Rv3840 Family assigned · medium auto-curated
H37Rv Rv3840 · MTBC0 - ·
137 aa · 4313567–4313980 (+) ·
RefSeq NP_218357.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator. Pfam: LytR_cpsA_psr (PF03816.20). |
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 |
P96238
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Possible transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | lytR2 |
| eggNOG description | transcriptional |
| Orthologous group | COG1316 |
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 | 0.927 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.67% of strains (3870) · 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 |
|---|---|---|---|---|
LytR_cpsA_psr | PF03816.20 | 3.1e-20 | 21–121 | LytR_cpsA_psr family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1151c cobB |
NAD-dependent protein deacylase | 862 | 862 | coexpression:860 |
Rv3263 |
DNA methylase | 865 | 860 | coexpression:860 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 865 | 860 | coexpression:860 |
Rv1674c |
transcriptional regulator | 860 | 860 | coexpression:860 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 860 | 860 | coexpression:860 |
Rv3830c |
TetR family transcriptional regulator | 860 | 860 | coexpression:860 |
Rv3167c |
TetR family transcriptional regulator | 860 | 860 | coexpression:860 |
Rv1359 |
transcriptional regulator | 860 | 860 | coexpression:860 |
Rv3736 |
AraC/XylS family transcriptional regulator | 860 | 860 | coexpression:860 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 860 | 860 | coexpression:860 |
Rv1267c embR |
transcriptional regulator EmbR | 857 | 857 | coexpression:857 |
Rv1931c |
transcriptional regulator | 850 | 850 | coexpression:850 |
Rv2282c |
LysR family HTH-type transcriptional regulator | 854 | 848 | coexpression:848 |
Rv3183 higA3 |
transcriptional regulator | 848 | 848 | coexpression:848 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 847 | 847 | coexpression:827 |
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): transcriptional regulator
- Pfam (hmmscan --cut_ga): LytR_cpsA_psr PF03816.20 (E=3e-20)
- (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_218357.1)
- Domains: Pfam-A via hmmscan --cut_ga — LytR_cpsA_psr (PF03816.20)
- 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
COG1316 - Curated reference: UniProt P96238 (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 — 100 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3840| MAGCIQRFSHVRCLGPGLASDNPTTLISIPRDSYVPIPGHGRDKINAAFALGGGRLLTQTVELATGLHLDHYAEVGFSEFADLVDAFDPLAGVDLPAGCQTLDGRAALGYVRTRATPRADLEGSDVPVPAAAFETQP