YRC Public Data Repository - Protein Structure Prediction

Protein:	PIM1
Organism:	Saccharomyces cerevisiae
Length:	1133 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 PIM1.

Description	E-value	Query Range	Subject Range
LONM_YEAST - Lon protease homolog, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PIM1... PIM1 - ATP-dependent Lon protease, involved in degradation of misfolded proteins in mitochondria; required ...	0.0	[1..1133]	[1..1133]
lon1 - Lon protease homolog Lon1 LONM_SCHPO - Lon protease homolog, mitochondrial OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pim1 P...	0.0	[91..1125]	[69..1056]
gi\|14719366 - gi\|14719366\|gb\|AAK73158.1\| lon proteinase [Paracoccidioides brasiliensis]	0.0	[90..1124]	[53..1055]
LONM_RAT - Lon protease homolog, mitochondrial OS=Rattus norvegicus GN=Lonp1 PE=2 SV=1	0.0	[142..1118]	[71..948]
gi\|126193574, gi... - gi\|254240196\|ref\|ZP_04933518.1\| Lon protease [Pseudomonas aeruginosa 2192], gi\|194551181\|ref\|YP_0020... gi\|126166828, gi... - gi\|254234897\|ref\|ZP_04928220.1\| Lon protease [Pseudomonas aeruginosa C3719], gi\|194545882\|ref\|YP_002... gi\|218772469, gi... - gi\|218892243\|ref\|YP_002441110.1\| Lon protease [Pseudomonas aeruginosa LESB58], gi\|218772469\|emb\|CAW2... gi\|15597000, gi\|... - gi\|9947786\|gb\|AAG05192.1\|AE004606_6 Lon protease [Pseudomonas aeruginosa PAO1], gi\|15597000\|ref\|NP_2... gi\|11350562 - pir\|\|G83420 Lon proteinase PA1803 [imported] - Pseudomonas aeruginosa (strain PAO1)	0.0	[261..1113]	[6..772]
gi\|146644 - gi\|146644\|gb\|AAA24079.1\| ATP-dependent proteinase (lon) [Escherichia coli]	0.0	[261..1112]	[10..776]
LON_RHIME - ATP-dependent protease La OS=Rhizobium meliloti GN=lon PE=3 SV=2 LON_RHIME - Lon protease OS=Rhizobium meliloti (strain 1021) GN=lon PE=3 SV=2	0.0	[261..1113]	[13..779]
gi\|70731344, gi\|... - gi\|70731344\|ref\|YP_261085.1\| ATP-dependent protease La [Pseudomonas fluorescens Pf-5], gi\|68345643\|g... gi\|7644385 - gi\|7644385\|gb\|AAF65564.1\|AF250140_1 protease Lon [Pseudomonas fluorescens]	0.0	[261..1113]	[6..772]
gi\|58037564, gi\|... - gi\|58037564\|ref\|NP_083058.1\| protease, serine, 15 [Mus musculus], gi\|12836291\|dbj\|BAB23591.1\| unname...	0.0	[142..1118]	[71..947]

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Predicted Domain #1

Region A:
Residues: [1-155]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLRTRTTKTL STVARTTRAI QYYRSIAKTA AVSQRRFAST LTVRDVENIK PSHIIKSPTW  60
   61 QEFQHQLKDP RYMEHFAQLD AQFARHFMAT NSGKSILAKD DSTSQKKDED VKIVPDEKDT 120
  121 DNDVEPTRDD EIVNKDQEGE ASKNSRSSAS GGGQS

[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.

Predicted Domain #2

Region A:
Residues: [156-387]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SSSRSDSGDG SSKQKPPKDV PEVYPQMLAL PIARRPLFPG FYKAVVISDE RVMKAIKEML  60
   61 DRQQPYIGAF MLKNSEEDTD VITDKNDVYD VGVLAQITSA FPSKDEKTGT ETMTALLYPH 120
  121 RRIKIDELFP PNEEKEKSKE QAKDTDTETT VVEDANNPED QESTSPATPK LEDIVVERIP 180
  181 DSELQHHKRV EATEEESEEL DDIQEGEDIN PTEFLKNYNV SLVNVLNLED EP

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	71.744727
Match:	PF02190
Description:	ATP-dependent protease La (LON) 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 functions:

