YRC Public Data Repository - Protein Structure Prediction

Protein:	HSP104
Organism:	Saccharomyces cerevisiae
Length:	908 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

[What does the above image mean?]

[Show Ginzu Version Information]

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 HSP104.

Description	E-value	Query Range	Subject Range
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	[1..880]	[57..931]
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	[1..865]	[4..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	[2..865]	[1..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	[2..865]	[1..854]
gi\|147365 - gi\|147365\|gb\|AAA24422.1\| ATP-dependent protease binding subunit [Escherichia coli]	0.0	[2..865]	[1..854]
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	[2..880]	[14..884]
CLPB_YERPE - Chaperone protein ClpB OS=Yersinia pestis GN=clpB PE=3 SV=2 gi\|16123432, gi\|... - gi\|218930300\|ref\|YP_002348175.1\| protein disaggregation chaperone [Yersinia pestis CO92], gi\|1612343...	0.0	[2..867]	[1..856]
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	[2..863]	[1..850]
CLPB_BRUSU - Chaperone protein ClpB OS=Brucella suis biovar 1 (strain 1330) GN=clpB PE=2 SV=1 CLPB_BRUSU - Chaperone protein clpB OS=Brucella suis GN=clpB PE=2 SV=1	0.0	[2..880]	[1..874]

Back

Predicted Domain #1

Region A:
Residues: [1-85]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNDQTQFTER ALTILTLAQK LASDHQHPQL QPIHILAAFI ETPEDGSVPY LQNLIEKGRY  60
   61 DYDLFKKVVN RNLVRIPQQQ PAPAE

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.971	0.127	nucleus	a.74.1	Cyclin-like

Predicted functions:

Term	Confidence	Notes
transporter activity	3.54081962055485	bayes_pls_golite062009
hydrogen ion transporting ATP synthase activity, rotational mechanism	3.36181317078971	bayes_pls_golite062009
transmembrane transporter activity	3.29578916194335	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.95079405147356	bayes_pls_golite062009
pyrophosphatase activity	2.87427509025394	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.85499564954033	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.85178667290149	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
hydrolase activity	2.55157966585974	bayes_pls_golite062009
ATPase activity	2.39535714892224	bayes_pls_golite062009
hydrogen ion transmembrane transporter activity	2.32451967319952	bayes_pls_golite062009
monovalent inorganic cation transmembrane transporter activity	2.20669061476179	bayes_pls_golite062009
ATPase activity, coupled	2.18396165590908	bayes_pls_golite062009
nucleic acid binding	2.11222585187695	bayes_pls_golite062009
DNA binding	1.7904783386531	bayes_pls_golite062009
protein transporter activity	1.71214667007262	bayes_pls_golite062009
transcription regulator activity	1.68903321260301	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.67543589693508	bayes_pls_golite062009
substrate-specific transporter activity	1.29730375126024	bayes_pls_golite062009
protein binding	1.22129154759482	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
motor activity	0.87979065815418	bayes_pls_golite062009
structural constituent of ribosome	0.860102064846772	bayes_pls_golite062009
structure-specific DNA binding	0.762584163889896	bayes_pls_golite062009
DNA-dependent ATPase activity	0.75383985982414	bayes_pls_golite062009
guanyl nucleotide binding	0.640772201693186	bayes_pls_golite062009
transcription activator activity	0.638755032892208	bayes_pls_golite062009
guanyl ribonucleotide binding	0.63468044350616	bayes_pls_golite062009
GTP binding	0.621689261700018	bayes_pls_golite062009
transcription factor activity	0.603758349693077	bayes_pls_golite062009
double-stranded DNA binding	0.49000746592281	bayes_pls_golite062009
protein transmembrane transporter activity	0.46552249844591	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
ion transmembrane transporter activity	0.355466224802969	bayes_pls_golite062009
helicase activity	0.33971254173831	bayes_pls_golite062009
sequence-specific DNA binding	0.334630071828653	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
DNA strand annealing activity	0.270268254152179	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
signal recognition particle binding	0.20866768220789	bayes_pls_golite062009
microtubule motor activity	0.11674780318211	bayes_pls_golite062009
structural molecule activity	0.11239762372728	bayes_pls_golite062009
cation transmembrane transporter activity	0.0254369227200564	bayes_pls_golite062009
ATP-dependent helicase activity	0.0136700590511267	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.0136700590511267	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [86-161]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ITPSYALGKV LQDAAKIQKQ QKDSFIAQDH ILFALFNDSS IQQIFKEAQV DIEAIKQQAL  60
   61 ELRGNTRIDS RGADTN

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	9.366532
Match:	PF02861
Description:	Clp amino terminal domain

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [162-353]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TPLEYLSKYA IDMTEQARQG KLDPVIGREE EIRSTIRVLA RRIKSNPCLI GEPGIGKTAI  60
   61 IEGVAQRIID DDVPTILQGA KLFSLDLAAL TAGAKYKGDF EERFKGVLKE IEESKTLIVL 120
  121 FIDEIHMLMG NGKDDAANIL KPALSRGQLK VIGATTNNEY RSIVEKDGAF ERRFQKIEVA 180
  181 EPSVRQTVAI LR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	679.69897
Match:	1jbkA_
Description:	ClpB
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [354-436]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GLQPKYEIHH GVRILDSALV TAAQLAKRYL PYRRLPDSAL DLVDISCAGV AVARDSKPEE  60
   61 LDSKERQLQL IQVEIKALER DED

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	9.02
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 #5

Region A:
Residues: [437-850]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ADSTTKDRLK LARQKEASLQ EELEPLRQRY NEEKHGHEEL TQAKKKLDEL ENKALDAERR  60
   61 YDTATAADLR YFAIPDIKKQ IEKLEDQVAE EERRAGANSM IQNVVDSDTI SETAARLTGI 120
  121 PVKKLSESEN EKLIHMERDL SSEVVGQMDA IKAVSNAVRL SRSGLANPRQ PASFLFLGLS 180
  181 GSGKTELAKK VAGFLFNDED MMIRVDCSEL SEKYAVSKLL GTTAGYVGYD EGGFLTNQLQ 240
  241 YKPYSVLLFD EVEKAHPDVL TVMLQMLDDG RITSGQGKTI DCSNCIVIMT SNLGAEFINS 300
  301 QQGSKIQEST KNLVMGAVRQ HFRPEFLNRI SSIVIFNKLS RKAIHKIVDI RLKEIEERFE 360
  361 QNDKHYKLNL TQEAKDFLAK YGYSDDMGAR PLNRLIQNEI LNKLALRILK NEIK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.0
Match:	1g4aE_
Description:	HslU
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [851-908]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DKETVNVVLK KGKSRDENVP EEAEECLEVL PNHEATIGAD TLGDDDNEDS MEIDDDLD

[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.

Found no confident structure predictions for this domain.

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: