Detailed information of TA system TA022006

Bioinformatically predicted

Overview

TA module

• Type: IV
• Classification (family/domain): ygfYX/Cpta(toxin)
• Location: 1208763..1209438
• Replicon: chromosome
• Accession: NC_009092
• Organism: Shewanella loihica PV-4

Toxin (Protein)

• Gene name: ygfX
• Uniprot ID: A3QBR9
• Locus tag: SHEW_RS05395
• Protein ID: WP_011864850.1
• Coordinates: 1208983..1209438 (+)
• Length: 152 a.a.

Antitoxin (Protein)

• Gene name: ygfY
• Uniprot ID: -
• Locus tag: SHEW_RS05390
• Protein ID: WP_041406484.1
• Coordinates: 1208763..1209002 (+)
• Length: 80 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SHEW_RS05365	1204127..1204921	+	795	WP_011864844.1	sulfite exporter TauE/SafE family protein	-
SHEW_RS05370	1205044..1205895	+	852	WP_011864845.1	thymidylate synthase	-
SHEW_RS05375	1206202..1207377	+	1176	WP_011864846.1	Na+/H+ antiporter NhaA	-
SHEW_RS05380	1207374..1207757	+	384	WP_011864847.1	hypothetical protein	-
SHEW_RS05385	1207778..1208686	+	909	WP_011864848.1	transcriptional activator NhaR	-
SHEW_RS05390	1208763..1209002	+	240	WP_041406484.1	succinate dehydrogenase assembly factor 2	Antitoxin
SHEW_RS05395	1208983..1209438	+	456	WP_011864850.1	hypothetical protein	Toxin
SHEW_RS05400	1209447..1211060	-	1614	WP_011864851.1	L-aspartate oxidase	-
SHEW_RS05405	1211260..1211838	+	579	WP_011864852.1	RNA polymerase sigma factor RpoE	-
SHEW_RS05410	1211878..1212480	+	603	WP_011864853.1	anti-sigma factor	-
SHEW_RS05415	1212546..1213478	+	933	WP_011864854.1	MucB/RseB C-terminal domain-containing protein	-
SHEW_RS05420	1213486..1213962	+	477	WP_011864855.1	SoxR reducing system RseC family protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)

Relative position:
(1) inside: TA loci is completely located inside the MGE;
(2) overlap: TA loci is partially overlapped with the MGE;
(3) flank: The TA loci is located in the 5 kb flanking regions of MGE.

Domains

Predicted by InterproScan

Toxin

• Inner membrane protein YgfX (5-149)

Antitoxin

• Flavinator of succinate dehydrogenase (4-75)

Sequences

Toxin

Protein

• Length: 152 a.a.
• Molecular weight: 18062.15 Da
• Isoelectric Point: 8.7156

>T22006 WP_011864850.1 NC_009092:1208983-1209438 [Shewanella loihica PV-4]
VAGRRHNFHLTASFDQRLSLVCFAALCLSAFLVWPPITSLWFLTLKYGFLLATITFFLYQFIVLRRWSLAFWLDESGRIG
LLRDELDSHTQVQQVEEAIEQRLSYRRIWVSPLVVLFWLYEGEQKRLVILWRDMFDDTGYRHLCRLLLRFG

Nucleotide

• Length: 456 bp

>T22006 NC_009092:1208983-1209438 [Shewanella loihica PV-4]
GTGGCCGGGCGGCGCCATAACTTTCACCTGACAGCCTCCTTCGACCAGCGACTCTCGCTGGTCTGTTTCGCCGCCCTGTG
CCTGAGTGCTTTTTTGGTCTGGCCGCCAATCACCTCTCTCTGGTTTCTCACCCTCAAGTATGGCTTCTTGCTGGCCACAA
TCACTTTCTTCCTCTATCAGTTTATTGTGCTAAGACGTTGGTCCCTTGCCTTTTGGCTGGATGAGTCGGGCAGAATAGGT
CTACTCCGCGACGAGTTAGATTCGCATACGCAAGTGCAGCAGGTTGAGGAAGCAATCGAGCAACGACTCAGTTATCGCAG
GATCTGGGTCAGTCCCTTGGTGGTGTTGTTCTGGTTATACGAGGGAGAGCAGAAACGCCTGGTTATCTTATGGCGGGATA
TGTTCGACGACACAGGTTATCGGCACCTGTGTCGCCTGCTACTGAGATTTGGCTAA

Antitoxin

Protein

• Length: 80 a.a.
• Molecular weight: 9169.66 Da
• Isoelectric Point: 4.5535

>AT22006 WP_041406484.1 NC_009092:1208763-1209002 [Shewanella loihica PV-4]
MNIARVRWACRRGMLELDVLFQPFVETQYEQLSIDDKAVFVRLLECEDPELFAWFMGHEACPDPQLADMVVKVRGRAAP

Nucleotide

• Length: 240 bp

>AT22006 NC_009092:1208763-1209002 [Shewanella loihica PV-4]
ATGAACATAGCCAGAGTAAGATGGGCGTGCCGACGGGGCATGTTAGAGCTTGATGTATTGTTTCAACCCTTTGTTGAGAC
CCAATATGAACAGCTGTCTATAGATGATAAGGCGGTTTTCGTTCGTCTGTTAGAGTGTGAAGATCCTGAGTTGTTTGCCT
GGTTTATGGGCCATGAGGCCTGTCCAGACCCGCAGCTTGCCGACATGGTGGTCAAAGTTCGTGGCCGGGCGGCGCCATAA

Structures

Toxin

• AlphaFold DB: A3QBR9