Protein Help

UBX3 / YDL091C 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
Summary
Clathrin-coated vesicle component; UBX (ubiquitin regulatory X) domain-containing protein that interacts with Cdc48p

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-life5.6 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
326SDuntreatedquantitative mass spectrometry evidenceS288Cde Godoy LM, et al. (2008)Ho B, et al. (2018)
4307SDuntreatedwide-field microscopy evidenceS288CDénervaud N, et al. (2013)Ho B, et al. (2018)
4596SD0.03% methyl methanesulfonate7 hrwide-field microscopy evidenceS288CDénervaud N, et al. (2013)Ho B, et al. (2018)
233YEPDuntreatedqualitative western immunoblotting evidenceS288CGhaemmaghami S, et al. (2003)Ho B, et al. (2018)
165YEPDuntreatedquantitative mass spectrometry evidenceS288CKulak NA, et al. (2014)Ho B, et al. (2018)
Showing 1 to 5 of 12 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.


ubx3-Δ | ubx3-ΔUBXd

View all UBX3 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 MDIFRHTFGN NDDSFIRIPG AFREEPPADL NGRTEDQNSN TNEPTQSRDG RLKSILHFLF
61 QAPLIVLYYL LNFIVRSSRL LKPLLRLHGF YQRKHNRLLD HSSQLHRLLE NLENEAQAVT
121 CSEGNGNNDD GSNTDSTSNN ESSGVQFSFG SLYNPENGTF SKSIMQNSYT ELLDACSEQV
181 KFGVIYLHDP LLDNHMDYVN KILCSEAFVN MIRKYQVLLW YGDVTTSEGL QVSNALKIRQ
241 YPLLGIISLK AEKKIELIAR VEGSISNYKA QDLEAIFSKN YSRLIQLRQQ RQNIEMQRLI
301 RQQQDSRYQD SLRRDQQRES ERLEQTQREQ MEREHQRIEN QWLLWRKSQL KPEPSSDKDA
361 SKVAIRLENG QRLVRKFDAS LPTEEIYAFV ELQLHDMLNS ENDTLPVYQP ANYQHQYSFK
421 LITPVPRREL DLSTKISDVS GIYPSGNIVM ERLDE*

* 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.

7 entries for 4 sites

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SiteModificationModifierReference
S14phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S39phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S39phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S39phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S39phosphorylated residueZhou X, et al. (2021) PMID: 33481703
S103phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S311phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
Showing 1 to 7 of 7 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
A173.74
C30.66
D275.93
E357.69
F173.74
G194.18
H112.42
I275.93
K204.40
L5411.87
M81.76
N327.03
P173.74
Q357.69
R357.69
S429.23
T163.52
V194.18
W30.66
Y183.96

Physical Details

Length (a.a): 455
Molecular Weight (Da): 52937.0
Isoelectric Point (pl): 6.31
Formula: C2324H3661N672O723S11
Aliphatic Index: 80.13
Instability Index: 43.22

Coding Region Translation Calculations

Codon Bias: 0.06
Codon Adaptation Index: 0.14
Frequence of Optimal Codons: 0.46
Hydropathicity of Protein: -0.7
Aromaticity Score: 0.08

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 43445.0
NO Cys residues appear as half cystines: 43320.0

Atomic Composition

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Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

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

19 entries for 9 sources


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External IDSource
AN0770AspGD
orf19.1595CGD
5024DIP
CAA64920.1GenBank/EMBL/DDBJ
CAA98657.1GenBank/EMBL/DDBJ
6320112GenBank/EMBL/DDBJ
Z74139GenBank/EMBL/DDBJ
X95644GenBank/EMBL/DDBJ
77416596GenBank/EMBL/DDBJ
1199556GenBank/EMBL/DDBJ
Showing 1 to 10 of 19 entries

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