensus        10 ~~GsGKTT~~l~~~~~~~~~--g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~--~~~~~dvvi   83 (190)
T PRK04296         10 AMNSGKSTELLQRAYNYEER--GMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE--EGEKIDCVL   83 (190)
T ss_pred             CCCCHHHHHHHHHHHHHHHc--CCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh--hCCCCCEEE
Confidence            45999999998888765432  22333331  1122222234456666543322   223344444444  332445899


Q ss_pred             EeCCC
Q 045120          219 LANIW  223 (374)
Q Consensus       219 lDdv~  223 (374)
                      +|.+.
T Consensus        84 IDEaq   88 (190)
T PRK04296         84 IDEAQ   88 (190)
T ss_pred             EEccc
Confidence            99983

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=91.09  E-value=1.5  Score=40.01  Aligned_cols=31  Identities=23%  Similarity=0.338  Sum_probs=22.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      .+|+||||||.++.......  =..++|++...
T Consensus        44 ~pGtGKT~l~~qf~~~~a~~--Ge~vlyis~Ee   74 (259)
T TIGR03878        44 VSDTGKSLMVEQFAVTQASR--GNPVLFVTVES   74 (259)
T ss_pred             CCCCCHHHHHHHHHHHHHhC--CCcEEEEEecC
Confidence            88999999999875543322  24678888764

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=91.03  E-value=1.6  Score=41.39  Aligned_cols=79  Identities=14%  Similarity=0.231  Sum_probs=48.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHh----CcC----------CchhhHHH------
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKL----GLE----------LSEEAEYR------  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l----~~~----------~~~~~~~~------  200 (374)
                      ..|+|||+|++++.+...    -+.++++-++... .+.+++.++-+.-    +..          ..+++...      
T Consensus       165 ~~G~GKT~L~~~Iak~~~----~dvvVyv~iGERg~Ev~e~l~ef~~l~~~~~~~~~m~rtvlV~nts~~p~~~R~~s~y  240 (369)
T cd01134         165 PFGCGKTVIQQSLSKYSN----SDIVIYVGCGERGNEMTEVLEEFPELTDPVTGEPLMKRTVLIANTSNMPVAAREASIY  240 (369)
T ss_pred             CCCCChHHHHHHHHhCCC----CCEEEEEEeCCChHHHHHHHHHHHhhccccccCCccceEEEEEECCCCCHHHHHHHHH
Confidence            679999999999988543    4678889888765 4555665543311    111          11122111      


Q ss_pred             HHHHHHHHHhc-CCeEEEEEeCCCC
Q 045120          201 RASRLYERLKN-ENKILVILANIWK  224 (374)
Q Consensus       201 ~~~~l~~~L~~-~kr~LlVlDdv~~  224 (374)
                      ..-.+.+++++ ++..|+++|++..
T Consensus       241 ta~tiAEYfrd~G~dVll~~Ds~tR  265 (369)
T cd01134         241 TGITIAEYFRDMGYNVALMADSTSR  265 (369)
T ss_pred             HHHHHHHHHHHcCCCEEEEEcChhH
Confidence            22345566642 5899999999853

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=91.00  E-value=0.28  Score=40.84  Aligned_cols=25  Identities=36%  Similarity=0.525  Sum_probs=20.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRV  167 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~  167 (374)
                      |+|+|||||++.+.+..+..+ |...
T Consensus        13 ~PGvGKtTl~~ki~e~L~~~g-~kvg   37 (179)
T COG1618          13 RPGVGKTTLVLKIAEKLREKG-YKVG   37 (179)
T ss_pred             CCCccHHHHHHHHHHHHHhcC-ceee
Confidence            899999999999998776443 6544

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=90.99  E-value=1.6  Score=43.67  Aligned_cols=77  Identities=14%  Similarity=0.232  Sum_probs=47.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch----------------hhHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE----------------EAEYRRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~----------------~~~~~~~~~l  205 (374)
                      ..|+|||||+.++......+  =..+++++...  +..++... ++.++.....                .+.++.+..+
T Consensus       271 ~~G~GKt~l~~~f~~~~~~~--ge~~~y~s~eE--s~~~i~~~-~~~lg~~~~~~~~~g~l~~~~~~p~~~~~~~~~~~i  345 (484)
T TIGR02655       271 ATGTGKTLLVSKFLENACAN--KERAILFAYEE--SRAQLLRN-AYSWGIDFEEMEQQGLLKIICAYPESAGLEDHLQII  345 (484)
T ss_pred             CCCCCHHHHHHHHHHHHHHC--CCeEEEEEeeC--CHHHHHHH-HHHcCCChHHHhhCCcEEEEEcccccCChHHHHHHH
Confidence            88999999999987755422  24566765443  44455444 3455432211                1235566777


Q ss_pred             HHHHhcCCeEEEEEeCCC
Q 045120          206 YERLKNENKILVILANIW  223 (374)
Q Consensus       206 ~~~L~~~kr~LlVlDdv~  223 (374)
                      .+.+...+.-.+|+|.+.
T Consensus       346 ~~~i~~~~~~~vvIDsi~  363 (484)
T TIGR02655       346 KSEIADFKPARIAIDSLS  363 (484)
T ss_pred             HHHHHHcCCCEEEEcCHH
Confidence            777765456688999874

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.

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=90.93  E-value=1.7  Score=42.30  Aligned_cols=69  Identities=19%  Similarity=0.287  Sum_probs=52.8

Q ss_pred             ccccHHHHHHHHHHhh---cC-------CC--CccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-------CHHHHHHH
Q 045120          124 FESRVSNLKSTQNALT---NA-------NG--GIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-------DIKKIQGD  184 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~---~~-------~g--GiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~  184 (374)
                      .|||+.+++.|.+-|.   .+       .|  |.|||.+.+.+.+...-+ .| .+..|.+|..-       ....+.++
T Consensus        27 ~VGr~~e~~~l~~~l~~v~~G~s~~kfi~G~YGsGKTf~l~~i~~~A~~~-~f-vvs~v~ls~e~~lh~~~g~~~~~Yr~  104 (416)
T PF10923_consen   27 AVGREREIEALDRDLDRVADGGSSFKFIRGEYGSGKTFFLRLIRERALEK-GF-VVSEVDLSPERPLHGTGGQLEALYRE  104 (416)
T ss_pred             eechHHHHHHHHHHHHHHhCCCCeEEEEEeCCCCcHHHHHHHHHHHHHHc-CC-EEEEEecCCCcccccccccHHHHHHH
Confidence            6899999999988875   33       44  999999999998876543 35 56777777642       56789999


Q ss_pred             HHHHhCcCCc
Q 045120          185 IAEKLGLELS  194 (374)
Q Consensus       185 i~~~l~~~~~  194 (374)
                      |++.+.....
T Consensus       105 l~~nL~t~~~  114 (416)
T PF10923_consen  105 LMRNLSTKTK  114 (416)
T ss_pred             HHHhcCCCCC
Confidence            9999986654

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=90.89  E-value=0.72  Score=49.43  Aligned_cols=37  Identities=24%  Similarity=0.364  Sum_probs=29.1

Q ss_pred             ccccccHHHHHHHHHHhhc------------C------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTN------------A------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~------------~------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|.+..++.|.+.+..            +      +.|+|||+||+.+.+..
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l  622 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM  622 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3588999998888777642            1      78999999999998743

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=90.84  E-value=2  Score=39.16  Aligned_cols=44  Identities=20%  Similarity=0.268  Sum_probs=28.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .+|+|||||+.++..+..... =..++|+++..  +..++...+...
T Consensus        38 ~~G~GKT~l~~~~~~~~~~~~-g~~vl~iS~E~--~~~~~~~r~~~~   81 (271)
T cd01122          38 GTGVGKTTFLREYALDLITQH-GVRVGTISLEE--PVVRTARRLLGQ   81 (271)
T ss_pred             CCCCCHHHHHHHHHHHHHHhc-CceEEEEEccc--CHHHHHHHHHHH
Confidence            789999999999877553221 23577887655  344555555443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=90.79  E-value=1.9  Score=38.48  Aligned_cols=43  Identities=16%  Similarity=0.259  Sum_probs=27.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      .+|+|||+++.++..+...... ..++|++...  +..++...++.
T Consensus        21 ~~G~GKT~~~~~~~~~~~~~~g-~~vly~s~E~--~~~~~~~r~~~   63 (242)
T cd00984          21 RPSMGKTAFALNIAENIAKKQG-KPVLFFSLEM--SKEQLLQRLLA   63 (242)
T ss_pred             CCCCCHHHHHHHHHHHHHHhCC-CceEEEeCCC--CHHHHHHHHHH
Confidence            7899999999988776554322 2456665444  44555555543

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.

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

Probab=90.78  E-value=1.4  Score=44.71  Aligned_cols=41  Identities=27%  Similarity=0.271  Sum_probs=29.7

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      ..-..+-|.|+-+.+|.+.+.-+                      ++|+|||++|+.+.+...
T Consensus       431 v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~  493 (693)
T KOG0730|consen  431 VSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAG  493 (693)
T ss_pred             CChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhc
Confidence            33344556777777776655433                      899999999999999655

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=90.77  E-value=0.86  Score=44.37  Aligned_cols=80  Identities=23%  Similarity=0.411  Sum_probs=46.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    .+..+++.++... .+.++.......=...       ..+++..      ...-.+.+
T Consensus       145 ~sG~GKTtLl~~I~~~~~----~~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~~~a~tiAE  220 (411)
T TIGR03496       145 GSGVGKSTLLGMMARYTE----ADVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAAFYATAIAE  220 (411)
T ss_pred             CCCCCHHHHHHHHhcCCC----CCEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            779999999998887433    3455556666654 3444555444331111       1112111      12334566


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      +++. +++.||++||+...
T Consensus       221 yfr~~G~~Vll~~Dsltr~  239 (411)
T TIGR03496       221 YFRDQGKDVLLLMDSLTRF  239 (411)
T ss_pred             HHHHCCCCEEEEEeChHHH
Confidence            6642 58999999998643

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=90.72  E-value=0.74  Score=49.37  Aligned_cols=97  Identities=20%  Similarity=0.217  Sum_probs=53.5

Q ss_pred             ccccccHHHHHHHHHHhhc-----------C-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTN-----------A-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQG  183 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~-----------~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  183 (374)
                      ..++|.+..++.+.+.+..           .       +.|+|||+||+.+.....  ..-...+.++++...+...+  
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~--~~~~~~i~~d~s~~~~~~~~--  640 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLF--DDEDAMVRIDMSEYMEKHSV--  640 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhc--CCCCcEEEEechhhcccchH--
Confidence            4588999999998888753           1       889999999999987432  11223445555543221111  


Q ss_pred             HHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 045120          184 DIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL  225 (374)
Q Consensus       184 ~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~  225 (374)
                        ...++.+..-..-+ ....+.+.++.....+|+||++...
T Consensus       641 --~~l~g~~~g~~g~~-~~g~l~~~v~~~p~~vlllDeieka  679 (852)
T TIGR03346       641 --ARLIGAPPGYVGYE-EGGQLTEAVRRKPYSVVLFDEVEKA  679 (852)
T ss_pred             --HHhcCCCCCccCcc-cccHHHHHHHcCCCcEEEEeccccC
Confidence              11122221100000 0123444444424459999999754

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=90.64  E-value=0.74  Score=42.00  Aligned_cols=48  Identities=23%  Similarity=0.236  Sum_probs=29.6

Q ss_pred             HHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHH
Q 045120          130 NLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQ  182 (374)
Q Consensus       130 ~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  182 (374)
                      -++++..++..+       ..|+|||+||+.+.+..  .  . ..+.++.+...+..+++
T Consensus        10 l~~~~l~~l~~g~~vLL~G~~GtGKT~lA~~la~~l--g--~-~~~~i~~~~~~~~~dll   64 (262)
T TIGR02640        10 VTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKR--D--R-PVMLINGDAELTTSDLV   64 (262)
T ss_pred             HHHHHHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHh--C--C-CEEEEeCCccCCHHHHh
Confidence            345555555544       88999999999998722  1  1 23455555555544443

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).

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

Probab=90.64  E-value=1  Score=43.02  Aligned_cols=18  Identities=22%  Similarity=0.209  Sum_probs=16.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+|||.+|+.+++...
T Consensus       156 PPGcGKTllAraiA~elg  173 (413)
T PLN00020        156 GKGQGKSFQCELVFKKMG  173 (413)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            789999999999999665

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=90.55  E-value=0.4  Score=41.90  Aligned_cols=44  Identities=27%  Similarity=0.364  Sum_probs=29.9

Q ss_pred             cHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEEE
Q 045120          127 RVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVFS  170 (374)
Q Consensus       127 r~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  170 (374)
                      +..+-...++.|...       ++|+|||.||.+..-+.-..+.|+..+++
T Consensus         5 ~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~   55 (205)
T PF02562_consen    5 KNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIIT   55 (205)
T ss_dssp             -SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE
T ss_pred             CCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            334445556666543       89999999999988776666889888877

; GO: 0005524 ATP binding; PDB: 3B85_A.

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

Probab=90.49  E-value=1.3  Score=44.54  Aligned_cols=113  Identities=19%  Similarity=0.265  Sum_probs=61.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ++|+|||-||++|.|...  -.|     ++|...    +++..   .+|     ++ +.....++..-+..-.|.|.||.
T Consensus       553 PPGCGKTLlAKAVANEag--~NF-----isVKGP----ELlNk---YVG-----ES-ErAVR~vFqRAR~saPCVIFFDE  612 (802)
T KOG0733|consen  553 PPGCGKTLLAKAVANEAG--ANF-----ISVKGP----ELLNK---YVG-----ES-ERAVRQVFQRARASAPCVIFFDE  612 (802)
T ss_pred             CCCccHHHHHHHHhhhcc--Cce-----EeecCH----HHHHH---Hhh-----hH-HHHHHHHHHHhhcCCCeEEEecc
Confidence            889999999999999655  334     544432    11111   111     11 22234455555555799999999


Q ss_pred             CCCcc-------------ccccccCcCCCC-----------CcchhHhhh---hcC-CCCceecCCCCHHHHHHHHHHhc
Q 045120          222 IWKLL-------------DLETVKIPFRND-----------SRDNNVVLL---SMG-SKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       222 v~~~~-------------~~~~l~~~~~~~-----------TR~~~va~~---~~~-~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                      +....             ...+|..-+...           |-+.++...   ..| -....-++.-+.+|-.++++...
T Consensus       613 iDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~t  692 (802)
T KOG0733|consen  613 IDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTIT  692 (802)
T ss_pred             hhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHh
Confidence            86320             122222222111           444333211   111 12355667778889999999888


Q ss_pred             C
Q 045120          274 G  274 (374)
Q Consensus       274 ~  274 (374)
                      .
T Consensus       693 k  693 (802)
T KOG0733|consen  693 K  693 (802)
T ss_pred             c
Confidence            6

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=90.48  E-value=1.1  Score=44.19  Aligned_cols=80  Identities=18%  Similarity=0.268  Sum_probs=47.2

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCeE-EEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHHH------HHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDRV-VFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEYR------RASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~------~~~~l  205 (374)
                      ..|+|||||| ..+.|..    .-|.+ +++-+++.. ...++.+.+...=...       ..+.+...      ..-.+
T Consensus       149 ~~g~GKt~Lal~~I~~q~----~~dv~cV~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atad~~~~~r~~ap~~a~ai  224 (485)
T CHL00059        149 DRQTGKTAVATDTILNQK----GQNVICVYVAIGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQYLAPYTGAAL  224 (485)
T ss_pred             CCCCCHHHHHHHHHHhcc----cCCeEEEEEEecCCchHHHHHHHHhhcccchhceEEEEeCCCCCHHHHHHHHHHHhhH
Confidence            6699999996 4465532    24555 888888765 4556666555432211       11111111      12345


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .++++. +++.|||+||+...
T Consensus       225 AEyfr~~G~~VLlv~DdlTr~  245 (485)
T CHL00059        225 AEYFMYRGRHTLIIYDDLSKQ  245 (485)
T ss_pred             HHHHHHcCCCEEEEEcChhHH
Confidence            566653 48999999999754

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=90.37  E-value=0.73  Score=40.86  Aligned_cols=76  Identities=18%  Similarity=0.338  Sum_probs=42.8

Q ss_pred             CCCccHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCC----------------c-----hhhHH
Q 045120          142 NGGIGKTTLAKEFAKQARED-KLFDRVVFSEVSQTSDIKKIQGDIAEKLGLEL----------------S-----EEAEY  199 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~-~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~----------------~-----~~~~~  199 (374)
                      ..|+|||+|+.++......+ +  ..++|++...++  .++.+.+- .++...                .     ..+..
T Consensus        27 ~~GsGKT~l~~q~l~~~~~~~g--e~vlyvs~ee~~--~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~~~~~~~~~  101 (226)
T PF06745_consen   27 PPGSGKTTLALQFLYNGLKNFG--EKVLYVSFEEPP--EELIENMK-SFGWDLEEYEDSGKLKIIDAFPERIGWSPNDLE  101 (226)
T ss_dssp             STTSSHHHHHHHHHHHHHHHHT----EEEEESSS-H--HHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGST-TSCCHH
T ss_pred             CCCCCcHHHHHHHHHHhhhhcC--CcEEEEEecCCH--HHHHHHHH-HcCCcHHHHhhcCCEEEEecccccccccccCHH
Confidence            88999999998865433222 1  356788765543  44444432 333210                0     12345


Q ss_pred             HHHHHHHHHHhcCCeEEEEEeCC
Q 045120          200 RRASRLYERLKNENKILVILANI  222 (374)
Q Consensus       200 ~~~~~l~~~L~~~kr~LlVlDdv  222 (374)
                      .....+.+.++..+...+|+|.+
T Consensus       102 ~l~~~i~~~i~~~~~~~vVIDsl  124 (226)
T PF06745_consen  102 ELLSKIREAIEELKPDRVVIDSL  124 (226)
T ss_dssp             HHHHHHHHHHHHHTSSEEEEETH
T ss_pred             HHHHHHHHHHHhcCCCEEEEECH
Confidence            56666777666535578888875

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 ....

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=90.33  E-value=1.3  Score=43.59  Aligned_cols=80  Identities=18%  Similarity=0.364  Sum_probs=46.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~------~~~~~~l~~  207 (374)
                      ..|+|||||++.+.+..    ..+.+++..++... +...+...+...-+..       ..+.+.      ...+-.+.+
T Consensus       176 ~sG~GKSTLl~~I~g~~----~~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~~~a~aiAE  251 (451)
T PRK05688        176 GTGVGKSVLLGMMTRFT----EADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAAMYCTRIAE  251 (451)
T ss_pred             CCCCCHHHHHHHHhCCC----CCCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            67999999999987632    23455555555443 4555555554443221       111111      112335666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       252 yfrd~G~~VLl~~DslTR~  270 (451)
T PRK05688        252 YFRDKGKNVLLLMDSLTRF  270 (451)
T ss_pred             HHHHCCCCEEEEecchhHH
Confidence            6643 58999999999654

>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit

Probab=90.30  E-value=1.2  Score=44.54  Aligned_cols=80  Identities=16%  Similarity=0.282  Sum_probs=48.8

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCeE-EEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDRV-VFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l  205 (374)
                      ..|+|||||| ..+.+..    ..|.+ +++-+++.. ...++.+.+...=...       ..+++..      ...-.+
T Consensus       169 ~~g~GKt~Lal~~i~~~~----~~dv~~V~~~IGer~rev~e~~~~~~~~~~l~~tvvV~atsd~p~~~r~~a~~~a~ai  244 (501)
T TIGR00962       169 DRQTGKTAVAIDTIINQK----DSDVYCVYVAIGQKASTVAQVVRKLEEHGAMDYTIVVAATASDSASLQYLAPYTGCTM  244 (501)
T ss_pred             CCCCCccHHHHHHHHhhc----CCCeEEEEEEccCChHHHHHHHHHHHhcCccceeEEEEecCCCCHHHHHHHHHHHHHH
Confidence            4499999996 5666643    35664 888888865 4566666665532211       1111111      123355


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .++++. +++.|||+||+...
T Consensus       245 AEyfrd~G~~VLlv~Ddltr~  265 (501)
T TIGR00962       245 AEYFRDNGKHALIIYDDLSKH  265 (501)
T ss_pred             HHHHHHcCCCEEEEecchHHH
Confidence            666653 48999999999754

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=90.29  E-value=14  Score=38.88  Aligned_cols=18  Identities=33%  Similarity=0.493  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||++..+.....
T Consensus       193 pnGvGKTTTiaKLA~~~~  210 (767)
T PRK14723        193 PTGVGKTTTTAKLAARCV  210 (767)
T ss_pred             CCCCcHHHHHHHHHhhHH
Confidence            889999998888876553

>PRK05922 type III secretion system ATPase; Validated

Probab=90.26  E-value=1.5  Score=42.99  Aligned_cols=80  Identities=19%  Similarity=0.313  Sum_probs=46.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~------~~~~~~l~~  207 (374)
                      ..|+|||||.+.+.+...    .+...++.++... .....+.+....+...       ..+++.      ....-.+.+
T Consensus       165 ~nG~GKSTLL~~Ia~~~~----~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~~~a~tiAE  240 (434)
T PRK05922        165 EPGSGKSSLLSTIAKGSK----STINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAGRAAMTIAE  240 (434)
T ss_pred             CCCCChHHHHHHHhccCC----CCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            569999999999987432    3445555555433 3345555544433221       111111      112345666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       241 yfrd~G~~VLl~~DslTR~  259 (434)
T PRK05922        241 YFRDQGHRVLFIMDSLSRW  259 (434)
T ss_pred             HHHHcCCCEEEeccchhHH
Confidence            6643 58999999999754

>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=90.22  E-value=1.5  Score=42.08  Aligned_cols=78  Identities=21%  Similarity=0.362  Sum_probs=52.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcC-------CchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLE-------LSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~------~~~~~~l~~  207 (374)
                      -.|+|||||.-++.+..+    +|..+-.-++.. -.+.++.++.+..-+..       ..+.+.      ...+..+.+
T Consensus       171 gsGVGKStLLgMiar~t~----aDv~ViaLIGERGREVrEFIE~~Lg~egl~rsViVvATSD~s~l~R~~aa~~At~IAE  246 (441)
T COG1157         171 GSGVGKSTLLGMIARNTE----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESALMRLKAAFTATTIAE  246 (441)
T ss_pred             cCCCcHHHHHHHHhcccc----CCEEEEEEeeccchhHHHHHHHhcchhhccceEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            669999999999998443    777666656654 35666766666655433       112221      224557888


Q ss_pred             HHhc-CCeEEEEEeCCC
Q 045120          208 RLKN-ENKILVILANIW  223 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~  223 (374)
                      +.++ +|+.||++|-+-
T Consensus       247 yFRDqG~~VLL~mDSlT  263 (441)
T COG1157         247 YFRDQGKRVLLIMDSLT  263 (441)
T ss_pred             HHHhCCCeEEEEeecHH
Confidence            8874 599999999884

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

Probab=90.20  E-value=2.5  Score=37.97  Aligned_cols=41  Identities=24%  Similarity=0.266  Sum_probs=31.1

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      ..+..+-|.+-.+.+|.+.+.-+                      ++|+|||-||++|.|+..
T Consensus       152 vsy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~  214 (408)
T KOG0727|consen  152 VSYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  214 (408)
T ss_pred             ccccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccc
Confidence            33445668887788777765433                      889999999999999665

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=90.18  E-value=0.61  Score=39.90  Aligned_cols=17  Identities=53%  Similarity=0.702  Sum_probs=15.3

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      .+|+||||+|+.+.+..
T Consensus         8 ~pGaGK~T~A~~La~~~   24 (178)
T COG0563           8 PPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            68999999999999874

>CHL00095 clpC Clp protease ATP binding subunit

Probab=90.18  E-value=0.76  Score=49.12  Aligned_cols=97  Identities=18%  Similarity=0.208  Sum_probs=52.4

Q ss_pred             ccccccHHHHHHHHHHhhcC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQG  183 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  183 (374)
                      ..++|-+..++.|.+.+...                  +.|+|||+||+.+.+..-  +.-...+-++++.-.+...+  
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~--~~~~~~~~~d~s~~~~~~~~--  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFF--GSEDAMIRLDMSEYMEKHTV--  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhc--CCccceEEEEchhccccccH--
Confidence            45889999998887776521                  789999999999987432  11123344444433222211  


Q ss_pred             HHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 045120          184 DIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL  225 (374)
Q Consensus       184 ~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~  225 (374)
                        ...++.+..-..- +....|.+.++.....+++||++...
T Consensus       585 --~~l~g~~~gyvg~-~~~~~l~~~~~~~p~~VvllDeieka  623 (821)
T CHL00095        585 --SKLIGSPPGYVGY-NEGGQLTEAVRKKPYTVVLFDEIEKA  623 (821)
T ss_pred             --HHhcCCCCcccCc-CccchHHHHHHhCCCeEEEECChhhC
Confidence              1112221100000 00123455555523468899999743

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=90.13  E-value=1.2  Score=40.13  Aligned_cols=18  Identities=44%  Similarity=0.676  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||+|+.+.....
T Consensus         7 ~pGSGKST~a~~La~~l~   24 (249)
T TIGR03574         7 LPGVGKSTFSKELAKKLS   24 (249)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            789999999999987654

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.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=90.06  E-value=1.5  Score=42.97  Aligned_cols=81  Identities=17%  Similarity=0.258  Sum_probs=43.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcC------CchhhH------HHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLE------LSEEAE------YRRASRLYERL  209 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~------~~~~~~------~~~~~~l~~~L  209 (374)
                      ..|+|||||++.+.....   ....+++..-.+.-++..+....+......      ..+++.      ....-.+.+++
T Consensus       173 ~SGsGKTTLL~~Ia~l~~---pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~a~~iAEyf  249 (450)
T PRK06002        173 GSGVGKSTLLAMLARADA---FDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLTATAIAEYF  249 (450)
T ss_pred             CCCCCHHHHHHHHhCCCC---CCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHHHHHHHHHH
Confidence            679999999998876332   122333333223345555444443332110      111111      11233455666


Q ss_pred             hc-CCeEEEEEeCCCCc
Q 045120          210 KN-ENKILVILANIWKL  225 (374)
Q Consensus       210 ~~-~kr~LlVlDdv~~~  225 (374)
                      +. ++..||++||+...
T Consensus       250 rd~G~~Vll~~DslTr~  266 (450)
T PRK06002        250 RDRGENVLLIVDSVTRF  266 (450)
T ss_pred             HHcCCCEEEeccchHHH
Confidence            43 58999999998643

>TIGR00416 sms DNA repair protein RadA

Probab=90.04  E-value=1.2  Score=44.08  Aligned_cols=78  Identities=22%  Similarity=0.315  Sum_probs=41.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchh--hHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEE--AEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      .+|+|||||+.++.......+  ..++|++....  ...+.. -+..++...+..  -.+.....+.+.+...+.-++|+
T Consensus       102 ~pGsGKTTL~lq~a~~~a~~g--~kvlYvs~EEs--~~qi~~-ra~rlg~~~~~l~~~~e~~~~~I~~~i~~~~~~~vVI  176 (454)
T TIGR00416       102 DPGIGKSTLLLQVACQLAKNQ--MKVLYVSGEES--LQQIKM-RAIRLGLPEPNLYVLSETNWEQICANIEEENPQACVI  176 (454)
T ss_pred             CCCCCHHHHHHHHHHHHHhcC--CcEEEEECcCC--HHHHHH-HHHHcCCChHHeEEcCCCCHHHHHHHHHhcCCcEEEE
Confidence            779999999999876543221  35778765433  333222 233444322110  00011234444454435678999


Q ss_pred             eCCCC
Q 045120          220 ANIWK  224 (374)
Q Consensus       220 Ddv~~  224 (374)
                      |.+..
T Consensus       177 DSIq~  181 (454)
T TIGR00416       177 DSIQT  181 (454)
T ss_pred             ecchh
Confidence            98853

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)).

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=90.03  E-value=0.68  Score=44.90  Aligned_cols=37  Identities=35%  Similarity=0.392  Sum_probs=26.6

Q ss_pred             cccccHHHHHHHHHHhhc-----------------------CCCCccHHHHHHHHHHHhh
Q 045120          123 AFESRVSNLKSTQNALTN-----------------------ANGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~-----------------------~~gGiGKTtLA~~v~~~~~  159 (374)
                      .++|.++.++.+.-.+..                       ++.|+|||+||+.+.....
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~   72 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLAN   72 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            466777777666544442                       1789999999999988654

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.

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

Probab=89.99  E-value=6.3  Score=38.39  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=16.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|.|||++..+++|...
T Consensus       243 PPGTGKSS~IaAmAn~L~  260 (457)
T KOG0743|consen  243 PPGTGKSSFIAAMANYLN  260 (457)
T ss_pred             CCCCCHHHHHHHHHhhcC
Confidence            999999999999999654

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=89.87  E-value=1.1  Score=43.84  Aligned_cols=80  Identities=13%  Similarity=0.218  Sum_probs=47.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~------~~~~~~l~~  207 (374)
                      ..|+|||||++.+.+..    +.+..+++.++... .+.+++.+....=...       ..+.+.      ....-.+.+
T Consensus       163 ~sG~GKSTLL~~I~~~~----~~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a~~~a~tiAE  238 (433)
T PRK07594        163 APGVGKSTLLAMLCNAP----DADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRALFVATTIAE  238 (433)
T ss_pred             CCCCCccHHHHHhcCCC----CCCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            77999999999998743    25556666666543 4445555543211100       111111      112335666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       239 yfrd~G~~VLl~~Dsltr~  257 (433)
T PRK07594        239 FFRDNGKRVVLLADSLTRY  257 (433)
T ss_pred             HHHHCCCcEEEEEeCHHHH
Confidence            6653 58999999999644

>PRK11823 DNA repair protein RadA; Provisional

Probab=89.85  E-value=0.87  Score=44.97  Aligned_cols=77  Identities=23%  Similarity=0.314  Sum_probs=42.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchh--hHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEE--AEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      .+|+|||||+.++.......  -..++|++....  ...+.. -++.++.....-  ..+.....+.+.+...+.-+||+
T Consensus        88 ~pG~GKTtL~lq~a~~~a~~--g~~vlYvs~Ees--~~qi~~-ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~~~~lVVI  162 (446)
T PRK11823         88 DPGIGKSTLLLQVAARLAAA--GGKVLYVSGEES--ASQIKL-RAERLGLPSDNLYLLAETNLEAILATIEEEKPDLVVI  162 (446)
T ss_pred             CCCCCHHHHHHHHHHHHHhc--CCeEEEEEcccc--HHHHHH-HHHHcCCChhcEEEeCCCCHHHHHHHHHhhCCCEEEE
Confidence            78999999999988765422  235678775443  333322 245555322110  00011233444444335668999


Q ss_pred             eCCC
Q 045120          220 ANIW  223 (374)
Q Consensus       220 Ddv~  223 (374)
                      |.+.
T Consensus       163 DSIq  166 (446)
T PRK11823        163 DSIQ  166 (446)
T ss_pred             echh
Confidence            9985

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=89.83  E-value=3.6  Score=36.39  Aligned_cols=32  Identities=25%  Similarity=0.353  Sum_probs=22.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      ..|+||||||.++......  .-..++|++....
T Consensus        28 ~~G~GKT~l~~~~~~~~~~--~g~~~~~is~e~~   59 (229)
T TIGR03881        28 EPGTGKTIFCLHFAYKGLR--DGDPVIYVTTEES   59 (229)
T ss_pred             CCCCChHHHHHHHHHHHHh--cCCeEEEEEccCC
Confidence            7899999999987654321  2346788876443

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.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=89.83  E-value=1.8  Score=40.76  Aligned_cols=80  Identities=19%  Similarity=0.354  Sum_probs=46.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    -+..++.-++.. -++..+.......-+..       ..+++..      ...-.+.+
T Consensus        77 ~sG~GKTtLl~~Ia~~~~----~~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~~~a~~~AE  152 (326)
T cd01136          77 GSGVGKSTLLGMIARGTT----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAAYTATAIAE  152 (326)
T ss_pred             CCCCChHHHHHHHhCCCC----CCEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHHHHHHHHHH
Confidence            679999999999887443    244555555543 35555555555443211       1111111      12334555


Q ss_pred             HHh-cCCeEEEEEeCCCCc
Q 045120          208 RLK-NENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~-~~kr~LlVlDdv~~~  225 (374)
                      ++. .+|..||++||+-..
T Consensus       153 yfr~~g~~Vll~~Dsltr~  171 (326)
T cd01136         153 YFRDQGKDVLLLMDSLTRF  171 (326)
T ss_pred             HHHHcCCCeEEEeccchHH
Confidence            554 258999999998643

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>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=89.79  E-value=0.78  Score=37.11  Aligned_cols=37  Identities=32%  Similarity=0.387  Sum_probs=26.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQG  183 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  183 (374)
                      ..|+|||+||+.++....     ....-+.++...+..++..
T Consensus         7 ~~G~GKt~l~~~la~~~~-----~~~~~i~~~~~~~~~dl~g   43 (139)
T PF07728_consen    7 PPGTGKTTLARELAALLG-----RPVIRINCSSDTTEEDLIG   43 (139)
T ss_dssp             SSSSSHHHHHHHHHHHHT-----CEEEEEE-TTTSTHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhh-----cceEEEEecccccccccee
Confidence            689999999999998552     1244567777777776654

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.

>PRK13849 putative crown gall tumor protein VirC1; Provisional

Probab=89.76  E-value=1.8  Score=38.70  Aligned_cols=38  Identities=26%  Similarity=0.358  Sum_probs=24.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKI  181 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~  181 (374)
                      -||+||||+|..+......++ + .++-|+.-...+....
T Consensus        10 KGGvGKTT~a~nLA~~la~~G-~-~VlliD~DpQ~s~~~w   47 (231)
T PRK13849         10 KGGAGKTTALMGLCAALASDG-K-RVALFEADENRPLTRW   47 (231)
T ss_pred             CCCccHHHHHHHHHHHHHhCC-C-cEEEEeCCCCCCHHHH
Confidence            699999999998877655332 2 3455555555554443

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=89.69  E-value=1.5  Score=43.76  Aligned_cols=80  Identities=15%  Similarity=0.263  Sum_probs=47.5

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCeE-EEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHHH------HHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDRV-VFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEYR------RASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~~-~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~~------~~~~l  205 (374)
                      ..|+|||||| ..+.+..    .-|.+ +++.+++..+ ..++.+.+...=...       ..+++...      ..-.+
T Consensus       170 ~~g~GKt~lal~~i~~~~----~~dv~~V~~~IGer~~ev~e~~~~~~~~~~l~~tvvv~atsd~p~~~r~~a~~~a~ti  245 (502)
T PRK09281        170 DRQTGKTAIAIDTIINQK----GKDVICIYVAIGQKASTVAQVVRKLEEHGAMEYTIVVAATASDPAPLQYLAPYAGCAM  245 (502)
T ss_pred             CCCCCchHHHHHHHHHhc----CCCeEEEEEEecCChHHHHHHHHHHhhcCCccceEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            6699999995 5555532    24564 8888888754 455555555432211       11111111      22345


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .++++. +++.|||+||+...
T Consensus       246 AEyfrd~G~~VLli~DdlTr~  266 (502)
T PRK09281        246 GEYFMDNGKDALIVYDDLSKQ  266 (502)
T ss_pred             HHHHHHcCCCEEEEecCchHH
Confidence            666653 48999999999754

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=89.55  E-value=9.7  Score=36.17  Aligned_cols=84  Identities=18%  Similarity=0.084  Sum_probs=49.4

Q ss_pred             CeEEEEEeCCCCcc--c----cccccCcCCCC------CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCc
Q 045120          213 NKILVILANIWKLL--D----LETVKIPFRND------SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENC  280 (374)
Q Consensus       213 kr~LlVlDdv~~~~--~----~~~l~~~~~~~------TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~  280 (374)
                      ++-.+|+|++..-.  .    +..+..|-+..      ++...+..+...--..+.+.+++.++..+.+... +.   ++
T Consensus       132 ~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~-~~---~~  207 (342)
T PRK06964        132 GARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQ-GV---AD  207 (342)
T ss_pred             CceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHc-CC---Ch
Confidence            56688899987542  2    44444444443      3333333222222347889999999999888765 21   11


Q ss_pred             chHHHHHHHHHHccCCchHHHHHHhc
Q 045120          281 KFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       281 ~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                           ...++..+ +|.|+.+..+..
T Consensus       208 -----~~~~l~~~-~Gsp~~Al~~~~  227 (342)
T PRK06964        208 -----ADALLAEA-GGAPLAALALAS  227 (342)
T ss_pred             -----HHHHHHHc-CCCHHHHHHHHC
Confidence                 12357788 999975554443

>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=89.36  E-value=0.27  Score=39.92  Aligned_cols=17  Identities=53%  Similarity=0.667  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus         7 ~pgsGKSt~a~~l~~~~   23 (143)
T PF13671_consen    7 PPGSGKSTLAKRLAKRL   23 (143)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHC
Confidence            78999999999998643

...

>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=89.25  E-value=1.4  Score=40.41  Aligned_cols=19  Identities=47%  Similarity=0.340  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      .+|+||||+|+.+......
T Consensus         9 ~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    9 LPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -TTSSHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHh
Confidence            6899999999999886553

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK13343 F0F1 ATP synthase subunit alpha; Provisional

Probab=89.21  E-value=1.5  Score=43.72  Aligned_cols=80  Identities=18%  Similarity=0.290  Sum_probs=47.6

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCeE-EEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH-H-----HHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDRV-VFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY-R-----RASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~-~-----~~~~l  205 (374)
                      ..|+|||||| ..+.+..    .-|.+ +++-+++.. ...++.+.+...=...       ..+.+.. .     ..-.+
T Consensus       170 ~~g~GKt~Lal~~i~~~~----~~dv~~V~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atsd~~~~~r~~ap~~a~ai  245 (502)
T PRK13343        170 DRQTGKTAIAIDAIINQK----DSDVICVYVAIGQKASAVARVIETLREHGALEYTTVVVAEASDPPGLQYLAPFAGCAI  245 (502)
T ss_pred             CCCCCccHHHHHHHHhhc----CCCEEEEEEEeccChHHHHHHHHHHHhcCccceeEEEEecccccHHHHHHHHHHHHHH
Confidence            6699999996 5666532    34654 888888775 3555665554432211       1111111 1     12245


Q ss_pred             HHHHh-cCCeEEEEEeCCCCc
Q 045120          206 YERLK-NENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~-~~kr~LlVlDdv~~~  225 (374)
                      .++++ .+++.|||+||+...
T Consensus       246 AEyfrd~G~~VLlv~DdlTr~  266 (502)
T PRK13343        246 AEYFRDQGQDALIVYDDLSKH  266 (502)
T ss_pred             HHHHHhCCCCEEEEecchHHH
Confidence            56664 358999999999754

>PRK09099 type III secretion system ATPase; Provisional

Probab=89.21  E-value=1.3  Score=43.37  Aligned_cols=80  Identities=19%  Similarity=0.365  Sum_probs=45.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.....    -+..+++-++.. -...++.+.+...-+..       ..+++..      ...-.+.+
T Consensus       171 ~sG~GKTtLl~~ia~~~~----~d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~~~a~tiAE  246 (441)
T PRK09099        171 PAGVGKSTLMGMFARGTQ----CDVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKAAYVATAIAE  246 (441)
T ss_pred             CCCCCHHHHHHHHhCCCC----CCeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            779999999999987443    234444444544 34555555554432211       1111111      12334666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       247 yfrd~G~~VLl~~DslTr~  265 (441)
T PRK09099        247 YFRDRGLRVLLMMDSLTRF  265 (441)
T ss_pred             HHHHcCCCEEEeccchhHH
Confidence            6642 58999999998654

>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=89.18  E-value=0.51  Score=42.81  Aligned_cols=33  Identities=27%  Similarity=0.427  Sum_probs=22.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      -||+||||+|-++.......+ -..++.|.....
T Consensus        11 KGGvGKTT~a~nLa~~La~~~-~~kVLliDlDpQ   43 (259)
T COG1192          11 KGGVGKTTTAVNLAAALAKRG-GKKVLLIDLDPQ   43 (259)
T ss_pred             CCCccHHHHHHHHHHHHHHhc-CCcEEEEeCCCc
Confidence            699999999999888665221 135667765544

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=89.18  E-value=1.8  Score=38.74  Aligned_cols=18  Identities=33%  Similarity=0.447  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +||+|||+||..+.-...
T Consensus         9 ~~G~GKS~lal~la~~va   26 (239)
T cd01125           9 PGGTGKSSLLLVLALAMA   26 (239)
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            799999999999877543

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK08233 hypothetical protein; Provisional

Probab=89.17  E-value=0.26  Score=41.87  Aligned_cols=17  Identities=35%  Similarity=0.487  Sum_probs=14.8

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      .+|+||||||..+....
T Consensus        11 ~~GsGKtTla~~L~~~l   27 (182)
T PRK08233         11 VSGGGKTTLTERLTHKL   27 (182)
T ss_pred             CCCCCHHHHHHHHHhhC
Confidence            67999999999998754

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=89.12  E-value=0.81  Score=48.98  Aligned_cols=37  Identities=22%  Similarity=0.284  Sum_probs=29.8

Q ss_pred             ccccccHHHHHHHHHHhhc-------C-----------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTN-------A-----------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~-------~-----------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|-+..++.+.+.+..       +           +.|+|||.||+.+....
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l  620 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELL  620 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            4588999999998888742       1           78999999999987753

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.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=89.02  E-value=2  Score=42.23  Aligned_cols=48  Identities=27%  Similarity=0.309  Sum_probs=28.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLE  192 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~  192 (374)
                      ..|+||||+|..+....... .+ .+..|+. ..+.  ..+-+..++.+++.+
T Consensus       103 ~~GsGKTTtaakLA~~L~~~-g~-kV~lV~~-D~~R~aa~eQL~~la~~~gvp  152 (437)
T PRK00771        103 LQGSGKTTTAAKLARYFKKK-GL-KVGLVAA-DTYRPAAYDQLKQLAEKIGVP  152 (437)
T ss_pred             CCCCcHHHHHHHHHHHHHHc-CC-eEEEecC-CCCCHHHHHHHHHHHHHcCCc
Confidence            89999999999988765532 23 3333433 2233  244456666666554

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

Probab=88.96  E-value=0.68  Score=44.06  Aligned_cols=18  Identities=44%  Similarity=0.518  Sum_probs=16.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|.|||-||++|+....
T Consensus       253 PPGTGKTlLAKAvATEc~  270 (491)
T KOG0738|consen  253 PPGTGKTLLAKAVATECG  270 (491)
T ss_pred             CCCCcHHHHHHHHHHhhc
Confidence            889999999999999665

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

Probab=88.95  E-value=0.98  Score=43.86  Aligned_cols=38  Identities=29%  Similarity=0.373  Sum_probs=28.9

Q ss_pred             ccccccHHHHHHHHHHhhc----------------C-------CCCccHHHHHHHHHHHhh
Q 045120          122 EAFESRVSNLKSTQNALTN----------------A-------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~----------------~-------~gGiGKTtLA~~v~~~~~  159 (374)
                      ..++|.+..++.+..++..                +       +.|+||||||+.+.....
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~   75 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            3477888888877766643                1       779999999999988643

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

Probab=88.93  E-value=0.91  Score=42.20  Aligned_cols=74  Identities=14%  Similarity=0.223  Sum_probs=40.5

Q ss_pred             CCCccHHHHHHHHHHHhhhc--CCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCC-eEEEE
Q 045120          142 NGGIGKTTLAKEFAKQARED--KLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNEN-KILVI  218 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~--~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~k-r~LlV  218 (374)
                      ++|.|||+|.+.++.+..++  +.|....-+.++    ...++...   ++.+  ..-...+-+++.+.+...+ =.++.
T Consensus       185 PPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEin----shsLFSKW---FsES--gKlV~kmF~kI~ELv~d~~~lVfvL  255 (423)
T KOG0744|consen  185 PPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEIN----SHSLFSKW---FSES--GKLVAKMFQKIQELVEDRGNLVFVL  255 (423)
T ss_pred             CCCCChhHHHHHHHHhheeeecCccccceEEEEe----hhHHHHHH---Hhhh--hhHHHHHHHHHHHHHhCCCcEEEEE
Confidence            99999999999999987654  334333333332    22333222   2111  1123344556666666533 34556


Q ss_pred             EeCCCC
Q 045120          219 LANIWK  224 (374)
Q Consensus       219 lDdv~~  224 (374)
                      +|.|.+
T Consensus       256 IDEVES  261 (423)
T KOG0744|consen  256 IDEVES  261 (423)
T ss_pred             eHHHHH
Confidence            677754

>PRK07667 uridine kinase; Provisional

Probab=88.82  E-value=0.47  Score=41.08  Aligned_cols=18  Identities=22%  Similarity=0.326  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||||+.+.....
T Consensus        25 ~~gsGKStla~~L~~~l~   42 (193)
T PRK07667         25 LSRSGKTTFVANLKENMK   42 (193)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            889999999999988654

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=88.64  E-value=0.44  Score=42.49  Aligned_cols=18  Identities=33%  Similarity=0.392  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+|||||++.+.....
T Consensus        41 ~~GsGKTTl~~~L~~~l~   58 (229)
T PRK09270         41 PPGAGKSTLAEFLEALLQ   58 (229)
T ss_pred             CCCCCHHHHHHHHHHHhh
Confidence            789999999999988654

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=88.62  E-value=2.9  Score=34.48  Aligned_cols=18  Identities=28%  Similarity=0.449  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||||+.+.....
T Consensus         7 ~~GsGKSTla~~L~~~l~   24 (149)
T cd02027           7 LSGSGKSTIARALEEKLF   24 (149)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            579999999999988653

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PTZ00088 adenylate kinase 1; Provisional

Probab=88.59  E-value=0.49  Score=42.22  Aligned_cols=17  Identities=35%  Similarity=0.583  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus        14 ~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088         14 APGVGKGTFAEILSKKE   30 (229)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            89999999999998754

>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots

Probab=88.58  E-value=7.4  Score=32.09  Aligned_cols=49  Identities=12%  Similarity=0.036  Sum_probs=30.5

Q ss_pred             hhHH-HHHHHHHHHHhhhhHHHhhhhhhhccchHHHHHHHHHHHHHHHHHHH
Q 045120            2 LEVI-VTLVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTS   52 (374)
Q Consensus         2 a~i~-~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~l~~   52 (374)
                      |+++ +|+++.+++.+...+.+.....  ..|+..++.+...++.+.-....
T Consensus         3 ~eL~~gaalG~~~~eLlk~v~~~~~k~--~~fk~~l~~L~sTl~~i~P~i~e   52 (147)
T PF05659_consen    3 AELVGGAALGAVFGELLKAVIDASKKS--LSFKSILKRLESTLESIIPIIKE   52 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH--HhhhhHHHHHHHHHHHhhhHHHH
Confidence            4444 6778888888888777776666  55555555555555555444443

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].

>PRK02118 V-type ATP synthase subunit B; Provisional

Probab=88.57  E-value=2.3  Score=41.51  Aligned_cols=80  Identities=19%  Similarity=0.223  Sum_probs=50.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      -.|+|||+|+..+.+...    -+.++|+-++...+ ...+.+++...=...       ..+++..      ..+-.+.+
T Consensus       148 gaGvgk~~L~~~ia~~~~----~~v~Vfa~iGeR~rE~~ef~~~~~~~~~l~rtvlv~~~adep~~~R~~~~~~AltiAE  223 (436)
T PRK02118        148 VSGEPYNALLARIALQAE----ADIIILGGMGLTFDDYLFFKDTFENAGALDRTVMFIHTASDPPVECLLVPDMALAVAE  223 (436)
T ss_pred             CCCCCHHHHHHHHHHhhC----CCeEEEEEeccchhHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            568999999999987554    35788999988754 444444444332111       1112221      12345677


Q ss_pred             HHhc--CCeEEEEEeCCCCc
Q 045120          208 RLKN--ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~--~kr~LlVlDdv~~~  225 (374)
                      +++.  ++..|+++||+-..
T Consensus       224 yfrd~g~~~VLli~DdlTr~  243 (436)
T PRK02118        224 KFALEGKKKVLVLLTDMTNF  243 (436)
T ss_pred             HHHhcCCCCEEEeccCchHH
Confidence            7764  28999999999754

>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=88.49  E-value=0.19  Score=40.29  Aligned_cols=23  Identities=43%  Similarity=0.569  Sum_probs=14.5

Q ss_pred             CCCCccHHHHHHHHHHHhhhcCCCC
Q 045120          141 ANGGIGKTTLAKEFAKQAREDKLFD  165 (374)
Q Consensus       141 ~~gGiGKTtLA~~v~~~~~~~~~F~  165 (374)
                      +..|+||||||+.+.....  ..|.
T Consensus         6 g~PG~GKT~la~~lA~~~~--~~f~   28 (131)
T PF07726_consen    6 GVPGVGKTTLAKALARSLG--LSFK   28 (131)
T ss_dssp             S---HHHHHHHHHHHHHTT----EE
T ss_pred             CCCccHHHHHHHHHHHHcC--Ccee
Confidence            3689999999999998544  4463

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.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=88.43  E-value=1.7  Score=42.56  Aligned_cols=80  Identities=14%  Similarity=0.304  Sum_probs=42.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcC-------Cchh------hHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLE-------LSEE------AEYRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~------~~~~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    .+..+...++.. .+..++....+..-+..       ..+.      ...+.+..+.+
T Consensus       163 ~sGaGKSTLl~~I~g~~~----~dv~vig~IGerg~ev~ef~~~~l~~~gl~rsvvv~~~~d~s~~~rl~a~e~a~~iAE  238 (434)
T PRK07196        163 GSGVGKSVLLGMITRYTQ----ADVVVVGLIGERGREVKEFIEHSLQAAGMAKSVVVAAPADESPLMRIKATELCHAIAT  238 (434)
T ss_pred             CCCCCccHHHHHHhcccC----CCeEEEEEEeeecHHHHHHHHHHhhhcccceEEEEEecCCCChhhhHHHHHHHHHHHH
Confidence            679999999999887432    344434444332 23333333333332211       1111      12223344555


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++.. +++.||++||+...
T Consensus       239 yfr~~g~~Vll~~Dsltr~  257 (434)
T PRK07196        239 YYRDKGHDVLLLVDSLTRY  257 (434)
T ss_pred             HhhhccCCEEEeecchhHH
Confidence            5532 48999999998654

>PRK06820 type III secretion system ATPase; Validated

Probab=88.28  E-value=2.5  Score=41.43  Aligned_cols=80  Identities=15%  Similarity=0.307  Sum_probs=43.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCc-------CCchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD-IKKIQGDIAEKLGL-------ELSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~-------~~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+..    +-+..++..++...+ ...+....+..=..       ...+.+..      ..+-.+.+
T Consensus       171 ~sG~GKStLl~~I~~~~----~~dv~V~~~iGergrEv~ef~e~~l~~~~~~rtvvv~atsd~p~~~r~~a~~~a~tiAE  246 (440)
T PRK06820        171 AAGVGKSTLLGMLCADS----AADVMVLALIGERGREVREFLEQVLTPEARARTVVVVATSDRPALERLKGLSTATTIAE  246 (440)
T ss_pred             CCCCChHHHHHHHhccC----CCCEEEEEEEccChHHHHHHHHHhhccCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHH
Confidence            77999999999888633    235566666666532 22222222110000       01111111      12335666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       247 yfrd~G~~VLl~~Dsltr~  265 (440)
T PRK06820        247 YFRDRGKKVLLMADSLTRY  265 (440)
T ss_pred             HHHHcCCCEEEEccchhHH
Confidence            6652 58999999998654

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

Probab=88.26  E-value=1.1  Score=47.09  Aligned_cols=93  Identities=13%  Similarity=0.198  Sum_probs=50.6

Q ss_pred             cccccHHHHHHHHHHhhc--------C----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTN--------A----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~--------~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      .++|-+..++.|.+.+..        .          +.|+|||+||+.+.....  .   ..+.++++......    .
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~--~---~~i~id~se~~~~~----~  529 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG--I---ELLRFDMSEYMERH----T  529 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC--C---CcEEeechhhcccc----c
Confidence            478888888888887762        1          779999999999987542  1   22334443322111    1


Q ss_pred             HHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 045120          185 IAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL  225 (374)
Q Consensus       185 i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~  225 (374)
                      +..-+|.+..-.. .+....+.+.+......+|+||++...
T Consensus       530 ~~~LiG~~~gyvg-~~~~g~L~~~v~~~p~sVlllDEieka  569 (758)
T PRK11034        530 VSRLIGAPPGYVG-FDQGGLLTDAVIKHPHAVLLLDEIEKA  569 (758)
T ss_pred             HHHHcCCCCCccc-ccccchHHHHHHhCCCcEEEeccHhhh
Confidence            2222232211000 011123444444434579999998754

>PRK03839 putative kinase; Provisional

Probab=88.21  E-value=0.34  Score=41.32  Aligned_cols=18  Identities=39%  Similarity=0.586  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.+...
T Consensus         8 ~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          8 TPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            789999999999998653

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=88.14  E-value=1.8  Score=42.36  Aligned_cols=77  Identities=21%  Similarity=0.264  Sum_probs=44.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH-HHHHHHHHHHhCcC---------CchhhHH------HHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI-KKIQGDIAEKLGLE---------LSEEAEY------RRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~-~~~~~~i~~~l~~~---------~~~~~~~------~~~~~l  205 (374)
                      ..|+|||||++.+.....    -+..+...++..... .+..+.   .++..         ..+++..      .....+
T Consensus       165 ~sG~GKStLl~~i~~~~~----~~v~vi~~iGergrev~e~~~~---~l~~~l~~tvvV~atsddsp~~R~~~~~~a~~i  237 (434)
T PRK08472        165 GSGVGKSTLMGMIVKGCL----APIKVVALIGERGREIPEFIEK---NLGGDLENTVIVVATSDDSPLMRKYGAFCAMSV  237 (434)
T ss_pred             CCCCCHHHHHHHHhhccC----CCEEEEEeeCccchhHHHHHHH---HhcCcccceEEEEECCCCCHHHhhHHHHHHHHH
Confidence            779999999999986432    345566666665443 333232   22221         1111111      123456


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .+++.+ +++.||++||+-..
T Consensus       238 AEyFrd~G~~Vll~~DslTr~  258 (434)
T PRK08472        238 AEYFKNQGLDVLFIMDSVTRF  258 (434)
T ss_pred             HHHHHHcCCCEEEecccchHH
Confidence            666642 58999999999654

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=88.13  E-value=2.1  Score=41.79  Aligned_cols=80  Identities=19%  Similarity=0.363  Sum_probs=44.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    -+..+..-++... ...++....+..-+..       ..+++..      ...-.+.+
T Consensus       145 ~sG~GKTtLl~~i~~~~~----~~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~~~~a~tiAE  220 (413)
T TIGR03497       145 GSGVGKSTLLGMIARNAK----ADINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKAAFTATAIAE  220 (413)
T ss_pred             CCCCCHHHHHHHHhCCCC----CCeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            779999999998887433    2333444455443 3444444433321111       1111111      22345666


Q ss_pred             HHh-cCCeEEEEEeCCCCc
Q 045120          208 RLK-NENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~-~~kr~LlVlDdv~~~  225 (374)
                      +++ .+++.||++||+...
T Consensus       221 yfr~~G~~Vll~~Dsltr~  239 (413)
T TIGR03497       221 YFRDQGKDVLLMMDSVTRF  239 (413)
T ss_pred             HHHHCCCCEEEEEcCcHHH
Confidence            664 358999999999643

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=88.07  E-value=27  Score=34.03  Aligned_cols=48  Identities=27%  Similarity=0.290  Sum_probs=28.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLE  192 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~  192 (374)
                      .-|.||||-|-.+.+..+-   ....+-+...+.+.  ..+-++.+.++++.+
T Consensus       108 LQGsGKTTt~~KLA~~lkk---~~~kvllVaaD~~RpAA~eQL~~La~q~~v~  157 (451)
T COG0541         108 LQGSGKTTTAGKLAKYLKK---KGKKVLLVAADTYRPAAIEQLKQLAEQVGVP  157 (451)
T ss_pred             ccCCChHhHHHHHHHHHHH---cCCceEEEecccCChHHHHHHHHHHHHcCCc
Confidence            6799999988887776553   22233333333333  334455666666654

>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=88.05  E-value=0.55  Score=43.11  Aligned_cols=16  Identities=38%  Similarity=0.646  Sum_probs=14.3

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      +.|+|||++++.....
T Consensus        41 ~~GtGKT~li~~~l~~   56 (272)
T PF12775_consen   41 PSGTGKTSLIQNFLSS   56 (272)
T ss_dssp             STTSSHHHHHHHHHHC
T ss_pred             CCCCchhHHHHhhhcc
Confidence            8899999999998864

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=87.95  E-value=0.39  Score=37.23  Aligned_cols=18  Identities=61%  Similarity=0.744  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+|||+||+.+..+..
T Consensus         6 ~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    6 PPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            579999999999887654

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

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=87.80  E-value=0.76  Score=42.96  Aligned_cols=18  Identities=44%  Similarity=0.667  Sum_probs=14.1

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|....-...
T Consensus         9 KGGVGKTT~aaA~A~~~A   26 (305)
T PF02374_consen    9 KGGVGKTTVAAALALALA   26 (305)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHh
Confidence            699999999977665444

...

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=87.78  E-value=1.9  Score=42.14  Aligned_cols=80  Identities=23%  Similarity=0.423  Sum_probs=45.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.....    -+..+.+.++... ...++....+..-+..       ..+++..      ...-.+.+
T Consensus       148 ~sG~GKTtLl~~I~~~~~----~~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~~a~~iAE  223 (418)
T TIGR03498       148 GSGVGKSTLLSMLARNTD----ADVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAYTATAIAE  223 (418)
T ss_pred             CCCCChHHHHHHHhCCCC----CCEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            679999999998887433    2333444444433 3455555444332211       1111111      12334666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       224 yfrd~G~~Vll~~DslTr~  242 (418)
T TIGR03498       224 YFRDQGKDVLLLMDSVTRF  242 (418)
T ss_pred             HHHHcCCCEEEeccchhHH
Confidence            6643 58999999998654

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases

Probab=87.73  E-value=0.43  Score=40.90  Aligned_cols=36  Identities=25%  Similarity=0.431  Sum_probs=23.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      .||+||||+|..+......++ + .++-++.....+..
T Consensus         7 kGG~GKTt~a~~la~~la~~g-~-~VlliD~D~~~~~~   42 (195)
T PF01656_consen    7 KGGVGKTTIAANLAQALARKG-K-KVLLIDLDPQAPNL   42 (195)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT-S--EEEEEESTTSHHH
T ss_pred             CCCccHHHHHHHHHhcccccc-c-cccccccCcccccH
Confidence            699999999998887665422 2 45556654443333

These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=87.71  E-value=0.54  Score=40.88  Aligned_cols=18  Identities=61%  Similarity=0.752  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||+|+++..-.+
T Consensus         9 yPgsGKTtfakeLak~L~   26 (261)
T COG4088           9 YPGSGKTTFAKELAKELR   26 (261)
T ss_pred             CCCCCchHHHHHHHHHHH
Confidence            789999999999988554

>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=87.70  E-value=0.48  Score=39.51  Aligned_cols=27  Identities=30%  Similarity=0.342  Sum_probs=19.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFS  170 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  170 (374)
                      ..|+||||||+.+.......+  ..+.++
T Consensus        10 lsGsGKtTlA~~L~~~L~~~g--~~~~~L   36 (156)
T PF01583_consen   10 LSGSGKTTLARALERRLFARG--IKVYLL   36 (156)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--S-EEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHcC--CcEEEe
Confidence            789999999999999766432  345555

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 ....

