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protein coding gene - vam6 (SPAC23H4.14) - HOPS complex RabGEF subunit Vam6

Gene summary

Standard name
vam6
Systematic ID
SPAC23H4.14
Product
HOPS complex RabGEF subunit Vam6
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
vps39
UniProt ID
O13955
ORFeome ID
47/47D12
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 1582412..1585585 reverse strand

Annotation

GO biological process

GO:0097352 - autophagosome maturation

References:

GO:0006886 - intracellular protein transport

References:

GO:1904263 - positive regulation of TORC1 signaling

References:

GO:0097576 - vacuole fusion

References:

GO:0140057 - vacuole-mitochondria membrane tethering

References:

GO:0016192 - vesicle-mediated transport

References:

GO cellular component

GO:0005829 - cytosol

References:

GO:0000329 - fungal-type vacuole membrane

References:

GO:0005634 - nucleus

References:

GO:1902500 - vacuolar HOPS complex

References:

GO:1990816 - vacuole-mitochondrion membrane contact site

References:

GO molecular function

GO:0005085 - guanyl-nucleotide exchange factor activity

References:

GO:0031267 - small GTPase binding

References:

Modification

MOD:00006 - N-glycosylated residue

References:

MOD:00046 - O-phospho-L-serine

References:

MOD:00047 - O-phospho-L-threonine

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Multi-locus phenotype

FYPO:0004482 - abnormal vacuole fusion during vegetative growth

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

Qualitative gene expression

PomGeneEx:0000018 - protein level increased

References:

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0001001 - abnormal cell cycle arrest at mitotic G2/M phase transition during nitrogen starvation

References:

Genotypes:

FYPO:0004482 - abnormal vacuole fusion during vegetative growth

References:

Genotypes:

FYPO:0001002 - abolished cell division prior to G0 entry

References:

Genotypes:

FYPO:0001283 - decreased protein level during cellular response to nitrogen starvation

References:

Genotypes:

FYPO:0001838 - decreased protein phosphorylation during vegetative growth

References:

Genotypes:

FYPO:0001178 - loss of viability upon nitrogen starvation

References:

Genotypes:

FYPO:0000997 - pear-shaped cell during nitrogen starvation

References:

Genotypes:

FYPO:0000764 - resistance to cycloheximide

References:

Genotypes:

FYPO:0009038 - resistance to egtazic acid

References:

Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

References:

Genotypes:

FYPO:0000830 - resistance to vanadate

References:

Genotypes:

FYPO:0000799 - sensitive to diamide

References:

Genotypes:

FYPO:0009086 - sensitive to lithium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0001234 - slow vegetative cell population growth

References:

Genotypes:

FYPO:0001003 - small vacuoles present in increased numbers during nitrogen starvation

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

FYPO:0001510 - viable vegetative cell, abnormal cell shape, normal cell size

References:

Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF10366Vps39_1VPS39/TGF_beta_rcpt-assoc_1PFAM
PF00780CNHCNH_domPFAM
PF10367zf-Vps39_CVPS39/TGFA1_ZnfPFAM
PS50219CNHCNH_domPROSITE_PROFILES
PS50236CHCRClathrin_H-chain/VPS_repeatPROSITE_PROFILES
SSF50978WD40 repeat-likeWD40_repeat_dom_sfSUPERFAMILY
G3DSA:2.130.10.10WD40/YVTN_repeat-like_dom_sfGENE3D
PTHR12894CNH DOMAIN CONTAININGVam6/VPS39/TRAP1PANTHER
CoilCoilCOILS

Orthologs

References / Literature

PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:19366728 - Genetic control of cellular quiescence in S. pombe.
Sajiki K et al. J Cell Sci 2009 May 01;122(Pt 9):1418-29
PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.
Rodríguez-López M et al. Elife 2023 Oct 03;12
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
PMID:2987072 - Hepatic triglyceride lipase and lipoprotein lipase activities in post-heparin plasma of patients with various cancers.
Masuno H et al. Jpn J Cancer Res 1985 Mar;76(3):202-7
PMID:22344254 - The Vam6 and Gtr1-Gtr2 pathway activates TORC1 in response to amino acids in fission yeast.
Valbuena N et al. J Cell Sci 2012 Apr 15;125(Pt 8):1920-8
PMID:22633491 - Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery.
Zielinska DF et al. Mol Cell 2012 May 25;46(4):542-8
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405
GO_REF:0000002 - Comments
PMID:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.
Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514