Rv2840c Family assigned · medium auto-curated
H37Rv Rv2840c · MTBC0 - ·
99 aa · 3147959–3148258 (-) ·
RefSeq NP_217356.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains YlxR (PF04296.19) 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 |
I6XFF7
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | YlxR domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | nucleic-acid-binding protein implicated in transcription termination |
| Orthologous group | COG2740 |
| KEGG orthology |
K07742
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 |
|---|---|---|---|---|
YlxR | PF04296.19 | 3.1e-19 | 2–81 | Protein of unknown function (DUF448) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nusA (transcription termination/antitermination protein NusA), high confidence from genomic context alone (score 960 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) |
|---|---|---|---|---|
Rv2841c nusA |
transcription termination/antitermination protein NusA | 960 | 960 ctx | neighborhood:760 coexpression:840 |
Rv2839c infB |
translation initiation factor IF-2 | 960 | 955 ctx | neighborhood:782 coexpression:804 |
Rv2842c rimP |
ribosome maturation factor RimP | 957 | 951 ctx | neighborhood:760 coexpression:805 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 870 | 870 ctx | neighborhood:782 coexpression:429 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 898 | 810 ctx | neighborhood:782 textmining:489 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 805 | 805 ctx | neighborhood:782 |
Rv0682 rpsL |
30S ribosomal protein S12 | 803 | 804 | coexpression:804 |
Rv0703 rplW |
50S ribosomal protein L23 | 681 | 681 | coexpression:681 |
Rv3459c rpsK |
30S ribosomal protein S11 | 671 | 671 | coexpression:661 |
Rv2442c rplU |
50S ribosomal protein L21 | 652 | 653 | coexpression:651 |
Rv0702 rplD |
50S ribosomal protein L4 | 643 | 644 | coexpression:644 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 590 | 590 | |
Rv0719 rplF |
50S ribosomal protein L6 | 570 | 570 | coexpression:570 |
Rv2843 hyp |
hypothetical protein | 523 | 523 ctx | neighborhood:521 |
Rv0716 rplE |
50S ribosomal protein L5 | 521 | 521 | coexpression:521 |
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): YlxR PF04296.19 (E=3e-19)
- (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_217356.3)
- Domains: Pfam-A via hmmscan --cut_ga — YlxR (PF04296.19)
- 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
COG2740 - Curated reference: UniProt I6XFF7 (TrEMBL, unreviewed; 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 —
66 functional partner(s); context anchor
nusA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2840c| MRTCVGCRKRGLAVELLRVVAVSTGNGNYAVIVDTATSLPGRGAWLHPLRQCAQQAIRRRAFARALRIAGSPDTSAVVEYLESLGELEPPGNRTGSNRT