Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|
| MTBC0 PGAP re-annotation | nucleotidyl transferase AbiEii/AbiGii toxin family protein |
|---|
| Revised (this work) | Nucleotidyl transferase AbiEii/AbiGii toxin family protein. Pfam: AbiEii (PF08843.18). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71626
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Nucleotidyl transferase AbiEii/AbiGii toxin family protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | Nucleotidyl transferase AbiEii toxin, Type IV TA system |
|---|
| Orthologous group | COG2253 |
|---|
| KEGG orthology |
K09144
|
|---|
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 |
0.0 · strong purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
4 synonymous, 0 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 |
|---|
AbiEii | PF08843.18 |
5.2e-24 | 36–272 |
Nucleotidyl transferase AbiEii toxin, Type IV TA system |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2827c hyp |
hypothetical protein |
990 |
884 ctx |
neighborhood:882 textmining:924 |
Rv2825c hyp |
hypothetical protein |
487 |
487 ctx |
neighborhood:480 |
Rv2828c hyp |
hypothetical protein |
437 |
437 ctx |
neighborhood:421 |
Rv2828A hyp |
hypothetical protein |
424 |
424 ctx |
neighborhood:424 |
Rv2829c vapC22 |
ribonuclease VapC22 |
416 |
403 |
|
Rv2830c vapB22 |
antitoxin VapB22 |
401 |
401 |
|
Rv1044 hyp |
hypothetical protein |
883 |
87 |
textmining:878 |
Rv1045 hyp |
hypothetical protein |
873 |
64 |
textmining:870 |
Rv0837c hyp |
hypothetical protein |
654 |
49 |
textmining:652 |
Rv0836c hyp |
hypothetical protein |
870 |
47 |
textmining:870 |
Rv0078A hyp |
hypothetical protein |
806 |
46 |
textmining:805 |
Rv1545 hyp |
hypothetical protein |
516 |
46 |
textmining:514 |
Rv3189 hyp |
hypothetical protein |
447 |
44 |
textmining:446 |
Rv0060 darG hyp |
hypothetical protein |
441 |
44 |
textmining:440 |
Rv0910 |
toxin |
512 |
42 |
textmining:512 |
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: nucleotidyl transferase AbiEii/AbiGii toxin family protein
- Pfam (hmmscan --cut_ga): AbiEii PF08843.18 (E=5e-24)
- (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_217342.1)
- Domains: Pfam-A via hmmscan --cut_ga — AbiEii (PF08843.18)
- 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
COG2253
- Curated reference: UniProt
P71626
(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 —
20 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003004|Rv2826c|
MAGLTRALVARHALGRAEAYDAALLDVAQDHLLYLLSQTVQFGDNRLVFKGGTSLRKCRLGNVGRFSTDLDFSAPDDEVVLEVCELIDGARVGGFEFGVQSTRGDGRHWQLRVRHTELGEPRIVASVEFARRPLALPSELLAFIQLPIHKAYGFGLPTLPVVAEAEACAEKLARYRRVALARDLYDLNHFASRTIDEPLVRRLWVLKVWGDVVDDRRGTRPLRVEDVLAARSEHDFQPDSIGVLTRPVAMAAWEARVRKRFAFLTDLDADEQRWAACDERHRREVENALAVLRS
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