Detailed information of TA system TA038043

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-VagC
• Location: 2043595..2044253
• Replicon: chromosome
• Accession: NZ_AP024145
• Organism: Methylobacterium indicum strain VL1

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: miv_RS09505
• Protein ID: WP_207182404.1
• Coordinates: 2043595..2043999 (-)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A0J6RC86
• Locus tag: miv_RS09510
• Protein ID: WP_048428143.1
• Coordinates: 2043996..2044253 (-)
• Length: 86 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
miv_RS09480	2039019..2040218	+	1200	WP_207182400.1	succinyl-diaminopimelate desuccinylase	-
miv_RS09485	2040270..2040842	+	573	WP_207182402.1	hypothetical protein	-
miv_RS09490	2041097..2042026	-	930	WP_048428147.1	histone deacetylase family protein	-
miv_RS09495	2042223..2042822	+	600	WP_048428146.1	L,D-transpeptidase	-
miv_RS09500	2043071..2043517	+	447	WP_048428145.1	hypothetical protein	-
miv_RS09505	2043595..2043999	-	405	WP_207182404.1	type II toxin-antitoxin system VapC family toxin	Toxin
miv_RS09510	2043996..2044253	-	258	WP_048428143.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
miv_RS09515	2044513..2044959	+	447	WP_048428142.1	hypothetical protein	-
miv_RS09520	2045145..2047148	+	2004	WP_207182405.1	acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha	-
miv_RS09525	2047159..2047575	+	417	WP_048428162.1	gamma-glutamylcyclotransferase	-
miv_RS09530	2047625..2048041	-	417	WP_207183446.1	phosphoribosyl-AMP cyclohydrolase	-
miv_RS09535	2048044..2048703	-	660	WP_048428139.1	GTP cyclohydrolase I FolE	-

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 (7-127)

Antitoxin

• SpoVT-AbrB domain (16-58)

Sequences

Toxin

Protein

• Length: 135 a.a.
• Molecular weight: 14304.54 Da
• Isoelectric Point: 6.3492

>T38043 WP_207182404.1 NZ_AP024145:c2043999-2043595 [Methylobacterium indicum]
MSGPRFLLDTNILSDLIRNPSGAVARQIARVGSKGIATSIVSVAELRYGCAKRGSARLLRQVEAVLEAIDVVPFETPADV
IYGRIRADLEAAGRPIGPNDLLIAAQALALEVPLVTANEAEFRRIGGLSVENWL

Nucleotide

• Length: 405 bp

>T38043 NZ_AP024145:c2043999-2043595 [Methylobacterium indicum]
ATGAGCGGCCCGCGCTTCCTGCTCGATACGAACATCCTCTCCGATCTGATCCGCAACCCGTCCGGTGCCGTGGCCCGGCA
GATCGCACGGGTCGGCAGCAAAGGCATCGCGACGAGCATCGTCTCGGTCGCGGAACTCCGCTACGGCTGCGCGAAGCGGG
GGTCGGCTCGCCTTCTCCGTCAGGTCGAAGCCGTGCTGGAAGCGATCGACGTGGTTCCGTTCGAGACTCCCGCCGATGTC
ATCTATGGAAGAATTCGCGCCGATCTCGAGGCTGCGGGTCGGCCGATCGGACCGAACGATCTCCTCATCGCGGCTCAGGC
GCTCGCGCTCGAGGTTCCGCTCGTGACGGCGAACGAGGCGGAGTTTCGGCGTATCGGCGGGCTGTCGGTCGAGAACTGGC
TCTGA

Antitoxin

Protein

• Length: 86 a.a.
• Molecular weight: 9659.09 Da
• Isoelectric Point: 4.5156

>AT38043 WP_048428143.1 NZ_AP024145:c2044253-2043996 [Methylobacterium indicum]
MARPTPIPQAREVKLFRNNRSQAVRIPAEFALPGDRVRISRDGDRLILEPIGKKDLLEVLATLEPIEEDFPDFDKTLPPL
DDDPL

Nucleotide

• Length: 258 bp

>AT38043 NZ_AP024145:c2044253-2043996 [Methylobacterium indicum]
ATGGCGAGACCGACCCCGATACCGCAGGCGCGGGAGGTGAAGCTGTTCCGCAACAATCGCAGCCAGGCCGTGCGCATCCC
GGCCGAATTCGCCTTGCCCGGGGACCGGGTCCGCATCAGCCGCGATGGCGACCGCCTCATCCTGGAGCCGATCGGCAAGA
AGGACCTTCTGGAGGTCCTGGCGACCCTGGAGCCGATCGAGGAGGATTTCCCGGACTTCGACAAGACGCTGCCGCCCCTG
GACGATGATCCGCTATGA

Structures

Antitoxin

• AlphaFold DB: A0A0J6RC86