YRC Public Data Repository - Protein Structure Prediction

Protein:	YME1
Organism:	Saccharomyces cerevisiae
Length:	747 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 YME1.

Description	E-value	Query Range	Subject Range
gi\|531752 - gi\|531752\|emb\|CAA56954.1\| YTA11 [Saccharomyces cerevisiae]	0.0	[1..747]	[1..747]
gi\|746401 - gi\|746401\|gb\|AAA97508.1\| ATP-binding protein gi\|188487047, gi... - gi\|188491848\|ref\|ZP_02999118.1\| ATP-dependent metallopeptidase HflB [Escherichia coli 53638], gi\|188... gi\|157068341, gi... - gi\|157162661\|ref\|YP_001459979.1\| ATP-dependent metalloprotease [Escherichia coli HS], gi\|157068341\|g... gi\|157080734, gi... - gi\|157158704\|ref\|YP_001464653.1\| ATP-dependent metalloprotease [Escherichia coli E24377A], gi\|157080... gi\|226839967, gi... - gi\|254038343\|ref\|ZP_04872401.1\| ATP-dependent metalloprotease [Escherichia sp. 1_1_43], gi\|226839967... gi\|253771988, gi... - gi\|253771988\|ref\|YP_003034819.1\| ATP-dependent metalloprotease FtsH [Escherichia coli BL21(DE3)], gi... gi\|237706070, gi... - gi\|237706070\|ref\|ZP_04536551.1\| ATP-dependent metalloprotease [Escherichia sp. 3_2_53FAA], gi\|226899... gi\|194411725, gi... - gi\|194430224\|ref\|ZP_03062722.1\| ATP-dependent metallopeptidase HflB [Escherichia coli B171], gi\|1944... tr\|A0A0G3HSQ2\|A0... - ATP-dependent zinc metalloprotease FtsH OS=Escherichia coli (strain K12) GN=ftsH PE=3 SV=1 gi\|191168060, gi... - gi\|191168060\|ref\|ZP_03029860.1\| ATP-dependent metallopeptidase HflB [Escherichia coli B7A], gi\|19090...	0.0	[120..746]	[1..638]
FTSH_SALTI - Cell division protease ftsH OS=Salmonella typhi GN=hflB PE=3 SV=1 FTSH_SALTY - Cell division protease ftsH OS=Salmonella typhimurium GN=hflB PE=3 SV=1 gi\|214000933 - gi\|214000933\|ref\|ZP_03411668.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica s... gi\|224585091, gi... - gi\|224585091\|ref\|YP_002638890.1\| cell division protein [Salmonella enterica subsp. enterica serovar ... gi\|56129482, gi\|... - gi\|56415225\|ref\|YP_152300.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica sero... gi\|238910089 - gi\|238910089\|ref\|ZP_04653926.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica s... gi\|207858544, gi... - gi\|207858544\|ref\|YP_002245195.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica ... gi\|213052988 - gi\|213052988\|ref\|ZP_03345866.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica s... lcl\|NC_016856.1_... - [gene=hflB] [protein=ATP-dependent metalloprotease] [protein_id=YP_005239474.1] [location=complement... gi\|213425426 - gi\|213425426\|ref\|ZP_03358176.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica s... gi\|213852786 - gi\|213852786\|ref\|ZP_03382318.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica s... gi\|29143547, gi\|... - gi\|29143547\|ref\|NP_806889.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica sero... gi\|160867488, gi... - gi\|161506141\|ref\|YP_001573253.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. arizonae ... FTSH_SALTY - ATP-dependent zinc metalloprotease FtsH OS=Salmonella typhimurium GN=ftsH PE=3 SV=1 gi\|16762058 - gi\|16762058\|ref\|NP_457675.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica sero... gi\|161616303, gi... - gi\|161616303\|ref\|YP_001590268.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica ... FTSH_SALTI - ATP-dependent zinc metalloprotease FtsH OS=Salmonella typhi GN=ftsH PE=3 SV=1 gi\|197364155, gi... - gi\|197364155\|ref\|YP_002143792.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica ... FTSH_SALTY - ATP-dependent zinc metalloprotease FtsH OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 7007... gi\|205273978, gi... - gi\|205354197\|ref\|YP_002227998.1\| ATP-dependent metalloprotease [Salmonella enterica subsp. enterica ...	0.0	[126..746]	[4..635]
FTSH_ECO57 - ATP-dependent zinc metalloprotease FtsH OS=Escherichia coli O157:H7 GN=ftsH PE=3 SV=1 gi\|13363530, gi\|... - gi\|15833311\|ref\|NP_312084.1\| ATP-dependent metalloprotease [Escherichia coli O157:H7 str. Sakai], gi... gi\|254594527, gi... - gi\|254795127\|ref\|YP_003079964.1\| subunit of integral membrane ATP-dependent zinc metallopeptidase [E... gi\|209758260, gi... - pir\|\|D85981 cell division protein HflB/FtsH proteinase [imported] - Escherichia coli (strain O157:H7... gi\|209160879, gi... - gi\|209399479\|ref\|YP_002272648.1\| ATP-dependent metallopeptidase HflB [Escherichia coli O157:H7 str. ... gi\|195938397 - gi\|195938397\|ref\|ZP_03083779.1\| ATP-dependent metalloprotease [Escherichia coli O157:H7 str. EC4024] gi\|15803718, gi\|... - gi\|15803718\|ref\|NP_289752.1\| ATP-dependent metalloprotease [Escherichia coli O157:H7 EDL933], gi\|125... gi\|217319989, gi... - gi\|217327622\|ref\|ZP_03443705.1\| ATP-dependent metallopeptidase HflB [Escherichia coli O157:H7 str. T...	0.0	[126..746]	[4..635]
gi\|218555748, gi... - gi\|218555748\|ref\|YP_002388661.1\| ATP-dependent metalloprotease [Escherichia coli IAI1], gi\|218362516... gi\|218358002, gi... - gi\|218550461\|ref\|YP_002384252.1\| ATP-dependent metalloprotease [Escherichia fergusonii ATCC 35469], ... gi\|218429032, gi... - gi\|218691468\|ref\|YP_002399680.1\| ATP-dependent metalloprotease [Escherichia coli ED1a], gi\|218429032... gi\|218367017, gi... - gi\|218560248\|ref\|YP_002393161.1\| ATP-dependent metalloprotease [Escherichia coli S88], gi\|218367017\|... gi\|218701947, gi... - gi\|218701947\|ref\|YP_002409576.1\| ATP-dependent metalloprotease [Escherichia coli IAI39], gi\|21837193... gi\|218696883, gi... - gi\|218696883\|ref\|YP_002404550.1\| ATP-dependent metalloprotease [Escherichia coli 55989], gi\|21835361... gi\|218706798, gi... - gi\|218706798\|ref\|YP_002414317.1\| ATP-dependent metalloprotease [Escherichia coli UMN026], gi\|2184338... FTSH_ECOLI - Cell division protease ftsH (EC 3.4.24.-) - Escherichia coli EG11506 - protease, ATP-dependent zinc-metallo / ATP-dependent membrane protease, complexed with HflCK; regula... FTSH_SHIFL - ATP-dependent zinc metalloprotease FtsH OS=Shigella flexneri GN=ftsH PE=3 SV=1 gi\|24053649, gi\|... - gi\|24114467\|ref\|NP_708977.1\| ATP-dependent metalloprotease [Shigella flexneri 2a str. 301], gi\|24053... gi\|30042775, gi\|... - gi\|30064516\|ref\|NP_838687.1\| ATP-dependent metalloprotease [Shigella flexneri 2a str. 2457T], gi\|300... EG11506 - protease, ATP-dependent zinc-metallo / ATP-dependent membrane protease, complexed with HflCK; regula... gi\|227887899, gi... - gi\|227887899\|ref\|ZP_04005704.1\| M41 family endopeptidase FtsH [Escherichia coli 83972], gi\|227835295... gi\|238863291, gi... - gi\|238902280\|ref\|YP_002928076.1\| protease, ATP-dependent