Detailed information of TA system TA000877

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/AbrB-PIN
• Location: 2611440..2612113
• Replicon: chromosome
• Accession: NC_003047
• Organism: Sinorhizobium meliloti 1021

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: SM_RS12380
• Protein ID: WP_010969926.1
• Coordinates: 2611709..2612113 (+)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: H0GA10
• Locus tag: SM_RS12375
• Protein ID: WP_003536345.1
• Coordinates: 2611440..2611712 (+)
• Length: 91 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SM_RS12355 (SMc01525)	2607431..2609071	-	1641	WP_003536336.1	ABC transporter substrate-binding protein	-
SM_RS12360 (SMc01524)	2609119..2610174	-	1056	WP_010969924.1	dipeptidase	-
SM_RS12365 (SMc01523)	2610354..2610695	-	342	WP_003536339.1	EamA family transporter	-
SM_RS12370 (SMc01522)	2610743..2611303	-	561	WP_010969925.1	TetR/AcrR family transcriptional regulator	-
SM_RS12375 (SMc03949)	2611440..2611712	+	273	WP_003536345.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
SM_RS12380 (SMc01521)	2611709..2612113	+	405	WP_010969926.1	type II toxin-antitoxin system VapC family toxin	Toxin
SM_RS12385 (SMc01520)	2612241..2612633	+	393	WP_003536349.1	globin	-
SM_RS12390 (SMc01519)	2612639..2613013	+	375	WP_010969927.1	DUF423 domain-containing protein	-
SM_RS12395 (SMc01748)	2613136..2613396	+	261	WP_010969928.1	type II toxin-antitoxin system Phd/YefM family antitoxin	-
SM_RS12400 (SMc01518)	2613511..2613825	-	315	WP_003536354.1	antibiotic biosynthesis monooxygenase	-
SM_RS12405 (SMc01517)	2613838..2614104	-	267	WP_010969929.1	hypothetical protein	-
SM_RS12410 (SMc01516)	2614157..2614570	-	414	WP_003536357.1	DUF2325 domain-containing protein	-
SM_RS12415 (SMc01515)	2614694..2615620	-	927	WP_010969930.1	energy transducer TonB	-
SM_RS12420 (SMc01514)	2615661..2616095	-	435	WP_010969931.1	hypothetical protein	-
SM_RS12425 (SMc01747)	2616325..2616465	+	141	WP_010969932.1	hemin uptake protein HemP	-

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 (4-124)

Antitoxin

• SpoVT-AbrB domain (16-54)

Sequences

Toxin

Protein

• Length: 135 a.a.
• Molecular weight: 14747.98 Da
• Isoelectric Point: 5.1974

>T877 WP_010969926.1 NC_003047:2611709-2612113 [Sinorhizobium meliloti 1021]
MNGYLLDTNIISDVIHNPFGPAAQRIERIGPKEIYTSIVVASELRYGCAKKGSAKLLAKVESLLEIVPVLPLDIPADTRY
GSIRAELESLGQTIGSNDLLIAAHAYALDLTLVTDNIREFSRVRGLSLENWLER

Nucleotide

• Length: 405 bp

>T877 NC_003047:2611709-2612113 [Sinorhizobium meliloti 1021]
TTGAACGGCTATCTTCTCGATACGAACATCATCAGCGACGTCATTCACAATCCGTTCGGACCGGCTGCGCAACGCATCGA
ACGGATCGGCCCGAAGGAGATTTACACCAGCATCGTCGTCGCGTCCGAGTTGCGGTATGGTTGCGCAAAAAAGGGATCGG
CGAAGTTGCTCGCCAAGGTCGAAAGCTTGCTGGAAATCGTCCCGGTGCTGCCATTGGATATTCCGGCCGACACCCGATAT
GGCAGCATTCGTGCGGAATTGGAGTCTCTGGGGCAGACCATCGGCTCCAACGATCTGTTGATTGCCGCGCATGCATATGC
GCTGGACCTGACGCTGGTGACGGACAATATCCGTGAGTTCAGCCGCGTTCGTGGCCTTAGTCTGGAAAACTGGCTTGAGC
GATAG

Antitoxin

Protein

• Length: 91 a.a.
• Molecular weight: 10334.02 Da
• Isoelectric Point: 6.3950

>AT877 WP_003536345.1 NC_003047:2611440-2611712 [Sinorhizobium meliloti 1021]
MPVPLPSSRPKEVKLFRNNRSQAVRIPAEFELPGDRVLIRREGTRLIIEPIARPADIVELLAEWKKEAPLGPEDRFPDVE
DIPARPEKIF

Nucleotide

• Length: 273 bp

>AT877 NC_003047:2611440-2611712 [Sinorhizobium meliloti 1021]
ATGCCCGTCCCGTTGCCGTCATCGCGACCTAAAGAAGTAAAGCTGTTCCGCAATAACCGCAGCCAGGCAGTCCGTATTCC
TGCGGAGTTCGAGTTGCCTGGAGACCGTGTGTTGATCCGTCGCGAAGGAACGAGACTCATTATCGAACCGATAGCCAGGC
CAGCCGATATCGTGGAGCTTCTCGCGGAGTGGAAGAAGGAAGCTCCCCTCGGACCTGAAGACCGGTTCCCGGATGTTGAG
GATATACCCGCCCGGCCGGAGAAAATCTTTTGA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T3856	Dichelobacter nodosus VCS1703A	42.188	96.241	0.406
T3858	Dichelobacter nodosus VCS1703A	42.188	96.241	0.406
T1070	Haemophilus influenzae Rd KW20	39.231	98.485	0.386
T4922	Actinobacillus pleuropneumoniae serovar 3 str. JL03	37.594	100	0.379
T10054	Bosea sp. PAMC 26642 strain PAMC26642	36.842	100	0.371
T10197	Klebsiella pneumoniae	36.567	100	0.366
T6111	uncultured bacterium	36.364	99.248	0.361
T652	Leptospira interrogans serovar Lai str. 56601	35.606	100	0.356
T4914	Actinobacillus pleuropneumoniae serovar 3 str. JL03	34.351	100	0.349
T439	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	34.848	100	0.348
T6112	uncultured bacterium	34.351	98.496	0.338
T10129	Haemophilus influenzae strain 69P2H1 N69P2H1_45_2	33.077	97.015	0.321
T1066	Haemophilus influenzae Rd KW20	32.308	97.015	0.313

Multiple sequence alignment

Structures

Antitoxin

• AlphaFold DB: H0GA10

References

(1) Monica Bodogai et al. (2006) The ntrPR operon of Sinorhizobium meliloti is organized and functions as a toxin-antitoxin module. Molecular Plant-microbe Interactions : MPMI 19(7):811-22. [PubMed:16838793]


 experimental literature