Protein Help

UBP2 / YOR124C 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.


Protein Product
ubiquitin-specific protease UBP2
Feature Type
ORF , Verified
EC Number
3.4.19.12

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-life11.1 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
1931SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
1601SD0.2 M hydroxyurea160 minconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
3277YEPDuntreatedflow cytometry evidenceS288CDavidson GS, et al. (2011)Ho B, et al. (2018)
3767YEPDcell quiescence7 dflow cytometry evidenceS288CDavidson GS, et al. (2011)Ho B, et al. (2018)
8337SDuntreatedquantitative mass spectrometry evidenceS288Cde Godoy LM, et al. (2008)Ho B, et al. (2018)
Showing 1 to 5 of 19 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.


ubp2-C745S | ubp2-C745V | ubp2-Δ

View all UBP2 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 MPNEDNELQK AIENHHNQLL NQDKENADRN GSVIEDLPLY GTSINQQSTP GDVDDGKHLL
61 YPDIATNLPL KTSDRLLDDI LCDTIFLNST DPKVMQKGLQ SRGILKESML SYSTFRSSIR
121 PNCLGSLTDQ VVFQTKSEYD SISCPKYNKI HVFQAVIFNP SLAEQQISTF DDIVKIPIYH
181 LKVSVKVRQE LERLKKHVGV TQFHSLDHLH EYDRVDLSTF DSSDPNLLDY GIYVSDDTNK
241 LILIEIFKPE FNSPEEHESF TADAIKKRYN AMCVKNESLD KSETPSQVDC FYTLFKIFKG
301 PLTRKSKAEP TKTIDSGNLA LNTHLNPEWL TSKYGFQASS EIDEETNEIF TEYVPPDMVD
361 YVNDLETRKI RESFVRKCLQ LIFWGQLSTS LLAPNSPLKN TKSVKGMSSL QTSFSTLPWF
421 HLLGESRARI LLNSNEQTHS PLDAEPHFIN LSVSHYYTDR DIIRNYESLS SLDPENIGLY
481 FDALTYIANR KGAYQLIAYC GKQDIIGQEA LENALLMFKI NPKECNISEL NEATLLSIYK
541 YETSNKSQVT SNHLTNLKNA LRLLAKYTKS DKLKFYVDHE PYRALSQAYD TLSIDESVDE
601 DIIKTAYSVK INDSPGLKLD CDRALYTIAI SKRSLDLFNF LTEECPQFSN YYGPEKLDYQ
661 EALKLLQVNE NASDETILKI FKQKWFDENV YEPDQFLILR AALTKISIER NSTLITNFLL
721 TGTIDPNSLP PENWPTGINN IGNTCYLNSL LQYYFSIAPL RRYVLEYQKT VENFNDHLSN
781 SGHIRRIGGR EISRGEVERS IQFIYQLRNL FYAMVHTRER CVTPSKELAY LAFAPSNVEV
841 EFEVEGNKVV DQTGVLSDSK KETTDDAFTT KIKDTSLIDL EMEDGLNGDV GTDANRKKNE
901 SNDAEVSENE DTTGLTSPTR VAKISSDQLE NALEMGRQQD VTECIGNVLF QIESGSEPIR
961 YDEDNEQYDL VKQLFYGTTK QSIVPLSATN KVRTKVERFL SLLINIGDHP KDIYDAFDSY
1021 FKDEYLTMEE YGDVIRTVAV TTFPTILQVQ IQRVYYDRER LMPFKSIEPL PFKEVIYMDR
1081 YADTENPLLL AKKKETEEMK QKLKVMKNRQ RELLSRDDSG LTRKDAFLES IKLLESDTIK
1141 KTPLKIEAAN DVIKTLRNNV QNIDNELMKL YNDINSLEEK ISHQFDDFKE YGYSLFSVFI
1201 HRGEASYGHY WIYIKDRNRN GIWRKYNDET ISEVQEEEVF NFNEGNTATP YFLVYVKQGQ
1261 EGDIEPLKRI LK*

* 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.

53 entries for 29 sites

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SiteModificationModifierReference
S32phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S32phosphorylated residueLeutert M, et al. (2023) PMID: 37845410
S43phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S43phosphorylated residueLeutert M, et al. (2023) PMID: 37845410
S48phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
T49phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S440phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S614phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S781phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
T823phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
Showing 1 to 10 of 53 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
A524.09
C131.02
D927.23
E1048.18
F544.25
G483.77
H241.89
I886.92
K927.23
L13510.61
M161.26
N846.60
P503.93
Q524.09
R554.32
S1017.94
T816.37
V634.95
W70.55
Y614.80

Physical Details

Length (a.a): 1272
Molecular Weight (Da): 146306.7
Isoelectric Point (pl): 4.84
Formula: C6523H10153N1720O2044S29
Aliphatic Index: 82.17
Instability Index: 38.33

Coding Region Translation Calculations

Codon Bias: 0.05
Codon Adaptation Index: 0.15
Frequence of Optimal Codons: 0.46
Hydropathicity of Protein: -0.54
Aromaticity Score: 0.1

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 130140.0
NO Cys residues appear as half cystines: 129390.0

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.

27 entries for 11 sources


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External IDSource
AN10722AspGD
orf19.457CGD
2647DIP
3.4.19.12ExPASy
1050825GenBank/EMBL/DDBJ
Z75032GenBank/EMBL/DDBJ
M94916GenBank/EMBL/DDBJ
X94335GenBank/EMBL/DDBJ
X90518GenBank/EMBL/DDBJ
1420324GenBank/EMBL/DDBJ
Showing 1 to 10 of 27 entries

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