Rv2175c Family assigned · medium auto-curated
H37Rv Rv2175c · MTBC0 - ·
146 aa · 2437446–2437886 (-) ·
RefSeq NP_216691.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | DNA-binding protein. Pfam: Rv2175c_wHTH (PF21531.4), Rv2175c_C (PF18367.7). |
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 |
O53509
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA-binding protein Rv2175c |
| Curated function | Binds DNA at low salt concentrations. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | transcriptional regulator |
| Orthologous group | 2E0H9 |
| Gene Ontology (38) |
GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0006464, GO:0006468, GO:0006793, GO:0006796, GO:0006807, GO:0008150, GO:0008152, GO:0009987 +26 more
|
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 | 1.092 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Rv2175c_wHTH | PF21531.4 | 3.1e-26 | 15–71 | DNA-binding protein Rv2175c, wHTH domain |
Rv2175c_C | PF18367.7 | 3.8e-28 | 78–145 | Rv2175c C-terminal domain of unknown function |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pknL (serine/threonine-protein kinase PknL), high confidence from genomic context alone (score 788 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2788 sirR |
transcriptional repressor SirR | 797 | 797 | coexpression:797 |
Rv2176 pknL |
serine/threonine-protein kinase PknL | 957 | 788 ctx | neighborhood:787 textmining:808 |
Rv1773c |
transcriptional regulator | 734 | 734 | coexpression:734 |
Rv1151c cobB |
NAD-dependent protein deacylase | 733 | 733 | coexpression:733 |
Rv0603 hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv1725c hyp |
hypothetical protein | 730 | 730 | coexpression:730 |
Rv0880 |
HTH-type transcriptional regulator | 730 | 730 | coexpression:730 |
Rv1027c kdpE |
transcriptional regulator KdpE | 729 | 729 | coexpression:729 |
Rv3736 |
AraC/XylS family transcriptional regulator | 729 | 729 | coexpression:729 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 726 | 716 | coexpression:716 |
Rv3840 |
transcriptional regulator | 716 | 716 | coexpression:716 |
Rv3488 hyp |
hypothetical protein | 615 | 615 | coexpression:615 |
Rv3263 |
DNA methylase | 615 | 615 | coexpression:615 |
Rv2488c |
LuxR family transcriptional regulator | 615 | 615 | coexpression:615 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 580 | 580 | coexpression:580 |
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): DNA-binding protein
- Pfam (hmmscan --cut_ga): Rv2175c_wHTH PF21531.4 (E=3e-26), Rv2175c_C PF18367.7 (E=4e-28)
- (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_216691.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv2175c_wHTH (PF21531.4), Rv2175c_C (PF18367.7)
- 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
2E0H9 - Curated reference: UniProt O53509 (SwissProt, reviewed; 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 —
36 functional partner(s); context anchor
pknL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2175c| MPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY