Rv2779c Family assigned · medium auto-curated
H37Rv Rv2779c · MTBC0 - ·
179 aa · 3086215–3086754 (-) ·
RefSeq NP_217295.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Lrp/AsnC family transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Lrp/AsnC family transcriptional regulator. Pfam: HTH_24 (PF13412.13), HTH_AsnC-type (PF13404.13), AsnC_trans_reg (PF01037.29). |
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 |
O33321
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator AldR |
| Curated function | Transcriptional regulator that might play a role under hypoxic conditions (Probable). Regulates the expression of ald, which encodes L-alanine dehydrogenase. Serves as both an activator for ald expression in the presence of L-alanine and a repressor in the absence of L-alanine. Acts by binding directly to the upstream region of the ald gene. Four AldR-binding sites (O2, O1, O4 and O3) were identified upstream of the ald gene. O2, O1 and O4 are required for the induction of ald expression by alanine, while O3 is directly involved in the repression of ald expression, by occluding the access of R. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | AsnC family |
| Orthologous group | COG1522 |
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 | 1.987 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.22% of strains (321) · 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_24 | PF13412.13 | 8.1e-16 | 32–79 | Winged helix-turn-helix DNA-binding |
HTH_AsnC-type | PF13404.13 | 4.3e-15 | 32–72 | AsnC-type helix-turn-helix domain |
AsnC_trans_reg | PF01037.29 | 6.9e-16 | 95–172 | Lrp/AsnC ligand binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ald (L-alanine dehydrogenase), medium confidence from genomic context alone (score 620 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2778c hyp |
hypothetical protein | 774 | 774 ctx | neighborhood:765 |
Rv0624 vapC30 |
ribonuclease VapC30 | 730 | 730 | coexpression:730 |
Rv2780 ald |
L-alanine dehydrogenase | 837 | 620 ctx | neighborhood:618 textmining:589 |
Rv2777c hyp |
hypothetical protein | 425 | 425 ctx | neighborhood:421 |
Rv3557c kstR2 |
HTH-type transcriptional regulator KstR2 | 605 | 339 | textmining:428 |
Rv3859c gltB |
glutamate synthase large subunit | 518 | 220 | textmining:408 |
Rv2272 |
transmembrane protein | 692 | 152 | textmining:652 |
Rv0880 |
HTH-type transcriptional regulator | 858 | 102 | textmining:849 |
Rv1219c raaS |
transcriptional regulator | 679 | 89 | textmining:663 |
Rv1218c |
tetronasin ABC transporter ATP-binding protein | 527 | 75 | textmining:510 |
Rv3549c |
short-chain type dehydrogenase/reductase | 806 | 63 | textmining:802 |
Rv3777 |
oxidoreductase | 872 | 58 | textmining:870 |
Rv0591 mce2C |
Mce family protein Mce2C | 656 | 52 | textmining:653 |
Rv1220c |
methyltransferase | 634 | 52 | textmining:630 |
Rv3489 hyp |
hypothetical protein | 555 | 52 | textmining:550 |
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): Lrp/AsnC family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_24 PF13412.13 (E=8e-16), HTH_AsnC-type PF13404.13 (E=4e-15), AsnC_trans_reg PF01037.29 (E=7e-16)
- (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_217295.2)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_24 (PF13412.13), HTH_AsnC-type (PF13404.13), AsnC_trans_reg (PF01037.29)
- 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
COG1522 - Curated reference: UniProt O33321 (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 —
21 functional partner(s); context anchor
ald - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2779c| MIILFRGHMRDNSTEHKTRRAASSKDVRPAELDEVDRRILSLLHGDARMPNNALADTVGIAPSTCHGRVRRLVDLGVIRGFYTDIDPVAVGLPLQAMISVNLQSSARGKIRSFIQQIRRKRQVMDVYFLAGADDFILHVAARDTEDLRSFVVENLNADADVAGTQTSLIFEHLRGAAPI