Protein Help

UFD4 / YKL010C 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
putative ubiquitin-protein ligase UFD4
Feature Type
ORF , Verified
EC Number
2.3.2.26
Summary
Ufd4p is 1483 amino acids long, shorter-lived, low in abundance; contains disordered region at N-terminus; ubiquitinylated on K174 and K488, sumoylated on 3 lysines, phosphorylated on 13 residues; relative distribution to the nucleus increases upon DNA replication stress

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.


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-life7.7 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
2551SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
2153SD0.2 M hydroxyurea160 min0.84confocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
3141YEPDuntreatedflow cytometry evidenceS288CDavidson GS, et al. (2011)Ho B, et al. (2018)
3806SDuntreatedquantitative mass spectrometry evidenceS288Cde Godoy LM, et al. (2008)Ho B, et al. (2018)
3544SD0.03% methyl methanesulfonate7 hrwide-field microscopy evidenceS288CDénervaud N, et al. (2013)Ho B, et al. (2018)
Showing 1 to 5 of 20 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.


ufd4-E1442A | ufd4-F313A,T315A,I316A | ufd4-H1433A | ufd4-H317A | ufd4-Q1471A | ufd4-R1468A | ufd4-Y276A,I277A,D278A | ... Show all

View all UFD4 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 MSENNSHNLD EHESHSENSD YMMDTQVEDD YDEDGHVQGE YSYYPDEDED EHMLSSVGSF
61 EADDGEDDDN DYHHEDDSGL LYGYHRTQNG SDEDRNEEED GLERSHDNNE FGSNPLHLPD
121 ILETFAQRLE QRRQTSEGLG QHPVGRTLPE ILSMIGGRME RSAESSARNE RISKLIENTG
181 NASEDPYIAM ESLKELSENI LMMNQMVVDR IIPMETLIGN IAAILSDKIL REELELQMQA
241 CRCMYNLFEV CPESISIAVD EHVIPILQGK LVEISYIDLA EQVLETVEYI SRVHGRDILK
301 TGQLSIYVQF FDFLTIHAQR KAIAIVSNAC SSIRTDDFKT IVEVLPTLKP IFSNATDQPI
361 LTRLVNAMYG ICGALHGVDK FETLFSLDLI ERIVQLVSIQ DTPLENKLKC LDILTVLAMS
421 SDVLSRELRE KTDIVDMATR SFQHYSKSPN AGLHETLIYV PNSLLISISR FIVVLFPPED
481 ERILSADKYT GNSDRGVISN QEKFDSLVQC LIPILVEIYT NAADFDVRRY VLIALLRVVS
541 CINNSTAKAI NDQLIKLIGS ILAQKETASN ANGTYSSEAG TLLVGGLSLL DLICKKFSEL
601 FFPSIKREGI FDLVKDLSVD FNNIDLKEDG NENISLSDEE GDLHSSIEEC DEGDEEYDYE
661 FTDMEIPDSV KPKKISIHIF RTLSLAYIKN KGVNLVNRVL SQMNVEQEAI TEELHQIEGV
721 VSILENPSTP DKTEEDWKGI WSVLKKCIFH EDFDVSGFEF TSTGLASSIT KRITSSTVSH
781 FILAKSFLEV FEDCIDRFLE ILQSALTRLE NFSIVDCGLH DGGGVSSLAK EIKIKLVYDG
841 DASKDNIGTD LSSTIVSVHC IASFTSLNEF LRHRMVRMRF LNSLIPNLTS SSTEADREEE
901 ENCLDHMRKK NFDFFYDNEK VDMESTVFGV IFNTFVRRNR DLKTLWDDTH TIKFCKSLEG
961 NNRESEAAEE ANEGKKLRDF YKKREFAQVD TGSSADILTL LDFLHSCGVK SDSFINSKLS
1021 AKLARQLDEP LVVASGALPD WSLFLTRRFP FLFPFDTRML FLQCTSFGYG RLIQLWKNKS
1081 KGSKDLRNDE ALQQLGRITR RKLRISRKTI FATGLKILSK YGSSPDVLEI EYQEEAGTGL
1141 GPTLEFYSVV SKYFARKSLN MWRCNSYSYR SEMDVDTTDD YITTLLFPEP LNPFSNNEKV
1201 IELFGYLGTF VARSLLDNRI LDFRFSKVFF ELLHRMSTPN VTTVPSDVET CLLMIELVDP
1261 LLAKSLKYIV ANKDDNMTLE SLSLTFTVPG NDDIELIPGG CNKSLNSSNV EEYIHGVIDQ
1321 ILGKGIEKQL KAFIEGFSKV FSYERMLILF PDELVDIFGR VEEDWSMATL YTNLNAEHGY
1381 TMDSSIIHDF ISIISAFGKH ERRLFLQFLT GSPKLPIGGF KSLNPKFTVV LKHAEDGLTA
1441 DEYLPSVMTC ANYLKLPKYT SKDIMRSRLC QAIEEGAGAF LLS*

* 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.

29 entries for 18 sites

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SiteModificationModifierReference
S14phosphorylated residueLeutert M, et al. (2023) PMID: 37845410
S14phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S19phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
T87phosphorylated residueSoulard A, et al. (2010) PMID: 20702584
S91phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S91phosphorylated residueAlbuquerque CP, et al. (2008) PMID: 18407956
S91phosphorylated residueHolt LJ, et al. (2009) PMID: 19779198
S91phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S91phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S91phosphorylated residueLeutert M, et al. (2023) PMID: 37845410
Showing 1 to 10 of 29 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
A664.45
C231.55
D1127.55
E1288.63
F775.19
G785.26
H342.29
I1107.42
K795.33
L16711.26
M332.23
N734.92
P442.97
Q382.56
R714.79
S1399.37
T785.26
V835.60
W70.47
Y432.90

Physical Details

Length (a.a): 1483
Molecular Weight (Da): 167753.9
Isoelectric Point (pl): 4.53
Formula: C7445H11617N1961O2335S56
Aliphatic Index: 89.89
Instability Index: 40.91

Coding Region Translation Calculations

Codon Bias: 0.04
Codon Adaptation Index: 0.14
Frequence of Optimal Codons: 0.45
Hydropathicity of Protein: -0.24
Aromaticity Score: 0.09

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 103945.0
NO Cys residues appear as half cystines: 102570.0

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.

20 entries for 10 sources


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External IDSource
orf19.3237CGD
4873DIP
2.3.2.26ExPASy
Z28010GenBank/EMBL/DDBJ
CAA81845.1GenBank/EMBL/DDBJ
AAB24903.1GenBank/EMBL/DDBJ
398364789GenBank/EMBL/DDBJ
S53418GenBank/EMBL/DDBJ
465668GenBank/EMBL/DDBJ
485993GenBank/EMBL/DDBJ
Showing 1 to 10 of 20 entries

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