Protein Help

TRE1 / YPL176C Protein

Protein abundance data, domains, shared domains with other proteins, protein sequence retrieval for various strains, sequence-based physico-chemical properties, protein modification sites, and external identifiers for the protein.


Feature Type
ORF , Verified
Paralog
TRE2 3

AlphaFold Protein Structure

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.


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Model Confidence

Very high
Confident
Low
Very low

Experimental Data

Contains experimentally-derived protein half-life data obtained using stable isotope labeling by amino acids (SILAC) coupled with mass spectrometry. This section also contains protein abundance data for both untreated and treated cells obtained from over 20 studies. These data have been normalized and converted to a common unit of molecules per cell.


Protein Half Life

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ExperimentResultReference
half-life1.2 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
1200SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
1205SD2 mM 1,4-dithiothreitol2 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
2032SD minus nitrogencellular response to nitrogen starvation15 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
1249SDuntreatedquantitative mass spectrometry evidenceS288Cde Godoy LM, et al. (2008)Ho B, et al. (2018)
396YEPDuntreatedqualitative western immunoblotting evidenceS288CGhaemmaghami S, et al. (2003)Ho B, et al. (2018)
Showing 1 to 5 of 9 entries

Domains and Classification - S288C

Collection of computationally identified domains and motifs, as determined by InterProScan analysis; includes protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain.


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Gene Protein Coordinates Accession ID Description Source No. of Genes with Domain

Domain Locations

Visual representation of the locations of the domains within the protein, as listed in the Domains and Classification table. Each row displays the domain(s) derived from a different Source, with domains color-coded according to this Source.

Scroll over a domain to view its exact coordinates and its Description.

Shared Domains

This diagram displays domains (colored squares) shared between the given protein (yellow circle) and other proteins (gray circles); the domains are color-coded according to their source, as displayed in the Domain Locations table, above.

Reset

Click on a gene or domain name to go to its specific page within SGD; drag any of the gene or domain objects around within the visualization for easier viewing; click “Reset” to automatically redraw the diagram.

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.


tre1-Δ

View all TRE1 alleles in SGD search

Sequence

Protein sequence for the given gene in S288C and other strains, when available. Use the pull-down menu under "Strain" to select the sequence for a specific strain. The displayed sequence can be downloaded in FASTA format as a .txt file. Amino acids displayed in blue represent modification sites. More detailed evidence for these modification sites is presented in the Post-translational Modifications table, located just below the protein sequence.


1 MVNTRGYTTL PNVEEPANNS QDELNSQDFE QAIGMPSEPP VYVEEMGMEE PQAPEAFSEK
61 VQRFRMCFEN NVVIPVKKNV VDPLAQMISL ASEKFDLFLS KIGNVMVMRR IFYIMMMSII
121 AALIIASDRL PNGKARGSNG SFSDHDLLLQ YARKSIDLSK IERDLEYISS MPHMSGTSGD
181 AAIRHYIKES FDKNGIRLAG EEEFMAYSNY PGNVSLRVYS KDDTEGFDIP LNEENFNPMS
241 HNGQLNNIPV IYANKASLDD MASMQDQGLL NGDFILLVHY GDYVFQQMLT AQEYGAKAII
301 FISEPYQDNK DVIQMKSVAL PQYGTGDALT PEWEGSIRDP IDATEAKCLP KIPSIPISAN
361 QGDKILAILS DTGVKFSNNL FSGSLNDCRL DLLVQTAIRE RHPVHDIVGK IEGSEQAGRA
421 IVIAAPRNSA SYGTMYPSFG TVVLLSLIQL YQEMVYKFDW KPLRNIYFIS FGGSEFNEAG
481 ATELMEKRTE ALKSEIYTII DVGQIGIWDD SNNLEIQCHP LLVDLFQKNM TSRKFNVKVD
541 NVHQFGDWTP YLAQGIPVAI ISSPGVMNRE HPIYTVEDKF DFIKDKLRDK KKGEVLSEIM
601 LYLVEKSLEL IDDPFIPFSI SNYVDFLSTT LKDLQKECPD TVNFDEVFLG TTLWENTKLQ
661 FEKWKSEWTE LMYGAGTYIE PTIIAINRWS WNYLLSLIGV TQCLEEGLMD RTFYKNVIFG
721 PKLWVDKGDP LRSWTFPEIR DTIAIKDWSS VQVQANTLGT ILQNTARYFL ENKNLHGINT
781 NEF*

* Blue amino acids indicate modification sites. More information below.

Post-translational Modifications - S288C

Modification sites for the protein in the selected strain, based on the presence of a residue in the specific strain, as inferred from experimental evidence.

1 entry for 1 site

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SiteModificationModifierReference
N213N-glycosylated residueZielinska DF, et al. (2012) PMID: 22633491
Showing 1 to 1 of 1 entries

Sequence-Based Physico-chemical Properties - S288C

Calculated protein properties, including amino acid composition, length, coding region calculations, and atomic composition.

Amino Acid Composition

Sort table using the arrow to the right of a column header to sort by that column; download all properties as a .txt file using the "Download Properties" button.

Amino AcidFrequencyPercentage
A435.49
C60.77
D516.51
E567.15
F384.85
G476.00
H111.40
I658.30
K445.62
L698.81
M273.45
N486.13
P384.85
Q324.09
R283.58
S577.28
T364.60
V455.75
W121.53
Y303.83

Physical Details

Length (a.a): 783
Molecular Weight (Da): 88721.6
Isoelectric Point (pl): 4.55
Formula: C3988H6142N1025O1201S33
Aliphatic Index: 84.68
Instability Index: 35.81

Coding Region Translation Calculations

Codon Bias: -0.01
Codon Adaptation Index: 0.11
Frequence of Optimal Codons: 0.43
Hydropathicity of Protein: -0.25
Aromaticity Score: 0.1

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 111075.0
NO Cys residues appear as half cystines: 110700.0

Atomic Composition

Sort table using the arrow to the right of a column header to sort by that column; download all properties as a .txt file using the "Download Properties" button.

Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

List of external identifiers for the protein from various database sources.

14 entries for 7 sources


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External IDSource
6325081GenBank/EMBL/DDBJ
CAA97883.1GenBank/EMBL/DDBJ
Z73532GenBank/EMBL/DDBJ
74627250GenBank/EMBL/DDBJ
1370371GenBank/EMBL/DDBJ
4726LoQAtE
855927NCBI
NP_015149.1NCBI
DAA11258.1NCBI
NM_001183990.1NCBI
Showing 1 to 10 of 14 entries

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