YRC Public Data Repository - Protein Structure Prediction

Protein:	HSP78
Organism:	Saccharomyces cerevisiae
Length:	811 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for HSP78.

Description	E-value	Query Range	Subject Range
CLPB_PASMU - Chaperone protein clpB OS=Pasteurella multocida GN=clpB PE=3 SV=1 CLPB_PASMU - Chaperone protein ClpB OS=Pasteurella multocida (strain Pm70) GN=clpB PE=3 SV=1	0.0	[1..792]	[59..850]
gi\|25289928 - pir\|\|AF3276 ATP-dependent clp proteinase, ATP-binding chain clpb BMEI0195 [imported] - Brucella meli... gi\|17986479, gi\|... - gi\|17986479\|ref\|NP_539113.1\| ATP-dependent Clp protease, ATP-binding subunit CLPB [Brucella melitens...	0.0	[3..807]	[137..927]
gi\|25289923 - pir\|\|F98216 endopeptidase clp ATP-binding chain B [imported] - Agrobacterium tumefaciens (strain C58... gi\|15890799, gi\|... - gi\|15890799\|ref\|NP_356471.1\| hypothetical protein AGR_L_1346 [Agrobacterium tumefaciens str. C58], g...	0.0	[4..809]	[94..884]
gi\|15803116, gi\|... - gi\|15803116\|ref\|NP_289147.1\| protein disaggregation chaperone [Escherichia coli O157:H7 EDL933], gi\|... gi\|227834799, gi... - gi\|227888159\|ref\|ZP_04005964.1\| endopeptidase Clp [Escherichia coli 83972], gi\|227834799\|gb\|EEJ45265... gi\|226839293, gi... - gi\|254037669\|ref\|ZP_04871727.1\| heat shock protein [Escherichia sp. 1_1_43], gi\|226839293\|gb\|EEH7131... gi\|26109361, gi\|... - gi\|26248955\|ref\|NP_754995.1\| protein disaggregation chaperone [Escherichia coli CFT073], gi\|26109361... gi\|209762704, gi... - gi\|25289895\|pir\|\|E85905 heat shock protein [imported] - Escherichia coli (strain O157:H7, substrain ...	0.0	[7..794]	[88..858]
CLPB_SALTY - Chaperone protein ClpB OS=Salmonella typhimurium GN=clpB PE=3 SV=1 CLPB_SALTY - Chaperone protein clpB OS=Salmonella typhimurium GN=clpB PE=3 SV=1 CLPB_SALTI - Chaperone protein clpB OS=Salmonella typhi GN=clpB PE=3 SV=1 gi\|213850142 - gi\|213850142\|ref\|ZP_03381040.1\| protein disaggregation chaperone [Salmonella enterica subsp. enteric... gi\|213999720 - gi\|213999720\|ref\|ZP_03410455.1\| protein disaggregation chaperone [Salmonella enterica subsp. enteric... gi\|194448814, gi... - gi\|194448814\|ref\|YP_002046666.1\| protein disaggregation chaperone [Salmonella enterica subsp. enteri... gi\|197244024, gi... - gi\|197265769\|ref\|ZP_03165843.1\| ATP-dependent chaperone protein ClpB [Salmonella enterica subsp. ent... gi\|213051813 - gi\|213051813\|ref\|ZP_03344691.1\| protein disaggregation chaperone [Salmonella enterica subsp. enteric... lcl\|NC_016856.1_... - [gene=clpB] [protein=protein disaggregation chaperone] [protein_id=YP_005238782.1] [location=complem... gi\|213649749 - gi\|213649749\|ref\|ZP_03379802.1\| protein disaggregation chaperone [Salmonella enterica subsp. enteric... gi\|29142985, gi\|... - gi\|29142985\|ref\|NP_806327.1\| protein disaggregation chaperone [Salmonella enterica subsp. enterica s... gi\|16761514 - gi\|16761514\|ref\|NP_457131.1\| protein disaggregation chaperone [Salmonella enterica subsp. enterica s... CLPB_SALTI - Chaperone protein ClpB OS=Salmonella typhi GN=clpB PE=3 SV=1 gi\|205329269, gi... - gi\|205329269\|gb\|EDZ16033.1\| chaperone protein clpB [Salmonella enterica subsp. enterica serovar 4,[5... CLPB_SALTY - Chaperone protein ClpB OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=clpB PE=3 ... gi\|168244680, gi... - gi\|205336469\|gb\|EDZ23233.1\| chaperone protein clpB [Salmonella enterica subsp. enterica serovar Heid...	0.0	[7..794]	[84..854]