zinc-metallo [Escherichia coli BW2952], gi\|... gi\|251786448, gi... - gi\|251786448\|ref\|YP_003000752.1\| hypothetical protein B21_02994 [Escherichia coli BL21], gi\|24237872... gi\|253975021, gi... - gi\|254163120\|ref\|YP_003046228.1\| protease, ATP-dependent zinc-metallo [Escherichia coli B str. REL60... gi\|253979177, gi... - gi\|254289870\|ref\|YP_003055618.1\| protease, ATP-dependent zinc-metallo [Escherichia coli BL21(DE3)], ... gi\|169890548, gi... - gi\|170082713\|ref\|YP_001732033.1\| subunit of integral membrane ATP-dependent zinc metallopeptidase [E... gi\|169753500, gi... - gi\|170018572\|ref\|YP_001723526.1\| ATP-dependent metalloprotease [Escherichia coli ATCC 8739], gi\|1697... gi\|215266566, gi... - gi\|215488494\|ref\|YP_002330925.1\| ATP-dependent metalloprotease [Escherichia coli O127:H6 str. E2348/... gi\|209920653, gi... - gi\|209920653\|ref\|YP_002294737.1\| ATP-dependent metalloprotease [Escherichia coli SE11], gi\|209913912... gi\|75197127 - gi\|75197127\|ref\|ZP_00707197.1\| COG0465: ATP-dependent Zn proteases [Escherichia coli HS] gi\|75208502 - gi\|75208502\|ref\|ZP_00708822.1\| COG0465: ATP-dependent Zn proteases [Escherichia coli B171] gi\|75187984 - gi\|75187984\|ref\|ZP_00701251.1\| COG0465: ATP-dependent Zn proteases [Escherichia coli E24377A] gi\|146028, gi\|89... - gi\|89109941\|ref\|AP_003721.1\| protease, ATP-dependent zinc-metallo [Escherichia coli str. K-12 substr... gi\|91074173, gi\|... - gi\|91212599\|ref\|YP_542585.1\| ATP-dependent metalloprotease [Escherichia coli UTI89], gi\|91074173\|gb\|... gi\|117625472, gi... - gi\|117625472\|ref\|YP_858795.1\| ATP-dependent metalloprotease [Escherichia coli APEC O1], gi\|115514596... gi\|110345010, gi... - gi\|110643418\|ref\|YP_671148.1\| ATP-dependent metalloprotease [Escherichia coli 536], gi\|110345010\|gb\|... gi\|75228765 - gi\|75228765\|ref\|ZP_00715374.1\| COG0465: ATP-dependent Zn proteases [Escherichia coli B7A] gi\|110616592, gi... - gi\|110807044\|ref\|YP_690564.1\| ATP-dependent metalloprotease [Shigella flexneri 5 str. 8401], gi\|1106... gi\|74313715, gi\|... - gi\|74313715\|ref\|YP_312134.1\| ATP-dependent metalloprotease [Shigella sonnei Ss046], gi\|73857192\|gb\|A...	0.0	[126..746]	[4..635]
gi\|11278954 - pir\|\|E82299 cell division protein FtsH VC0637 [imported] - Vibrio cholerae (strain N16961 serogroup ... gi\|229357964, gi... - gi\|229505741\|ref\|ZP_04395251.1\| cell division protein FtsH [Vibrio cholerae BX 330286], gi\|229357964... gi\|229509226, gi... - gi\|229509226\|ref\|ZP_04398711.1\| cell division protein FtsH [Vibrio cholerae B33], gi\|229353798\|gb\|EE... gi\|146315175, gi... - gi\|227117012\|ref\|YP_002818908.1\| cell division protein FtsH [Vibrio cholerae O395], gi\|227012462\|gb\|... gi\|227008706, gi... - gi\|227080818\|ref\|YP_002809369.1\| cell division protein FtsH [Vibrio cholerae M66-2], gi\|227008706\|gb... gi\|254850871, gi... - gi\|254850871\|ref\|ZP_05240221.1\| cell division protein FtsH [Vibrio cholerae MO10], gi\|254846576\|gb\|E... gi\|229519565, gi... - gi\|229519565\|ref\|ZP_04409008.1\| cell division protein FtsH [Vibrio cholerae RC9], gi\|229344254\|gb\|EE... gi\|15640657, gi\|... - gi\|9655072\|gb\|AAF93803.1\| cell division protein FtsH [Vibrio cholerae O1 biovar El Tor str. N16961],... gi\|229371507, gi... - gi\|229608852\|ref\|YP_002879500.1\| cell division protein FtsH [Vibrio cholerae MJ-1236], gi\|229371507\|...	0.0	[120..747]	[1..637]
gi\|22124596, gi\|... - gi\|22124596\|ref\|NP_668019.1\| ATP-dependent metalloprotease [Yersinia pestis KIM], gi\|21957399\|gb\|AAM... gi\|165937451, gi... - gi\|165937451\|ref\|ZP_02226014.1\| ATP-dependent metallopeptidase HflB [Yersinia pestis biovar Oriental... gi\|45435292, gi\|... - gi\|45440435\|ref\|NP_991974.1\| ATP-dependent metalloprotease [Yersinia pestis biovar Microtus str. 910... gi\|165989729, gi... - gi\|166011345\|ref\|ZP_02232243.1\| ATP-dependent metallopeptidase HflB [Yersinia pestis biovar Antiqua ... gi\|165919868, gi... - gi\|165928181\|ref\|ZP_02224013.1\| ATP-dependent metallopeptidase HflB [Yersinia pestis biovar Oriental... gi\|170025951, gi... - gi\|170025951\|ref\|YP_001722456.1\| ATP-dependent metalloprotease [Yersinia pseudotuberculosis YPIII], ... gi\|167420745, gi... - gi\|167420745\|ref\|ZP_02312498.1\| ATP-dependent metallopeptidase HflB [Yersinia pestis biovar Oriental... gi\|167057456, gi... - gi\|167423286\|ref\|ZP_02315039.1\| ATP-dependent metallopeptidase HflB [Yersinia pestis biovar Mediaeva... gi\|166214009, gi... - gi\|166214009\|ref\|ZP_02240044.1\| ATP-dependent metallopeptidase HflB [Yersinia pestis biovar Antiqua ... gi\|167049379, gi... - gi\|167401354\|ref\|ZP_02306854.1\| ATP-dependent metallopeptidase HflB [Yersinia pestis biovar Antiqua ...	0.0	[120..746]	[1..638]
gi\|108806050, gi... - gi\|108806050\|ref\|YP_649966.1\| ATP-dependent metalloprotease [Yersinia pestis Antiqua], gi\|108777963\|... gi\|186893835, gi... - gi\|186893835\|ref\|YP_001870947.1\| ATP-dependent metalloprotease [Yersinia pseudotuberculosis PB1/+], ... gi\|229687210, gi... - gi\|229899718\|ref\|ZP_04514859.1\| subunit of integral membrane ATP-dependent zinc metallopeptidase [Ye... gi\|229679650, gi... - gi\|229903880\|ref\|ZP_04518993.1\| subunit of integral membrane ATP-dependent zinc metallopeptidase [Ye... Q66F66\|Q66F66_YERPS - Cell division protein precursor - Yersinia pseudotuberculosis gi\|89104072 - gi\|89104072\|ref\|ZP_01176626.1\| COG0465: ATP-dependent Zn proteases [Yersinia pestis biovar Orientali... gi\|117675037, gi... - gi\|77631471\|ref\|ZP_00794057.1\| COG0465: ATP-dependent Zn proteases [Yersinia pseudotuberculosis IP 3... gi\|153997279, gi... - gi\|153997279\|ref\|ZP_02022379.1\| subunit of integral membrane ATP-dependent zinc metallopeptidase [Ye... gi\|145212494, gi... - gi\|145600798\|ref\|YP_001164874.1\| ATP-dependent metalloprotease [Yersinia pestis Pestoides F], gi\|145... gi\|51588108, gi\|... - gi\|51594826\|ref\|YP_069017.1\| ATP-dependent metalloprotease [Yersinia pseudotuberculosis IP 32953], g... gi\|25308060 - pir\|\|AG0425 cell division protein (EC 3.4.24.-) [imported] - Yersinia pestis (strain CO92) gi\|218930516, gi... - gi\|218930516\|ref\|YP_002348391.1\| ATP-dependent metalloprotease [Yersinia pestis CO92], gi\|16123648\|r... gi\|229695520, gi... - gi\|229839154\|ref\|ZP_04459313.1\| subunit of integral membrane ATP-dependent zinc metallopeptidase [Ye... gi\|229700421, gi... - gi\|229896643\|ref\|ZP_04511810.1\| subunit of integral membrane ATP-dependent zinc metallopeptidase [Ye...	0.0	[126..746]	[4..635]

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Predicted Domain #1

Region A:
Residues: [1-182]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNVSKILVSP TVTTNVLRIF APRLPQIGAS LLVQKKWALR SKKFYRFYSE KNSGEMPPKK  60
   61 EADSSGKASN KSTISSIDNS QPPPPSNTND KTKQANVAVS HAMLATREQE ANKDLTSPDA 120
  121 QAAFYKLLLQ SNYPQYVVSR FETPGIASSP ECMELYMEAL QRIGRHSEAD AVRQNLLTAS 180
  181 SA

[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.

Predicted Domain #2

Region A:
Residues: [183-254]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GAVNPSLASS SSNQSGYHGN FPSMYSPLYG SRKEPLHVVV SESTFTVVSR WVKWLLVFGI  60
   61 LTYSFSEGFK YI

[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 functions:

Term	Confidence	Notes
hydrolase activity	1.62872031361523	bayes_pls_golite062009
binding	1.49433277484566	bayes_pls_golite062009
catalytic activity	0.767627914425245	bayes_pls_golite062009
protein binding	0.657913936613888	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.578045489085857	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.576706256405554	bayes_pls_golite062009
SNARE binding	0.1851395346962	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [255-447]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TENTTLLKSS EVADKSVDVA KTNVKFDDVC GCDEARAELE EIVDFLKDPT KYESLGGKLP  60
   61 KGVLLTGPPG TGKTLLARAT AGEAGVDFFF MSGSEFDEVY VGVGAKRIRD LFAQARSRAP 120
  121 AIIFIDELDA IGGKRNPKDQ AYAKQTLNQL LVELDGFSQT SGIIIIGATN FPEALDKALT 180
  181 RPGRFDKVVN VDL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	959.0
Match:	1lv7A_
Description:	AAA domain of cell division protein FtsH
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	2.55157966585974	bayes_pls_golite062009
binding	2.0681607836408	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.85030653553169	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.84811666933472	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
motor activity	0.677658554107	bayes_pls_golite062009
purine nucleotide binding	0.569910969126728	bayes_pls_golite062009
purine ribonucleotide binding	0.568840867400671	bayes_pls_golite062009
ribonucleotide binding	0.568779924702229	bayes_pls_golite062009
nucleotide binding	0.564275755355315	bayes_pls_golite062009
pyrophosphatase activity	0.540750418412449	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.517457589081898	bayes_pls_golite062009
nucleic acid binding	0.318452816722389	bayes_pls_golite062009
protein binding	0.193768631623192	bayes_pls_golite062009
ATP binding	0.1860481660648	bayes_pls_golite062009
adenyl ribonucleotide binding	0.152859582615242	bayes_pls_golite062009
adenyl nucleotide binding	0.138615225841109	bayes_pls_golite062009
microtubule motor activity	0.11674780318211	bayes_pls_golite062009
DNA strand annealing activity	0.0887104483353087	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [448-552]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PDVRGRADIL KHHMKKITLA DNVDPTIIAR GTPGLSGAEL ANLVNQAAVY ACQKNAVSVD  60
   61 MSHFEWAKDK ILMGAERKTM VLTDAARKAT AFHEAGHAIM AKYTN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	959.0
Match:	1lv7A_
Description:	AAA domain of cell division protein FtsH
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [553-632]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GATPLYKATI LPRGRALGIT FQLPEMDKVD ITKRECQARL DVCMGGKIAE ELIYGKDNTT  60
   61 SGCGSDLQSA TGTARAMVTQ

[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.

Predicted Domain #6

Region A:
Residues: [633-747]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YGMSDDVGPV NLSENWESWS NKIRDIADNE VIELLKDSEE RARRLLTKKN VELHRLAQGL  60
   61 IEYETLDAHE IEQVCKGEKL DKLKTSTNTV VEGPDSDERK DIGDDKPKIP TMLNA

[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: