PF3D7_0727000 (VPS53)

Genome location: Pf3D7_07_v3:1,147,264..1,151,617(-)

Genome classification: Core

Function and Localization

Product Description: vacuolar protein sorting-associated protein 53, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: None

Curated GO (PlasmoDB):

Type	GO Term	Name
Component	GO:0000938	GARP complex
Process	GO:0042147	retrograde transport, endosome to Golgi

Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):

Stage	LR class	MCA mean	MCA prop. zeros
Sporozoite	not expressed	N/A	N/A
Ring	not expressed	0.09	0.95
Trophozoite	not expressed	0.53	0.69
Schizont	possibly expressed	0.21	0.86
Gametocyte	expressed	0.47	0.73

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_0727000

Resistome Missense Mutations: None

Resistome Compounds with Missense Mutations: None

Resistome # Samples with Disruptive Mutations: 1 (0 missense, 0 "interesting" missense)

Essentiality (ABS)

Zhang Phenotype: Mutable in CDS

MIS: 0.882 | MFS: -2.948 | #Insertions: 1

PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_0211100)

Relative Growth Rate: 0.09 ± 0.10
Confidence: 5.90

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8IBI7

"Best" AlphaFill ligand hit: TAR (d(-)-tartaric acid, Local RMSD=0.42) with 3OPS (Global RMSD=15.07)

No associated EC numbers

No evidence of orthology to BindingDB entries

Orthology Information

Ortholog Group (OrthoMCL): OG6_102035

Most Similar Human Ortholog: A0A7P0TA82

TM-align score: 0.87 | RMSD: 1.42

Seq Identity: 0.23 | Length: 80 / 1162

All Human Orthologs (OrthoMCL):

Gene ID	Description
ENSG00000141252	VPS53 subunit of GARP complex
ENSG00000283883	VPS53 subunit of GARP complex

Genetic Variation

MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	26	68	29	71
disruptive	117	198	100	217
missense	56	135	65	159

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	35	120	41	71
disruptive	176	370	137	300
missense	80	254	94	196

PlasmoDB Total SNPs: 305

Non-coding: 75 | Synonymous: 92 | Nonsynonymous: 138 | Stop Codon: 0

Protein Information

Protein Length: 1162 | Molecular Weight (kDa): 136.866

UniProt ID(s): Q8IBI7

PDB ID(s): None

Isoelectric Point: 6.46

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR007234	Vps53-like, N-terminal
InterPro	IPR039766	Vacuolar protein sorting-associated protein 53
PFam	PF04100	Vps53-like, N-terminal
Superfamily	N/A	N/A