YRC Public Data Repository - Protein Structure Prediction

Protein:	YTA12
Organism:	Saccharomyces cerevisiae
Length:	825 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 YTA12.

Description	E-value	Query Range	Subject Range
YTA12_YEAST - Mitochondrial respiratory chain complexes assembly protein YTA12 OS=Saccharomyces cerevisiae (strain... YTA12 - Component, with Afg3p, of the mitochondrial inner membrane m-AAA protease that mediates degradation ...	0.0	[1..825]	[1..825]
AFG3L2 - AFG3 ATPase family gene 3-like 2 (yeast)	0.0	[102..816]	[70..780]
gi\|220947456 - gi\|220947456\|gb\|ACL86271.1\| CG6512-PA [synthetic construct] CG6512-PA - This gene is referred to in FlyBase by the symbol Dmel\CG6512 (CG6512, FBgn0036702). It is a protein...	0.0	[102..820]	[67..802]
gi\|15021761 - gi\|15021761\|gb\|AAK77908.1\|AF397903_1 AAA-metalloprotease FtsH [Pisum sativum]	0.0	[85..819]	[59..797]
gi\|15891238, gi\|... - gi\|15891238\|ref\|NP_356910.1\| hypothetical protein AGR_L_2253 [Agrobacterium tumefaciens str. C58], g... gi\|25308068 - pir\|\|E98271 metalloproteinase ftsH (AJ243808) [imported] - Agrobacterium tumefaciens (strain C58, Ce...	0.0	[171..822]	[15..661]
gi\|12082993 - gi\|12082993\|gb\|AAG48697.1\|AF323912_1 matrix AAA protease MAP-1 [Neurospora crassa]	0.0	[67..821]	[166..901]

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Predicted Domain #1

Region A:
Residues: [1-162]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLLLSWSRIA TKVVRRPVRF RSYYGLTHIK SLHTQYRLLN RLQENKSGNK NEDNNEDAKL  60
   61 NKEIPTDEEV EAIRKQVEKY IEQTKNNTIP ANWKEQKRKI DESIRRLEDA VLKQESNRIQ 120
  121 EERKEKEEEN GPSKAKSNRT KEQGYFEGNN SRNIPPPPPP PP

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.255	a.47.2	t-snare proteins

Predicted Domain #2

Region A:
Residues: [163-264]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PKPPLNDPSN PVSKNVNLFQ IGLTFFLLSF LLDLLNSLEE QSEITWQDFR EKLLAKGYVA  60
   61 KLIVVNKSMV KVMLNDNGKN QADNYGRNFY YFTIGSIDSF EH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	564.54902
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
nucleoside-triphosphatase activity	1.66565132432505	bayes_pls_golite062009
hydrolase activity	1.62872031361523	bayes_pls_golite062009
pyrophosphatase activity	1.59966904665651	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.5827346030945	bayes_pls_golite062009
ATPase activity	1.58256263495768	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.58037625997232	bayes_pls_golite062009
binding	1.49433277484566	bayes_pls_golite062009
SNARE binding	1.43448416553145	bayes_pls_golite062009
syntaxin binding	0.951634505775889	bayes_pls_golite062009
protein binding	0.842371133121818	bayes_pls_golite062009
ATPase activity, coupled	0.787685249362834	bayes_pls_golite062009
catalytic activity	0.767627914425245	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [265-344]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KLQKAQDELD IDKDFRIPVL YVQEGNWAKA MFQILPTVLM IAGIIWLTRR SAQAAGGSRG  60
   61 GIFGLSRSKA KKFNTETDVK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	564.54902
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
hydrogen ion transporting ATP synthase activity, rotational mechanism	3.57926427233638	bayes_pls_golite062009
transporter activity	3.10463051760206	bayes_pls_golite062009
transmembrane transporter activity	2.95886887664984	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
primary active transmembrane transporter activity	2.61775212528604	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	2.61467977505707	bayes_pls_golite062009
hydrogen ion transmembrane transporter activity	2.61311581579476	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	2.57552435627908	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	2.57107347424517	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	2.57054427875021	bayes_pls_golite062009
hydrolase activity	2.55157966585974	bayes_pls_golite062009
monovalent inorganic cation transmembrane transporter activity	2.50934147358924	bayes_pls_golite062009
active transmembrane transporter activity	2.50494515048649	bayes_pls_golite062009
ATPase activity, coupled	2.43862163407966	bayes_pls_golite062009
ATPase activity	2.39535714892224	bayes_pls_golite062009
binding	2.0681607836408	bayes_pls_golite062009
substrate-specific transporter activity	1.91091452720653	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.56325751172863	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
ion transmembrane transporter activity	0.977237423302079	bayes_pls_golite062009
P-P-bond-hydrolysis-driven protein transmembrane transporter activity	0.97313818590443	bayes_pls_golite062009
macromolecule transmembrane transporter activity	0.97313818590443	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
nucleic acid binding	0.831762535895849	bayes_pls_golite062009
guanyl nucleotide binding	0.640772201693186	bayes_pls_golite062009
guanyl ribonucleotide binding	0.63468044350616	bayes_pls_golite062009
GTP binding	0.621689261700018	bayes_pls_golite062009
cation transmembrane transporter activity	0.557919489256916	bayes_pls_golite062009
protein transporter activity	0.498432226280822	bayes_pls_golite062009
drug transmembrane transporter activity	0.46842047319323	bayes_pls_golite062009
protein transmembrane transporter activity	0.46552249844591	bayes_pls_golite062009
GTPase activity	0.437665353870877	bayes_pls_golite062009
ATP binding	0.41092997612902	bayes_pls_golite062009
adenyl ribonucleotide binding	0.385813421701492	bayes_pls_golite062009
protein binding	0.378225828131122	bayes_pls_golite062009
adenyl nucleotide binding	0.377870145186619	bayes_pls_golite062009
	0.3586311431823	bayes_pls_golite062009
signal recognition particle binding	0.29390189699022	bayes_pls_golite062009
DNA binding	0.143403729737365	bayes_pls_golite062009
inorganic cation transmembrane transporter activity	0.123304946374679	bayes_pls_golite062009
microtubule motor activity	0.11674780318211	bayes_pls_golite062009
transcription regulator activity	0.0147430141176288	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [345-518]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IKFKDVAGCD EAKEEIMEFV SFLKEPSRYE KMGAKIPRGA ILSGPPGTGK TLLAKATAGE  60
   61 AGVPFYFVSG SEFVEMFVGV GAARVRDLFK TARENAPSIV FIDEIDAIGK ARQKGNFSGA 120
  121 NDERENTLNQ MLVEMDGFTP ADHVVVLAGT NRPDILDKAL LRPGRFDRHI NIDK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	564.54902
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 #5

Region A:
Residues: [519-602]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PELEGRKAIF AVHLHHLKLA GEIFDLKNRL AALTPGFSGA DIANVCNEAA LIAARSDEDA  60
   61 VKLNHFEQAI ERVIGGVERK SKLL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	564.54902
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 #6

Region A:
Residues: [603-721]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SPEEKKVVAY HEAGHAVCGW YLKYADPLLK VSIIPRGQGA LGYAQYLPGD IFLLTEQQLK  60
   61 DRMTMSLGGR VSEELHFPSV TSGASDDFKK VTSMATAMVT ELGMSDKIGW VNYQKRDDS

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.710	0.396	protein complex assembly	d.109.1	Actin depolymerizing proteins
View	Download	0.345	0.382	protein complex assembly	a.29.2	Bromodomain
View	Download	0.335	0.012	mitochondrion	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.310	0.001	protein complex assembly	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.306	N/A	N/A	a.7.6	Ribosomal protein S20
View	Download	0.283	N/A	N/A	c.44.2	Enzyme IIB-cellobiose
View	Download	0.282	N/A	N/A	a.1.1	Globin-like
View	Download	0.270	N/A	N/A	c.84.1	Phosphoglucomutase, first 3 domains
View	Download	0.241	N/A	N/A	b.34.8	Fumarylacetoacetate hydrolase, FAH, N-terminal domain
View	Download	0.235	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.232	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.227	N/A	N/A	a.29.2	Bromodomain
View	Download	0.206	N/A	N/A	d.58.8	Viral DNA-binding domain
View	Download	0.203	N/A	N/A	a.26.1	4-helical cytokines

Predicted Domain #7

Region A:
Residues: [722-825]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DLTKPFSDET GDIIDSEVYR IVQECHDRCT KLLKEKAEDV EKIAQVLLKK EVLTREDMID  60
   61 LLGKRPFPER NDAFDKYLND YETEKIRKEE EKNEKRNEPK PSTN

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.431	0.050	mitochondrion	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.536	0.031	mitochondrion	a.23.4	Mitochondrial import receptor subunit Tom20
View	Download	0.756	0.031	proteolysis	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.525	0.000	protein complex assembly	a.49.1	C-terminal domain of B transposition protein
View	Download	0.424	N/A	N/A	a.24.10	Histidine-containing phosphotransfer domain, HPT domain
View	Download	0.394	N/A	N/A	a.1.1	Globin-like
View	Download	0.365	N/A	N/A	a.118.11	Cytochrome c oxidase subunit E
View	Download	0.363	N/A	N/A	a.7.6	Ribosomal protein S20
View	Download	0.336	N/A	N/A	a.71.1	Endoplasmic reticulum protein ERP29, C-domain
View	Download	0.313	N/A	N/A	a.118.8	TPR-like
View	Download	0.313	N/A	N/A	a.1.1	Globin-like
View	Download	0.269	N/A	N/A	a.118.8	TPR-like
View	Download	0.266	N/A	N/A	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.213	N/A	N/A	a.92.1	Carbamoyl phosphate synthetase, large subunit connection domain
View	Download	0.210	N/A	N/A	d.102.1	Regulatory factor Nef
View	Download	0.203	N/A	N/A	a.4.1	Homeodomain-like

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: