Rv2409c Family assigned · medium auto-curated
H37Rv Rv2409c · MTBC0 mtbc0_002565 ·
279 aa · 2730762–2731601 (-) ·
RefSeq NP_216925.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | transglutaminase family protein |
| Revised (this work) | Transglutaminase family protein. Pfam: Bact_transglu_N (PF08379.16), Transglut_core (PF01841.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71734
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | transglutaminase-like |
| Orthologous group | COG1305 |
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 | 0.447 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Bact_transglu_N | PF08379.16 | 6.7e-21 | 5–82 | Bacterial transglutaminase-like N-terminal region |
Transglut_core | PF01841.26 | 2.8e-24 | 126–232 | Transglutaminase-like superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsT (30S ribosomal protein S20), medium confidence from genomic context alone (score 631 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2410c hyp |
hypothetical protein | 994 | 995 ctx | neighborhood:882 cooccurence:774 coexpression:818 |
Rv2411c hyp |
hypothetical protein | 993 | 993 ctx | neighborhood:882 cooccurence:774 coexpression:754 |
Rv2567 hyp |
hypothetical protein | 840 | 827 ctx | cooccurence:774 |
Rv2566 hyp |
hypothetical protein | 676 | 677 ctx | cooccurence:629 |
Rv2412 rpsT |
30S ribosomal protein S20 | 631 | 631 ctx | neighborhood:630 |
Rv2568c hyp |
hypothetical protein | 411 | 411 |
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: transglutaminase family protein
- Pfam (hmmscan --cut_ga): Bact_transglu_N PF08379.16 (E=7e-21), Transglut_core PF01841.26 (E=3e-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_216925.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bact_transglu_N (PF08379.16), Transglut_core (PF01841.26)
- 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
COG1305 - Curated reference: UniProt P71734 (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 —
6 functional partner(s); context anchor
rpsT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002565|Rv2409c| MWRTRVVHTTGYVYQSPVTASYNEARLTPRSSSRQNLVLNRVETIPATRSYRYIDYWGTAVTAFDLHAPHTELTVTSSSVVETERPEPLAAKATWADLQSTAVIDRFDEVLRPTPHTPASARVDAVGRRIRKCHEPSEAVVAAARWARSELDYIPGTTSVHSSGLDALEQGKGVCQDFVHLSLMVLRSMGIPCRYVSGYLHPKRDAVVGKTVDGRSHAWVQAWTGGWWHYDPTNDNEITEQYISVGVGRDYTDVSPLKGIYSGEGVTDLDVVVEITRLA