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=87.70  E-value=0.37  Score=41.75  Aligned_cols=18  Identities=50%  Similarity=0.597  Sum_probs=15.8

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||||+.+.....
T Consensus         7 ~sgSGKTTla~~L~~~L~   24 (194)
T PF00485_consen    7 PSGSGKTTLAKRLAQILN   24 (194)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            689999999999988654

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 ....

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

Probab=87.60  E-value=3.5  Score=42.48  Aligned_cols=83  Identities=18%  Similarity=0.256  Sum_probs=51.4

Q ss_pred             ccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          122 EAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      ..+-|..+.++-+.+.+.-+                      ++|+|||.||.++......       -||+|..+   +
T Consensus       667 ~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~-------~fisvKGP---E  736 (952)
T KOG0735|consen  667 EDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNL-------RFISVKGP---E  736 (952)
T ss_pred             eecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCe-------eEEEecCH---H
Confidence            34667777776666666544                      8899999999999875442       25666543   1


Q ss_pred             HHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 045120          180 KIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWK  224 (374)
Q Consensus       180 ~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~  224 (374)
                       ++   -+.+|.+      ++..+.+++.-+.-|.|.|.+|...+
T Consensus       737 -lL---~KyIGaS------Eq~vR~lF~rA~~a~PCiLFFDEfdS  771 (952)
T KOG0735|consen  737 -LL---SKYIGAS------EQNVRDLFERAQSAKPCILFFDEFDS  771 (952)
T ss_pred             -HH---HHHhccc------HHHHHHHHHHhhccCCeEEEeccccc
Confidence             11   1122211      22344555555544899999998764

>PRK04192 V-type ATP synthase subunit A; Provisional

Probab=87.47  E-value=2.7  Score=42.49  Aligned_cols=80  Identities=18%  Similarity=0.230  Sum_probs=51.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHh----CcC----------CchhhHHH------
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKL----GLE----------LSEEAEYR------  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l----~~~----------~~~~~~~~------  200 (374)
                      ..|+|||+|++++.+..    +-|.++++-++... .+.+++.++-+..    +.+          ..+++...      
T Consensus       235 ~~G~GKTvl~~~iak~a----~adivVyvg~GERg~E~~e~l~ef~~l~dp~~g~~~m~RTvlVanTSn~Pv~aR~~s~y  310 (586)
T PRK04192        235 PFGSGKTVTQHQLAKWA----DADIVIYVGCGERGNEMTEVLEEFPELIDPKTGRPLMERTVLIANTSNMPVAAREASIY  310 (586)
T ss_pred             CCCCCHHHHHHHHHhcC----CCCEEEEEEcCcChHHHHHHHHHHHhhcccccccccceeEEEEEECCCCCHHHHHHHHH
Confidence            66999999999998753    24789999888775 4566666654422    111          11222221      


Q ss_pred             HHHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          201 RASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       201 ~~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      ..-.+.+++++ ++..||++|++...
T Consensus       311 tgiTiAEYfRd~G~~Vllm~DStSR~  336 (586)
T PRK04192        311 TGITIAEYYRDMGYDVLLMADSTSRW  336 (586)
T ss_pred             HHHHHHHHHHHCCCCEEEEecChHHH
Confidence            22356666653 58999999999643

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=87.47  E-value=4.1  Score=41.03  Aligned_cols=77  Identities=17%  Similarity=0.204  Sum_probs=46.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc----------------hhhHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS----------------EEAEYRRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~----------------~~~~~~~~~~l  205 (374)
                      ..|+|||+||.++..+....  -..++|++....  ...+.+.. ..++.+..                ..+.++....+
T Consensus       281 ~~G~GKT~l~~~~~~~~~~~--g~~~~yis~e~~--~~~i~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~~~~i  355 (509)
T PRK09302        281 ATGTGKTLLASKFAEAACRR--GERCLLFAFEES--RAQLIRNA-RSWGIDLEKMEEKGLLKIICARPESYGLEDHLIII  355 (509)
T ss_pred             CCCCCHHHHHHHHHHHHHhC--CCcEEEEEecCC--HHHHHHHH-HHcCCChHHHhhcCCceeecCCcccCCHHHHHHHH
Confidence            78999999999987765422  356888876654  44444433 34442210                11234455566


Q ss_pred             HHHHhcCCeEEEEEeCCC
Q 045120          206 YERLKNENKILVILANIW  223 (374)
Q Consensus       206 ~~~L~~~kr~LlVlDdv~  223 (374)
                      .+.+...+.-++|+|.+.
T Consensus       356 ~~~i~~~~~~~vVIDslt  373 (509)
T PRK09302        356 KREIEEFKPSRVAIDPLS  373 (509)
T ss_pred             HHHHHHcCCCEEEEcCHH
Confidence            666655355689999874

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=87.46  E-value=3.2  Score=36.75  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=15.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||||+.+.....
T Consensus         7 ~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           7 SVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            579999999999988553

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>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=87.43  E-value=0.48  Score=33.46  Aligned_cols=17  Identities=47%  Similarity=0.689  Sum_probs=14.8

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||+++.+.+..
T Consensus         7 ~~gsGKst~~~~l~~~l   23 (69)
T cd02019           7 GSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            57999999999998864

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.

>PRK06762 hypothetical protein; Provisional

Probab=87.43  E-value=0.41  Score=40.13  Aligned_cols=17  Identities=47%  Similarity=0.730  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+.+..
T Consensus        10 ~~GsGKST~A~~L~~~l   26 (166)
T PRK06762         10 NSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=87.34  E-value=2.4  Score=41.50  Aligned_cols=80  Identities=25%  Similarity=0.417  Sum_probs=46.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcC-------CchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLE-------LSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~------~~~~~~l~~  207 (374)
                      ..|+|||||++.+......    +.....-+++. ....+++...+..-+..       ..+.+.      ...+..+.+
T Consensus       164 ~sG~GKTtLl~~Ia~~~~~----~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~~~a~~iAE  239 (432)
T PRK06793        164 GSGVGKSTLLGMIAKNAKA----DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAAKLATSIAE  239 (432)
T ss_pred             CCCCChHHHHHHHhccCCC----CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            6799999999999875432    22222334433 55666666555543221       111111      122335556


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      +++. ++..||++||+-..
T Consensus       240 yfr~~G~~VLlilDslTr~  258 (432)
T PRK06793        240 YFRDQGNNVLLMMDSVTRF  258 (432)
T ss_pred             HHHHcCCcEEEEecchHHH
Confidence            6643 58999999998654

>PHA02518 ParA-like protein; Provisional

Probab=87.29  E-value=0.46  Score=41.41  Aligned_cols=37  Identities=27%  Similarity=0.468  Sum_probs=23.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKK  180 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  180 (374)
                      -||+||||+|..+..-....+  ..++-++.....+...
T Consensus         9 KGGvGKTT~a~~la~~la~~g--~~vlliD~D~q~~~~~   45 (211)
T PHA02518          9 KGGAGKTTVATNLASWLHADG--HKVLLVDLDPQGSSTD   45 (211)
T ss_pred             CCCCCHHHHHHHHHHHHHhCC--CeEEEEeCCCCCChHH
Confidence            699999999998876544222  2455566655544443

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=87.25  E-value=5  Score=36.35  Aligned_cols=45  Identities=20%  Similarity=0.288  Sum_probs=31.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      .+|+|||++|.++..+...... ..++|++.  .-+..++...++...
T Consensus        27 ~pg~GKT~~~l~ia~~~a~~~~-~~vly~Sl--Em~~~~l~~R~la~~   71 (259)
T PF03796_consen   27 RPGVGKTAFALQIALNAALNGG-YPVLYFSL--EMSEEELAARLLARL   71 (259)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTS-SEEEEEES--SS-HHHHHHHHHHHH
T ss_pred             cccCCchHHHHHHHHHHHHhcC-CeEEEEcC--CCCHHHHHHHHHHHh
Confidence            7899999999999988765433 46666654  445566666666655

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. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation

Probab=87.20  E-value=0.41  Score=36.63  Aligned_cols=18  Identities=44%  Similarity=0.634  Sum_probs=14.6

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|..+..-..
T Consensus         8 kgG~Gkst~~~~la~~~~   25 (104)
T cd02042           8 KGGVGKTTTAVNLAAALA   25 (104)
T ss_pred             CCCcCHHHHHHHHHHHHH
Confidence            699999999988866543

ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=87.19  E-value=0.43  Score=39.20  Aligned_cols=61  Identities=20%  Similarity=0.223  Sum_probs=34.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhc
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKN  211 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~  211 (374)
                      .+|+||||||..+.....       .-|+++|+-..-..+...-=+...  ...-+++.+.+.|...+.+
T Consensus        15 TPG~GKstl~~~lae~~~-------~~~i~isd~vkEn~l~~gyDE~y~--c~i~DEdkv~D~Le~~m~~   75 (176)
T KOG3347|consen   15 TPGTGKSTLAERLAEKTG-------LEYIEISDLVKENNLYEGYDEEYK--CHILDEDKVLDELEPLMIE   75 (176)
T ss_pred             CCCCCchhHHHHHHHHhC-------CceEehhhHHhhhcchhccccccc--CccccHHHHHHHHHHHHhc
Confidence            789999999999986333       236666654332222221111111  1112556667777777765

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=86.99  E-value=2.9  Score=37.91  Aligned_cols=80  Identities=18%  Similarity=0.144  Sum_probs=45.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-----CCCHHHHHHHHHHHhCcCCch-------hhHHHHH-HHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-----TSDIKKIQGDIAEKLGLELSE-------EAEYRRA-SRLYER  208 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-----~~~~~~~~~~i~~~l~~~~~~-------~~~~~~~-~~l~~~  208 (374)
                      -.|+|||||++.+..=..   .-.+.++..-.+     .....+-..++++.++.....       -+..+++ -.+.+.
T Consensus        47 ESG~GKSTlgr~i~~L~~---pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQRi~IARA  123 (268)
T COG4608          47 ESGCGKSTLGRLILGLEE---PTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQRIGIARA  123 (268)
T ss_pred             cCCCCHHHHHHHHHcCcC---CCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhhHHHHHH
Confidence            779999999999987333   222333332111     112334455666666644211       1223322 356667


Q ss_pred             HhcCCeEEEEEeCCCCc
Q 045120          209 LKNENKILVILANIWKL  225 (374)
Q Consensus       209 L~~~kr~LlVlDdv~~~  225 (374)
                      |.- +.-|||.|..-+.
T Consensus       124 Lal-~P~liV~DEpvSa  139 (268)
T COG4608         124 LAL-NPKLIVADEPVSA  139 (268)
T ss_pred             Hhh-CCcEEEecCchhh
Confidence            776 7899999986544

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=86.99  E-value=0.76  Score=38.35  Aligned_cols=40  Identities=30%  Similarity=0.407  Sum_probs=29.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS  194 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~  194 (374)
                      .+|+||||+|+.+.++....       +|      +.-.+++++++..+.+..
T Consensus         8 ~pGsG~TTva~~lAe~~gl~-------~v------saG~iFR~~A~e~gmsl~   47 (179)
T COG1102           8 LPGSGKTTVARELAEHLGLK-------LV------SAGTIFREMARERGMSLE   47 (179)
T ss_pred             CCCCChhHHHHHHHHHhCCc-------ee------eccHHHHHHHHHcCCCHH
Confidence            68999999999999876533       11      334677888888887643

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=86.91  E-value=1.1  Score=39.71  Aligned_cols=36  Identities=28%  Similarity=0.493  Sum_probs=22.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      -||+||||+|..+......++.|+ ++=|+...++++
T Consensus         8 KGG~GKTtiaalll~~l~~~~~~~-VLvVDaDpd~nL   43 (255)
T COG3640           8 KGGVGKTTIAALLLKRLLSKGGYN-VLVVDADPDSNL   43 (255)
T ss_pred             CCCccHHHHHHHHHHHHHhcCCce-EEEEeCCCCCCh
Confidence            599999999988666544343332 344444445553

>COG1158 Rho Transcription termination factor [Transcription]

Probab=86.88  E-value=5.7  Score=37.23  Aligned_cols=80  Identities=13%  Similarity=0.204  Sum_probs=49.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC--CCHHHHHHHHHHHhC-cCCchhh--HHH----HHHHHHHHHhcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT--SDIKKIQGDIAEKLG-LELSEEA--EYR----RASRLYERLKNE  212 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i~~~l~-~~~~~~~--~~~----~~~~l~~~L~~~  212 (374)
                      ++-.|||||.+.|+|... .+|-++.+||-+-..  -.+.++++.+--.+- ..+++..  .-+    .+++-++....+
T Consensus       181 PPkaGKT~lLq~IA~aIt-~N~Pe~~LiVLLIDERPEEVTdmqrsV~geViaSTFDepp~~HvqVAE~viEkAKRlVE~~  259 (422)
T COG1158         181 PPKAGKTTLLQNIANAIT-TNHPECELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPPSRHVQVAEMVIEKAKRLVEHG  259 (422)
T ss_pred             CCCCCchHHHHHHHHHHh-cCCCceEEEEEEecCCchHHHHHHHhhcceEEeecCCCcchhhHHHHHHHHHHHHHHHHcC
Confidence            889999999999999654 467799999865443  244555555432221 1222211  111    234444555556


Q ss_pred             CeEEEEEeCC
Q 045120          213 NKILVILANI  222 (374)
Q Consensus       213 kr~LlVlDdv  222 (374)
                      |...|+||-+
T Consensus       260 kDVVILLDSI  269 (422)
T COG1158         260 KDVVILLDSI  269 (422)
T ss_pred             CcEEEEehhH
Confidence            7888888876

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=86.86  E-value=0.71  Score=46.67  Aligned_cols=38  Identities=24%  Similarity=0.402  Sum_probs=31.3

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      ..+++|.+..++.+...+...         ..|+|||++|+.+++..
T Consensus        64 f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~  110 (531)
T TIGR02902        64 FDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEA  110 (531)
T ss_pred             HHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            446899999999988877643         88999999999998743

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.

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=86.85  E-value=3.5  Score=40.39  Aligned_cols=80  Identities=18%  Similarity=0.336  Sum_probs=45.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||.+.+.+...    .+...++.++.. .++..+..+........       ..+.+..      ...-.+.+
T Consensus       153 ~sG~GKStLl~~I~~~~~----~~~~vi~~iG~~~~ev~~~~~~~~~~~~~~~tvvv~~~s~~p~~~r~~~~~~a~~~AE  228 (422)
T TIGR02546       153 GAGVGKSTLLGMIARGAS----ADVNVIALIGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPSLERLKAAYTATAIAE  228 (422)
T ss_pred             CCCCChHHHHHHHhCCCC----CCEEEEEEEccCCcCHHHHHHHHhccccccceEEEeccccCCHHHHHHHHHHHHHHHH
Confidence            779999999999987443    344555555554 34555554444332111       1111111      12234555


Q ss_pred             HHh-cCCeEEEEEeCCCCc
Q 045120          208 RLK-NENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~-~~kr~LlVlDdv~~~  225 (374)
                      ++. .+++.|+++|++...
T Consensus       229 ~f~~~g~~Vl~~~Dsltr~  247 (422)
T TIGR02546       229 YFRDQGKRVLLMMDSLTRF  247 (422)
T ss_pred             HHHHCCCcEEEEEeCchHH
Confidence            554 258999999999643

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=86.72  E-value=0.81  Score=43.26  Aligned_cols=38  Identities=16%  Similarity=0.193  Sum_probs=28.8

Q ss_pred             ccccccccHHHHHHHHHHhh-cC--------CCCccHHHHHHHHHHH
Q 045120          120 VYEAFESRVSNLKSTQNALT-NA--------NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~-~~--------~gGiGKTtLA~~v~~~  157 (374)
                      +...++|.+..++.+.-.+. .+        ..|+||||||+.+.+-
T Consensus         6 ~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~l   52 (334)
T PRK13407          6 PFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAAL   52 (334)
T ss_pred             CHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence            34568899999888765443 22        7899999999998663

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=86.70  E-value=2.9  Score=42.90  Aligned_cols=101  Identities=19%  Similarity=0.144  Sum_probs=67.0

Q ss_pred             cccccccHHHHHHHHHHhhcC--------------CCCccHHHHHHHHHHHhh---hcCCCC--eEEEEEeCCCCCHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA--------------NGGIGKTTLAKEFAKQAR---EDKLFD--RVVFSEVSQTSDIKKI  181 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~--------------~gGiGKTtLA~~v~~~~~---~~~~F~--~~~wv~vs~~~~~~~~  181 (374)
                      +..+-+||.+..+|-+.+..-              .+|+|||..+..|.+...   .++.-.  ..+.|+.-.-..+.++
T Consensus       395 p~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~  474 (767)
T KOG1514|consen  395 PESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREI  474 (767)
T ss_pred             cccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHH
Confidence            345678999999998887532              679999999999988654   122222  2344554455679999


Q ss_pred             HHHHHHHhCcCCchhhHHHHHHHHHHHHh----cCCeEEEEEeCCC
Q 045120          182 QGDIAEKLGLELSEEAEYRRASRLYERLK----NENKILVILANIW  223 (374)
Q Consensus       182 ~~~i~~~l~~~~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~  223 (374)
                      ...|...+.......  ...++.|..+..    ..+.+++++|++.
T Consensus       475 Y~~I~~~lsg~~~~~--~~al~~L~~~f~~~k~~~~~~VvLiDElD  518 (767)
T KOG1514|consen  475 YEKIWEALSGERVTW--DAALEALNFRFTVPKPKRSTTVVLIDELD  518 (767)
T ss_pred             HHHHHHhcccCcccH--HHHHHHHHHhhccCCCCCCCEEEEeccHH
Confidence            999999997654322  222334444443    2367899999875

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

Probab=86.69  E-value=2.4  Score=42.53  Aligned_cols=23  Identities=26%  Similarity=0.225  Sum_probs=18.9

Q ss_pred             CceecCCCCHHHHHHHHHHhcCC
Q 045120          253 DNFLIANITEEEAWRLFKIMNGD  275 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~  275 (374)
                      ..+.+.+-+.++..+.|+.+..+
T Consensus       403 ~~i~v~~pd~~~r~~i~~~~~~~  425 (494)
T COG0464         403 RLIYVPLPDLEERLEIFKIHLRD  425 (494)
T ss_pred             eEeecCCCCHHHHHHHHHHHhcc
Confidence            46778888899999999988863

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=86.63  E-value=1  Score=41.01  Aligned_cols=33  Identities=24%  Similarity=0.393  Sum_probs=20.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      -||+||||++..+..-....+ + .++-|+.....
T Consensus         9 KGGvGKTT~~~nLA~~La~~G-~-kVlliD~Dpq~   41 (270)
T cd02040           9 KGGIGKSTTTQNLSAALAEMG-K-KVMIVGCDPKA   41 (270)
T ss_pred             CCcCCHHHHHHHHHHHHHhCC-C-eEEEEEcCCCC
Confidence            599999999988877654332 2 34445444433

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=86.58  E-value=3.1  Score=41.55  Aligned_cols=30  Identities=27%  Similarity=0.400  Sum_probs=19.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC-CeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF-DRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F-~~~~wv~vs  173 (374)
                      .+|+||||||.++..+-..+  + ..++||+..
T Consensus        29 ~pGsGKT~la~qfl~~g~~~--~ge~~lyvs~e   59 (484)
T TIGR02655        29 TSGTGKTLFSIQFLYNGIIH--FDEPGVFVTFE   59 (484)
T ss_pred             CCCCCHHHHHHHHHHHHHHh--CCCCEEEEEEe
Confidence            88999999999875432211  2 345566543

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=86.53  E-value=3.6  Score=39.81  Aligned_cols=79  Identities=19%  Similarity=0.143  Sum_probs=39.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcCCch-hhHHHHHHHHHHHHhcCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLELSE-EAEYRRASRLYERLKNENKILVI  218 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~~kr~LlV  218 (374)
                      .+|+||||++..+......+ .+ .+..++. +.+.  ..+-+....+.++.+... .+...+...+...-...+.=+|+
T Consensus       249 ptGvGKTTTiaKLA~~L~~~-Gk-kVglI~a-Dt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~~~DvVL  325 (436)
T PRK11889        249 PTGVGKTTTLAKMAWQFHGK-KK-TVGFITT-DHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEARVDYIL  325 (436)
T ss_pred             CCCCcHHHHHHHHHHHHHHc-CC-cEEEEec-CCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhccCCCEEE
Confidence            88999999999988755422 22 3344443 3333  222333444455544321 23444444333322111235777


Q ss_pred             EeCCC
Q 045120          219 LANIW  223 (374)
Q Consensus       219 lDdv~  223 (374)
                      +|-.-
T Consensus       326 IDTaG  330 (436)
T PRK11889        326 IDTAG  330 (436)
T ss_pred             EeCcc
Confidence            78653

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=86.35  E-value=0.56  Score=37.43  Aligned_cols=19  Identities=32%  Similarity=0.429  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      .=|.|||||++.+.....+
T Consensus        23 dLGaGKTtf~r~l~~~lg~   41 (123)
T PF02367_consen   23 DLGAGKTTFVRGLARALGI   41 (123)
T ss_dssp             STTSSHHHHHHHHHHHTT-
T ss_pred             CCCCCHHHHHHHHHHHcCC
Confidence            4599999999999886543

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.

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=86.22  E-value=1.2  Score=41.88  Aligned_cols=39  Identities=26%  Similarity=0.440  Sum_probs=23.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQ  182 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  182 (374)
                      .||+||||+|-+..-.....+  ..++-|+.....++.+++
T Consensus        10 KGGVGKTT~aaA~A~~lA~~g--~kvLlvStDPAhsL~d~f   48 (322)
T COG0003          10 KGGVGKTTIAAATAVKLAESG--KKVLLVSTDPAHSLGDVF   48 (322)
T ss_pred             CCcccHHHHHHHHHHHHHHcC--CcEEEEEeCCCCchHhhh
Confidence            799999999988555444222  336666554444444433

>PRK05480 uridine/cytidine kinase; Provisional

Probab=86.16  E-value=0.51  Score=41.29  Aligned_cols=17  Identities=35%  Similarity=0.493  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||||+.+....
T Consensus        14 ~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480         14 GSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999999854

>PRK06547 hypothetical protein; Provisional

Probab=86.15  E-value=0.91  Score=38.57  Aligned_cols=17  Identities=47%  Similarity=0.622  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||||+.+....
T Consensus        23 ~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         23 RSGSGKTTLAGALAART   39 (172)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998753

>PLN02924 thymidylate kinase

Probab=86.15  E-value=4.2  Score=36.04  Aligned_cols=78  Identities=12%  Similarity=0.149  Sum_probs=40.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhh--------HHHHHHHHHHHHhcCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEA--------EYRRASRLYERLKNEN  213 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~--------~~~~~~~l~~~L~~~k  213 (374)
                      .-|+||||+|+.+....... .+....+-..+.........+.++.... ......        ..+....+...|..  
T Consensus        24 iDGsGKsTq~~~L~~~l~~~-g~~v~~~~ep~~~~~~g~~ir~~l~~~~-~~~~~~~~llf~adR~~~~~~I~pal~~--   99 (220)
T PLN02924         24 LDRSGKSTQCAKLVSFLKGL-GVAAELWRFPDRTTSVGQMISAYLSNKS-QLDDRAIHLLFSANRWEKRSLMERKLKS--   99 (220)
T ss_pred             CCCCCHHHHHHHHHHHHHhc-CCCceeeeCCCCCChHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHC--
Confidence            77999999999999977644 3444333222222334455555554321 111111        11112335555555  


Q ss_pred             eEEEEEeCCC
Q 045120          214 KILVILANIW  223 (374)
Q Consensus       214 r~LlVlDdv~  223 (374)
                      ...+|.|--.
T Consensus       100 g~vVI~DRy~  109 (220)
T PLN02924        100 GTTLVVDRYS  109 (220)
T ss_pred             CCEEEEccch
Confidence            3468888754

>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=86.14  E-value=0.68  Score=41.61  Aligned_cols=29  Identities=24%  Similarity=0.353  Sum_probs=19.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV  172 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v  172 (374)
                      |+|+||||+++.+.+.....+  ..++-|+.
T Consensus         4 paGSGKTT~~~~~~~~~~~~~--~~~~~vNL   32 (238)
T PF03029_consen    4 PAGSGKTTFCKGLSEWLESNG--RDVYIVNL   32 (238)
T ss_dssp             STTSSHHHHHHHHHHHHTTT---S-EEEEE-
T ss_pred             CCCCCHHHHHHHHHHHHHhcc--CCceEEEc
Confidence            789999999999998765432  23444543

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []

Probab=86.08  E-value=0.47  Score=39.67  Aligned_cols=39  Identities=31%  Similarity=0.407  Sum_probs=26.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe-----CCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV-----SQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v-----s~~~~~~~~~~~i~~~l  189 (374)
                      .-|+||||+|..+.+      -|+.  |-++     +.+ ....+.+.+++.|
T Consensus         7 tiGCGKTTva~aL~~------LFg~--wgHvQnDnI~~k-~~~~f~~~~l~~L   50 (168)
T PF08303_consen    7 TIGCGKTTVALALSN------LFGE--WGHVQNDNITGK-RKPKFIKAVLELL   50 (168)
T ss_pred             CCCcCHHHHHHHHHH------HcCC--CCccccCCCCCC-CHHHHHHHHHHHH
Confidence            359999999999886      2543  4433     333 5677777777777

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>PTZ00301 uridine kinase; Provisional

Probab=86.06  E-value=0.53  Score=41.44  Aligned_cols=17  Identities=24%  Similarity=0.501  Sum_probs=14.6

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      .+|+||||||+.+....
T Consensus        11 ~SgSGKTTla~~l~~~l   27 (210)
T PTZ00301         11 ASGSGKSSLSTNIVSEL   27 (210)
T ss_pred             CCcCCHHHHHHHHHHHH
Confidence            67999999999988754

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=86.05  E-value=5.6  Score=38.58  Aligned_cols=27  Identities=7%  Similarity=-0.044  Sum_probs=22.1

Q ss_pred             hcCCCCceecCCCCHHHHHHHHHHhcC
Q 045120          248 SMGSKDNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       248 ~~~~~~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      .+...-++.+.+.+.+....++.+.+.
T Consensus       232 R~~~Gl~~~I~~Pd~e~r~aiL~kka~  258 (408)
T COG0593         232 RLEWGLVVEIEPPDDETRLAILRKKAE  258 (408)
T ss_pred             HHhceeEEeeCCCCHHHHHHHHHHHHH
Confidence            444456899999999999999998764

>TIGR00235 udk uridine kinase

Probab=86.05  E-value=0.5  Score=41.37  Aligned_cols=17  Identities=41%  Similarity=0.589  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||||+.+....
T Consensus        14 ~sGsGKSTl~~~l~~~l   30 (207)
T TIGR00235        14 GSGSGKTTVARKIYEQL   30 (207)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=85.98  E-value=0.51  Score=41.14  Aligned_cols=18  Identities=39%  Similarity=0.471  Sum_probs=16.0

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      |=|+||||||+.+.++..
T Consensus        12 ~IG~GKSTLa~~La~~l~   29 (216)
T COG1428          12 MIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             ccccCHHHHHHHHHHHhC
Confidence            779999999999998665

>PRK08760 replicative DNA helicase; Provisional

Probab=85.90  E-value=5  Score=40.00  Aligned_cols=45  Identities=20%  Similarity=0.127  Sum_probs=28.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      .+|+||||+|..+..+...+.... ++++  |-.-+..++...++...
T Consensus       237 rPg~GKTafal~iA~~~a~~~g~~-V~~f--SlEMs~~ql~~Rl~a~~  281 (476)
T PRK08760        237 RPAMGKTTFALNIAEYAAIKSKKG-VAVF--SMEMSASQLAMRLISSN  281 (476)
T ss_pred             CCCCChhHHHHHHHHHHHHhcCCc-eEEE--eccCCHHHHHHHHHHhh
Confidence            779999999999987665443343 3444  33444556666655543

>PRK05748 replicative DNA helicase; Provisional

Probab=85.89  E-value=38  Score=33.45  Aligned_cols=46  Identities=15%  Similarity=0.115  Sum_probs=29.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      .+|+|||+||..+..+...+... .++|++  -.-+..++...++...+
T Consensus       211 rpg~GKT~~al~ia~~~a~~~g~-~v~~fS--lEms~~~l~~R~l~~~~  256 (448)
T PRK05748        211 RPSVGKTAFALNIAQNVATKTDK-NVAIFS--LEMGAESLVMRMLCAEG  256 (448)
T ss_pred             CCCCCchHHHHHHHHHHHHhCCC-eEEEEe--CCCCHHHHHHHHHHHhc
Confidence            77999999999988765433233 344543  34455666666665443

>PRK00625 shikimate kinase; Provisional

Probab=85.88  E-value=0.56  Score=39.90  Aligned_cols=18  Identities=33%  Similarity=0.381  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      |.|+||||+++.+.+...
T Consensus         8 ~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          8 LPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            899999999999987543

>PRK06217 hypothetical protein; Validated

Probab=85.86  E-value=0.55  Score=40.22  Aligned_cols=18  Identities=33%  Similarity=0.488  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||||+.+.....
T Consensus         9 ~~GsGKSTla~~L~~~l~   26 (183)
T PRK06217          9 ASGSGTTTLGAALAERLD   26 (183)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            689999999999998654

>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=85.82  E-value=1.2  Score=38.92  Aligned_cols=35  Identities=20%  Similarity=0.268  Sum_probs=26.0

Q ss_pred             ccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAK  156 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~  156 (374)
                      ..++|-+..+..+.-.....       ..|+|||+||+.+-.
T Consensus         3 ~dI~GQe~aKrAL~iAAaG~h~lLl~GppGtGKTmlA~~l~~   44 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAAGGHHLLLIGPPGTGKTMLARRLPS   44 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHHCC--EEEES-CCCTHHHHHHHHHH
T ss_pred             hhhcCcHHHHHHHHHHHcCCCCeEEECCCCCCHHHHHHHHHH
Confidence            45778887777776555544       889999999999865

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.

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=85.81  E-value=1.7  Score=42.74  Aligned_cols=80  Identities=19%  Similarity=0.367  Sum_probs=43.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    -+.++...+.... +..++.+.++..-...       ..+++..      ...-.+.+
T Consensus       183 ~sG~GKTTLL~~Ia~~~~----~d~iv~g~Igerg~ev~e~~~~~~~~~~~~~tvVv~~~ad~~~~~r~~~~~~a~tiAE  258 (455)
T PRK07960        183 GSGVGKSVLLGMMARYTQ----ADVIVVGLIGERGREVKDFIENILGAEGRARSVVIAAPADVSPLLRMQGAAYATRIAE  258 (455)
T ss_pred             CCCCCccHHHHHHhCCCC----CCEEEEEEEEECCeEHHHHHHhhcCcCCCceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            779999999999887432    2344444444332 4444444433211110       1111111      12234556


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.|+++||+-..
T Consensus       259 yfrd~G~~Vll~~DslTr~  277 (455)
T PRK07960        259 DFRDRGQHVLLIMDSLTRY  277 (455)
T ss_pred             HHHHcCCCeEEEecchhHH
Confidence            6643 58999999998654

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=85.80  E-value=4.5  Score=40.72  Aligned_cols=33  Identities=24%  Similarity=0.351  Sum_probs=21.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      .+|+|||+||.++......+ +=..++|++....
T Consensus        39 ~pGsGKT~l~~qf~~~~~~~-~ge~~lyis~ee~   71 (509)
T PRK09302         39 TAGTGKTLFALQFLVNGIKR-FDEPGVFVTFEES   71 (509)
T ss_pred             CCCCCHHHHHHHHHHHHHHh-cCCCEEEEEccCC
Confidence            88999999999876543322 1135677765543

>cd01131 PilT Pilus retraction ATPase PilT

Probab=85.79  E-value=0.74  Score=40.04  Aligned_cols=80  Identities=10%  Similarity=0.156  Sum_probs=39.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI--KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      +.|+||||++..+.....  .+....+++- ..+...  .. ...++.+-..   ..+.....+.++..|.. ..=.|++
T Consensus         9 ptGSGKTTll~~ll~~~~--~~~~~~i~t~-e~~~E~~~~~-~~~~i~q~~v---g~~~~~~~~~i~~aLr~-~pd~ii~   80 (198)
T cd01131           9 PTGSGKSTTLAAMIDYIN--KNKTHHILTI-EDPIEFVHES-KRSLINQREV---GLDTLSFENALKAALRQ-DPDVILV   80 (198)
T ss_pred             CCCCCHHHHHHHHHHHhh--hcCCcEEEEE-cCCccccccC-ccceeeeccc---CCCccCHHHHHHHHhcC-CcCEEEE
Confidence            679999999998877543  2233343332 211110  00 0011111000   01112234556777766 5668899


Q ss_pred             eCCCCccccc
Q 045120          220 ANIWKLLDLE  229 (374)
Q Consensus       220 Ddv~~~~~~~  229 (374)
                      |.+.+.+.+.
T Consensus        81 gEird~e~~~   90 (198)
T cd01131          81 GEMRDLETIR   90 (198)
T ss_pred             cCCCCHHHHH
Confidence            9987654433

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=85.75  E-value=2.2  Score=40.09  Aligned_cols=36  Identities=17%  Similarity=0.196  Sum_probs=25.4

Q ss_pred             ccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhh
Q 045120          124 FESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~  159 (374)
                      ++=.......++.+|..+       ..|+||||||+.+.....
T Consensus        47 y~f~~~~~~~vl~~l~~~~~ilL~G~pGtGKTtla~~lA~~l~   89 (327)
T TIGR01650        47 YLFDKATTKAICAGFAYDRRVMVQGYHGTGKSTHIEQIAARLN   89 (327)
T ss_pred             ccCCHHHHHHHHHHHhcCCcEEEEeCCCChHHHHHHHHHHHHC
Confidence            333344555677776544       889999999999988543

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.

>PRK00279 adk adenylate kinase; Reviewed

Probab=85.74  E-value=2.6  Score=37.00  Aligned_cols=17  Identities=41%  Similarity=0.364  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus         8 ~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          8 PPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998643

>PF07015 VirC1: VirC1 protein; InterPro: IPR009744 This family consists of several bacterial VirC1 proteins

Probab=85.74  E-value=0.63  Score=41.29  Aligned_cols=32  Identities=31%  Similarity=0.444  Sum_probs=21.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      -||.||||++..++.....++  ..+.-+....+
T Consensus        10 KGGaGKTT~~~~LAs~la~~G--~~V~lIDaDpn   41 (231)
T PF07015_consen   10 KGGAGKTTAAMALASELAARG--ARVALIDADPN   41 (231)
T ss_pred             CCCCcHHHHHHHHHHHHHHCC--CeEEEEeCCCC
Confidence            699999999999988765433  23444444433

In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon, which enhances T-DNA processing probably, does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA [].

>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell

Probab=85.73  E-value=0.63  Score=39.26  Aligned_cols=18  Identities=33%  Similarity=0.599  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .||+||||+|..+.....
T Consensus         8 kgG~GKtt~a~~la~~l~   25 (179)
T cd02036           8 KGGVGKTTTTANLGTALA   25 (179)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            799999999999877655

The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=85.69  E-value=2.4  Score=44.04  Aligned_cols=23  Identities=4%  Similarity=0.016  Sum_probs=17.9

Q ss_pred             CceecCCCCHHHHHHHHHHhcCC
Q 045120          253 DNFLIANITEEEAWRLFKIMNGD  275 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~  275 (374)
                      ..+.++..+.++-.++|..+...
T Consensus       315 r~i~v~~Pd~~~R~~Il~~~~~~  337 (644)
T PRK10733        315 RQVVVGLPDVRGREQILKVHMRR  337 (644)
T ss_pred             eEEEcCCCCHHHHHHHHHHHhhc
Confidence            46778888888888888887753

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=85.67  E-value=4.1  Score=39.80  Aligned_cols=52  Identities=21%  Similarity=0.202  Sum_probs=27.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCcCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-TSDIKKIQGDIAEKLGLEL  193 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~  193 (374)
                      .-|+||||++..+..........+.+..+.... .....+-+....+.++.+.
T Consensus       199 pnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~  251 (420)
T PRK14721        199 PTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSV  251 (420)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCce
Confidence            679999999988876433222223444443222 1223333445555655553

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=85.64  E-value=3.3  Score=40.72  Aligned_cols=80  Identities=14%  Similarity=0.273  Sum_probs=41.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHh------C-cCCchhhH------HHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKL------G-LELSEEAE------YRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l------~-~~~~~~~~------~~~~~~l~~  207 (374)
                      ..|+|||||++.+.+....    +.....-++.. -+..++....+..-      . ....+++.      ....-.+.+
T Consensus       166 ~sG~GKStLl~~I~~~~~~----~~gvI~~~Gerg~ev~e~~~~~l~~~~l~r~v~vv~~~~~~~~~r~~~~~~a~~iAE  241 (438)
T PRK07721        166 GSGVGKSTLMGMIARNTSA----DLNVIALIGERGREVREFIERDLGPEGLKRSIVVVATSDQPALMRIKGAYTATAIAE  241 (438)
T ss_pred             CCCCCHHHHHHHHhcccCC----CeEEEEEEecCCccHHHHHHhhcChhhhcCeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            6799999999988874432    22222233333 23444433322111      0 01111111      122335666


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      ++++ +++.||++||+...
T Consensus       242 yfr~~g~~Vll~~Dsltr~  260 (438)
T PRK07721        242 YFRDQGLNVMLMMDSVTRV  260 (438)
T ss_pred             HHHHCCCcEEEEEeChHHH
Confidence            6642 58999999999643

>TIGR01042 V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit

Probab=85.56  E-value=3.9  Score=41.27  Aligned_cols=80  Identities=15%  Similarity=0.190  Sum_probs=50.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHh------CcC----------CchhhHHH----
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKL------GLE----------LSEEAEYR----  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l------~~~----------~~~~~~~~----  200 (374)
                      ..|+|||+|++++.+.    ..-|.++++-++..- .+.+++.++-+..      +.+          ..+++...    
T Consensus       234 g~G~GKT~l~~~lak~----s~aDviVyvg~GERG~Em~evle~fp~l~dp~~g~~~~~m~rtvlVa~tsd~p~~~R~~s  309 (591)
T TIGR01042       234 AFGCGKTVISQSLSKY----SNSDAIVYVGCGERGNEMAEVLMDFPELTMEVDGREESIMKRTTLVANTSNMPVAAREAS  309 (591)
T ss_pred             CCCcCHHHHHHHHHhc----cCcCEEEEEEEeechHHHHHHHHHhHhhcccccccccccccceEEEEEcCCCCHHHHHHH
Confidence            5699999999998662    236789999887764 4566666643221      001          11122211    


Q ss_pred             --HHHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          201 --RASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       201 --~~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                        ..-.+.+++++ +++.||++|++...
T Consensus       310 ~ytg~tiAEYfRD~G~~Vll~~DS~tR~  337 (591)
T TIGR01042       310 IYTGITLAEYFRDMGYNVSMMADSTSRW  337 (591)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEecChHHH
Confidence              22356667753 58999999998643

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=85.54  E-value=1.1  Score=36.23  Aligned_cols=19  Identities=32%  Similarity=0.345  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      .-|+|||||++.+......
T Consensus        30 ~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        30 DLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCCCCHHHHHHHHHHHcCC
Confidence            6699999999999986543

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.

>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily

Probab=85.54  E-value=0.62  Score=39.23  Aligned_cols=19  Identities=37%  Similarity=0.629  Sum_probs=15.6

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      -||+||||+|..+......
T Consensus         8 kgG~GKTt~a~~LA~~la~   26 (169)
T cd02037           8 KGGVGKSTVAVNLALALAK   26 (169)
T ss_pred             CCcCChhHHHHHHHHHHHH
Confidence            6999999999888776543

Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.

>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=85.47  E-value=9  Score=32.05  Aligned_cols=33  Identities=27%  Similarity=0.386  Sum_probs=24.0

Q ss_pred             ccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHh
Q 045120          126 SRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       126 Gr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~  158 (374)
                      |-+...+.|.+.+..+          ..|+||+|+|..+.+..
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~l   43 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARAL   43 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHH
Confidence            3455666777777665          78999999998887753

...

>PHA02244 ATPase-like protein

Probab=85.33  E-value=1.8  Score=41.40  Aligned_cols=36  Identities=14%  Similarity=0.226  Sum_probs=24.5

Q ss_pred             cccccHHHH----HHHHHHhhcC-------CCCccHHHHHHHHHHHh
Q 045120          123 AFESRVSNL----KSTQNALTNA-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       123 ~~vGr~~~~----~~i~~~L~~~-------~gGiGKTtLA~~v~~~~  158 (374)
                      .++|.....    ..+..++..+       +.|+|||+||+++.+..
T Consensus        97 ~~ig~sp~~~~~~~ri~r~l~~~~PVLL~GppGtGKTtLA~aLA~~l  143 (383)
T PHA02244         97 TKIASNPTFHYETADIAKIVNANIPVFLKGGAGSGKNHIAEQIAEAL  143 (383)
T ss_pred             cccCCCHHHHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHh
Confidence            355544333    3455555554       88999999999999854

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=85.28  E-value=0.76  Score=41.66  Aligned_cols=51  Identities=20%  Similarity=0.242  Sum_probs=31.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEE-------EeCCCCCHHHH--HHHHHHHhCcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFS-------EVSQTSDIKKI--QGDIAEKLGLE  192 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv-------~vs~~~~~~~~--~~~i~~~l~~~  192 (374)
                      |+|+||||+.+.++.+...++.-..++=.       ...-+.++++.  .++++++.+..
T Consensus        27 MAGSGKTTF~QrL~~hl~~~~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LG   86 (366)
T KOG1532|consen   27 MAGSGKTTFMQRLNSHLHAKKTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLG   86 (366)
T ss_pred             cCCCCchhHHHHHHHHHhhccCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCC
Confidence            99999999999999987644332222221       12223355544  34677776554

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=85.23  E-value=0.61  Score=38.30  Aligned_cols=16  Identities=38%  Similarity=0.613  Sum_probs=14.4

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      +.|+||||+|+.+...
T Consensus         7 ~~GsGKST~a~~l~~~   22 (150)
T cd02021           7 VSGSGKSTVGKALAER   22 (150)
T ss_pred             CCCCCHHHHHHHHHhh
Confidence            7899999999999874

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

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.22  E-value=4.3  Score=39.26  Aligned_cols=78  Identities=15%  Similarity=0.120  Sum_probs=42.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcC--CCCeEEEEEeCCCCCHH--HHHHHHHHHhCcCCchh-hHHHHHHHHHHHHhcCCeEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDK--LFDRVVFSEVSQTSDIK--KIQGDIAEKLGLELSEE-AEYRRASRLYERLKNENKIL  216 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~--~F~~~~wv~vs~~~~~~--~~~~~i~~~l~~~~~~~-~~~~~~~~l~~~L~~~kr~L  216 (374)
                      ..|+||||.+..+........  +=..+..++.. ++...  .-++..++.++.+.... +..+....+.+ + . +.-+
T Consensus       182 ptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~D-t~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~-~-~-~~Dl  257 (388)
T PRK12723        182 PTGVGKTTTIAKLAAIYGINSDDKSLNIKIITID-NYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ-S-K-DFDL  257 (388)
T ss_pred             CCCCCHHHHHHHHHHHHHhhhccCCCeEEEEecc-CccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH-h-C-CCCE
Confidence            789999999888877554221  11234455443 43333  23555666666653322 22333333333 2 2 4568


Q ss_pred             EEEeCCC
Q 045120          217 VILANIW  223 (374)
Q Consensus       217 lVlDdv~  223 (374)
                      |++|..-
T Consensus       258 VLIDTaG  264 (388)
T PRK12723        258 VLVDTIG  264 (388)
T ss_pred             EEEcCCC
Confidence            8888874

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=85.20  E-value=0.97  Score=42.97  Aligned_cols=38  Identities=13%  Similarity=0.177  Sum_probs=31.0

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      ...++|-++.+..|+..+.++         ..|+||||+|+.+++-.
T Consensus        16 f~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l   62 (350)
T CHL00081         16 FTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLL   62 (350)
T ss_pred             HHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHH
Confidence            456899999888888777665         67999999999997753

>PRK13695 putative NTPase; Provisional

Probab=85.14  E-value=1.1  Score=37.94  Aligned_cols=28  Identities=32%  Similarity=0.402  Sum_probs=19.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFS  170 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  170 (374)
                      ..|+|||||++.+++..... .|....|+
T Consensus         8 ~~G~GKTTll~~i~~~l~~~-G~~~~g~~   35 (174)
T PRK13695          8 PPGVGKTTLVLKIAELLKEE-GYKVGGFY   35 (174)
T ss_pred             CCCCCHHHHHHHHHHHHHHC-CCeEEEEE
Confidence            68999999999998865432 34444343

>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=85.14  E-value=0.95  Score=42.75  Aligned_cols=67  Identities=16%  Similarity=0.337  Sum_probs=44.7

Q ss_pred             ccccccHHHHHHHHHHhhcC---------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC----CCC---CHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS----QTS---DIK  179 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs----~~~---~~~  179 (374)
                      ..|+|.++.+++|++.+...               +-|.||||||..+-+-.+  . |  .+|+-..    ..+   =+.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le--~-y--~~Y~l~~~Pm~e~PL~L~P~  135 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLE--E-Y--PIYTLKGCPMHEEPLHLFPK  135 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhh--e-E--EEEEecCCccccChhhhCCH
Confidence            36999999999999998754               779999999999987443  2 2  3443211    111   134


Q ss_pred             HHHHHHHHHhCcCC
Q 045120          180 KIQGDIAEKLGLEL  193 (374)
Q Consensus       180 ~~~~~i~~~l~~~~  193 (374)
                      ++-..+.+.++...
T Consensus       136 ~~r~~~~~~~~~~i  149 (358)
T PF08298_consen  136 ELRREFEDELGIRI  149 (358)
T ss_pred             hHHHHHHHHhCccc
Confidence            55556666666543

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=85.13  E-value=0.63  Score=39.06  Aligned_cols=17  Identities=35%  Similarity=0.474  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus        12 ~~GsGKstla~~La~~l   28 (175)
T PRK00131         12 FMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            89999999999999854

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=85.09  E-value=0.8  Score=39.15  Aligned_cols=17  Identities=35%  Similarity=0.646  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.++.+.
T Consensus        12 PSG~GKsTl~k~L~~~~   28 (191)
T COG0194          12 PSGVGKSTLVKALLEDD   28 (191)
T ss_pred             CCCCCHHHHHHHHHhhc
Confidence            88999999999999854

>PRK07773 replicative DNA helicase; Validated

Probab=85.00  E-value=39  Score=36.62  Aligned_cols=43  Identities=16%  Similarity=0.247  Sum_probs=26.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      -+|+|||++|..+..+...+... .+++++.  .-+..++...++.
T Consensus       225 rPg~GKT~fal~ia~~~a~~~~~-~V~~fSl--Ems~~ql~~R~~s  267 (886)
T PRK07773        225 RPSMGKTTFGLDFARNCAIRHRL-AVAIFSL--EMSKEQLVMRLLS  267 (886)
T ss_pred             CCCCCcHHHHHHHHHHHHHhcCC-eEEEEec--CCCHHHHHHHHHH
Confidence            67999999999998776544322 3445443  3334444444443

>COG4167 SapF ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=84.93  E-value=1.6  Score=37.28  Aligned_cols=15  Identities=53%  Similarity=0.685  Sum_probs=12.9

Q ss_pred             CCCccHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAK  156 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~  156 (374)
                      --|+||+|||+.+..
T Consensus        47 ~NGSGKSTLakMlaG   61 (267)
T COG4167          47 ENGSGKSTLAKMLAG   61 (267)
T ss_pred             cCCCcHhHHHHHHhc
Confidence            569999999999854

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=84.76  E-value=2.3  Score=37.28  Aligned_cols=46  Identities=15%  Similarity=0.158  Sum_probs=23.9

Q ss_pred             CCCccHHHHHHHHHHHhh-----hcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAR-----EDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~-----~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      ++|.||||++..+.....     ....-+..+-++...+..+..++..+.+
T Consensus        25 pPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   25 PPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            889999987666655441     1122344444444444444444444433

>PRK10037 cell division protein; Provisional

Probab=84.70  E-value=0.72  Score=41.68  Aligned_cols=18  Identities=28%  Similarity=0.588  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|..+..-..
T Consensus        10 KGGvGKTT~a~nLA~~La   27 (250)
T PRK10037         10 RGGVGTTSITAALAWSLQ   27 (250)
T ss_pred             CCCccHHHHHHHHHHHHH
Confidence            699999999988877654

>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein

Probab=84.44  E-value=0.73  Score=42.01  Aligned_cols=18  Identities=33%  Similarity=0.573  Sum_probs=13.8

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||++..+.....
T Consensus         8 KGGVGKTT~~~nLA~~La   25 (268)
T TIGR01281         8 KGGIGKSTTSSNLSVAFA   25 (268)
T ss_pred             CCcCcHHHHHHHHHHHHH
Confidence            599999998877765443

The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=84.33  E-value=0.71  Score=39.16  Aligned_cols=17  Identities=18%  Similarity=0.399  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus        10 ~~gsGKst~a~~l~~~~   26 (175)
T cd00227          10 GSSAGKSSIARALQSVL   26 (175)
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            78999999999998753

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK07165 F0F1 ATP synthase subunit alpha; Validated

Probab=84.31  E-value=4.4  Score=40.35  Aligned_cols=80  Identities=18%  Similarity=0.271  Sum_probs=47.8

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCe-EEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH-----HHHHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDR-VVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY-----RRASRLY  206 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~-----~~~~~l~  206 (374)
                      ..|+|||||| ..+.+...    -+. ++++.+++..+ ...+.+.+...=...       ..+....     ...-.+.
T Consensus       151 ~~gtGKT~lal~~I~~q~~----~dv~~V~~~IGer~~ev~~~~~~l~~~gal~~tvvV~atsd~~~~r~~ap~~a~tiA  226 (507)
T PRK07165        151 DRQTGKTHIALNTIINQKN----TNVKCIYVAIGQKRENLSRIYETLKEHDALKNTIIIDAPSTSPYEQYLAPYVAMAHA  226 (507)
T ss_pred             CCCCCccHHHHHHHHHhcC----CCeEEEEEEccCChHHHHHHHHHhhhcCceeeeEEEEeCCCCHHHHHHHHHHHHHHH
Confidence            5799999996 45666432    344 48888888754 455555554432111       1111111     1234566


Q ss_pred             HHHhcCCeEEEEEeCCCCc
Q 045120          207 ERLKNENKILVILANIWKL  225 (374)
Q Consensus       207 ~~L~~~kr~LlVlDdv~~~  225 (374)
                      ++++.++..|||+||+...
T Consensus       227 Eyfrd~~dVLlv~DdLTr~  245 (507)
T PRK07165        227 ENISYNDDVLIVFDDLTKH  245 (507)
T ss_pred             HHHHhcCceEEEEcChHHH
Confidence            7776558999999999754

>PRK05636 replicative DNA helicase; Provisional

Probab=84.28  E-value=5  Score=40.30  Aligned_cols=45  Identities=27%  Similarity=0.311  Sum_probs=29.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      .+|+||||||..+..+...+......+|   |-.-+..++...++...
T Consensus       273 rpg~GKT~~al~~a~~~a~~~g~~v~~f---SlEMs~~ql~~R~ls~~  317 (505)
T PRK05636        273 RPGVGKSTLALDFMRSASIKHNKASVIF---SLEMSKSEIVMRLLSAE  317 (505)
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCCeEEEE---EeeCCHHHHHHHHHHHh
Confidence            7799999999998876654444433333   44455566666665554

>KOG2859 consensus DNA repair protein, member of the recA/RAD51 family [Replication, recombination and repair]

Probab=84.26  E-value=11  Score=33.12  Aligned_cols=49  Identities=20%  Similarity=0.347  Sum_probs=39.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCe----EEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDR----VVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~----~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      +||.|||...+++.-+.-+-+.|.+    +.|++....+|..++.+.+-..+.
T Consensus        46 p~~sgKt~vL~ql~a~CilPk~~GGl~~~VLfidld~~fd~lrL~~~l~hrL~   98 (293)
T KOG2859|consen   46 PGNSGKTLVLQQLVAHCILPKKFGGLQWSVLFIDLDHKFDRLRLAKSLRHRLK   98 (293)
T ss_pred             CCCccHHHHHHHHHHHeecccccCCceeEEEEEeccccccHHHHHHHHHHHHH
Confidence            9999999998888777666666753    688899999998888777766553

>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=84.20  E-value=0.76  Score=38.87  Aligned_cols=18  Identities=39%  Similarity=0.610  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+|||||++.+.+..+
T Consensus         7 ~pG~GKTTll~k~i~~l~   24 (168)
T PF03266_consen    7 PPGVGKTTLLKKVIEELK   24 (168)
T ss_dssp             -TTSSHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHhh
Confidence            679999999999998764

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=84.19  E-value=1.3  Score=44.47  Aligned_cols=45  Identities=22%  Similarity=0.305  Sum_probs=32.1

Q ss_pred             cccccHHHHHHHHHHhhcC--------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEE
Q 045120          123 AFESRVSNLKSTQNALTNA--------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSE  171 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~~--------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~  171 (374)
                      +++--...++++.+||...              ++|+||||.++.+.+...    |+.+=|.+
T Consensus        20 eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg----~~v~Ew~n   78 (519)
T PF03215_consen   20 ELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG----FEVQEWIN   78 (519)
T ss_pred             HhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC----CeeEEecC
Confidence            3444455677777777642              899999999999998643    66666753

>PF13245 AAA_19: Part of AAA domain

Probab=84.12  E-value=2.1  Score=30.91  Aligned_cols=17  Identities=35%  Similarity=0.347  Sum_probs=11.4

Q ss_pred             CCCccHHHHH-HHHHHHh
Q 045120          142 NGGIGKTTLA-KEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~  158 (374)
                      .+|.|||+++ ..+..-.
T Consensus        18 ~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   18 PPGTGKTTTLAARIAELL   35 (76)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            8899999554 4444433

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=84.10  E-value=0.71  Score=39.80  Aligned_cols=17  Identities=41%  Similarity=0.360  Sum_probs=14.8

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      .+|+||||||+.+....
T Consensus         7 ~sgsGKTtla~~l~~~~   23 (187)
T cd02024           7 VTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            57999999999998853

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.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=83.99  E-value=1.3  Score=41.93  Aligned_cols=36  Identities=17%  Similarity=0.167  Sum_probs=28.2

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~  157 (374)
                      ..++|-+..+..++-.+.++         ..|+|||||++.+..-
T Consensus         4 ~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~   48 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAAL   48 (337)
T ss_pred             cccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHh
Confidence            45789998888876655543         7799999999999753

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.

>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=83.95  E-value=1.1  Score=38.00  Aligned_cols=34  Identities=18%  Similarity=0.294  Sum_probs=24.7

Q ss_pred             ccccHHHHHHHHHHhhc----C-------CCCccHHHHHHHHHHH
Q 045120          124 FESRVSNLKSTQNALTN----A-------NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~~----~-------~gGiGKTtLA~~v~~~  157 (374)
                      ++|.+..+.++++.+..    +       ..|+||+.+|+.+++.
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~   45 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNN   45 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHC
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            36777777777776653    2       7799999999999983

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 ....

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=83.94  E-value=3.5  Score=38.73  Aligned_cols=150  Identities=17%  Similarity=0.123  Sum_probs=84.1

Q ss_pred             cccccccHHHHHHHHHHhhcC-------------CCCccHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCH-HHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA-------------NGGIGKTTLAKEFAKQAREDKLFD-RVVFSEVSQTSDI-KKIQGDI  185 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~-------------~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~vs~~~~~-~~~~~~i  185 (374)
                      ..+++|-.++-.++-.+|...             +.|.|||+|...+..+.   ..|. ..+-|......-. .-.++.|
T Consensus        23 ~~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~---q~~~E~~l~v~Lng~~~~dk~al~~I   99 (408)
T KOG2228|consen   23 HINLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDI---QENGENFLLVRLNGELQTDKIALKGI   99 (408)
T ss_pred             CcceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhH---HhcCCeEEEEEECccchhhHHHHHHH
Confidence            456888888888888887653             88999999998888772   2242 3344444444322 2355666


Q ss_pred             HHHhCcCCc-----hhhHHHHHHHHHHHHhc-----CCeEEEEEeCCCCc----cc--cccccCc-----CCCC-----C
Q 045120          186 AEKLGLELS-----EEAEYRRASRLYERLKN-----ENKILVILANIWKL----LD--LETVKIP-----FRND-----S  239 (374)
Q Consensus       186 ~~~l~~~~~-----~~~~~~~~~~l~~~L~~-----~kr~LlVlDdv~~~----~~--~~~l~~~-----~~~~-----T  239 (374)
                      ..++.....     ..+-.+....|-..|+.     +-+...|+|..+-.    .+  +-.+...     -|-+     |
T Consensus       100 ~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Tt  179 (408)
T KOG2228|consen  100 TRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTT  179 (408)
T ss_pred             HHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeec
Confidence            666643321     12334455666677753     23578888876522    11  1111111     1111     3


Q ss_pred             cchhHh------hhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          240 RDNNVV------LLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       240 R~~~va------~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                      |-...-      ...+..-.++-+++++-++...++++..
T Consensus       180 rld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  180 RLDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             cccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHh
Confidence            322111      1223333366677788888888888776

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=83.92  E-value=5.2  Score=35.27  Aligned_cols=32  Identities=22%  Similarity=0.433  Sum_probs=22.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      ..|+|||++|.++......++  ..++|++....
T Consensus        24 ~~G~GKt~~~~~~~~~~~~~g--~~~~y~s~e~~   55 (224)
T TIGR03880        24 EYGTGKTTFSLQFLYQGLKNG--EKAMYISLEER   55 (224)
T ss_pred             CCCCCHHHHHHHHHHHHHhCC--CeEEEEECCCC
Confidence            679999999988876433222  35778877653

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=83.89  E-value=8.3  Score=37.75  Aligned_cols=45  Identities=20%  Similarity=0.188  Sum_probs=30.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      .+|+|||++|..+..+......+ .++|++  -.-+..++...++...
T Consensus       202 ~pg~GKT~~al~ia~~~a~~~g~-~v~~fS--lEm~~~~l~~Rl~~~~  246 (421)
T TIGR03600       202 RPSMGKTTLALNIAENVALREGK-PVLFFS--LEMSAEQLGERLLASK  246 (421)
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCC-cEEEEE--CCCCHHHHHHHHHHHH
Confidence            78999999999998665433333 355654  3456677777766654

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

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

Probab=83.86  E-value=1.6  Score=44.20  Aligned_cols=42  Identities=26%  Similarity=0.247  Sum_probs=31.9

Q ss_pred             ccccccccHHHHH---HHHHHhhcC------------------CCCccHHHHHHHHHHHhhhc
Q 045120          120 VYEAFESRVSNLK---STQNALTNA------------------NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       120 ~~~~~vGr~~~~~---~i~~~L~~~------------------~gGiGKTtLA~~v~~~~~~~  161 (374)
                      ....+.|.|+.++   ++++.|.++                  ++|.|||.||+++.....+-
T Consensus       148 ~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VP  210 (596)
T COG0465         148 TFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP  210 (596)
T ss_pred             ChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCC
Confidence            3456778876555   567777765                  88999999999999977654

>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]

Probab=83.74  E-value=2.4  Score=37.17  Aligned_cols=43  Identities=23%  Similarity=0.309  Sum_probs=26.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      +=|+||||+++.++...+..+.  .++|.--.....+.+..++++
T Consensus        11 iDGaGKTT~~~~L~~~l~~~g~--~v~~trEP~~~~ige~iR~~l   53 (208)
T COG0125          11 IDGAGKTTQAELLKERLEERGI--KVVLTREPGGTPIGEKIRELL   53 (208)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCC--eEEEEeCCCCChHHHHHHHHH
Confidence            5599999999999997765432  445543333333344444433

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=83.73  E-value=0.74  Score=39.87  Aligned_cols=17  Identities=47%  Similarity=0.634  Sum_probs=14.6

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||||+.+....
T Consensus         7 ~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           7 GSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            67999999999998754

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.

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

Probab=83.73  E-value=1.2  Score=40.84  Aligned_cols=40  Identities=28%  Similarity=0.381  Sum_probs=31.8

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      .+..+-|-|..+.+|.+.+.-+                      .+|.|||-||++|.|...
T Consensus       183 ty~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTS  244 (440)
T KOG0726|consen  183 TYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTS  244 (440)
T ss_pred             hhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccc
Confidence            3455668899999998887543                      779999999999999543

>TIGR00665 DnaB replicative DNA helicase

Probab=83.71  E-value=46  Score=32.62  Aligned_cols=45  Identities=18%  Similarity=0.178  Sum_probs=29.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      .+|+|||++|..+..+....... .++|++..  -+..++...++...
T Consensus       203 ~pg~GKT~~~l~~a~~~a~~~g~-~vl~~SlE--m~~~~i~~R~~~~~  247 (434)
T TIGR00665       203 RPSMGKTAFALNIAENAAIKEGK-PVAFFSLE--MSAEQLAMRMLSSE  247 (434)
T ss_pred             CCCCChHHHHHHHHHHHHHhCCC-eEEEEeCc--CCHHHHHHHHHHHh
Confidence            78999999999987765433232 45566443  45566666665543

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=83.70  E-value=5.7  Score=38.31  Aligned_cols=76  Identities=22%  Similarity=0.221  Sum_probs=38.3

Q ss_pred             CCCccHHH-HHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcCCchh-hHHHHHHHHHHHHhcCCeEEE
Q 045120          142 NGGIGKTT-LAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLELSEE-AEYRRASRLYERLKNENKILV  217 (374)
Q Consensus       142 ~gGiGKTt-LA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~~~~-~~~~~~~~l~~~L~~~kr~Ll  217 (374)
                      +-|+|||| ||+..+.-....+ =..+..|+.. ++.  ..+=++.-++-++.+..-. +..++...+. .|++  +=+|
T Consensus       211 PTGVGKTTTlAKLAar~~~~~~-~~kVaiITtD-tYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~-~l~~--~d~I  285 (407)
T COG1419         211 PTGVGKTTTLAKLAARYVMLKK-KKKVAIITTD-TYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIE-ALRD--CDVI  285 (407)
T ss_pred             CCCCcHHHHHHHHHHHHHhhcc-CcceEEEEec-cchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHH-Hhhc--CCEE
Confidence            77999998 7776655331122 2345666543 333  3344455666666664432 3333333322 3333  2455


Q ss_pred             EEeCC
Q 045120          218 ILANI  222 (374)
Q Consensus       218 VlDdv  222 (374)
                      .+|-+
T Consensus       286 LVDTa  290 (407)
T COG1419         286 LVDTA  290 (407)
T ss_pred             EEeCC
Confidence            55654

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=83.67  E-value=0.8  Score=38.23  Aligned_cols=17  Identities=35%  Similarity=0.540  Sum_probs=14.8

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+.+..
T Consensus         6 ~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         6 VAGSGKSTIASALAHRL   22 (163)
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            68999999999998754

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.

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=83.64  E-value=4.7  Score=39.71  Aligned_cols=80  Identities=18%  Similarity=0.351  Sum_probs=42.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.+...    -+..+...++... ....+....+..-...       ..+.+..      ...-.+.+
T Consensus       171 ~sG~GKStLl~~I~~~~~----~~~~vi~~iG~r~~ev~~~~~~~~~~~~l~~tvvv~~~~d~~p~~r~~~~~~a~t~AE  246 (440)
T TIGR01026       171 GSGVGKSTLLGMIARNTE----ADVNVIALIGERGREVREFIEHDLGEEGLKRSVVVVATSDQSPLLRLKGAYVATAIAE  246 (440)
T ss_pred             CCCCCHHHHHHHHhCCCC----CCEEEEEEEeecchHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            679999999999887432    2344445554433 3444443333321111       1111111      12234555


Q ss_pred             HHh-cCCeEEEEEeCCCCc
Q 045120          208 RLK-NENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~-~~kr~LlVlDdv~~~  225 (374)
                      ++. .+++.||++||+...
T Consensus       247 ~frd~G~~Vll~~DslTr~  265 (440)
T TIGR01026       247 YFRDQGKDVLLLMDSVTRF  265 (440)
T ss_pred             HHHHCCCCEEEEEeChHHH
Confidence            553 358999999998643

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>PRK14529 adenylate kinase; Provisional

Probab=83.63  E-value=4.1  Score=36.15  Aligned_cols=77  Identities=14%  Similarity=0.088  Sum_probs=38.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeE--EEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRV--VFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~--~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      +.|+||||+|+.+....... |++.-  +.-.+..........+.++..    ...-+++-....+.+.|.....--+||
T Consensus         8 ~PGsGK~T~a~~La~~~~~~-~is~gdllr~~i~~~t~lg~~i~~~i~~----G~lvpdei~~~lv~~~l~~~~~~g~iL   82 (223)
T PRK14529          8 PNGSGKGTQGALVKKKYDLA-HIESGAIFREHIGGGTELGKKAKEYIDR----GDLVPDDITIPMILETLKQDGKNGWLL   82 (223)
T ss_pred             CCCCCHHHHHHHHHHHHCCC-CcccchhhhhhccCCChHHHHHHHHHhc----cCcchHHHHHHHHHHHHhccCCCcEEE
Confidence            78999999999998865432 22211  111122222222223333322    111233444556666665422345788


Q ss_pred             eCCC
Q 045120          220 ANIW  223 (374)
Q Consensus       220 Ddv~  223 (374)
                      |+.-
T Consensus        83 DGfP   86 (223)
T PRK14529         83 DGFP   86 (223)
T ss_pred             eCCC
Confidence            8753

>PRK14531 adenylate kinase; Provisional

Probab=83.60  E-value=3.3  Score=35.40  Aligned_cols=17  Identities=29%  Similarity=0.323  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+++.+....
T Consensus        10 ~pGsGKsT~~~~la~~~   26 (183)
T PRK14531         10 PPGAGKGTQAARLCAAH   26 (183)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=83.53  E-value=6.1  Score=38.66  Aligned_cols=78  Identities=21%  Similarity=0.174  Sum_probs=45.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc--------hhhHHHHHHHHHHHHhcCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS--------EEAEYRRASRLYERLKNEN  213 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~--------~~~~~~~~~~l~~~L~~~k  213 (374)
                      -+|+||||+|-.+..+......=. +++.  |-..+..++...++...+.-..        ...+.+........|.+ .
T Consensus       204 RP~mGKTafalnia~n~a~~~~~~-v~iF--SLEM~~eql~~R~Ls~~s~v~~~kirtg~l~~~d~~~l~~a~~~l~~-~  279 (435)
T COG0305         204 RPGMGKTALALNIALNAAADGRKP-VAIF--SLEMSEEQLVMRLLSSESGIESSKLRTGRLSDDEWERLIKAASELSE-A  279 (435)
T ss_pred             CCCCChHHHHHHHHHHHHHhcCCC-eEEE--EccCCHHHHHHHhhccccccchhccccccccHHHHHHHHHHHHHHhh-C
Confidence            779999999999888776532222 3333  3445566666666665543211        12233344555556665 4


Q ss_pred             eEEEEEeCCCCc
Q 045120          214 KILVILANIWKL  225 (374)
Q Consensus       214 r~LlVlDdv~~~  225 (374)
                      +  |.+||....
T Consensus       280 ~--i~IdD~~~~  289 (435)
T COG0305         280 P--IFIDDTPGL  289 (435)
T ss_pred             C--eeecCCCcC
Confidence            5  888887654

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=83.52  E-value=1.3  Score=40.29  Aligned_cols=32  Identities=22%  Similarity=0.354  Sum_probs=25.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      .+|+|||+++.++...-.  .+...++||+....
T Consensus        31 ~pGsGKT~f~~qfl~~~~--~~ge~vlyvs~~e~   62 (260)
T COG0467          31 PPGTGKTIFALQFLYEGA--REGEPVLYVSTEES   62 (260)
T ss_pred             CCCCcHHHHHHHHHHHHH--hcCCcEEEEEecCC
Confidence            889999999999887554  34778999987755

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=83.45  E-value=1  Score=33.24  Aligned_cols=18  Identities=50%  Similarity=0.756  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||++..+.....
T Consensus         7 ~~G~Gktt~~~~l~~~l~   24 (99)
T cd01983           7 KGGVGKTTLAANLAAALA   24 (99)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            469999999999888654

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=83.20  E-value=5.3  Score=37.27  Aligned_cols=62  Identities=21%  Similarity=0.357  Sum_probs=37.7

Q ss_pred             HHHHHHHhhcC-------CCCccHHHHHHHHHHHhh-hcCCC-------CeEEEEEeCCC-CCHHHHHHHHHHHhCcC
Q 045120          131 LKSTQNALTNA-------NGGIGKTTLAKEFAKQAR-EDKLF-------DRVVFSEVSQT-SDIKKIQGDIAEKLGLE  192 (374)
Q Consensus       131 ~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~-~~~~F-------~~~~wv~vs~~-~~~~~~~~~i~~~l~~~  192 (374)
                      -+-|-+++..+       .||+|||||+..++=... -++-|       ..+++|++... .++..=++.+..+++.+
T Consensus        79 P~lId~~fr~g~~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~L~Rl~~v~a~mgLs  156 (402)
T COG3598          79 PQLIDEFFRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILERLEPVRARMGLS  156 (402)
T ss_pred             hhhhhHHhhcCeeEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccChHHHHHHHHHHHHHcCCC
Confidence            34455555555       899999999876643321 12223       35677776554 34555566777777765

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=83.16  E-value=0.81  Score=38.84  Aligned_cols=17  Identities=29%  Similarity=0.300  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.+....
T Consensus         9 ~sGsGKttl~~~l~~~~   25 (179)
T TIGR02322         9 PSGAGKDTLLDYARARL   25 (179)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            78999999999998754

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.

>PRK13947 shikimate kinase; Provisional

Probab=83.15  E-value=0.86  Score=38.30  Aligned_cols=18  Identities=39%  Similarity=0.396  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.+...
T Consensus         9 ~~GsGKst~a~~La~~lg   26 (171)
T PRK13947          9 FMGTGKTTVGKRVATTLS   26 (171)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            889999999999988543

>PRK10646 ADP-binding protein; Provisional

Probab=83.14  E-value=0.77  Score=38.13  Aligned_cols=20  Identities=30%  Similarity=0.494  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhhhc
Q 045120          142 NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~  161 (374)
                      -=|.|||||++.+.....+.
T Consensus        36 dLGaGKTtf~rgl~~~Lg~~   55 (153)
T PRK10646         36 DLGAGKTTFSRGFLQALGHQ   55 (153)
T ss_pred             CCCCCHHHHHHHHHHHcCCC
Confidence            34999999999999866443

>PRK13231 nitrogenase reductase-like protein; Reviewed

Probab=83.02  E-value=1.3  Score=40.29  Aligned_cols=29  Identities=34%  Similarity=0.509  Sum_probs=19.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      -||+||||++..+....... .  .++-+..-
T Consensus        10 KGGvGKTT~a~nLA~~La~~-G--rVLliD~D   38 (264)
T PRK13231         10 KGGIGKSTTVSNMAAAYSND-H--RVLVIGCD   38 (264)
T ss_pred             CCCCcHHHHHHHHhcccCCC-C--EEEEEeEc
Confidence            59999999999988755422 2  34445443

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

Probab=83.01  E-value=2.2  Score=38.23  Aligned_cols=45  Identities=24%  Similarity=0.330  Sum_probs=31.8

Q ss_pred             ccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          124 FESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      +-|.+..+++|.+-+.-+                      +.|.|||-||+.|+++.       .+.|+-||..
T Consensus       149 iGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht-------~c~firvsgs  215 (404)
T KOG0728|consen  149 IGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT-------DCTFIRVSGS  215 (404)
T ss_pred             hccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc-------ceEEEEechH
Confidence            335677777777665432                      88999999999999844       3556777643

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=82.97  E-value=0.9  Score=38.16  Aligned_cols=17  Identities=41%  Similarity=0.538  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||||+.+....
T Consensus         3 ~sGsGKSTla~~la~~l   19 (163)
T PRK11545          3 VSGSGKSAVASEVAHQL   19 (163)
T ss_pred             CCCCcHHHHHHHHHHHh
Confidence            46999999999998855

>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional

Probab=82.97  E-value=0.94  Score=41.37  Aligned_cols=18  Identities=33%  Similarity=0.597  Sum_probs=14.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||++..+.....
T Consensus        10 KGGVGKTT~~~nLA~~la   27 (270)
T PRK13185         10 KGGIGKSTTSSNLSAAFA   27 (270)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            599999998888776554

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=82.94  E-value=0.93  Score=41.67  Aligned_cols=18  Identities=39%  Similarity=0.551  Sum_probs=14.8

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|..+..-..
T Consensus         9 KGGVGKTT~a~nLA~~La   26 (279)
T PRK13230          9 KGGIGKSTTVCNIAAALA   26 (279)
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            599999999888777554

>TIGR01969 minD_arch cell division ATPase MinD, archaeal

Probab=82.90  E-value=0.94  Score=40.61  Aligned_cols=18  Identities=33%  Similarity=0.573  Sum_probs=14.6

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|..+.....
T Consensus         9 KGGvGKTt~a~~LA~~la   26 (251)
T TIGR01969         9 KGGTGKTTITANLGVALA   26 (251)
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            699999999988776543

This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=82.87  E-value=12  Score=29.92  Aligned_cols=37  Identities=16%  Similarity=0.207  Sum_probs=25.0

Q ss_pred             ccccccHHHHHHHHHHhhc----C------------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTN----A------------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~----~------------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|-.-..+.|++.|..    +            ..|+|||.+++.+.++.
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            3466766555555555542    2            78999999888887763

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

>PRK06321 replicative DNA helicase; Provisional

Probab=82.63  E-value=7.9  Score=38.54  Aligned_cols=44  Identities=18%  Similarity=0.133  Sum_probs=28.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      -+|+|||++|..++.+....... .++|++  -.-+..++...++..
T Consensus       234 rPgmGKTafal~ia~~~a~~~g~-~v~~fS--LEMs~~ql~~Rlla~  277 (472)
T PRK06321        234 RPAMGKTALALNIAENFCFQNRL-PVGIFS--LEMTVDQLIHRIICS  277 (472)
T ss_pred             CCCCChHHHHHHHHHHHHHhcCC-eEEEEe--ccCCHHHHHHHHHHh
Confidence            67999999999998876433332 345554  334555666665543

>TIGR01351 adk adenylate kinases

Probab=82.58  E-value=4.5  Score=35.36  Aligned_cols=17  Identities=41%  Similarity=0.429  Sum_probs=14.6

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus         7 ~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         7 PPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            68999999999998643

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=82.58  E-value=7.3  Score=36.91  Aligned_cols=78  Identities=21%  Similarity=0.205  Sum_probs=40.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCcCCch----hhHHHHH-HHHHHHHhcCCe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI--KKIQGDIAEKLGLELSE----EAEYRRA-SRLYERLKNENK  214 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~~~----~~~~~~~-~~l~~~L~~~kr  214 (374)
                      +.|+||||++..+...... ..+. ++.+. ...+..  ..-++.....++.+...    .+..... +.+...... ..
T Consensus       148 ~~GvGKTTtiakLA~~l~~-~g~~-V~li~-~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai~~~~~~-~~  223 (336)
T PRK14974        148 VNGTGKTTTIAKLAYYLKK-NGFS-VVIAA-GDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIEHAKAR-GI  223 (336)
T ss_pred             CCCCCHHHHHHHHHHHHHH-cCCe-EEEec-CCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHHHHHHhC-CC
Confidence            8999999988887765442 2232 33333 333433  33355566777654321    1222222 222222223 23


Q ss_pred             EEEEEeCCC
Q 045120          215 ILVILANIW  223 (374)
Q Consensus       215 ~LlVlDdv~  223 (374)
                      =+|++|-.-
T Consensus       224 DvVLIDTaG  232 (336)
T PRK14974        224 DVVLIDTAG  232 (336)
T ss_pred             CEEEEECCC
Confidence            388999874

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=82.49  E-value=11  Score=34.64  Aligned_cols=78  Identities=17%  Similarity=0.203  Sum_probs=39.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH--HHHHHHHHHhCcCCc----hhhHHH-HHHHHHHHHhcCCe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK--KIQGDIAEKLGLELS----EEAEYR-RASRLYERLKNENK  214 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~~~~~i~~~l~~~~~----~~~~~~-~~~~l~~~L~~~kr  214 (374)
                      ++|+||||++..+....... . ..+..++. +.+...  .-+....+..+.+..    ..+... ....+.....+ ..
T Consensus        80 ~~G~GKTTt~akLA~~l~~~-g-~~V~li~~-D~~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~l~~~~~~-~~  155 (272)
T TIGR00064        80 VNGVGKTTTIAKLANKLKKQ-G-KSVLLAAG-DTFRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDAIQKAKAR-NI  155 (272)
T ss_pred             CCCCcHHHHHHHHHHHHHhc-C-CEEEEEeC-CCCCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHHHHHHHC-CC
Confidence            89999999988887655422 1 24455543 334332  233344555553321    112222 22334333334 45


Q ss_pred             EEEEEeCCC
Q 045120          215 ILVILANIW  223 (374)
Q Consensus       215 ~LlVlDdv~  223 (374)
                      =++++|-.-
T Consensus       156 D~ViIDT~G  164 (272)
T TIGR00064       156 DVVLIDTAG  164 (272)
T ss_pred             CEEEEeCCC
Confidence            678888763

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=82.49  E-value=2.6  Score=40.44  Aligned_cols=19  Identities=32%  Similarity=0.419  Sum_probs=16.7

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      .||+|||+|.+.+.+..+.
T Consensus        30 ~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   30 PAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             CCCCChhHHHHHHHHHhcc
Confidence            9999999999999986653

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PF02223 Thymidylate_kin: Thymidylate kinase; InterPro: IPR018094 Thymidylate kinase (2

Probab=82.43  E-value=2.1  Score=36.57  Aligned_cols=43  Identities=21%  Similarity=0.281  Sum_probs=25.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAE  187 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~  187 (374)
                      .-|+||||+++.+.+.....++ .  +.++.... .......++++.
T Consensus         4 iDGsGKtT~~~~L~~~l~~~~~-~--~~~~~~~~~~~~g~~ir~~l~   47 (186)
T PF02223_consen    4 IDGSGKTTQIRLLAEALKEKGY-K--VIITFPPGSTPIGELIRELLR   47 (186)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTE-E--EEEEESSTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHcCC-c--ccccCCCCCChHHHHHHHHHh
Confidence            4599999999999997764432 2  23332222 224455555555

7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process; PDB: 2PLR_B 1NMX_A 1NN0_A 2XX3_A 1NN3_A 1E9F_A 1E2Q_A 1E2D_A 1E9A_A 1E99_A ....

>TIGR01287 nifH nitrogenase iron protein

Probab=82.37  E-value=1  Score=41.30  Aligned_cols=20  Identities=40%  Similarity=0.586  Sum_probs=15.6

Q ss_pred             CCCccHHHHHHHHHHHhhhc
Q 045120          142 NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~  161 (374)
                      -||+||||++..+.....-+
T Consensus         8 KGGVGKTT~a~nLA~~La~~   27 (275)
T TIGR01287         8 KGGIGKSTTTQNIAAALAEM   27 (275)
T ss_pred             CCcCcHHHHHHHHHHHHHHC
Confidence            59999999988887765533

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=82.31  E-value=0.97  Score=38.52  Aligned_cols=17  Identities=24%  Similarity=0.349  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        11 ~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360        11 GPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998743

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.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=82.28  E-value=1.3  Score=37.10  Aligned_cols=30  Identities=20%  Similarity=0.453  Sum_probs=23.5

Q ss_pred             HHHHHHHHHhhcC------CCCccHHHHHHHHHHHh
Q 045120          129 SNLKSTQNALTNA------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       129 ~~~~~i~~~L~~~------~gGiGKTtLA~~v~~~~  158 (374)
                      ..+++|.+.|...      ..|+|||||...+..+.
T Consensus        24 ~g~~~l~~~l~~k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   24 EGIEELKELLKGKTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             cCHHHHHHHhcCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3466777777666      78999999999998754

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=82.16  E-value=1.2  Score=37.79  Aligned_cols=19  Identities=26%  Similarity=0.392  Sum_probs=16.7

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      ..|.||||||..++.....
T Consensus        31 LSGsGKSTiA~ale~~L~~   49 (197)
T COG0529          31 LSGSGKSTIANALEEKLFA   49 (197)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            8999999999999986653

>PRK13233 nifH nitrogenase reductase; Reviewed

Probab=82.05  E-value=0.84  Score=41.83  Aligned_cols=18  Identities=39%  Similarity=0.589  Sum_probs=14.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|..+..-..
T Consensus        10 KGGVGKTT~a~nLA~~La   27 (275)
T PRK13233         10 KGGIGKSTTTQNTAAAMA   27 (275)
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            599999999887766543

>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=81.99  E-value=0.99  Score=35.14  Aligned_cols=18  Identities=28%  Similarity=0.549  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+|||||.+.+.+...
T Consensus         7 ~~g~GKTsLi~~l~~~~~   24 (119)
T PF08477_consen    7 DSGVGKTSLIRRLCGGEF   24 (119)
T ss_dssp             STTSSHHHHHHHHHHSS-
T ss_pred             cCCCCHHHHHHHHhcCCC
Confidence            579999999999987543

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.

>cd02032 Bchl_like This family of proteins contains bchL and chlL

Probab=81.82  E-value=1.1  Score=40.85  Aligned_cols=18  Identities=33%  Similarity=0.593  Sum_probs=14.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|..+.....
T Consensus         8 KGGvGKTT~a~nLA~~la   25 (267)
T cd02032           8 KGGIGKSTTSSNLSVALA   25 (267)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            599999998887766544

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.

>PRK05595 replicative DNA helicase; Provisional

Probab=81.76  E-value=57  Score=32.22  Aligned_cols=45  Identities=18%  Similarity=0.097  Sum_probs=29.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      .+|+|||++|..+..+...+... .++|++.  .-+..++...++...
T Consensus       209 rpg~GKT~~al~ia~~~a~~~g~-~vl~fSl--Ems~~~l~~R~~a~~  253 (444)
T PRK05595        209 RPSMGKTTFALNIAEYAALREGK-SVAIFSL--EMSKEQLAYKLLCSE  253 (444)
T ss_pred             cCCCChHHHHHHHHHHHHHHcCC-cEEEEec--CCCHHHHHHHHHHHh
Confidence            77999999999988764433333 3445543  445666666666554

>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=81.66  E-value=1.1  Score=36.76  Aligned_cols=17  Identities=41%  Similarity=0.458  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus         7 ~~GsGKstla~~la~~l   23 (154)
T cd00464           7 MMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

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.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=81.56  E-value=2.2  Score=34.84  Aligned_cols=32  Identities=19%  Similarity=0.303  Sum_probs=22.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      ..|+|||||++.+.+....+ .+...+..+...
T Consensus         8 ~~~sGKTTl~~~Li~~l~~~-g~~v~~ik~~~~   39 (140)
T PF03205_consen    8 PKNSGKTTLIRKLINELKRR-GYRVAVIKHTDH   39 (140)
T ss_dssp             STTSSHHHHHHHHHHHHHHT-T--EEEEEE-ST
T ss_pred             CCCCCHHHHHHHHHHHHhHc-CCceEEEEEccC
Confidence            46899999999999987543 455666666655

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=81.55  E-value=7.2  Score=38.20  Aligned_cols=18  Identities=33%  Similarity=0.298  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||++..+.....
T Consensus       108 ~~GvGKTTtaaKLA~~l~  125 (429)
T TIGR01425       108 LQGSGKTTTCTKLAYYYQ  125 (429)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            899999999888876544

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK13235 nifH nitrogenase reductase; Reviewed

Probab=81.46  E-value=1.1  Score=40.98  Aligned_cols=18  Identities=33%  Similarity=0.523  Sum_probs=14.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||++..+..-..
T Consensus         9 KGGVGKTT~~~nLA~~La   26 (274)
T PRK13235          9 KGGIGKSTTTQNTVAGLA   26 (274)
T ss_pred             CCCccHHHHHHHHHHHHH
Confidence            599999999887766543

>PRK13975 thymidylate kinase; Provisional

Probab=81.44  E-value=1.1  Score=38.65  Aligned_cols=18  Identities=44%  Similarity=0.451  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.....
T Consensus        10 ~~GsGKtT~~~~L~~~l~   27 (196)
T PRK13975         10 IDGSGKTTQAKLLAEKLN   27 (196)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            789999999999998654

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=81.42  E-value=1.1  Score=40.96  Aligned_cols=18  Identities=33%  Similarity=0.632  Sum_probs=14.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|..+..-..
T Consensus         9 KGGVGKTT~a~nLA~~La   26 (273)
T PRK13232          9 KGGIGKSTTTQNLTAALS   26 (273)
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            599999998888766543

>PRK04040 adenylate kinase; Provisional

Probab=81.29  E-value=1.1  Score=38.65  Aligned_cols=17  Identities=29%  Similarity=0.419  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+++.+....
T Consensus        10 ~pG~GKtt~~~~l~~~l   26 (188)
T PRK04040         10 VPGVGKTTVLNKALEKL   26 (188)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998854

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=81.26  E-value=1  Score=39.67  Aligned_cols=18  Identities=50%  Similarity=0.671  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||+|+.++....
T Consensus        16 ~SgSGKTTva~~l~~~~~   33 (218)
T COG0572          16 GSGSGKTTVAKELSEQLG   33 (218)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            678999999999998554

>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=81.18  E-value=1.1  Score=38.36  Aligned_cols=18  Identities=50%  Similarity=0.704  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||||+.+.....
T Consensus         7 ~sgsGKttla~~l~~~l~   24 (179)
T cd02028           7 PSGSGKTTFAKKLSNQLR   24 (179)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            579999999999988654

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd03110 Fer4_NifH_child This protein family's function is unkown

Probab=81.14  E-value=0.97  Score=38.37  Aligned_cols=17  Identities=41%  Similarity=0.616  Sum_probs=13.8

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      -||+||||+|..+..-.
T Consensus         8 kgG~GKSt~a~nLA~~l   24 (179)
T cd03110           8 KGGTGKTTVTAALAALL   24 (179)
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            69999999988876643

It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=81.09  E-value=1.1  Score=37.96  Aligned_cols=18  Identities=44%  Similarity=0.676  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||+|+.+.....
T Consensus        12 ~~GsGKST~a~~la~~l~   29 (175)
T PRK00889         12 LSGAGKTTIARALAEKLR   29 (175)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            789999999999998654

>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=81.02  E-value=5  Score=36.70  Aligned_cols=15  Identities=40%  Similarity=0.514  Sum_probs=13.6

Q ss_pred             CCCccHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAK  156 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~  156 (374)
                      .||+||+||++.+..
T Consensus        39 ~~GsGr~sl~rLaa~   53 (268)
T PF12780_consen   39 VGGSGRQSLARLAAF   53 (268)
T ss_dssp             TTTSCHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHH
Confidence            999999999998776

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.

>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ

Probab=80.79  E-value=1.3  Score=39.72  Aligned_cols=30  Identities=30%  Similarity=0.403  Sum_probs=20.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      -||+||||+|..+.......+ + .++-|+..
T Consensus        10 KGGvGKTt~a~nla~~la~~g-~-~VlliD~D   39 (246)
T TIGR03371        10 KGGVGKTTLTANLASALKLLG-E-PVLAIDLD   39 (246)
T ss_pred             CCCccHHHHHHHHHHHHHhCC-C-cEEEEeCC
Confidence            699999999998877654322 2 35555544

Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=80.78  E-value=6.8  Score=38.22  Aligned_cols=16  Identities=19%  Similarity=0.345  Sum_probs=14.4

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      +.|+|||.||..+...
T Consensus       217 p~GTGKThla~~l~~~  232 (449)
T TIGR02688       217 PKGTGKSYIYNNLSPY  232 (449)
T ss_pred             CCCCCHHHHHHHHhHH
Confidence            8899999999998776

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.

>PRK13949 shikimate kinase; Provisional

Probab=80.77  E-value=1.2  Score=37.67  Aligned_cols=18  Identities=44%  Similarity=0.556  Sum_probs=15.8

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+|||||++.+.+...
T Consensus         9 ~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          9 YMGAGKTTLGKALARELG   26 (169)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            789999999999998654

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=80.71  E-value=6.5  Score=39.13  Aligned_cols=50  Identities=18%  Similarity=0.167  Sum_probs=28.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLE  192 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~  192 (374)
                      +-|+||||++..+......+..-..+..|.. ..+.  ..+-+....+.++.+
T Consensus       264 pnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~-Dt~RigA~EQLr~~AeilGVp  315 (484)
T PRK06995        264 PTGVGKTTTTAKLAARCVMRHGASKVALLTT-DSYRIGGHEQLRIYGKILGVP  315 (484)
T ss_pred             CCCccHHHHHHHHHHHHHHhcCCCeEEEEeC-CccchhHHHHHHHHHHHhCCC
Confidence            7799999999998876543322223444543 3333  233344455555544

>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

Probab=80.41  E-value=1.7  Score=39.32  Aligned_cols=28  Identities=32%  Similarity=0.406  Sum_probs=19.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSE  171 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~  171 (374)
                      -||+||||++..+.--..  ..|..++.-+
T Consensus        10 KGGtGKTTva~~la~~l~--~~~~~~l~Dc   37 (284)
T COG1149          10 KGGTGKTTVAANLAVLLG--DKYKLVLADC   37 (284)
T ss_pred             CCCCChhhHHHHHHHHhc--cccceEEEec
Confidence            699999999988876433  4466555543

>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=80.28  E-value=2.5  Score=40.25  Aligned_cols=41  Identities=24%  Similarity=0.331  Sum_probs=29.6

Q ss_pred             cccccccHHHHHH---HHHHhhcC-----------CCCccHHHHHHHHHHHhhhc
Q 045120          121 YEAFESRVSNLKS---TQNALTNA-----------NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       121 ~~~~vGr~~~~~~---i~~~L~~~-----------~gGiGKTtLA~~v~~~~~~~  161 (374)
                      ...+||..+..+.   +++++...           ++|.|||+||..+.......
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~   77 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGED   77 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTT
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCC
Confidence            3468998766654   57777665           88999999999999966533

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.

>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=80.15  E-value=1.7  Score=36.70  Aligned_cols=27  Identities=22%  Similarity=0.352  Sum_probs=22.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSE  171 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~  171 (374)
                      ..|+||+||.+.+|.++.+.   ...+||.
T Consensus        45 ~SG~GKStllr~LYaNY~~d---~G~I~v~   71 (235)
T COG4778          45 PSGSGKSTLLRSLYANYLPD---EGQILVR   71 (235)
T ss_pred             CCCCcHHHHHHHHHhccCCC---CceEEEE
Confidence            88999999999999987754   3577774

>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=80.15  E-value=1.3  Score=35.84  Aligned_cols=17  Identities=47%  Similarity=0.602  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||+|+.+....
T Consensus         7 ~~GsGKst~a~~la~~~   23 (147)
T cd02020           7 PAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            67999999999998754

>TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit

Probab=80.07  E-value=4.9  Score=40.69  Aligned_cols=80  Identities=16%  Similarity=0.188  Sum_probs=48.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHH----hCcC----------CchhhHHH------
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD-IKKIQGDIAEK----LGLE----------LSEEAEYR------  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~----l~~~----------~~~~~~~~------  200 (374)
                      ..|+|||+|.+++.+..    +-|.++++-++...+ +.+++.+.-+.    ++.+          ..+++...      
T Consensus       230 g~G~GKT~l~~~lak~~----~adivVyvg~GERG~E~~e~le~f~~l~dp~~g~~~m~RTvlVanTSn~p~~aR~~s~y  305 (578)
T TIGR01043       230 PFGSGKTVTQHQLAKWS----DADIVVYIGCGERGNEMTDVLEEFPELKDPKTGKPLMERTVLIANTSNMPVAAREASIY  305 (578)
T ss_pred             CCCCCHHHHHHHHHhcC----CCCEEEEEEeccChHHHHHHHHHhHhhcccccccccccceEEEEECCCCCHHHHHHHHH
Confidence            56999999999887632    357889998887753 45555554221    1111          11222211      


Q ss_pred             HHHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          201 RASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       201 ~~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      ..-.+.+++++ ++..||+.|++...
T Consensus       306 tg~TiAEYfRD~G~~Vllm~DS~sR~  331 (578)
T TIGR01043       306 TGITIAEYFRDMGYDVALMADSTSRW  331 (578)
T ss_pred             HHHHHHHHHHHCCCCEEEEecChhHH
Confidence            12346666653 58999999998643

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>KOG1547 consensus Septin CDC10 and related P-loop GTPases [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms; Cytoskeleton]

Probab=80.04  E-value=3.5  Score=36.76  Aligned_cols=38  Identities=16%  Similarity=0.249  Sum_probs=30.9

Q ss_pred             ccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhh
Q 045120          122 EAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~  159 (374)
                      -.+||.|..++++...+...          ..|.|||||..-+|...-
T Consensus        24 lgyvGidtI~~Qm~~k~mk~GF~FNIMVVgqSglgkstlinTlf~s~v   71 (336)
T KOG1547|consen   24 LGYVGIDTIIEQMRKKTMKTGFDFNIMVVGQSGLGKSTLINTLFKSHV   71 (336)
T ss_pred             cccccHHHHHHHHHHHHHhccCceEEEEEecCCCCchhhHHHHHHHHH
Confidence            46899999999997777654          679999999988887543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	374
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-20
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	1e-15
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-09
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	1e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 91.1 bits (225), Expect = 6e-20
 Identities = 58/396 (14%), Positives = 131/396 (33%), Gaps = 92/396 (23%)

Query: 40  KAELEKLKVERTSIQ--LRVSEA-KEKGEEIEEK-VE-------KWL-TRYQLSKKAKT- 86
           K E++ + + + ++   LR+      K EE+ +K VE       K+L +  +  ++  + 
Sbjct: 48  KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSM 107

Query: 87  -------EVKALIELGEEVKKFDIVSHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALT 139
                  +   L    +   K+++    +  +        + E        L+  +N L 
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNV----SRLQPYLKLRQALLE--------LRPAKNVLI 155

Query: 140 NANGGIGKTTLAKEFAKQAREDKLFDRVVF----SEVSQTSDIKKIQGDIAEKLGLELSE 195
           +   G GKT +A +     +     D  +F       +    + ++   +  ++    + 
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS 215

Query: 196 EAEY-----RRASRLYERL------KNENKILVILANIWKLLDLETVKIPFRND------ 238
            +++      R   +   L      K     L++L N+    + +     F         
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ---NAKAWN-AFNLSCKILLT 271

Query: 239 SRDNNV--VLLSMGSKDNFLI---ANITEEEAWRLF-KIMNGDD----VENCKFKSTAIN 288
           +R   V   L +  +    L      +T +E   L  K ++        E        ++
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331

Query: 289 VAKACGAGL---FCT----LTTNASK-----SSSIYSHVSNDYQSIYKPKPYLAVFQD-- 334
           +       +     T       N  K      SS+      +Y+ ++     L+VF    
Sbjct: 332 I---IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD---RLSVFPPSA 385

Query: 335 LEPTIVKTAFVDPKWYLALKEEFEA-LQRNQTWSLV 369
             PTI+ +      W+  +K +    + +   +SLV
Sbjct: 386 HIPTILLSLI----WFDVIKSDVMVVVNKLHKYSLV 417

>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* Length = 549

 Score = 77.3 bits (190), Expect = 1e-15
 Identities = 22/173 (12%), Positives = 54/173 (31%), Gaps = 22/173 (12%)

Query: 143 GGIGKTTLAKEFAKQARE--DKLFDRVVFSEVSQTS---------DIKKIQGDIAEKLGL 191
            G GK+ +A +   ++ +     +D +V+ + S T+         DI  +     + L  
Sbjct: 161 AGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNF 220

Query: 192 ELSEEAEYRRASRLYER-LKNENKILVILANIWKLLDLETVKIPFRNDS------RDNNV 244
              E        R+    L +    L +  ++      ET++             RD  +
Sbjct: 221 PSVEHVTSVVLKRMICNALIDRPNTLFVFDDVV---QEETIRWAQELRLRCLVTTRDVEI 277

Query: 245 VLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL 297
              +  + +   + ++  +E +   +          K +       +    G 
Sbjct: 278 SNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSS-GN 329

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 57.9 bits (140), Expect = 2e-09
 Identities = 36/281 (12%), Positives = 90/281 (32%), Gaps = 49/281 (17%)

Query: 45  KLKVERTSIQLRVSEAKEKGEEIEEKVEKWLTRYQLSKKAKTEVKALIELGEEVKKFDIV 104
             K   + +    +   E  +++   +   +        + +   ++  +   V+   ++
Sbjct: 61  LKKDNDSYVSFYNALLHEGYKDLAALLHDGIPV----VSSSSGKDSVSGITSYVRT--VL 114

Query: 105 SHCTIPEEIWLKSNKVYEAFESRVSNLKSTQNALTNAN-----------GGIGKTTLAKE 153
               +P+        V+   +  V+ ++     L+               G GK+ LA E
Sbjct: 115 CEGGVPQR-----PVVFVTRKKLVNAIQ---QKLSKLKGEPGWVTIHGMAGCGKSVLAAE 166

Query: 154 FAKQAREDKLF--DRVVFSEVSQTSDIKKIQG--DIAEKLGLELSEEAEYRR-----ASR 204
             +     +      V +  V +      +    ++  +L  + S              R
Sbjct: 167 AVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDR 226

Query: 205 LYERLKN-ENKILVILANIWKLLDLETVKIPFRNDS------RDNNVVLLSMGSKDN-FL 256
           L   +     + L+IL ++W    L+     F +        RD +V    MG K    +
Sbjct: 227 LRILMLRKHPRSLLILDDVWDSWVLKA----FDSQCQILLTTRDKSVTDSVMGPKYVVPV 282

Query: 257 IANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL 297
            +++ +E+   +  +       +   ++ +I   K C  G 
Sbjct: 283 ESSLGKEKGLEILSLFVNMKKADLPEQAHSI--IKECK-GS 320

>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* Length = 1249

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 48/274 (17%), Positives = 89/274 (32%), Gaps = 52/274 (18%)

Query: 143 GGIGKTTLAKEFAKQAR--EDKLFDRVVFSEVSQT--SDIKKIQGDIAEKLGLELS---- 194
            G GK+ LA E  +     E      V +  + +   S +     ++  +L  E S    
Sbjct: 156 AGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQR 215

Query: 195 -----EEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRN--DSRDNNVVLL 247
                EEA+ R    +  +     + L+IL ++W    L+      +    +RD +V   
Sbjct: 216 LPLNIEEAKDRLRVLMLRK---HPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTDS 272

Query: 248 SMGSKDNFLI-ANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACG---------AGL 297
            MG K    + + +  E+   +  +      E     + A ++ K C            L
Sbjct: 273 VMGPKHVVPVESGLGREKGLEILSLFVNMKKE--DLPAEAHSIIKECKGSPLVVSLIGAL 330

Query: 298 FCTLTTN---------ASKSSSIYSHVSNDYQSIYK---------PKPYLAVFQDL---- 335
                             +   I    S DY+++ +          +     + DL    
Sbjct: 331 LRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQ 390

Query: 336 EPTIVKTAFVDPKWYLALKEEFEALQRNQTWSLV 369
           +   V T  +   W L  +E  + LQ     SL+
Sbjct: 391 KDVKVPTKVLCVLWDLETEEVEDILQEFVNKSLL 424

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	374
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.96
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.96
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.93
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.32
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.17
2fna_A	357	Conserved hypothetical protein; structural genomic	99.1
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.91
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.89
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.88
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.78
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.71
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.51
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.38
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	98.26
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.07
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.06
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.02
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.85
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.81
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.72
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.63
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.63
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.52
3pvs_A	447	Replication-associated recombination protein A; ma	97.44
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.19
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.17
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.14
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.04
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	96.99
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.91
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.91
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.89
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.88
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	96.78
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.76
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	96.76
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.69
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.69
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.63
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.59
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.57
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.55
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.54
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.5
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.47
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.43
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.43
3bos_A	242	Putative DNA replication factor; P-loop containing	96.38
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.36
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.3
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.3
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.26
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.25
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	96.2
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.2
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	95.85
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	95.82
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	95.81
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	95.71
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.71
3io5_A	333	Recombination and repair protein; storage dimer, i	95.6
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.56
3co5_A	143	Putative two-component system transcriptional RES	95.53
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	95.42
2z43_A	324	DNA repair and recombination protein RADA; archaea	95.42
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	95.35
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.28
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	95.27
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	95.23
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.12
1xp8_A	366	RECA protein, recombinase A; recombination, radior	95.11
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.01
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.94
2cvh_A	220	DNA repair and recombination protein RADB; filamen	94.87
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.86
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	94.85
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.77
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	94.74
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	94.72
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	94.42
2qgz_A	308	Helicase loader, putative primosome component; str	94.38
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	94.3
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	94.23
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.21
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	94.19
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	93.93
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	93.91
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	93.71
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	93.6
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	93.46
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	93.13
2r44_A	331	Uncharacterized protein; putative ATPase, structur	93.04
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	93.03
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	92.76
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	92.74
2r6a_A	454	DNAB helicase, replicative helicase; replication,	92.71
3ice_A	422	Transcription termination factor RHO; transcriptio	92.63
4a74_A	231	DNA repair and recombination protein RADA; hydrola	92.31
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	92.27
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	92.27
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	92.15
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	91.78
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	91.73
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	91.37
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	91.36
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.15
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	91.04
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	90.64
3l0o_A	427	Transcription termination factor RHO; helicase, RH	90.43
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	90.4
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	90.37
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	90.32
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	90.25
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	90.11
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	90.09
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	90.03
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	89.92
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	89.53
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	89.48
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	89.45
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	88.99
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	88.87
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	88.76
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	88.76
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	88.49
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	88.32
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	88.32
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	88.19
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	88.14
3cwq_A	209	Para family chromosome partitioning protein; alpha	87.83
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	87.8
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	87.69
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	87.56
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	87.41
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	87.36
2xxa_A	433	Signal recognition particle protein; protein trans	87.32
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	87.23
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	87.12
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	87.08
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	86.98
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	86.75
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	86.61
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	86.35
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	85.73
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	85.7
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	85.57
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	85.21
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	85.12
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	85.1
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	85.1
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	84.87
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	84.85
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	84.65
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	84.36
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	84.32
1via_A	175	Shikimate kinase; structural genomics, transferase	84.31
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	84.28
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	84.15
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	84.07
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	83.85
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	83.84
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	83.8
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	83.78
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	83.46
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	83.39
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	82.88
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	82.69
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	82.67
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	82.66
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	82.15
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	82.12
3gqb_A	578	V-type ATP synthase alpha chain; A3B3, V-ATPase, A	82.08
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	82.08
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	81.92
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	81.82
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	81.81
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	81.73
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	81.68
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	81.64
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	81.62
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	81.52
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	81.45
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	81.44
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	81.35
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	81.18
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	80.89
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	80.8
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	80.79
3end_A	307	Light-independent protochlorophyllide reductase ir	80.63
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	80.2
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	80.1
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	80.04
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	80.03

>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=100.00  E-value=1.9e-36  Score=303.94  Aligned_cols=234  Identities=11%  Similarity=0.049  Sum_probs=181.4

Q ss_pred             cccHHHHHHHHHHhhcC------------CCCccHHHHHHHHHH--HhhhcCCCCeEEEEEeCCCC--CHHHHHHHHHHH
Q 045120          125 ESRVSNLKSTQNALTNA------------NGGIGKTTLAKEFAK--QAREDKLFDRVVFSEVSQTS--DIKKIQGDIAEK  188 (374)
Q Consensus       125 vGr~~~~~~i~~~L~~~------------~gGiGKTtLA~~v~~--~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~  188 (374)
                      +||+.++++|.++|..+            |||+||||||+++|+  +.++..+|++++||++++.+  ++..++..|+.+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            49999999999999632            999999999999999  67888999999999999985  899999999999


Q ss_pred             hCcCCc--------hhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcCCCC-----CcchhHhhhhcC-CCCc
Q 045120          189 LGLELS--------EEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND-----SRDNNVVLLSMG-SKDN  254 (374)
Q Consensus       189 l~~~~~--------~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~~~~-----TR~~~va~~~~~-~~~~  254 (374)
                      ++....        ..+...+...+++.|.++|||||||||||+..++ .+. ..+.+     ||+..++. .++ ...+
T Consensus       211 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~-~~~gs~ilvTTR~~~v~~-~~~~~~~~  287 (549)
T 2a5y_B          211 LKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWA-QELRLRCLVTTRDVEISN-AASQTCEF  287 (549)
T ss_dssp             HTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHH-HHTTCEEEEEESBGGGGG-GCCSCEEE
T ss_pred             HhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-ccc-ccCCCEEEEEcCCHHHHH-HcCCCCeE
Confidence            986521        1234567789999999833999999999998754 221 11333     99999974 444 3467


Q ss_pred             eecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc--CCCccccccccccc-----CCCCccc
Q 045120          255 FLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS--KSSSIYSHVSNDYQ-----SIYKPKP  327 (374)
Q Consensus       255 ~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~~~~~W~~~~~~-----~~~~~~~  327 (374)
                      |+|++|+.++||+||.+.++....++.+.+++++|+++| +|+||||+++|+  +.++ .+|......     ...++.+
T Consensus       288 ~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c-~GlPLAl~~~g~~l~~~~-w~~~~~l~~~l~~~~~~~i~~  365 (549)
T 2a5y_B          288 IEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELS-SGNPATLMMFFKSCEPKT-FEKMAQLNNKLESRGLVGVEC  365 (549)
T ss_dssp             EECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHH-TTCHHHHHHHHTTCCSSS-HHHHHHHHHHHHHHCSSTTCC
T ss_pred             EECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHh-CCChHHHHHHHHHhccch-HHHHHHhHHHhhcccHHHHHH
Confidence            999999999999999999986554578889999999999 999999999999  4432 223111110     1233334


Q ss_pred             chhh-cccCCchhhhhhhc---------------CchhhhhcHHHHHHHHHhC--Ccce
Q 045120          328 YLAV-FQDLEPTIVKTAFV---------------DPKWYLALKEEFEALQRNQ--TWSL  368 (374)
Q Consensus       328 ~~~l-y~~Lp~~~lk~cfL---------------fp~~~~i~~~~Li~~W~~~--~~~~  368 (374)
                      .+.+ |++||++ +|.||+               ||+++.|+    |++|+|+  ||..
T Consensus       366 ~l~~Sy~~L~~~-lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~  419 (549)
T 2a5y_B          366 ITPYSYKSLAMA-LQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDIC  419 (549)
T ss_dssp             CSSSSSSSHHHH-HHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC---
T ss_pred             HHhcccccccHH-HHHHHhccchhhhhHhhheeeeCCCCeee----eeeeeeeccceec
Confidence            5666 9999885 999973               99999999    8999999  7764

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.96  E-value=6.5e-31  Score=271.08  Aligned_cols=226  Identities=14%  Similarity=0.050  Sum_probs=172.7

Q ss_pred             ccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCe-EEEEEeCCCCCHHHHHHHHHHHhCcC
Q 045120          124 FESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDR-VVFSEVSQTSDIKKIQGDIAEKLGLE  192 (374)
Q Consensus       124 ~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~~~~~i~~~l~~~  192 (374)
                      .+||+.++++|.++|...          |||+||||||+++|++.++..+|+. ++|+++++.++...++..|+..++..
T Consensus       130 ~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i  209 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI  209 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhc
Confidence            499999999999999862          9999999999999998888888986 99999999999988888887754321


Q ss_pred             ---C----c-----hhhHHHHHHHHHHHHh--cCCeEEEEEeCCCCccccccccCcCCCC----CcchhHhhhhcCCCCc
Q 045120          193 ---L----S-----EEAEYRRASRLYERLK--NENKILVILANIWKLLDLETVKIPFRND----SRDNNVVLLSMGSKDN  254 (374)
Q Consensus       193 ---~----~-----~~~~~~~~~~l~~~L~--~~kr~LlVlDdv~~~~~~~~l~~~~~~~----TR~~~va~~~~~~~~~  254 (374)
                         .    .     ..+.+.....+++.|+  .+||+||||||||+.+.|+.+.  .++.    ||+..++. .+.....
T Consensus       210 ~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~--pGSRILVTTRd~~Va~-~l~g~~v  286 (1221)
T 1vt4_I          210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN--LSCKILLTTRFKQVTD-FLSAATT  286 (1221)
T ss_dssp             CSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH--SSCCEEEECSCSHHHH-HHHHHSS
T ss_pred             CcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC--CCeEEEEeccChHHHH-hcCCCeE
Confidence               0    0     1133455667777762  2389999999999988888763  1222    99999874 2333346


Q ss_pred             eecC------CCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc--CCC--cccccccccccCCCC
Q 045120          255 FLIA------NITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS--KSS--SIYSHVSNDYQSIYK  324 (374)
Q Consensus       255 ~~l~------~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~--~~~~W~~~~~~~~~~  324 (374)
                      |.|+      +|+.+|||+||++..+..     ..++..+|   | +|+||||+++|+  +.+  +.++|.....   ..
T Consensus       287 y~LeL~d~dL~LS~eEA~eLF~~~~g~~-----~eeL~~eI---C-gGLPLALkLaGs~Lr~k~~s~eeW~~~~~---~~  354 (1221)
T 1vt4_I          287 THISLDHHSMTLTPDEVKSLLLKYLDCR-----PQDLPREV---L-TTNPRRLSIIAESIRDGLATWDNWKHVNC---DK  354 (1221)
T ss_dssp             CEEEECSSSSCCCHHHHHHHHHHHHCCC-----TTTHHHHH---C-CCCHHHHHHHHHHHHHSCSSHHHHHHCSC---HH
T ss_pred             EEecCccccCCcCHHHHHHHHHHHcCCC-----HHHHHHHH---h-CCCHHHHHHHHHHHhCCCCCHHHHhcCCh---hH
Confidence            7777      999999999999986432     12333344   9 999999999999  333  6778876522   12


Q ss_pred             cccchhh-cccCCchhh-hhhhc----CchhhhhcHHHHHHHHHhCC
Q 045120          325 PKPYLAV-FQDLEPTIV-KTAFV----DPKWYLALKEEFEALQRNQT  365 (374)
Q Consensus       325 ~~~~~~l-y~~Lp~~~l-k~cfL----fp~~~~i~~~~Li~~W~~~~  365 (374)
                      ....+.+ |+.||++ . |+||+    ||+++.|+++.++.+|+++|
T Consensus       355 I~aaLelSYd~Lp~e-elK~cFL~LAIFPed~~I~~elLa~LW~aeG  400 (1221)
T 1vt4_I          355 LTTIIESSLNVLEPA-EYRKMFDRLSVFPPSAHIPTILLSLIWFDVI  400 (1221)
T ss_dssp             HHHHHHHHHHHSCTT-HHHHHHHHTTSSCTTSCEEHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHhCCHH-HHHHHHHHHhCCCCCCCCCHHHHHHHhcCCC
Confidence            2224555 9999986 7 99995    99999999999999999886

>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=99.96  E-value=4.4e-29  Score=272.05  Aligned_cols=242  Identities=17%  Similarity=0.180  Sum_probs=181.9

Q ss_pred             cccccccccccHHHHHHHHHHhhcC-----------CCCccHHHHHHHHHHHhhh-cCCC-CeEEEEEeCCCCC--HHHH
Q 045120          117 SNKVYEAFESRVSNLKSTQNALTNA-----------NGGIGKTTLAKEFAKQARE-DKLF-DRVVFSEVSQTSD--IKKI  181 (374)
Q Consensus       117 ~~~~~~~~vGr~~~~~~i~~~L~~~-----------~gGiGKTtLA~~v~~~~~~-~~~F-~~~~wv~vs~~~~--~~~~  181 (374)
                      +|.....|+||+.++++|.++|...           |||+||||||+++|++... ..+| +.++||++++..+  ....
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~  198 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMK  198 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHH
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHH
Confidence            4455667999999999999999532           9999999999999997643 4445 6788999998543  4555


Q ss_pred             HHHHHHHhCcCCc-----hhhHHHHHHHHHHHHhc-CCeEEEEEeCCCCccccccccCcCCCC-----CcchhHhhhhcC
Q 045120          182 QGDIAEKLGLELS-----EEAEYRRASRLYERLKN-ENKILVILANIWKLLDLETVKIPFRND-----SRDNNVVLLSMG  250 (374)
Q Consensus       182 ~~~i~~~l~~~~~-----~~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~~~~~l~~~~~~~-----TR~~~va~~~~~  250 (374)
                      +..++..+.....     ..+.+.....++..|.+ ++|+||||||||+..+|..+.   +..     ||+..++...++
T Consensus       199 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~~---~~~~ilvTtR~~~~~~~~~~  275 (1249)
T 3sfz_A          199 LQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFD---NQCQILLTTRDKSVTDSVMG  275 (1249)
T ss_dssp             HHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTTC---SSCEEEEEESSTTTTTTCCS
T ss_pred             HHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhhc---CCCEEEEEcCCHHHHHhhcC
Confidence            7777777765421     23556777888888876 139999999999998888762   222     999998743456


Q ss_pred             CCCceecCC-CCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc--CCCccccccc-----------
Q 045120          251 SKDNFLIAN-ITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS--KSSSIYSHVS-----------  316 (374)
Q Consensus       251 ~~~~~~l~~-L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~~~~~W~~-----------  316 (374)
                      ....+++++ |+.++|++||...++..  .+.+.+++++|+++| +|+||||+++|+  +.+. ..|..           
T Consensus       276 ~~~~~~~~~~l~~~~a~~l~~~~~~~~--~~~~~~~~~~i~~~~-~glPLal~~~~~~l~~~~-~~~~~~l~~l~~~~~~  351 (1249)
T 3sfz_A          276 PKHVVPVESGLGREKGLEILSLFVNMK--KEDLPAEAHSIIKEC-KGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFK  351 (1249)
T ss_dssp             CBCCEECCSSCCHHHHHHHHHHHHTSC--STTCCTHHHHHHHHT-TTCHHHHHHHHHHHHHSS-SCHHHHHHHHHSCCCC
T ss_pred             CceEEEecCCCCHHHHHHHHHHhhCCC--hhhCcHHHHHHHHHh-CCCHHHHHHHHHHhhcCh-hHHHHHHHHHhhhhhh
Confidence            677899996 99999999999998633  344567789999999 999999999999  3333 34521           


Q ss_pred             -ccccCCC---Ccccchhh-cccCCchhhhhhhc----CchhhhhcHHHHHHHHHhCCc
Q 045120          317 -NDYQSIY---KPKPYLAV-FQDLEPTIVKTAFV----DPKWYLALKEEFEALQRNQTW  366 (374)
Q Consensus       317 -~~~~~~~---~~~~~~~l-y~~Lp~~~lk~cfL----fp~~~~i~~~~Li~~W~~~~~  366 (374)
                       +......   .....+.+ |+.||++ +|+||+    ||+++.|+++.++.+|.+++.
T Consensus       352 ~~~~~~~~~~~~~~~~l~~s~~~L~~~-~~~~~~~l~~f~~~~~i~~~~~~~~~~~~~~  409 (1249)
T 3sfz_A          352 RIRKSSSYDYEALDEAMSISVEMLRED-IKDYYTDLSILQKDVKVPTKVLCVLWDLETE  409 (1249)
T ss_dssp             CSSCTTCTTHHHHHHHHHHHHHTSCTT-THHHHHHGGGSCTTCCEEHHHHHHHHTCCHH
T ss_pred             hcccccccchHHHHHHHHHHHHhCCHH-HHHHHHHhCccCCCCeeCHHHHHHHhCCCHH
Confidence             1111111   11123444 9999986 999995    999999999999999987643

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.93  E-value=5.5e-26  Score=230.02  Aligned_cols=235  Identities=15%  Similarity=0.201  Sum_probs=168.4

Q ss_pred             ccccccccccHHHHHHHHHHhhc---C--------CCCccHHHHHHHHHHHhhh-cCCC-CeEEEEEeCCCCCHHHHHHH
Q 045120          118 NKVYEAFESRVSNLKSTQNALTN---A--------NGGIGKTTLAKEFAKQARE-DKLF-DRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~~---~--------~gGiGKTtLA~~v~~~~~~-~~~F-~~~~wv~vs~~~~~~~~~~~  184 (374)
                      |..+..||||+.++++|.++|..   +        |||+||||||.+++++..+ ..+| +.++|++++.. +...++..
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~  198 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMK  198 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHH
T ss_pred             CCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHH
Confidence            44556799999999999999973   1        9999999999999997655 6779 58999999876 33333333


Q ss_pred             ---HHHHhCcC-----CchhhHHHHHHHHHHHHhcC-CeEEEEEeCCCCccccccccCcCCCC------CcchhHhhhhc
Q 045120          185 ---IAEKLGLE-----LSEEAEYRRASRLYERLKNE-NKILVILANIWKLLDLETVKIPFRND------SRDNNVVLLSM  249 (374)
Q Consensus       185 ---i~~~l~~~-----~~~~~~~~~~~~l~~~L~~~-kr~LlVlDdv~~~~~~~~l~~~~~~~------TR~~~va~~~~  249 (374)
                         ++..++..     ....+.......+.+.|.+. +++||||||||+...+..+    +.+      ||+..++. ..
T Consensus       199 l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l----~~~~~ilvTsR~~~~~~-~~  273 (591)
T 1z6t_A          199 LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF----DSQCQILLTTRDKSVTD-SV  273 (591)
T ss_dssp             HHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTT----CSSCEEEEEESCGGGGT-TC
T ss_pred             HHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHh----cCCCeEEEECCCcHHHH-hc
Confidence               34455421     12234566777888888753 6899999999988776654    222      88888753 22


Q ss_pred             CCCCceec---CCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc--CCCccccccccc------
Q 045120          250 GSKDNFLI---ANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS--KSSSIYSHVSND------  318 (374)
Q Consensus       250 ~~~~~~~l---~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~~~~~W~~~~------  318 (374)
                      . ...+++   ++|+.+++++||...++..  .....+.+.+|+++| +|+||||.++|+  +.. ...|....      
T Consensus       274 ~-~~~~~v~~l~~L~~~ea~~L~~~~~~~~--~~~~~~~~~~i~~~~-~G~PLal~~~a~~l~~~-~~~w~~~l~~l~~~  348 (591)
T 1z6t_A          274 M-GPKYVVPVESSLGKEKGLEILSLFVNMK--KADLPEQAHSIIKEC-KGSPLVVSLIGALLRDF-PNRWEYYLKQLQNK  348 (591)
T ss_dssp             C-SCEEEEECCSSCCHHHHHHHHHHHHTSC--GGGSCTHHHHHHHHH-TTCHHHHHHHHHHHHHS-TTCHHHHHHHHHSC
T ss_pred             C-CCceEeecCCCCCHHHHHHHHHHHhCCC--cccccHHHHHHHHHh-CCCcHHHHHHHHHHhcC-chhHHHHHHHHHHh
Confidence            2 234554   5899999999999998742  223346788999999 999999999999  332 23573211      


Q ss_pred             -ccCCC--------Ccccchhh-cccCCchhhhhhhc----CchhhhhcHHHHHHHHHhC
Q 045120          319 -YQSIY--------KPKPYLAV-FQDLEPTIVKTAFV----DPKWYLALKEEFEALQRNQ  364 (374)
Q Consensus       319 -~~~~~--------~~~~~~~l-y~~Lp~~~lk~cfL----fp~~~~i~~~~Li~~W~~~  364 (374)
                       ...+.        .....+.. |+.||++ .|.||+    ||+++.|+.+.++.+|.++
T Consensus       349 ~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~-~~~~l~~la~f~~~~~i~~~~l~~l~~~~  407 (591)
T 1z6t_A          349 QFKRIRKSSSYDYEALDEAMSISVEMLRED-IKDYYTDLSILQKDVKVPTKVLCILWDME  407 (591)
T ss_dssp             CCCCSSCCCSSCCHHHHHHHHHHHHTSCTT-THHHHHHGGGCCTTCCEEHHHHHHHHTCC
T ss_pred             HHHHhhhccccchHHHHHHHHHHHHhCCHH-HHHHHHHccccCCCCccCHHHHHHHhccC
Confidence             01111        11112333 9999986 999995    9999999999999999765

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.32  E-value=1.8e-11  Score=114.77  Aligned_cols=181  Identities=10%  Similarity=0.079  Sum_probs=114.9

Q ss_pred             cccccccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC------CHHHHHH
Q 045120          117 SNKVYEAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS------DIKKIQG  183 (374)
Q Consensus       117 ~~~~~~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~------~~~~~~~  183 (374)
                      ++..+..|+||+.++++|.+++..+       ++|+|||||++++.+..      + .+|+++....      +...++.
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~~~~v~i~G~~G~GKT~Ll~~~~~~~------~-~~~~~~~~~~~~~~~~~~~~~~~   79 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLENYPLTLLLGIRRVGKSSLLRAFLNER------P-GILIDCRELYAERGHITREELIK   79 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHS------S-EEEEEHHHHHHTTTCBCHHHHHH
T ss_pred             CCCChHhcCChHHHHHHHHHHHhcCCeEEEECCCcCCHHHHHHHHHHHc------C-cEEEEeecccccccCCCHHHHHH
Confidence            3444567999999999999998754       99999999999998753      2 6777765432      5666777


Q ss_pred             HHHHHhCc-----------------CC--chhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc---------cccccC--
Q 045120          184 DIAEKLGL-----------------EL--SEEAEYRRASRLYERLKNENKILVILANIWKLLD---------LETVKI--  233 (374)
Q Consensus       184 ~i~~~l~~-----------------~~--~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~---------~~~l~~--  233 (374)
                      .+...+..                 ..  ...+..+....+.+.+...++++|||||++....         +..+..  
T Consensus        80 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~  159 (350)
T 2qen_A           80 ELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAY  159 (350)
T ss_dssp             HHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHH
Confidence            77665542                 00  0123344555565555431389999999986432         122211  


Q ss_pred             -cCCCC-----CcchhHhhh----------hcCC-CCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC
Q 045120          234 -PFRND-----SRDNNVVLL----------SMGS-KDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG  296 (374)
Q Consensus       234 -~~~~~-----TR~~~va~~----------~~~~-~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G  296 (374)
                       ..+..     ++.......          ..+. ...+.+.+|+.+++.+++........... -.+....|+..| ||
T Consensus       160 ~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~-~~~~~~~i~~~t-gG  237 (350)
T 2qen_A          160 DSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV-PENEIEEAVELL-DG  237 (350)
T ss_dssp             HHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHH-TT
T ss_pred             HhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHh-CC
Confidence             11111     232221110          0111 23789999999999999987643211111 135667999999 99


Q ss_pred             chHHHHHHhc
Q 045120          297 LFCTLTTNAS  306 (374)
Q Consensus       297 lPLai~~ig~  306 (374)
                      +|+++..++.
T Consensus       238 ~P~~l~~~~~  247 (350)
T 2qen_A          238 IPGWLVVFGV  247 (350)
T ss_dssp             CHHHHHHHHH
T ss_pred             CHHHHHHHHH
Confidence            9999999885

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.17  E-value=3.7e-10  Score=108.42  Aligned_cols=181  Identities=16%  Similarity=0.152  Sum_probs=118.5

Q ss_pred             ccccccHHHHHHHHHHh-h--------cC---------CCCccHHHHHHHHHHHhhhc---CCCC-eEEEEEeCCCCCHH
Q 045120          122 EAFESRVSNLKSTQNAL-T--------NA---------NGGIGKTTLAKEFAKQARED---KLFD-RVVFSEVSQTSDIK  179 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L-~--------~~---------~gGiGKTtLA~~v~~~~~~~---~~F~-~~~wv~vs~~~~~~  179 (374)
                      ..|+||+.++++|.++| .        ..         ++|+||||||+.+++.....   ..|+ .++|++.....+..
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            56999999999999988 3        22         78999999999999865431   1233 35788777778899


Q ss_pred             HHHHHHHHHhCcCCc--hhhHHHHHHHHHHHHh-cCCeEEEEEeCCCCc--------cccccccCc---CC-----CC--
Q 045120          180 KIQGDIAEKLGLELS--EEAEYRRASRLYERLK-NENKILVILANIWKL--------LDLETVKIP---FR-----ND--  238 (374)
Q Consensus       180 ~~~~~i~~~l~~~~~--~~~~~~~~~~l~~~L~-~~kr~LlVlDdv~~~--------~~~~~l~~~---~~-----~~--  238 (374)
                      .++..|+..++...+  ..+.......+.+.|. .+++++|||||++..        ..+..+...   ++     ..  
T Consensus       102 ~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~  181 (412)
T 1w5s_A          102 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIG  181 (412)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEE
T ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEE
Confidence            999999999976533  2234455666777765 237999999999863        222222111   11     12  


Q ss_pred             ----CcchhHhhh-------h-cCCCCceecCCCCHHHHHHHHHHhcC---CCCCCcchHHHHHHHHHHccC------Cc
Q 045120          239 ----SRDNNVVLL-------S-MGSKDNFLIANITEEEAWRLFKIMNG---DDVENCKFKSTAINVAKACGA------GL  297 (374)
Q Consensus       239 ----TR~~~va~~-------~-~~~~~~~~l~~L~~~~s~~Lf~~~a~---~~~~~~~l~~~~~~I~~~c~~------Gl  297 (374)
                          |+...+...       . ......+.+++|+.++++++|...+.   ...  .--.+....|++.| +      |.
T Consensus       182 lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~--~~~~~~~~~i~~~~-~~~~~~~G~  258 (412)
T 1w5s_A          182 FLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDT--VWEPRHLELISDVY-GEDKGGDGS  258 (412)
T ss_dssp             EEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTT--SCCHHHHHHHHHHH-CGGGTSCCC
T ss_pred             EEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCC--CCChHHHHHHHHHH-HHhccCCCc
Confidence                444332100       0 01112399999999999999976542   211  11145677899999 8      99


Q ss_pred             hHHHHHHh
Q 045120          298 FCTLTTNA  305 (374)
Q Consensus       298 PLai~~ig  305 (374)
                      |..+..+.
T Consensus       259 p~~~~~l~  266 (412)
T 1w5s_A          259 ARRAIVAL  266 (412)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            97655443

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.10  E-value=2.5e-10  Score=107.14  Aligned_cols=178  Identities=12%  Similarity=0.162  Sum_probs=106.1

Q ss_pred             ccccccccccHHHHHHHHHHhhcC------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-----CCHHHHHHHHH
Q 045120          118 NKVYEAFESRVSNLKSTQNALTNA------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-----SDIKKIQGDIA  186 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~~~------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~~~~~i~  186 (374)
                      +..+..|+||+.+++.|.+ +...      ++|+|||||++++.+...  .   ..+|+++...     .+...++..+.
T Consensus         9 ~~~~~~~~gR~~el~~L~~-l~~~~v~i~G~~G~GKT~L~~~~~~~~~--~---~~~~~~~~~~~~~~~~~~~~~~~~l~   82 (357)
T 2fna_A            9 KDNRKDFFDREKEIEKLKG-LRAPITLVLGLRRTGKSSIIKIGINELN--L---PYIYLDLRKFEERNYISYKDFLLELQ   82 (357)
T ss_dssp             CCSGGGSCCCHHHHHHHHH-TCSSEEEEEESTTSSHHHHHHHHHHHHT--C---CEEEEEGGGGTTCSCCCHHHHHHHHH
T ss_pred             CCCHHHhcChHHHHHHHHH-hcCCcEEEECCCCCCHHHHHHHHHHhcC--C---CEEEEEchhhccccCCCHHHHHHHHH
Confidence            3345679999999999999 7645      999999999999998653  2   2578887642     34455555554


Q ss_pred             HHhCc------------------CCc----hhh----HHHHHHHHHHHHhc-C-CeEEEEEeCCCCcc-----ccc-ccc
Q 045120          187 EKLGL------------------ELS----EEA----EYRRASRLYERLKN-E-NKILVILANIWKLL-----DLE-TVK  232 (374)
Q Consensus       187 ~~l~~------------------~~~----~~~----~~~~~~~l~~~L~~-~-kr~LlVlDdv~~~~-----~~~-~l~  232 (374)
                      +.+..                  ..+    ..+    .......+.+.|.. . ++++|||||++...     .+. .+.
T Consensus        83 ~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~~~~~~l~  162 (357)
T 2fna_A           83 KEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALA  162 (357)
T ss_dssp             HHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHHHH
T ss_pred             HHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccCchhHHHHHH
Confidence            44310                  000    000    01112334444432 1 38999999997532     221 121


Q ss_pred             C---cCCCC-----CcchhHhhhh---------c-CC-CCceecCCCCHHHHHHHHHHhcCC-CCCCcchHHHHHHHHHH
Q 045120          233 I---PFRND-----SRDNNVVLLS---------M-GS-KDNFLIANITEEEAWRLFKIMNGD-DVENCKFKSTAINVAKA  292 (374)
Q Consensus       233 ~---~~~~~-----TR~~~va~~~---------~-~~-~~~~~l~~L~~~~s~~Lf~~~a~~-~~~~~~l~~~~~~I~~~  292 (374)
                      .   ..+..     +|........         . +. ...+.+.+|+.+++.+++...... ....+..    ..|+..
T Consensus       163 ~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~----~~i~~~  238 (357)
T 2fna_A          163 YAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY----EVVYEK  238 (357)
T ss_dssp             HHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH----HHHHHH
T ss_pred             HHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcH----HHHHHH
Confidence            1   11111     3433221100         1 11 247899999999999999876431 1111221    689999


Q ss_pred             ccCCchHHHHHHhc
Q 045120          293 CGAGLFCTLTTNAS  306 (374)
Q Consensus       293 c~~GlPLai~~ig~  306 (374)
                      | +|+|+++..++.
T Consensus       239 t-~G~P~~l~~~~~  251 (357)
T 2fna_A          239 I-GGIPGWLTYFGF  251 (357)
T ss_dssp             H-CSCHHHHHHHHH
T ss_pred             h-CCCHHHHHHHHH
Confidence            9 999999999886

>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=98.91  E-value=4.8e-09  Score=99.36  Aligned_cols=182  Identities=15%  Similarity=0.110  Sum_probs=115.4

Q ss_pred             cccccccHHHHHHHHHHhhc----C---------CCCccHHHHHHHHHHHhhhcCC-CCeEEEEEeCCCCCHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTN----A---------NGGIGKTTLAKEFAKQAREDKL-FDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~----~---------~gGiGKTtLA~~v~~~~~~~~~-F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      +..|+||+.+++.+.+++..    .         ++|+||||||+.+++....... --..+|++.....+...++..++
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~   98 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLL   98 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHT
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHH
Confidence            35699999999999998873    1         8999999999999986543210 12467777766677888888888


Q ss_pred             HHhCcCCch--hhHHHHHHHHHHHHhc-CCeEEEEEeCCCCc------cccccccCcC---CC-C------CcchhHh--
Q 045120          187 EKLGLELSE--EAEYRRASRLYERLKN-ENKILVILANIWKL------LDLETVKIPF---RN-D------SRDNNVV--  245 (374)
Q Consensus       187 ~~l~~~~~~--~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~------~~~~~l~~~~---~~-~------TR~~~va--  245 (374)
                      ..++.....  .+..+....+.+.+.. +++.+||||+++..      ..+..+...+   +. .      |+.....  
T Consensus        99 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~  178 (386)
T 2qby_A           99 ESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDL  178 (386)
T ss_dssp             TTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGG
T ss_pred             HHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhh
Confidence            888654322  2345556667777764 24899999999752      2222221111   11 1      3332211  


Q ss_pred             -----hhhcCCCCceecCCCCHHHHHHHHHHhcCC-CCCCcchHHHHHHHHHHccC---CchHHHHHH
Q 045120          246 -----LLSMGSKDNFLIANITEEEAWRLFKIMNGD-DVENCKFKSTAINVAKACGA---GLFCTLTTN  304 (374)
Q Consensus       246 -----~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~-~~~~~~l~~~~~~I~~~c~~---GlPLai~~i  304 (374)
                           .... ....+.+++++.++..++|...+.. .....--.++...|++.+ +   |.|..+..+
T Consensus       179 ~~~~~~~r~-~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~G~~r~~~~l  244 (386)
T 2qby_A          179 LDPRVKSSL-SEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALA-AREHGDARRALDL  244 (386)
T ss_dssp             CTTHHHHTT-TTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHH-HHTTCCHHHHHHH
T ss_pred             hCHHHhccC-CCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHH-HHhcCCHHHHHHH
Confidence                 0111 1147999999999999999986531 001111235566777777 7   999854433

>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=98.89  E-value=1.7e-08  Score=95.87  Aligned_cols=177  Identities=16%  Similarity=0.117  Sum_probs=114.3

Q ss_pred             ccccccHHHHHHHHHHhhc------C-------CCCccHHHHHHHHHHHhhhc----CC--CCeEEEEEeCCCC-CHHHH
Q 045120          122 EAFESRVSNLKSTQNALTN------A-------NGGIGKTTLAKEFAKQARED----KL--FDRVVFSEVSQTS-DIKKI  181 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~------~-------~gGiGKTtLA~~v~~~~~~~----~~--F~~~~wv~vs~~~-~~~~~  181 (374)
                      ..++||+.+++++.++|..      .       ++|+||||||+.+++.....    ..  ....+|++.+... +...+
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            5699999999999988764      1       89999999999999865321    11  2346788777766 88889


Q ss_pred             HHHHHHHh-CcCCc--hhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc------c-cccccCcCCCC-----Ccchh---
Q 045120          182 QGDIAEKL-GLELS--EEAEYRRASRLYERLKNENKILVILANIWKLL------D-LETVKIPFRND-----SRDNN---  243 (374)
Q Consensus       182 ~~~i~~~l-~~~~~--~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~------~-~~~l~~~~~~~-----TR~~~---  243 (374)
                      +..++..+ +....  ..+.......+.+.+.. ++.+|||||++...      . +..+....+..     |+...   
T Consensus       100 ~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~-~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~~~~~  178 (384)
T 2qby_B          100 LSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRN-IRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRD  178 (384)
T ss_dssp             HHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSS-SCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSSTTTTT
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhcc-CCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCCchHh
Confidence            99998888 32211  12334556777778876 45599999997532      1 22332222111     43321   


Q ss_pred             -Hh---hhhcCCCCceecCCCCHHHHHHHHHHhcC---C-CCCCcchHHHHHHHHHHccC---CchH-HHHHHh
Q 045120          244 -VV---LLSMGSKDNFLIANITEEEAWRLFKIMNG---D-DVENCKFKSTAINVAKACGA---GLFC-TLTTNA  305 (374)
Q Consensus       244 -va---~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~---~-~~~~~~l~~~~~~I~~~c~~---GlPL-ai~~ig  305 (374)
                       +.   ....+  ..+.+++++.++..++|...+.   . ...+   .+....|++.| +   |.|. ++.++-
T Consensus       179 ~l~~~l~sr~~--~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~---~~~~~~i~~~~-~~~~G~~r~a~~~l~  246 (384)
T 2qby_B          179 YMEPRVLSSLG--PSVIFKPYDAEQLKFILSKYAEYGLIKGTYD---DEILSYIAAIS-AKEHGDARKAVNLLF  246 (384)
T ss_dssp             TSCHHHHHTCC--CEEEECCCCHHHHHHHHHHHHHHTSCTTSCC---SHHHHHHHHHH-HTTCCCHHHHHHHHH
T ss_pred             hhCHHHHhcCC--CeEEECCCCHHHHHHHHHHHHHhhcccCCcC---HHHHHHHHHHH-HhccCCHHHHHHHHH
Confidence             11   11222  2899999999999999998753   1 1122   24556788888 7   8776 444433

>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=98.88  E-value=2e-08  Score=88.35  Aligned_cols=178  Identities=11%  Similarity=0.143  Sum_probs=97.9

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++||+..++.+..++..+          ++|+||||||+.+++.......+..      ........ ...+....
T Consensus        21 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~------~~~~~~~~-~~~~~~~~   93 (250)
T 1njg_A           21 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA------TPCGVCDN-CREIEQGR   93 (250)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCS------SCCSCSHH-HHHHHTTC
T ss_pred             cHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC------CCCcccHH-HHHHhccC
Confidence            3456999999999999998754          8899999999999986543221100      00000000 00111000


Q ss_pred             Cc-----CCchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCc--cccccccCcC---CCC------Ccch-hHhhhh
Q 045120          190 GL-----ELSEEAEYRRASRLYERLK----NENKILVILANIWKL--LDLETVKIPF---RND------SRDN-NVVLLS  248 (374)
Q Consensus       190 ~~-----~~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~--~~~~~l~~~~---~~~------TR~~-~va~~~  248 (374)
                      ..     .............+.+.+.    .+++.+|||||++..  ..+..+...+   +..      |+.. .+....
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l  173 (250)
T 1njg_A           94 FVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTI  173 (250)
T ss_dssp             CSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHH
T ss_pred             CcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHH
Confidence            00     0000011111222222221    126799999999753  2333332211   222      3222 221111


Q ss_pred             cCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          249 MGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       249 ~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      ......+.+++++.++..+++...+...... --.+....|++.| +|.|..+..+..
T Consensus       174 ~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~-~~~~~~~~l~~~~-~G~~~~~~~~~~  229 (250)
T 1njg_A          174 LSRCLQFHLKALDVEQIRHQLEHILNEEHIA-HEPRALQLLARAA-EGSLRDALSLTD  229 (250)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHTTCC-BCHHHHHHHHHHH-TTCHHHHHHHHH
T ss_pred             HHHhhhccCCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHc-CCCHHHHHHHHH
Confidence            2223579999999999999999877522111 1135567899999 999999887764

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.78  E-value=5.4e-08  Score=92.16  Aligned_cols=172  Identities=16%  Similarity=0.173  Sum_probs=112.7

Q ss_pred             ccccccHHHHHHHHHHhhc----C---------CCCccHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTN----A---------NGGIGKTTLAKEFAKQARED----KLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~----~---------~gGiGKTtLA~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      ..++||+.+++++.++|..    .         ++|+||||||+.+++.....    +.--..+|++.....+...++..
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   98 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASA   98 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHH
Confidence            6699999999999998842    1         88999999999999865321    10124577887888888999999


Q ss_pred             HHHHhCcCCch--hhHHHHHHHHHHHHhc-CCeEEEEEeCCCCcc-------ccccccCc---C--CCC------Ccch-
Q 045120          185 IAEKLGLELSE--EAEYRRASRLYERLKN-ENKILVILANIWKLL-------DLETVKIP---F--RND------SRDN-  242 (374)
Q Consensus       185 i~~~l~~~~~~--~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~-------~~~~l~~~---~--~~~------TR~~-  242 (374)
                      ++..++...+.  .+..+....+.+.+.. +++.+||||++....       .+..+...   .  +..      |+.. 
T Consensus        99 l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~  178 (387)
T 2v1u_A           99 IAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLG  178 (387)
T ss_dssp             HHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCST
T ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCc
Confidence            99999765332  2345556677777753 368999999998532       12221111   1  111      3322 


Q ss_pred             -------hHhhhhcCCCCceecCCCCHHHHHHHHHHhcC---C-CCCCcchHHHHHHHHHHccC---CchH
Q 045120          243 -------NVVLLSMGSKDNFLIANITEEEAWRLFKIMNG---D-DVENCKFKSTAINVAKACGA---GLFC  299 (374)
Q Consensus       243 -------~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~---~-~~~~~~l~~~~~~I~~~c~~---GlPL  299 (374)
                             .+. ... ....+.+++++.++..+++...+.   . ...++   +....|++.+ +   |.|-
T Consensus       179 ~~~~l~~~l~-~r~-~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~---~~~~~l~~~~-~~~~G~~r  243 (387)
T 2v1u_A          179 FVENLEPRVK-SSL-GEVELVFPPYTAPQLRDILETRAEEAFNPGVLDP---DVVPLCAALA-AREHGDAR  243 (387)
T ss_dssp             TSSSSCHHHH-TTT-TSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCS---SHHHHHHHHH-HSSSCCHH
T ss_pred             hHhhhCHHHH-hcC-CCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCH---HHHHHHHHHH-HHhccCHH
Confidence                   111 111 114789999999999999998753   1 11222   3456777888 7   9994

>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=98.71  E-value=2.2e-07  Score=80.44  Aligned_cols=169  Identities=10%  Similarity=0.061  Sum_probs=95.5

Q ss_pred             ccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          120 VYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ....++|++..++.+.+++...         ++|+|||+||+.+++.......-...+.++.+...+...+...+.....
T Consensus        15 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (226)
T 2chg_A           15 TLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKIKEFAR   94 (226)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHHHHHHHT
T ss_pred             CHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHHHHHHhc
Confidence            3456999999999999998764         7899999999999886432211112334443333333222221111111


Q ss_pred             cCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccccC---cCCCC------Ccch-hHhhhhcCCCCceecC
Q 045120          191 LELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVKI---PFRND------SRDN-NVVLLSMGSKDNFLIA  258 (374)
Q Consensus       191 ~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~~---~~~~~------TR~~-~va~~~~~~~~~~~l~  258 (374)
                      ..               .+...++.+|||||++...  ..+.+..   ..+.+      |+.. .+..........+.+.
T Consensus        95 ~~---------------~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~  159 (226)
T 2chg_A           95 TA---------------PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFK  159 (226)
T ss_dssp             SC---------------CSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             cc---------------CCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecC
Confidence            00               0111368899999997542  2222211   11222      2221 1111111222378999


Q ss_pred             CCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          259 NITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       259 ~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      +++.++..+++.+.+...... --.+....|++.+ +|.|..+..+.
T Consensus       160 ~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~-~g~~r~l~~~l  204 (226)
T 2chg_A          160 PVPKEAMKKRLLEICEKEGVK-ITEDGLEALIYIS-GGDFRKAINAL  204 (226)
T ss_dssp             CCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHH-TTCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            999999999999877421111 1134566888999 99999655443

>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=98.51  E-value=3.2e-06  Score=80.03  Aligned_cols=170  Identities=16%  Similarity=0.165  Sum_probs=109.7

Q ss_pred             ccccccHHHHHHHHHHhhc----------C-----CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTN----------A-----NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~----------~-----~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      ..++||+.+++++.+++..          .     +.|+||||||+.+++....... -..++++.+...+...+...++
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHHHH
Confidence            5699999999999988864          2     7899999999999986542211 2467777777788889999999


Q ss_pred             HHhCcCCch--hhHHHHHHHHHHHHhc-CCeEEEEEeCCCCc--cccccccCcC---C----CC------CcchhHhh--
Q 045120          187 EKLGLELSE--EAEYRRASRLYERLKN-ENKILVILANIWKL--LDLETVKIPF---R----ND------SRDNNVVL--  246 (374)
Q Consensus       187 ~~l~~~~~~--~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~--~~~~~l~~~~---~----~~------TR~~~va~--  246 (374)
                      ..++.....  .+.......+.+.+.. +++.+||||++...  ..+..+...+   +    .+      |+......  
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l  175 (389)
T 1fnn_A           96 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNL  175 (389)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTS
T ss_pred             HHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHh
Confidence            998764332  2345555666666653 36899999999764  2222221111   1    12      33322110  


Q ss_pred             -----hhcCCCCceecCCCCHHHHHHHHHHhcCCC-CCCcchHHHHHHHHHHc
Q 045120          247 -----LSMGSKDNFLIANITEEEAWRLFKIMNGDD-VENCKFKSTAINVAKAC  293 (374)
Q Consensus       247 -----~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~-~~~~~l~~~~~~I~~~c  293 (374)
                           ... ....+.+++++.++..+++...+... ....--.+....|++.+
T Consensus       176 ~~~~~~r~-~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~  227 (389)
T 1fnn_A          176 DPSTRGIM-GKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADIT  227 (389)
T ss_dssp             CHHHHHHH-TTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHH
T ss_pred             CHHhhhcC-CCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Confidence                 111 12369999999999999998876310 00111135566788888

>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=98.38  E-value=2.3e-06  Score=78.90  Aligned_cols=171  Identities=13%  Similarity=0.120  Sum_probs=95.8

Q ss_pred             ccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          120 VYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ....++|++..++.+.+++..+         ++|+||||+|+.+++...........++++.+...+...+ ++++..+.
T Consensus        19 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~~~   97 (323)
T 1sxj_B           19 VLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVV-RNQIKHFA   97 (323)
T ss_dssp             SGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHH-HTHHHHHH
T ss_pred             CHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHH-HHHHHHHH
Confidence            3456999999999999998765         8899999999999986432111112344443333232221 12222111


Q ss_pred             cCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccccCc---CCCC------Ccc-hhHhhhhcCCCCceecC
Q 045120          191 LELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVKIP---FRND------SRD-NNVVLLSMGSKDNFLIA  258 (374)
Q Consensus       191 ~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~~~---~~~~------TR~-~~va~~~~~~~~~~~l~  258 (374)
                      ...             ..+..+++.+||+||++...  .++.+...   .+.+      |+. ..+..........+.+.
T Consensus        98 ~~~-------------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~  164 (323)
T 1sxj_B           98 QKK-------------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYS  164 (323)
T ss_dssp             HBC-------------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             hcc-------------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeec
Confidence            000             00102258999999997532  22222211   1222      222 11111111223379999


Q ss_pred             CCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH-HHHHHhc
Q 045120          259 NITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC-TLTTNAS  306 (374)
Q Consensus       259 ~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL-ai~~ig~  306 (374)
                      +++.++..+++...+...... --.+....|++.| +|.|. |+..+..
T Consensus       165 ~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~-~G~~r~a~~~l~~  211 (323)
T 1sxj_B          165 KLSDEDVLKRLLQIIKLEDVK-YTNDGLEAIIFTA-EGDMRQAINNLQS  211 (323)
T ss_dssp             CCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHH-TTCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-CCCHHHHHHHHHH
Confidence            999999999999876421111 1135567899999 99995 4555543

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=98.26  E-value=3.4e-06  Score=65.72  Aligned_cols=66  Identities=24%  Similarity=0.325  Sum_probs=59.3

Q ss_pred             HHHHHHHHhhhhHHHhhhhhhhccchHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHhchhhHHHHHHHH
Q 045120            8 LVLELVKWLAPPTERQLVYLRKRNYNANLENLKAELEKLKVERTS------------IQLRVSEAKEKGEEIEEKVEKWL   75 (374)
Q Consensus         8 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~l~~------------v~~~i~~a~~~~~~~~~~v~~wl   75 (374)
                      +++.++++|.+.+.+++..+  .++.++++.++++|+.|++.|.+            ++.|+.++++.+|++||++++|.
T Consensus         2 ~v~~ll~KL~~ll~~E~~l~--~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD~f~   79 (115)
T 3qfl_A            2 AISNLIPKLGELLTEEFKLH--KGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDKFL   79 (115)
T ss_dssp             TTCSHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHH--hchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667788889999999999  99999999999999999999865            57799999999999999999998

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.07  E-value=3e-05  Score=71.43  Aligned_cols=151  Identities=10%  Similarity=0.097  Sum_probs=91.0

Q ss_pred             cccccHHHHHHHHHHhhcC-------------CCCccHHHHHHHHHHHhhhcCC---CC--eEEEEEeCCCCCHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTNA-------------NGGIGKTTLAKEFAKQAREDKL---FD--RVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~~-------------~gGiGKTtLA~~v~~~~~~~~~---F~--~~~wv~vs~~~~~~~~~~~  184 (374)
                      .+.|||+++++|...|...             ++|+|||++++.|.+.......   ..  .+++|+.....+...++..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~  100 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEK  100 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHH
Confidence            3789999999998877642             8999999999999997643211   11  3456666666788899999


Q ss_pred             HHHHhCcCCch-hhHHHHHHHHHHHH--hcCCeEEEEEeCCCCcc---ccccccC--cCCCC----------Ccc--hhH
Q 045120          185 IAEKLGLELSE-EAEYRRASRLYERL--KNENKILVILANIWKLL---DLETVKI--PFRND----------SRD--NNV  244 (374)
Q Consensus       185 i~~~l~~~~~~-~~~~~~~~~l~~~L--~~~kr~LlVlDdv~~~~---~~~~l~~--~~~~~----------TR~--~~v  244 (374)
                      |++++...... .........+.+.+  ..++.++++||++....   .+..+..  .....          +-.  ..+
T Consensus       101 I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~L  180 (318)
T 3te6_A          101 IWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQI  180 (318)
T ss_dssp             HHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHHH
T ss_pred             HHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccchhhc
Confidence            99999644211 11122333444443  12368999999997642   1221110  01111          111  111


Q ss_pred             h---hhhcCCCCceecCCCCHHHHHHHHHHhcC
Q 045120          245 V---LLSMGSKDNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       245 a---~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      .   ...++ ...+.+.+++.++-.+++...+.
T Consensus       181 ~~~v~SR~~-~~~i~F~pYt~~el~~Il~~Rl~  212 (318)
T 3te6_A          181 NIMPSLKAH-FTEIKLNKVDKNELQQMIITRLK  212 (318)
T ss_dssp             HTCHHHHTT-EEEEECCCCCHHHHHHHHHHHHH
T ss_pred             chhhhccCC-ceEEEeCCCCHHHHHHHHHHHHH
Confidence            0   11222 23688999999999999988763

>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=98.06  E-value=1e-05  Score=74.57  Aligned_cols=162  Identities=10%  Similarity=0.096  Sum_probs=90.9

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCC-CeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLF-DRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|++..++.+.+++..+         +.|+||||+|+.+++..... .+ ...+.++.+.......          
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~-~~~~~~~~~~~~~~~~~~~----------   92 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINV----------   92 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG-GHHHHEEEEETTCHHHHHT----------
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCC-cccCceEEeeccccCchHH----------
Confidence            456999999999999998765         88999999999999864311 11 1123333222111100          


Q ss_pred             cCCchhhHHHHHHHHHHHH-----hcCCeEEEEEeCCCCc--cccccccCc---CCCC------Ccc-hhHhhhhcCCCC
Q 045120          191 LELSEEAEYRRASRLYERL-----KNENKILVILANIWKL--LDLETVKIP---FRND------SRD-NNVVLLSMGSKD  253 (374)
Q Consensus       191 ~~~~~~~~~~~~~~l~~~L-----~~~kr~LlVlDdv~~~--~~~~~l~~~---~~~~------TR~-~~va~~~~~~~~  253 (374)
                                ....+.+..     ..+++.+||+|+++..  .....+...   .+..      |.. ..+.........
T Consensus        93 ----------~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~  162 (327)
T 1iqp_A           93 ----------IREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCA  162 (327)
T ss_dssp             ----------THHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEE
T ss_pred             ----------HHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCc
Confidence                      001111111     1126789999998754  222222111   1222      211 111110011123


Q ss_pred             ceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          254 NFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       254 ~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      .+.+.+++.++..+++...+...... --.+....|++.+ +|.|..+..+.
T Consensus       163 ~~~~~~l~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~-~g~~r~~~~~l  212 (327)
T 1iqp_A          163 IFRFRPLRDEDIAKRLRYIAENEGLE-LTEEGLQAILYIA-EGDMRRAINIL  212 (327)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCE-ECHHHHHHHHHHH-TTCHHHHHHHH
T ss_pred             EEEecCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHC-CCCHHHHHHHH
Confidence            68999999999999998876432211 1135567889999 99988654443

>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=98.02  E-value=4e-05  Score=72.05  Aligned_cols=176  Identities=10%  Similarity=0.123  Sum_probs=92.5

Q ss_pred             cccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|++..++.+.+.+..+          +.|+||||||+.+.+.......+.       ...+........+.....
T Consensus        15 ~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~-------~~~~~~~~~~~~~~~~~~   87 (373)
T 1jr3_A           15 FADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGIT-------ATPCGVCDNCREIEQGRF   87 (373)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSC-------SSCCSSSHHHHHHHTSCC
T ss_pred             hhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCC-------CCCCcccHHHHHHhccCC
Confidence            356999999999999988764          889999999999988654221110       000000000111110000


Q ss_pred             cC-----CchhhHHHHHHHHHHHHh----cCCeEEEEEeCCCCcc--ccccccC---cCCCC-------CcchhHhhhhc
Q 045120          191 LE-----LSEEAEYRRASRLYERLK----NENKILVILANIWKLL--DLETVKI---PFRND-------SRDNNVVLLSM  249 (374)
Q Consensus       191 ~~-----~~~~~~~~~~~~l~~~L~----~~kr~LlVlDdv~~~~--~~~~l~~---~~~~~-------TR~~~va~~~~  249 (374)
                      ..     .......+....+.+.+.    .+++.+||+||+....  ..+.+..   ..+..       ++...+.....
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~  167 (373)
T 1jr3_A           88 VDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTIL  167 (373)
T ss_dssp             SSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHH
T ss_pred             CceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHH
Confidence            00     000000001122233332    1357899999986532  2222211   11222       22222211112


Q ss_pred             CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHh
Q 045120          250 GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNA  305 (374)
Q Consensus       250 ~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig  305 (374)
                      .....+.+.+++.++..+++...+......- -.+....|++.+ +|.|..+..+.
T Consensus       168 sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~~-~~~a~~~l~~~~-~G~~r~~~~~l  221 (373)
T 1jr3_A          168 SRCLQFHLKALDVEQIRHQLEHILNEEHIAH-EPRALQLLARAA-EGSLRDALSLT  221 (373)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHHHHHTCCB-CHHHHHHHHHHS-SSCHHHHHHHH
T ss_pred             hheeEeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHC-CCCHHHHHHHH
Confidence            2235789999999999999987763111111 134566899999 99998876554

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.85  E-value=4.6e-05  Score=63.94  Aligned_cols=39  Identities=21%  Similarity=0.373  Sum_probs=33.5

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~  159 (374)
                      ...++||+.+++++.+.+...         +.|+||||||+.+++...
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~   68 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHH
Confidence            456999999999999998754         889999999999988653

>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=97.81  E-value=0.00013  Score=66.85  Aligned_cols=163  Identities=9%  Similarity=0.077  Sum_probs=90.5

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFD-RVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|++..++.+.+++..+         +.|+||||+|+.+.+..... .+. ..+.++.+.......+.        
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~-~~~~~~~~~~~~~~~~~~~~~--------   86 (319)
T 2chq_A           16 LDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGIDVVR--------   86 (319)
T ss_dssp             GGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTT-CHHHHCEEEETTSTTCTTTSS--------
T ss_pred             HHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCC-cccCCeEEEeCccccChHHHH--------
Confidence            456999999999999988765         78999999999998864211 111 12333333321111000        


Q ss_pred             cCCchhhHHHHHHHHHHH--HhcCCeEEEEEeCCCCcc--ccccccC---cCCCC------C-cchhHhhhhcCCCCcee
Q 045120          191 LELSEEAEYRRASRLYER--LKNENKILVILANIWKLL--DLETVKI---PFRND------S-RDNNVVLLSMGSKDNFL  256 (374)
Q Consensus       191 ~~~~~~~~~~~~~~l~~~--L~~~kr~LlVlDdv~~~~--~~~~l~~---~~~~~------T-R~~~va~~~~~~~~~~~  256 (374)
                               +........  +..+++.++|+|++....  ..+.+..   ..+..      | +...+..........+.
T Consensus        87 ---------~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~  157 (319)
T 2chq_A           87 ---------HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFR  157 (319)
T ss_dssp             ---------HHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEE
T ss_pred             ---------HHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEE
Confidence                     000111100  111368899999987532  2222222   22222      2 22211111112223799


Q ss_pred             cCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHH
Q 045120          257 IANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTT  303 (374)
Q Consensus       257 l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~  303 (374)
                      +.+++.++..+++...+......- -.+....|+..+ +|.|-.+..
T Consensus       158 ~~~~~~~~~~~~l~~~~~~~~~~i-~~~~l~~l~~~~-~G~~r~~~~  202 (319)
T 2chq_A          158 FKPVPKEAMKKRLLEICEKEGVKI-TEDGLEALIYIS-GGDFRKAIN  202 (319)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTCCCB-CHHHHHHHHHTT-TTCHHHHHH
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHHHH
Confidence            999999999999988764322111 134566888899 888876543

>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=97.72  E-value=0.00041  Score=63.73  Aligned_cols=52  Identities=10%  Similarity=-0.148  Sum_probs=38.5

Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      ..+.+.+++.++..+++...+...... --.+....++..| +|.|-.+.-+..
T Consensus       161 ~~i~l~~~~~~e~~~~l~~~~~~~~~~-~~~~~~~~l~~~~-~G~~r~l~~~l~  212 (324)
T 1hqc_A          161 IVEHLEYYTPEELAQGVMRDARLLGVR-ITEEAALEIGRRS-RGTMRVAKRLFR  212 (324)
T ss_dssp             CEEECCCCCHHHHHHHHHHHHHTTTCC-CCHHHHHHHHHHS-CSCHHHHHHHHH
T ss_pred             EEEecCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHc-cCCHHHHHHHHH
Confidence            478999999999999998877532211 1135667899999 999988866654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.63  E-value=0.00021  Score=59.56  Aligned_cols=38  Identities=18%  Similarity=0.384  Sum_probs=33.1

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      ...++||+.+++.+.+.+...         ..|+||||||+.+.+..
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~   67 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKI   67 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             cchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            456999999999999998764         78999999999998865

>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=97.63  E-value=0.00012  Score=72.25  Aligned_cols=174  Identities=10%  Similarity=-0.006  Sum_probs=93.7

Q ss_pred             cccccccccHHHHHHHHHHhhc--------------------C------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 045120          119 KVYEAFESRVSNLKSTQNALTN--------------------A------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV  172 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~--------------------~------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v  172 (374)
                      .....++|++..++++.++|..                    .      +.|+||||||+.+.+...    + ..+.++.
T Consensus        36 ~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~----~-~~i~in~  110 (516)
T 1sxj_A           36 TNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG----Y-DILEQNA  110 (516)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT----C-EEEEECT
T ss_pred             CCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC----C-CEEEEeC
Confidence            3456799999999999999875                    1      889999999999998652    2 2344555


Q ss_pred             CCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHH-hcCCeEEEEEeCCCCccc-----cccccCcC---CCC-----
Q 045120          173 SQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERL-KNENKILVILANIWKLLD-----LETVKIPF---RND-----  238 (374)
Q Consensus       173 s~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L-~~~kr~LlVlDdv~~~~~-----~~~l~~~~---~~~-----  238 (374)
                      +...+.. +....+........-.   .......+.+ ..+++.+|+||++.....     +..+...+   ...     
T Consensus       111 s~~~~~~-~~~~~i~~~~~~~~~~---~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~~~~iIli~  186 (516)
T 1sxj_A          111 SDVRSKT-LLNAGVKNALDNMSVV---GYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILIC  186 (516)
T ss_dssp             TSCCCHH-HHHHTGGGGTTBCCST---TTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEE
T ss_pred             CCcchHH-HHHHHHHHHhccccHH---HHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHhcCCCEEEEE
Confidence            5444433 2222222111100000   0000000011 123688999999964311     11111110   000     


Q ss_pred             -C-cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCC--CCCCcchHHHHHHHHHHccCC-chHHHHHHhc
Q 045120          239 -S-RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGD--DVENCKFKSTAINVAKACGAG-LFCTLTTNAS  306 (374)
Q Consensus       239 -T-R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~--~~~~~~l~~~~~~I~~~c~~G-lPLai~~ig~  306 (374)
                       + ....+.. .......+.+++++.++..+++...+..  ...++   +....|++.+ +| ++-++..+..
T Consensus       187 ~~~~~~~l~~-l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~---~~l~~la~~s-~GdiR~~i~~L~~  254 (516)
T 1sxj_A          187 NERNLPKMRP-FDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NVIDRLIQTT-RGDIRQVINLLST  254 (516)
T ss_dssp             SCTTSSTTGG-GTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHT-TTCHHHHHHHHTH
T ss_pred             cCCCCccchh-hHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHc-CCcHHHHHHHHHH
Confidence             1 1111211 1112236899999999999998877641  11222   3356888999 77 6666766543

>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=97.52  E-value=0.0019  Score=57.15  Aligned_cols=164  Identities=13%  Similarity=0.106  Sum_probs=84.0

Q ss_pred             cccccccHHHHHHHHHHhh---c------------------CCCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          121 YEAFESRVSNLKSTQNALT---N------------------ANGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~---~------------------~~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      ...++|.+..++.|.+.+.   .                  ++.|+|||+||+.+++...  ..   .+.++.+.-.+  
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~--~~---~~~~~~~~~~~--   77 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQ--VP---FLAMAGAEFVE--   77 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHT--CC---EEEEETTTTSS--
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhC--CC---EEEechHHHHh--
Confidence            4568899888877765542   1                  1889999999999998553  21   23344332211  


Q ss_pred             HHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc-----------------ccccccCc---C--CC
Q 045120          180 KIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL-----------------DLETVKIP---F--RN  237 (374)
Q Consensus       180 ~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~-----------------~~~~l~~~---~--~~  237 (374)
                                  ....... .....+.+........+|+||++....                 .+..+...   .  +.
T Consensus        78 ------------~~~~~~~-~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~  144 (262)
T 2qz4_A           78 ------------VIGGLGA-ARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTD  144 (262)
T ss_dssp             ------------SSTTHHH-HHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTC
T ss_pred             ------------hccChhH-HHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCC
Confidence                        0111111 122223333333257999999997530                 01111110   0  11


Q ss_pred             C------Ccchh-Hhhhhc---CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH-HHHHHh
Q 045120          238 D------SRDNN-VVLLSM---GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC-TLTTNA  305 (374)
Q Consensus       238 ~------TR~~~-va~~~~---~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL-ai~~ig  305 (374)
                      .      |.... +.....   --...+.++..+.++-.++|..++...............+++.+ .|.+- .|..+.
T Consensus       145 ~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~-~g~~~~~l~~l~  222 (262)
T 2qz4_A          145 HVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELT-PGFSGADIANIC  222 (262)
T ss_dssp             CEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTC-TTCCHHHHHHHH
T ss_pred             CEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHC-CCCCHHHHHHHH
Confidence            1      22111 110011   11246778999999999999887752222222222346788888 87754 554443

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.44  E-value=0.0013  Score=63.50  Aligned_cols=160  Identities=14%  Similarity=0.186  Sum_probs=87.9

Q ss_pred             cccccccccHHHH---HHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHH
Q 045120          119 KVYEAFESRVSNL---KSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDI  185 (374)
Q Consensus       119 ~~~~~~vGr~~~~---~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i  185 (374)
                      .....++|.+..+   ..+...+..+         ..|+||||||+.+.+...  ..     |+.++.. .....+ +.+
T Consensus        23 ~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~--~~-----f~~l~a~~~~~~~i-r~~   94 (447)
T 3pvs_A           23 ENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYAN--AD-----VERISAVTSGVKEI-REA   94 (447)
T ss_dssp             CSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTT--CE-----EEEEETTTCCHHHH-HHH
T ss_pred             CCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhC--CC-----eEEEEeccCCHHHH-HHH
Confidence            3345689999888   6777777654         889999999999998543  11     2333222 122211 111


Q ss_pred             HHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc--cccccccCcCCCC--------Ccchh--HhhhhcCCCC
Q 045120          186 AEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL--LDLETVKIPFRND--------SRDNN--VVLLSMGSKD  253 (374)
Q Consensus       186 ~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~--~~~~~l~~~~~~~--------TR~~~--va~~~~~~~~  253 (374)
                                      ..........+++.+|+||++...  ...+.|...+..+        |.+..  +.........
T Consensus        95 ----------------~~~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~~~v~lI~att~n~~~~l~~aL~sR~~  158 (447)
T 3pvs_A           95 ----------------IERARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIEDGTITFIGATTENPSFELNSALLSRAR  158 (447)
T ss_dssp             ----------------HHHHHHHHHTTCCEEEEEETTTCC------CCHHHHHTTSCEEEEEESSCGGGSSCHHHHTTEE
T ss_pred             ----------------HHHHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhcCceEEEecCCCCcccccCHHHhCcee
Confidence                            111111112236899999999754  2233332222222        22221  1111112233


Q ss_pred             ceecCCCCHHHHHHHHHHhcCCC------CCCcchHHHHHHHHHHccCCchHHHHH
Q 045120          254 NFLIANITEEEAWRLFKIMNGDD------VENCKFKSTAINVAKACGAGLFCTLTT  303 (374)
Q Consensus       254 ~~~l~~L~~~~s~~Lf~~~a~~~------~~~~~l~~~~~~I~~~c~~GlPLai~~  303 (374)
                      ++.+.+++.++-..++.+.+...      ....--.+....|++.+ +|.+-.+.-
T Consensus       159 v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~-~Gd~R~lln  213 (447)
T 3pvs_A          159 VYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELV-NGDARRALN  213 (447)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHH-CSCHHHHHH
T ss_pred             EEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHC-CCCHHHHHH
Confidence            78899999999999998876421      11111235566788888 887765543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.19  E-value=0.0018  Score=60.54  Aligned_cols=48  Identities=4%  Similarity=-0.018  Sum_probs=33.1

Q ss_pred             ceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccC-CchHHHHH
Q 045120          254 NFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGA-GLFCTLTT  303 (374)
Q Consensus       254 ~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~-GlPLai~~  303 (374)
                      .+.+++++.++..+++...+...... --.+....|++.+ . |.|-.+..
T Consensus       253 ~i~~~~~~~~e~~~il~~~~~~~~~~-~~~~~l~~l~~~~-~~G~~r~~~~  301 (368)
T 3uk6_A          253 IVSTTPYSEKDTKQILRIRCEEEDVE-MSEDAYTVLTRIG-LETSLRYAIQ  301 (368)
T ss_dssp             EEEECCCCHHHHHHHHHHHHHHTTCC-BCHHHHHHHHHHH-HHSCHHHHHH
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHh-cCCCHHHHHH
Confidence            47999999999999999876421111 1135567888888 6 77765543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.17  E-value=0.0017  Score=58.42  Aligned_cols=164  Identities=15%  Similarity=0.129  Sum_probs=87.7

Q ss_pred             cccccccccHHHHHHHHHHhhc--------------C--------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTN--------------A--------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~--------------~--------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      .....++|.+..+++|.+.+..              .        ++|+|||+||+.+++....     ..+.+..+.-.
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~-----~~~~v~~~~~~   88 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNA-----TFIRVVGSELV   88 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTC-----EEEEEEGGGGC
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCC-----CEEEEehHHHH
Confidence            3456799999999999887732              1        8899999999999985431     12233322111


Q ss_pred             CHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc----------------cccccccCc-----C
Q 045120          177 DIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL----------------LDLETVKIP-----F  235 (374)
Q Consensus       177 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~----------------~~~~~l~~~-----~  235 (374)
                                    ...... .......+.......+..+|+||++...                ..+..+...     .
T Consensus        89 --------------~~~~~~-~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~  153 (285)
T 3h4m_A           89 --------------KKFIGE-GASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDA  153 (285)
T ss_dssp             --------------CCSTTH-HHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCS
T ss_pred             --------------Hhccch-HHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCC
Confidence                          111111 1222333333443336789999999642                011111110     1


Q ss_pred             CCC------Ccchh-Hhhhhc---CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC-chHHHHHH
Q 045120          236 RND------SRDNN-VVLLSM---GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG-LFCTLTTN  304 (374)
Q Consensus       236 ~~~------TR~~~-va~~~~---~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G-lPLai~~i  304 (374)
                      ..+      |.... +.....   .-...+.+++.+.++..++|...+.........  -...++..+ .| .|-.|..+
T Consensus       154 ~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~--~~~~l~~~~-~g~~~~~i~~l  230 (285)
T 3h4m_A          154 RGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDV--NLEEIAKMT-EGCVGAELKAI  230 (285)
T ss_dssp             SSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHHC-TTCCHHHHHHH
T ss_pred             CCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcC--CHHHHHHHc-CCCCHHHHHHH
Confidence            111      32221 110011   112368999999999999999887633221111  124677777 66 55455444


Q ss_pred             h
Q 045120          305 A  305 (374)
Q Consensus       305 g  305 (374)
                      .
T Consensus       231 ~  231 (285)
T 3h4m_A          231 C  231 (285)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.14  E-value=0.0012  Score=61.27  Aligned_cols=177  Identities=11%  Similarity=0.104  Sum_probs=90.1

Q ss_pred             ccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFD-RVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....++|++..++.+..++..+         +.|+||||||+.+.+.......+. ....++.+.......+ .+.+..+
T Consensus        35 ~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  113 (353)
T 1sxj_D           35 NLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIV-REKVKNF  113 (353)
T ss_dssp             STTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHH-TTHHHHH
T ss_pred             CHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHH-HHHHHHH
Confidence            3456899999999999998765         789999999999988643111111 2233443333233222 2211111


Q ss_pred             CcC-CchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccccC---cCCCC-------CcchhHhhhhcCCCCcee
Q 045120          190 GLE-LSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVKI---PFRND-------SRDNNVVLLSMGSKDNFL  256 (374)
Q Consensus       190 ~~~-~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~~---~~~~~-------TR~~~va~~~~~~~~~~~  256 (374)
                      ... .......     ........+.-+|++|++....  ....+..   ..+..       +....+..........+.
T Consensus       114 ~~~~~~~~~~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~  188 (353)
T 1sxj_D          114 ARLTVSKPSKH-----DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFR  188 (353)
T ss_dssp             HHSCCCCCCTT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEE
T ss_pred             hhhcccccchh-----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEE
Confidence            100 0000000     0000111245688888875431  1111111   11111       111111100001113688


Q ss_pred             cCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHH
Q 045120          257 IANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       257 l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                      +.+++.++....+...+...... --.+....|++.+ +|.|-.+..+
T Consensus       189 ~~~~~~~~~~~~l~~~~~~~~~~-i~~~~l~~l~~~~-~G~~r~~~~~  234 (353)
T 1sxj_D          189 FKALDASNAIDRLRFISEQENVK-CDDGVLERILDIS-AGDLRRGITL  234 (353)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCC-CCHHHHHHHHHHT-SSCHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHc-CCCHHHHHHH
Confidence            99999999999998876422111 1135667899999 9998865443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.04  E-value=0.011  Score=55.98  Aligned_cols=154  Identities=14%  Similarity=0.168  Sum_probs=84.7

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      .....+.|.+..+++|.+.+.-+                      ++|+|||.||+++.+.....  |   +.|+.+.-.
T Consensus       145 v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~--f---~~v~~s~l~  219 (405)
T 4b4t_J          145 STYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK--F---IRVSGAELV  219 (405)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCE--E---EEEEGGGGS
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCC--c---eEEEhHHhh
Confidence            33456889999888887765432                      89999999999999965422  2   333332211


Q ss_pred             CHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc----------------cccccC---cCCC
Q 045120          177 DIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD----------------LETVKI---PFRN  237 (374)
Q Consensus       177 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~----------------~~~l~~---~~~~  237 (374)
                                    ..+... .+.....+++.-+....++|.+|++.....                +..+..   .+..
T Consensus       220 --------------sk~vGe-se~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  284 (405)
T 4b4t_J          220 --------------QKYIGE-GSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFET  284 (405)
T ss_dssp             --------------CSSTTH-HHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTC
T ss_pred             --------------ccccch-HHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCC
Confidence                          111111 223334444444444789999999874310                011110   1111


Q ss_pred             C--------CcchhH---hhhhc-CCCCceecCCCCHHHHHHHHHHhcCCCCCC--cchHHHHHHHHHHccCCc
Q 045120          238 D--------SRDNNV---VLLSM-GSKDNFLIANITEEEAWRLFKIMNGDDVEN--CKFKSTAINVAKACGAGL  297 (374)
Q Consensus       238 ~--------TR~~~v---a~~~~-~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~--~~l~~~~~~I~~~c~~Gl  297 (374)
                      .        |.....   |-... --...+.++.-+.++-.++|+.+.......  -++    ..|++.+ .|+
T Consensus       285 ~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl----~~lA~~t-~G~  353 (405)
T 4b4t_J          285 SKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINL----RKVAEKM-NGC  353 (405)
T ss_dssp             CCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCH----HHHHHHC-CSC
T ss_pred             CCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCH----HHHHHHC-CCC
Confidence            1        211111   11111 123478888889999999998887533222  233    3667777 664

>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=96.99  E-value=0.014  Score=54.56  Aligned_cols=165  Identities=9%  Similarity=0.030  Sum_probs=89.6

Q ss_pred             ccccccccHHHHHHHHHHhhc--------------C-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          120 VYEAFESRVSNLKSTQNALTN--------------A-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~--------------~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ....++|.+..++.|.+.+..              .       +.|+|||+||+.+++...  .   ..+.++.+.-.+ 
T Consensus        82 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~--~---~~~~i~~~~l~~-  155 (357)
T 3d8b_A           82 NWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSG--A---TFFSISASSLTS-  155 (357)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTT--C---EEEEEEGGGGCC-
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcC--C---eEEEEehHHhhc-
Confidence            345689999999999887742              1       889999999999988542  1   233444432211 


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc-------------cccccccCc-------CCCC
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL-------------LDLETVKIP-------FRND  238 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~-------------~~~~~l~~~-------~~~~  238 (374)
                                   ..... .......+.......+..+|+||++...             ..+..+...       .+..
T Consensus       156 -------------~~~g~-~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~  221 (357)
T 3d8b_A          156 -------------KWVGE-GEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDR  221 (357)
T ss_dssp             -------------SSTTH-HHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCC
T ss_pred             -------------cccch-HHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCC
Confidence                         11111 1122233333333336789999998421             001111110       0111


Q ss_pred             ------Ccc-hhHhhh-hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC-chHHHHHHhc
Q 045120          239 ------SRD-NNVVLL-SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG-LFCTLTTNAS  306 (374)
Q Consensus       239 ------TR~-~~va~~-~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G-lPLai~~ig~  306 (374)
                            |.. ..+... .......+.+...+.++..+++...+...... --......|++.+ .| .|-.|..+..
T Consensus       222 v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-l~~~~l~~la~~t-~G~s~~dl~~l~~  296 (357)
T 3d8b_A          222 ILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCC-LSEEEIEQIVQQS-DAFSGADMTQLCR  296 (357)
T ss_dssp             EEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBC-CCHHHHHHHHHHT-TTCCHHHHHHHHH
T ss_pred             EEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCC-ccHHHHHHHHHHc-CCCCHHHHHHHHH
Confidence                  211 111100 01122367888899999999988776422111 1134556888889 77 6667777664

>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=96.91  E-value=0.0037  Score=58.03  Aligned_cols=53  Identities=9%  Similarity=-0.033  Sum_probs=35.5

Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                      ..+++.+++.++..+.+...+......-.-.+....|++.+ +|.+-.+..+-.
T Consensus       186 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~-~G~~r~a~~~l~  238 (354)
T 1sxj_E          186 LLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQAS-NGNLRVSLLMLE  238 (354)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHH-TTCHHHHHHHHT
T ss_pred             eEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHc-CCCHHHHHHHHH
Confidence            57899999999999999887642111100024556888999 888776654443

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.91  E-value=0.0024  Score=62.08  Aligned_cols=37  Identities=24%  Similarity=0.444  Sum_probs=32.6

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      .+++||+.++..++..|...         .+|+|||+||+.+.+..
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l  225 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQI  225 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            46999999999999998654         88999999999998864

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.89  E-value=0.011  Score=54.55  Aligned_cols=48  Identities=10%  Similarity=-0.040  Sum_probs=33.8

Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHH
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLT  302 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~  302 (374)
                      ..+.+.+++.++...++.+.+..... .--.+....|+..+ +|.|-.+.
T Consensus       177 ~~i~l~~~~~~e~~~il~~~~~~~~~-~~~~~~~~~l~~~~-~G~~r~l~  224 (338)
T 3pfi_A          177 MQFRLEFYKDSELALILQKAALKLNK-TCEEKAALEIAKRS-RSTPRIAL  224 (338)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHHHTTC-EECHHHHHHHHHTT-TTCHHHHH
T ss_pred             EEeeCCCcCHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHH-CcCHHHHH
Confidence            47999999999999999887742211 11135566788889 99884443

>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=96.88  E-value=0.025  Score=52.22  Aligned_cols=87  Identities=11%  Similarity=0.029  Sum_probs=51.2

Q ss_pred             CeEEEEEeCCCCcc--c----cccccCcCCCC-----C-cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCc
Q 045120          213 NKILVILANIWKLL--D----LETVKIPFRND-----S-RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENC  280 (374)
Q Consensus       213 kr~LlVlDdv~~~~--~----~~~l~~~~~~~-----T-R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~  280 (374)
                      ++-++|+|++..-.  .    +..+..+-+..     | +...+..........+.+.+++.++..+.+.....  . + 
T Consensus       108 ~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~~--~-~-  183 (334)
T 1a5t_A          108 GAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT--M-S-  183 (334)
T ss_dssp             SCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC--C-C-
T ss_pred             CcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhcC--C-C-
Confidence            57788899987532  1    22222222221     2 22222211222234799999999999999888751  1 1 


Q ss_pred             chHHHHHHHHHHccCCchHHHHHHhc
Q 045120          281 KFKSTAINVAKACGAGLFCTLTTNAS  306 (374)
Q Consensus       281 ~l~~~~~~I~~~c~~GlPLai~~ig~  306 (374)
                        .+....++..+ +|.|..+..+..
T Consensus       184 --~~~~~~l~~~s-~G~~r~a~~~l~  206 (334)
T 1a5t_A          184 --QDALLAALRLS-AGSPGAALALFQ  206 (334)
T ss_dssp             --HHHHHHHHHHT-TTCHHHHHHTTS
T ss_pred             --HHHHHHHHHHc-CCCHHHHHHHhc
Confidence              24456788999 999987755543

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=96.78  E-value=0.0049  Score=56.74  Aligned_cols=167  Identities=11%  Similarity=0.116  Sum_probs=89.2

Q ss_pred             cccccccccHHHHHHHHHHhhc-------------C--------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTN-------------A--------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD  177 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~-------------~--------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~  177 (374)
                      .....++|.+..++.|.+.+..             .        +.|+|||+||+.+++... ..   ..+.++.+.-.+
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~-~~---~~~~i~~~~l~~   84 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN-NS---TFFSISSSDLVS   84 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTT-SC---EEEEEECCSSCC
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcC-CC---cEEEEEhHHHHh
Confidence            3456788999888888776631             1        889999999999998541 11   123333332111


Q ss_pred             HHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc-------------cccccC---cC---CCC
Q 045120          178 IKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD-------------LETVKI---PF---RND  238 (374)
Q Consensus       178 ~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~-------------~~~l~~---~~---~~~  238 (374)
                                    ...... ......+.+.....+..+|+||++.....             ...+..   .+   +.+
T Consensus        85 --------------~~~g~~-~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~  149 (322)
T 1xwi_A           85 --------------KWLGES-EKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDG  149 (322)
T ss_dssp             --------------SSCCSC-HHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTT
T ss_pred             --------------hhhhHH-HHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCC
Confidence                          111111 12233344444333689999999975310             011100   00   111


Q ss_pred             ------Ccch-hHhh-hhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCc-hHHHHHHhc
Q 045120          239 ------SRDN-NVVL-LSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL-FCTLTTNAS  306 (374)
Q Consensus       239 ------TR~~-~va~-~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~Gl-PLai~~ig~  306 (374)
                            |... .+-. ....-...+.++..+.++-.++|..+.......-. ......|++.+ .|. +-.|..+..
T Consensus       150 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~-~~~l~~la~~t-~G~sgadl~~l~~  224 (322)
T 1xwi_A          150 ILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSLT-EADFRELGRKT-DGYSGADISIIVR  224 (322)
T ss_dssp             EEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCCC-HHHHHHHHHTC-TTCCHHHHHHHHH
T ss_pred             EEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHc-CCCCHHHHHHHHH
Confidence                  2111 1100 00122246788889999999999988753321111 23456788888 776 545655544

>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=96.76  E-value=0.0049  Score=56.54  Aligned_cols=40  Identities=18%  Similarity=0.237  Sum_probs=33.8

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~  158 (374)
                      .....++|.+..++.+.+++..+          +.|+|||++|+.+.+..
T Consensus        23 ~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l   72 (324)
T 3u61_B           23 STIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV   72 (324)
T ss_dssp             CSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT
T ss_pred             CCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            33567999999999999999865          57999999999998854

>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=96.76  E-value=0.021  Score=55.04  Aligned_cols=168  Identities=14%  Similarity=0.170  Sum_probs=87.5

Q ss_pred             ccccccccccHHHHHHHHHHhh-------------cC--------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          118 NKVYEAFESRVSNLKSTQNALT-------------NA--------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~-------------~~--------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      +.....++|.+..++.|.+.+.             ..        +.|+|||+||+.+++...      ..-++.++.. 
T Consensus       130 ~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~------~~~~~~v~~~-  202 (444)
T 2zan_A          130 NVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN------NSTFFSISSS-  202 (444)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCC------SSEEEEECCC-
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcC------CCCEEEEeHH-
Confidence            3445679999999999888762             11        889999999999998541      1123333322 


Q ss_pred             CHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc-------------ccccccCcC------CC
Q 045120          177 DIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL-------------DLETVKIPF------RN  237 (374)
Q Consensus       177 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~-------------~~~~l~~~~------~~  237 (374)
                      +   +...   ..+..  ..    ....+.......+..+|+||++....             ....+...+      +.
T Consensus       203 ~---l~~~---~~g~~--~~----~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~  270 (444)
T 2zan_A          203 D---LVSK---WLGES--EK----LVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDND  270 (444)
T ss_dssp             ---------------C--CC----THHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCS
T ss_pred             H---HHhh---hcchH--HH----HHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCC
Confidence            1   1110   11111  01    12233333333367999999997531             011111111      11


Q ss_pred             C------Ccch-hHhhh-hcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC-chHHHHHHhc
Q 045120          238 D------SRDN-NVVLL-SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG-LFCTLTTNAS  306 (374)
Q Consensus       238 ~------TR~~-~va~~-~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G-lPLai~~ig~  306 (374)
                      +      |... .+... ..-....+.++..+.++-..+|..++........ ......|++.+ .| .+-.|..+..
T Consensus       271 ~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~-~~~l~~la~~t-~G~sgadl~~l~~  346 (444)
T 2zan_A          271 GILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLT-EADFQELGRKT-DGYSGADISIIVR  346 (444)
T ss_dssp             SCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEECC-HHHHHHHHHHT-TTCCHHHHHHHHH
T ss_pred             CEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHc-CCCCHHHHHHHHH
Confidence            1      2211 11100 0112246778888899999999888753321111 23445788888 77 4545555443

>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=96.69  E-value=0.006  Score=63.84  Aligned_cols=38  Identities=18%  Similarity=0.363  Sum_probs=33.3

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      ..+++||+.++.++++.|...         .+|+||||||+.+.+..
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l  215 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRI  215 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            356999999999999998764         88999999999999865

>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=96.69  E-value=0.0052  Score=51.20  Aligned_cols=66  Identities=21%  Similarity=0.233  Sum_probs=37.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+||||||+.+++.......+. ++++      +..++...+...+......        .+.+.+.  +.-+|||||
T Consensus        46 ~~G~GKTtL~~~i~~~~~~~~g~~-~~~~------~~~~~~~~~~~~~~~~~~~--------~~~~~~~--~~~llilDE  108 (180)
T 3ec2_A           46 SPGVGKTHLAVATLKAIYEKKGIR-GYFF------DTKDLIFRLKHLMDEGKDT--------KFLKTVL--NSPVLVLDD  108 (180)
T ss_dssp             SSSSSHHHHHHHHHHHHHHHSCCC-CCEE------EHHHHHHHHHHHHHHTCCS--------HHHHHHH--TCSEEEEET
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCe-EEEE------EHHHHHHHHHHHhcCchHH--------HHHHHhc--CCCEEEEeC
Confidence            779999999999998764232222 2333      3444555544443221111        2222333  357999999


Q ss_pred             CCC
Q 045120          222 IWK  224 (374)
Q Consensus       222 v~~  224 (374)
                      +..
T Consensus       109 ~~~  111 (180)
T 3ec2_A          109 LGS  111 (180)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            873

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.63  E-value=0.0083  Score=54.22  Aligned_cols=164  Identities=13%  Similarity=0.101  Sum_probs=87.7

Q ss_pred             cccccccccHHHHHHHHHHhhc--------------C-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTN--------------A-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD  177 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~--------------~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~  177 (374)
                      .....++|.+..++.+.+.+..              .       +.|+||||||+.+.+...  .   ..+.++.+.-.+
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~--~---~~~~i~~~~l~~   92 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECS--A---TFLNISAASLTS   92 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTT--C---EEEEEESTTTSS
T ss_pred             CCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhC--C---CeEEeeHHHHhh
Confidence            3356799999999998887632              1       889999999999998543  1   123333332111


Q ss_pred             HHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc-------------ccccc---CcCC-----
Q 045120          178 IKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD-------------LETVK---IPFR-----  236 (374)
Q Consensus       178 ~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~-------------~~~l~---~~~~-----  236 (374)
                                    ..... .......+.......+..+|+||++.....             ...+.   ..++     
T Consensus        93 --------------~~~~~-~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  157 (297)
T 3b9p_A           93 --------------KYVGD-GEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDG  157 (297)
T ss_dssp             --------------SSCSC-HHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC-----
T ss_pred             --------------cccch-HHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCC
Confidence                          11111 122222333333333678999999964310             00010   0011     


Q ss_pred             CC------Ccch-hHh---hhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH-HHHHHh
Q 045120          237 ND------SRDN-NVV---LLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC-TLTTNA  305 (374)
Q Consensus       237 ~~------TR~~-~va---~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL-ai~~ig  305 (374)
                      ..      |... .+.   ...+  ...+.++..+.++...++...+......- -......|++.+ .|.+- ++..+.
T Consensus       158 ~~v~vi~~tn~~~~l~~~l~~R~--~~~i~~~~p~~~~r~~il~~~~~~~~~~~-~~~~~~~la~~~-~g~~~~~l~~l~  233 (297)
T 3b9p_A          158 DRIVVLAATNRPQELDEAALRRF--TKRVYVSLPDEQTRELLLNRLLQKQGSPL-DTEALRRLAKIT-DGYSGSDLTALA  233 (297)
T ss_dssp             -CEEEEEEESCGGGBCHHHHHHC--CEEEECCCCCHHHHHHHHHHHHGGGSCCS-CHHHHHHHHHHT-TTCCHHHHHHHH
T ss_pred             CcEEEEeecCChhhCCHHHHhhC--CeEEEeCCcCHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHc-CCCCHHHHHHHH
Confidence            11      2211 110   1111  23577778888888888887764221111 124456888899 88775 565554


Q ss_pred             c
Q 045120          306 S  306 (374)
Q Consensus       306 ~  306 (374)
                      .
T Consensus       234 ~  234 (297)
T 3b9p_A          234 K  234 (297)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=96.59  E-value=0.025  Score=52.19  Aligned_cols=167  Identities=10%  Similarity=0.101  Sum_probs=83.5

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCC-eEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFD-RVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      ...++|.+..++.|...+..+         +.|+||||+|+.+.+..... .+. .+.-++.+.......+. +++..+.
T Consensus        24 ~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~-~~~~~~~~~~~~~~~~~~~ir-~~i~~~~  101 (340)
T 1sxj_C           24 LDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGK-NYSNMVLELNASDDRGIDVVR-NQIKDFA  101 (340)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTT-SHHHHEEEECTTSCCSHHHHH-THHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCC-CccceEEEEcCcccccHHHHH-HHHHHHH
Confidence            455889998899888888765         78999999999998864311 111 12223333222222221 1111110


Q ss_pred             cCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--cccccc---CcCCCC------C-cchhHhhhhcCCCCceecC
Q 045120          191 LELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVK---IPFRND------S-RDNNVVLLSMGSKDNFLIA  258 (374)
Q Consensus       191 ~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~---~~~~~~------T-R~~~va~~~~~~~~~~~l~  258 (374)
                      ....             .+.. .+-++|+|++....  ..+.+.   ...+..      | ....+..........+.+.
T Consensus       102 ~~~~-------------~~~~-~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~  167 (340)
T 1sxj_C          102 STRQ-------------IFSK-GFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQ  167 (340)
T ss_dssp             HBCC-------------SSSC-SCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             hhcc-------------cCCC-CceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEecc
Confidence            0000             0011 35677788775321  111111   001111      0 0001100011112367899


Q ss_pred             CCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH-HHHHh
Q 045120          259 NITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT-LTTNA  305 (374)
Q Consensus       259 ~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa-i~~ig  305 (374)
                      +++.++..+.+...+......- -......|++.+ +|-+-- +..+-
T Consensus       168 ~l~~~~~~~~l~~~~~~~~~~i-~~~~~~~i~~~s-~G~~r~~~~~l~  213 (340)
T 1sxj_C          168 PLPQEAIERRIANVLVHEKLKL-SPNAEKALIELS-NGDMRRVLNVLQ  213 (340)
T ss_dssp             CCCHHHHHHHHHHHHHTTTCCB-CHHHHHHHHHHH-TTCHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHc-CCCHHHHHHHHH
Confidence            9999998888887663211111 134566888999 887764 44443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.57  E-value=0.0048  Score=63.70  Aligned_cols=38  Identities=24%  Similarity=0.433  Sum_probs=33.2

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      ..+++||+.+++++...|...         .+|+|||++|+.+.+..
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l  225 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQI  225 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            346999999999999999654         88999999999998864

>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=96.55  E-value=0.0091  Score=54.86  Aligned_cols=166  Identities=12%  Similarity=0.090  Sum_probs=91.0

Q ss_pred             cccccccccccHHHHHHHHHHhhc----------C-----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          117 SNKVYEAFESRVSNLKSTQNALTN----------A-----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       117 ~~~~~~~~vGr~~~~~~i~~~L~~----------~-----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      +......++|.+..++.|.+.+..          .           +.|+|||+||+.+++...  ..   .+.++.   
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~--~~---~~~v~~---   84 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN--ST---FFSVSS---   84 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHT--CE---EEEEEH---
T ss_pred             CCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHC--CC---EEEEch---
Confidence            334456799999999999887721          0           889999999999998643  21   222321   


Q ss_pred             CCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc-------------cccccCc------CC
Q 045120          176 SDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD-------------LETVKIP------FR  236 (374)
Q Consensus       176 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~-------------~~~l~~~------~~  236 (374)
                         ..+.    .    .... ........+.+.....+..+|+||++.....             ...+...      ..
T Consensus        85 ---~~l~----~----~~~g-~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~  152 (322)
T 3eie_A           85 ---SDLV----S----KWMG-ESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDS  152 (322)
T ss_dssp             ---HHHH----T----TTGG-GHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSC
T ss_pred             ---HHHh----h----cccc-hHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccC
Confidence               1111    1    1111 1223334444444443678999999974311             1111100      11


Q ss_pred             CC------Ccch-hHh---hhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC-chHHHHHHh
Q 045120          237 ND------SRDN-NVV---LLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG-LFCTLTTNA  305 (374)
Q Consensus       237 ~~------TR~~-~va---~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G-lPLai~~ig  305 (374)
                      .+      |... .+-   ...  -...+.++..+.++-.++|..++......-. ......|++.+ .| .+-.|..+.
T Consensus       153 ~~v~vi~atn~~~~ld~al~~R--f~~~i~~~~p~~~~r~~il~~~~~~~~~~~~-~~~l~~la~~t-~g~sg~di~~l~  228 (322)
T 3eie_A          153 QGVLVLGATNIPWQLDSAIRRR--FERRIYIPLPDLAARTTMFEINVGDTPCVLT-KEDYRTLGAMT-EGYSGSDIAVVV  228 (322)
T ss_dssp             CCEEEEEEESCGGGSCHHHHHH--CCEEEECCCCCHHHHHHHHHHHHTTCCCCCC-HHHHHHHHHTT-TTCCHHHHHHHH
T ss_pred             CceEEEEecCChhhCCHHHHcc--cCeEEEeCCCCHHHHHHHHHHHhccCCCCCC-HHHHHHHHHHc-CCCCHHHHHHHH
Confidence            11      2211 110   111  2236778889999999999998864321111 23445788888 66 455555544


Q ss_pred             c
Q 045120          306 S  306 (374)
Q Consensus       306 ~  306 (374)
                      .
T Consensus       229 ~  229 (322)
T 3eie_A          229 K  229 (322)
T ss_dssp             H
T ss_pred             H
Confidence            3

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.54  E-value=0.01  Score=56.76  Aligned_cols=84  Identities=18%  Similarity=0.306  Sum_probs=52.1

Q ss_pred             cccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ...+.|.+..+++|.+.+.-+                      ++|+|||+||+++++.....     .+.++.+.-.+ 
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~-----~~~v~~s~l~s-  253 (437)
T 4b4t_L          180 FDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGAN-----FIFSPASGIVD-  253 (437)
T ss_dssp             SGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGTCC-
T ss_pred             hhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehhhhcc-
Confidence            456789998888887765431                      89999999999999965422     23344332211 


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWK  224 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~  224 (374)
                                   .+...+ ......++...+....++|.+|++..
T Consensus       254 -------------k~~Ges-e~~ir~~F~~A~~~~P~IifiDEiDa  285 (437)
T 4b4t_L          254 -------------KYIGES-ARIIREMFAYAKEHEPCIIFMDEVDA  285 (437)
T ss_dssp             -------------SSSSHH-HHHHHHHHHHHHHSCSEEEEEECCCS
T ss_pred             -------------ccchHH-HHHHHHHHHHHHhcCCceeeeecccc
Confidence                         111111 22334444444444789999999974

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.50  E-value=0.0081  Score=54.56  Aligned_cols=38  Identities=21%  Similarity=0.203  Sum_probs=29.2

Q ss_pred             cccccHHHHHHHHHHhh---------------cC---------CCCccHHHHHHHHHHHhhh
Q 045120          123 AFESRVSNLKSTQNALT---------------NA---------NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~---------------~~---------~gGiGKTtLA~~v~~~~~~  160 (374)
                      .++|.+..++.|.+.+.               ..         +.|+|||+||+.+.+....
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~   93 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHR   93 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            48899988888776543               11         8899999999998886543

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.47  E-value=0.051  Score=51.18  Aligned_cols=166  Identities=16%  Similarity=0.119  Sum_probs=87.8

Q ss_pred             cccccccccHHHHHHHHHHhhc--------------C-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTN--------------A-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD  177 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~--------------~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~  177 (374)
                      .....++|.+..++.|.+.+..              .       ..|+|||+||+.+.+...  .   ..+.++.+.-.+
T Consensus       112 ~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~--~---~~~~v~~~~l~~  186 (389)
T 3vfd_A          112 VKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESN--A---TFFNISAASLTS  186 (389)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTT--C---EEEEECSCCC--
T ss_pred             CChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhc--C---cEEEeeHHHhhc
Confidence            3456799999999999888721              1       889999999999987532  1   223333322111


Q ss_pred             HHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc-------------ccccccC-------cCCC
Q 045120          178 IKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL-------------DLETVKI-------PFRN  237 (374)
Q Consensus       178 ~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~-------------~~~~l~~-------~~~~  237 (374)
                        .            ..... ......+.+.....+..+|+||++....             ....+..       ..+.
T Consensus       187 --~------------~~g~~-~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  251 (389)
T 3vfd_A          187 --K------------YVGEG-EKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDD  251 (389)
T ss_dssp             -------------------C-HHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----
T ss_pred             --c------------ccchH-HHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCC
Confidence              0            00001 1122333333333256899999995330             0011100       0011


Q ss_pred             C------C-cchhHhhhhc-CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCc-hHHHHHHhc
Q 045120          238 D------S-RDNNVVLLSM-GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGL-FCTLTTNAS  306 (374)
Q Consensus       238 ~------T-R~~~va~~~~-~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~Gl-PLai~~ig~  306 (374)
                      .      | +...+..... -....+.+...+.++-.+++...+......- .......|++.+ .|. +-+|..+..
T Consensus       252 ~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l-~~~~~~~la~~~-~g~~~~~l~~L~~  327 (389)
T 3vfd_A          252 RVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPL-TQKELAQLARMT-DGYSGSDLTALAK  327 (389)
T ss_dssp             CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCCS-CHHHHHHHHHHT-TTCCHHHHHHHHH
T ss_pred             CEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHc-CCCCHHHHHHHHH
Confidence            1      1 1111110011 1223678889999999999998875322111 123556888888 774 446666654

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.43  E-value=0.01  Score=56.84  Aligned_cols=86  Identities=16%  Similarity=0.164  Sum_probs=52.0

Q ss_pred             ccccccccccHHHHHHHHHHhhc----C------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC
Q 045120          118 NKVYEAFESRVSNLKSTQNALTN----A------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT  175 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~~----~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~  175 (374)
                      ......+.|.+..+++|.+.+..    +                  ++|+|||.||+++++.....     .+.++.+.-
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~-----f~~v~~s~l  251 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNAT-----FLKLAAPQL  251 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGG
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCC-----EEEEehhhh
Confidence            34456788999999888776432    2                  89999999999999965421     233332221


Q ss_pred             CCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          176 SDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       176 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                                    ...+... .......++..-+....++|.+|++.
T Consensus       252 --------------~~~~vGe-se~~ir~lF~~A~~~aP~IifiDEiD  284 (434)
T 4b4t_M          252 --------------VQMYIGE-GAKLVRDAFALAKEKAPTIIFIDELD  284 (434)
T ss_dssp             --------------CSSCSSH-HHHHHHHHHHHHHHHCSEEEEEECTH
T ss_pred             --------------hhcccch-HHHHHHHHHHHHHhcCCeEEeecchh
Confidence                          1111111 12233344443333368999999985

>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=96.43  E-value=0.067  Score=51.37  Aligned_cols=140  Identities=14%  Similarity=0.111  Sum_probs=76.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+||||||+.+++.......--.+++++.+      .+...+...+....        ...+.+.+.. +.-+|+|||
T Consensus       138 p~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~------~~~~~~~~~~~~~~--------~~~~~~~~~~-~~~vL~IDE  202 (440)
T 2z4s_A          138 GVGLGKTHLLQSIGNYVVQNEPDLRVMYITSE------KFLNDLVDSMKEGK--------LNEFREKYRK-KVDILLIDD  202 (440)
T ss_dssp             SSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHH------HHHHHHHHHHHTTC--------HHHHHHHHTT-TCSEEEEEC
T ss_pred             CCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH------HHHHHHHHHHHccc--------HHHHHHHhcC-CCCEEEEeC
Confidence            78999999999999865422101123455432      33344444332110        1223344442 467999999


Q ss_pred             CCCccc----cccccCc----CCCC------Cc---------chhHhhhhcCCCCceecCCCCHHHHHHHHHHhcC--CC
Q 045120          222 IWKLLD----LETVKIP----FRND------SR---------DNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNG--DD  276 (374)
Q Consensus       222 v~~~~~----~~~l~~~----~~~~------TR---------~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~--~~  276 (374)
                      +.....    .+.+...    ...+      |.         ...+. ..+....++.+++++.++-.+++.+.+.  +.
T Consensus       203 i~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~-sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~  281 (440)
T 2z4s_A          203 VQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLV-SRFQMGLVAKLEPPDEETRKSIARKMLEIEHG  281 (440)
T ss_dssp             GGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHH-HHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTC
T ss_pred             cccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHH-hhccCCeEEEeCCCCHHHHHHHHHHHHHHcCC
Confidence            864321    1111111    1111      11         12222 2233335789999999999999988774  11


Q ss_pred             CCCcchHHHHHHHHHHccCCchHHH
Q 045120          277 VENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       277 ~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      ..++   ++...|+..+ +|.+-.+
T Consensus       282 ~i~~---e~l~~la~~~-~gn~R~l  302 (440)
T 2z4s_A          282 ELPE---EVLNFVAENV-DDNLRRL  302 (440)
T ss_dssp             CCCT---THHHHHHHHC-CSCHHHH
T ss_pred             CCCH---HHHHHHHHhc-CCCHHHH
Confidence            1222   3456788888 8877544

>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=96.38  E-value=0.015  Score=50.20  Aligned_cols=50  Identities=8%  Similarity=-0.060  Sum_probs=35.4

Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHH
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTN  304 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~i  304 (374)
                      ..+.+.+++.++..+++...+...... --.+....|++.| +|.+-.+.-+
T Consensus       167 ~~i~l~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~-~g~~r~l~~~  216 (242)
T 3bos_A          167 LTYQLQPMMDDEKLAALQRRAAMRGLQ-LPEDVGRFLLNRM-ARDLRTLFDV  216 (242)
T ss_dssp             EEEECCCCCGGGHHHHHHHHHHHTTCC-CCHHHHHHHHHHT-TTCHHHHHHH
T ss_pred             ceEEeCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHc-cCCHHHHHHH
Confidence            478999999999999999876421111 1135667888999 8888766543

>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=96.36  E-value=0.015  Score=59.95  Aligned_cols=137  Identities=15%  Similarity=0.272  Sum_probs=76.0

Q ss_pred             cccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcC----CCCeEEEE-EeCCCCCHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDK----LFDRVVFS-EVSQTSDIKKIQGDIA  186 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv-~vs~~~~~~~~~~~i~  186 (374)
                      ..+++||+.++.++++.|...         ..|+||||||+.+.+......    .+++.+|. +.+.-.          
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~----------  254 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLL----------  254 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-------------
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHh----------
Confidence            346899999999999998754         889999999999988643211    12333332 111100          


Q ss_pred             HHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc----------cc-cccccCcCCCC-------CcchhHh---
Q 045120          187 EKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL----------LD-LETVKIPFRND-------SRDNNVV---  245 (374)
Q Consensus       187 ~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~----------~~-~~~l~~~~~~~-------TR~~~va---  245 (374)
                        .+... ..........+.+.+...+..+|++|++...          .+ ...+...+..+       |......   
T Consensus       255 --~~~~~-~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~~~~~~I~at~~~~~~~~~  331 (758)
T 1r6b_X          255 --AGTKY-RGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIF  331 (758)
T ss_dssp             --CCCCC-SSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCC
T ss_pred             --ccccc-cchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhCCCeEEEEEeCchHHhhhh
Confidence              00111 1122223334444444335799999999743          11 11233333332       2221110   


Q ss_pred             ------hhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          246 ------LLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       246 ------~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                            ...+   ..+.+++.+.++..+++....
T Consensus       332 ~~d~aL~~Rf---~~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          332 EKDRALARRF---QKIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             CCTTSSGGGE---EEEECCCCCHHHHHHHHHHHH
T ss_pred             hcCHHHHhCc---eEEEcCCCCHHHHHHHHHHHH
Confidence                  0111   258899999999988887654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.30  E-value=0.0033  Score=53.38  Aligned_cols=65  Identities=15%  Similarity=0.183  Sum_probs=37.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      .+|+||||||+.+++....  ....++|++.+      .+...+...+...    ..    ..+.+.+..  .-+|||||
T Consensus        62 ~~GtGKT~la~~i~~~~~~--~~~~~~~~~~~------~~~~~~~~~~~~~----~~----~~~~~~~~~--~~~lilDe  123 (202)
T 2w58_A           62 SFGVGKTYLLAAIANELAK--RNVSSLIVYVP------ELFRELKHSLQDQ----TM----NEKLDYIKK--VPVLMLDD  123 (202)
T ss_dssp             STTSSHHHHHHHHHHHHHT--TTCCEEEEEHH------HHHHHHHHC---C----CC----HHHHHHHHH--SSEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHH--cCCeEEEEEhH------HHHHHHHHHhccc----hH----HHHHHHhcC--CCEEEEcC
Confidence            8899999999999986652  23345666543      4444443332211    11    122333443  24999999


Q ss_pred             CCC
Q 045120          222 IWK  224 (374)
Q Consensus       222 v~~  224 (374)
                      ++.
T Consensus       124 i~~  126 (202)
T 2w58_A          124 LGA  126 (202)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            964

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.30  E-value=0.015  Score=55.91  Aligned_cols=154  Identities=15%  Similarity=0.181  Sum_probs=83.6

Q ss_pred             cccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      .....+.|.+..+++|.+.+.-+                      ++|+|||+||+++.+....  .|   +.++.+.- 
T Consensus       206 vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~--~f---i~vs~s~L-  279 (467)
T 4b4t_H          206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDA--TF---IRVIGSEL-  279 (467)
T ss_dssp             CCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTC--EE---EEEEGGGG-
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCC--Ce---EEEEhHHh-
Confidence            33456889999888887765321                      8899999999999996542  12   33332211 


Q ss_pred             CHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc----------------cccccC---cCCC
Q 045120          177 DIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD----------------LETVKI---PFRN  237 (374)
Q Consensus       177 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~----------------~~~l~~---~~~~  237 (374)
                                   ....... .+.....++...+....++|++|++.....                +..+..   .+..
T Consensus       280 -------------~sk~vGe-sek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  345 (467)
T 4b4t_H          280 -------------VQKYVGE-GARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDP  345 (467)
T ss_dssp             -------------CCCSSSH-HHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCC
T ss_pred             -------------hcccCCH-HHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCC
Confidence                         1111111 122334444444444789999999874310                000100   0111


Q ss_pred             C--------CcchhH---hhhhcC-CCCceecCCCCHHHHHHHHHHhcCCCCC--CcchHHHHHHHHHHccCCc
Q 045120          238 D--------SRDNNV---VLLSMG-SKDNFLIANITEEEAWRLFKIMNGDDVE--NCKFKSTAINVAKACGAGL  297 (374)
Q Consensus       238 ~--------TR~~~v---a~~~~~-~~~~~~l~~L~~~~s~~Lf~~~a~~~~~--~~~l~~~~~~I~~~c~~Gl  297 (374)
                      .        |.....   |....| -...+.++.-+.++-.++|+.+......  .-++    ..|++.| .|+
T Consensus       346 ~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl----~~LA~~T-~Gf  414 (467)
T 4b4t_H          346 RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRW----ELISRLC-PNS  414 (467)
T ss_dssp             TTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCH----HHHHHHC-CSC
T ss_pred             CCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCH----HHHHHHC-CCC
Confidence            1        222111   111111 2347888888889999999888753222  2233    3567777 665

>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=96.26  E-value=0.0086  Score=54.49  Aligned_cols=40  Identities=25%  Similarity=0.278  Sum_probs=31.4

Q ss_pred             cccccccccHHHHHHHHHHhhc--------------C--------CCCccHHHHHHHHHHHh
Q 045120          119 KVYEAFESRVSNLKSTQNALTN--------------A--------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~--------------~--------~gGiGKTtLA~~v~~~~  158 (374)
                      .....++|.+..+++|.+.+..              .        +.|+||||||+.+++..
T Consensus        12 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~   73 (301)
T 3cf0_A           12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC   73 (301)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHh
Confidence            3345689999988888776642              1        88999999999999854

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.25  E-value=0.02  Score=54.64  Aligned_cols=84  Identities=14%  Similarity=0.184  Sum_probs=51.6

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD  177 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~  177 (374)
                      ....+.|.+..+++|.+.+.-.                      ++|+|||+||+++++....  +   .+.|+.+.-.+
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~--~---~~~v~~~~l~~  244 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKA--A---FIRVNGSEFVH  244 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTC--E---EEEEEGGGTCC
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCC--C---eEEEecchhhc
Confidence            3456889999988887765421                      8999999999999996542  1   23343332211


Q ss_pred             HHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          178 IKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       178 ~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                                    .....+ ......++...+....++|.+|++.
T Consensus       245 --------------~~~Ge~-e~~ir~lF~~A~~~aP~IifiDEiD  275 (428)
T 4b4t_K          245 --------------KYLGEG-PRMVRDVFRLARENAPSIIFIDEVD  275 (428)
T ss_dssp             --------------SSCSHH-HHHHHHHHHHHHHTCSEEEEEECTH
T ss_pred             --------------cccchh-HHHHHHHHHHHHHcCCCeeechhhh
Confidence                          111111 2233444444443368999999985

>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=96.20  E-value=0.013  Score=54.77  Aligned_cols=165  Identities=13%  Similarity=0.125  Sum_probs=88.2

Q ss_pred             ccccccccHHHHHHHHHHhhc----------------C-----CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          120 VYEAFESRVSNLKSTQNALTN----------------A-----NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~----------------~-----~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ....++|.+..++.|.+.+..                +     +.|+|||+||+.+++...  ..   .+.++.+     
T Consensus        49 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~--~~---~~~v~~~-----  118 (355)
T 2qp9_X           49 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN--ST---FFSVSSS-----  118 (355)
T ss_dssp             CGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHT--CE---EEEEEHH-----
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhC--CC---EEEeeHH-----
Confidence            345689999999998887631                1     889999999999998653  11   2223221     


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc-------------cccccCc---C---CCC-
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD-------------LETVKIP---F---RND-  238 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~-------------~~~l~~~---~---~~~-  238 (374)
                       .+.    ..    ..... ......+.......+..+|+||++.....             ...+...   +   +.+ 
T Consensus       119 -~l~----~~----~~g~~-~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v  188 (355)
T 2qp9_X          119 -DLV----SK----WMGES-EKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGV  188 (355)
T ss_dssp             -HHH----SC----C---C-HHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCE
T ss_pred             -HHh----hh----hcchH-HHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCe
Confidence             111    11    11111 12233333433333689999999874310             1111110   0   111 


Q ss_pred             -----Ccch-hHhh-hhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC-chHHHHHHhc
Q 045120          239 -----SRDN-NVVL-LSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG-LFCTLTTNAS  306 (374)
Q Consensus       239 -----TR~~-~va~-~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G-lPLai~~ig~  306 (374)
                           |... .+.. ........+.++..+.++-.++|..+.......-. ......|++.+ .| .|-.|..+..
T Consensus       189 ~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~-~~~l~~la~~t-~G~sg~dl~~l~~  262 (355)
T 2qp9_X          189 LVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLT-KEDYRTLGAMT-EGYSGSDIAVVVK  262 (355)
T ss_dssp             EEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCCC-HHHHHHHHHHT-TTCCHHHHHHHHH
T ss_pred             EEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCC-HHHHHHHHHHc-CCCCHHHHHHHHH
Confidence                 2111 1100 00122346788899999999999988763321111 23446788888 77 4545555443

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.20  E-value=0.018  Score=54.80  Aligned_cols=86  Identities=19%  Similarity=0.212  Sum_probs=52.4

Q ss_pred             cccccccccHHHHHHHHHHhhc----C------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC
Q 045120          119 KVYEAFESRVSNLKSTQNALTN----A------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS  176 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~----~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~  176 (374)
                      .....+.|.++.+++|.+.+.-    +                  ++|+|||.||+++.+.....  |   +.++.+.- 
T Consensus       179 v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~--f---i~v~~s~l-  252 (437)
T 4b4t_I          179 ESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSAT--F---LRIVGSEL-  252 (437)
T ss_dssp             CCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCE--E---EEEESGGG-
T ss_pred             CcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCC--E---EEEEHHHh-
Confidence            3445688999888888776532    1                  89999999999999965522  2   23332211 


Q ss_pred             CHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 045120          177 DIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWK  224 (374)
Q Consensus       177 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~  224 (374)
                                   ...+... .+.....++...+....++|.+|++..
T Consensus       253 -------------~sk~vGe-sek~ir~lF~~Ar~~aP~IIfiDEiDa  286 (437)
T 4b4t_I          253 -------------IQKYLGD-GPRLCRQIFKVAGENAPSIVFIDEIDA  286 (437)
T ss_dssp             -------------CCSSSSH-HHHHHHHHHHHHHHTCSEEEEEEEESS
T ss_pred             -------------hhccCch-HHHHHHHHHHHHHhcCCcEEEEehhhh
Confidence                         1111111 223344455544444789999999863

>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=95.85  E-value=0.0045  Score=56.71  Aligned_cols=62  Identities=10%  Similarity=0.171  Sum_probs=39.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe--CCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV--SQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v--s~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      ++|+||||||.++....     -..++|+++  ....+.               ...+.+.....+.+.+.. .+ +||+
T Consensus       131 pPGsGKTtLAlqlA~~~-----G~~VlyIs~~~eE~v~~---------------~~~~le~~l~~i~~~l~~-~~-LLVI  188 (331)
T 2vhj_A          131 KGNSGKTPLVHALGEAL-----GGKDKYATVRFGEPLSG---------------YNTDFNVFVDDIARAMLQ-HR-VIVI  188 (331)
T ss_dssp             SCSSSHHHHHHHHHHHH-----HTTSCCEEEEBSCSSTT---------------CBCCHHHHHHHHHHHHHH-CS-EEEE
T ss_pred             CCCCCHHHHHHHHHHhC-----CCCEEEEEecchhhhhh---------------hhcCHHHHHHHHHHHHhh-CC-EEEE
Confidence            89999999999998751     113456766  222111               002344555667777776 45 9999


Q ss_pred             eCCCCc
Q 045120          220 ANIWKL  225 (374)
Q Consensus       220 Ddv~~~  225 (374)
                      |++...
T Consensus       189 DsI~aL  194 (331)
T 2vhj_A          189 DSLKNV  194 (331)
T ss_dssp             ECCTTT
T ss_pred             eccccc
Confidence            998653

>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=95.82  E-value=0.031  Score=49.71  Aligned_cols=47  Identities=13%  Similarity=0.218  Sum_probs=28.7

Q ss_pred             CceecCCCCH-HHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC------chHHHHHHhc
Q 045120          253 DNFLIANITE-EEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG------LFCTLTTNAS  306 (374)
Q Consensus       253 ~~~~l~~L~~-~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G------lPLai~~ig~  306 (374)
                      ..+.+++++. ++-..++.....  . +   .+....|++.+ .|      ++-++.++-.
T Consensus       191 ~~i~~p~l~~r~~i~~i~~~~~~--~-~---~~~~~~l~~~~-~g~~~~g~ir~l~~~l~~  244 (272)
T 1d2n_A          191 TTIHVPNIATGEQLLEALELLGN--F-K---DKERTTIAQQV-KGKKVWIGIKKLLMLIEM  244 (272)
T ss_dssp             EEEECCCEEEHHHHHHHHHHHTC--S-C---HHHHHHHHHHH-TTSEEEECHHHHHHHHHH
T ss_pred             eEEcCCCccHHHHHHHHHHhcCC--C-C---HHHHHHHHHHh-cCCCccccHHHHHHHHHH
Confidence            4688899988 666666655321  1 1   24456788888 66      5555555544

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=95.81  E-value=0.032  Score=49.21  Aligned_cols=39  Identities=23%  Similarity=0.277  Sum_probs=29.0

Q ss_pred             ccccccccHHHHHHHHHHh---hc-----------C-------CCCccHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNAL---TN-----------A-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L---~~-----------~-------~gGiGKTtLA~~v~~~~  158 (374)
                      ....++|.+..++++.+.+   ..           +       ..|+||||||+.+.+..
T Consensus        10 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~   69 (257)
T 1lv7_A           10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA   69 (257)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHc
Confidence            3566889988877665543   21           1       88999999999999864

>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=95.71  E-value=0.08  Score=45.81  Aligned_cols=83  Identities=16%  Similarity=0.121  Sum_probs=49.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc----------hhhHH---HHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDK----LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS----------EEAEY---RRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~----------~~~~~---~~~~~  204 (374)
                      ..|+|||||+..+........    .-..++|++....++...+. .+++.++....          ..+..   .....
T Consensus        32 ~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (243)
T 1n0w_A           32 EFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQ  110 (243)
T ss_dssp             CTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCHHHHHHHHHH
Confidence            789999999999987532211    12468888877655554443 34445543210          11112   23344


Q ss_pred             HHHHHhcCCeEEEEEeCCCCc
Q 045120          205 LYERLKNENKILVILANIWKL  225 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~~~  225 (374)
                      +.+.+...+.-+||||.+...
T Consensus       111 ~~~~~~~~~~~lliiD~~~~~  131 (243)
T 1n0w_A          111 ASAMMVESRYALLIVDSATAL  131 (243)
T ss_dssp             HHHHHHHSCEEEEEEETSSGG
T ss_pred             HHHHHhcCCceEEEEeCchHH
Confidence            556665446789999998643

>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=95.71  E-value=0.029  Score=54.66  Aligned_cols=161  Identities=13%  Similarity=0.146  Sum_probs=84.8

Q ss_pred             cccccccHHHHHHHHHHhhc-------------C---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          121 YEAFESRVSNLKSTQNALTN-------------A---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~-------------~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ...++|.+..+++|.+++..             .         ..|+|||+||+.+.+...  .   ..+.++.      
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~--~---~fv~vn~------  271 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG--A---FFFLING------  271 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCS--S---EEEEEEH------
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhC--C---CEEEEEc------
Confidence            34689999999998887642             1         889999999999988542  1   1233331      


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc--------c-----cccccc---CcC--CCC--
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL--------L-----DLETVK---IPF--RND--  238 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~--------~-----~~~~l~---~~~--~~~--  238 (374)
                      ..+    .    ........... ..+.+....++..+|+||++...        .     ....|.   ..+  +..  
T Consensus       272 ~~l----~----~~~~g~~~~~~-~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~  342 (489)
T 3hu3_A          272 PEI----M----SKLAGESESNL-RKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVI  342 (489)
T ss_dssp             HHH----H----TSCTTHHHHHH-HHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEE
T ss_pred             hHh----h----hhhcchhHHHH-HHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceE
Confidence            111    1    11111112222 22233333336789999998311        0     011111   111  111  


Q ss_pred             ----Ccch-hHhhh--hc-CCCCceecCCCCHHHHHHHHHHhcCCCCC--CcchHHHHHHHHHHccCC-chHHHHHHhc
Q 045120          239 ----SRDN-NVVLL--SM-GSKDNFLIANITEEEAWRLFKIMNGDDVE--NCKFKSTAINVAKACGAG-LFCTLTTNAS  306 (374)
Q Consensus       239 ----TR~~-~va~~--~~-~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~--~~~l~~~~~~I~~~c~~G-lPLai~~ig~  306 (374)
                          |... .+...  .. .-...+.+...+.++-.++|..++.....  ...+    .+++..+ .| .+-.|..+..
T Consensus       343 vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l----~~la~~t-~g~s~~dL~~L~~  416 (489)
T 3hu3_A          343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDL----EQVANET-HGHVGADLAALCS  416 (489)
T ss_dssp             EEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCH----HHHHHTC-TTCCHHHHHHHHH
T ss_pred             EEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhH----HHHHHHc-cCCcHHHHHHHHH
Confidence                2221 11110  11 11236889999999999999988763221  2223    3566677 55 4655655543

>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=95.60  E-value=0.056  Score=49.31  Aligned_cols=78  Identities=9%  Similarity=0.095  Sum_probs=50.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHH-HHHHHHHH---hc
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRR-ASRLYERL---KN  211 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~-~~~l~~~L---~~  211 (374)
                      ..|+||||||.++.........=..++||+....++..     .+++++...+.      .+.++. .. +.+.|   +.
T Consensus        36 ~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~-i~~~l~~i~~  109 (333)
T 3io5_A           36 PSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRID-MVNQLDAIER  109 (333)
T ss_dssp             SSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHH-HHHHHHTCCT
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHH-HHHHHHHhhc
Confidence            88999999998887765422112468899888887754     36777765332      233443 33 33333   44


Q ss_pred             CCeEEEEEeCCCCc
Q 045120          212 ENKILVILANIWKL  225 (374)
Q Consensus       212 ~kr~LlVlDdv~~~  225 (374)
                      ++.-|||+|-|...
T Consensus       110 ~~~~lvVIDSI~aL  123 (333)
T 3io5_A          110 GEKVVVFIDSLGNL  123 (333)
T ss_dssp             TCCEEEEEECSTTC
T ss_pred             cCceEEEEeccccc
Confidence            47889999998644

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.56  E-value=0.054  Score=48.49  Aligned_cols=39  Identities=23%  Similarity=0.233  Sum_probs=26.9

Q ss_pred             cccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhh
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      ...+.|.++.+++|.+.+..+                      +.|+||||||+.+.+...
T Consensus         9 ~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~   69 (274)
T 2x8a_A            9 WADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESG   69 (274)
T ss_dssp             ---CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcC
Confidence            445778777777776644211                      889999999999998543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.53  E-value=0.0043  Score=49.75  Aligned_cols=35  Identities=14%  Similarity=0.183  Sum_probs=26.4

Q ss_pred             cccccHHHHHHHHHHhhc----C-------CCCccHHHHHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTN----A-------NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~----~-------~gGiGKTtLA~~v~~~  157 (374)
                      .++|++..++++.+.+..    +       ..|+|||++|+.+.+.
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            578999888888887653    1       8899999999999873

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=95.42  E-value=0.086  Score=48.81  Aligned_cols=82  Identities=16%  Similarity=0.233  Sum_probs=51.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc-------------hhhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDK----LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS-------------EEAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-------------~~~~~~~~~~  204 (374)
                      ..|+||||||.++........    .-..++|++....++...+.. ++..++....             .....+....
T Consensus       130 ~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g~~~~~~l~~l~~~~~~~~e~~~~ll~~  208 (343)
T 1v5w_A          130 EFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFNVDHDAVLDNVLYARAYTSEHQMELLDY  208 (343)
T ss_dssp             CTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCSTTHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcCCCHHHHHhceeEeecCCHHHHHHHHHH
Confidence            789999999999887643211    124688999888777766553 4455543321             1122234445


Q ss_pred             HHHHHhc--CCeEEEEEeCCCC
Q 045120          205 LYERLKN--ENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~--~kr~LlVlDdv~~  224 (374)
                      +.+.+..  .+--+||+|.+..
T Consensus       209 l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          209 VAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             HHHHHHHSCSSEEEEEEETSGG
T ss_pred             HHHHHHhcCCCccEEEEechHH
Confidence            5566654  4677999998753

>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=95.42  E-value=0.077  Score=48.65  Aligned_cols=82  Identities=18%  Similarity=0.267  Sum_probs=52.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc----------hhhHH---HHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKL----FDRVVFSEVSQTSDIKKIQGDIAEKLGLELS----------EEAEY---RRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~----------~~~~~---~~~~~  204 (374)
                      ..|+||||||.++.........    -..++|++....++...+.+ +++.++....          ..+.+   +....
T Consensus       115 ~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~l~~~~~~~~~~~~~~l~~  193 (324)
T 2z43_A          115 EFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIEN-MAKALGLDIDNVMNNIYYIRAINTDHQIAIVDD  193 (324)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCSHHHHHHHHHH
T ss_pred             CCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHhCCCHHHHhccEEEEeCCCHHHHHHHHHH
Confidence            8899999999998875432210    24689999888877776653 4555554321          01112   34556


Q ss_pred             HHHHHhc-CCeEEEEEeCCCC
Q 045120          205 LYERLKN-ENKILVILANIWK  224 (374)
Q Consensus       205 l~~~L~~-~kr~LlVlDdv~~  224 (374)
                      +...+.. .+--+||+|.+..
T Consensus       194 l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          194 LQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHHHHHHCTTEEEEEETTTTH
T ss_pred             HHHHHHhccCCCEEEEeCcHH
Confidence            6666654 4678999998853

>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=95.35  E-value=0.062  Score=52.05  Aligned_cols=39  Identities=21%  Similarity=0.363  Sum_probs=29.1

Q ss_pred             cccccccHHHHHHHHHHh---hcC------------------CCCccHHHHHHHHHHHhh
Q 045120          121 YEAFESRVSNLKSTQNAL---TNA------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L---~~~------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      ...++|.+..++++.+.+   ...                  +.|+||||||+.+.+...
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~   74 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEAN   74 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            456889988777665543   221                  889999999999998553

>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=95.28  E-value=0.042  Score=56.59  Aligned_cols=153  Identities=12%  Similarity=0.200  Sum_probs=79.6

Q ss_pred             ccccccccHHHHHHHHHHhh----cC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC
Q 045120          120 VYEAFESRVSNLKSTQNALT----NA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD  177 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~----~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~  177 (374)
                      ....+.|.+..+++|.+.+.    .+                  ++|+|||+||+++++...  .+   .+.|+.+    
T Consensus       202 ~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg--~~---~~~v~~~----  272 (806)
T 3cf2_A          202 GYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG--AF---FFLINGP----  272 (806)
T ss_dssp             CGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTT--CE---EEEEEHH----
T ss_pred             ChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC--Ce---EEEEEhH----
Confidence            34557888888877776643    22                  889999999999998543  11   2333321    


Q ss_pred             HHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--------c-----cccccC---cCCCC---
Q 045120          178 IKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--------D-----LETVKI---PFRND---  238 (374)
Q Consensus       178 ~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--------~-----~~~l~~---~~~~~---  238 (374)
                        ++    .    ......+ +.....+.+..+....++|+||++....        .     ...|..   .+...   
T Consensus       273 --~l----~----sk~~ges-e~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V  341 (806)
T 3cf2_A          273 --EI----M----SKLAGES-ESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  341 (806)
T ss_dssp             --HH----H----SSCTTHH-HHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCE
T ss_pred             --Hh----h----cccchHH-HHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCE
Confidence              11    1    1111222 2233344444443378999999986321        0     011110   01110   


Q ss_pred             -----CcchhHhhhhc----CCCCceecCCCCHHHHHHHHHHhcCCCC--CCcchHHHHHHHHHHccCCc
Q 045120          239 -----SRDNNVVLLSM----GSKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKACGAGL  297 (374)
Q Consensus       239 -----TR~~~va~~~~----~~~~~~~l~~L~~~~s~~Lf~~~a~~~~--~~~~l~~~~~~I~~~c~~Gl  297 (374)
                           |.+........    --...+.++..+.++-.++|..+.....  ...++    ..|++++ .|+
T Consensus       342 ~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl----~~lA~~T-~Gf  406 (806)
T 3cf2_A          342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDL----EQVANET-HGH  406 (806)
T ss_dssp             EEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCH----HHHHHHC-CSC
T ss_pred             EEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCH----HHHHHhc-CCC
Confidence                 22211110000    1123678888888888999988775322  12223    3566777 555

>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=95.27  E-value=0.074  Score=48.63  Aligned_cols=81  Identities=17%  Similarity=0.219  Sum_probs=51.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcC---------CC-----CeEEEEEeCCCCCHHHHHHHHHHHhCcCCc----------hhh
Q 045120          142 NGGIGKTTLAKEFAKQAREDK---------LF-----DRVVFSEVSQTSDIKKIQGDIAEKLGLELS----------EEA  197 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~---------~F-----~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~----------~~~  197 (374)
                      ..|+||||||.++..+.....         ..     ..++|++....++...+.+ +++.++....          ..+
T Consensus       106 ~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~~l~~~~~~~  184 (322)
T 2i1q_A          106 VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLDNTFVARAYN  184 (322)
T ss_dssp             STTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHHTEEEEECSS
T ss_pred             CCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhcCEEEEeCCC
Confidence            889999999999887532211         11     4688999888887776664 3455554321          011


Q ss_pred             H---HHHHHHHHHHHhc-CCeEEEEEeCCC
Q 045120          198 E---YRRASRLYERLKN-ENKILVILANIW  223 (374)
Q Consensus       198 ~---~~~~~~l~~~L~~-~kr~LlVlDdv~  223 (374)
                      .   .+....+.+.+.. .+--+||+|.+.
T Consensus       185 ~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          185 SDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             HHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             HHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence            1   2344556666654 456799999875

>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=95.23  E-value=0.079  Score=49.29  Aligned_cols=77  Identities=21%  Similarity=0.240  Sum_probs=50.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc------hhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS------EEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.++.......+  ..++|++....++..     .++.++....      ..+.++....+...++..+.-
T Consensus        69 ppGsGKSTLal~la~~~~~~g--g~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~~~~d  141 (356)
T 3hr8_A           69 QESSGKTTLALHAIAEAQKMG--GVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVDELVRSGVVD  141 (356)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTSCCS
T ss_pred             CCCCCHHHHHHHHHHHHHhcC--CeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHHHHhhhcCCC
Confidence            889999999999988654322  347888877777654     4555654422      123445555555555544567


Q ss_pred             EEEEeCCCCc
Q 045120          216 LVILANIWKL  225 (374)
Q Consensus       216 LlVlDdv~~~  225 (374)
                      ++|+|.+...
T Consensus       142 lvVIDSi~~l  151 (356)
T 3hr8_A          142 LIVVDSVAAL  151 (356)
T ss_dssp             EEEEECTTTC
T ss_pred             eEEehHhhhh
Confidence            9999998644

>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=95.12  E-value=0.1  Score=47.70  Aligned_cols=113  Identities=17%  Similarity=0.193  Sum_probs=59.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+||||||+.+++..... .+ ..++++.      ..+...+...+...        ....+.+.+.  +..+|+|||
T Consensus        45 ~~GtGKT~la~~i~~~~~~~-~~-~~~~i~~------~~~~~~~~~~~~~~--------~~~~~~~~~~--~~~vL~iDE  106 (324)
T 1l8q_A           45 SVGTGKTHLLQAAGNEAKKR-GY-RVIYSSA------DDFAQAMVEHLKKG--------TINEFRNMYK--SVDLLLLDD  106 (324)
T ss_dssp             SSSSSHHHHHHHHHHHHHHT-TC-CEEEEEH------HHHHHHHHHHHHHT--------CHHHHHHHHH--TCSEEEEEC
T ss_pred             CCCCcHHHHHHHHHHHHHHC-CC-EEEEEEH------HHHHHHHHHHHHcC--------cHHHHHHHhc--CCCEEEEcC
Confidence            88999999999999865432 12 2345542      33333333333211        0112222332  367899999


Q ss_pred             CCCccc----cccccCc----CCCC-------Cc--------chhHhhhhcCCCCceecCCCCHHHHHHHHHHhcC
Q 045120          222 IWKLLD----LETVKIP----FRND-------SR--------DNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNG  274 (374)
Q Consensus       222 v~~~~~----~~~l~~~----~~~~-------TR--------~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~  274 (374)
                      +.....    .+.+...    ...+       ++        ...+. ........+.+++ +.++..+++...+.
T Consensus       107 i~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~-sR~~~~~~i~l~~-~~~e~~~il~~~~~  180 (324)
T 1l8q_A          107 VQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLV-SRFEGGILVEIEL-DNKTRFKIIKEKLK  180 (324)
T ss_dssp             GGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHH-HHHHTSEEEECCC-CHHHHHHHHHHHHH
T ss_pred             cccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhh-hcccCceEEEeCC-CHHHHHHHHHHHHH
Confidence            864321    1111111    1111       11        11221 1233334689999 99999999988764

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=95.11  E-value=0.079  Score=49.53  Aligned_cols=76  Identities=18%  Similarity=0.187  Sum_probs=49.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc------hhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS------EEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      .+|+||||||.++.......+  ..++|++....++..     .++.++....      ..+.++....+...++..+--
T Consensus        82 ~pGsGKTtlal~la~~~~~~g--~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~~~~~~  154 (366)
T 1xp8_A           82 PESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMELLVRSGAID  154 (366)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             CCCCChHHHHHHHHHHHHHCC--CeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHHHHHhcCCCC
Confidence            889999999999877654322  368999988777654     2455554321      123445555555555543566


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      +||+|.+..
T Consensus       155 lVVIDsl~~  163 (366)
T 1xp8_A          155 VVVVDSVAA  163 (366)
T ss_dssp             EEEEECTTT
T ss_pred             EEEEeChHH
Confidence            999999863

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.01  E-value=0.014  Score=46.88  Aligned_cols=36  Identities=17%  Similarity=0.200  Sum_probs=28.3

Q ss_pred             cccccHHHHHHHHHHhhc----C-------CCCccHHHHHHHHHHHh
Q 045120          123 AFESRVSNLKSTQNALTN----A-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~----~-------~gGiGKTtLA~~v~~~~  158 (374)
                      .++|++..+.++.+.+..    +       ..|+|||+||+.+++..
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhC
Confidence            478999999988887742    1       88999999999998853

>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=94.94  E-value=0.11  Score=45.54  Aligned_cols=40  Identities=25%  Similarity=0.401  Sum_probs=27.9

Q ss_pred             ccccccccHHHHHHHHHHhh---c------------------CCCCccHHHHHHHHHHHhh
Q 045120          120 VYEAFESRVSNLKSTQNALT---N------------------ANGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~---~------------------~~gGiGKTtLA~~v~~~~~  159 (374)
                      ....++|.+..+.++.+...   .                  +..|+||||||+.+.+...
T Consensus        14 ~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~   74 (254)
T 1ixz_A           14 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   74 (254)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            34568888876665544322   1                  0889999999999998653

>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=94.87  E-value=0.069  Score=45.46  Aligned_cols=77  Identities=23%  Similarity=0.247  Sum_probs=45.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcC-----------C-ch-hhHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLE-----------L-SE-EAEYRRASRLYER  208 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~-----------~-~~-~~~~~~~~~l~~~  208 (374)
                      .+|+||||||..+.. ..    -..++|++....++...+.. +.+.++..           . .. .........++..
T Consensus        28 ~~GsGKTtl~~~l~~-~~----~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  101 (220)
T 2cvh_A           28 PYASGKTTLALQTGL-LS----GKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQRRVIGSLKKT  101 (220)
T ss_dssp             STTSSHHHHHHHHHH-HH----CSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH-Hc----CCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHHHHHHHHHHH
Confidence            889999999999987 21    24678888776556555443 33333221           0 01 1112334444444


Q ss_pred             HhcCCeEEEEEeCCCCc
Q 045120          209 LKNENKILVILANIWKL  225 (374)
Q Consensus       209 L~~~kr~LlVlDdv~~~  225 (374)
                      +.. +.-+||+|.+...
T Consensus       102 ~~~-~~~lliiD~~~~~  117 (220)
T 2cvh_A          102 VDS-NFALVVVDSITAH  117 (220)
T ss_dssp             CCT-TEEEEEEECCCCC
T ss_pred             hhc-CCCEEEEcCcHHH
Confidence            444 5789999987643

>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=94.86  E-value=0.1  Score=48.64  Aligned_cols=75  Identities=16%  Similarity=0.224  Sum_probs=46.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      .+|+||||||.++.......+  ..++|++....++..     .+..++.....      .+.++....+....+..+--
T Consensus        71 ~pGsGKTtLal~la~~~~~~g--~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~~~~~~  143 (356)
T 1u94_A           71 PESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  143 (356)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHHHHHhccCCC
Confidence            889999999999887654332  368899988777643     24555543211      12334444444444333566


Q ss_pred             EEEEeCCC
Q 045120          216 LVILANIW  223 (374)
Q Consensus       216 LlVlDdv~  223 (374)
                      +||+|.+.
T Consensus       144 lVVIDsl~  151 (356)
T 1u94_A          144 VIVVDSVA  151 (356)
T ss_dssp             EEEEECGG
T ss_pred             EEEEcCHH
Confidence            99999875

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=94.85  E-value=0.14  Score=45.71  Aligned_cols=42  Identities=24%  Similarity=0.375  Sum_probs=29.7

Q ss_pred             ccccccccccHHHHHHHHHHhh---c------------------CCCCccHHHHHHHHHHHhh
Q 045120          118 NKVYEAFESRVSNLKSTQNALT---N------------------ANGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       118 ~~~~~~~vGr~~~~~~i~~~L~---~------------------~~gGiGKTtLA~~v~~~~~  159 (374)
                      ......++|.+..+.++.+...   .                  +..|+||||||+.+.+...
T Consensus        36 ~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~   98 (278)
T 1iy2_A           36 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   98 (278)
T ss_dssp             CCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcC
Confidence            3445678898877766654432   1                  0789999999999998653

>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=94.77  E-value=0.11  Score=48.13  Aligned_cols=76  Identities=16%  Similarity=0.193  Sum_probs=48.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      .+|+||||||.++.......+  ..++|++....++..     .++.++.....      .+.++....+.......+.-
T Consensus        69 ~pGsGKTtLal~la~~~~~~g--~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~~~~~~  141 (349)
T 2zr9_A           69 PESSGKTTVALHAVANAQAAG--GIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIADMLVRSGALD  141 (349)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             CCCCCHHHHHHHHHHHHHhCC--CeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            889999999999887654322  357899888776653     25555543221      23344444444444443567


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      +||+|.+..
T Consensus       142 lIVIDsl~~  150 (349)
T 2zr9_A          142 IIVIDSVAA  150 (349)
T ss_dssp             EEEEECGGG
T ss_pred             EEEEcChHh
Confidence            999998753

>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=94.74  E-value=0.19  Score=47.44  Aligned_cols=81  Identities=14%  Similarity=0.213  Sum_probs=48.2

Q ss_pred             CCCccHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc-------------hhhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQARED----KLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS-------------EEAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-------------~~~~~~~~~~  204 (374)
                      ..|+|||||+..+.-.....    ..-..++|++....++...+. .+++.++....             .....+....
T Consensus       186 ~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~-~~a~~~gl~~~~vleni~~~~~~~~~~~~~~l~~  264 (400)
T 3lda_A          186 EFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLV-SIAQRFGLDPDDALNNVAYARAYNADHQLRLLDA  264 (400)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHHH-HHHHHcCCChHhHhhcEEEeccCChHHHHHHHHH
Confidence            88999999999876432211    123468898877766655543 36666654311             0111233344


Q ss_pred             HHHHHhcCCeEEEEEeCCC
Q 045120          205 LYERLKNENKILVILANIW  223 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~  223 (374)
                      +.+.+...+.-+||+|.+.
T Consensus       265 ~~~~l~~~~~~llVIDs~t  283 (400)
T 3lda_A          265 AAQMMSESRFSLIVVDSVM  283 (400)
T ss_dssp             HHHHHHHSCEEEEEEETGG
T ss_pred             HHHHHHhcCCceEEecchh
Confidence            5555554467899999864

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=94.72  E-value=0.052  Score=49.10  Aligned_cols=96  Identities=15%  Similarity=0.204  Sum_probs=49.9

Q ss_pred             cccccHHHHHHHHHHhhc------------C------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTN------------A------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~------------~------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      .++|.+..++.+...+..            .      ..|+||||||+.+.+.....  -...+.++.+....... .. 
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~--~~~~~~~~~~~~~~~~~-~~-   93 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKHA-VS-   93 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC--GGGEEEEEGGGCCSTTH-HH-
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC--CcceEEeeccccccccc-HH-
Confidence            467777777776666542            1      88999999999999865321  12244555443322111 11 


Q ss_pred             HHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc
Q 045120          185 IAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL  225 (374)
Q Consensus       185 i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~  225 (374)
                        ..++......... ....+...+......+|+||++...
T Consensus        94 --~l~g~~~~~~~~~-~~~~~~~~~~~~~~~vl~lDEi~~l  131 (311)
T 4fcw_A           94 --RLIGAPPGYVGYE-EGGQLTEAVRRRPYSVILFDAIEKA  131 (311)
T ss_dssp             --HHHCCCTTSTTTT-TCCHHHHHHHHCSSEEEEEETGGGS
T ss_pred             --HhcCCCCcccccc-ccchHHHHHHhCCCeEEEEeChhhc
Confidence              1122211100000 0012334444324579999998743

>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=94.42  E-value=0.21  Score=45.33  Aligned_cols=125  Identities=14%  Similarity=0.090  Sum_probs=66.5

Q ss_pred             HHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhc--CCCCeEEEEEeCC-CCCHHHHHHHHHHHhCcCCchh
Q 045120          129 SNLKSTQNALTNA---------NGGIGKTTLAKEFAKQARED--KLFDRVVFSEVSQ-TSDIKKIQGDIAEKLGLELSEE  196 (374)
Q Consensus       129 ~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~--~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~~~~  196 (374)
                      +.++.|.+.+..+         +.|+||||+|..+.+.....  .+.|. ..++.+. ...+..+ +++.+.+.....  
T Consensus         4 ~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~-~~l~~~~~~~~id~i-r~li~~~~~~p~--   79 (305)
T 2gno_A            4 DQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDDI-RTIKDFLNYSPE--   79 (305)
T ss_dssp             CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHHH-HHHHHHHTSCCS--
T ss_pred             HHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCE-EEEcCCcCCCCHHHH-HHHHHHHhhccc--
Confidence            3444555555443         88999999999998753211  23333 4555432 3333332 334444422110  


Q ss_pred             hHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccc----cccCcCCCC------CcchhHhhhhcCCCCceecCCCCHHH
Q 045120          197 AEYRRASRLYERLKNENKILVILANIWKLL--DLE----TVKIPFRND------SRDNNVVLLSMGSKDNFLIANITEEE  264 (374)
Q Consensus       197 ~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~----~l~~~~~~~------TR~~~va~~~~~~~~~~~l~~L~~~~  264 (374)
                                    .+++-++|+|++..-.  ..+    .+..|-+..      +....+.. ..... .+++.++++++
T Consensus        80 --------------~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~-tI~SR-~~~f~~l~~~~  143 (305)
T 2gno_A           80 --------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLP-TIKSR-VFRVVVNVPKE  143 (305)
T ss_dssp             --------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCH-HHHTT-SEEEECCCCHH
T ss_pred             --------------cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChH-HHHce-eEeCCCCCHHH
Confidence                          1246788888886431  122    222222222      22222322 22222 89999999999


Q ss_pred             HHHHHHHhc
Q 045120          265 AWRLFKIMN  273 (374)
Q Consensus       265 s~~Lf~~~a  273 (374)
                      ..+.+.+..
T Consensus       144 i~~~L~~~~  152 (305)
T 2gno_A          144 FRDLVKEKI  152 (305)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999988876

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=94.38  E-value=0.039  Score=50.31  Aligned_cols=44  Identities=18%  Similarity=0.258  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHhhc-----C-------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 045120          128 VSNLKSTQNALTN-----A-------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV  172 (374)
Q Consensus       128 ~~~~~~i~~~L~~-----~-------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v  172 (374)
                      ...++.+.+++..     .       ..|+|||+||..+++.......+ .++++++
T Consensus       134 ~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~-~v~~~~~  189 (308)
T 2qgz_A          134 MEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGV-STTLLHF  189 (308)
T ss_dssp             HHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCC-CEEEEEH
T ss_pred             HHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCC-cEEEEEH
Confidence            3344555566653     2       88999999999999865512223 3455554

>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=94.23  E-value=0.11  Score=50.08  Aligned_cols=39  Identities=18%  Similarity=0.198  Sum_probs=29.5

Q ss_pred             cccccccHHHHHHHHH---HhhcC-----------CCCccHHHHHHHHHHHhh
Q 045120          121 YEAFESRVSNLKSTQN---ALTNA-----------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~---~L~~~-----------~gGiGKTtLA~~v~~~~~  159 (374)
                      ...++|.+..++.+..   .+..+           ++|+|||+||+.+.+...
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~   88 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELG   88 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhC
Confidence            4679999988776544   33332           889999999999998654

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.21  E-value=0.26  Score=44.87  Aligned_cols=42  Identities=21%  Similarity=0.233  Sum_probs=29.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      .+|+||||||.++..+...++  ..++|++..  -+...+...++.
T Consensus        76 ~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~  117 (315)
T 3bh0_A           76 RPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIV  117 (315)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHH
Confidence            789999999999887655433  567787655  445555555544

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=94.19  E-value=0.17  Score=38.78  Aligned_cols=71  Identities=17%  Similarity=0.144  Sum_probs=50.6

Q ss_pred             hhHHHh-hhhhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-hhhHHHHHHHHHhh-hhHHHHHHHHHH
Q 045120           18 PPTERQ-LVYLRKRNYNANLENLKAELEKLKVERTSIQLRVSEAKEKG-EEIEEKVEKWLTRY-QLSKKAKTEVKA   90 (374)
Q Consensus        18 ~~~~~~-~~~~~~~~~~~~~~~l~~~l~~L~~~l~~v~~~i~~a~~~~-~~~~~~v~~wl~r~-~~~~~i~~~~~~   90 (374)
                      +.+..+ .+++  ..-...+.+++++++.|++.|..+++++.+|++.. ...+..++.|+... .++.+++++.+.
T Consensus         4 ~~ll~KL~~ll--~~E~~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD~   77 (115)
T 3qfl_A            4 SNLIPKLGELL--TEEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDK   77 (115)
T ss_dssp             CSHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--HHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444 4455  56677888999999999999999999999999874 23468899998222 344455554444

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=93.93  E-value=0.063  Score=48.52  Aligned_cols=18  Identities=17%  Similarity=0.200  Sum_probs=16.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+|||+||+.+++...
T Consensus        44 ppGtGKT~la~aiA~~l~   61 (293)
T 3t15_A           44 GKGQGKSFQCELVFRKMG   61 (293)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            899999999999999663

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=93.91  E-value=0.27  Score=47.31  Aligned_cols=83  Identities=18%  Similarity=0.290  Sum_probs=53.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------------CchhhHH------HH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------------LSEEAEY------RR  201 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------------~~~~~~~------~~  201 (374)
                      ..|+|||+|++.+.++.. +.+-+.++++-++... ...++.+++...=...             ..+++..      ..
T Consensus       161 g~G~GKT~L~~~i~~~~~-~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~~~~rtvvV~~t~d~p~~~r~~~~~~  239 (482)
T 2ck3_D          161 GAGVGKTVLIMELINNVA-KAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALT  239 (482)
T ss_dssp             CTTSSHHHHHHHHHHHTT-TTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHhhH-hhCCCEEEEEECCCcchHHHHHHHHhhhccccccccCCceEEEEEECCCCCHHHHHHHHHH
Confidence            789999999999988643 2345778888888875 4566777776542211             1111111      12


Q ss_pred             HHHHHHHHhc--CCeEEEEEeCCCCc
Q 045120          202 ASRLYERLKN--ENKILVILANIWKL  225 (374)
Q Consensus       202 ~~~l~~~L~~--~kr~LlVlDdv~~~  225 (374)
                      .-.+.++++.  ++..||++||+...
T Consensus       240 a~tiAEyfrd~~G~dVLll~DsitR~  265 (482)
T 2ck3_D          240 GLTVAEYFRDQEGQDVLLFIDNIFRF  265 (482)
T ss_dssp             HHHHHHHHHHTTCSCEEEEEECTHHH
T ss_pred             HHHHHHHHHHhcCCcEEEEeccHHHH
Confidence            3345666654  68999999998643

>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=93.71  E-value=0.22  Score=47.95  Aligned_cols=82  Identities=17%  Similarity=0.282  Sum_probs=47.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCc-------CCchhhHH------HHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGL-------ELSEEAEY------RRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~-------~~~~~~~~------~~~~~l~~  207 (374)
                      ..|+|||||++.+.++..... -+.++++-+++.. ...++..++...-..       ....++..      ...-.+.+
T Consensus       159 ~sGvGKTtL~~~l~~~~~~~~-~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~~~~ltiAE  237 (473)
T 1sky_E          159 GAGVGKTVLIQELIHNIAQEH-GGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVALTGLTMAE  237 (473)
T ss_dssp             CSSSCHHHHHHHHHHHHHHHT-CCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHhhhhhcc-CcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHHHHHHHHHH
Confidence            889999999999988765432 2456777777664 344555544432100       01111111      11124455


Q ss_pred             HHhc--CCeEEEEEeCCCC
Q 045120          208 RLKN--ENKILVILANIWK  224 (374)
Q Consensus       208 ~L~~--~kr~LlVlDdv~~  224 (374)
                      ++..  +++.||++||+..
T Consensus       238 yFrd~~G~~VLl~~D~itR  256 (473)
T 1sky_E          238 YFRDEQGQDGLLFIDNIFR  256 (473)
T ss_dssp             HHHHHSCCEEEEEEECTHH
T ss_pred             HHHHhcCCcEEEEeccHHH
Confidence            5543  5899999999853

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=93.60  E-value=0.27  Score=47.50  Aligned_cols=82  Identities=21%  Similarity=0.304  Sum_probs=54.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCcC--------------CchhhHH------H
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGLE--------------LSEEAEY------R  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~~--------------~~~~~~~------~  200 (374)
                      ..|+|||+|++.+.++... .+-+.++|+-++... ...++.+++...=...              ..+++..      .
T Consensus       173 g~GvGKT~L~~~l~~~~a~-~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtvvV~~t~d~p~~~R~~~~~  251 (498)
T 1fx0_B          173 GAGVGKTVLIMELINNIAK-AHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPGARMRVGL  251 (498)
T ss_dssp             CSSSSHHHHHHHHHHHTTT-TCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEEEEEECTTSCHHHHTTHHH
T ss_pred             CCCCCchHHHHHHHHHHHh-hCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceEEEEeCCCCCHHHHHHHHH
Confidence            7799999999999886432 345788999988876 4566777766532111              1111111      2


Q ss_pred             HHHHHHHHHhc--CCeEEEEEeCCCC
Q 045120          201 RASRLYERLKN--ENKILVILANIWK  224 (374)
Q Consensus       201 ~~~~l~~~L~~--~kr~LlVlDdv~~  224 (374)
                      ..-.+.++++.  ++..||++||+..
T Consensus       252 ~altiAEyfrd~~G~dVLl~~DsitR  277 (498)
T 1fx0_B          252 TALTMAEYFRDVNEQDVLLFIDNIFR  277 (498)
T ss_dssp             HHHHTHHHHTTTSCCEEEEEEECSHH
T ss_pred             HHHHHHHHHHHhcCCcEEEEeccHHH
Confidence            23456677765  6899999999864

>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=93.46  E-value=0.06  Score=47.61  Aligned_cols=39  Identities=23%  Similarity=0.289  Sum_probs=29.5

Q ss_pred             cccccccHHHHHHHHHHhhc----------------C-----CCCccHHHHHHHHHHHhh
Q 045120          121 YEAFESRVSNLKSTQNALTN----------------A-----NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~----------------~-----~gGiGKTtLA~~v~~~~~  159 (374)
                      ...++|.+..++.+.+.+..                +     +.|+|||+||+.+++...
T Consensus        10 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~   69 (268)
T 2r62_A           10 FKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAH   69 (268)
T ss_dssp             STTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHT
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhC
Confidence            45688988877777665541                1     789999999999998653

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=93.13  E-value=0.068  Score=43.05  Aligned_cols=31  Identities=23%  Similarity=0.334  Sum_probs=21.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      ..|+|||||++.+++..... .+ ..+++....
T Consensus        44 ~~G~GKTtL~~~i~~~~~~~-g~-~~~~~~~~~   74 (149)
T 2kjq_A           44 EEGAGKSHLLQAWVAQALEA-GK-NAAYIDAAS   74 (149)
T ss_dssp             SSTTTTCHHHHHHHHHHHTT-TC-CEEEEETTT
T ss_pred             CCCCCHHHHHHHHHHHHHhc-CC-cEEEEcHHH
Confidence            78999999999999866532 12 256665443

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=93.04  E-value=0.065  Score=49.09  Aligned_cols=37  Identities=14%  Similarity=0.121  Sum_probs=31.2

Q ss_pred             ccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|++..++.+...+..+       ..|+|||+||+.+.+..
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~~vll~G~pGtGKT~la~~la~~~   70 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGGHILLEGVPGLAKTLSVNTLAKTM   70 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTCCEEEESCCCHHHHHHHHHHHHHT
T ss_pred             cceeCcHHHHHHHHHHHHcCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            45889999999888887655       88999999999998854

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=93.03  E-value=0.39  Score=40.87  Aligned_cols=39  Identities=21%  Similarity=0.356  Sum_probs=24.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGD  184 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  184 (374)
                      ..|+|||||++.+.......+  ..++|++...  ....+...
T Consensus        31 ~~GsGKTtl~~~l~~~~~~~~--~~v~~~~~~~--~~~~~~~~   69 (235)
T 2w0m_A           31 EPGTGKTIFSLHFIAKGLRDG--DPCIYVTTEE--SRDSIIRQ   69 (235)
T ss_dssp             STTSSHHHHHHHHHHHHHHHT--CCEEEEESSS--CHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CeEEEEEccc--CHHHHHHH
Confidence            789999999999986544222  2456665433  34444433

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=92.76  E-value=0.16  Score=49.41  Aligned_cols=41  Identities=24%  Similarity=0.378  Sum_probs=29.8

Q ss_pred             cccccccccHHHHHHHHHHh---hcC------------------CCCccHHHHHHHHHHHhh
Q 045120          119 KVYEAFESRVSNLKSTQNAL---TNA------------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L---~~~------------------~gGiGKTtLA~~v~~~~~  159 (374)
                      .....++|.+..+.++.+.+   ...                  +.|+||||||+.+.+...
T Consensus        28 ~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~   89 (499)
T 2dhr_A           28 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   89 (499)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             CCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            33556899988777665543   221                  889999999999998653

>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=92.74  E-value=0.093  Score=47.23  Aligned_cols=37  Identities=30%  Similarity=0.425  Sum_probs=30.3

Q ss_pred             ccccccHHHHHHHHHHhhc----------------C-------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTN----------------A-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~----------------~-------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|.+..++.+...+..                +       ..|+|||+||+.+.+..
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l   74 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3588999999888877754                1       88999999999998855

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=92.71  E-value=4.3  Score=38.71  Aligned_cols=42  Identities=14%  Similarity=0.226  Sum_probs=27.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      .+|+||||||..+..+...... ..++|++...  +...+...++
T Consensus       211 ~pG~GKTtl~l~ia~~~~~~~g-~~Vl~~s~E~--s~~~l~~r~~  252 (454)
T 2r6a_A          211 RPSVGKTAFALNIAQNVATKTN-ENVAIFSLEM--SAQQLVMRML  252 (454)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHSS-CCEEEEESSS--CHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHhCC-CcEEEEECCC--CHHHHHHHHH
Confidence            7799999999999887654321 2567776443  3445555443

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=92.63  E-value=0.16  Score=47.68  Aligned_cols=80  Identities=14%  Similarity=0.164  Sum_probs=42.5

Q ss_pred             CCCccHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCCCHHHHHHHHHHHhCc----CCchhhHH------HHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQARED-KLFDRVVFSEVSQTSDIKKIQGDIAEKLGL----ELSEEAEY------RRASRLYERLK  210 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~-~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~----~~~~~~~~------~~~~~l~~~L~  210 (374)
                      ..|+|||||++.+.+..... ..++ ++++-+++..+-..   ++.+.+..    ...+++..      ...-.+.+++.
T Consensus       182 ~sG~GKTtLl~~Iar~i~~~~~~v~-~I~~lIGER~~Ev~---~~~~~~~~~vV~atadep~~~r~~~a~~alt~AEyfr  257 (422)
T 3ice_A          182 PPKAGKTMLLQNIAQSIAYNHPDCV-LMVLLIDERPEEVT---EMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLV  257 (422)
T ss_dssp             CSSSSHHHHHHHHHHHHHHHCTTSE-EEEEEESSCHHHHH---HHHTTCSSEEEEECTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCChhHHHHHHHHHHhhcCCCee-EEEEEecCChHHHH---HHHHHhCeEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            78999999999987754321 1233 34677776643221   22233211    11111111      11122344443


Q ss_pred             -cCCeEEEEEeCCCCc
Q 045120          211 -NENKILVILANIWKL  225 (374)
Q Consensus       211 -~~kr~LlVlDdv~~~  225 (374)
                       .++..||++||+...
T Consensus       258 d~G~dVLil~DslTR~  273 (422)
T 3ice_A          258 EHKKDVIILLDSITRL  273 (422)
T ss_dssp             HTSCEEEEEEECHHHH
T ss_pred             hcCCCEEEEEeCchHH
Confidence             258999999998643

>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=92.31  E-value=1  Score=38.24  Aligned_cols=81  Identities=21%  Similarity=0.273  Sum_probs=44.0

Q ss_pred             CCCccHHHHHHHHHHHhhhc---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc-------------hhhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQARED---K-LFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS-------------EEAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~-------------~~~~~~~~~~  204 (374)
                      ..|+|||||++.+.......   . .-...+|+.-...+.... ...+.+.++....             ..........
T Consensus        33 ~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (231)
T 4a74_A           33 EFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQ  111 (231)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH-HHHHHHHTTSCHHHHHHTEEEEECCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH-HHHHHHHcCCCHHHHhhcEEEEecCChHHHHHHHHH
Confidence            88999999999998743321   1 124577877555444333 2334444432211             1111122344


Q ss_pred             HHHHHh-----cCCeEEEEEeCCC
Q 045120          205 LYERLK-----NENKILVILANIW  223 (374)
Q Consensus       205 l~~~L~-----~~kr~LlVlDdv~  223 (374)
                      +.+.+.     ..+.-+||||...
T Consensus       112 ~~~~~~~~~~~~~~~~llilDe~~  135 (231)
T 4a74_A          112 AEDKIKELLNTDRPVKLLIVDSLT  135 (231)
T ss_dssp             HHHHHHHHTTSSSCEEEEEEETSS
T ss_pred             HHHHHHHhcccCCceeEEEECChH
Confidence            444444     3367799999764

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=92.27  E-value=0.35  Score=46.24  Aligned_cols=81  Identities=25%  Similarity=0.318  Sum_probs=51.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCC----eEEEEEeCCCC-CHHHHHHHHHHHhCc-------CCchhhHH------HHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFD----RVVFSEVSQTS-DIKKIQGDIAEKLGL-------ELSEEAEY------RRAS  203 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~----~~~wv~vs~~~-~~~~~~~~i~~~l~~-------~~~~~~~~------~~~~  203 (374)
                      ..|+|||+|+.++.+....  +-+    .++++-+++.. ...++.+++...=..       ...+++..      ...-
T Consensus       159 g~G~GKt~L~~~Ia~~~~~--~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~~a~~~a~  236 (465)
T 3vr4_D          159 GSGLPHKELAAQIARQATV--LDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPRMAL  236 (465)
T ss_dssp             CTTSCHHHHHHHHHHHCBC--SSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHHHHHHHHH
T ss_pred             CCCcChHHHHHHHHHHHHh--ccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHHHHHHHHH
Confidence            6799999999999986653  223    67788888765 455666665443111       11112211      1234


Q ss_pred             HHHHHHhc--CCeEEEEEeCCCC
Q 045120          204 RLYERLKN--ENKILVILANIWK  224 (374)
Q Consensus       204 ~l~~~L~~--~kr~LlVlDdv~~  224 (374)
                      .+.++++.  ++..||++||+..
T Consensus       237 tiAEyfrd~~G~~VLl~~DslTr  259 (465)
T 3vr4_D          237 TAAEYLAYEKGMHVLVIMTDMTN  259 (465)
T ss_dssp             HHHHHHHHTTCCEEEEEEECHHH
T ss_pred             HHHHHHHHhcCCeEEEEEcChHH
Confidence            56777763  6899999999864

>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=92.27  E-value=0.075  Score=46.98  Aligned_cols=37  Identities=11%  Similarity=0.239  Sum_probs=26.7

Q ss_pred             ccccccHHHHHHHHHHhhc----C-------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTN----A-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~----~-------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|.+..+.++.+.+..    +       ..|+|||+||+.+++..
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~   53 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLS   53 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTS
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhc
Confidence            4578999888888776643    1       78999999999998853

>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=92.15  E-value=0.3  Score=50.31  Aligned_cols=84  Identities=14%  Similarity=0.218  Sum_probs=51.1

Q ss_pred             cccccccHHHHHHHHHHhhcC----------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          121 YEAFESRVSNLKSTQNALTNA----------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~----------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ...+.|.++.+++|.+.+.-.                      ++|+|||.||+++.+....       -++.++    .
T Consensus       476 w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~-------~f~~v~----~  544 (806)
T 3cf2_A          476 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQA-------NFISIK----G  544 (806)
T ss_dssp             STTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTC-------EEEECC----H
T ss_pred             HHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCC-------ceEEec----c
Confidence            445778888888877665422                      8899999999999985431       233332    1


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWK  224 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~  224 (374)
                      .++    +.    .+-..+ +.....+++.-+....+.|+||++..
T Consensus       545 ~~l----~s----~~vGes-e~~vr~lF~~Ar~~~P~IifiDEiDs  581 (806)
T 3cf2_A          545 PEL----LT----MWFGES-EANVREIFDKARQAAPCVLFFDELDS  581 (806)
T ss_dssp             HHH----HT----TTCSSC-HHHHHHHHHHHHTTCSEEEECSCGGG
T ss_pred             chh----hc----cccchH-HHHHHHHHHHHHHcCCceeechhhhH
Confidence            221    11    111122 23345555555544689999999863

>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=91.78  E-value=0.16  Score=46.74  Aligned_cols=47  Identities=15%  Similarity=-0.113  Sum_probs=34.0

Q ss_pred             ceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHH
Q 045120          254 NFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLT  302 (374)
Q Consensus       254 ~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~  302 (374)
                      .+.+++.+.++-.+++.+.+..... .--.+.+..|+..+ +|.|-.+.
T Consensus       174 ~~~Ld~~~~~~l~~iL~~~~~~~~~-~~~~~~~~~ia~~~-~G~~R~a~  220 (334)
T 1in4_A          174 ILELDFYTVKELKEIIKRAASLMDV-EIEDAAAEMIAKRS-RGTPRIAI  220 (334)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHTTC-CBCHHHHHHHHHTS-TTCHHHHH
T ss_pred             eeeCCCCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHhc-CCChHHHH
Confidence            4789999999999999987642111 11235677899999 99996553

>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=91.73  E-value=0.67  Score=42.86  Aligned_cols=83  Identities=20%  Similarity=0.266  Sum_probs=47.2

Q ss_pred             CCCccHHHHHHHHHHHhhhc---CCC-CeEEEEEeCCCCCHHHHHHHHHHHhCcCC-------------chhhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQARED---KLF-DRVVFSEVSQTSDIKKIQGDIAEKLGLEL-------------SEEAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~---~~F-~~~~wv~vs~~~~~~~~~~~i~~~l~~~~-------------~~~~~~~~~~~  204 (374)
                      ..|+|||||+.++.......   +.. ..++|++....+....+ ..+++.++...             ......+....
T Consensus       139 ~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~~~~~~~l~~  217 (349)
T 1pzn_A          139 EFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQ  217 (349)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCChHHHHHHHHH
Confidence            88999999999998754211   111 24588887665544433 33444443221             11112234445


Q ss_pred             HHHHHhc-----CCeEEEEEeCCCCc
Q 045120          205 LYERLKN-----ENKILVILANIWKL  225 (374)
Q Consensus       205 l~~~L~~-----~kr~LlVlDdv~~~  225 (374)
                      +...+..     .+.-+||+|.+-..
T Consensus       218 ~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          218 AEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             HHHHHHHhccccCCCCEEEEeCchHh
Confidence            5555543     36789999988543

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=91.37  E-value=0.11  Score=50.65  Aligned_cols=37  Identities=16%  Similarity=0.183  Sum_probs=31.3

Q ss_pred             ccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|++..++.+...+..+       .+|+|||+||+.+.+..
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHHHHHHHHHH
Confidence            34889999999888887765       88999999999998854

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=91.36  E-value=0.29  Score=46.99  Aligned_cols=83  Identities=27%  Similarity=0.310  Sum_probs=51.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC--CeEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhHH------HHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF--DRVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAEY------RRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F--~~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l  205 (374)
                      ..|+|||+|+..+.++....+.=  +.++++-++... ...++.+++...=...       ..+++..      ...-.+
T Consensus       160 g~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~r~~~~~~a~ti  239 (469)
T 2c61_A          160 ASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTA  239 (469)
T ss_dssp             CTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHHHHHHHHHHHHH
Confidence            77999999999999876542211  367788888765 4556666665431111       1111111      123356


Q ss_pred             HHHHh--cCCeEEEEEeCCCC
Q 045120          206 YERLK--NENKILVILANIWK  224 (374)
Q Consensus       206 ~~~L~--~~kr~LlVlDdv~~  224 (374)
                      .++++  .++..||++||+..
T Consensus       240 AEyfrdd~G~dVLl~~DsltR  260 (469)
T 2c61_A          240 AEYLAYEHGMHVLVILTDITN  260 (469)
T ss_dssp             HHHHHHHHCCEEEEEEECHHH
T ss_pred             HHHHHHhcCCeEEEEEeCHHH
Confidence            66666  36999999999854

>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=91.15  E-value=4.7  Score=41.93  Aligned_cols=37  Identities=24%  Similarity=0.406  Sum_probs=29.3

Q ss_pred             ccccccHHHHHHHHHHhhc-------------C-----CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTN-------------A-----NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~-------------~-----~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|.+..++.+...+..             .     ..|+|||+||+.+.+..
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~  612 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL  612 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3578999988888776642             1     77999999999998864

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=91.04  E-value=1  Score=42.97  Aligned_cols=43  Identities=16%  Similarity=0.090  Sum_probs=28.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      .+|+||||||..+..+...... ..++|++..  -+...+...++.
T Consensus       208 ~pg~GKT~lal~ia~~~a~~~g-~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          208 RPAMGKTAFALTIAQNAALKEG-VGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             CTTSCHHHHHHHHHHHHHHTTC-CCEEEEESS--SCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHhCC-CeEEEEECC--CCHHHHHHHHHH
Confidence            8899999999998887653321 246776654  445566666554

>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=90.64  E-value=0.15  Score=46.88  Aligned_cols=39  Identities=15%  Similarity=0.173  Sum_probs=28.4

Q ss_pred             ccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~  158 (374)
                      ....++|.+..+..+...+...         ..|+|||+||+.+.+..
T Consensus        22 ~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~   69 (350)
T 1g8p_A           22 PFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALL   69 (350)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             CchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhC
Confidence            3456899988666654444321         78999999999999854

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=90.43  E-value=0.13  Score=48.15  Aligned_cols=92  Identities=14%  Similarity=0.121  Sum_probs=46.9

Q ss_pred             HHHHHhhcC----------CCCccHHHHHHHHHHHhhhc-CCCCeEEEEEeCCCCCH-HHHHHHHHHHhCcCCchhhHH-
Q 045120          133 STQNALTNA----------NGGIGKTTLAKEFAKQARED-KLFDRVVFSEVSQTSDI-KKIQGDIAEKLGLELSEEAEY-  199 (374)
Q Consensus       133 ~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~-~~F~~~~wv~vs~~~~~-~~~~~~i~~~l~~~~~~~~~~-  199 (374)
                      ++++.|..-          ..|+|||+|++.+.+..... ..+. ++++-+++..+- .++.+.+...+-....+++.. 
T Consensus       164 raID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~-~V~~lIGER~~EV~d~~~~~~G~VV~atadep~~~  242 (427)
T 3l0o_A          164 RLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTI-RIILLIDERPEEVTDIRESTNAIVIAAPFDMPPDK  242 (427)
T ss_dssp             HHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSE-EEEEECSCCHHHHSSSSSSCCSEEEECCTTSCHHH
T ss_pred             hhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhhcCCCeE-EEEEEeccCcchHHHHHHHhCCeEEEECCCCCHHH
Confidence            566666542          78999999999998865422 1232 356766655321 111111100010111111111 


Q ss_pred             -----HHHHHHHHHHh-cCCeEEEEEeCCCCc
Q 045120          200 -----RRASRLYERLK-NENKILVILANIWKL  225 (374)
Q Consensus       200 -----~~~~~l~~~L~-~~kr~LlVlDdv~~~  225 (374)
                           ...-.+.+++. .++..||++||+...
T Consensus       243 r~~~a~~altiAEyfrd~G~dVLil~DslTR~  274 (427)
T 3l0o_A          243 QVKVAELTLEMAKRLVEFNYDVVILLDSLTRL  274 (427)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCEEEecccchHH
Confidence                 11223444444 258999999998643

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=90.40  E-value=0.9  Score=39.02  Aligned_cols=31  Identities=16%  Similarity=0.331  Sum_probs=21.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      ..|+||||||.++.......+  ..++|++...
T Consensus        31 ~~GsGKTtl~~~~~~~~~~~~--~~v~~~~~e~   61 (247)
T 2dr3_A           31 GPGTGKTIFSQQFLWNGLKMG--EPGIYVALEE   61 (247)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTT--CCEEEEESSS
T ss_pred             CCCCCHHHHHHHHHHHHHhcC--CeEEEEEccC
Confidence            889999999988866543221  3567776543

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=90.37  E-value=1.1  Score=43.48  Aligned_cols=84  Identities=15%  Similarity=0.272  Sum_probs=49.2

Q ss_pred             CCCccHHHHH-HHHHHHhhh----cCCCC-eEEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH------HH
Q 045120          142 NGGIGKTTLA-KEFAKQARE----DKLFD-RVVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY------RR  201 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~----~~~F~-~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~------~~  201 (374)
                      ..|+|||+|| ..+.|....    .++-+ .++++-+++..+ ..++.+.+...=...       ..+++..      ..
T Consensus       170 ~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~a~~~  249 (510)
T 2ck3_A          170 DRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYS  249 (510)
T ss_dssp             STTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceEEEECCCCCHHHHHHHHHH
Confidence            7799999995 567765542    12345 478888887754 556666655422111       1111111      11


Q ss_pred             HHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          202 ASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       202 ~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .-.+.++++. ++..||++||+...
T Consensus       250 a~tiAEyfrd~G~dVLli~Dsltr~  274 (510)
T 2ck3_A          250 GCSMGEYFRDNGKHALIIYDDLSKQ  274 (510)
T ss_dssp             HHHHHHHHHTTTCEEEEEEETHHHH
T ss_pred             HHHHHHHHHHcCCcEEEEEcCHHHH
Confidence            2345555553 58999999998643

>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=90.32  E-value=0.82  Score=41.20  Aligned_cols=76  Identities=17%  Similarity=0.075  Sum_probs=37.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCcCCch-hhHHHHHHHHHHHHhcCCeEEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-TSDIKKIQGDIAEKLGLELSE-EAEYRRASRLYERLKNENKILVIL  219 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~~kr~LlVl  219 (374)
                      .+|+||||++..+.......... .+..+.... .....+.+....+..+.+... .+...+...+. .+ . +.=++|+
T Consensus       113 ~~GsGKTTl~~~LA~~l~~~~G~-~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~~~~~l~~al~-~~-~-~~dlvIi  188 (296)
T 2px0_A          113 STGAGKTTTLAKLAAISMLEKHK-KIAFITTDTYRIAAVEQLKTYAELLQAPLEVCYTKEEFQQAKE-LF-S-EYDHVFV  188 (296)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTCC-CEEEEECCCSSTTHHHHHHHHHTTTTCCCCBCSSHHHHHHHHH-HG-G-GSSEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCC-EEEEEecCcccchHHHHHHHHHHhcCCCeEecCCHHHHHHHHH-Hh-c-CCCEEEE
Confidence            78999999999988765532222 344444322 223333344444444433211 12222322233 23 3 3457888


Q ss_pred             eC
Q 045120          220 AN  221 (374)
Q Consensus       220 Dd  221 (374)
                      |-
T Consensus       189 DT  190 (296)
T 2px0_A          189 DT  190 (296)
T ss_dssp             EC
T ss_pred             eC
Confidence            83

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=90.25  E-value=0.17  Score=45.95  Aligned_cols=36  Identities=14%  Similarity=0.249  Sum_probs=29.5

Q ss_pred             cccccHHHHHHHHHHhhc----C-------CCCccHHHHHHHHHHHh
Q 045120          123 AFESRVSNLKSTQNALTN----A-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~----~-------~gGiGKTtLA~~v~~~~  158 (374)
                      .++|++..+.++.+.+..    +       ..|+|||++|+.+.+..
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~   49 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS   49 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHS
T ss_pred             CcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhC
Confidence            478999888888887753    1       78999999999998853

>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=90.11  E-value=0.23  Score=46.04  Aligned_cols=36  Identities=25%  Similarity=0.182  Sum_probs=28.7

Q ss_pred             cccccHHHHHHHHHHhh-----------------cC-------CCCccHHHHHHHHHHHh
Q 045120          123 AFESRVSNLKSTQNALT-----------------NA-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~-----------------~~-------~gGiGKTtLA~~v~~~~  158 (374)
                      .++|.+..++.+...+.                 ..       +.|+|||++|+.+.+..
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~   75 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL   75 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            36888888888877772                 11       88999999999999855

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=90.09  E-value=0.48  Score=53.46  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=50.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc------hhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS------EEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      +.|+|||+||.++.......+  ..++|+++...++...     ++.++.+..      ..+.++....+++..+..+.-
T Consensus      1435 ppGtGKT~LA~ala~ea~~~G--~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~~~~~ 1507 (2050)
T 3cmu_A         1435 PESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD 1507 (2050)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHHHHHHcC--CcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHHHHHhcCCCC
Confidence            899999999999987554222  3578888888877665     455553211      122344555566565555778


Q ss_pred             EEEEeCCC
Q 045120          216 LVILANIW  223 (374)
Q Consensus       216 LlVlDdv~  223 (374)
                      +||+|.+.
T Consensus      1508 lVVIDsi~ 1515 (2050)
T 3cmu_A         1508 VIVVDSVA 1515 (2050)
T ss_dssp             EEEESCGG
T ss_pred             EEEEcChh
Confidence            99999984

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=90.03  E-value=0.19  Score=51.67  Aligned_cols=51  Identities=20%  Similarity=0.241  Sum_probs=35.7

Q ss_pred             ccccccHHHHHHHHHHhhcC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          122 EAFESRVSNLKSTQNALTNA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      ..++|.+..++.+.+.+...                  +.|+|||+||+.+.+...  ..-...+.++++.
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~--~~~~~~i~i~~s~  559 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIF--GDEESMIRIDMSE  559 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHH--SCTTCEEEEEGGG
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc--CCCcceEEEechh
Confidence            45889999888887776521                  789999999999998652  1122345555543

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=89.92  E-value=0.28  Score=41.33  Aligned_cols=33  Identities=21%  Similarity=0.220  Sum_probs=23.5

Q ss_pred             cHHHHHHHHHHhhcC------------CCCccHHHHHHHHHHHhh
Q 045120          127 RVSNLKSTQNALTNA------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       127 r~~~~~~i~~~L~~~------------~gGiGKTtLA~~v~~~~~  159 (374)
                      |++.+++|.+.+...            ..|+|||||++.+.....
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~   47 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            455566666665531            889999999999987543

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=89.53  E-value=0.71  Score=44.12  Aligned_cols=83  Identities=23%  Similarity=0.292  Sum_probs=50.3

Q ss_pred             CCCccHHHHHHHHHHHhhhc--------CCCC-eEEEEEeCCCC-CHHHHHHHHHHHhCcC-------CchhhH------
Q 045120          142 NGGIGKTTLAKEFAKQARED--------KLFD-RVVFSEVSQTS-DIKKIQGDIAEKLGLE-------LSEEAE------  198 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~--------~~F~-~~~wv~vs~~~-~~~~~~~~i~~~l~~~-------~~~~~~------  198 (374)
                      ..|+|||+|+.++.+.....        ++=+ .++++-+++.. ...++.+++...=...       ..+++.      
T Consensus       155 g~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~rtvvv~~t~d~p~~~r~~~  234 (464)
T 3gqb_B          155 GSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDPTIERILT  234 (464)
T ss_dssp             ETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGGEEEEEEETTSCTHHHHHH
T ss_pred             CCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccceEEEEECCCCCHHHHHHH
Confidence            67999999999998876531        1222 56788888765 3455555544321010       111111      


Q ss_pred             HHHHHHHHHHHhc--CCeEEEEEeCCCC
Q 045120          199 YRRASRLYERLKN--ENKILVILANIWK  224 (374)
Q Consensus       199 ~~~~~~l~~~L~~--~kr~LlVlDdv~~  224 (374)
                      ....-.+.++++.  ++..||++||+..
T Consensus       235 ~~~a~tiAEyfrd~~G~~VLl~~DdlTr  262 (464)
T 3gqb_B          235 PRMALTVAEYLAFEHDYHVLVILTDMTN  262 (464)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEcChHH
Confidence            1123456777763  6899999999864

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=89.48  E-value=1.6  Score=40.10  Aligned_cols=43  Identities=16%  Similarity=0.183  Sum_probs=29.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .+|+||||||..+..+....+  ..++|++.  .-+...+...++..
T Consensus        54 ~pG~GKTt~al~ia~~~a~~g--~~Vl~fSl--Ems~~ql~~Rlls~   96 (338)
T 4a1f_A           54 RPSMGKTSLMMNMVLSALNDD--RGVAVFSL--EMSAEQLALRALSD   96 (338)
T ss_dssp             CTTSCHHHHHHHHHHHHHHTT--CEEEEEES--SSCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHcC--CeEEEEeC--CCCHHHHHHHHHHH
Confidence            789999999999988765422  35666654  44556666666544

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=89.45  E-value=0.85  Score=39.25  Aligned_cols=41  Identities=24%  Similarity=0.415  Sum_probs=24.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDI  185 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i  185 (374)
                      .+|+||||||.++..+..... -..++|++..  .+...+.+.+
T Consensus        38 ~pG~GKT~l~l~~~~~~~~~~-~~~v~~~s~E--~~~~~~~~~~   78 (251)
T 2zts_A           38 GTGTGKTTFAAQFIYKGAEEY-GEPGVFVTLE--ERARDLRREM   78 (251)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS--SCHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHhc-CCCceeeccc--CCHHHHHHHH
Confidence            789999999988765432221 2345666544  3444444443

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=88.99  E-value=1  Score=43.54  Aligned_cols=80  Identities=18%  Similarity=0.225  Sum_probs=48.2

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCe-EEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHHH------HHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDR-VVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEYR------RASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~~------~~~~l  205 (374)
                      ..|+|||+|| ..+.|..    +-+. ++++-+++..+ ..++.+.+...=...       ..+++...      ..-.+
T Consensus       170 ~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~a~~~a~ti  245 (502)
T 2qe7_A          170 DRQTGKTTIAIDTIINQK----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLYLAPYAGCAM  245 (502)
T ss_dssp             CSSSCHHHHHHHHHHGGG----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCchHHHHHHHHHhh----cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHHHHHHHHHHH
Confidence            7799999996 5777744    2564 57888888753 556666665422111       11111111      12345


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .++++. ++..||++||+...
T Consensus       246 AEyfrd~G~dVLl~~Dsltr~  266 (502)
T 2qe7_A          246 GEYFMYKGKHALVVYDDLSKQ  266 (502)
T ss_dssp             HHHHHTTTCEEEEEEECHHHH
T ss_pred             HHHHHHcCCcEEEEEecHHHH
Confidence            555653 58999999998643

>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=88.87  E-value=0.47  Score=48.73  Aligned_cols=37  Identities=16%  Similarity=0.253  Sum_probs=29.3

Q ss_pred             ccccccHHHHHHHHHHhhc-------------C-----CCCccHHHHHHHHHHHh
Q 045120          122 EAFESRVSNLKSTQNALTN-------------A-----NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~-------------~-----~gGiGKTtLA~~v~~~~  158 (374)
                      ..++|.+..++.+...+..             .     ..|+|||+||+.+.+..
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l  512 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            3588999988887776642             1     78999999999998855

>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=88.76  E-value=0.93  Score=50.46  Aligned_cols=76  Identities=16%  Similarity=0.212  Sum_probs=49.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCC------chhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLEL------SEEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~------~~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.++.......+  ..++|++.....+..     .++.++...      ...+.++....+++.....+--
T Consensus       740 ~PG~GKTtLal~lA~~aa~~g--~~VlyiS~Ees~~ql-----~A~~lGvd~~~L~i~~~~~leei~~~l~~lv~~~~~~  812 (1706)
T 3cmw_A          740 PESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  812 (1706)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEECTTSCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCcHHHHHHHHHHHHHcC--CCeEEEeccchHHHH-----HHHHcCCChhheEEecCCcHHHHHHHHHHHHHccCCC
Confidence            789999999999988665332  357888777766543     255665432      1224455555665555444667


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      +||+|.+..
T Consensus       813 lVVIDsLq~  821 (1706)
T 3cmw_A          813 VIVVDSVAA  821 (1706)
T ss_dssp             EEEESCSTT
T ss_pred             EEEEechhh
Confidence            999999864

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=88.76  E-value=1.5  Score=36.80  Aligned_cols=77  Identities=13%  Similarity=0.108  Sum_probs=39.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      .-|+||||+++.+.+.....+ ++ +++..-.......+....++..-......      .+..+....+...|..+  .
T Consensus         8 ~DGsGKsTq~~~L~~~L~~~g-~~-v~~treP~~t~~~~~ir~~l~~~~~~~~~~~ll~~a~r~~~~~~I~~~L~~g--~   83 (197)
T 3hjn_A            8 IDGSGKSTQIQLLAQYLEKRG-KK-VILKREPGGTETGEKIRKILLEEEVTPKAELFLFLASRNLLVTEIKQYLSEG--Y   83 (197)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT-CC-EEEEESSCSSHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHHHTTT--C
T ss_pred             CCCCCHHHHHHHHHHHHHHCC-Cc-EEEEECCCCCcHHHHHHHHhhcccCChHHHHHHHHHHHHHHHHHHHHHHHCC--C
Confidence            459999999999998766433 23 33333232223344444444322111100      01222334566666653  4


Q ss_pred             EEEEeCC
Q 045120          216 LVILANI  222 (374)
Q Consensus       216 LlVlDdv  222 (374)
                      .+|.|--
T Consensus        84 ~Vi~DRy   90 (197)
T 3hjn_A           84 AVLLDRY   90 (197)
T ss_dssp             EEEEESC
T ss_pred             eEEeccc
Confidence            5677754

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=88.49  E-value=1.1  Score=43.98  Aligned_cols=78  Identities=17%  Similarity=0.253  Sum_probs=47.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHH----HhCcC----------CchhhHHH------
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAE----KLGLE----------LSEEAEYR------  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~----~l~~~----------~~~~~~~~------  200 (374)
                      ..|+|||+|+.++.+...    -+.++++-++... ...++++++-+    .++..          ..+++...      
T Consensus       240 g~g~GKT~L~~~ia~~~~----~~v~V~~~iGER~~Ev~e~~~~~~el~d~~~G~~~m~rtvvV~~tsd~p~~~R~~~~~  315 (600)
T 3vr4_A          240 PFGAGKTVVQHQIAKWSD----VDLVVYVGCGERGNEMTDVVNEFPELIDPNTGESLMERTVLIANTSNMPVAAREASIY  315 (600)
T ss_dssp             CTTSCHHHHHHHHHHHSS----CSEEEEEEEEECHHHHHHHHHHTTTCBCTTTCSBGGGGEEEEEEETTSCHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHhccC----CCEEEEEEecccHHHHHHHHHHHHhhcccccccccccceEEEEECCCCCHHHHHHHHH
Confidence            679999999999988533    4678898888774 34455544322    11211          11111111      


Q ss_pred             HHHHHHHHHhc-CCeEEEEEeCCC
Q 045120          201 RASRLYERLKN-ENKILVILANIW  223 (374)
Q Consensus       201 ~~~~l~~~L~~-~kr~LlVlDdv~  223 (374)
                      ..-.+.++++. ++..||++|++.
T Consensus       316 ~altiAEyfrd~G~dVLl~~Ds~t  339 (600)
T 3vr4_A          316 TGITIAEYFRDMGYDVAIMADSTS  339 (600)
T ss_dssp             HHHHHHHHHHTTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHcCCCEEEEecchH
Confidence            12345556653 589999999986

>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=88.32  E-value=0.22  Score=40.77  Aligned_cols=17  Identities=12%  Similarity=0.245  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        11 ~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A           11 GSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CTTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            88999999999998754

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=88.32  E-value=1.5  Score=41.86  Aligned_cols=31  Identities=26%  Similarity=0.357  Sum_probs=22.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      .+|+||||||.++..+...++  ..++|++...
T Consensus       205 ~pG~GKTtlal~ia~~~a~~g--~~vl~fSlEm  235 (444)
T 3bgw_A          205 RPSMGKTAFALKQAKNMSDND--DVVNLHSLEM  235 (444)
T ss_dssp             CSSSSHHHHHHHHHHHHHHTT--CEEEEECSSS
T ss_pred             CCCCChHHHHHHHHHHHHHcC--CEEEEEECCC
Confidence            889999999999988765442  2567775543

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=88.19  E-value=1.4  Score=43.13  Aligned_cols=80  Identities=14%  Similarity=0.214  Sum_probs=48.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHH----HhCc----------CCchhhHHH------
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD-IKKIQGDIAE----KLGL----------ELSEEAEYR------  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~----~l~~----------~~~~~~~~~------  200 (374)
                      ..|+|||+|++.+.+..    +-+.++++-+++..+ ..++.+++-+    ..+.          ...+++...      
T Consensus       235 ~~g~GKT~L~~~ia~~~----~~~~~V~~~iGER~~Ev~e~~~~~~el~d~~~g~~~m~rtvvV~~tsd~p~~~r~~~~~  310 (588)
T 3mfy_A          235 PAGSGKTVTQHQLAKWS----DAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIY  310 (588)
T ss_dssp             CCSHHHHHHHHHHHHHS----SCSEEEEEECCSSSSHHHHHHHHTTTCEETTTTEEGGGGEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHHHHhcccccccccccceEEEEECCCCCHHHHHHHHH
Confidence            66899999999987743    246788999998765 4455555422    1110          011111111      


Q ss_pred             HHHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          201 RASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       201 ~~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      ..-.+.+++++ ++..||++||+...
T Consensus       311 ~a~tiAEyfrd~G~dVLl~~DsltR~  336 (588)
T 3mfy_A          311 TGITIAEYFRDMGYDVALMADSTSRW  336 (588)
T ss_dssp             HHHHHHHHHHHTTCEEEEEEECTTTC
T ss_pred             HHHHHHHHHHHcCCCEEEeecchHHH
Confidence            12244555543 58999999999743

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=88.14  E-value=1.1  Score=43.40  Aligned_cols=80  Identities=16%  Similarity=0.214  Sum_probs=47.9

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCe-EEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH------HHHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDR-VVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY------RRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l  205 (374)
                      ..|+|||+|| ..+.|..    .-+. ++++-+++..+ ..++.+.+...=...       ..+++..      ...-.+
T Consensus       183 ~~g~GKT~Lal~~I~~~~----~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~~~a~ti  258 (515)
T 2r9v_A          183 DRQTGKTAIAIDTIINQK----GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIAPYAGCAM  258 (515)
T ss_dssp             ETTSSHHHHHHHHHHTTT----TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHHHHHHHHH
Confidence            7799999996 5777743    2564 57888887753 556666665421111       1111111      122345


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .++++. ++..||++||+...
T Consensus       259 AEyfrd~G~dVLli~DslTr~  279 (515)
T 2r9v_A          259 GEYFAYSGRDALVVYDDLSKH  279 (515)
T ss_dssp             HHHHHTTTCEEEEEEETHHHH
T ss_pred             HHHHHHcCCcEEEEeccHHHH
Confidence            556653 58999999998643

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=87.83  E-value=0.58  Score=39.67  Aligned_cols=36  Identities=19%  Similarity=0.270  Sum_probs=25.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKK  180 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  180 (374)
                      -||+||||+|..+..-....+   .++-|+.....+...
T Consensus         9 KGGvGKTT~a~~LA~~la~~g---~VlliD~D~q~~~~~   44 (209)
T 3cwq_A            9 KGGVGKTTTAVHLSAYLALQG---ETLLIDGDPNRSATG   44 (209)
T ss_dssp             STTSSHHHHHHHHHHHHHTTS---CEEEEEECTTCHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHhcC---CEEEEECCCCCCHHH
Confidence            699999999999887655332   566776665544433

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=87.69  E-value=2.1  Score=41.34  Aligned_cols=80  Identities=19%  Similarity=0.278  Sum_probs=46.7

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCCe-EEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH------HHHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFDR-VVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY------RRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~------~~~~~l  205 (374)
                      ..|+|||+|| ..+.|.    .+-+. ++++-+++..+ ..++.+++...=...       ..+++..      ...-.+
T Consensus       170 ~~g~GKT~l~l~~I~n~----~~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~~a~~~a~ti  245 (513)
T 3oaa_A          170 DRQTGKTALAIDAIINQ----RDSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQYLAPYAGCAM  245 (513)
T ss_dssp             SSSSSHHHHHHHHHHTT----SSSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCcchHHHHHHHhh----ccCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHHHHHHHHHHH
Confidence            5599999996 567663    23443 67888888754 556666654431111       1111111      112244


Q ss_pred             HHHHhc-CCeEEEEEeCCCCc
Q 045120          206 YERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .+++++ ++..||++||+...
T Consensus       246 AEyfrd~G~dVLli~Dsltr~  266 (513)
T 3oaa_A          246 GEYFRDRGEDALIIYDDLSKQ  266 (513)
T ss_dssp             HHHHHHTTCEEEEEEETHHHH
T ss_pred             HHHHHhcCCCEEEEecChHHH
Confidence            555543 58999999998643

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=87.56  E-value=0.41  Score=47.82  Aligned_cols=40  Identities=18%  Similarity=0.281  Sum_probs=33.2

Q ss_pred             cccccccccHHHHHHHHHHhhcC-------CCCccHHHHHHHHHHHh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA-------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~-------~gGiGKTtLA~~v~~~~  158 (374)
                      .....++|.+..++.+...+..+       ..|+||||||+.+.+..
T Consensus        38 ~~l~~i~G~~~~l~~l~~~i~~g~~vll~Gp~GtGKTtlar~ia~~l   84 (604)
T 3k1j_A           38 KLIDQVIGQEHAVEVIKTAANQKRHVLLIGEPGTGKSMLGQAMAELL   84 (604)
T ss_dssp             SHHHHCCSCHHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHTS
T ss_pred             cccceEECchhhHhhccccccCCCEEEEEeCCCCCHHHHHHHHhccC
Confidence            34456899999998888888766       88999999999998844

>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=87.41  E-value=2  Score=40.82  Aligned_cols=78  Identities=22%  Similarity=0.241  Sum_probs=39.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHH--HHHHHHHhCcCC----chhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKI--QGDIAEKLGLEL----SEEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~--~~~i~~~l~~~~----~~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      .+|+||||++..+.......+  ..+..+. ...+.....  +.......+.+.    ...++.+......+.++...-=
T Consensus       106 ~~GsGKTT~~~~LA~~l~~~g--~~Vllvd-~D~~r~aa~~qL~~~~~~~gv~v~~~~~~~~p~~i~~~~l~~~~~~~~D  182 (425)
T 2ffh_A          106 LQGSGKTTTAAKLALYYKGKG--RRPLLVA-ADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARD  182 (425)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTT--CCEEEEE-CCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCCCHHHHHHHHHHHHHHcC--CeEEEee-ccccCchhHHHHHHhcccCCccEEecCCCCCHHHHHHHHHHHHHHCCCC
Confidence            899999999999887665332  1234443 344444332  344455555431    1123333333344444321223


Q ss_pred             EEEEeCC
Q 045120          216 LVILANI  222 (374)
Q Consensus       216 LlVlDdv  222 (374)
                      ++|+|-.
T Consensus       183 vVIIDTa  189 (425)
T 2ffh_A          183 LILVDTA  189 (425)
T ss_dssp             EEEEECC
T ss_pred             EEEEcCC
Confidence            6777754

>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=87.36  E-value=0.16  Score=43.85  Aligned_cols=77  Identities=10%  Similarity=0.053  Sum_probs=40.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch---hhHHHHHHHHHHHHhcCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE---EAEYRRASRLYERLKNENKILVI  218 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~---~~~~~~~~~l~~~L~~~kr~LlV  218 (374)
                      ..|+||||++..+.++....+ . .++.+.-....  . ....|++.++.....   .+..+....+.+.+..++.-+||
T Consensus        20 ~mGsGKTT~ll~~~~r~~~~g-~-kVli~~~~~d~--r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvVi   94 (223)
T 2b8t_A           20 PMFAGKTAELIRRLHRLEYAD-V-KYLVFKPKIDT--R-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIG   94 (223)
T ss_dssp             STTSCHHHHHHHHHHHHHHTT-C-CEEEEEECCCG--G-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEE
T ss_pred             CCCCcHHHHHHHHHHHHHhcC-C-EEEEEEeccCc--h-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEEE
Confidence            669999999988887665332 2 33444322221  1 222445555544322   12233344444444332345999


Q ss_pred             EeCCC
Q 045120          219 LANIW  223 (374)
Q Consensus       219 lDdv~  223 (374)
                      +|.+.
T Consensus        95 IDEaQ   99 (223)
T 2b8t_A           95 IDEVQ   99 (223)
T ss_dssp             ECSGG
T ss_pred             EecCc
Confidence            99885

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=87.32  E-value=2.7  Score=39.99  Aligned_cols=20  Identities=40%  Similarity=0.425  Sum_probs=16.4

Q ss_pred             CCCccHHHHHHHHHHHhhhc
Q 045120          142 NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~  161 (374)
                      .||+||||++..+......+
T Consensus       108 ~~GvGKTT~a~~LA~~l~~~  127 (433)
T 2xxa_A          108 LQGAGKTTSVGKLGKFLREK  127 (433)
T ss_dssp             STTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHh
Confidence            79999999998888766543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=87.23  E-value=1.3  Score=49.95  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=50.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCc------hhhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELS------EEAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~~kr~  215 (374)
                      .+|+||||||.++..+....+  ..++|++....++...     ++.++....      ..+.++....+....+..+.-
T Consensus       391 ~pGsGKTtLaLqia~~~a~~G--~~vlyis~E~s~~~~~-----a~~lGvd~~~L~I~~~~~~e~il~~~~~lv~~~~~~  463 (2050)
T 3cmu_A          391 PESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  463 (2050)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHHHHHhcC--CeEEEEEcCCCHHHHH-----HHHcCCCHHHeEEeCCCCHHHHHHHHHHHHHhcCCc
Confidence            889999999999988665332  3688998887776542     556665321      224455555555555444567


Q ss_pred             EEEEeCCC
Q 045120          216 LVILANIW  223 (374)
Q Consensus       216 LlVlDdv~  223 (374)
                      +||+|-+.
T Consensus       464 lIVIDSL~  471 (2050)
T 3cmu_A          464 VIVVDSVA  471 (2050)
T ss_dssp             EEEESCGG
T ss_pred             EEEECCHH
Confidence            99999875

>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=87.12  E-value=1.6  Score=39.30  Aligned_cols=79  Identities=19%  Similarity=0.204  Sum_probs=41.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcCC----chhhHHHHHHHHHHHHhcCCeEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLEL----SEEAEYRRASRLYERLKNENKIL  216 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~~----~~~~~~~~~~~l~~~L~~~kr~L  216 (374)
                      .+|+||||++..+.......+  ..+.++..... +.....+.......+.+.    ...+..+......+.++.+.-=+
T Consensus       106 ~~G~GKTT~~~~la~~~~~~g--~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~~~~~~~~D~  183 (297)
T 1j8m_F          106 VQGTGKTTTAGKLAYFYKKKG--FKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEKFLSEKMEI  183 (297)
T ss_dssp             SSCSSTTHHHHHHHHHHHHTT--CCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHHHHHTTCSE
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHHHHHhCCCCE
Confidence            799999999999887654332  23445543322 222333444455554432    11233444444444554213337


Q ss_pred             EEEeCC
Q 045120          217 VILANI  222 (374)
Q Consensus       217 lVlDdv  222 (374)
                      +|+|-.
T Consensus       184 ViIDTp  189 (297)
T 1j8m_F          184 IIVDTA  189 (297)
T ss_dssp             EEEECC
T ss_pred             EEEeCC
Confidence            888864

>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=87.08  E-value=0.28  Score=39.72  Aligned_cols=17  Identities=24%  Similarity=0.196  Sum_probs=14.9

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus         9 ~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            9 PDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             SSSSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>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=86.98  E-value=0.5  Score=43.95  Aligned_cols=17  Identities=41%  Similarity=0.550  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||+||+.+.+..
T Consensus        80 p~GtGKT~la~~la~~l   96 (376)
T 1um8_A           80 PTGSGKTLMAQTLAKHL   96 (376)
T ss_dssp             CTTSSHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            88999999999999854

>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=86.75  E-value=0.26  Score=39.86  Aligned_cols=13  Identities=38%  Similarity=0.488  Sum_probs=12.5

Q ss_pred             CCCccHHHHHHHH
Q 045120          142 NGGIGKTTLAKEF  154 (374)
Q Consensus       142 ~gGiGKTtLA~~v  154 (374)
                      +.|+||||+|+.+
T Consensus         9 ~~GsGKsT~a~~L   21 (179)
T 3lw7_A            9 MPGSGKSEFAKLL   21 (179)
T ss_dssp             CTTSCHHHHHHHH
T ss_pred             CCCCCHHHHHHHH
Confidence            7899999999999

>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=86.61  E-value=3  Score=40.43  Aligned_cols=43  Identities=14%  Similarity=0.186  Sum_probs=28.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  187 (374)
                      .+|+||||||.++..+...... ..++|++...  +..++...++.
T Consensus       250 ~pG~GKT~lal~~a~~~a~~~g-~~vl~~s~E~--s~~~l~~r~~~  292 (503)
T 1q57_A          250 GSGMVMSTFVRQQALQWGTAMG-KKVGLAMLEE--SVEETAEDLIG  292 (503)
T ss_dssp             SSCHHHHHHHHHHHHHHTTTSC-CCEEEEESSS--CHHHHHHHHHH
T ss_pred             cCCCCchHHHHHHHHHHHHhcC-CcEEEEeccC--CHHHHHHHHHH
Confidence            8899999999998876653311 2567776543  45566665543

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=86.35  E-value=0.31  Score=39.73  Aligned_cols=15  Identities=47%  Similarity=0.645  Sum_probs=14.0

Q ss_pred             CCCccHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAK  156 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~  156 (374)
                      +.|+||||+|+.+..
T Consensus        10 ~~GsGKST~a~~L~~   24 (181)
T 1ly1_A           10 CPGSGKSTWAREFIA   24 (181)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHh
Confidence            789999999999987

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=85.73  E-value=0.72  Score=39.73  Aligned_cols=36  Identities=31%  Similarity=0.422  Sum_probs=24.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      -||+||||+|..+.......+  ..++-|+.....++.
T Consensus         8 kGGvGKTt~a~~LA~~la~~g--~~VlliD~D~~~~l~   43 (254)
T 3kjh_A            8 KGGVGKTTVAAGLIKIMASDY--DKIYAVDGDPDSCLG   43 (254)
T ss_dssp             SSSHHHHHHHHHHHHHHTTTC--SCEEEEEECTTSCHH
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCcChH
Confidence            599999999999887665332  345666655444433

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=85.70  E-value=0.43  Score=41.20  Aligned_cols=31  Identities=19%  Similarity=0.146  Sum_probs=21.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      .||+||||+|..+......++ ++. +++.+..
T Consensus        14 kgGvGKTt~a~~la~~l~~~G-~~V-~v~d~D~   44 (228)
T 2r8r_A           14 APGVGKTYAMLQAAHAQLRQG-VRV-MAGVVET   44 (228)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT-CCE-EEEECCC
T ss_pred             CCCCcHHHHHHHHHHHHHHCC-CCE-EEEEeCC
Confidence            899999999988887665333 443 4444443

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=85.57  E-value=0.66  Score=41.58  Aligned_cols=16  Identities=31%  Similarity=0.476  Sum_probs=14.6

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      +.|+||||||+.+...
T Consensus        41 ~sGsGKSTla~~L~~~   56 (287)
T 1gvn_B           41 QPGSGKTSLRSAIFEE   56 (287)
T ss_dssp             CTTSCTHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            8899999999999874

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=85.21  E-value=0.4  Score=39.46  Aligned_cols=17  Identities=35%  Similarity=0.468  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        13 ~~GsGKst~a~~La~~l   29 (185)
T 3trf_A           13 LMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=85.12  E-value=0.41  Score=40.14  Aligned_cols=17  Identities=53%  Similarity=0.702  Sum_probs=15.3

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        33 ~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           33 YMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            89999999999998754

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=85.10  E-value=0.39  Score=38.96  Aligned_cols=17  Identities=35%  Similarity=0.595  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.+....
T Consensus        12 ~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A           12 PMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CTTSCHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998753

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=85.10  E-value=0.42  Score=39.38  Aligned_cols=18  Identities=22%  Similarity=0.335  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.....
T Consensus         9 ~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            9 IPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            789999999999988654

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=84.87  E-value=0.59  Score=39.46  Aligned_cols=18  Identities=33%  Similarity=0.455  Sum_probs=15.6

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+|||||++.+..-..
T Consensus        30 ~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           30 APGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CTTSCTHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            789999999999987654

>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=84.85  E-value=0.44  Score=39.24  Aligned_cols=18  Identities=28%  Similarity=0.316  Sum_probs=15.6

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.....
T Consensus        11 ~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A           11 VPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            789999999999988543

>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=84.65  E-value=0.37  Score=39.83  Aligned_cols=16  Identities=38%  Similarity=0.588  Sum_probs=14.4

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      +.|+|||||++.+...
T Consensus        17 ~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A           17 HPGSGKSTIAEALANL   32 (191)
T ss_dssp             CTTSCHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHhc
Confidence            8899999999999863

>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=84.36  E-value=0.52  Score=39.39  Aligned_cols=35  Identities=20%  Similarity=0.298  Sum_probs=23.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      -||+||||+|..+.......+  ..++.|+.....+.
T Consensus        10 kgG~GKTt~a~~la~~la~~g--~~vlliD~D~~~~~   44 (206)
T 4dzz_A           10 KGGSGKTTAVINIATALSRSG--YNIAVVDTDPQMSL   44 (206)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEECCTTCHH
T ss_pred             CCCccHHHHHHHHHHHHHHCC--CeEEEEECCCCCCH
Confidence            699999999998877655332  24566666544443

>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=84.32  E-value=4.2  Score=36.70  Aligned_cols=77  Identities=22%  Similarity=0.209  Sum_probs=40.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH--HHHHHHHHhCcCC----chhhHHHH-HHHHHHHHhcCCe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKK--IQGDIAEKLGLEL----SEEAEYRR-ASRLYERLKNENK  214 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~--~~~~i~~~l~~~~----~~~~~~~~-~~~l~~~L~~~kr  214 (374)
                      .+|+||||++..+.......+  ..+.++.. ..+....  -+...++.++.+.    ...+.... ...+...+.. +.
T Consensus       112 ~~GsGKTTl~~~LA~~l~~~g--~kV~lv~~-D~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~al~~a~~~-~~  187 (306)
T 1vma_A          112 VNGTGKTTSCGKLAKMFVDEG--KSVVLAAA-DTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAHALAR-NK  187 (306)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTT--CCEEEEEE-CTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHHHHHHHT-TC
T ss_pred             CCCChHHHHHHHHHHHHHhcC--CEEEEEcc-ccccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHHHHhc-CC
Confidence            789999999999887655332  23444443 3333322  2334455554331    11122221 2345555555 45


Q ss_pred             EEEEEeCC
Q 045120          215 ILVILANI  222 (374)
Q Consensus       215 ~LlVlDdv  222 (374)
                      -++|+|-.
T Consensus       188 dvvIiDtp  195 (306)
T 1vma_A          188 DVVIIDTA  195 (306)
T ss_dssp             SEEEEEEC
T ss_pred             CEEEEECC
Confidence            58888854

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=84.31  E-value=0.48  Score=38.70  Aligned_cols=17  Identities=47%  Similarity=0.558  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        12 ~~GsGKsTla~~La~~l   28 (175)
T 1via_A           12 FMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            88999999999998754

>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=84.28  E-value=1.8  Score=48.28  Aligned_cols=76  Identities=16%  Similarity=0.181  Sum_probs=55.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      +.|+||||||.++.....  +.=..++|+...+..++.-     ++.+|.....      .+.++.+..+...++.+.--
T Consensus      1439 ~~~sGkttl~~~~~a~~~--~~g~~~~~i~~e~~~~~~~-----~~~~Gv~~~~l~~~~p~~~e~~l~~~~~~~~s~~~~ 1511 (1706)
T 3cmw_A         1439 PESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD 1511 (1706)
T ss_dssp             STTSSHHHHHHHHHHHHH--HTTCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCHHHHHHHHHHHHH--hcCCeEEEEecCCCCCHHH-----HHHcCCCHHHeEEeCCCcHHHHHHHHHHHHHcCCCC
Confidence            889999999999887543  2335689999888888663     7788766432      23455666677777776778


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      +||+|-|..
T Consensus      1512 ~vvvDsv~a 1520 (1706)
T 3cmw_A         1512 VIVVDSVAA 1520 (1706)
T ss_dssp             EEEESCSTT
T ss_pred             EEEEccHHh
Confidence            999998853

>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=84.15  E-value=3.1  Score=39.62  Aligned_cols=18  Identities=33%  Similarity=0.372  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||++..+.....
T Consensus       108 ~~G~GKTTt~~kLA~~l~  125 (443)
T 3dm5_A          108 IQGSGKTTTVAKLARYFQ  125 (443)
T ss_dssp             CTTSSHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHH
Confidence            799999999988877554

>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=84.07  E-value=3.5  Score=39.19  Aligned_cols=19  Identities=37%  Similarity=0.335  Sum_probs=15.6

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      .+|+||||++..+......
T Consensus       105 ~~GsGKTTt~~kLA~~l~~  123 (433)
T 3kl4_A          105 VQGSGKTTTAGKLAYFYKK  123 (433)
T ss_dssp             CTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            7899999999888776543

>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=83.85  E-value=0.5  Score=38.73  Aligned_cols=17  Identities=53%  Similarity=0.819  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        19 ~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           19 TPGVGKTTLGKELASKS   35 (180)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            89999999999998754

>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=83.84  E-value=0.5  Score=39.04  Aligned_cols=17  Identities=35%  Similarity=0.456  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        13 ~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A           13 HPATGKTTLSQALATGL   29 (193)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            78999999999998754

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=83.80  E-value=0.5  Score=39.62  Aligned_cols=17  Identities=24%  Similarity=0.476  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||||+.+....
T Consensus        26 ~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           26 VSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             STTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            88999999999998754

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=83.78  E-value=0.51  Score=39.33  Aligned_cols=18  Identities=33%  Similarity=0.529  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+++.+.....
T Consensus         8 ~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            8 TVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             CTTSCHHHHHHHHHHHHC
T ss_pred             CCccCHHHHHHHHHHhcC
Confidence            779999999999988543

>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=83.46  E-value=6.2  Score=35.24  Aligned_cols=77  Identities=18%  Similarity=0.133  Sum_probs=39.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHH--HHHHHHHHhCcCCc----hhhHHHHHH-HHHHHHhcCCe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKK--IQGDIAEKLGLELS----EEAEYRRAS-RLYERLKNENK  214 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~--~~~~i~~~l~~~~~----~~~~~~~~~-~l~~~L~~~kr  214 (374)
                      .+|+||||++..+.......+  ..+.++.. .......  -+..+....+...-    ..++.++.. .+...... +.
T Consensus       106 ~~G~GKTT~~~~la~~~~~~~--~~v~l~~~-d~~~~~~~~ql~~~~~~~~l~~~~~~~~~~p~~l~~~~l~~~~~~-~~  181 (295)
T 1ls1_A          106 LQGSGKTTTAAKLALYYKGKG--RRPLLVAA-DTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLE-AR  181 (295)
T ss_dssp             CTTTTHHHHHHHHHHHHHHTT--CCEEEEEC-CSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHHHHHH-TC
T ss_pred             CCCCCHHHHHHHHHHHHHHcC--CeEEEecC-CcccHhHHHHHHHhcccCCeEEEEcCCCCCHHHHHHHHHHHHHhC-CC
Confidence            789999999999987655332  23444443 2223222  23344455544321    123333333 33333334 45


Q ss_pred             EEEEEeCC
Q 045120          215 ILVILANI  222 (374)
Q Consensus       215 ~LlVlDdv  222 (374)
                      =++|+|-.
T Consensus       182 D~viiDtp  189 (295)
T 1ls1_A          182 DLILVDTA  189 (295)
T ss_dssp             CEEEEECC
T ss_pred             CEEEEeCC
Confidence            57888864

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=83.39  E-value=0.95  Score=41.87  Aligned_cols=18  Identities=33%  Similarity=0.547  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+++.+.....
T Consensus        32 ~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A           32 SPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             CTTSSHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhC
Confidence            889999999999887544

>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=82.88  E-value=0.61  Score=40.70  Aligned_cols=18  Identities=44%  Similarity=0.656  Sum_probs=15.6

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .||+|||||+..+.....
T Consensus        22 kgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           22 TAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            799999999999987554

>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=82.69  E-value=0.55  Score=39.35  Aligned_cols=18  Identities=33%  Similarity=0.349  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+|||||++.+.....
T Consensus        33 ~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           33 LSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            889999999999988654

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=82.67  E-value=0.59  Score=40.98  Aligned_cols=17  Identities=29%  Similarity=0.364  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||||+.+....
T Consensus         9 ~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            9 PTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHhcC
Confidence            77999999999998754

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=82.66  E-value=0.57  Score=38.57  Aligned_cols=17  Identities=12%  Similarity=0.430  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.+....
T Consensus        13 psGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A           13 AHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CTTSSHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHhhC
Confidence            78999999999998753

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=82.15  E-value=0.9  Score=39.69  Aligned_cols=17  Identities=35%  Similarity=0.448  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        40 ~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           40 QSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             CGGGTTHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            88999999999998743

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=82.12  E-value=0.67  Score=38.06  Aligned_cols=17  Identities=35%  Similarity=0.436  Sum_probs=14.9

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        12 ~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A           12 PPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998744

>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A 3j0j_A* 1um2_C

Probab=82.08  E-value=1.2  Score=43.65  Aligned_cols=79  Identities=16%  Similarity=0.196  Sum_probs=46.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHH----HhCcC----------CchhhHHH------
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAE----KLGLE----------LSEEAEYR------  200 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~----~l~~~----------~~~~~~~~------  200 (374)
                      ..|+|||+|+..+.+...    -+.++++-++... ...++++++-+    ..+..          ..+++...      
T Consensus       229 ~~g~GKT~l~~~ia~~~~----~~v~V~~~iGER~~Ev~e~~~~~~el~d~~~G~~~~~rtvvv~~tsd~p~~~R~~~~~  304 (578)
T 3gqb_A          229 PFGSGKSVTQQSLAKWSN----ADVVVYVGSGERGNEMTDVLVEFPELTDPKTGGPLMHRTVLIANTSNMPVAAREASIY  304 (578)
T ss_dssp             CTTSCHHHHHHHHHHHSS----CSEEEEEEEEECHHHHHHHHTTGGGCBCTTTSSBSGGGEEEEEEETTSCHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHhccC----CCEEEEEEecccHHHHHHHHHHHHhhcccccccccccceEEEEECCCCCHHHHHHHHH
Confidence            679999999999988542    4678888888774 34444444322    11111          11111111      


Q ss_pred             HHHHHHHHHhc-CCeEEEEEeCCCC
Q 045120          201 RASRLYERLKN-ENKILVILANIWK  224 (374)
Q Consensus       201 ~~~~l~~~L~~-~kr~LlVlDdv~~  224 (374)
                      ..-.+.+++++ ++..||++|++..
T Consensus       305 ~altiAEyfrd~G~dVLl~~Ds~tR  329 (578)
T 3gqb_A          305 VGVTIAEYFRDQGFSVALMADSTSR  329 (578)
T ss_dssp             HHHHHHHHHHHTTCEEEECCSCHHH
T ss_pred             HHHHHHHHHHHcCCCEEEEecChHH
Confidence            12234555542 5899999999863

>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=82.08  E-value=0.61  Score=37.95  Aligned_cols=17  Identities=41%  Similarity=0.538  Sum_probs=14.8

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.+....
T Consensus        16 ~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A           16 VSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             STTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            78999999999998743

>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=81.92  E-value=0.95  Score=43.23  Aligned_cols=38  Identities=29%  Similarity=0.411  Sum_probs=28.3

Q ss_pred             ccccccHHHHHHHHHHhhc------------------C-----CCCccHHHHHHHHHHHhh
Q 045120          122 EAFESRVSNLKSTQNALTN------------------A-----NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~------------------~-----~gGiGKTtLA~~v~~~~~  159 (374)
                      ..++|-+..++.|...+..                  +     +.|+||||+|+.+.....
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~   75 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3478888877777665521                  1     889999999999998553

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=81.82  E-value=0.67  Score=38.96  Aligned_cols=17  Identities=35%  Similarity=0.518  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.+....
T Consensus        20 ~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           20 PSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CTTSCHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHhC
Confidence            88999999999998754

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=81.81  E-value=0.68  Score=38.17  Aligned_cols=19  Identities=37%  Similarity=0.448  Sum_probs=16.4

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      +.|+||||+++.+......
T Consensus        21 ~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           21 LPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            8899999999999886553

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=81.73  E-value=0.73  Score=40.43  Aligned_cols=30  Identities=20%  Similarity=0.340  Sum_probs=20.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      -||+||||+|..+.......+ + .++-|...
T Consensus         9 KGGvGKTT~a~nLA~~la~~G-~-~VlliD~D   38 (269)
T 1cp2_A            9 KGGIGKSTTTQNLTSGLHAMG-K-TIMVVGCD   38 (269)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTT-C-CEEEEEEC
T ss_pred             CCCCcHHHHHHHHHHHHHHCC-C-cEEEEcCC
Confidence            599999999998887655322 2 35555544

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=81.68  E-value=0.69  Score=38.12  Aligned_cols=17  Identities=24%  Similarity=0.321  Sum_probs=14.7

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        11 ~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A           11 GPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998743

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=81.64  E-value=2.9  Score=36.53  Aligned_cols=35  Identities=26%  Similarity=0.477  Sum_probs=24.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      -||+||||+|..+..-.. ++  ..++-|+.....+..
T Consensus        36 kGGvGKTT~a~~LA~~la-~g--~~VlliD~D~~~~~~   70 (267)
T 3k9g_A           36 KGGVGKSTSAIILATLLS-KN--NKVLLIDMDTQASIT   70 (267)
T ss_dssp             SSSSCHHHHHHHHHHHHT-TT--SCEEEEEECTTCHHH
T ss_pred             CCCchHHHHHHHHHHHHH-CC--CCEEEEECCCCCCHH
Confidence            899999999999988666 43  345666665544433

>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=81.62  E-value=0.7  Score=37.36  Aligned_cols=17  Identities=35%  Similarity=0.563  Sum_probs=14.9

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        10 ~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A           10 ARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=81.52  E-value=0.72  Score=37.27  Aligned_cols=17  Identities=35%  Similarity=0.423  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        15 ~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A           15 FMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=81.45  E-value=0.7  Score=38.70  Aligned_cols=18  Identities=22%  Similarity=0.224  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.....
T Consensus        12 ~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A           12 IDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            789999999999988654

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=81.44  E-value=0.67  Score=38.83  Aligned_cols=17  Identities=41%  Similarity=0.552  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.+....
T Consensus        37 ~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           37 VSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            78999999999998754

>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=81.35  E-value=0.67  Score=38.29  Aligned_cols=15  Identities=40%  Similarity=0.665  Sum_probs=13.6

Q ss_pred             CCCccHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAK  156 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~  156 (374)
                      +.|+|||||++.+..
T Consensus        10 ~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A           10 PAGVGKSTTCKRLAA   24 (189)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHhc
Confidence            679999999999975

>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=81.18  E-value=0.72  Score=37.84  Aligned_cols=17  Identities=35%  Similarity=0.522  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        10 ~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A           10 LPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            78999999999998754

>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=80.89  E-value=0.73  Score=38.07  Aligned_cols=18  Identities=39%  Similarity=0.628  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+|||||++.+.....
T Consensus         8 ~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            8 EPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             CTTSSHHHHHHHHHHHHG
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999988654

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=80.80  E-value=3.5  Score=39.88  Aligned_cols=79  Identities=19%  Similarity=0.289  Sum_probs=44.7

Q ss_pred             CCCccHHHHH-HHHHHHhhhcCCCC-eEEEEEeCCCCC-HHHHHHHHHHHhCcC-------Cchh------hHHHHHHHH
Q 045120          142 NGGIGKTTLA-KEFAKQAREDKLFD-RVVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEE------AEYRRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA-~~v~~~~~~~~~F~-~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~------~~~~~~~~l  205 (374)
                      ..|+|||+|| ..+.|...    -+ .++++-+++..+ ..++.+.+...=...       ..++      -.....-.+
T Consensus       171 ~~g~GKT~Lal~~I~~~~~----~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~~~a~ti  246 (507)
T 1fx0_A          171 DRQTGKTAVATDTILNQQG----QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYTGAAL  246 (507)
T ss_dssp             SSSSSHHHHHHHHHHTCCT----TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHHHhhc----CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHHHHHHHHH
Confidence            7799999996 57777432    45 358888887754 444544443321110       1111      011122334


Q ss_pred             HHHHhc-CCeEEEEEeCCCC
Q 045120          206 YERLKN-ENKILVILANIWK  224 (374)
Q Consensus       206 ~~~L~~-~kr~LlVlDdv~~  224 (374)
                      .++++. ++..||++||+..
T Consensus       247 AEyfrd~G~dVLli~Dsltr  266 (507)
T 1fx0_A          247 AEYFMYRERHTLIIYDDLSK  266 (507)
T ss_dssp             HHHHHHTTCEEEEEEECHHH
T ss_pred             HHHHHHcCCcEEEEEecHHH
Confidence            444442 4899999999854

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=80.79  E-value=0.74  Score=37.05  Aligned_cols=17  Identities=18%  Similarity=0.155  Sum_probs=14.9

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus         8 ~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            8 FMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            68999999999998754

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=80.20  E-value=0.85  Score=37.68  Aligned_cols=17  Identities=24%  Similarity=0.354  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        17 ~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A           17 GPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            88999999999998744

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=80.10  E-value=0.79  Score=38.25  Aligned_cols=16  Identities=38%  Similarity=0.646  Sum_probs=14.4

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      +.|+|||||++.+...
T Consensus        15 p~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A           15 PSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CTTSCHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHhh
Confidence            7799999999999874

>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=80.04  E-value=0.77  Score=40.36  Aligned_cols=17  Identities=41%  Similarity=0.600  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        12 ~pGSGKSTla~~La~~L   28 (260)
T 3a4m_A           12 LPGVGKSTFSKNLAKIL   28 (260)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            88999999999998753

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=80.03  E-value=0.84  Score=37.80  Aligned_cols=17  Identities=24%  Similarity=0.368  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        20 ~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           20 GPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            88999999999998754

---

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	374
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-11

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

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]

 Score = 62.5 bits (151), Expect = 1e-11
 Identities = 16/167 (9%), Positives = 49/167 (29%), Gaps = 15/167 (8%)

Query: 143 GGIGKTTLAKEFAKQARE--DKLFDRVVFSEVSQTSDIKKIQGDIAEKLGL--------- 191
            G GK+ +A +   ++ +     +D +V+ + S T+            L L         
Sbjct: 53  AGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNF 112

Query: 192 -ELSEEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRN---DSRDNNVVLL 247
             +           +   L +    L +  ++ +   +   +         +RD  +   
Sbjct: 113 PSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNA 172

Query: 248 SMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACG 294
           +  + +   + ++  +E +   +          K +       +   
Sbjct: 173 ASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSS 219

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	374
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.87
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.13
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.08
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.05
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.89
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.88
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.85
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.79
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.68
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.64
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.6
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.22
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.15
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.15
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.15
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.95
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.92
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.68
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.62
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.44
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.39
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.19
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.96
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	95.25
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.0
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	94.92
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.48
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	93.66
d1xpua3	289	Transcription termination factor Rho, ATPase domai	93.48
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	93.02
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	92.85
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	92.7
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	92.68
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	92.63
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	92.57
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.56
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	92.3
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	92.13
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.78
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	91.71
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	91.59
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.44
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	91.4
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	91.17
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	91.1
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	91.01
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	90.91
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	90.6
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	90.44
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	90.44
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	90.03
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	89.6
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	89.28
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	89.25
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	89.15
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	89.04
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	88.96
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	88.87
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	88.71
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	88.6
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	88.52
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	88.5
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	87.84
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	87.76
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	87.58
d1ls1a2	207	GTPase domain of the signal sequence recognition p	87.48
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	87.41
d2qy9a2	211	GTPase domain of the signal recognition particle r	87.08
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	87.01
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	87.01
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	86.79
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	86.63
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	86.58
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	86.54
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	86.41
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	86.39
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	86.38
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	86.25
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	86.1
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	85.94
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	85.67
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	85.65
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	85.38
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	85.34
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	85.27
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	84.98
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	84.82
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	84.73
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	84.73
d1okkd2	207	GTPase domain of the signal recognition particle r	84.54
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	84.22
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	83.92
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	83.51
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	83.34
d1vmaa2	213	GTPase domain of the signal recognition particle r	82.98
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	82.96
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	81.6
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	81.27
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	80.42

>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=100.00  E-value=2.9e-38  Score=287.84  Aligned_cols=221  Identities=9%  Similarity=0.029  Sum_probs=169.5

Q ss_pred             cccccccHHHHHHHHHHhhcC------------CCCccHHHHHHHHHHHhh--hcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          121 YEAFESRVSNLKSTQNALTNA------------NGGIGKTTLAKEFAKQAR--EDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~~------------~gGiGKTtLA~~v~~~~~--~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      ...++||+.++++|+++|...            |||+||||||+++|++..  ...+|++++||++++.++...+...+.
T Consensus        19 ~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~   98 (277)
T d2a5yb3          19 QMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTD   98 (277)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHH
T ss_pred             CCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHH
Confidence            345789999999999999641            999999999999999754  667899999999999998777766654


Q ss_pred             HHh---CcCCc--------hhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccccccccCcCCCC---CcchhHhhhhcCCC
Q 045120          187 EKL---GLELS--------EEAEYRRASRLYERLKNENKILVILANIWKLLDLETVKIPFRND---SRDNNVVLLSMGSK  252 (374)
Q Consensus       187 ~~l---~~~~~--------~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~~~~l~~~~~~~---TR~~~va~~~~~~~  252 (374)
                      ..+   +....        ..........+.+.|.+ +|+|+||||||+..+|+.+...-...   ||+..++.......
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~-kr~LlVLDDv~~~~~~~~~~~~~srilvTTR~~~v~~~~~~~~  177 (277)
T d2a5yb3          99 ILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDR-PNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTC  177 (277)
T ss_dssp             HHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTS-TTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGCCSCE
T ss_pred             HHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhcc-CCeeEecchhhHHhhhhhhcccCceEEEEeehHHHHHhcCCCC
Confidence            443   22111        11233344567778887 89999999999998887664321111   99999975333344


Q ss_pred             CceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHHHHHhc--CCCcccccccc----cccCCCCcc
Q 045120          253 DNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTLTTNAS--KSSSIYSHVSN----DYQSIYKPK  326 (374)
Q Consensus       253 ~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai~~ig~--~~~~~~~W~~~----~~~~~~~~~  326 (374)
                      +.|+|++|+.++||+||+++++.....+...+++++|+++| ||+||||+++|+  +.++.+.|.+.    ...+..++.
T Consensus       178 ~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c-~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~~~~~~~v~  256 (277)
T d2a5yb3         178 EFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELS-SGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVGVE  256 (277)
T ss_dssp             EEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHH-TTCHHHHHHHHTTCCSSSHHHHHHHHHHHHHHCSSTTC
T ss_pred             ceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHh-CCCHHHHHHHHHHhccCCHHHHHHHHHHHhcCcHHHHH
Confidence            68999999999999999999986666677789999999999 999999999999  77788888442    223344444


Q ss_pred             cchhh-cccCCchhhhhhh
Q 045120          327 PYLAV-FQDLEPTIVKTAF  344 (374)
Q Consensus       327 ~~~~l-y~~Lp~~~lk~cf  344 (374)
                      +.+.+ |++||++ +|+||
T Consensus       257 ~il~~sY~~L~~~-lk~c~  274 (277)
T d2a5yb3         257 CITPYSYKSLAMA-LQRCV  274 (277)
T ss_dssp             CCSSSSSSSHHHH-HHHHH
T ss_pred             HHHHHHHhcccHH-HHHHH
Confidence            46677 9999986 99998

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.87  E-value=7.9e-10  Score=97.63  Aligned_cols=180  Identities=11%  Similarity=0.051  Sum_probs=98.4

Q ss_pred             cccccccccccHHHHHHHHHHhhcC-----CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-----CCCHHHHHHHHH
Q 045120          117 SNKVYEAFESRVSNLKSTQNALTNA-----NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-----TSDIKKIQGDIA  186 (374)
Q Consensus       117 ~~~~~~~~vGr~~~~~~i~~~L~~~-----~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-----~~~~~~~~~~i~  186 (374)
                      |....+.|+||+.++++|.+.....     ++|+|||+|++++.+...  .   ...|+.+..     ......+...+.
T Consensus         7 p~~~~~~f~GR~~el~~l~~~~~~~i~i~G~~G~GKTsLl~~~~~~~~--~---~~~~i~~~~~~~~~~~~~~~~~~~~~   81 (283)
T d2fnaa2           7 PKDNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELN--L---PYIYLDLRKFEERNYISYKDFLLELQ   81 (283)
T ss_dssp             CCCSGGGSCCCHHHHHHHHHTCSSEEEEEESTTSSHHHHHHHHHHHHT--C---CEEEEEGGGGTTCSCCCHHHHHHHHH
T ss_pred             CCCChhhCCChHHHHHHHHhccCCEEEEEcCCCCcHHHHHHHHHHHCC--C---CeEEEEeccccccccccHHHHHHHHH
Confidence            3344678999999999998754332     999999999999987543  2   234554322     123444444444


Q ss_pred             HHhCcC---------------------C--chhhH----HHHHHHHHHHHh-cCCeEEEEEeCCCCccc------ccccc
Q 045120          187 EKLGLE---------------------L--SEEAE----YRRASRLYERLK-NENKILVILANIWKLLD------LETVK  232 (374)
Q Consensus       187 ~~l~~~---------------------~--~~~~~----~~~~~~l~~~L~-~~kr~LlVlDdv~~~~~------~~~l~  232 (374)
                      ......                     .  .....    ......+..... .++++++|+|++.....      +..+.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~l~  161 (283)
T d2fnaa2          82 KEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALA  161 (283)
T ss_dssp             HHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHHHH
T ss_pred             HHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHHHH
Confidence            332210                     0  00000    011222222222 24789999998753211      11110


Q ss_pred             Cc---CCCC------CcchhHhh--hh--------cCCCCceecCCCCHHHHHHHHHHhcCCC-CCCcchHHHHHHHHHH
Q 045120          233 IP---FRND------SRDNNVVL--LS--------MGSKDNFLIANITEEEAWRLFKIMNGDD-VENCKFKSTAINVAKA  292 (374)
Q Consensus       233 ~~---~~~~------TR~~~va~--~~--------~~~~~~~~l~~L~~~~s~~Lf~~~a~~~-~~~~~l~~~~~~I~~~  292 (374)
                      ..   .+..      ++...+..  ..        ......+.|++++.+++.+++.+..... ...++    ..+|.+.
T Consensus       162 ~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~~----~~~i~~~  237 (283)
T d2fnaa2         162 YAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKD----YEVVYEK  237 (283)
T ss_dssp             HHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCC----HHHHHHH
T ss_pred             HHHHhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHHH----HHHHHHH
Confidence            00   0000      22111100  00        0112468899999999999998765321 11222    3589999


Q ss_pred             ccCCchHHHHHHhc
Q 045120          293 CGAGLFCTLTTNAS  306 (374)
Q Consensus       293 c~~GlPLai~~ig~  306 (374)
                      + ||.|..+..+|.
T Consensus       238 ~-~G~P~~L~~~~~  250 (283)
T d2fnaa2         238 I-GGIPGWLTYFGF  250 (283)
T ss_dssp             H-CSCHHHHHHHHH
T ss_pred             h-CCCHHHHHHHHH
Confidence            9 999999998885

>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=98.13  E-value=5.8e-06  Score=70.21  Aligned_cols=166  Identities=14%  Similarity=0.138  Sum_probs=93.9

Q ss_pred             cccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....+++|-+..++.|.+++..+         +.|+||||+|+.+.+.......-..++-++.+...+...+...+....
T Consensus        12 ~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~   91 (224)
T d1sxjb2          12 QVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFA   91 (224)
T ss_dssp             SSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHHHHH
Confidence            34567999999999999999876         889999999999988644221111234444444444433332222221


Q ss_pred             CcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc--ccccc---CcCCCC-------CcchhHhhhhcCCCCceec
Q 045120          190 GLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD--LETVK---IPFRND-------SRDNNVVLLSMGSKDNFLI  257 (374)
Q Consensus       190 ~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~--~~~l~---~~~~~~-------TR~~~va~~~~~~~~~~~l  257 (374)
                      .....              ....+.-++|+|++.....  ...+.   ...+..       +....+..........+++
T Consensus        92 ~~~~~--------------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~  157 (224)
T d1sxjb2          92 QKKLH--------------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRY  157 (224)
T ss_dssp             HBCCC--------------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             Hhhcc--------------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhh
Confidence            11100              0012566888999875421  11111   111111       2222221112223347899


Q ss_pred             CCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHH
Q 045120          258 ANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       258 ~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      ++++.++-...+.+.+......-. .+....|++.| +|-+-.
T Consensus       158 ~~~~~~~i~~~l~~i~~~e~~~i~-~~~l~~I~~~s-~Gd~R~  198 (224)
T d1sxjb2         158 SKLSDEDVLKRLLQIIKLEDVKYT-NDGLEAIIFTA-EGDMRQ  198 (224)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCCBC-HHHHHHHHHHH-TTCHHH
T ss_pred             cccchhhhHHHHHHHHHhcccCCC-HHHHHHHHHHc-CCcHHH
Confidence            999999999999887752111111 34567999999 887653

>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=98.08  E-value=1.1e-05  Score=68.46  Aligned_cols=169  Identities=10%  Similarity=0.120  Sum_probs=91.8

Q ss_pred             cccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ....+++|.+..++.|.+++..+         +.|+||||+|+.+.+..........+.-.+.+...+.......+....
T Consensus        11 ~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~   90 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFA   90 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhcc
Confidence            34567999999999999999875         899999999999998654222112223333333333222211111111


Q ss_pred             CcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc--ccccc---CcCCCC-------CcchhHhhhhcCCCCceec
Q 045120          190 GLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD--LETVK---IPFRND-------SRDNNVVLLSMGSKDNFLI  257 (374)
Q Consensus       190 ~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~--~~~l~---~~~~~~-------TR~~~va~~~~~~~~~~~l  257 (374)
                      ..               ..+..+++-.+|+|++.....  -..+.   ...+..       +....+..........+.+
T Consensus        91 ~~---------------~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~  155 (227)
T d1sxjc2          91 ST---------------RQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRF  155 (227)
T ss_dssp             HB---------------CCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             cc---------------ccccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhcc
Confidence            00               001112455788888865421  11111   111111       1112221111223347899


Q ss_pred             CCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch-HHHHHH
Q 045120          258 ANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF-CTLTTN  304 (374)
Q Consensus       258 ~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP-Lai~~i  304 (374)
                      .+++.++-..++.+.+......-. .+....|++.| +|-. -||..+
T Consensus       156 ~~~~~~~i~~~l~~I~~~e~i~i~-~~~l~~i~~~s-~Gd~R~ain~L  201 (227)
T d1sxjc2         156 QPLPQEAIERRIANVLVHEKLKLS-PNAEKALIELS-NGDMRRVLNVL  201 (227)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCCBC-HHHHHHHHHHH-TTCHHHHHHHT
T ss_pred             ccccccccccccccccccccccCC-HHHHHHHHHHc-CCcHHHHHHHH
Confidence            999999999998887753221111 35567899999 7765 444433

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.05  E-value=1.9e-05  Score=68.37  Aligned_cols=149  Identities=15%  Similarity=0.194  Sum_probs=95.1

Q ss_pred             ccccccHHHHHHHHHHhhc----C-----------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTN----A-----------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIA  186 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~----~-----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  186 (374)
                      ..++|||.++++|.++|..    .           +.|+||||+|+.+++...-...| ..+++..........+...+.
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~   94 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTA-RFVYINGFIYRNFTAIIGEIA   94 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCC-EEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCC-cEEEecchhhhhhhhhhhhhH
Confidence            4589999999999998853    1           89999999999999976532222 346777777788888889988


Q ss_pred             HHhCcCCch--hhHHHHHHHHHHHHhc-CCeEEEEEeCCCCccc-----cccccCc---CCCC-------Ccc-------
Q 045120          187 EKLGLELSE--EAEYRRASRLYERLKN-ENKILVILANIWKLLD-----LETVKIP---FRND-------SRD-------  241 (374)
Q Consensus       187 ~~l~~~~~~--~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~~-----~~~l~~~---~~~~-------TR~-------  241 (374)
                      ..++.....  .........+.+.+.. .....+++|++.+...     ...+...   ....       +..       
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  174 (276)
T d1fnna2          95 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNL  174 (276)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTS
T ss_pred             HhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhc
Confidence            888765433  2344555555555543 3567788888775421     1111110   0000       111       


Q ss_pred             -hhHhhhhcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          242 -NNVVLLSMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       242 -~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                       ..+. ... ....+.+.+.+.++.++++.+.+
T Consensus       175 ~~~~~-~r~-~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         175 DPSTR-GIM-GKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             CHHHH-HHH-TTCEEECCCCBHHHHHHHHHHHH
T ss_pred             chhhh-hhh-cchhccccchhHHHHHHHHHHHH
Confidence             1111 111 22457899999999999998765

>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=97.89  E-value=1.9e-05  Score=67.21  Aligned_cols=179  Identities=13%  Similarity=0.147  Sum_probs=95.3

Q ss_pred             cccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcC-CCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          119 KVYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDK-LFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       119 ~~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~-~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      ....+++|.+..++.+.+++...         +.|+||||||+.+.+...... .......++.+.......+...+-..
T Consensus         9 ~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (237)
T d1sxjd2           9 KNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNF   88 (237)
T ss_dssp             SSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHH
Confidence            33556899999999999998765         899999999999988642111 12233445555554544333333222


Q ss_pred             hCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccc---cCcCCCC-------CcchhHhhhhcCCCCcee
Q 045120          189 LGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETV---KIPFRND-------SRDNNVVLLSMGSKDNFL  256 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l---~~~~~~~-------TR~~~va~~~~~~~~~~~  256 (374)
                      ..........    ..+...... +.-.+|+|++....  ....+   ....+..       +....+..........++
T Consensus        89 ~~~~~~~~~~----~~~~~~~~~-~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~  163 (237)
T d1sxjd2          89 ARLTVSKPSK----HDLENYPCP-PYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFR  163 (237)
T ss_dssp             HHSCCCCCCT----THHHHSCCC-SCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEE
T ss_pred             hhhhhhhhhH----HHHhhcccc-CceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhhc
Confidence            1111110000    011111122 34478999887442  11111   1111111       111111111111124789


Q ss_pred             cCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCC-chHHHHHH
Q 045120          257 IANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAG-LFCTLTTN  304 (374)
Q Consensus       257 l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~G-lPLai~~i  304 (374)
                      +.+++.++..+++.+.+......-. .+..+.|++.+ +| +--||..+
T Consensus       164 f~~~~~~~~~~~L~~i~~~e~i~i~-~~~l~~ia~~s-~gd~R~ai~~L  210 (237)
T d1sxjd2         164 FKALDASNAIDRLRFISEQENVKCD-DGVLERILDIS-AGDLRRGITLL  210 (237)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCCCC-HHHHHHHHHHT-SSCHHHHHHHH
T ss_pred             cccccccccchhhhhhhhhhcCcCC-HHHHHHHHHHc-CCCHHHHHHHH
Confidence            9999999999999887753221111 35567899999 66 45556554

>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=97.88  E-value=6.3e-06  Score=70.27  Aligned_cols=162  Identities=11%  Similarity=0.124  Sum_probs=87.4

Q ss_pred             ccccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhcCCCCe-EEEEEeCCCCCHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAREDKLFDR-VVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      ...+++|-+..+++|.+++..+         +.|+||||+|+.+.+..... .++. .+-++.+...+...+...+....
T Consensus        22 ~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~-~~~~~~~e~n~s~~~~~~~~~~~~~~~~  100 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKEFA  100 (231)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG-GHHHHEEEEETTCHHHHHTTHHHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhc-ccCCCeeEEecCcccchhHHHHHHHHHH
Confidence            3567999999999999999876         88999999999998854321 1211 22233222111111111111000


Q ss_pred             CcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc--cccccccCc---CCCC-------CcchhHhhhhcCCCCceec
Q 045120          190 GLELSEEAEYRRASRLYERLKNENKILVILANIWKL--LDLETVKIP---FRND-------SRDNNVVLLSMGSKDNFLI  257 (374)
Q Consensus       190 ~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~--~~~~~l~~~---~~~~-------TR~~~va~~~~~~~~~~~l  257 (374)
                      .               .......++.++++|++...  .....+...   .+..       ++...+..........+.+
T Consensus       101 ~---------------~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~  165 (231)
T d1iqpa2         101 R---------------TKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRF  165 (231)
T ss_dssp             H---------------SCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEEC
T ss_pred             h---------------hhhccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccc
Confidence            0               00011236778889988643  112222111   1111       2222221111122247899


Q ss_pred             CCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH
Q 045120          258 ANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC  299 (374)
Q Consensus       258 ~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL  299 (374)
                      .+.+.++....+.+.+...... --.+..+.|++.| +|-+-
T Consensus       166 ~~~~~~~~~~~l~~~~~~e~i~-i~~~~l~~I~~~~-~gdiR  205 (231)
T d1iqpa2         166 RPLRDEDIAKRLRYIAENEGLE-LTEEGLQAILYIA-EGDMR  205 (231)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCE-ECHHHHHHHHHHH-TTCHH
T ss_pred             cccchhhHHHHHHHHHHHhCCC-CCHHHHHHHHHHc-CCCHH
Confidence            9999999999998887533221 1135567899999 77543

>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=97.85  E-value=6.5e-05  Score=65.19  Aligned_cols=138  Identities=14%  Similarity=0.223  Sum_probs=82.3

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhc----CCCCeEEEE-EeCCCCCHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQARED----KLFDRVVFS-EVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~----~~F~~~~wv-~vs~~~~~~~~~~~i~~  187 (374)
                      .+++||+++++++++.|...         .+|+|||+|+..+.....-.    ...+..+|. +++.-.           
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~li-----------   86 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLL-----------   86 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC--------------
T ss_pred             CcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHh-----------
Confidence            35889999999999999754         89999999998887753321    112345554 222110           


Q ss_pred             HhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc----------ccccc-ccCcCCCC-------CcchhHhhhhc
Q 045120          188 KLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL----------LDLET-VKIPFRND-------SRDNNVVLLSM  249 (374)
Q Consensus       188 ~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~----------~~~~~-l~~~~~~~-------TR~~~va~~~~  249 (374)
                        ........-++....+.+.+...++.++++|++...          .+... +.+.+..+       |....... ..
T Consensus        87 --ag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey~~-~~  163 (268)
T d1r6bx2          87 --AGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSN-IF  163 (268)
T ss_dssp             --CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHC-CC
T ss_pred             --ccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHHHH-HH
Confidence              011111223444455555555446899999997643          12333 34455555       33333321 11


Q ss_pred             C-------CCCceecCCCCHHHHHHHHHHhc
Q 045120          250 G-------SKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       250 ~-------~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                      .       .-..+.|++.+.+++.+++...+
T Consensus       164 e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         164 EKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             CCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence            1       12378999999999999987654

>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=97.79  E-value=8.3e-05  Score=64.48  Aligned_cols=103  Identities=22%  Similarity=0.248  Sum_probs=70.7

Q ss_pred             cccccccHHHHHHHHHHhhc------------------CCCCccHHHHHHHHHHHhhh----cCCCCeEEEEEeCCCCCH
Q 045120          121 YEAFESRVSNLKSTQNALTN------------------ANGGIGKTTLAKEFAKQARE----DKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~L~~------------------~~gGiGKTtLA~~v~~~~~~----~~~F~~~~wv~vs~~~~~  178 (374)
                      +..+.||+.++++|.+++..                  ++.|+||||+++.+++....    ........++........
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~   94 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNL   94 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccch
Confidence            35688999999999887632                  17899999999999986421    122245677787888888


Q ss_pred             HHHHHHHHHHhCcCCch--hhHHHHHHHHHHHHhc-CCeEEEEEeCCC
Q 045120          179 KKIQGDIAEKLGLELSE--EAEYRRASRLYERLKN-ENKILVILANIW  223 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~--~~~~~~~~~l~~~L~~-~kr~LlVlDdv~  223 (374)
                      ......+...++.....  .........+.+.+.. +...++++|.+.
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          95 YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             hhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEE
Confidence            88888888887654322  2334444455555532 357788888775

>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=97.68  E-value=0.00031  Score=59.81  Aligned_cols=166  Identities=11%  Similarity=0.161  Sum_probs=89.7

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCC-------------------eEEEE
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFD-------------------RVVFS  170 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~-------------------~~~wv  170 (374)
                      ....++|.+..++.+.+++..+          +.|+||||+|+.+.+........+                   ..+.+
T Consensus        10 ~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   89 (239)
T d1njfa_          10 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEI   89 (239)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEE
T ss_pred             CHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEEEe
Confidence            3567999999999999998765          789999999999877543221111                   01222


Q ss_pred             EeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc--ccccccCc---CCCC-------
Q 045120          171 EVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL--DLETVKIP---FRND-------  238 (374)
Q Consensus       171 ~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~--~~~~l~~~---~~~~-------  238 (374)
                      +.+....... .+.+.+.+....                ..+++-++|||++....  ....|...   .+..       
T Consensus        90 ~~~~~~~i~~-ir~~~~~~~~~~----------------~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~t  152 (239)
T d1njfa_          90 DAASRTKVED-TRDLLDNVQYAP----------------ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLAT  152 (239)
T ss_dssp             ETTCSSSHHH-HHHHHHSCCCSC----------------SSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEE
T ss_pred             cchhcCCHHH-HHHHHHHHHhcc----------------ccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEc
Confidence            2221111111 111222211100                01255688999987542  11112111   1222       


Q ss_pred             CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH-HHHHH
Q 045120          239 SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC-TLTTN  304 (374)
Q Consensus       239 TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL-ai~~i  304 (374)
                      ++...+..........+.+.+++.++-.+.+...+...... --.+....|++.+ +|.|- |+..+
T Consensus       153 n~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~-~~~~~l~~i~~~s-~Gd~R~ain~l  217 (239)
T d1njfa_         153 TDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA-HEPRALQLLARAA-EGSLRDALSLT  217 (239)
T ss_dssp             SCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHT-TTCHHHHHHHH
T ss_pred             CCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccC-CCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            22222211112223478999999999988888776411111 1134567899999 88884 55443

>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=97.64  E-value=0.0001  Score=63.03  Aligned_cols=39  Identities=13%  Similarity=0.101  Sum_probs=32.8

Q ss_pred             ccccccccHHHHHHHHHHhhcC----------CCCccHHHHHHHHHHHh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA----------NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~----------~gGiGKTtLA~~v~~~~  158 (374)
                      ...+++|.+...+.|.+++...          ++|+||||+|+.+.+..
T Consensus         9 ~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2           9 SLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            3567999999888888887644          99999999999999864

>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=97.60  E-value=0.00022  Score=58.51  Aligned_cols=91  Identities=18%  Similarity=0.276  Sum_probs=55.1

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQARED----KLFDRVVFSEVSQTSDIKKIQGDIAEK  188 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~~~~~i~~~  188 (374)
                      .+++||+++++++++.|...         .+|+|||+|+..++......    ..-+.++|.-     +...++      
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~l-----d~~~Li------   90 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL-----DMGALV------   90 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE-----CHHHHH------
T ss_pred             CCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEe-----eHHHHh------
Confidence            35889999999999999864         88999999988887754321    1224455532     222222      


Q ss_pred             hCcCCchhhHHHHHHHHHHHH-hcCCeEEEEEeCCCC
Q 045120          189 LGLELSEEAEYRRASRLYERL-KNENKILVILANIWK  224 (374)
Q Consensus       189 l~~~~~~~~~~~~~~~l~~~L-~~~kr~LlVlDdv~~  224 (374)
                       ........-++....+.+.+ ....+.+|++|++..
T Consensus        91 -Ag~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~  126 (195)
T d1jbka_          91 -AGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHT  126 (195)
T ss_dssp             -TTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGG
T ss_pred             -ccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHH
Confidence             11111112333344444444 333589999999853

>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=97.22  E-value=0.0024  Score=54.76  Aligned_cols=160  Identities=13%  Similarity=0.139  Sum_probs=85.7

Q ss_pred             ccccccHHHHHHHHHHhh----cC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          122 EAFESRVSNLKSTQNALT----NA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~----~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      ..+.|.+..+++|.+.+.    ..                  +.|+|||+||+.+.+....  +   .+.++.      .
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~--~---~~~i~~------~   72 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA--F---FFLING------P   72 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTC--E---EEEECH------H
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCC--e---EEEEEc------h
Confidence            458899988888877642    11                  8899999999999985431  1   222221      1


Q ss_pred             HHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCcc---------c----ccccc---Cc--CCCC---
Q 045120          180 KIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLL---------D----LETVK---IP--FRND---  238 (374)
Q Consensus       180 ~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~---------~----~~~l~---~~--~~~~---  238 (374)
                              .+.......+.. ....+.+.-...++++|+|||+....         .    ...+.   ..  ...+   
T Consensus        73 --------~l~~~~~g~~~~-~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlv  143 (258)
T d1e32a2          73 --------EIMSKLAGESES-NLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIV  143 (258)
T ss_dssp             --------HHTTSCTTHHHH-HHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEE
T ss_pred             --------hhcccccccHHH-HHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccE
Confidence                    111112222222 23333333333378999999987431         0    01110   00  1111   


Q ss_pred             ---CcchhHh---hhhc-CCCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchH-HHHHH
Q 045120          239 ---SRDNNVV---LLSM-GSKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFC-TLTTN  304 (374)
Q Consensus       239 ---TR~~~va---~~~~-~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPL-ai~~i  304 (374)
                         |....-.   .... .-.+.+.++..+.++-.++|..+.......+++ + -..|++.+ .|+-- -|..+
T Consensus       144 i~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~-~-~~~la~~t-~G~s~adl~~l  214 (258)
T d1e32a2         144 MAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDV-D-LEQVANET-HGHVGADLAAL  214 (258)
T ss_dssp             EEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTC-C-HHHHHHHC-TTCCHHHHHHH
T ss_pred             EEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCccccccc-c-hhhhhhcc-cCCCHHHHHHH
Confidence               3222211   1111 134589999999999999999887633222221 1 24788888 77533 24444

>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=97.15  E-value=0.0065  Score=50.97  Aligned_cols=48  Identities=10%  Similarity=-0.147  Sum_probs=33.4

Q ss_pred             CCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCchHHH
Q 045120          252 KDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLFCTL  301 (374)
Q Consensus       252 ~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlPLai  301 (374)
                      ...+.+...+.++..++..+.+..... ..-.+....|++.+ +|-+-.+
T Consensus       157 ~~~~~~~~~~~~~~~~i~~~~~~~~~i-~~~~~~l~~ia~~s-~gd~R~a  204 (239)
T d1ixsb2         157 GIVEHLEYYTPEELAQGVMRDARLLGV-RITEEAALEIGRRS-RGTMRVA  204 (239)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHGGGCC-CBCHHHHHHHHHHT-TSSHHHH
T ss_pred             ceeeEeeccChhhhhHHHHHHHHHhCC-ccchHHHHHHHHHc-CCCHHHH
Confidence            346788899999998888877652221 12245677999999 8876554

>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=97.15  E-value=0.00074  Score=61.57  Aligned_cols=139  Identities=12%  Similarity=0.220  Sum_probs=73.5

Q ss_pred             ccccccHHHHHHHHHHhhcC---------CCCccHHHHHHHHHHHhh----hcCCCCeEEEE-EeCCCCCHHHHHHHHHH
Q 045120          122 EAFESRVSNLKSTQNALTNA---------NGGIGKTTLAKEFAKQAR----EDKLFDRVVFS-EVSQTSDIKKIQGDIAE  187 (374)
Q Consensus       122 ~~~vGr~~~~~~i~~~L~~~---------~gGiGKTtLA~~v~~~~~----~~~~F~~~~wv-~vs~~~~~~~~~~~i~~  187 (374)
                      .+++||+.+++++++.|...         .+|+|||+|+..+.....    ...-.+.++|. +++.      ++.    
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~------l~a----   91 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS------LLA----   91 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC---------------
T ss_pred             CCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh------hhc----
Confidence            35889999999999999754         889999998876665422    12223555554 3221      110    


Q ss_pred             HhCcCCchhhHHHHHHHHHHHHhc-CCeEEEEEeCCCCcc---------cccc-ccCcCCCC-------CcchhHhhh--
Q 045120          188 KLGLELSEEAEYRRASRLYERLKN-ENKILVILANIWKLL---------DLET-VKIPFRND-------SRDNNVVLL--  247 (374)
Q Consensus       188 ~l~~~~~~~~~~~~~~~l~~~L~~-~kr~LlVlDdv~~~~---------~~~~-l~~~~~~~-------TR~~~va~~--  247 (374)
                        |.... ..-++....+...+.. ..+++|++|++...-         +... |.+.+..+       |........  
T Consensus        92 --g~~~~-g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~~~e~  168 (387)
T d1qvra2          92 --GAKYR-GEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYREIEK  168 (387)
T ss_dssp             ---------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTTCCCEEEEECHHHHHHHTT
T ss_pred             --ccCcc-hhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHHHhcc
Confidence              00111 1122333334334432 247999999986431         2222 22333333       333322110  


Q ss_pred             ---hcCCCCceecCCCCHHHHHHHHHHhc
Q 045120          248 ---SMGSKDNFLIANITEEEAWRLFKIMN  273 (374)
Q Consensus       248 ---~~~~~~~~~l~~L~~~~s~~Lf~~~a  273 (374)
                         ....-..+.|.+.+.+++..++....
T Consensus       169 d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         169 DPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             CTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             cHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence               01122478999999999999988654

>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=97.15  E-value=0.00077  Score=57.40  Aligned_cols=173  Identities=10%  Similarity=0.022  Sum_probs=91.4

Q ss_pred             ccccccccHHHHHHHHHHhhc--------------------C------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          120 VYEAFESRVSNLKSTQNALTN--------------------A------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~--------------------~------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      ....++|.+..+++|.++|..                    .      +.|+||||+|+.+++...    + ..++++.+
T Consensus        12 ~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~----~-~~~~~~~~   86 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG----Y-DILEQNAS   86 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT----C-EEEEECTT
T ss_pred             CHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHH----h-hhhccccc
Confidence            356799999999999998853                    0      899999999999998543    2 24566666


Q ss_pred             CCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCccc-----cccccC---cCCCC------C
Q 045120          174 QTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKLLD-----LETVKI---PFRND------S  239 (374)
Q Consensus       174 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~~~-----~~~l~~---~~~~~------T  239 (374)
                      ...+...+-. .....-.......... ....... ...+..++++|++.....     +..+..   .....      +
T Consensus        87 ~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~-~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~~~  163 (253)
T d1sxja2          87 DVRSKTLLNA-GVKNALDNMSVVGYFK-HNEEAQN-LNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNE  163 (253)
T ss_dssp             SCCCHHHHHH-TGGGGTTBCCSTTTTT-C----CC-SSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEESC
T ss_pred             cchhhHHHHH-HHHHHhhcchhhhhhh-hhhhccc-ccccceEEEeeeccccccchhhhhHHHhhhhccccccccccccc
Confidence            5555433322 2222211110000000 0000001 123678888999764311     111110   01101      1


