Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|
| MTBC0 PGAP re-annotation | type IV toxin-antitoxin system AbiEi family antitoxin |
|---|
| Revised (this work) | Type IV toxin-antitoxin system AbiEi family antitoxin. Pfam: AbiEi_1 (PF09407.17). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71625
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | AbiEi antitoxin C-terminal domain-containing protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|
| eggNOG description | AbiEi antitoxin C-terminal domain |
|---|
| Orthologous group | COG5340 |
|---|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are
computed annotations, not manual curation; cross-check against the primary literature
before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS |
1.524 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 synonymous, 4 missense, 0 nonsense, 0 frameshift
|
|---|
pN/pS from segregating SNPs (singletons removed) normalised by possible sites.
Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene).
A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic
variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A
clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a
convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|
AbiEi_1 | PF09407.17 |
2.8e-39 | 97–236 |
AbiEi antitoxin C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2826c hyp |
hypothetical protein |
990 |
884 ctx |
neighborhood:882 textmining:924 |
Rv3183 higA3 |
transcriptional regulator |
617 |
617 |
coexpression:615 |
Rv3060c |
GntR family transcriptional regulator |
533 |
533 |
coexpression:533 |
Rv2825c hyp |
hypothetical protein |
493 |
492 ctx |
neighborhood:480 |
Rv2828c hyp |
hypothetical protein |
432 |
432 ctx |
neighborhood:421 |
Rv2828A hyp |
hypothetical protein |
424 |
424 ctx |
neighborhood:424 |
Rv2829c vapC22 |
ribonuclease VapC22 |
434 |
417 |
|
Rv2830c vapB22 |
antitoxin VapB22 |
401 |
401 |
|
Rv1045 hyp |
hypothetical protein |
877 |
98 |
textmining:870 |
Rv0909 |
antitoxin |
526 |
55 |
textmining:519 |
Rv0837c hyp |
hypothetical protein |
807 |
54 |
textmining:805 |
Rv0078A hyp |
hypothetical protein |
806 |
50 |
textmining:805 |
Rv0836c hyp |
hypothetical protein |
870 |
49 |
textmining:869 |
Rv1044 hyp |
hypothetical protein |
870 |
47 |
textmining:870 |
Rv1545 hyp |
hypothetical protein |
529 |
47 |
textmining:527 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression,
experimental, database, text-mining) into a 0–1000 score. The ctx
badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion,
phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an
unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not
depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with
the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: type IV toxin-antitoxin system AbiEi family antitoxin
- Pfam (hmmscan --cut_ga): AbiEi_1 PF09407.17 (E=3e-39)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024),
An imputed ancestral reference genome for the MTBC,
doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217343.1)
- Domains: Pfam-A via hmmscan --cut_ga — AbiEi_1 (PF09407.17)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG5340
- Curated reference: UniProt
P71625
(TrEMBL, unreviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of
145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
23 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003005|Rv2827c|
MVSPAGADRRIPTWASRVVSGLARDRPVVVTKEDLTQRLTEAGCGRDPDSAIRELRRIGWLVQLPVKGTWAFIPPGEAAISDPYLPLRSWLARDQNAGFMLAGASAAWHLGYLDRQPDGRIPIWLPPAKRLPDGLASYVSVVRIPWNAADTALLAPRPALLVRRRLDLVAWATGLPALGPEALLVQIATRPASFGPWADLVPHLDDLVADCSDERLERLLSGRPTSAWQRASYLLDSGGEPARGQALLAKRHTEVMPVTRFTTAHSRDRGESVWAPEYQLVDELVVPLLRVIGKA
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