Term	Confidence	Notes
binding	1.20426875618254	bayes_pls_golite062009
protein binding	0.594610587848879	bayes_pls_golite062009
ubiquitin-protein ligase activity	0.533622874557729	bayes_pls_golite062009
small conjugating protein ligase activity	0.505301584684092	bayes_pls_golite062009
catalytic activity	0.174240748624544	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [388-449]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FDRKSPVINA LTSEILKVFK EISQLNTMFR EQIATFSASI QSATTNIFEE PARLADFAAA  60
   61 VS

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.54
Match:	1jqjC
Description:	delta subunit; delta subunit of DNA polymerase III, N-domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [450-581]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AGEEDELQDI LSSLNIEHRL EKSLLVLKKE LMNAELQNKI SKDVETKIQK RQREYYLMEQ  60
   61 LKGIKRELGI DDGRDKLIDT YKERIKSLKL PDSVQKIFDD EITKLSTLET SMSEFGVIRN 120
  121 YLDWLTSIPW GK

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.54
Match:	1jqjC
Description:	delta subunit; delta subunit of DNA polymerase III, N-domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [582-768]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HSKEQYSIPR AKKILDEDHY GMVDVKDRIL EFIAVGKLLG KVDGKIICFV GPPGVGKTSI  60
   61 GKSIARALNR KFFRFSVGGM TDVAEIKGHR RTYIGALPGR VVQALKKCQT QNPLILIDEI 120
  121 DKIGHGGIHG DPSAALLEVL DPEQNNSFLD NYLDIPIDLS KVLFVCTANS LETIPRPLLD 180
  181 RMEVIEL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	62.221849
Match:	1e32A_
Description:	Membrane fusion atpase p97 N-terminal domain , P97-Nn; Membrane fusion atpase p97, D1 domain; Membrane fusion atpase p97 domain 2, P97-Nc
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ribonuclease activity	2.03745175432755	bayes_pls_golite062009
nuclease activity	1.83032641679211	bayes_pls_golite062009
structural constituent of ribosome	1.38482286547386	bayes_pls_golite062009
hydrolase activity	1.18773479836745	bayes_pls_golite062009
3'-5'-exoribonuclease activity	1.16726450662143	bayes_pls_golite062009
exoribonuclease activity	1.1604717842042	bayes_pls_golite062009
structural molecule activity	1.14918348313691	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	1.13566902804592	bayes_pls_golite062009
ATP-dependent peptidase activity	0.99253423929971	bayes_pls_golite062009
binding	0.923114523007774	bayes_pls_golite062009
catalytic activity	0.878454819018611	bayes_pls_golite062009
peptidase activity	0.46678532223973	bayes_pls_golite062009
protein binding	0.398523921130957	bayes_pls_golite062009
endopeptidase activity	0.227419965943609	bayes_pls_golite062009
peptidase activity, acting on L-amino acid peptides	0.161393552073973	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	0.0709817198603016	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	6.9430052008157E-5	bayes_pls_golite062009

Predicted Domain #6

Region A:
Residues: [769-890]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TGYVAEDKVK IAEQYLVPSA KKSAGLENSH VDMTEDAITA LMKYYCRESG VRNLKKHIEK  60
   61 IYRKAALQVV KKLSIEDSPT SSADSKPKES VSSEEKAENN AKSSSEKTKD NNSEKTSDDI 120
  121 EA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	62.221849
Match:	1e32A_
Description:	Membrane fusion atpase p97 N-terminal domain , P97-Nn; Membrane fusion atpase p97, D1 domain; Membrane fusion atpase p97 domain 2, P97-Nc
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [891-988]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LKTSEKINVS ISQKNLKDYV GPPVYTTDRL YETTPPGVVM GLAWTNMGGC SLYVESVLEQ  60
   61 PLHNCKHPTF ERTGQLGDVM KESSRLAYSF AKMYLAQK

[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	0.865	N/A	N/A	d.50.2	Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain

Predicted Domain #8

Region A:
Residues: [989-1133]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FPENRFFEKA SIHLHCPEGA TPKDGPSAGV TMATSFLSLA LNKSIDPTVA MTGELTLTGK  60
   61 VLRIGGLREK AVAAKRSGAK TIIFPKDNLN DWEELPDNVK EGLEPLAADW YNDIFQKLFK 120
  121 DVNTKEGNSV WKAEFEILDA KKEKD

[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.

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:

Predicted functions: