Rv2515c Family assigned · medium auto-curated
H37Rv Rv2515c · MTBC0 mtbc0_002678 ·
415 aa · 2854234–2855481 (-) ·
RefSeq NP_217031.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | XRE family transcriptional regulator |
| Revised (this work) | XRE family transcriptional regulator. Pfam: HTH_3 (PF01381.29), Peptidase_M78 (PF06114.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XEH5
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | HTH cro/C1-type domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | IrrE N-terminal-like domain |
| Orthologous group | COG1396 |
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 | 0.121 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 20 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (156) · 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 |
|---|---|---|---|---|
HTH_3 | PF01381.29 | 4.8e-08 | 29–82 | Helix-turn-helix |
Peptidase_M78 | PF06114.20 | 8.0e-22 | 190–325 | IrrE N-terminal-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1371 (membrane protein), medium confidence from genomic context alone (score 698 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) |
|---|---|---|---|---|
Rv2514c hyp |
hypothetical protein | 998 | 994 ctx | neighborhood:882 cooccurence:774 coexpression:802 textmining:803 |
Rv0332 hyp |
hypothetical protein | 936 | 927 | experimental:916 |
Rv1371 |
membrane protein | 846 | 698 ctx | cooccurence:695 textmining:511 |
Rv2608 PPE42 |
PPE family protein PPE42 | 651 | 651 ctx | cooccurence:650 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 592 | 592 ctx | cooccurence:590 |
Rv2516c hyp |
hypothetical protein | 578 | 578 ctx | neighborhood:566 |
Rv2517c hyp |
hypothetical protein | 515 | 516 ctx | neighborhood:513 |
Rv2017 |
transcriptional regulator | 636 | 484 | |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 447 | 447 ctx | cooccurence:447 |
Rv3190c hyp |
hypothetical protein | 654 | 437 | textmining:412 |
Rv0878c PPE13 |
PPE family protein PPE13 | 437 | 437 ctx | cooccurence:437 |
Rv1917c PPE34 |
PPE family protein PPE34 | 433 | 433 ctx | cooccurence:425 |
Rv1959c parE1 |
toxin ParE1 | 416 | 417 | |
Rv2021c higA2 |
transcriptional regulator | 400 | 312 | |
Rv0341 iniB |
isoniazid inducible protein IniB | 403 | 276 |
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: XRE family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_3 PF01381.29 (E=5e-08), Peptidase_M78 PF06114.20 (E=8e-22)
- (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_217031.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_3 (PF01381.29), Peptidase_M78 (PF06114.20)
- 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
COG1396 - Curated reference: UniProt I6XEH5 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
38 functional partner(s); context anchor
Rv1371 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002678|Rv2515c| MGIGHPMWVGWCIIIAMRSIPASVESSVLRWARESCGLTEVAAARKLGLPDDRVAAWEVGEVVPTIAQLRKAAEVYKRSLAVFFLSEPPEGFDTLRDFRRLDGAASGQWTPGLHEEFRRAHTQRDFALELADAEDREIPGAWRLPLSGDEADADIAARIRKALIEVSPLPIPVASVDPYEHLNAWVSAIETSGVLVLATRGGKVAIDEMRGMCLYFDELPVIVLNGSDHPRPRLFSLLHEFVHVVLHTEGLCDVIADAHPSTQDRSLEARCNAIAAAVLMPADVVRARPEVIVRSETPSSWDYESLRPVAAHFGVSAEAFLRRLSTLGIVPVEVYRQRRAEFIAAHEDEAERARSAGGGNWYRNTVRDLGKGYVRAVTDAHRRRVIDSNTAAIYLDAKVSQIPKLAESAELRSVV