Rv2248 Family assigned · medium auto-curated
H37Rv Rv2248 · MTBC0 - ·
271 aa · 2522360–2523175 (+) ·
RefSeq NP_216764.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains AbiEi_1 (PF09407.17) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLG5
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2248 |
UniProt still lists this protein as Uncharacterized protein Rv2248; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein conserved in bacteria |
| Orthologous group | COG2852 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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) pseudogene candidate
| pN/pS | 0.591 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 1.35% of strains (1964) · clonal |
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 | 1.6e-33 | 45–158 | AbiEi antitoxin C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsmA (anti-sigma-M factor RsmA), medium confidence from genomic context alone (score 630 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) |
|---|---|---|---|---|
Rv3912 rsmA |
anti-sigma-M factor RsmA | 630 | 630 ctx | cooccurence:628 |
Rv3779 |
transmembrane protein | 589 | 589 ctx | cooccurence:589 |
Rv0204c |
transmembrane protein | 582 | 583 ctx | cooccurence:581 |
Rv0955 |
integral membrane protein | 540 | 540 ctx | cooccurence:540 |
Rv1353c |
HTH-type transcriptional regulator | 539 | 539 ctx | cooccurence:538 |
Rv2246 kasB |
3-oxoacyl-ACP synthase 2 | 539 | 538 | |
Rv0048c |
membrane protein | 525 | 525 ctx | cooccurence:525 |
Rv3859c gltB |
glutamate synthase large subunit | 522 | 522 | coexpression:515 |
Rv0256c PPE2 |
PPE family protein PPE2 | 513 | 514 ctx | cooccurence:505 |
Rv1060 hyp |
hypothetical protein | 512 | 512 ctx | cooccurence:512 |
Rv3773c hyp |
hypothetical protein | 509 | 510 ctx | cooccurence:507 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 501 | 501 ctx | cooccurence:494 |
Rv2247 accD6 |
acetyl-/propionyl-CoA carboxylase subunit beta | 494 | 494 ctx | neighborhood:451 |
Rv3594 hyp |
hypothetical protein | 478 | 479 ctx | cooccurence:471 |
Rv2687c |
antibiotic ABC transporter permease | 473 | 474 ctx | cooccurence:471 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): AbiEi_1 PF09407.17 (E=2e-33)
- (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_216764.1)
- 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
COG2852 - Curated reference: UniProt P9WLG5 (SwissProt, reviewed; Predicted)
- 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 —
30 functional partner(s); context anchor
rsmA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2248| MTRQQLDVQVKNGGLVRVWYGVYAAQEPDLLGRLAALDVFMGGHAVACLGTAAALYGFDTENTVAIHMLDPGVRMRPTVGLMVHQRVGARLQRVSGRLATAPAWTAVEVARQLRRPRALATLDAALRSMRCARSEIENAVAEQRGRRGIVAARELLPFADGRAESAMESEARLVMIDHGLPLPELQYPIHGHGGEMWRVDFAWPDMRLAAEYESIEWHAGPAEMLRDKTRWAKLQELGWTIVPIVVDDVRREPGRLAARIARHLDRARMAG