Detailed information of TA system
Overview
TA module
| Type | II | Classification (family/domain) | ccdAB/- |
| Location | 863257..863807 | Replicon | chromosome |
| Accession | NC_014500 | ||
| Organism | Dickeya dadantii 3937 | ||
Toxin (Protein)
| Gene name | ccdB | Uniprot ID | E0SMR8 |
| Locus tag | DDA3937_RS03885 | Protein ID | WP_013316491.1 |
| Coordinates | 863499..863807 (+) | Length | 103 a.a. |
Antitoxin (Protein)
| Gene name | ccdA | Uniprot ID | E0SMR7 |
| Locus tag | DDA3937_RS03880 | Protein ID | WP_013316490.1 |
| Coordinates | 863257..863496 (+) | Length | 80 a.a. |
Genomic Context
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| DDA3937_RS03855 (Dda3937_01705) | 858294..859532 | - | 1239 | WP_013316485.1 | integrase | - |
| DDA3937_RS03860 (Dda3937_01706) | 859910..861085 | - | 1176 | WP_013316486.1 | site-specific integrase | - |
| DDA3937_RS03870 (Dda3937_01707) | 861642..862151 | + | 510 | WP_033111620.1 | DNA repair protein RadC | - |
| DDA3937_RS03875 (Dda3937_01708) | 862746..863057 | + | 312 | WP_012768885.1 | DUF736 domain-containing protein | - |
| DDA3937_RS03880 (Dda3937_01709) | 863257..863496 | + | 240 | WP_013316490.1 | type II toxin-antitoxin system CcdA family antitoxin | Antitoxin |
| DDA3937_RS03885 (Dda3937_01710) | 863499..863807 | + | 309 | WP_013316491.1 | CcdB family protein | Toxin |
| DDA3937_RS03890 (Dda3937_01711) | 863993..864589 | + | 597 | WP_148226861.1 | hypothetical protein | - |
| DDA3937_RS21875 (Dda3937_01712) | 864924..865721 | + | 798 | WP_013316493.1 | DUF2285 domain-containing protein | - |
| DDA3937_RS03895 | 865805..866101 | + | 297 | WP_033111622.1 | helix-turn-helix domain-containing protein | - |
| DDA3937_RS03900 (Dda3937_01714) | 866128..866940 | + | 813 | WP_013316495.1 | replication initiator protein A | - |
| DDA3937_RS03905 (Dda3937_01716) | 867230..867796 | + | 567 | WP_148226862.1 | S26 family signal peptidase | - |
Associated MGEs
| MGE detail |
Similar MGEs |
Relative position |
MGE Type | Cargo ARG | Virulence gene | Coordinates | Length (bp) |
|---|---|---|---|---|---|---|---|
| - | inside | Integrative and Conjugative Element | - | hcp | 756565..934986 | 178421 |
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.
Sequences
Toxin
Download Length: 103 a.a. Molecular weight: 11671.49 Da Isoelectric Point: 5.6557
>T10064 WP_013316491.1 NC_014500:863499-863807 [Dickeya dadantii 3937]
MQYMVYRNNDNSRAYPYLLDVQSDIIGELHTRLVIPLFPEEKVNASVVKRLTPVLPVEGRDYLVMTHEMASVRLSQLGPQ
VMDAQAYRQSIKAALDFLLDGF
MQYMVYRNNDNSRAYPYLLDVQSDIIGELHTRLVIPLFPEEKVNASVVKRLTPVLPVEGRDYLVMTHEMASVRLSQLGPQ
VMDAQAYRQSIKAALDFLLDGF
Download Length: 309 bp
>T10064 NC_014500:863499-863807 [Dickeya dadantii 3937]
ATGCAGTACATGGTGTATCGCAATAACGATAACAGCAGGGCATACCCTTATCTGCTTGATGTGCAGAGTGATATCATCGG
GGAGCTGCATACACGCCTGGTTATCCCACTGTTCCCAGAGGAAAAGGTGAACGCCAGTGTGGTAAAACGCCTGACACCTG
TCTTACCGGTTGAGGGCCGTGATTATCTGGTGATGACGCATGAAATGGCCAGCGTTCGGCTTTCCCAGCTTGGTCCGCAA
GTGATGGATGCCCAGGCGTATCGCCAGAGTATCAAGGCGGCGCTGGACTTTTTGCTAGACGGGTTTTGA
ATGCAGTACATGGTGTATCGCAATAACGATAACAGCAGGGCATACCCTTATCTGCTTGATGTGCAGAGTGATATCATCGG
GGAGCTGCATACACGCCTGGTTATCCCACTGTTCCCAGAGGAAAAGGTGAACGCCAGTGTGGTAAAACGCCTGACACCTG
TCTTACCGGTTGAGGGCCGTGATTATCTGGTGATGACGCATGAAATGGCCAGCGTTCGGCTTTCCCAGCTTGGTCCGCAA
GTGATGGATGCCCAGGCGTATCGCCAGAGTATCAAGGCGGCGCTGGACTTTTTGCTAGACGGGTTTTGA
Antitoxin
Download Length: 80 a.a. Molecular weight: 9003.13 Da Isoelectric Point: 7.2047
>AT10064 WP_013316490.1 NC_014500:863257-863496 [Dickeya dadantii 3937]
MPTTSIRHKKTVSVTLEPALLQQAREAGINLSATLAEALKREIRASEAERWQRENRAGLQELNRITDEHGLLSDDYRTF
MPTTSIRHKKTVSVTLEPALLQQAREAGINLSATLAEALKREIRASEAERWQRENRAGLQELNRITDEHGLLSDDYRTF
Download Length: 240 bp
>AT10064 NC_014500:863257-863496 [Dickeya dadantii 3937]
ATGCCGACTACAAGCATACGACACAAAAAAACCGTCAGCGTCACACTGGAGCCCGCCTTGTTGCAGCAGGCCCGGGAGGC
GGGAATTAATCTCTCGGCCACGCTTGCTGAGGCCCTGAAGCGGGAAATTCGAGCGTCAGAAGCGGAACGGTGGCAGCGAG
AAAATCGCGCCGGCCTGCAGGAACTCAACCGTATCACGGATGAGCATGGCTTGCTGTCCGATGATTACAGGACGTTTTAA
ATGCCGACTACAAGCATACGACACAAAAAAACCGTCAGCGTCACACTGGAGCCCGCCTTGTTGCAGCAGGCCCGGGAGGC
GGGAATTAATCTCTCGGCCACGCTTGCTGAGGCCCTGAAGCGGGAAATTCGAGCGTCAGAAGCGGAACGGTGGCAGCGAG
AAAATCGCGCCGGCCTGCAGGAACTCAACCGTATCACGGATGAGCATGGCTTGCTGTCCGATGATTACAGGACGTTTTAA
Similar Proteins
Only experimentally validated proteins are listed.
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| T10099 | Escherichia coli Nissle 1917 |
48.544 |
100 |
0.49 |
| T10018 | Escherichia coli O157:H7 str. Sakai |
47.573 |
100 |
0.48 |
| T190 | Escherichia coli O157:H7 str. EDL933 |
47.573 |
100 |
0.48 |
| T6109 | uncultured bacterium |
36.275 |
100 |
0.366 |
| T6145 | Escherichia coli K-12 |
36.275 |
100 |
0.366 |
Multiple sequence alignment
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| AT10018 | Escherichia coli O157:H7 str. Sakai |
43.421 |
98.701 |
0.429 |
| AT10099 | Escherichia coli Nissle 1917 |
43.421 |
98.701 |
0.429 |
| AT190 | Escherichia coli O157:H7 str. EDL933 |
43.421 |
98.701 |
0.429 |
| AT6157 | Escherichia coli str. K-12 substr. MG1655 |
34.247 |
92.405 |
0.316 |
Multiple sequence alignment
References
(1) Lidia Boss et al. (2021) Identification of Three Type II Toxin-Antitoxin Systems in Model Bacterial Plant Pathogen Dickeya dadantii 3937. International Journal of Molecular Sciences 22(11):5932. [PubMed:34073004]