Detailed information of TA system TA024167

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC(toxin)
• Location: 4855..5498
• Replicon: chromosome
• Accession: NC_012988
• Organism: Methylobacterium extorquens DM4 (Methylobacterium)

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: C7C6G0
• Locus tag: METD_RS00020
• Protein ID: WP_012778865.1
• Coordinates: 4855..5259 (-)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: -
• Locus tag: METD_RS00025
• Protein ID: WP_012251834.1
• Coordinates: 5259..5498 (-)
• Length: 80 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
METD_RS00005	710..2215	+	1506	WP_012778864.1	chromosomal replication initiator protein DnaA	-
METD_RS00010	2535..3656	+	1122	WP_003598299.1	DNA polymerase III subunit beta	-
METD_RS00015	3697..4851	+	1155	WP_012251832.1	DNA replication/repair protein RecF	-
METD_RS00020	4855..5259	-	405	WP_012778865.1	type II toxin-antitoxin system VapC family toxin	Toxin
METD_RS00025	5259..5498	-	240	WP_012251834.1	type II toxin-antitoxin system VapB family antitoxin	Antitoxin
METD_RS00030	5601..7448	+	1848	WP_012778866.1	DNA helicase RecQ	-
METD_RS00035	7506..7844	-	339	WP_041357188.1	hypothetical protein	-
METD_RS00040	8160..8846	+	687	WP_003598308.1	hypothetical 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

• PIN domain (1-128)

Antitoxin

• Antitoxin VapB-like (1-75)

Sequences

Toxin

Protein

• Length: 135 a.a.
• Molecular weight: 14294.31 Da
• Isoelectric Point: 5.1418

>T24167 WP_012778865.1 NC_012988:c5259-4855 [Methylorubrum extorquens AM1]
MFVDASAIVAIIAREPQAETLTARLEEAPVRYTSAVAVLETVMALRRLGAGSIAQAEQLVRHLLEHADIEEVPITTRESA
AAIAAYARYGKGQGHPAQLNLGDCFAYACARTRNVPLLFVGNDFSQTDIAAALA

Nucleotide

• Length: 405 bp

>T24167 NC_012988:c5259-4855 [Methylorubrum extorquens AM1]
ATGTTCGTAGACGCGTCGGCGATCGTCGCGATCATCGCACGCGAGCCGCAGGCGGAAACATTGACGGCCCGGCTCGAGGA
GGCGCCCGTCCGCTATACCTCGGCAGTGGCCGTCTTGGAAACGGTGATGGCCTTGCGGCGCCTCGGTGCGGGATCGATCG
CGCAAGCAGAGCAACTGGTGCGACATCTGCTCGAGCATGCGGATATTGAGGAAGTCCCCATCACAACGCGGGAGTCGGCT
GCGGCCATCGCCGCATACGCGCGCTACGGCAAGGGCCAGGGCCACCCTGCCCAACTCAACCTCGGCGACTGCTTCGCCTA
TGCCTGCGCTCGAACGCGCAACGTCCCGCTTCTCTTCGTCGGCAACGACTTCTCGCAGACCGACATCGCCGCTGCATTGG
CCTGA

Antitoxin

Protein

• Length: 80 a.a.
• Molecular weight: 8977.27 Da
• Isoelectric Point: 10.0862

>AT24167 WP_012251834.1 NC_012988:c5498-5259 [Methylorubrum extorquens AM1]
MPLNIRSEEVNRLAEKLASQARVSKTEAVRMALANELQRRESSLPLSERIKPIQDAFARWPKTGMKADKAFFDDMNGES

Nucleotide

• Length: 240 bp

>AT24167 NC_012988:c5498-5259 [Methylorubrum extorquens AM1]
ATGCCCTTGAACATCCGCAGCGAGGAGGTGAACCGCCTCGCCGAGAAGCTGGCATCGCAGGCTCGGGTGAGCAAGACCGA
GGCGGTGCGTATGGCGTTGGCCAACGAACTGCAACGCCGGGAATCGTCGCTGCCGCTGTCAGAGCGGATCAAGCCGATCC
AAGATGCCTTCGCGCGTTGGCCGAAGACGGGTATGAAAGCCGACAAGGCCTTCTTCGACGACATGAACGGCGAGTCCTGA

Structures

Toxin

• AlphaFold DB: A0A1S1P7Q0