Q ss_pred             cchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcC--CCCCCcchHHHHHHHHHHccCCch-HHHHHH
Q 045120          240 RDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNG--DDVENCKFKSTAINVAKACGAGLF-CTLTTN  304 (374)
Q Consensus       240 R~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~--~~~~~~~l~~~~~~I~~~c~~GlP-Lai~~i  304 (374)
                      ...............+.+.+++.++-...+.....  +-..++   +....|++.| +|-. -||..+
T Consensus       164 ~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~---~~l~~i~~~s-~GDiR~ai~~L  227 (253)
T d1sxja2         164 RNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NVIDRLIQTT-RGDIRQVINLL  227 (253)
T ss_dssp             TTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHT-TTCHHHHHHHH
T ss_pred             ccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCH---HHHHHHHHhC-CCcHHHHHHHH
Confidence            11111111112234789999999999888887663  111122   2346889999 8855 554433

>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=96.95  E-value=0.006  Score=51.13  Aligned_cols=40  Identities=33%  Similarity=0.349  Sum_probs=33.1

Q ss_pred             ccccccccHHHHHHHHHHhhcC--------------CCCccHHHHHHHHHHHhh
Q 045120          120 VYEAFESRVSNLKSTQNALTNA--------------NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~~~--------------~gGiGKTtLA~~v~~~~~  159 (374)
                      ....++|-+..+++|..++...              ++|+||||+|+.+.+...
T Consensus         7 ~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~   60 (238)
T d1in4a2           7 SLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQ   60 (238)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHT
T ss_pred             cHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccC
Confidence            3567999999999998887521              999999999999998654

>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=96.92  E-value=0.017  Score=47.34  Aligned_cols=82  Identities=11%  Similarity=0.050  Sum_probs=49.2

Q ss_pred             CeEEEEEeCCCCcc--cccc----ccCcCCCC------Ccc-hhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCCC
Q 045120          213 NKILVILANIWKLL--DLET----VKIPFRND------SRD-NNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVEN  279 (374)
Q Consensus       213 kr~LlVlDdv~~~~--~~~~----l~~~~~~~------TR~-~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~  279 (374)
                      ++-++|+|++....  ....    +..+ +.+      |++ ..+......-...+.+.+++.++....+.+...-.   
T Consensus       108 ~~kviIide~d~l~~~a~n~Llk~lEep-~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~~~~L~~~~~~~---  183 (207)
T d1a5ta2         108 GAKVVWVTDAALLTDAAANALLKTLEEP-PAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVTMS---  183 (207)
T ss_dssp             SCEEEEESCGGGBCHHHHHHHHHHHTSC-CTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCCCC---
T ss_pred             ccceEEechhhhhhhhhhHHHHHHHHhh-cccceeeeeecChhhhhhhhcceeEEEecCCCCHHHHHHHHHHcCCCC---
Confidence            56789999987542  1222    2222 222      322 22322122233578999999999999887754311   


Q ss_pred             cchHHHHHHHHHHccCCchHHHH
Q 045120          280 CKFKSTAINVAKACGAGLFCTLT  302 (374)
Q Consensus       280 ~~l~~~~~~I~~~c~~GlPLai~  302 (374)
                         .+....|++.+ +|.|-.+.
T Consensus       184 ---~~~~~~i~~~s-~Gs~r~al  202 (207)
T d1a5ta2         184 ---QDALLAALRLS-AGSPGAAL  202 (207)
T ss_dssp             ---HHHHHHHHHHT-TTCHHHHH
T ss_pred             ---HHHHHHHHHHc-CCCHHHHH
Confidence               35567889999 99886553

>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=96.68  E-value=0.0027  Score=54.02  Aligned_cols=82  Identities=16%  Similarity=0.175  Sum_probs=45.6

Q ss_pred             cccccHHHHHHHHHHhh-------cC------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHH
Q 045120          123 AFESRVSNLKSTQNALT-------NA------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQG  183 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~-------~~------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~  183 (374)
                      .++|..+.++.+++.+.       .+            +.|+|||+||+.+++...  .+|   +.++.+...       
T Consensus        10 ~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~--~~~---~~i~~~~~~-------   77 (246)
T d1d2na_          10 GIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESN--FPF---IKICSPDKM-------   77 (246)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHT--CSE---EEEECGGGC-------
T ss_pred             CCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhccc--ccc---ccccccccc-------
Confidence            47777766665554433       11            889999999999998643  222   223322111       


Q ss_pred             HHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCC
Q 045120          184 DIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIW  223 (374)
Q Consensus       184 ~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~  223 (374)
                             ......+.......+.+......+++|+||++.
T Consensus        78 -------~g~~~~~~~~~i~~if~~A~~~~p~il~iDEid  110 (246)
T d1d2na_          78 -------IGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIE  110 (246)
T ss_dssp             -------TTCCHHHHHHHHHHHHHHHHTSSEEEEEECCHH
T ss_pred             -------ccccccchhhhhhhhhhhhhhcccceeehhhhh
Confidence                   011112222333344444443368999999985

>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=96.62  E-value=0.0038  Score=53.09  Aligned_cols=153  Identities=17%  Similarity=0.238  Sum_probs=82.2

Q ss_pred             ccccccccHHHHHHHHHH---hhcC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH
Q 045120          120 VYEAFESRVSNLKSTQNA---LTNA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI  178 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~---L~~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~  178 (374)
                      ....++|-+..+++|.+.   +..+                  +.|+|||+||+.+.+....  +   .+.++.      
T Consensus         7 ~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~--~---~~~i~~------   75 (247)
T d1ixza_           7 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV--P---FITASG------   75 (247)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTC--C---EEEEEH------
T ss_pred             cHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCC--C---EEEEEh------
Confidence            345688988877665443   2211                  8899999999999985431  1   223322      


Q ss_pred             HHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc-------c---------cccccc---CcCCC--
Q 045120          179 KKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL-------L---------DLETVK---IPFRN--  237 (374)
Q Consensus       179 ~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~-------~---------~~~~l~---~~~~~--  237 (374)
                      ..+..        .....+ ......+.+..+...+++|+|||+...       .         .+..+.   ..+..  
T Consensus        76 ~~l~~--------~~~g~~-~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~  146 (247)
T d1ixza_          76 SDFVE--------MFVGVG-AARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDT  146 (247)
T ss_dssp             HHHHH--------SCTTHH-HHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTC
T ss_pred             HHhhh--------ccccHH-HHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCC
Confidence            22211        111112 223344555544447899999998521       0         011111   01111  


Q ss_pred             C------CcchhHhhhhc---C-CCCceecCCCCHHHHHHHHHHhcCCCC--CCcchHHHHHHHHHHccCCc
Q 045120          238 D------SRDNNVVLLSM---G-SKDNFLIANITEEEAWRLFKIMNGDDV--ENCKFKSTAINVAKACGAGL  297 (374)
Q Consensus       238 ~------TR~~~va~~~~---~-~~~~~~l~~L~~~~s~~Lf~~~a~~~~--~~~~l~~~~~~I~~~c~~Gl  297 (374)
                      +      |....-....+   + -.+.+.+++.+.++-.++|+.+.....  ....+    ..+++.| .|+
T Consensus       147 ~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~----~~la~~t-~g~  213 (247)
T d1ixza_         147 AIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDL----ALLAKRT-PGF  213 (247)
T ss_dssp             CEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCH----HHHHHTC-TTC
T ss_pred             CEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCH----HHHHHHC-CCC
Confidence            1      33222111111   1 234789999999999999998886322  22233    3666777 765

>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=96.44  E-value=0.002  Score=55.50  Aligned_cols=44  Identities=14%  Similarity=0.054  Sum_probs=29.8

Q ss_pred             CCceecCCCCHHHHHHHHHHhcCCCCC--CcchHHHHHHHHHHccCCchHH
Q 045120          252 KDNFLIANITEEEAWRLFKIMNGDDVE--NCKFKSTAINVAKACGAGLFCT  300 (374)
Q Consensus       252 ~~~~~l~~L~~~~s~~Lf~~~a~~~~~--~~~l~~~~~~I~~~c~~GlPLa  300 (374)
                      ...+++++.+.++-.++|..+......  ..++    .+|++++ .|+--+
T Consensus       170 ~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l----~~la~~t-~g~s~~  215 (265)
T d1r7ra3         170 DQLIYIPLPDEKSRVAILKANLRKSPVAKDVDL----EFLAKMT-NGFSGA  215 (265)
T ss_dssp             EEEEECCCCCCHHHHHHHHHHTTCC----CCCC----HHHHHHH-CSSCCH
T ss_pred             cEEEEecchHHHHHHHHHHHHhccCCchhhhhH----HHHHhcC-CCCCHH
Confidence            347899999999999999987753221  2233    3667777 766543

>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=96.39  E-value=0.006  Score=52.07  Aligned_cols=155  Identities=14%  Similarity=0.152  Sum_probs=82.5

Q ss_pred             cccccccHHHHHHHHHH---hhcC------------------CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHH
Q 045120          121 YEAFESRVSNLKSTQNA---LTNA------------------NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIK  179 (374)
Q Consensus       121 ~~~~vGr~~~~~~i~~~---L~~~------------------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~  179 (374)
                      ...++|.++.+++|.+.   +...                  ++|+|||+||+.+.+....  +   .+-++.+.-.+  
T Consensus        11 ~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~--~---~~~i~~~~l~~--   83 (256)
T d1lv7a_          11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKV--P---FFTISGSDFVE--   83 (256)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTC--C---EEEECSCSSTT--
T ss_pred             HHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCC--C---EEEEEhHHhhh--
Confidence            45788999888777543   3211                  8999999999999986541  1   23333322211  


Q ss_pred             HHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeCCCCc------------cc----cccccCc---CCC--C
Q 045120          180 KIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILANIWKL------------LD----LETVKIP---FRN--D  238 (374)
Q Consensus       180 ~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDdv~~~------------~~----~~~l~~~---~~~--~  238 (374)
                                  .....++. ....+.+..+...+++|+|||+...            ..    +..+...   +..  +
T Consensus        84 ------------~~~g~~~~-~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~  150 (256)
T d1lv7a_          84 ------------MFVGVGAS-RVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEG  150 (256)
T ss_dssp             ------------SCCCCCHH-HHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSC
T ss_pred             ------------cchhHHHH-HHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCC
Confidence                        11111222 2334444444447899999998521            00    1111111   111  1


Q ss_pred             ------Ccch-hHhhhhc--C-CCCceecCCCCHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHccCCch
Q 045120          239 ------SRDN-NVVLLSM--G-SKDNFLIANITEEEAWRLFKIMNGDDVENCKFKSTAINVAKACGAGLF  298 (374)
Q Consensus       239 ------TR~~-~va~~~~--~-~~~~~~l~~L~~~~s~~Lf~~~a~~~~~~~~l~~~~~~I~~~c~~GlP  298 (374)
                            |... .+-....  + -.+.+.+++.+.++-.++|+.+........+..  ...+++.+ .|+.
T Consensus       151 v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~--~~~la~~t-~G~s  217 (256)
T d1lv7a_         151 IIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDID--AAIIARGT-PGFS  217 (256)
T ss_dssp             EEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCC--HHHHHHTC-TTCC
T ss_pred             EEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccC--HHHHHHhC-CCCC
Confidence                  2222 2111111  1 235788999999999999998875332222111  23667777 7764

>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=96.19  E-value=0.014  Score=49.92  Aligned_cols=76  Identities=17%  Similarity=0.191  Sum_probs=54.0

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.+++......+  ..++|++....++.+.     +++++...+.      .+.++..+.+...++.++.-
T Consensus        68 ~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~~~~~~  140 (269)
T d1mo6a1          68 PESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALD  140 (269)
T ss_dssp             SSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTTCEE
T ss_pred             CCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            789999999988887655443  4689999999998764     4556655322      34555555555555655688


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      |||+|.+-.
T Consensus       141 liIiDSi~a  149 (269)
T d1mo6a1         141 IVVIDSVAA  149 (269)
T ss_dssp             EEEEECSTT
T ss_pred             EEEEecccc
Confidence            999998854

>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=95.96  E-value=0.015  Score=49.76  Aligned_cols=76  Identities=20%  Similarity=0.205  Sum_probs=54.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.++.....-.+  ..++|++....+++.     +++.++...+.      .+.++..+.+...++.+..-
T Consensus        65 ~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~~~~~  137 (268)
T d1xp8a1          65 PESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMELLVRSGAID  137 (268)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             CCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhcCCCc
Confidence            889999999998887655333  358999999888874     67777765332      24455556666555554677


Q ss_pred             EEEEeCCCC
Q 045120          216 LVILANIWK  224 (374)
Q Consensus       216 LlVlDdv~~  224 (374)
                      |||+|-+-.
T Consensus       138 liIiDSi~a  146 (268)
T d1xp8a1         138 VVVVDSVAA  146 (268)
T ss_dssp             EEEEECTTT
T ss_pred             EEEEecccc
Confidence            999998854

>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=95.25  E-value=0.039  Score=47.13  Aligned_cols=82  Identities=18%  Similarity=0.273  Sum_probs=53.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCc-------------CCchhhHH------HH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTS-DIKKIQGDIAEKLGL-------------ELSEEAEY------RR  201 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~l~~-------------~~~~~~~~------~~  201 (374)
                      ..|+|||+|+..+.++.. +.+=+.++++-+++.. ...++.+++.+.--.             ...+++..      ..
T Consensus        76 ~~g~GKt~l~~~i~~~~~-~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~~~r~~~~~~  154 (276)
T d2jdid3          76 GAGVGKTVLIMELINNVA-KAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALT  154 (276)
T ss_dssp             CTTSSHHHHHHHHHHHHT-TTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH-hhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEEEEEECCCCCHHHHHHHHHH
Confidence            779999999999988643 1334678899888775 456677777663110             01112211      12


Q ss_pred             HHHHHHHHh-c-CCeEEEEEeCCCC
Q 045120          202 ASRLYERLK-N-ENKILVILANIWK  224 (374)
Q Consensus       202 ~~~l~~~L~-~-~kr~LlVlDdv~~  224 (374)
                      .-.+.+++. . ++..|+++||+..
T Consensus       155 a~~iAEyf~~~~G~~VLv~~Dsltr  179 (276)
T d2jdid3         155 GLTVAEYFRDQEGQDVLLFIDNIFR  179 (276)
T ss_dssp             HHHHHHHHHHTTCSCEEEEEECTHH
T ss_pred             HHHHHHHHHhcCCCeEEEEEcchhH
Confidence            345777776 3 5899999999854

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=95.00  E-value=0.04  Score=46.89  Aligned_cols=75  Identities=16%  Similarity=0.224  Sum_probs=51.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCch------hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSE------EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~~kr~  215 (374)
                      ..|+||||||.++.....-.+  ..++|++....++..     .++.++...+.      .+.++..+.+...++.++.-
T Consensus        62 ~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~~~~~~  134 (263)
T d1u94a1          62 PESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVD  134 (263)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCS
T ss_pred             CCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            789999999999888765443  357999988888864     35666665322      23455555555555554556


Q ss_pred             EEEEeCCC
Q 045120          216 LVILANIW  223 (374)
Q Consensus       216 LlVlDdv~  223 (374)
                      |||+|-+-
T Consensus       135 liViDSi~  142 (263)
T d1u94a1         135 VIVVDSVA  142 (263)
T ss_dssp             EEEEECGG
T ss_pred             EEEEECcc
Confidence            99999874

>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=94.92  E-value=0.022  Score=46.91  Aligned_cols=131  Identities=15%  Similarity=0.134  Sum_probs=69.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ..|+|||.|++++++.....  ...+++++.      .++...+...+...        ....+.+.+.+  --+|+|||
T Consensus        44 ~~G~GKTHLl~A~~~~~~~~--~~~~~~~~~------~~~~~~~~~~~~~~--------~~~~~~~~~~~--~dll~iDD  105 (213)
T d1l8qa2          44 SVGTGKTHLLQAAGNEAKKR--GYRVIYSSA------DDFAQAMVEHLKKG--------TINEFRNMYKS--VDLLLLDD  105 (213)
T ss_dssp             SSSSSHHHHHHHHHHHHHHT--TCCEEEEEH------HHHHHHHHHHHHHT--------CHHHHHHHHHT--CSEEEEEC
T ss_pred             CCCCcHHHHHHHHHHHhccC--ccceEEech------HHHHHHHHHHHHcc--------chhhHHHHHhh--ccchhhhh
Confidence            88999999999999976533  345666643      34444444443211        11233333443  56888888


Q ss_pred             CCCc---ccccc-ccCc----CCCC---------------CcchhHhhhhcCCCCceecCCCCHHHHHHHHHHhcCCCCC
Q 045120          222 IWKL---LDLET-VKIP----FRND---------------SRDNNVVLLSMGSKDNFLIANITEEEAWRLFKIMNGDDVE  278 (374)
Q Consensus       222 v~~~---~~~~~-l~~~----~~~~---------------TR~~~va~~~~~~~~~~~l~~L~~~~s~~Lf~~~a~~~~~  278 (374)
                      +...   ..|+. +..-    ...+               ....++. .+.....++.++ +++++-.+++++.+.....
T Consensus       106 i~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~-SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl  183 (213)
T d1l8qa2         106 VQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLV-SRFEGGILVEIE-LDNKTRFKIIKEKLKEFNL  183 (213)
T ss_dssp             GGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHH-HHHHTSEEEECC-CCHHHHHHHHHHHHHHTTC
T ss_pred             hhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHH-HHhhCceEEEEC-CCcHHHHHHHHHHHHHcCC
Confidence            8633   22332 1110    0011               1223332 234445577786 5777788888888752221


Q ss_pred             CcchHHHHHHHHHHc
Q 045120          279 NCKFKSTAINVAKAC  293 (374)
Q Consensus       279 ~~~l~~~~~~I~~~c  293 (374)
                      .-. .++..-|++.+
T Consensus       184 ~l~-~~v~~yl~~~~  197 (213)
T d1l8qa2         184 ELR-KEVIDYLLENT  197 (213)
T ss_dssp             CCC-HHHHHHHHHHC
T ss_pred             CCC-HHHHHHHHHhc
Confidence            111 24555666666

>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=94.48  E-value=0.12  Score=42.63  Aligned_cols=76  Identities=13%  Similarity=0.201  Sum_probs=46.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCC----------------chhhHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLEL----------------SEEAEYRRASRL  205 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~----------------~~~~~~~~~~~l  205 (374)
                      .+|+|||+||.++..+..  .+...++|++....  ...+.+ .+..++...                ......+....+
T Consensus        34 ~pGsGKT~l~~qia~~~~--~~~~~~~~is~e~~--~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  108 (242)
T d1tf7a2          34 ATGTGKTLLVSRFVENAC--ANKERAILFAYEES--RAQLLR-NAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHLQII  108 (242)
T ss_dssp             CTTSSHHHHHHHHHHHHH--TTTCCEEEEESSSC--HHHHHH-HHHTTSCCHHHHHHTTSEEECCCCGGGSCHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH--HhccccceeeccCC--HHHHHH-HHHHcCCChHHHhhcCceEEEEeecchhhHHHHHHHH
Confidence            899999999999988754  45667888876543  233222 223332210                112344555666


Q ss_pred             HHHHhcCCeEEEEEeCC
Q 045120          206 YERLKNENKILVILANI  222 (374)
Q Consensus       206 ~~~L~~~kr~LlVlDdv  222 (374)
                      ...+...+.-++|+|.+
T Consensus       109 ~~~i~~~~~~~vviDs~  125 (242)
T d1tf7a2         109 KSEINDFKPARIAIDSL  125 (242)
T ss_dssp             HHHHHTTCCSEEEEECH
T ss_pred             HHHHHhcCCceeeeecc
Confidence            66666556678888875

>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=93.66  E-value=0.014  Score=45.02  Aligned_cols=17  Identities=35%  Similarity=0.595  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        10 ~~GsGKSTvak~La~~L   26 (169)
T d1kaga_          10 PMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CTTSCHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            89999999999999854

>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=93.48  E-value=0.069  Score=45.81  Aligned_cols=89  Identities=16%  Similarity=0.213  Sum_probs=49.2

Q ss_pred             HHHHHhhcC----------CCCccHHHHHHHHHHHhhhcCCCCeEEEE-EeCCCCCHHHHHHHHHHHhCcC----Cchhh
Q 045120          133 STQNALTNA----------NGGIGKTTLAKEFAKQAREDKLFDRVVFS-EVSQTSDIKKIQGDIAEKLGLE----LSEEA  197 (374)
Q Consensus       133 ~i~~~L~~~----------~gGiGKTtLA~~v~~~~~~~~~F~~~~wv-~vs~~~~~~~~~~~i~~~l~~~----~~~~~  197 (374)
                      ++++.|..-          ..|+|||+|+..+.++.... +-++++.+ .+.....  ++ .++.+.....    ..+++
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~-~~~~v~~~~~iger~~--ev-~~~~~~~~~~vv~~t~d~~  107 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN-HPDCVLMVLLIDERPE--EV-TEMQRLVKGEVVASTFDEP  107 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHHH-CTTSEEEEEEEEECHH--HH-HHHHHHCSSEEEEEETTSC
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhhc-CCCeEEEEEeeceeHH--HH-HhHHhhcceEEEeccCCCc
Confidence            567777542          77999999999998876543 33444444 3333322  21 2222222111    11111


Q ss_pred             H------HHHHHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          198 E------YRRASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       198 ~------~~~~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .      ....-.+.+++.+ ++..||++||+...
T Consensus       108 ~~~r~~~~~~a~~iAEyfrd~G~dVLli~Dsltr~  142 (289)
T d1xpua3         108 ASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRL  142 (289)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTCEEEEEESCHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHhccCceeecCcHHHH
Confidence            1      1233456666653 58999999998643

>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=93.02  E-value=0.17  Score=41.40  Aligned_cols=81  Identities=14%  Similarity=0.232  Sum_probs=45.2

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCC----CeEEEEEeCCCCCHHHHHHHHHHHhCcCC-------------chhhHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLF----DRVVFSEVSQTSDIKKIQGDIAEKLGLEL-------------SEEAEYRRASR  204 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~~~~~i~~~l~~~~-------------~~~~~~~~~~~  204 (374)
                      .+|+||||||.++..+......+    ...+|++....++...+. .....++...             ...........
T Consensus        42 ~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (251)
T d1szpa2          42 EFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLV-SIAQRFGLDPDDALNNVAYARAYNADHQLRLLDA  120 (251)
T ss_dssp             STTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGGGH-HHHHHTCCCHHHHGGGEEEEECCSTTTHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHHHH-HHHHhcCCchhhhhcceEEEeccchhHHHHHHHH
Confidence            88999999999887654322222    457888877766544333 2233333221             11122233344


Q ss_pred             HHHHHhcCCeEEEEEeCCC
Q 045120          205 LYERLKNENKILVILANIW  223 (374)
Q Consensus       205 l~~~L~~~kr~LlVlDdv~  223 (374)
                      +.+.+......++++|.+-
T Consensus       121 ~~~~~~~~~~~~~~~ds~~  139 (251)
T d1szpa2         121 AAQMMSESRFSLIVVDSVM  139 (251)
T ss_dssp             THHHHHHSCEEEEEEETGG
T ss_pred             HHHHhhccccceeeehhhh
Confidence            4555554467788888763

>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=92.85  E-value=0.037  Score=43.22  Aligned_cols=28  Identities=14%  Similarity=0.074  Sum_probs=20.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFS  170 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  170 (374)
                      +.|+||||+|+.+....... +++...++
T Consensus        14 ~~GsGKTTia~~La~~L~~~-~~~~~~~~   41 (183)
T d1m8pa3          14 YMNSGKDAIARALQVTLNQQ-GGRSVSLL   41 (183)
T ss_dssp             STTSSHHHHHHHHHHHHHHH-CSSCEEEE
T ss_pred             CCCCCHHHHHHHHHHHHhhc-CCCchhhh
Confidence            89999999999999865432 34555554

>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=92.70  E-value=0.034  Score=48.56  Aligned_cols=17  Identities=47%  Similarity=0.718  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||.||+.+++..
T Consensus        57 PpG~GKT~lAkalA~~~   73 (309)
T d1ofha_          57 PTGVGKTEIARRLAKLA   73 (309)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHhhcc
Confidence            89999999999999854

>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=92.68  E-value=0.024  Score=44.17  Aligned_cols=17  Identities=53%  Similarity=0.819  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus        12 ~pGsGKTTia~~La~~l   28 (173)
T d1rkba_          12 TPGVGKTTLGKELASKS   28 (173)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            88999999999998754

>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=92.63  E-value=0.048  Score=47.68  Aligned_cols=35  Identities=20%  Similarity=0.310  Sum_probs=26.1

Q ss_pred             cccccHHHHHHHHHHhhcC------------------CCCccHHHHHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTNA------------------NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~~------------------~gGiGKTtLA~~v~~~  157 (374)
                      .++|-+..++.|...+...                  +.|+|||.||+.+..-
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~   75 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA   75 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhh
Confidence            4677777777776655311                  8899999999999874

>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=92.57  E-value=0.026  Score=43.18  Aligned_cols=15  Identities=47%  Similarity=0.645  Sum_probs=13.6

Q ss_pred             CCCccHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAK  156 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~  156 (374)
                      +.|+||||||+.+..
T Consensus        10 ~pGsGKTTla~~L~~   24 (152)
T d1ly1a_          10 CPGSGKSTWAREFIA   24 (152)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            789999999998865

>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=92.56  E-value=0.023  Score=44.73  Aligned_cols=17  Identities=24%  Similarity=0.311  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||||+.+.+..
T Consensus        15 ~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2          15 GESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             CTTSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998843

>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=92.30  E-value=0.059  Score=45.34  Aligned_cols=18  Identities=28%  Similarity=0.462  Sum_probs=16.1

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+||||||+.+++...
T Consensus        40 pPGtGKT~la~~la~~~~   57 (273)
T d1gvnb_          40 QPGSGKTSLRSAIFEETQ   57 (273)
T ss_dssp             CTTSCTHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhh
Confidence            899999999999998553

>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=92.13  E-value=0.036  Score=43.43  Aligned_cols=18  Identities=33%  Similarity=0.501  Sum_probs=16.1

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+|||||++++.....
T Consensus         9 ~~GtGKTtl~~~i~~~l~   26 (189)
T d2i3ba1           9 PPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCSSCHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            789999999999998764

>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=91.78  E-value=0.035  Score=43.07  Aligned_cols=16  Identities=44%  Similarity=0.679  Sum_probs=14.4

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      +.|+||||+|+.+...
T Consensus        10 ~~GsGKTTva~~L~~~   25 (176)
T d2bdta1          10 PAGVGKSTTCKRLAAQ   25 (176)
T ss_dssp             STTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            7899999999999864

>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=91.71  E-value=0.044  Score=42.47  Aligned_cols=18  Identities=39%  Similarity=0.405  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+|||||+.++.+...
T Consensus        10 ~~GSGKTTL~~~L~~~l~   27 (170)
T d1np6a_          10 WSGTGKTTLLKKLIPALC   27 (170)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            679999999999998654

>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=91.59  E-value=0.088  Score=45.92  Aligned_cols=77  Identities=18%  Similarity=0.268  Sum_probs=36.3

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      +.|+|||.||+.+....-  +.-...+-++.+.-.+...+..    -+|.+..-.. .+....|.+.++......++||+
T Consensus        61 p~G~GKt~lak~la~~l~--~~~~~~~~~~~~~~~~~~~~~~----L~g~~~gyvG-~~~~~~l~~~~~~~p~~Vvl~DE  133 (315)
T d1qvra3          61 PTGVGKTELAKTLAATLF--DTEEAMIRIDMTEYMEKHAVSR----LIGAPPGYVG-YEEGGQLTEAVRRRPYSVILFDE  133 (315)
T ss_dssp             CSSSSHHHHHHHHHHHHH--SSGGGEEEECTTTCCSSGGGGG----C---------------CHHHHHHHCSSEEEEESS
T ss_pred             CCcchHHHHHHHHHHHhc--CCCcceEEEeccccccchhhhh----hcCCCCCCcC-cccCChHHHHHHhCCCcEEEEeh
Confidence            889999999999987542  1112233344433322111100    0011100000 00112345555544678999999


Q ss_pred             CCCc
Q 045120          222 IWKL  225 (374)
Q Consensus       222 v~~~  225 (374)
                      +...
T Consensus       134 ieK~  137 (315)
T d1qvra3         134 IEKA  137 (315)
T ss_dssp             GGGS
T ss_pred             Hhhc
Confidence            9854

>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=91.44  E-value=0.86  Score=38.02  Aligned_cols=45  Identities=18%  Similarity=0.198  Sum_probs=28.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKL  189 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l  189 (374)
                      .+|+|||||+.++..+......+. +++++.  ..+...+...++...
T Consensus        43 ~~G~GKT~~~~~la~~~a~~~g~~-v~~~s~--E~~~~~~~~r~~~~~   87 (277)
T d1cr2a_          43 GSGMGKSTFVRQQALQWGTAMGKK-VGLAML--EESVEETAEDLIGLH   87 (277)
T ss_dssp             STTSSHHHHHHHHHHHHHHTSCCC-EEEEES--SSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhhhhcccc-eeEeee--ccchhhHHhHHHHHh
Confidence            779999999998876654443343 444443  345566666665544

>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=91.40  E-value=0.041  Score=42.96  Aligned_cols=18  Identities=33%  Similarity=0.475  Sum_probs=16.1

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      |.|+||||+++.+.....
T Consensus         9 ~~G~GKSTig~~La~~l~   26 (165)
T d2iyva1           9 LPGSGKSTIGRRLAKALG   26 (165)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            899999999999998654

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=91.17  E-value=0.3  Score=41.48  Aligned_cols=82  Identities=17%  Similarity=0.233  Sum_probs=47.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC-HHHHHHHHHHHhCcC-------Cchhh------HHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEA------EYRRASRLYE  207 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~------~~~~~~~l~~  207 (374)
                      ..|+|||+|+........  .+-+.++++-++.... ..++..++...=...       ..+++      .....-.+.+
T Consensus        75 ~~g~GKt~l~~~~~~~~~--~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~a~tiAE  152 (276)
T d1fx0a3          75 DRQTGKTAVATDTILNQQ--GQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYTGAALAE  152 (276)
T ss_dssp             SSSSSHHHHHHHHHHTCC--TTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHhhhc--ccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHHHHHHHHH
Confidence            669999999987655433  3456778888887643 333333333221000       11111      1123345566


Q ss_pred             HHhc-CCeEEEEEeCCCCc
Q 045120          208 RLKN-ENKILVILANIWKL  225 (374)
Q Consensus       208 ~L~~-~kr~LlVlDdv~~~  225 (374)
                      +++. +++.|+++||+...
T Consensus       153 yfrd~G~~Vlll~Dsltr~  171 (276)
T d1fx0a3         153 YFMYRERHTLIIYDDLSKQ  171 (276)
T ss_dssp             HHHHTTCEEEEEEECHHHH
T ss_pred             HHHHcCCceeEEeeccHHH
Confidence            6653 58999999998643

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.10  E-value=0.4  Score=40.83  Aligned_cols=84  Identities=12%  Similarity=0.195  Sum_probs=46.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcC-----CC-CeEEEEEeCCCCC-HHHHHHHHHHHhCcC-------CchhhHH------HH
Q 045120          142 NGGIGKTTLAKEFAKQAREDK-----LF-DRVVFSEVSQTSD-IKKIQGDIAEKLGLE-------LSEEAEY------RR  201 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~-----~F-~~~~wv~vs~~~~-~~~~~~~i~~~l~~~-------~~~~~~~------~~  201 (374)
                      ..|+|||+|+..+.++....+     .- ..++++-++...+ ..++...+...-...       ..+++..      ..
T Consensus        76 ~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvvv~~ts~~~~~~r~~~~~~  155 (285)
T d2jdia3          76 DRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYS  155 (285)
T ss_dssp             STTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceEEEEECCCCCHHHHHHHHHH
Confidence            779999999987766543211     11 1456777777653 344555444332111       1111111      12


Q ss_pred             HHHHHHHHhc-CCeEEEEEeCCCCc
Q 045120          202 ASRLYERLKN-ENKILVILANIWKL  225 (374)
Q Consensus       202 ~~~l~~~L~~-~kr~LlVlDdv~~~  225 (374)
                      .-.+.+++++ +|+.|+++||+...
T Consensus       156 a~tiAEyfrd~G~~VLll~Dsltr~  180 (285)
T d2jdia3         156 GCSMGEYFRDNGKHALIIYDDLSKQ  180 (285)
T ss_dssp             HHHHHHHHHHTTCEEEEEEETHHHH
T ss_pred             HHHHHHHHHHcCCcEEEEEcChHHH
Confidence            2245555543 59999999998543

>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=91.01  E-value=0.048  Score=42.44  Aligned_cols=18  Identities=44%  Similarity=0.521  Sum_probs=16.1

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      |+|+||||+|+.+..+..
T Consensus         8 ~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           8 FMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            899999999999998653

>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=90.91  E-value=0.049  Score=42.44  Aligned_cols=17  Identities=35%  Similarity=0.522  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        13 ~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_          13 TPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            88999999999998753

>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=90.60  E-value=0.055  Score=42.40  Aligned_cols=18  Identities=33%  Similarity=0.514  Sum_probs=16.0

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.....
T Consensus        10 ~~GsGKSTia~~LA~~Lg   27 (170)
T d1e6ca_          10 ARGCGMTTVGRELARALG   27 (170)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            889999999999998654

>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=90.44  E-value=0.17  Score=39.87  Aligned_cols=19  Identities=42%  Similarity=0.527  Sum_probs=16.3

Q ss_pred             CCCccHHHHHHHHHHHhhh
Q 045120          142 NGGIGKTTLAKEFAKQARE  160 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~  160 (374)
                      ..|+||||||+.+......
T Consensus        30 ~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          30 LSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             CTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhcc
Confidence            8899999999999876553

>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=90.44  E-value=0.058  Score=42.83  Aligned_cols=18  Identities=28%  Similarity=0.331  Sum_probs=15.9

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||||+.+.....
T Consensus        27 ~pGSGKTTiAk~La~~l~   44 (195)
T d1x6va3          27 LSGAGKTTVSMALEEYLV   44 (195)
T ss_dssp             SCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            889999999999988654

>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=90.03  E-value=0.48  Score=37.47  Aligned_cols=17  Identities=29%  Similarity=0.415  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+..+.
T Consensus        16 ppGSGKsT~a~~La~~~   32 (196)
T d1ukza_          16 GPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            88999999999998754

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=89.60  E-value=0.16  Score=43.21  Aligned_cols=30  Identities=30%  Similarity=0.475  Sum_probs=19.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      -||+||||+|..+.....-+++  .++-|+..
T Consensus        16 KGGVGKTTvaa~lA~~lA~~G~--rVLlvD~D   45 (296)
T d1ihua1          16 KGGVGKTSISCATAIRLAEQGK--RVLLVSTD   45 (296)
T ss_dssp             STTSSHHHHHHHHHHHHHHTTC--CEEEEECC
T ss_pred             CCcChHHHHHHHHHHHHHHCCC--CEEEEeCC
Confidence            7999999988877665543332  24455433

>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=89.28  E-value=0.082  Score=40.95  Aligned_cols=17  Identities=41%  Similarity=0.538  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        14 ~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_          14 VSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             STTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>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=89.25  E-value=0.094  Score=42.13  Aligned_cols=18  Identities=22%  Similarity=0.277  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      .+|+||||||+++.....
T Consensus        10 lpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1          10 LPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            689999999999997654

>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=89.15  E-value=0.11  Score=45.56  Aligned_cols=37  Identities=16%  Similarity=0.164  Sum_probs=26.6

Q ss_pred             ccccccccHHHHHHHHHHhh---cC------CCCccHHHHHHHHHH
Q 045120          120 VYEAFESRVSNLKSTQNALT---NA------NGGIGKTTLAKEFAK  156 (374)
Q Consensus       120 ~~~~~vGr~~~~~~i~~~L~---~~------~gGiGKTtLA~~v~~  156 (374)
                      +...++|.+..+..|.-.+.   .+      ..|+||||||+.+..
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHH
Confidence            35578999887776543332   12      789999999999864

>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=89.04  E-value=0.19  Score=40.79  Aligned_cols=17  Identities=41%  Similarity=0.438  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||||+.+....
T Consensus        32 lsGsGKTTia~~L~~~l   48 (208)
T d1m7ga_          32 LSASGKSTLAVELEHQL   48 (208)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            89999999999998754

>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=88.96  E-value=1  Score=36.35  Aligned_cols=48  Identities=19%  Similarity=0.198  Sum_probs=29.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCC--------------CCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKL--------------FDRVVFSEVSQTSDIKKIQGDIAEKLG  190 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~--------------F~~~~wv~vs~~~~~~~~~~~i~~~l~  190 (374)
                      .+|+|||+||.++..+....+.              ...++|++.....+.. ....+...+.
T Consensus        42 ~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~~-~~~~~~~~~~  103 (258)
T d2i1qa2          42 VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPE-RIMQMAEHAG  103 (258)
T ss_dssp             STTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHH-HHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCHH-HHHHHHhhcc
Confidence            8899999999999876532211              1246788766555533 3344455443

>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=88.87  E-value=0.09  Score=40.73  Aligned_cols=17  Identities=12%  Similarity=0.245  Sum_probs=14.9

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ..|+||||+|+.+....
T Consensus        11 ~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_          11 GSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CTTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            78999999999998843

>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=88.71  E-value=0.41  Score=38.67  Aligned_cols=20  Identities=15%  Similarity=0.214  Sum_probs=16.5

Q ss_pred             CCCccHHHHHHHHHHHhhhc
Q 045120          142 NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~  161 (374)
                      +-|+||||+++.+.+.....
T Consensus        11 ~dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_          11 VDRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             STTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            66999999999998876543

>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=88.60  E-value=0.1  Score=40.66  Aligned_cols=18  Identities=39%  Similarity=0.628  Sum_probs=15.7

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+|||||++.+.....
T Consensus         8 ~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           8 EPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             CTTSSHHHHHHHHHHHHG
T ss_pred             CCCcHHHHHHHHHHhcCC
Confidence            689999999999998654

>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=88.52  E-value=0.88  Score=36.28  Aligned_cols=18  Identities=6%  Similarity=-0.060  Sum_probs=15.5

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||+|..+.+...
T Consensus        23 ~~g~gk~~~a~~l~~~i~   40 (198)
T d2gnoa2          23 EDLSYPREVSLELPEYVE   40 (198)
T ss_dssp             SSSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            889999999999887543

>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=88.50  E-value=0.099  Score=41.17  Aligned_cols=15  Identities=33%  Similarity=0.406  Sum_probs=13.5

Q ss_pred             CCCccHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAK  156 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~  156 (374)
                      ++|+||||+|+.+..
T Consensus        22 ~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          22 FPGAGKSTFIQEHLV   36 (172)
T ss_dssp             CTTSSHHHHHHHHTG
T ss_pred             CCCCCHHHHHHHHHH
Confidence            899999999998865

>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=87.84  E-value=0.75  Score=39.73  Aligned_cols=63  Identities=8%  Similarity=0.159  Sum_probs=35.6

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCHHHHHHHHHHHhCcCCchhhHHHHHHHHHHHHhcCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDIKKIQGDIAEKLGLELSEEAEYRRASRLYERLKNENKILVILAN  221 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~~kr~LlVlDd  221 (374)
                      ++|+|||.||+.+......+..|   +-+..+.-.+              .+-.. -+.....+.+..+.  .++|.+|.
T Consensus       131 ~pG~GKT~la~ala~~~~~~~~~---~~~~~~~~~~--------------~~~G~-~e~~~~~~f~~a~~--~~ilf~DE  190 (321)
T d1w44a_         131 KGNSGKTPLVHALGEALGGKDKY---ATVRFGEPLS--------------GYNTD-FNVFVDDIARAMLQ--HRVIVIDS  190 (321)
T ss_dssp             SSSSCHHHHHHHHHHHHHTTSCC---EEEEBSCSST--------------TCBCC-HHHHHHHHHHHHHH--CSEEEEEC
T ss_pred             CCCccHHHHHHHHHHHhcCCCCe---EEEEhhHhhh--------------cccch-HHHHHHHHHHHHhh--ccEEEeeh
Confidence            89999999999999865422223   1233332221              11111 22333445444443  57999998


Q ss_pred             CCC
Q 045120          222 IWK  224 (374)
Q Consensus       222 v~~  224 (374)
                      +..
T Consensus       191 id~  193 (321)
T d1w44a_         191 LKN  193 (321)
T ss_dssp             CTT
T ss_pred             hhh
Confidence            754

>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=87.76  E-value=0.098  Score=40.57  Aligned_cols=15  Identities=40%  Similarity=0.663  Sum_probs=13.6

Q ss_pred             CCCccHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAK  156 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~  156 (374)
                      +.|+||||+|+.+..
T Consensus        12 ~~GsGKSTia~~La~   26 (176)
T d1zp6a1          12 HPGSGKSTIAEALAN   26 (176)
T ss_dssp             CTTSCHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHH
Confidence            889999999999875

>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=87.58  E-value=0.65  Score=37.92  Aligned_cols=41  Identities=27%  Similarity=0.305  Sum_probs=28.7

Q ss_pred             CCCccHHHHHHHHHHHhhhc----CCCCeEEEEEeCCCCCHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQARED----KLFDRVVFSEVSQTSDIKKIQ  182 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~~~  182 (374)
                      .+|+||||||.++..+....    ......+|+......+...+.
T Consensus        44 ~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (254)
T d1pzna2          44 EFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIR   88 (254)
T ss_dssp             STTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHHH
Confidence            88999999999987754322    223567888877777754443

>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=87.48  E-value=0.97  Score=36.34  Aligned_cols=49  Identities=24%  Similarity=0.247  Sum_probs=29.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCC--HHHHHHHHHHHhCcCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSD--IKKIQGDIAEKLGLEL  193 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~~~~~i~~~l~~~~  193 (374)
                      +.|+||||.+..+......+ .. .+..++. +.+.  ..+-++...+.++.+.
T Consensus        18 p~GvGKTTTiaKLA~~~~~~-g~-kV~lit~-Dt~R~gA~eQL~~~a~~l~v~~   68 (207)
T d1ls1a2          18 LQGSGKTTTAAKLALYYKGK-GR-RPLLVAA-DTQRPAAREQLRLLGEKVGVPV   68 (207)
T ss_dssp             CTTTTHHHHHHHHHHHHHHT-TC-CEEEEEC-CSSCHHHHHHHHHHHHHHTCCE
T ss_pred             CCCCCHHHHHHHHHHHHHHC-CC-cEEEEec-ccccchHHHHHHHHHHhcCCcc
Confidence            89999999666665554432 23 3455544 4444  3455567777777653

>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=87.41  E-value=0.14  Score=39.69  Aligned_cols=26  Identities=23%  Similarity=0.236  Sum_probs=18.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVV  168 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~  168 (374)
                      ..|+|||||+.++......++ +...+
T Consensus         9 ~~gSGKTTli~~l~~~L~~~g-~~v~v   34 (165)
T d1xjca_           9 YKHSGKTTLMEKWVAAAVREG-WRVGT   34 (165)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTT-CCEEE
T ss_pred             CCCCCHHHHHHHHHHHHHhCC-CeEEE
Confidence            569999999999988766443 44433

>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=87.08  E-value=1.7  Score=34.97  Aligned_cols=79  Identities=15%  Similarity=0.086  Sum_probs=43.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCcCCch----hhHHHHHHHHHHHHhcCCeE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQTSDI--KKIQGDIAEKLGLELSE----EAEYRRASRLYERLKNENKI  215 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~~~~~i~~~l~~~~~~----~~~~~~~~~l~~~L~~~kr~  215 (374)
                      +-|+||||-+..+......   ....+.+-..+.+..  .+-++...+.++.+...    .+....+....+..+.+..=
T Consensus        17 ptGvGKTTTiAKLA~~~~~---~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~a~~~~~d   93 (211)
T d2qy9a2          17 VNGVGKTTTIGKLARQFEQ---QGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAAKARNID   93 (211)
T ss_dssp             CTTSCHHHHHHHHHHHHHT---TTCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCCCHHHHHHHHHHHHHH---CCCcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHHHHHHHcCCC
Confidence            8899999966666655442   233455555567765  45556677777766422    22333333333332221334


Q ss_pred             EEEEeCCC
Q 045120          216 LVILANIW  223 (374)
Q Consensus       216 LlVlDdv~  223 (374)
                      +|++|-.-
T Consensus        94 ~ilIDTaG  101 (211)
T d2qy9a2          94 VLIADTAG  101 (211)
T ss_dssp             EEEECCCC
T ss_pred             EEEeccCC
Confidence            77777653

>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=87.01  E-value=0.14  Score=40.67  Aligned_cols=18  Identities=17%  Similarity=0.128  Sum_probs=15.6

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+|+.+.+...
T Consensus        11 ppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1          11 APASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            789999999999987653

>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=87.01  E-value=0.14  Score=40.25  Aligned_cols=18  Identities=33%  Similarity=0.366  Sum_probs=15.8

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+||||+|+.+.....
T Consensus         8 ~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           8 PPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            789999999999998653

>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=86.79  E-value=0.16  Score=39.53  Aligned_cols=18  Identities=28%  Similarity=0.316  Sum_probs=15.8

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+++.+.....
T Consensus         9 ~~GsGKsT~~~~L~~~l~   26 (190)
T d1khta_           9 VPGVGSTTSSQLAMDNLR   26 (190)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            789999999999988654

>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=86.63  E-value=0.16  Score=43.41  Aligned_cols=30  Identities=27%  Similarity=0.410  Sum_probs=20.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      -||+||||+|..+.......+ + .++-|..-
T Consensus        10 KGGVGKTT~a~NLA~~LA~~G-~-rVLlID~D   39 (289)
T d2afhe1          10 KGGIGKSTTTQNLVAALAEMG-K-KVMIVGCD   39 (289)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTT-C-CEEEEEEC
T ss_pred             CCCCCHHHHHHHHHHHHHHCC-C-CEEEEecC
Confidence            599999999988776554332 2 35555554

>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=86.58  E-value=0.16  Score=42.77  Aligned_cols=29  Identities=21%  Similarity=0.349  Sum_probs=19.8

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEe
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEV  172 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~v  172 (374)
                      -||+||||+|..+..-....+ +. ++-|+.
T Consensus         9 KGGvGKTT~a~nLA~~LA~~G-~r-VllID~   37 (269)
T d1cp2a_           9 KGGIGKSTTTQNLTSGLHAMG-KT-IMVVGC   37 (269)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTT-CC-EEEEEE
T ss_pred             CCcCCHHHHHHHHHHHHHhCC-Cc-EEEEec
Confidence            499999999988877665332 44 444444

>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=86.54  E-value=0.15  Score=40.54  Aligned_cols=17  Identities=24%  Similarity=0.327  Sum_probs=15.3

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+..+.
T Consensus        14 ~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_          14 GPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            89999999999998754

>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=86.41  E-value=0.17  Score=41.35  Aligned_cols=30  Identities=23%  Similarity=0.337  Sum_probs=21.7

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      -||+||||+|..+.......  =..++.|...
T Consensus        10 KGGvGKTtia~nlA~~la~~--g~~VlliD~D   39 (232)
T d1hyqa_          10 KGGTGKTTITANLGVALAQL--GHDVTIVDAD   39 (232)
T ss_dssp             SSCSCHHHHHHHHHHHHHHT--TCCEEEEECC
T ss_pred             CCCChHHHHHHHHHHHHHhC--CCCEEEEeCC
Confidence            59999999999888765533  2356777654

>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=86.39  E-value=0.42  Score=40.10  Aligned_cols=18  Identities=44%  Similarity=0.706  Sum_probs=14.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      -||+||||+|-.+.....
T Consensus        28 KGGVGKTT~a~nLA~~lA   45 (279)
T d1ihua2          28 KGGVGKTTMAAAIAVRLA   45 (279)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            899999998777766544

>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=86.38  E-value=0.16  Score=39.81  Aligned_cols=17  Identities=29%  Similarity=0.274  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus         8 ~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           8 LPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            78999999999998854

>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=86.25  E-value=3.7  Score=31.70  Aligned_cols=40  Identities=13%  Similarity=0.124  Sum_probs=25.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCC----CCeEEEEEeCCCCCHHHH
Q 045120          142 NGGIGKTTLAKEFAKQAREDKL----FDRVVFSEVSQTSDIKKI  181 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~  181 (374)
                      .+|+||||||.++..+......    +....++..........+
T Consensus        31 ~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (242)
T d1n0wa_          31 EFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL   74 (242)
T ss_dssp             CTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHHHH
Confidence            8899999999998876543222    234555555555554433

>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=86.10  E-value=0.18  Score=39.02  Aligned_cols=20  Identities=30%  Similarity=0.423  Sum_probs=16.4

Q ss_pred             CCCccHHHHHHHHHHHhhhc
Q 045120          142 NGGIGKTTLAKEFAKQARED  161 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~  161 (374)
                      .=|+||||+++.+.+...+.
T Consensus        41 ~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          41 DLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             STTSSHHHHHHHHHHHTTCC
T ss_pred             CCCccHHHHHHHHHhhcccc
Confidence            44999999999999876544

>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=85.94  E-value=0.86  Score=36.70  Aligned_cols=18  Identities=28%  Similarity=0.226  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +=|+||||+++.+.....
T Consensus        11 ~DGsGKST~~~~L~~~L~   28 (214)
T d1tmka_          11 LDRTGKTTQCNILYKKLQ   28 (214)
T ss_dssp             STTSSHHHHHHHHHHHTT
T ss_pred             CCCCcHHHHHHHHHHHHH
Confidence            569999999999987544

>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=85.67  E-value=0.18  Score=39.68  Aligned_cols=17  Identities=29%  Similarity=0.309  Sum_probs=15.4

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+..+.
T Consensus         8 ~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           8 LPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            78999999999999865

>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=85.65  E-value=0.21  Score=39.01  Aligned_cols=18  Identities=22%  Similarity=0.335  Sum_probs=15.8

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      +.|+||||+++.+.....
T Consensus         9 ~~GsGKTT~~~~La~~L~   26 (194)
T d1nksa_           9 IPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            789999999999988664

>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=85.38  E-value=0.2  Score=40.88  Aligned_cols=30  Identities=23%  Similarity=0.365  Sum_probs=21.4

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVS  173 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs  173 (374)
                      -||+||||+|..+.....-.+ + .++.++..
T Consensus        11 kGGvGKTtia~nLA~~la~~g-~-~VlliD~D   40 (237)
T d1g3qa_          11 KGGTGKTTVTANLSVALGDRG-R-KVLAVDGD   40 (237)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT-C-CEEEEECC
T ss_pred             CCCCcHHHHHHHHHHHHHhCC-C-CEEEEeCC
Confidence            699999999999887665332 3 46666653

>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=85.34  E-value=0.18  Score=40.84  Aligned_cols=18  Identities=39%  Similarity=0.388  Sum_probs=16.1

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+||||+|+.+..+..
T Consensus        11 p~GsGKgT~ak~La~~lg   28 (223)
T d1q3ta_          11 PASSGKSTVAKIIAKDFG   28 (223)
T ss_dssp             SSCSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            789999999999998664

>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=85.27  E-value=0.18  Score=40.09  Aligned_cols=17  Identities=29%  Similarity=0.417  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+..+.
T Consensus        14 ~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1          14 APGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CTTSSHHHHHHHHHHHB
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            89999999999998744

>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=84.98  E-value=1.2  Score=35.61  Aligned_cols=32  Identities=22%  Similarity=0.263  Sum_probs=19.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ  174 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~  174 (374)
                      ..|+|||+||.++..+....+ -..++|++...
T Consensus        34 ~~G~GKT~la~~~~~~~~~~~-~~~~~~~s~e~   65 (242)
T d1tf7a1          34 TSGTGKTLFSIQFLYNGIIEF-DEPGVFVTFEE   65 (242)
T ss_dssp             STTSSHHHHHHHHHHHHHHHH-CCCEEEEESSS
T ss_pred             CCCCCHHHHHHHHHHHHHHhc-CCCcccccccC
Confidence            889999999977544322221 12456665443

>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=84.82  E-value=0.21  Score=39.60  Aligned_cols=17  Identities=24%  Similarity=0.321  Sum_probs=15.3

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.++++.
T Consensus         9 ppGSGKsT~a~~La~~~   25 (194)
T d1teva_           9 GPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999999854

>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=84.73  E-value=0.27  Score=40.98  Aligned_cols=35  Identities=17%  Similarity=0.335  Sum_probs=27.7

Q ss_pred             cccccHHHHHHHHHHhhcC-----------CCCccHHHHHHHHHHH
Q 045120          123 AFESRVSNLKSTQNALTNA-----------NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       123 ~~vGr~~~~~~i~~~L~~~-----------~gGiGKTtLA~~v~~~  157 (374)
                      +|||....++++.+.+..-           ..|+|||++|+.+...
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            3788888888887776532           6699999999999763

>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=84.73  E-value=0.21  Score=39.17  Aligned_cols=17  Identities=29%  Similarity=0.350  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+....
T Consensus        10 ~pGSGKtT~a~~La~~~   26 (180)
T d1akya1          10 PPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>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=84.54  E-value=2.1  Score=34.22  Aligned_cols=50  Identities=16%  Similarity=0.257  Sum_probs=33.1

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCcCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQ-TSDIKKIQGDIAEKLGLEL  193 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~~~~~i~~~l~~~~  193 (374)
                      +.|+||||.+..+.......+  ..+..|+.-. ...-.+-++..++.++.+.
T Consensus        14 ptGvGKTTTiaKLA~~~~~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   64 (207)
T d1okkd2          14 VNGVGKTTTIAKLGRYYQNLG--KKVMFCAGDTFRAAGGTQLSEWGKRLSIPV   64 (207)
T ss_dssp             STTSSHHHHHHHHHHHHHTTT--CCEEEECCCCSSTTHHHHHHHHHHHHTCCE
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CcEEEEEeccccccchhhHhhcccccCceE
Confidence            789999997666666554322  2466665543 3456677778888888764

>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=84.22  E-value=1.7  Score=34.43  Aligned_cols=28  Identities=25%  Similarity=0.260  Sum_probs=19.5

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEE
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFS  170 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  170 (374)
                      +-|+||||+++.+.+..... .+..+++.
T Consensus        10 ~dGsGKsT~~~~L~~~L~~~-g~~~~~~~   37 (210)
T d4tmka_          10 LEGAGKTTARNVVVETLEQL-GIRDMVFT   37 (210)
T ss_dssp             CTTSCHHHHHHHHHHHHHHT-TCCCEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHhC-CCCeEEEe
Confidence            56999999999998865433 24444444

>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=83.92  E-value=0.24  Score=38.73  Aligned_cols=17  Identities=24%  Similarity=0.089  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+||||+|+.+..+.
T Consensus         8 ~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           8 APVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            78999999999998754

>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=83.51  E-value=0.25  Score=39.79  Aligned_cols=18  Identities=39%  Similarity=0.547  Sum_probs=16.3

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ++|+||||+|+.+.++..
T Consensus        11 ppGSGKgT~ak~La~~~g   28 (225)
T d1ckea_          11 PSGAGKGTLCKAMAEALQ   28 (225)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            899999999999998664

>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=83.34  E-value=0.25  Score=39.85  Aligned_cols=18  Identities=11%  Similarity=0.237  Sum_probs=15.2

Q ss_pred             CCCccHHHHHHHHHHHhh
Q 045120          142 NGGIGKTTLAKEFAKQAR  159 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~  159 (374)
                      ..|+||||||+.+.....
T Consensus        10 ~~gSGKSTla~~L~~~l~   27 (213)
T d1uj2a_          10 GTASGKSSVCAKIVQLLG   27 (213)
T ss_dssp             STTSSHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhc
Confidence            679999999999987643

>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=82.98  E-value=2.7  Score=33.77  Aligned_cols=50  Identities=22%  Similarity=0.250  Sum_probs=29.9

Q ss_pred             CCCccHHHHHHHHHHHhhhcCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCcCC
Q 045120          142 NGGIGKTTLAKEFAKQAREDKLFDRVVFSEVSQT-SDIKKIQGDIAEKLGLEL  193 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~~~~~i~~~l~~~~  193 (374)
                      +-|+||||-+-.++.....++  ..+..++.-.. ....+-++..++.++.+.
T Consensus        19 ptGvGKTTTiAKLAa~~~~~~--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   69 (213)
T d1vmaa2          19 VNGTGKTTSCGKLAKMFVDEG--KSVVLAAADTFRAAAIEQLKIWGERVGATV   69 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHHHTT--CCEEEEEECTTCHHHHHHHHHHHHHHTCEE
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CceEEEeecccccchhHHHHHHhhhcCccc
Confidence            889999996655555543332  34566654422 234455666777777653

>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=82.96  E-value=0.28  Score=38.73  Aligned_cols=17  Identities=41%  Similarity=0.430  Sum_probs=15.1

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      ++|+||||+|+.+....
T Consensus        11 ~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1          11 PPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            88999999999998754

>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=81.60  E-value=0.16  Score=40.46  Aligned_cols=16  Identities=50%  Similarity=0.571  Sum_probs=13.7

Q ss_pred             CCCccHHHHHHHHHHH
Q 045120          142 NGGIGKTTLAKEFAKQ  157 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~  157 (374)
                      .-|+||||+++.+...
T Consensus        17 ~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1          17 NIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             STTSCHHHHHHTTGGG
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            6799999999998753

>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=81.27  E-value=1.5  Score=35.47  Aligned_cols=39  Identities=18%  Similarity=0.192  Sum_probs=27.7

Q ss_pred             CCCccHHHHHHHHHHHhhh----cCCCCeEEEEEeCCCCCHHH
Q 045120          142 NGGIGKTTLAKEFAKQARE----DKLFDRVVFSEVSQTSDIKK  180 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~~~----~~~F~~~~wv~vs~~~~~~~  180 (374)
                      .+|+|||+||.++..+...    ...+..+.|+.....+....
T Consensus        45 ~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (258)
T d1v5wa_          45 EFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDR   87 (258)
T ss_dssp             CTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHH
Confidence            8899999999998765432    23356678888777766443

>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=80.42  E-value=0.39  Score=38.07  Aligned_cols=17  Identities=35%  Similarity=0.558  Sum_probs=15.0

Q ss_pred             CCCccHHHHHHHHHHHh
Q 045120          142 NGGIGKTTLAKEFAKQA  158 (374)
Q Consensus       142 ~gGiGKTtLA~~v~~~~  158 (374)
                      +.|+|||||++.+....
T Consensus         8 PsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           8 PSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhC
Confidence            78999999999998754