Rv2141c Family assigned · medium auto-curated
H37Rv Rv2141c · MTBC0 - ·
448 aa · 2400376–2401722 (-) ·
RefSeq YP_177864.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Peptidase_M28 (PF04389.23), Peptidase_M20 (PF01546.34), M20_dimer (PF07687.20) 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 |
L7N684
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
|
|---|---|
| Preferred name | dapE2 |
| eggNOG description | deacetylase Succinyl-diaminopimelate desuccinylase and related deacylases |
| Orthologous group | COG0624 |
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 | 1.179 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 |
|---|---|---|---|---|
Peptidase_M28 | PF04389.23 | 8.9e-10 | 69–169 | Peptidase family M28 |
Peptidase_M20 | PF01546.34 | 5.2e-31 | 85–446 | Peptidase family M20/M25/M40 |
M20_dimer | PF07687.20 | 3.3e-14 | 206–332 | Peptidase dimerisation domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ctaF (cytochrome c oxidase polypeptide 4), medium confidence from genomic context alone (score 492 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) |
|---|---|---|---|---|
Rv2140c TB18.6 hyp |
hypothetical protein | 832 | 827 ctx | neighborhood:816 |
Rv1652 argC |
N-acetyl-gamma-glutamyl-phoshate reductase | 545 | 497 | coexpression:403 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 492 | 492 ctx | cooccurence:473 |
Rv1658 argG |
argininosuccinate synthase | 520 | 468 | |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 497 | 443 | experimental:419 |
Rv2146c |
transmembrane protein | 439 | 440 | |
Rv2096c pafB |
proteasome accessory factor B | 430 | 430 ctx | cooccurence:430 |
Rv2467 pepN |
aminopeptidase PepN | 414 | 352 | |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 504 | 199 | textmining:407 |
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): Peptidase_M28 PF04389.23 (E=9e-10), Peptidase_M20 PF01546.34 (E=5e-31), M20_dimer PF07687.20 (E=3e-14)
- (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 YP_177864.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M28 (PF04389.23), Peptidase_M20 (PF01546.34), M20_dimer (PF07687.20)
- 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
COG0624 - Curated reference: UniProt L7N684 (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 —
9 functional partner(s); context anchor
ctaF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2141c| MTDETGASSDHSDDVAQVVSRLIRFDTTNSGEPGTTKGEAECARWVAEQLAEVGYQPEYVESGAPGRGNVFARLAGADSSRGALLIHGHLDVVPAEPAEWSVHPFSGAIEDGYVWGRGAVDMKDMVGMMIVVARHLRQAAIVPPRDLVFAFVADEEHGGKYGSHWLVDNRPDLFDGITEAIGEVGGFSLTVPRHDGGERRLYLIETAEKGIQWMRLTARGRAGHGSMVHDQNAVTAVCEAVARLGRHQFPLVCTDTVAQFLAVVGEETGLAFDLDSPDLAGTIDKLGPMARMLKAVLHDTANPTMLKAGYKANVVPATAEAVVDCRVLPGRRAAFEAEVDALIGPDVTREWVSDLPSYETTFDGDLVAAMNAAVLAVDPDGRTVPYMLSGGTDAKAFARLGIRCFGFSPLRLPPDLDFTSLFHGVDERVPIDGLRFGTEVLTHLLTHC