Detailed information of TA system TA024171

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 2503222..2503934
• Replicon: chromosome
• Accession: NC_012988
• Organism: Methylobacterium extorquens DM4 (Methylobacterium)

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: C7CBU9
• Locus tag: METD_RS11465
• Protein ID: WP_015822437.1
• Coordinates: 2503222..2503659 (-)
• Length: 146 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: C7CBV0
• Locus tag: METD_RS11470
• Protein ID: WP_015822438.1
• Coordinates: 2503656..2503934 (-)
• Length: 93 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
METD_RS11445	2498541..2499524	-	984	WP_111772144.1	plasmid partitioning protein RepB	-
METD_RS11450	2499521..2500744	-	1224	WP_041357685.1	plasmid partitioning protein RepA	-
METD_RS11455	2500951..2502123	-	1173	WP_015822435.1	site-specific integrase	-
METD_RS11460	2502137..2503225	-	1089	WP_015822436.1	hypothetical protein	-
METD_RS11465	2503222..2503659	-	438	WP_015822437.1	type II toxin-antitoxin system VapC family toxin	Toxin
METD_RS11470	2503656..2503934	-	279	WP_015822438.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
METD_RS11475	2504056..2504355	+	300	WP_015822439.1	hypothetical protein	-
METD_RS11485	2505901..2507145	-	1245	WP_015822441.1	TniQ family protein	-
METD_RS11490	2507142..2508020	-	879	WP_015822442.1	TniB family NTP-binding 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 (3-125)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (13-58)

Sequences

Toxin

Protein

• Length: 146 a.a.
• Molecular weight: 15923.21 Da
• Isoelectric Point: 4.5209

>T24171 WP_015822437.1 NC_012988:c2503659-2503222 [Methylorubrum extorquens AM1]
MNVLLDTNVLSEVRRPAPDQKVLAWLDTVDEDRAFISVASIAELRRGIALMDDGRRREALTAWLAEDLPARFAGRILPID
PAIAERWGDLMAHARQSGFALSVMDGFFAATALDRELVLATRNTKDFAPLGVPLLNPWTDEGAPG

Nucleotide

• Length: 438 bp

>T24171 NC_012988:c2503659-2503222 [Methylorubrum extorquens AM1]
ATGAACGTCCTGCTCGACACCAATGTGCTGTCGGAGGTGCGCCGGCCGGCGCCGGACCAAAAGGTGCTCGCCTGGCTCGA
TACGGTCGACGAGGACCGGGCCTTTATCAGCGTGGCGTCGATCGCCGAGCTCCGGCGCGGCATCGCCCTGATGGACGATG
GCCGTCGGCGCGAGGCGCTGACCGCCTGGCTTGCCGAGGATCTGCCGGCGCGCTTCGCCGGGCGGATCCTGCCGATCGAC
CCGGCAATCGCCGAACGCTGGGGCGATCTGATGGCGCATGCCCGCCAGAGCGGCTTCGCGCTCTCGGTCATGGACGGGTT
TTTCGCAGCCACCGCGCTTGACCGCGAGCTCGTGCTCGCGACCCGCAACACCAAGGATTTTGCGCCGCTGGGCGTACCAC
TGTTGAACCCCTGGACCGATGAAGGAGCACCGGGATGA

Antitoxin

Protein

• Length: 93 a.a.
• Molecular weight: 10306.70 Da
• Isoelectric Point: 8.8444

>AT24171 WP_015822438.1 NC_012988:c2503934-2503656 [Methylorubrum extorquens AM1]
VTIPRKTPAHESDHWTVAGAKARLSEVIERAQSDPQIITRHGKPSVVIVSAEEWARKTVRKGTLAEFLMASPLRNADLDL
DRARDQPRDLDL

Nucleotide

• Length: 279 bp

>AT24171 NC_012988:c2503934-2503656 [Methylorubrum extorquens AM1]
GTGACAATCCCCCGAAAAACCCCTGCTCACGAATCGGATCACTGGACGGTCGCTGGCGCCAAGGCGCGTCTCTCCGAAGT
GATCGAGCGCGCCCAGAGCGACCCGCAGATCATCACCCGCCACGGCAAGCCGAGCGTCGTCATCGTCTCGGCCGAGGAAT
GGGCGCGCAAGACCGTCCGCAAAGGCACCCTGGCCGAGTTCCTGATGGCCTCGCCGCTGCGCAACGCCGATCTCGACCTC
GATCGGGCCCGCGACCAACCGCGCGACCTCGATCTATGA

Structures

Toxin

• AlphaFold DB: C7CBU9

Antitoxin

• AlphaFold DB: C7CBV0