Protein Help

NAP1 / YKR048C 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
histone chaperone NAP1
Feature Type
ORF , Verified
Summary
Phosphorylated by CK2; protein abundance increases in response to 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.


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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-life10.5 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
10431SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
9043SD2 mM 1,4-dithiothreitol2 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
9798SD1 mM hydrogen peroxide1 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
8151SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
8344SD0.2 M hydroxyurea160 minconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
Showing 1 to 5 of 28 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.


nap1-T20A | nap1-Δ

View all NAP1 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 MSDPIRTKPK SSMQIDNAPT PHNTPASVLN PSYLKNGNPV RAQAQEQDDK IGTINEEDIL
61 ANQPLLLQSI QDRLGSLVGQ DSGYVGGLPK NVKEKLLSLK TLQSELFEVE KEFQVEMFEL
121 ENKFLQKYKP IWEQRSRIIS GQEQPKPEQI AKGQEIVESL NETELLVDEE EKAQNDSEEE
181 QVKGIPSFWL TALENLPIVC DTITDRDAEV LEYLQDIGLE YLTDGRPGFK LLFRFDSSAN
241 PFFTNDILCK TYFYQKELGY SGDFIYDHAE GCEISWKDNA HNVTVDLEMR KQRNKTTKQV
301 RTIEKITPIE SFFNFFDPPK IQNEDQDEEL EEDLEERLAL DYSIGEQLKD KLIPRAVDWF
361 TGAALEFEFE EDEEEADEDE DEEEDDDHGL EDDDGESAEE QDDFAGRPEQ APECKQS*

* 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.

76 entries for 18 sites

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SiteModificationModifierReference
S2phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S11phosphorylated residueHolt LJ, et al. (2009) PMID: 19779198
T20phosphorylated residueAlbuquerque CP, et al. (2008) PMID: 18407956
T20phosphorylated residueChen YC, et al. (2018) PMID: 30516470
T20phosphorylated residueSoulard A, et al. (2010) PMID: 20702584
T20phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
T20phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
T20phosphorylated residueZhou X, et al. (2021) PMID: 33481703
T20phosphorylated residueHolt LJ, et al. (2009) PMID: 19779198
T20phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
Showing 1 to 10 of 76 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
A204.80
C40.96
D399.35
E6014.39
F204.80
G215.04
H40.96
I245.76
K286.71
L399.35
M40.96
N194.56
P225.28
Q286.71
R143.36
S235.52
T184.32
V163.84
W40.96
Y102.40

Physical Details

Length (a.a): 417
Molecular Weight (Da): 47827.6
Isoelectric Point (pl): 3.96
Formula: C2105H3191N546O714S8
Aliphatic Index: 70.72
Instability Index: 53.97

Coding Region Translation Calculations

Codon Bias: 0.2
Codon Adaptation Index: 0.15
Frequence of Optimal Codons: 0.55
Hydropathicity of Protein: -0.85
Aromaticity Score: 0.08

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 37150.0
NO Cys residues appear as half cystines: 36900.0

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.

46 entries for 10 sources


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External IDSource
orf19.7501CGD
1380DIP
M63555GenBank/EMBL/DDBJ
AY692777GenBank/EMBL/DDBJ
6322901GenBank/EMBL/DDBJ
CAA82124.2GenBank/EMBL/DDBJ
AAT92796.1GenBank/EMBL/DDBJ
CAA82125.1GenBank/EMBL/DDBJ
AAA34811.1GenBank/EMBL/DDBJ
Z28272GenBank/EMBL/DDBJ
Showing 1 to 10 of 46 entries

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