Detailed information of TA system TA076016

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-Phd
• Location: 950928..951646
• Replicon: chromosome
• Accession: NZ_CP021124
• Organism: Rhizobium sp. Kim5

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: KIM5_RS04780
• Protein ID: WP_009996200.1
• Coordinates: 950928..951386 (-)
• Length: 153 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A060I3H0
• Locus tag: KIM5_RS04785
• Protein ID: WP_009996202.1
• Coordinates: 951383..951646 (-)
• Length: 88 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
KIM5_RS33535	946038..946670	+	633	WP_125461960.1	hypothetical protein	-
KIM5_RS04760	946713..948350	-	1638	WP_038687103.1	chaperonin GroEL	-
KIM5_RS04765	948422..948718	-	297	WP_004675403.1	co-chaperone GroES	-
KIM5_RS04770	949054..949902	+	849	WP_038687105.1	TIGR01459 family HAD-type hydrolase	-
KIM5_RS04775	949917..950900	+	984	WP_039623031.1	bifunctional riboflavin kinase/FAD synthetase	-
KIM5_RS04780	950928..951386	-	459	WP_009996200.1	type II toxin-antitoxin system VapC family toxin	Toxin
KIM5_RS04785	951383..951646	-	264	WP_009996202.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
KIM5_RS04790	951999..954905	+	2907	WP_086156068.1	isoleucine--tRNA ligase	-
KIM5_RS04795	955037..955666	+	630	WP_038687111.1	hypothetical protein	-
KIM5_RS04800	955953..956390	-	438	WP_077991088.1	nucleoside deaminase	-

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 (5-125)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (7-58)

Sequences

Toxin

Protein

• Length: 153 a.a.
• Molecular weight: 17029.08 Da
• Isoelectric Point: 5.2132

>T76016 WP_009996200.1 NZ_CP021124:c951386-950928 [Rhizobium sp. Kim5]
VIGWLLDTNVIAALINPNGAPSVKSWAAAQDENQMFISVLTLAEYDEGIENLPEDDRNRYRYIAARDALEERFSQRTLSL
SDAGVRHWGAISGRTKLRTGHTQPVIDTMLAATAIEHNLYLVTRNVKDTRFSGAAVFDPWTNDPDQFPLSRK

Nucleotide

• Length: 459 bp

>T76016 NZ_CP021124:c951386-950928 [Rhizobium sp. Kim5]
GTGATCGGATGGCTGCTCGACACCAACGTCATTGCGGCGCTGATCAATCCGAACGGCGCGCCCTCCGTGAAGTCCTGGGC
TGCCGCGCAGGACGAGAACCAGATGTTCATCAGCGTGCTCACCCTCGCAGAATATGACGAAGGCATCGAAAACCTGCCTG
AAGACGACCGGAACCGCTATCGTTATATAGCGGCGCGCGACGCTCTGGAGGAGCGGTTCTCACAGCGTACTCTCTCGCTG
AGCGACGCGGGCGTCAGGCACTGGGGTGCTATTTCAGGGCGCACAAAACTGCGAACCGGACATACGCAACCGGTCATCGA
CACGATGCTGGCCGCCACCGCCATTGAGCACAATCTCTATCTGGTGACGCGGAACGTAAAGGATACGCGCTTCTCCGGCG
CGGCAGTTTTCGATCCGTGGACAAACGATCCGGATCAATTTCCATTGAGCCGGAAATAA

Antitoxin

Protein

• Length: 88 a.a.
• Molecular weight: 10124.70 Da
• Isoelectric Point: 8.5600

>AT76016 WP_009996202.1 NZ_CP021124:c951646-951383 [Rhizobium sp. Kim5]
MRKVIKQSWKLEDAKARFSEVVRRARSEGPQRVTVRGKDSVVIISVEELERLTKAEPKKPLVDFMESLALKELDLEREPD
YGRDVEL

Nucleotide

• Length: 264 bp

>AT76016 NZ_CP021124:c951646-951383 [Rhizobium sp. Kim5]
ATGAGAAAAGTCATTAAGCAAAGCTGGAAGCTCGAGGACGCCAAAGCGCGCTTCAGCGAAGTCGTGCGCCGTGCCCGCAG
CGAAGGGCCACAGCGCGTCACAGTGCGCGGCAAAGACAGCGTCGTCATCATCAGCGTCGAAGAACTCGAACGGTTGACGA
AGGCCGAGCCCAAAAAGCCCCTGGTCGACTTCATGGAGAGCCTCGCTCTGAAAGAGCTCGATCTGGAGCGGGAGCCCGAT
TACGGGCGGGACGTCGAACTGTGA

Structures

Antitoxin

• AlphaFold DB: A0A060I3H0