gi\|188487823, gi... - gi\|75513198\|ref\|ZP_00735640.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|74313151, gi\|... - gi\|74313151\|ref\|YP_311570.1\| protein disaggregation chaperone [Shigella sonnei Ss046], gi\|73856628\|g... gi\|75236016, gi\|... - gi\|75236016\|ref\|ZP_00720150.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|193064051, gi... - gi\|75258013\|ref\|ZP_00729487.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|81246456, gi\|... - gi\|82545045\|ref\|YP_408992.1\| protein disaggregation chaperone [Shigella boydii Sb227], gi\|81246456\|g... gi\|83585276, gi\|... - gi\|83585276\|ref\|ZP_00923925.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|189354548, gi... - gi\|189354548\|gb\|EDU72967.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4401], gi\|... gi\|157080262, gi... - gi\|75187341\|ref\|ZP_00700608.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|189367288, gi... - gi\|189367288\|gb\|EDU85704.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4501], gi\|... gi\|168771698, gi... - gi\|189359601\|gb\|EDU78020.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4486], gi\|... gi\|187770676, gi... - gi\|187770676\|gb\|EDU34520.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4196], gi\|... gi\|75214716 - gi\|75214716\|ref\|ZP_00713224.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|189003333, gi... - gi\|189003333\|gb\|EDU72319.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4076], gi\|... gi\|75227675, gi\|... - gi\|75227675\|ref\|ZP_00714416.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|189370894, gi... - gi\|189370894\|gb\|EDU89310.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC869], gi\|1... gi\|157067748, gi... - gi\|75196607\|ref\|ZP_00706677.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|168801710, gi... - gi\|189376181\|gb\|EDU94597.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC508], gi\|1... gi\|194411789, gi... - gi\|75208572\|ref\|ZP_00708885.1\| COG0542: ATPases with chaperone activity, ATP-binding subunit [Escher... gi\|170019129, gi... - gi\|170019129\|ref\|YP_001724083.1\| protein disaggregation chaperone [Escherichia coli ATCC 8739], gi\|1... gi\|254593940, gi... - gi\|254794540\|ref\|YP_003079377.1\| protein disaggregation chaperone [Escherichia coli O157:H7 str. TW1... gi\|253974464, gi... - gi\|254162563\|ref\|YP_003045671.1\| protein disaggregation chaperone [Escherichia coli B str. REL606], ... gi\|254289324, gi... - gi\|254289324\|ref\|YP_003055072.1\| protein disaggregation chaperone [Escherichia coli BL21(DE3)], gi\|2... gi\|251785915, gi... - gi\|251785915\|ref\|YP_003000219.1\| hypothetical protein B21_02446 [Escherichia coli BL21], gi\|24237818... gi\|238901753, gi... - gi\|238901753\|ref\|YP_002927549.1\| protein disaggregation chaperone [Escherichia coli BW2952], gi\|2388... gi\|188014008, gi... - gi\|188014008\|gb\|EDU52130.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4113], gi\|... EG10157 - protein disaggregation chaperone / Bichaperone with DnaK for protein disaggregation; disaggregase; p... CLPB_ECOLI - Chaperone clpB (Heat-shock protein F84.1) - Escherichia coli CLPB_ECOL6 - Chaperone protein ClpB OS=Escherichia coli O6 GN=clpB PE=3 SV=1 gi\|89109394, gi\|... - gi\|89109394\|ref\|AP_003174.1\| protein disaggregation chaperone [Escherichia coli str. K-12 substr. W3... gi\|13362926, gi\|... - gi\|15832709\|ref\|NP_311482.1\| protein disaggregation chaperone [Escherichia coli O157:H7 str. Sakai],... gi\|110642755, gi... - gi\|110642755\|ref\|YP_670485.1\| protein disaggregation chaperone [Escherichia coli 536], gi\|110344347\|... CLPB_ECO57 - Chaperone protein ClpB OS=Escherichia coli O157:H7 GN=clpB PE=3 SV=1 EG10157 - protein disaggregation chaperone / Bichaperone with DnaK for protein disaggregation; disaggregase; p... gi\|215266003, gi... - gi\|215487931\|ref\|YP_002330362.1\| protein disaggregation chaperone [Escherichia coli O127:H6 str. E23... gi\|217326744, gi... - gi\|217326744\|ref\|ZP_03442827.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. TW14588]... gi\|218361940, gi... - gi\|218555172\|ref\|YP_002388085.1\| protein disaggregation chaperone [Escherichia coli IAI1], gi\|218361... gi\|218428275, gi... - gi\|218690711\|ref\|YP_002398923.1\| protein disaggregation chaperone [Escherichia coli ED1a], gi\|218428... gi\|218696217, gi... - gi\|218696217\|ref\|YP_002403884.1\| protein disaggregation chaperone [Escherichia coli 55989], gi\|21835... gi\|218371090, gi... - gi\|218701104\|ref\|YP_002408733.1\| protein disaggregation chaperone [Escherichia coli IAI39], gi\|21837... gi\|218433191, gi... - gi\|218706094\|ref\|YP_002413613.1\| protein disaggregation chaperone [Escherichia coli UMN026], gi\|2184... gi\|169890032, gi... - gi\|170082197\|ref\|YP_001731517.1\| protein disaggregation chaperone [Escherichia coli str. K-12 substr... gi\|170683980, gi... - gi\|170683980\|ref\|YP_001744777.1\| ATP-dependent chaperone protein ClpB [Escherichia coli SMS-3-5], gi... gi\|195940187 - gi\|195940187\|ref\|ZP_03085569.1\| protein disaggregation chaperone [Escherichia coli O157:H7 str. EC40... gi\|208805997, gi... - gi\|208805997\|ref\|ZP_03248334.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4206],... gi\|208813052, gi... - gi\|208813052\|ref\|ZP_03254381.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4045],... gi\|124500885, gi... - gi\|124527993\|ref\|ZP_01699346.1\| ATPase AAA-2 domain protein [Escherichia coli B], gi\|124500885\|gb\|EA... gi\|208819305, gi... - gi\|208819305\|ref\|ZP_03259625.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4042],... gi\|209397795, gi... - gi\|209397795\|ref\|YP_002272065.1\| ATP-dependent chaperone ClpB [Escherichia coli O157:H7 str. EC4115]... gi\|209920069, gi... - gi\|209920069\|ref\|YP_002294153.1\| protein disaggregation chaperone [Escherichia coli SE11], gi\|209913... CLPB_ECOL6 - Chaperone protein ClpB OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=clpB PE=3 S...	0.0	[7..794]	[84..854]
gi\|147365 - gi\|147365\|gb\|AAA24422.1\| ATP-dependent protease binding subunit [Escherichia coli]	0.0	[2..794]	[60..854]
gi\|17232576, gi\|... - gi\|17232576\|ref\|NP_489124.1\| endopeptidase Clp ATP-binding chain B [Nostoc sp. PCC 7120], gi\|1713422... gi\|25289937 - pir\|\|AD2441 endopeptidase Clp ATP-binding chain B [imported] - Nostoc sp. (strain PCC 7120)	0.0	[4..795]	[46..825]
HSP78 - Oligomeric mitochondrial matrix chaperone that cooperates with Ssc1p in mitochondrial thermotoleranc... gi\|207346524 - gi\|207346524\|gb\|EDZ72997.1\| YDR258Cp-like protein [Saccharomyces cerevisiae AWRI1631] HSP78_YEAST - Heat shock protein 78, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HSP...	0.0	[1..799]	[1..799]

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Predicted Domain #1

Region A:
Residues: [1-91]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLRQATKAPI QKYLQRTQLL RRSTPRIYTI VQCKRSICSF NARPRVANKL LSDIKTNALN  60
   61 EVAISTCALK SSYGLPNFKR TYVQMRMDPN Q

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.852	0.631	mitochondrial genome maintenance	a.4.5	"Winged helix" DNA-binding domain

Predicted functions:

Term	Confidence	Notes
transporter activity	3.04833973586251	bayes_pls_golite062009
hydrogen ion transmembrane transporter activity	2.97325763395103	bayes_pls_golite062009
transmembrane transporter activity	2.88860382281825	bayes_pls_golite062009
monovalent inorganic cation transmembrane transporter activity	2.82839518806942	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.62748401933955	bayes_pls_golite062009
pyrophosphatase activity	2.55282098898104	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.5316131833172	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.53035702378505	bayes_pls_golite062009
binding	2.21604035604783	bayes_pls_golite062009
hydrolase activity	2.18454736627863	bayes_pls_golite062009
hydrogen ion transporting ATP synthase activity, rotational mechanism	2.11085913752215	bayes_pls_golite062009
ATPase activity	2.04651885449197	bayes_pls_golite062009
ATPase activity, coupled	1.87142752786895	bayes_pls_golite062009
substrate-specific transporter activity	1.61003954220885	bayes_pls_golite062009
nucleic acid binding	1.52921795164482	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.35976511031033	bayes_pls_golite062009
protein binding	1.22129154759482	bayes_pls_golite062009
DNA binding	1.19966224604123	bayes_pls_golite062009
transcription regulator activity	1.09075553688438	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
purine nucleotide binding	0.929901285538132	bayes_pls_golite062009
nucleotide binding	0.922442819194247	bayes_pls_golite062009
purine ribonucleotide binding	0.920987930180051	bayes_pls_golite062009
ribonucleotide binding	0.920926158369519	bayes_pls_golite062009
structural constituent of ribosome	0.738234102557832	bayes_pls_golite062009
motor activity	0.70874549510465	bayes_pls_golite062009
guanyl nucleotide binding	0.640772201693186	bayes_pls_golite062009
guanyl ribonucleotide binding	0.63468044350616	bayes_pls_golite062009
DNA-dependent ATPase activity	0.62832939629645	bayes_pls_golite062009
GTP binding	0.621689261700018	bayes_pls_golite062009
ion transmembrane transporter activity	0.613335848236039	bayes_pls_golite062009
GTPase activity	0.437665353870877	bayes_pls_golite062009
active transmembrane transporter activity	0.434775387083003	bayes_pls_golite062009
ATP binding	0.41092997612902	bayes_pls_golite062009
adenyl ribonucleotide binding	0.385813421701492	bayes_pls_golite062009
adenyl nucleotide binding	0.377870145186619	bayes_pls_golite062009
inorganic cation transmembrane transporter activity	0.314819889840159	bayes_pls_golite062009
primary active transmembrane transporter activity	0.294474570607914	bayes_pls_golite062009
translation regulator activity	0.29096092258568	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	0.282352478532746	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.274994961137851	bayes_pls_golite062009
cation transmembrane transporter activity	0.226483101618176	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.220608508617331	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	0.219533217661421	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	0.219157471322311	bayes_pls_golite062009
transcription activator activity	0.129948034606198	bayes_pls_golite062009
transcription factor activity	0.0612932659603008	bayes_pls_golite062009
structural molecule activity	0.0558641287316701	bayes_pls_golite062009
structure-specific DNA binding	0.050232896280066	bayes_pls_golite062009
helicase activity	0.0450969969658499	bayes_pls_golite062009
protein transporter activity	0.0071389922757723	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [92-286]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QPEKPALEQF GTNLTKLARD GKLDPVIGRD EEIARAIQIL SRRTKNNPCL IGRAGVGKTA  60
   61 LIDGLAQRIV AGEVPDSLKD KDLVALDLGS LIAGAKYRGE FEERLKKVLE EIDKANGKVI 120
  121 VFIDEVHMLL GLGKTDGSMD ASNILKPKLA RGLRCISATT LDEFKIIEKD PALSRRFQPI 180
  181 LLNEPSVSDT ISILR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	688.124002
Match:	1jbkA_
Description:	ClpB
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [287-425]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GLKERYEVHH GVRITDTALV SAAVLSNRYI TDRFLPDKAI DLVDEACAVL RLQHESKPDE  60
   61 IQKLDRAIMK IQIELESLKK ETDPVSVERR EALEKDLEMK NDELNRLTKI WDAERAEIES 120
  121 IKNAKANLEQ ARIELEKCQ

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.9
Match:	1ksfX
Description:	N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone; ClpA, an Hsp100 chaperone, AAA+ modules
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [426-688]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 REGDYTKASE LRYSRIPDLE KKVALSEKSK DGDKVNLLHD SVTSDDISKV VAKMTGIPTE  60
   61 TVMKGDKDRL LYMENSLKER VVGQDEAIAA ISDAVRLQRA GLTSEKRPIA SFMFLGPTGT 120
  121 GKTELTKALA EFLFDDESNV IRFDMSEFQE KHTVSRLIGA PPGYVLSESG GQLTEAVRRK 180
  181 PYAVVLFDEF EKAHPDVSKL LLQVLDEGKL TDSLGHHVDF RNTIIVMTSN IGQDILLNDT 240
  241 KLGDDGKIDT ATKNKVIEAM KRS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.522879
Match:	1iqpA_
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [689-811]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YPPEFINRID DILVFNRLSK KVLRSIVDIR IAEIQDRLAE KRMKIDLTDE AKDWLTDKGY  60
   61 DQLYGARPLN RLIHRQILNS MATFLLKGQI RNGETVRVVV KDTKLVVLPN HEEGEVVEEE 120
  121 AEK

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	12.61
Match:	1e94E
Description:	HslU
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: